{"text": "Sodium Taurocholate Co-transporting Polypeptide (NTCP) and Bile Salt Export Pump (BSEP) play significant roles as membrane transporters because of their presence in the enterohepatic circulation of bile salts. They have emerged as promising drug targets in related liver disease.\n\nThe Role of the Sodium-taurocholate Co-transporting Polypeptide (NTCP) and Bile Salt Export Pump (BSEP) in Related Liver Disease.", "token_count": 117, "char_count": 410, "word_count": 57, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:18.261364", "source": {"split": "train_shard_00000", "doc_id": 2990}, "chunk_id": "train_shard_00000_2990_0", "global_id": 3300}
{"text": "Advances in whole-genome sequencing (WGS) technologies have documented genetic diversity and epidemiology of the major foodborne pathogen Listeria monocytogenes (Lm) in Europe and North America, but data concerning South America are scarce. Here, we examined the population structure and genetic diversity of this major foodborne pathogen collected in Brazil. Based on core genome multilocus sequence typing (cgMLST), isolates from lineages I (n = 22; 63%) and II (n = 13; 37%) were distributed into 10 different sublineages (SLs) and represented 31 new cgMLST types (CTs). The most prevalent SLs were SL9 (n = 9; 26%), SL3 (n = 6; 17%) and SL2 and SL218 (n = 5; 14%). Isolates belonging to CTs L2-SL9-ST9-CT4420 and L1-SL315-ST520-CT4429 were collected 3 and 9 years apart, respectively, revealing long-term persistence of Lm in Brazil. Genetic elements associated with stress survival were present in 60% of isolates (57% SSI-1 and 3% SSI-2). Pathogenic islands were present in 100% (LIPI-1), 43% (LIPI-3) and 6% (LIPI-4) of the isolates. Mutations leading to premature stop codons were detected in the prfA and inlA virulence genes. This study is an important contribution to understanding the genomic diversity and epidemiology of Lm in South America. In addition, the results highlight the importance of using WGS to reveal Lm long-term persistence.\n\nWhole-genome sequencing reveals Listeria monocytogenes diversity and allows identification of long-term persistent strains in Brazil.", "token_count": 452, "char_count": 1489, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": {"genes": ["SL9", "SL2", "SL3", "SL218", "SL315", "CT4429", "ST9", "CT4420", "ST520"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:18.869328", "source": {"split": "train_shard_00000", "doc_id": 2991}, "chunk_id": "train_shard_00000_2991_0", "global_id": 3301}
{"text": "Probiotics used in aquaculture are mostly from non-fish sources, as a result ineffective in eliciting the desired effects in aquatic animals. In this study, three Bacillus species were isolated from the digestive tract of freshwater fish Oreochromis niloticus and characterised based on their morphological, biochemical and evolutionary relationships. Their probiotic potentials were evaluated based on their ability to tolerate low pH, bile salt concentration, high temperatures, adhesion ability (auto-aggregation and hydrophobicity), haemolytic activity and antimicrobial activity including biosafety assay. Three Bacillus strains identified as Bacillus velezensis TPS3N (MK130897), Bacillus subtilis TPS4 (MK130899) and Bacillus amyloliquefaciens TPS17 (MK130898) were designated as TPS3N, TPS4 and TPS17, respectively. TPS3N and TPS17 were α-haemolytic, while TPS4 was γ-haemolytic. The three isolates had higher viability ability after exposure to higher temperatures (80 °C, 90 °C and 100 °C) and were resistant to low pH (1) and bile salt concentration (0.5%) as well as high cell surface hydrophobicity and auto-aggregation. The three isolates were compatible with one another and thus can be used in consortia. These strains were susceptible to gentamicin, cephalexin, ampicillin, ceftriaxone, kanamycin, amikacin, penicillin, cefoperazone, chloramphenicol, erythromycin, tetracycline, doxycycline, ciprofloxacin, clindamycin (except TPS4) and furazolidone (except TPS17)", "token_count": 471, "char_count": 1481, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6907, "quality_score": 0.8454, "entities": {"genes": ["TPS3N", "TPS4", "MK130898", "TPS17", "MK130897", "MK130899"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph", "temperature"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:19.487163", "source": {"split": "train_shard_00000", "doc_id": 2992}, "chunk_id": "train_shard_00000_2992_0", "global_id": 3302}
{"text": "The antimicrobial assessment showed that among the three isolates, TPS3N and TPS17 exhibited good antimicrobial activity against the three fish pathogens (Streptococcus agalactiae, Aeromonas hydrophila, Vibrio harveyi), while TPS4 was effective against Streptococcus agalactiae only. The results of this work suggest that Bacillus strains TPS3N, TPS4 and TPS17 could be considered as potential probiotics in tilapia aquaculture.\n\nIn vitro Assessment of the Probiotic Characteristics of Three Bacillus Species from the Gut of Nile Tilapia, Oreochromis niloticus.", "token_count": 172, "char_count": 561, "word_count": 76, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": {"genes": ["TPS3N", "TPS17", "TPS4"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:19.913971", "source": {"split": "train_shard_00000", "doc_id": 2992}, "chunk_id": "train_shard_00000_2992_1", "global_id": 3303}
{"text": "The present study aimed to evaluate the probiotic characteristics of certain microbial strains for potential use as feed additives. Three bacterial strains and a yeast previously isolated from different environments were investigated. The strains were subjected to molecular identification and established as Lactobacillus paracasei CP133, Lactobacillus plantarum CP134, Bacillus subtilis CP350 and Saccharomyces cerevisiae CP605. Lactobacillus sp. CP133 and CP134 exhibited antibiosis, antibiotic activity, and relative odor reduction ability. Bacillus subtilis CP350 was thermotolerant, reduced hydrogen sulfide gas and showed significant proteolytic activity, whereas Saccharomyces cerevisiae CP605 exhibited high acid and bile salt tolerance. In general, the isolates in this study demonstrated improved functional characteristics, particularly acid and bile tolerance and relative cell adhesion to HT-29 monolayer cell line. Results in this work provides multifunctional probiotic characteristics of the strains for potential development of probiotics and cleaning of the environment.\n\nInvestigating the probiotic characteristics of four microbial strains with potential application in feed industry.", "token_count": 293, "char_count": 1205, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": {"genes": ["CP133", "CP605", "CP350", "CP134"], "proteins": [], "pathways": [], "organisms": ["yeast", "saccharomyces"], "conditions": ["acid", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:20.453008", "source": {"split": "train_shard_00000", "doc_id": 2993}, "chunk_id": "train_shard_00000_2993_0", "global_id": 3304}
{"text": "The genus\n\nThe poplar pangenome provides insights into the evolutionary history of the genus.", "token_count": 21, "char_count": 93, "word_count": 14, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:20.798388", "source": {"split": "train_shard_00000", "doc_id": 2994}, "chunk_id": "train_shard_00000_2994_0", "global_id": 3305}
{"text": "The application of phytases for animal feed in developing countries is limited due to the high cost of these enzymes, determined by the importation fees and the expensive substrates used for their production. In this work, we have used agroindustrial byproducts for the production of extracts containing phytases, which were accessed for their stability focusing on the conditions found in the gastrointestinal tract of pigs. The fungus Acremonim zeae presented higher phytase production in medium containing cornmeal, while the yeast Kluyveromyces marxianus produced 10-fold more phytase when cultivated on rice bran. Process optimization increased the difference in productivity to more than 300 fold. The phytase from A. zeae was thermostable, with higher activity at neutral pH and 50 °C, but was inhibited at pH 2.5 and by various ions. The phytase activity in the K. marxianus extract was stable at a wide range of conditions, which indicates the presence of at least two enzymes. As far as we know, this manuscript describes for the first time the phytase production and the characteristics of the extracts produced by both these microbial species. These enzymes could be produced at low cost and have potential to replace enzymes currently imported for this purpose.\n\nProduction of Fungal Phytases from Agroindustrial Byproducts for Pig Diets.", "token_count": 323, "char_count": 1351, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6048, "quality_score": 0.8024, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:21.347430", "source": {"split": "train_shard_00000", "doc_id": 2995}, "chunk_id": "train_shard_00000_2995_0", "global_id": 3306}
{"text": "In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of primary to secondary bile acids have been known to be involved in the immune regulation of human physiology. Several 16S amplicon-based studies with inflammatory bowel disease (IBD) subjects were found to have an association with the level of fecal bile acids. However, a detailed investigation of all the bile salt biotransformation genes in the gut microbiome of healthy and IBD subjects has not been performed.\n\nMetagenomic analysis of bile salt biotransformation in the human gut microbiome.", "token_count": 159, "char_count": 637, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6531, "quality_score": 0.8265, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:21.770885", "source": {"split": "train_shard_00000", "doc_id": 2996}, "chunk_id": "train_shard_00000_2996_0", "global_id": 3307}
{"text": "Bile salts tend to form micelles in aqueous media and can thereby contribute to drug solubilization; they also exhibit crystallization inhibition properties that can stabilize supersaturated drug solutions. Herein, we explore conjugation of bile salts with polysaccharides to create new, amphiphilic polysaccharide derivatives with intriguing properties, portending broad utility in various applications. We introduce efficient conjugation of cholesterol (as a model steroid), lithocholic acid, and deoxycholic acid by mild, modular olefin cross-metathesis reactions. These small molecules were first modified with an acrylate group from the A-ring hydroxyl, then reacted with cellulose derivatives bearing olefin-terminated metathesis \"handles\". Successful conjugation of bile acids has demonstrated chemoselective cross-metathesis with complex, polyfunctional structures, and large multi-ring systems. It also enabled an efficient, general pathway for polysaccharide-bile salt conjugates, which promise synergy for applications such as amorphous solid dispersion (ASD).\n\nConjugation of bile esters to cellulose by olefin cross-metathesis: A strategy for accessing complex polysaccharide structures.", "token_count": 299, "char_count": 1200, "word_count": 151, "semantic_coherence": 1, "information_density": 0.7748, "quality_score": 0.8874, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:22.320223", "source": {"split": "train_shard_00000", "doc_id": 2997}, "chunk_id": "train_shard_00000_2997_0", "global_id": 3308}
{"text": "t-Butyl 6-cyano-(3R,5R)-dihydroxyhexanoate ((3R,5R)-2) is an important chiral diol synthon of atorvastatin calcium. Previously, we constructed a variant KmAKR-W297H (M1) of Kluyveromyces marxianus aldo-keto reductase (KmAKR, designated as M0), possessing excellent diastereoselectivity but moderate activity towards t-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate ((5R)-1). In this work, KmAKR-W297H/Y296W/K29H (M3) was developed via semi-rational design. It exhibited much improved catalytic efficiency towards (5R)-1. The K\n\nImproving the catalytic efficiency of aldo-keto reductase KmAKR towards t-butyl 6-cyano-(3R,5R)-dihydroxyhexanoate via semi-rational design.", "token_count": 253, "char_count": 663, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:22.787895", "source": {"split": "train_shard_00000", "doc_id": 2998}, "chunk_id": "train_shard_00000_2998_0", "global_id": 3309}
{"text": "The study was conducted to investigate the expression and activity of key lipolytic enzymes during the ontogenetic development of Clarias magur. After partial characterization, the messenger RNA (mRNA) expression analysis of lipoprotein lipase (LPL), pancreatic triacylglycerol lipase (PL), and bile salt-activated lipase (BAL) genes along with the specific lipase activity were performed in larvae from Day 1 after hatching till 34-day posthatch (dph). Heterogeneous patterns of mRNA expression were shown by the important lipolytic enzymes and were detected before first exogenous feeding during the yolk-sac stage. LPL started increasing from 13 dph and peaked at 16 dph followed by a declining trend till 34 dph. However, the PL observed to be peaking at 9, 22, and 30 dph. Similarly, BAL showed an increasing trend from 11 to 22 dph with a significantly high level of mRNA expression at 16 dph. Later, the specific lipase activity was evaluated which appears at Day 1 after hatching with a progressive increase from 7 to 16 dph and a further declining trend afterwards with a peak at 22 dph. The results indicated the development of exocrine pancreas at 16 dph. Furthermore, the transcript levels and the activity of lipases were regulated with the age. Hence, the present study can be helpful in devising different strategies containing optimum lipid levels at a suitable stage of development for improving the survival during larval rearing. Furthermore, the study could be a baseline for elucidating the optimized dietary lipid levels of this catfish during its larval rearing.\n\nExpression and activity of key lipases during the larval development of walking catfish (Clarias magur).", "token_count": 437, "char_count": 1691, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5379, "quality_score": 0.7689, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:23.397485", "source": {"split": "train_shard_00000", "doc_id": 2999}, "chunk_id": "train_shard_00000_2999_0", "global_id": 3310}
{"text": "GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops.", "token_count": 518, "char_count": 1927, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6993, "quality_score": 0.8496, "entities": {"genes": ["PIECE2"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:14:24.036306", "source": {"split": "train_shard_00000", "doc_id": 3000}, "chunk_id": "train_shard_00000_3000_0", "global_id": 3311}
{"text": "GrainGenes: centralized small grain resources and digital platform for geneticists and breeders.", "token_count": 20, "char_count": 96, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:24.383207", "source": {"split": "train_shard_00000", "doc_id": 3000}, "chunk_id": "train_shard_00000_3000_1", "global_id": 3312}
{"text": "Bile salt export pump (BSEP) have been confirmed to play an important role for bile acid canalicular export in the treatment of cholestasis. In this study, we investigated the stimulatory effect of emodin on BSEP signaling pathway in cholestasis.\n\nEmodin Rescues Intrahepatic Cholestasis via Stimulating FXR/BSEP Pathway in Promoting the Canalicular Export of Accumulated Bile.", "token_count": 107, "char_count": 377, "word_count": 55, "semantic_coherence": 1, "information_density": 0.7455, "quality_score": 0.8727, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:25.064480", "source": {"split": "train_shard_00000", "doc_id": 3001}, "chunk_id": "train_shard_00000_3001_0", "global_id": 3313}
{"text": "Hydrophilic bile salts, ursodeoxycholate and hyodeoxycholate, have choleretic effects. ABCB4, a member of the ABC transporter family, is essential for the secretion of phospholipids from hepatocytes into bile. In this study, we assessed the effects of taurine- or glycine-conjugated cholate, ursodeoxycholate and hyodeoxycholate on the ABCB4-mediated phosphatidylcholine (PC) efflux using Abcb4 knockout mice and HEK293 cells stably expressing ABCB4. To evaluate the effects of bile salts on bile formation in Abcb4\n\nEnhancing effect of taurohyodeoxycholate on ABCB4-mediated phospholipid efflux.", "token_count": 194, "char_count": 596, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7595, "quality_score": 0.8797, "entities": {"genes": ["HEK293", "ABCB4"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:25.505152", "source": {"split": "train_shard_00000", "doc_id": 3002}, "chunk_id": "train_shard_00000_3002_0", "global_id": 3314}
{"text": "Fermented cereal doughs constitute a predominant part of West African diets. The environment of fermented doughs can be hostile for microbial survival due to high levels of microbial metabolites such as weak carboxylic organic acids and ethanol. In order to get a better understanding of the intrinsic factors affecting the microbial successions of yeasts during dough fermentation, survival and physiological responses of the yeasts associated with West African fermented cereal doughs were investigated at exposure to relevant concentrations of microbial inhibitory compounds. Three strains each of the predominant species, i.e. Saccharomyces cerevisiae, Kluyveromyces marxianus, Pichia kudriavzevii as well as the opportunistic pathogen Candida glabrata were studied. The strains were exposed to individual stress factors of cereal doughs, i.e. (i) pH 3.4, (ii) 3% (v/v) ethanol (EtOH\n\nEffects of intrinsic microbial stress factors on viability and physiological condition of yeasts isolated from spontaneously fermented cereal doughs.", "token_count": 272, "char_count": 1038, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6483, "quality_score": 0.8241, "entities": {"genes": [], "proteins": [], "pathways": ["fermentation"], "organisms": ["marxianus", "kluyveromyces", "yeast", "saccharomyces"], "conditions": ["acid", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:26.037060", "source": {"split": "train_shard_00000", "doc_id": 3003}, "chunk_id": "train_shard_00000_3003_0", "global_id": 3315}
{"text": "Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried bla\n\nCore genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain.", "token_count": 344, "char_count": 1259, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": {"genes": ["ST469"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:26.589907", "source": {"split": "train_shard_00000", "doc_id": 3004}, "chunk_id": "train_shard_00000_3004_0", "global_id": 3316}
{"text": "Bile salts (BS) form hydrophobic Small's primary micelles at concentrations above the critical micelle concentration (CMC), while at concentrations above 3CMC they form secondary micelles (by the association of primary micelles via H-bonds). In this paper the self-associations of the anions of isohenodeoxycholic acid (3-epimer of henodeoxycholic acid, ICD) and the anions of isoursodeoxycholic acid (3-epimer of ursodeoxycholic acid, IUD) are examined, since the thermodynamic parameters of their self-association have not yet been published. Forming of IUD aggregates with two or three building units is slightly more favorable via α sides of steroid skeletons, regarding hydrophobicity, while regarding steric repulsive interactions it is more favorable to associate via β sides. Due to this, IUD in the vicinity of the CMC can form primary micelles by association of IUD particles both from the convex side and from the concave side of the steroid ring system. Therefore, IUD is significantly more prone to initial micellization than bile salt derivatives whose steroidal skeletons contain equatorially oriented OH groups.\n\nSelf-association of sodium isoursodeoxycholate and sodium isohenodeoxycholate in water.", "token_count": 309, "char_count": 1216, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:27.133518", "source": {"split": "train_shard_00000", "doc_id": 3005}, "chunk_id": "train_shard_00000_3005_0", "global_id": 3317}
{"text": "The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intragroup but limited intergroup recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly overrepresented in Group A compared with Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly overrepresented in Group B compared with Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts.\n\nThe Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages.", "token_count": 390, "char_count": 1634, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5863, "quality_score": 0.7932, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:27.726318", "source": {"split": "train_shard_00000", "doc_id": 3006}, "chunk_id": "train_shard_00000_3006_0", "global_id": 3318}
{"text": "The endo-polygalacturonase enzyme (endoPG: EC 3.2.1.15) plays an important role in the fruit juice and wine industries, so the development of new tools for the quantitative and qualitative analysis of its enzymatic action is necessary. In this work, we report the development of a simple, fast and practical method that did not use any chemical reagent to identify and evaluate the action of the endoPG enzyme, produced by the yeast Kluyveromyces marxianus CCT3172, using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy combined with principal component analysis-linear discriminant analysis (PCA-LDA). This method evaluated the action of the endoPG enzyme on the polygalacturonic acid (PGA) substrate at 5 different times (0, 10, 15, 20 and 30 minutes), and at each time interval the samples were analyzed by ATR-FTIR. It was demonstrated that there was clear segregation between the samples that were and that were not subjected to the action of the endoPG enzyme, and it was also possible to distinguish the samples that were subjected to different incubation times with the enzyme. Through PCA-LDA it was possible to obtain wavelengths that are biomarkers for this enzymatic reaction and the observed changes as a function of hydrolysis duration were found to be in agreement with the breakdown of the glycosidic chain (1011 cm\n\nEvaluation of Kluyveromyces marxianus endo-polygalacturonase activity through ATR-FTIR.", "token_count": 385, "char_count": 1451, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8005, "entities": {"genes": ["CCT3172"], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["acid"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:28.324571", "source": {"split": "train_shard_00000", "doc_id": 3007}, "chunk_id": "train_shard_00000_3007_0", "global_id": 3319}
{"text": "Enterococcus faecium is a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing-based study on 96 multidrug-resistant E. faecium strains that asymptomatically colonized five patients with the aim of describing the genome dynamics of this species. The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged to E. faecium clade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which consisted entirely of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalization. We estimated the evolutionary rate of two clonal groups that each colonized single patients at 12.6 and 25.2 single-nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of 12 different insertion sequence (IS) elements, with ISEfa5 showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5 excision and insertion into the genome during gut colonization. Our findings show that the E. faecium genome is highly dynamic during asymptomatic colonization of the human gut. We observed considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.\n\nEnterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization.", "token_count": 506, "char_count": 2202, "word_count": 318, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["gut", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:28.968614", "source": {"split": "train_shard_00000", "doc_id": 3008}, "chunk_id": "train_shard_00000_3008_0", "global_id": 3320}
{"text": "The aim of this study was to analyze the alarming spread of NDM-1- and OXA-48-co-producing Klebsiella pneumoniae clinical isolates, collected between October 2016 and January 2018 in a neonatal intensive care unit of the University Hospital, Catania, Italy, through whole genome sequencing. All confirmed carbapenem-resistant K. pneumoniae (CRKp) isolates were characterized pheno- and geno-typically, as well as by whole genome sequencing (WGS). A total of 13 CRKp isolates were identified from 13 patients. Pulsed-field gel electrophoresis (PFGE) was performed, and the multilocus sequence typing (MLST) scheme used was based on the gene sequence as published on the MLST Pasteur website. Core genome MLST (cgMLST) was also performed. All isolates co-carried bla\n\nEmergence of two novel sequence types (3366 and 3367) NDM-1- and OXA-48-co-producing K. pneumoniae in Italy.", "token_count": 267, "char_count": 874, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:29.523740", "source": {"split": "train_shard_00000", "doc_id": 3009}, "chunk_id": "train_shard_00000_3009_0", "global_id": 3321}
{"text": "Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone-responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.\n\nPhylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species.", "token_count": 379, "char_count": 1542, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6295, "quality_score": 0.8147, "entities": {"genes": ["ST16", "ST82", "ST55", "ST170"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:30.118230", "source": {"split": "train_shard_00000", "doc_id": 3010}, "chunk_id": "train_shard_00000_3010_0", "global_id": 3322}
{"text": "Weissella cibaria CMU and CMS1 are known to exert beneficial effects on the oral cavity but have not yet been determined to be generally recognized as safe (GRAS), although they are used as commercial strains in Korea. We aimed to verify the safety of W. cibaria CMU and CMS1 strains through phenotypic and genotypic analyses. Their safety was evaluated by a minimum inhibitory concentration assay for 14 antibiotics, DNA analysis for 28 antibiotic resistance genes (ARGs) and one conjugative element, antibiotic resistance gene transferability, virulence gene analysis, hemolysis, mucin degradation, toxic metabolite production, and platelet aggregation reaction. W. cibaria CMU showed higher kanamycin resistance than the European Food Safety Authority (EFSA) cut-off, but this resistance was not transferred to the recipient strain. W. cibaria CMU and CMS1 lacked ARGs in chromosomes and plasmids, and genetic analysis confirmed that antibiotic resistance of kanamycin was an intrinsic characteristic of W. cibaria. Additionally, these strains did not harbor virulence genes associated with pathogenic bacteria and lacked toxic metabolite production, β-hemolysis, mucin degradation, bile salt deconjugation, β-glucuronidase, nitroreductase activity, gelatin liquefaction, phenylalanine degradation, and platelet aggregation. Our findings demonstrate that W. cibaria CMU and CMS1 can achieve the GRAS status in future.\n\nSafety Evaluation of Oral Care Probiotics", "token_count": 380, "char_count": 1463, "word_count": 204, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": {"genes": ["CMS1"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:30.685251", "source": {"split": "train_shard_00000", "doc_id": 3011}, "chunk_id": "train_shard_00000_3011_0", "global_id": 3323}
{"text": "This study aimed to evaluate the functional and probiotic properties of Lactobacillus acidophilus SJLH001 (La-SJLH001) isolated from fermented food via mechanism analysis based on transcriptomics and culturomics. La-SJLH001 exhibited good tolerance to acid and bile salt conditions with anti-diabetic ability and cholesterol assimilation activity in vitro. Supplementation with La-SJLH001 also resulted in a significant reduction in host oral glucose and serum total cholesterol levels in vivo. Transcriptome profiles and qPCR analysis suggested that La-SJLH001 significantly regulated the transcription of key genes involved in glucose transportation, cholesterol metabolism, ion channels, and immune response, resulting in improved glucose homeostasis and cholesterol metabolism. La-SJLH001 significantly affected the structure of intestinal microbiota when analyzed by using culturomics coupled with MALDI-TOF MS. These results indicated that La-SJLH001 may be a mechanistic target for the control of diabetes with great potential in the application of probiotic products.\n\nMechanism analysis of improved glucose homeostasis and cholesterol metabolism in high-fat-induced obese mice treated with La-SJLH001 via transcriptomics and culturomics.", "token_count": 339, "char_count": 1246, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6646, "quality_score": 0.8323, "entities": {"genes": ["SJLH001"], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:31.237156", "source": {"split": "train_shard_00000", "doc_id": 3012}, "chunk_id": "train_shard_00000_3012_0", "global_id": 3324}
{"text": "Microbial bile salt hydrolases (BSHs), a member of cholylglycine hydrolase (CGH) family, catalyze the hydrolysis of glycine and taurine-linked bile salts in the small intestine of human. BSH is evolutionarily related to penicillin V acylase (PVA) which hydrolyses a penicillin V and is also a member of CGH family. Although, five of the six amino acids, C2, R16, D19, N170, N79 and R223, supposed to be responsible for catalytic activity of BSH enzyme, are strictly conserved in all CGH family members, N79 is partially conserved in this family. In this study, in order to analyze the correlation between N79 and catalytic activity or substrate specificity of BSH, the polar and acidic N79 was substituted for the aliphatic and hydrophobic V79 by PCR-based site directed mutagenesis and mutant recombinant BSH was expressed in E. coli BLR(DE3). While the effects of the mutation on catalytic activity and substrate specificity of BSH were detected by ninhydrin assay. The effect of this mutation on the stability of the BSH was observed by SDS-PAGE analysis. Although V79 mutation resulted in stable BSH, it reduced the catalytic activity and altered substrate specificity of BSH. The results suggested that N79 might be important for substrate binding and catalytic turnover of BSH.\n\nAsparagine 79 is an important amino acid for catalytic activity and substrate specificity of bile salt hydrolase (BSH).", "token_count": 402, "char_count": 1404, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5495, "quality_score": 0.7748, "entities": {"genes": ["DE3"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:31.834727", "source": {"split": "train_shard_00000", "doc_id": 3013}, "chunk_id": "train_shard_00000_3013_0", "global_id": 3325}
{"text": "To study the formation and characterize the structure of mixed complexes of oppositely charged block copolymers and surfactants are of great significance for practical applications, e.g., in drug carrier formulations that are based on electrostatically assisted assembly. In this context, biocompatible block copolymers and biosurfactants (like bile salts) are particularly interesting. In this work, we report on the co-assembly in dilute aqueous solution between a cationic poly(N-isopropyl acryl amide) (PNIPAM) diblock copolymer and the oppositely charged bile salt surfactant sodium deoxycholate at ambient temperature. The cryogenic transmission electron microscopy (cryo-TEM) experiments revealed the co-existence of two types of co-assembled complexes of radically different morphology and inner structure. They are formed mainly as a result of the electrostatic attraction between the positively charged copolymer blocks and bile salt anions and highlight the potential of using linear amphiphilic block copolymers as bile salt sequestrants in the treatment of bile acid malabsorption and hypercholesterolemia. The first complex of globular morphology has a coacervate core of deoxycholate anions and charged copolymer blocks surrounded by a PNIPAM corona. The second complex has an intriguing tape-like supramolecular morphology of several micrometer in length that is striped in the direction of the long axis. A model is presented in which the stretched cationic blocks of several block copolymers interact electrostatically with the bile salt molecules that are associated to form a zipper-like structure. The tape is covered on both sides by the PNIPAM chains that stabilize the overall complex in solution. In addition to cryo-TEM, the mixed system was investigated in a range of molar charge fractions at a constant copolymer concentration by static light scattering, small angle X-ray scattering, and electrophoretic mobility measurements.\n\nBlock copolymers as bile salt sequestrants: intriguing structures formed in a mixture of an oppositely charged amphiphilic block copolymer and bile salt.", "token_count": 504, "char_count": 2111, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5518, "quality_score": 0.7759, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph", "temperature"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:32.457062", "source": {"split": "train_shard_00000", "doc_id": 3014}, "chunk_id": "train_shard_00000_3014_0", "global_id": 3326}
{"text": "Comparative genomics has proven useful in exploring the biodiversity of phages and understanding phage-host interactions. This knowledge is particularly useful for phages infecting Streptococcus thermophilus, as they constitute a constant threat during dairy fermentations. Here, we explore the genetic diversity of S. thermophilus phages to identify genetic determinants with a signature for host specificity, which could be linked to the bacterial receptor genotype. A comparative genomic analysis was performed on 142 S. thermophilus phage genomes, 55 of which were sequenced in this study. Effectively, 94 phages were assigned to the group cos (DT1), 36 to the group pac (O1205), six to the group 5093, and six to the group 987. The core genome-based phylogeny of phages from the two dominating groups and their receptor binding protein (RBP) phylogeny corresponded to the phage host-range. A role of RBP in host recognition was confirmed by constructing a fluorescent derivative of the RBP of phage CHPC951, followed by studying the binding of the protein to the host strain. Furthermore, the RBP phylogeny of the cos group was found to correlate with the host genotype of the exocellular polysaccharide-encoding operon. These findings provide novel insights towards developing strategies to combat phage infections in dairies.\n\nA comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages.", "token_count": 365, "char_count": 1451, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": {"genes": ["CHPC951", "DT1"], "proteins": [], "pathways": ["fermentation"], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:33.015113", "source": {"split": "train_shard_00000", "doc_id": 3015}, "chunk_id": "train_shard_00000_3015_0", "global_id": 3327}
{"text": "The metagenome of the gut microbiome encodes tremendous potential for biosynthesizing and transforming small-molecule metabolites through the activities of enzymes expressed by intestinal bacteria. Accordingly, elucidating this metabolic network is critical for understanding how the gut microbiota contributes to health and disease. Bile acids, which are first biosynthesized in the liver, are modified in the gut by enzymes expressed by commensal bacteria into secondary bile acids, which regulate myriad host processes, including lipid metabolism, glucose metabolism, and immune homeostasis. The gateway reaction of secondary bile acid biosynthesis is mediated by bile salt hydrolases (BSHs), bacterial cysteine hydrolases whose action precedes other bile acid modifications within the gut. To assess how changes in bile acid metabolism mediated by certain intestinal microbiota impact gut physiology and pathobiology, methods are needed to directly examine the activities of BSHs because they are master regulators of intestinal bile acid metabolism. Here, we developed chemoproteomic tools to profile changes in gut microbiome-associated BSH activity. We showed that these probes can label active BSHs in model microorganisms, including relevant gut anaerobes, and in mouse gut microbiomes. Using these tools, we identified altered BSH activities in a murine model of inflammatory bowel disease, in this case, colitis induced by dextran sodium sulfate, leading to changes in bile acid metabolism that could impact host metabolism and immunity. Importantly, our findings reveal that alterations in BSH enzymatic activities within the gut microbiome do not correlate with changes in gene abundance as determined by metagenomic sequencing, highlighting the utility of chemoproteomic approaches for interrogating the metabolic activities of the gut microbiota.\n\nChemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity.", "token_count": 470, "char_count": 1946, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5799, "quality_score": 0.79, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["gut", "acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:33.636445", "source": {"split": "train_shard_00000", "doc_id": 3016}, "chunk_id": "train_shard_00000_3016_0", "global_id": 3328}
{"text": "Probiotic bacteria are usually encapsulated to increase their survival through passage of the simulated gastrointestinal tract (GIT). Four\n\nViability of 4 Probiotic Bacteria Microencapsulated with Arrowroot Starch in the Simulated Gastrointestinal Tract (GIT) and Yoghurt.", "token_count": 74, "char_count": 272, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:34.002893", "source": {"split": "train_shard_00000", "doc_id": 3017}, "chunk_id": "train_shard_00000_3017_0", "global_id": 3329}
{"text": "Lyme disease, initially described as Lyme arthritis, was reported before nucleic-acid based detection technologies were available. The most widely used diagnostic tests for Lyme disease are based on the serologic detection of antibodies produced against antigens derived from a single strain of\n\nSingle Core Genome Sequencing for Detection of both", "token_count": 74, "char_count": 347, "word_count": 50, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:34.371693", "source": {"split": "train_shard_00000", "doc_id": 3018}, "chunk_id": "train_shard_00000_3018_0", "global_id": 3330}
{"text": "Active secretion of bile salts into the canalicular lumen drives bile formation and promotes biliary cholesterol and phospholipid output. Disrupting hepatic bile salt uptake, by inhibition of sodium-taurocholate cotransporting polypetide (NTCP; Slc10a1) with Myrcludex B, is expected to limit bile salt flux through the liver and thereby to decrease biliary lipid excretion. Here, we show that Myrcludex B-mediated NTCP inhibition actually causes an increase in biliary cholesterol and phospholipid excretion whereas biliary bile salt output and bile salt composition remains unchanged. Increased lysosomal discharge into bile was excluded as a potential contributor to increased biliary lipid secretion. Induction of cholesterol secretion was not a consequence of increased ATP-binding cassette subfamily G member 5/8 activity given that NTCP inhibition still promoted cholesterol excretion in Abcg8\n\nBlocking Sodium-Taurocholate Cotransporting Polypeptide Stimulates Biliary Cholesterol and Phospholipid Secretion in Mice.", "token_count": 282, "char_count": 1024, "word_count": 136, "semantic_coherence": 1, "information_density": 0.6397, "quality_score": 0.8199, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:34.913306", "source": {"split": "train_shard_00000", "doc_id": 3019}, "chunk_id": "train_shard_00000_3019_0", "global_id": 3331}
{"text": "Two-component systems (TCSs) are dominant regulating components in bacteria for responding to environmental stimuli. However, little information is available on how TCSs in\n\nThe LiaFSR and BsrXRS Systems Contribute to Bile Salt Resistance in", "token_count": 57, "char_count": 241, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:35.271920", "source": {"split": "train_shard_00000", "doc_id": 3020}, "chunk_id": "train_shard_00000_3020_0", "global_id": 3332}
{"text": "In recent years, the fast and accurate identification of the Candida species is of great importance as the response to antifungal treatment differs among species. Following the treatment of several immunosuppressive diseases, fungal infections can emerge. The aim of this study was to compare the accuracy, costs and time of result periods of the methods used in the identification of the most common human fungal infectious agent, Candida strains. From various clinical samples sent to the Microbiology Laboratory of Karabuk University Training and Research Hospital between July 2016-December 2017, a total of 91 yeast isolates cultivated in blood agar (Becton Dickinson, USA) and/or Sabouraud dextrose agar (SDA-Oxoid, UK), confirmed with colony morphology and microscopic appearance, identified as Candida species with a fully automated identification system (Phoenix™ Yeast ID Panel, Becton Dickinson Diagnostics, USA) were included in the study. All the samples were examined with sequence analysis using ITS1 forward 5'-TCC GTA GGT GAA CCT GCG G-3' and ITS4 reverse 5'-TCC TCC GCT TAT TGA TAT GC-3' primers (Iontek, Turkey) and the matrix-assisted laser desorption-ionisation time of flight mass spectrometry (MALDI TOF-MS) systems. Molecular sequence analysis was accepted as the gold standard method and the results were compared with those of the other methods MALDI TOF-MS and Phoenix™ Yeast ID Panel in respect of the accuracy of the identification of Candida strains. According to the results of the DNA sequence analysis of the 91 Candida isolates included in the study, 24 were identified as Candida albicans, 20 Candida tropicalis, 16 Candida parapsilosis, 13 Candida glabrata, seven Candida kefyr, six Candida krusei, two of each Candida dubliniensis, Candida guilliermondi and one Candida lusitaniae", "token_count": 477, "char_count": 1817, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.81, "entities": {"genes": ["ITS1", "ITS4"], "proteins": [], "pathways": [], "organisms": ["yeast"], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:35.894891", "source": {"split": "train_shard_00000", "doc_id": 3021}, "chunk_id": "train_shard_00000_3021_0", "global_id": 3333}
{"text": "Compared to the results of the DNA sequence analysis, the accurate identification of the fully automated Phoenix™ system and the MALDI TOF-MS system was found as 92.3% and 97.8%, respectively. In addition to accuracy, costs and time of result periods of the three methods were also compared. Disregarding the cost of the device in the 3 methods, when the comparison was made of the cost per test and the time to results after pure production in SDA agar, the MALDI TOF-MS system was determined to have the lowest costs and provided results in the shortest time. As some of the Candida strains have antifungal resistance, identification of the strains must be a priority in respect of starting early treatment. The MALDI TOF-MS system has high performance in accurate identification, low costs and the system provides the results within minutes, thereby allowing immediate decision to be made for the antifungal treatment to be started. Thus, the morbidity, mortality and cost rates will be reduced. In conclusion, as the MALDI TOF-MS is a rapid, reliable and low cost per test system, it can be considered suitable for routine use in laboratories.\n\n[A comparison of the costs, reliability and time of result periods of widely used methods, new molecular methods and MALDI TOF-MS in the routine diagnosis of Candida strains].", "token_count": 302, "char_count": 1324, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5115, "quality_score": 0.7558, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:36.435358", "source": {"split": "train_shard_00000", "doc_id": 3021}, "chunk_id": "train_shard_00000_3021_1", "global_id": 3334}
{"text": "Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.\n\nAnalysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages.", "token_count": 441, "char_count": 1896, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6241, "quality_score": 0.812, "entities": {"genes": ["SPO1"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:37.047818", "source": {"split": "train_shard_00000", "doc_id": 3022}, "chunk_id": "train_shard_00000_3022_0", "global_id": 3335}
{"text": "Whole-genome sequencing is increasingly adopted in clinical settings to identify pathogen transmissions, though largely as a retrospective tool. Prospective monitoring, in which samples are continuously added and compared to previous samples, can generate more actionable information. To enable prospective pathogen comparison, genomic relatedness metrics based on single-nucleotide differences must be consistent across time, efficient to compute and reliable for a large variety of samples. The choice of genomic regions to compare, i.e., the core genome, is critical to obtain a good metric. We propose a novel core genome method that selects conserved sequences in the reference genome by comparing its k-mer content to that of publicly available genome assemblies. The conserved-sequence genome is sample set-independent, which enables prospective pathogen monitoring. Based on clinical data sets of 3436 S. aureus, 1362 K. pneumoniae and 348 E. faecium samples, ROC curves demonstrate that the conserved-sequence genome disambiguates same-patient samples better than a core genome consisting of conserved genes. The conserved-sequence genome confirms outbreak samples with high sensitivity: in a set of 2335 S. aureus samples, it correctly identifies 44 out of 44 known outbreak samples, whereas the conserved-gene method confirms 38 known outbreak samples.\n\nA core genome approach that enables prospective and dynamic monitoring of infectious outbreaks.", "token_count": 336, "char_count": 1460, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:37.599212", "source": {"split": "train_shard_00000", "doc_id": 3023}, "chunk_id": "train_shard_00000_3023_0", "global_id": 3336}
{"text": "Food animals are considered reservoirs of methicillin-resistant Staphylococcus aureus (MRSA) and are implicated in their zoonotic transmission in the farm-to-plate continuum. LA-MRSA has been reported as a zoonotic agent that has the potential to spread to humans and may cause infections in at-risk groups. In this study, whole genome sequencing was used to describe the genetic environment (resistance mechanisms, virulence factors and mobile genetic elements) and investigate the genetic lineages of MRSA isolates from pigs in Cameroonian and South African abattoirs. During March-October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were de novo-assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated, and antibiotic resistance genes, virulence factors, plasmids, SCCmec and phage elements were identified with ResFinder, Virulence Finder, PlasmidFinder, SCCmec Finder and PHAST, respectively. Core genome single nucleotide analysis was undertaken to assess clonal relatedness among isolates. A lower MRSA prevalence was observed in pigs in Cameroon (n = 1/13; 0.07%) compared with South Africa (n = 4/22; 18.18%), and none of the workers were colonized by MRSA. Genome analysis identified various antibiotic resistance genes along with six virulence factors in all isolates. All MRSA isolates belonged to the clonal lineage ST398 (spa-type t011) and harboured the type Vc SCCmec and several plasmids. Our study shows that the livestock-associated MRSA clonal lineage ST398 is already present in both Cameroon and South Africa and is probably underestimated in the absence of molecular epidemiological studies. It reveals the serious food safety and public health threat associated with this animal strain and underscores the need for interventions to contain this resistant clone.", "token_count": 519, "char_count": 1979, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": {"genes": ["ST398"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:14:38.230680", "source": {"split": "train_shard_00000", "doc_id": 3024}, "chunk_id": "train_shard_00000_3024_0", "global_id": 3337}
{"text": "Genome analysis of methicillin-resistant Staphylococcus aureus isolated from pigs: Detection of the clonal lineage ST398 in Cameroon and South Africa.", "token_count": 45, "char_count": 150, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": {"genes": ["ST398"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:38.579789", "source": {"split": "train_shard_00000", "doc_id": 3024}, "chunk_id": "train_shard_00000_3024_1", "global_id": 3338}
{"text": "The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals. Soils and surface waters also host a high diversity of non-pathogenic Leptospira and species for which the virulence status is not clearly established. The genus Leptospira is currently divided into 35 species classified into three phylogenetic clusters, which supposedly correlate with the virulence of the bacteria. In this study, a total of 90 Leptospira strains isolated from different environments worldwide including Japan, Malaysia, New Caledonia, Algeria, mainland France, and the island of Mayotte in the Indian Ocean were sequenced. A comparison of average nucleotide identity (ANI) values of genomes of the 90 isolates and representative genomes of known species revealed 30 new Leptospira species. These data also supported the existence of two clades and 4 subclades. To avoid classification that strongly implies assumption on the virulence status of the lineages, we called them P1, P2, S1, S2. One of these subclades has not yet been described and is composed of Leptospira idonii and 4 novel species that are phylogenetically related to the saprophytes. We then investigated genome diversity and evolutionary relationships among members of the genus Leptospira by studying the pangenome and core gene sets. Our data enable the identification of genome features, genes and domains that are important for each subclade, thereby laying the foundation for refining the classification of this complex bacterial genus. We also shed light on atypical genomic features of a group of species that includes the species often associated with human infection, suggesting a specific and ongoing evolution of this group of species that will require more attention. In conclusion, we have uncovered a massive species diversity and revealed a novel subclade in environmental samples collected worldwide and we have redefined the classification of species in the genus. The implication of several new potentially infectious Leptospira species for human and animal health remains to be determined but our data also provide new insights into the emergence of virulence in the pathogenic species.", "token_count": 507, "char_count": 2342, "word_count": 354, "semantic_coherence": 1, "information_density": 0.5678, "quality_score": 0.7839, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:39.182425", "source": {"split": "train_shard_00000", "doc_id": 3025}, "chunk_id": "train_shard_00000_3025_0", "global_id": 3339}
{"text": "Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics.", "token_count": 27, "char_count": 109, "word_count": 16, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:39.533486", "source": {"split": "train_shard_00000", "doc_id": 3025}, "chunk_id": "train_shard_00000_3025_1", "global_id": 3340}
{"text": "This study was undertaken to investigate the impact of culture pH (4.5-6.5) and temperature (32-37 °C) on the stress resilience of Lactobacillus reuteri DSM 17938 during freeze-drying and post freeze-drying exposure to low pH (pH 2) and bile salts. Response-surface methodology analysis revealed that freeze-drying survival rates [Formula: see text] were linearly related to pH with the highest survival rate of 80% when cells were cultured at pH 6.5 and the lowest was 40% when cells were cultured at pH 4.5. The analysis further revealed that within the chosen temperature range the culture temperature did not significantly affect the freeze-drying survival rate. However, fermentation at pH 4.5 led to better survival rates when rehydrated cells were exposed to low pH shock or bile salts. Thus, the effect of pH on freeze-drying survival was in contrast to effects on low pH and bile salts stress tolerance. The rationale behind this irreconcilability is based on the responses being dissimilar and are not tuned to each other. Culturing strain DSM 17938 at pH values higher than 5.5 could be a useful option to improve the survivability and increase viable cell numbers in the final freeze-dried product. However, the dissimilar responses for the process- and application parameters tested here suggest that an optimal compromise has to be found in order to obtain the most functional probiotic product possible.\n\nImpact of the fermentation parameters pH and temperature on stress resilience of Lactobacillus reuteri DSM 17938.", "token_count": 397, "char_count": 1533, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5583, "quality_score": 0.7792, "entities": {"genes": [], "proteins": [], "pathways": ["fermentation"], "organisms": [], "conditions": ["bile", "ph", "temperature"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:40.126284", "source": {"split": "train_shard_00000", "doc_id": 3026}, "chunk_id": "train_shard_00000_3026_0", "global_id": 3341}
{"text": "Thermotolerance is a highly desirable trait of microbial cell factories and has been the focus of extensive research. Yeast usually tolerate only a narrow temperature range and just two species, Kluyveromyces marxianus and Ogataea polymorpha have been described to grow at reasonable rates above 40 °C. However, the complex mechanisms of thermotolerance in yeast impede its full comprehension and the rare physiological data at elevated temperatures has so far not been matched with corresponding metabolic analyses.\n\nElevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts.", "token_count": 146, "char_count": 622, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7865, "quality_score": 0.8933, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["ph", "temperature"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:40.566796", "source": {"split": "train_shard_00000", "doc_id": 3027}, "chunk_id": "train_shard_00000_3027_0", "global_id": 3342}
{"text": "Catechin hydrate is a phytopharmaceutical with promising anticancer effects but poor bioavailability. This study aimed to elaborate catechin loaded chitosan-tethered liposomes (chitosomes) to enhance catechin oral bioavailability. Nanocarriers were optimized via ethanol injection method followed by physicochemical, ex vivo and biological appraisal in male Wistar albino rats. Results demonstrated that chitosomes possessed excellent nanosize of 137 nm, monodispersity (PDI < 0.2) and high Zeta potential of +36.8 mV. Additionally, chitosomes showed significant improvement in digestive stability against bile salt with enhanced ex-vivo intestinal permeation. Pharmacokinetic studies revealed the significant potential of chitosomes to enhance catechin bioavailability (AUC, Cmax) and sustain its effect (Tmax). In conclusion, elaborated chitosomes are promising nanoplatforms to enhance catechin oral efficacy with lower dose, side effects, administration frequency and higher patient compliance.\n\nImproved oral bioavailability of the anticancer drug catechin using chitosomes: Design, in-vitro appraisal and in-vivo studies.", "token_count": 308, "char_count": 1127, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:41.126317", "source": {"split": "train_shard_00000", "doc_id": 3028}, "chunk_id": "train_shard_00000_3028_0", "global_id": 3343}
{"text": "A microbiota-generated bile salt induces biofilm formation in", "token_count": 15, "char_count": 61, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:41.475608", "source": {"split": "train_shard_00000", "doc_id": 3029}, "chunk_id": "train_shard_00000_3029_0", "global_id": 3344}
{"text": "Hydrophobic bile salts, such as glycochenodeoxycholate (GCDC) can trigger hepatocyte apoptosis, which is prevented by tauroursodesoxycholate (TUDC), but the effects of GCDC and TUDC on sinusoidal bile salt uptake via the Na⁺-taurocholate transporting polypeptide (Ntcp) are unclear.\n\nRegulation of Plasma Membrane Localization of the Na⁺-Taurocholate Co-Transporting Polypeptide by Glycochenodeoxycholate and Tauroursodeoxycholate.", "token_count": 150, "char_count": 431, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8039, "quality_score": 0.902, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:41.933158", "source": {"split": "train_shard_00000", "doc_id": 3030}, "chunk_id": "train_shard_00000_3030_0", "global_id": 3345}
{"text": "Here we are presenting a novel method to study the sumoylation of proteins and their sub-cellular localization in mammalian cells and nematode oocytes. This method utilizes a recombinant modified SUMO-trapping protein fragment, kmUTAG, derived from the Ulp1 SUMO protease of the stress-tolerant budding yeast Kluyveromyces marxianus. We have adapted the properties of the kmUTAG for the purpose of studying sumoylation in a variety of model systems without the use of antibodies. For the study of SUMO, KmUTAG has several advantages when compared to antibody-based approaches. This stress-tolerant SUMO-trapping reagent is produced recombinantly, it recognizes native SUMO isoforms from many species, and unlike commercially available antibodies it shows reduced affinity for free, unconjugated SUMO. Representative results shown here include the localization of SUMO conjugates in mammalian tissue culture cells and nematode oocytes.\n\nLocalization of SUMO-modified Proteins Using Fluorescent Sumo-trapping Proteins.", "token_count": 257, "char_count": 1016, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.8309, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:42.464137", "source": {"split": "train_shard_00000", "doc_id": 3031}, "chunk_id": "train_shard_00000_3031_0", "global_id": 3346}
{"text": "The number of poorly soluble new drugs is increasing and one of the effective ways to deliver such pharmaceutically active molecules is using hydrophilic polymers to form a solid dispersion. Bile salts play an important role in the solubilisation of poorly soluble compounds in the gastrointestinal tract (gut) prior to absorption. When a poorly water-soluble drug is delivered using a hydrophilic polymer based solid dispersion oral formulation, it is still unclear whether there are any polymer-bile salt interactions, which may influence the drug dissolution and solubilisation. This study, using two widely used hydrophilic model polymers, Hydroxypropyl methylcellulose (HPMC) and polyvynilpirrolidone (PVP), and sodium taurocholate (NaTC) as the model bile salt, aims to investigate the interactions between the polymers and bile salts in simulated fed state (FeSSIF) and fasted state (FaSSIF) gut fluids. The nature of the interactions was characterised using a range of NMR techniques. The results revealed that the aggregation behaviour of NaTC in FaSSIF and FeSSIF is much more complex than in water. The addition of hydrophilic polymers led to the occurrences of NaTC-HPMC and NaTC-PVP aggregation. For both systems, pH and ionic strength strongly influenced the aggregation behavior, while the ion type played a less significant role. The outcome of this study enriched the understanding of the aggregation behaviour of bile salts and typical hydrophilic pharmaceutical polymers in bio-relevant media. Due to the high surface-activity of the bile salts and their ability to interact with polymers, such aggregation behaviour is expected to play a role in drug solubilisation in the gut when the drug is delivered by hydrophilic polymer based dispersions.\n\nProbing the molecular interactions between pharmaceutical polymeric carriers and bile salts in simulated gastrointestinal fluids using NMR spectroscopy.", "token_count": 476, "char_count": 1919, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5603, "quality_score": 0.7801, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:43.085055", "source": {"split": "train_shard_00000", "doc_id": 3032}, "chunk_id": "train_shard_00000_3032_0", "global_id": 3347}
{"text": "Lactic acid bacteria (LAB) are major probiotics in food supplements. Survival in gastrointestinal (GI) tract is important for the effective use of LAB as probiotics. Bile salt hydrolase (BSH), which catalyzes the conversion of conjugated bile salts into free bile salts, can significantly modulate the gut microbiome. Here, we hypothesize that BSH is important for LAB survival and adhesion in the gut. The aim of this study is to investigate the effect of BSH on the survival of LAB in the GI tract. A panel of bsh genes from murine gut microbiota were amplified, cloned and expressed into Lactobacillus plantarum, which were then administered to mice by gavage. Our data indicated that the survival of BSH-positive L. plantarum was significantly prolonged in the GI tract compared with wild type L. plantarum. Furthermore, BSH-positive strains exhibited increased adhesion to Caco-2 intestinal cells than BSH-deleted L. plantarum. Enhanced adhesion to intestinal cells of BSH positive LAB can therefore be an important criterion for selecting effective probiotic strains in food industry.\n\nBile salt hydrolase can improve Lactobacillus plantarum survival in gastrointestinal tract by enhancing their adhesion ability.", "token_count": 322, "char_count": 1219, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "acid", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:43.630892", "source": {"split": "train_shard_00000", "doc_id": 3033}, "chunk_id": "train_shard_00000_3033_0", "global_id": 3348}
{"text": "During the last two decades, there has been a public health concern of severe invasive infections caused by Group A Streptococcus (GAS) of the emm1 genotype. This study investigated the dynamics of emm1 GAS during 1994-2013 in Belgium. emm1 GAS isolated from blood, tissue, and wounds of patients with invasive infections (n = 23, S1-S23), and from patients with uncomplicated pharyngitis (n = 15, NS1-NS15) were subjected to whole-genome mapping (WGM; kpn) (Opgen). Whole-genome sequencing was performed on 25 strains (WGS; S1-S23 and NS6-NS7) (Illumina Inc.). Belgian GAS belonged to the M1T1 clone typified by the 36-kb chromosomal region encoding extracellular toxins, NAD+-glycohydrolase and streptolysin O. Strains from 1994-1999 clustered together with published strains (MGAS5005 and M1476). From 2001 onward, invasive GAS showed higher genomic divergence in the accessory genome and harbored on average 7% prophage content. Low evolutionary rate (2.49E-008; P > 0.05) was observed in this study, indicating a highly stable genome. The studied invasive and pharyngitis isolates were no genetically distinct populations based on the WGM and core genome phylogeny analyses. Two copies of the speJ superantigen were present in the 1999 and 2010 study strains (n = 3), one being chromosomal and one being truncated and associated with phage remnants. This study showed that emm1 GAS in Belgium, compared with Canada and UK M1 strains, were highly conserved by harboring a remarkable genome stability over a 19-year period with variations observed in the accessory genome.", "token_count": 504, "char_count": 1575, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": {"genes": ["NS7", "NS1", "MGAS5005", "NS6", "NS15"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:44.266792", "source": {"split": "train_shard_00000", "doc_id": 3034}, "chunk_id": "train_shard_00000_3034_0", "global_id": 3349}
{"text": "Remarkable Genome Stability among emm1 Group A Streptococcus in Belgium over 19 Years.", "token_count": 26, "char_count": 86, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:44.616185", "source": {"split": "train_shard_00000", "doc_id": 3034}, "chunk_id": "train_shard_00000_3034_1", "global_id": 3350}
{"text": "Vancomycin-resistant enterococci (VRE) can rapidly spread through hospitals. Therefore, our hospital employs a screening program whereby rectal swabs are screened for the presence of vanA and vanB, and only PCR-positive broths are cultured on VRE selection agar. Early November 2016, a clinical vanA-/vanB-negative VRE isolate was detected in a vanA/vanB-screening-negative patient, giving the possibility that an undetected VRE might be spreading within our hospital. Whole-genome-sequencing of the isolate showed that resistance was vanD-mediated and core genome multilocus sequence typing showed it was a rare type: ST17/CT154. To determine the prevalence of vanA/B/C/D-carrying enterococci, we designed a real-time PCR for vanC1/2/3 and vanD and screened rectal swabs from 360 patients. vanD was found in 27.8% of the patients, yet culture demonstrated only E. faecium from vanA-positive broths and E. gallinarum from vanC1-positive broths. No vanD-positive VRE were found, limiting the possibility of nosocomial spread of this VRE. Moreover, the high prevalence of non-VRE vanD in rectal swabs makes it unfeasible to include the vanD PCR in our VRE screening. However, having validated the vanC1/2/3 and vanD PCRs allows us to rapidly check future vanA/B-negative VRE for the presence of vanC and vanD genes.\n\nAppearance of vanD-positive Enterococcus faecium in a tertiary hospital in the Netherlands: prevalence of vanC and vanD in hospitalized patients.", "token_count": 422, "char_count": 1460, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7972, "entities": {"genes": ["ST17", "CT154"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:45.221775", "source": {"split": "train_shard_00000", "doc_id": 3035}, "chunk_id": "train_shard_00000_3035_0", "global_id": 3351}
{"text": "The overall goal of this study was to determine whether the genome of an important plant pathogen in Africa, Ceratocystis albifundus, is structured into subgenomic compartments, and if so, to establish how these compartments are distributed across the genome. For this purpose, the publicly available genome of C. albifundus was complemented with the genome sequences for four additional isolates using the Illumina HiSeq platform. In addition, a reference genome for one of the individuals was assembled using both PacBio and Illumina HiSeq technologies. Our results showed a high degree of synteny between the five genomes, although several regions lacked detectable long-range synteny. These regions were associated with the presence of accessory genes, lower genetic similarity, variation in read-map depth, as well as transposable elements and genes associated with host-pathogen interactions (e.g. effectors and CAZymes). Such patterns are regarded as hallmarks of accelerated evolution, particularly of accessory subgenomic compartments in fungal pathogens. Our findings thus showed that the genome of C. albifundus is made-up of core and accessory subgenomic compartments, which is an important step towards characterizing its pangenome. This study also highlights the value of comparative genomics for understanding mechanisms that may underly and influence the biology and evolution of pathogens.\n\nGenomic analysis of the aggressive tree pathogen Ceratocystis albifundus.", "token_count": 336, "char_count": 1481, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.819, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:45.768337", "source": {"split": "train_shard_00000", "doc_id": 3036}, "chunk_id": "train_shard_00000_3036_0", "global_id": 3352}
{"text": "Yeast are usually responsible for spoilage of soft drinks and fruit beverages, because of the particular characteristics of these products (low pH, high C/N ratio). The microbial stability is guaranteed by thermal treatments. However, excessive heat treatments can affect food sensorial quality. In this work the thermal resistance of different yeasts strains (seven belonging to the species Saccharomyces cerevisiae and six belonging to the species Kluyveromyces marxianus, Zygosaccharomyces bisporus, Z. mellis, Z. rouxii, Schizosaccharomyces pombe and Saccharomycodes ludwigii) was assessed in a model system. The results showed non-linear death curves and a high variability also within the same species. The most resistant strain, belonging to the species S. cerevisiae, was chosen for further experiments in orange juice based industrial beverages: first, death curves were performed; then, the probability of beverage spoilage in relation to process parameters (initial inoculum, temperature, treatment time) was evaluated using a logistic regression model. Finally, a cross-validation was performed to investigate the predictive capability of the fitted model. Pasteurization in the soft drink industry is commonly applied according to parameters defined several decades ago, which does not consider the successive findings concerning microbial physiology and stress response, the process improvement and the more recent tools provided by predictive microbiology. In this perspective, this study can fill a gap in the literature on this subject, going to be a basis for optimizing thermal processes. In fact, the data obtained indicated an interesting possibility for food industry to better modulated (and even reduce) thermal treatments, with the aim to guarantee microbial stability while reducing thermal damage and energy costs.\n\nModeling of yeast thermal resistance and optimization of the pasteurization treatment applied to soft drinks.", "token_count": 411, "char_count": 1952, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast", "saccharomyces"], "conditions": ["ph", "temperature"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:46.370079", "source": {"split": "train_shard_00000", "doc_id": 3037}, "chunk_id": "train_shard_00000_3037_0", "global_id": 3353}
{"text": "Prey are under selection to minimize predation losses. In aquatic environments, many prey use chemical cues released by predators, which initiate predator avoidance. A prominent example of behavioral predator-avoidance constitutes diel vertical migration (DVM) in the freshwater microcrustacean\n\n5α-cyprinol sulfate, a bile salt from fish, induces diel vertical migration in", "token_count": 93, "char_count": 374, "word_count": 50, "semantic_coherence": 1, "information_density": 0.86, "quality_score": 0.93, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:46.736944", "source": {"split": "train_shard_00000", "doc_id": 3038}, "chunk_id": "train_shard_00000_3038_0", "global_id": 3354}
{"text": "Xylitol is a valuable substance utilized by food and biochemical industries. NAD(P)H-dependent xylose reductase (XR)-encoded by the yeast KmXYL1 gene-is the key enzyme which facilitates reduction of xylose to xylitol. Multi-copy integration of a mutant KmXYL1 (mKmXYL1) gene was carried out using thermotolerant yeast Kluyveromyces marxianus KCTC17555ΔURA3, in order to enhance xylitol production. After multi-copy integration, the highest xylitol producing strain was isolated and named K. marxianus 17555-JBP2. This strain exhibited 440% higher xylitol production than the parental strain at 30 °C. Due to a multi-copy integration of the mKmXYL1 gene, various additional differences between K. marxianus 17555-JBP2 and the parental strain were observed, including a 66% increase in NAD(P)H-dependent XR activity at high temperature (45 °C). Quantitative real-time PCR and transcriptome analysis demonstrated that, relative to the parent strain, K. marxianus 17555-JBP2 exhibited two more copies of mKmXY1 genes and a 9.63-fold elevation in transcription of NAD(P)H-dependent XR. After optimization of bioreactor fermentation conditions (agitation speed), high-temperature (40 °C) xylitol productivity of K. marxianus 17555-JBP2 exhibited an 81% improvement relative to the parental strain. In this study, we demonstrated that the overexpression of endogenous XR could enhance xylitol productivity at 40 °C by thermotolerant K. marxianus.\n\nOverexpression of Endogenous Xylose Reductase Enhanced Xylitol Productivity at 40 °C by Thermotolerant Yeast Kluyveromyces marxianus.", "token_count": 489, "char_count": 1574, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": {"genes": ["JBP2"], "proteins": [], "pathways": ["fermentation"], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["temperature"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:47.366050", "source": {"split": "train_shard_00000", "doc_id": 3039}, "chunk_id": "train_shard_00000_3039_0", "global_id": 3355}
{"text": "Simultaneous cofermentation of glucose and xylose mixtures would be a cost-effective solution for the conversion of cellulosic biomass to high-value products. However, most yeasts ferment glucose and xylose sequentially due to glucose catabolite repression. A well known thermotolerant yeast,\n\nAlleviation of catabolite repression in", "token_count": 89, "char_count": 333, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7955, "quality_score": 0.8977, "entities": {"genes": [], "proteins": [], "pathways": ["fermentation"], "organisms": ["yeast"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:47.729151", "source": {"split": "train_shard_00000", "doc_id": 3040}, "chunk_id": "train_shard_00000_3040_0", "global_id": 3356}
{"text": "Albeit its well known potency as a postmenopausal osteoporosis treatment, Risedronate suffers from poor oral bioavailability and high oral toxicity. This is the first work to assess the potential of bilosomes to address challenges of RS oral delivery. Furthermore, impact of integrating cationic moiety into bilosomes on intestinal digestability and toxicity of RS nanovesicles was first investigated in this article. Prepared formulations were optimized based on physicochemical properties, digestibility, intestinal permeation and local toxicity studies. Optimized preparations were prepared by reversed phase evaporation technique with three extrusion cycles and loaded by 10 mg/ml RS. Molar lipid to bile salt to cholesterol ratio was adjusted to 4:1:1 at pH 5. Addition of cholesterol had significantly improved bilosomes stability to digestive media. Results also revealed that permeation of anionic vesicles increased permeation by 1.5 times more than RS solution and reduced drug toxicity by 2 folds. On the other hand, Cationic bilosomes showed good stability in GIT fluids but their induced oral toxicity could limit their use. In conclusion, bilosomes are superior over liposomes regarding protection of delivery system from the damaging effect of external in digestive bile salts. In addition, it decreases toxicity issues of orally administered drugs.\n\nAnionic versus cationic bilosomes as oral nanocarriers for enhanced delivery of the hydrophilic drug risedronate.", "token_count": 362, "char_count": 1479, "word_count": 212, "semantic_coherence": 1, "information_density": 0.684, "quality_score": 0.842, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:48.289647", "source": {"split": "train_shard_00000", "doc_id": 3041}, "chunk_id": "train_shard_00000_3041_0", "global_id": 3357}
{"text": "Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus", "token_count": 465, "char_count": 1794, "word_count": 243, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": {"genes": ["CG6"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:48.904080", "source": {"split": "train_shard_00000", "doc_id": 3042}, "chunk_id": "train_shard_00000_3042_0", "global_id": 3358}
{"text": "The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.\n\nGenus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance.", "token_count": 100, "char_count": 400, "word_count": 47, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:49.270124", "source": {"split": "train_shard_00000", "doc_id": 3042}, "chunk_id": "train_shard_00000_3042_1", "global_id": 3359}
{"text": "Bile salts (BS) are biosurfactants crucial for emulsification and intestinal absorption of cholesterol and other hydrophobic compounds such as vitamins and fatty acids. Interaction of BS with lipid bilayers is important for understanding their effects on membranes properties. The latter have relevance in passive diffusion processes through intestinal epithelium such as reabsorption of BS, as well as their degree of toxicity to intestinal flora and their potential applications in drug delivery. In this work, we used molecular dynamics simulations to address at the atomic scale the interactions of cholate, deoxycholate, and chenodeoxycholate, as well as their glycine conjugates with POPC bilayers. In this set of BS, variation of three structural aspects was addressed, namely conjugation with glycine, number and position of hydroxyl substituents, and ionization state. From atomistic simulations, the location and orientation of BS inside the bilayer, and their specific interactions with water and host lipid, such as hydrogen bonding and ion-pair formation, were studied in detail. Membrane properties were also investigated to obtain information on the degree of perturbation induced by the different BS. The results are described and related to a recent experimental study (Coreta-Gomes et al., 2015). Differences in macroscopic membrane partition thermodynamics and translocation kinetics are rationalized in terms of the distinct structures and atomic-scale behavior of the bile salt species. In particular, the faster translocation of cholate is explained by its higher degree of local membrane perturbation. On the other hand, the relatively high partition of the polar glycine conjugates is related to the longer and more flexible side chain, which allows simultaneous efficient solvation of the ionized carboxylate and deep insertion of the ring system.\n\nInteraction of Bile Salts With Lipid Bilayers: An Atomistic Molecular Dynamics Study.", "token_count": 447, "char_count": 1959, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:49.874245", "source": {"split": "train_shard_00000", "doc_id": 3043}, "chunk_id": "train_shard_00000_3043_0", "global_id": 3360}
{"text": "Drug-induced cholestasis poses a major hurdle for the pharmaceutical industry as it is one the primary mechanisms of drug-induced liver injury. Hence, detection of drug-induced cholestasis during the early stages of drug development is of utmost importance. The most commonly used in vitro models rely on the extent of inhibition of bile salt export pump-mediated taurocholic acid transport, thereby assuming that drug-induced cholestasis mechanisms are merely restricted to the interaction with this sole hepatic transporter. Sandwich-cultured human hepatocytes represent a more holistic in vitro tool to investigate drug-induced cholestasis as they preserve all relevant disposition pathways and cellular functions involved in bile acid homeostasis. We developed and validated a sandwich-cultured human hepatocytes-based in vitro assay which is able to identify compounds causing cholestasis by altering bile acid disposition. The in vitro cholestatic potential is expressed by calculating a drug-induced cholestasis index value, which reflects the relative residual urea formation of sandwich-cultured human hepatocytes co-incubated with bile acids and test compound as compared to sandwich-cultured human hepatocytes treated with test compound alone. In addition, a safety margin can be calculated to determine the in vivo risk for cholestasis based on the determination of the drug-induced cholestasis index at various concentrations and the peak plasma concentration of the drug candidate. This chapter outlines the various steps involved in performing our sandwich-cultured human hepatocytes-based in vitro assay.\n\nDetection of Drug-Induced Cholestasis Potential in Sandwich-Cultured Human Hepatocytes.", "token_count": 402, "char_count": 1709, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5708, "quality_score": 0.7854, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:50.471007", "source": {"split": "train_shard_00000", "doc_id": 3044}, "chunk_id": "train_shard_00000_3044_0", "global_id": 3361}
{"text": "Drug-induced liver injury is an important reason for drug candidate failure. Alterations in the hepatobiliary disposition of bile acids are a proposed mechanism of cholestatic hepatotoxicity. Bile acids are synthesized in the hepatocyte, and excreted into the bile primarily by the bile salt export pump. Therefore, inhibition of the bile salt export pump by drugs has been postulated as a risk factor in the development of cholestatic hepatotoxicity. However, recent publications have shown a lack of correlation between bile salt export pump inhibition potency and drug-induced liver injury incidence. Following inhibition of the bile salt export pump mediated efflux of bile acids, the liver compensates through various mechanisms (adaptive response) including upregulation of basolateral bile acid efflux mediated by the farnesoid X receptor, the master regulator of bile acid homeostasis. The C-DILI™ assay integrates the effects of bile salt export pump inhibition, farnesoid X receptor antagonism, and basolateral efflux inhibition of bile acids to more accurately predict a drug's potential to cause cholestatic hepatotoxicity and drug-induced liver injury.\n\nThe C-DILI™ Assay: An Integrated In Vitro Approach to Predict Cholestatic Hepatotoxicity.", "token_count": 324, "char_count": 1256, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5333, "quality_score": 0.7667, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:51.008499", "source": {"split": "train_shard_00000", "doc_id": 3045}, "chunk_id": "train_shard_00000_3045_0", "global_id": 3362}
{"text": "Transporters play a crucial role in the uptake of endo- and exogenous molecules in hepatocytes and efflux into the bile. The bile salt export pump (BSEP; ABCB11) is of major importance for efflux of bile salts to the bile and BSEP inhibition frequently provokes drug-induced cholestasis. This chapter describes two assays to determine inhibition of BSEP-mediated bile salt excretion. The first assay uses inside-out membrane vesicles, prepared from BSEP-transfected cell lines. The cholestasis potential of compounds can be determined by specifically investigating the ability to inhibit BSEP-mediated uptake of tauro-nor-THCA-24-DBD, a fluorescent bile salt derivative. For the second assay, relative accumulation of tauro-nor-THCA-24-DBD in sandwich-cultured hepatocytes, which represents a more biorelevant in vitro system, is investigated. Through incubation with standard or Ca\n\nVesicle- and Hepatocyte-Based Assays for Identification of Drug Candidates Inhibiting BSEP Function.", "token_count": 282, "char_count": 984, "word_count": 134, "semantic_coherence": 1, "information_density": 0.709, "quality_score": 0.8545, "entities": {"genes": ["ABCB11"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:51.537041", "source": {"split": "train_shard_00000", "doc_id": 3046}, "chunk_id": "train_shard_00000_3046_0", "global_id": 3363}
{"text": "Gypenosides (GPS) have been used as traditional medicine for centuries with various pharmacological effects. However, its therapeutic effects were restricted owing to the poor lipid and water solubility and low absorption. This study aimed to develop nanostructured lipid carriers (NLCs) containing a bile salt formulation (sodium glycocholate, SGC) for GPS, and to evaluate the potential of the GPS-SGC-NLCs as an oral delivery system.\n\nFormulation design, characterization, and in vitro and in vivo evaluation of nanostructured lipid carriers containing a bile salt for oral delivery of gypenosides.", "token_count": 153, "char_count": 601, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7093, "quality_score": 0.8547, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:51.959202", "source": {"split": "train_shard_00000", "doc_id": 3047}, "chunk_id": "train_shard_00000_3047_0", "global_id": 3364}
{"text": "A 27-month-old girl presented with a short history of jaundice initially attributed to drug-induced liver injury. During the preceding 20 days, she had received a 10-day course of cefprozil and 2 doses of a homeopathic preparation of cantharidin for cystitis. Severe conjugated hyperbilirubinemia was present with normal γ-glutamyl transpeptidase activity. Liver biopsy revealed marked canalicular and hepatocellular cholestasis, with moderate hepatocellular disarray, as well as evidence of chronicity, including moderate portal-tract and perisinusoidal fibrosis. Immunohistochemical studies revealed that bile salt export pump expression was preserved, whereas canalicular γ-glutamyl transpeptidase expression was largely absent. An inherited cholestatic disorder was suspected. The entire coding region of\n\nBeyond an Obvious Cause of Cholestasis in a Toddler: Compound Heterozygosity for", "token_count": 241, "char_count": 890, "word_count": 116, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:52.459606", "source": {"split": "train_shard_00000", "doc_id": 3048}, "chunk_id": "train_shard_00000_3048_0", "global_id": 3365}
{"text": "In our study, the potential of bilosomes as novel vesicular carrier for the cutaneous delivery of the sulphone compound, Dapsone, for topical treatment of acne was investigated. The effect of different formulation variables (type and concentration of bile salt, and molar ratio of Span 60:cholesterol) on the properties of DPS-loaded bilosomes was investigated using a full factorial design. Design Expert software was used for data analysis and optimization of DPS-loaded bilosomes. The optimized bilosomes, chosen on the basis of their superior properties giving maximum entrapment,\n\nBilosomes as a novel carrier for the cutaneous delivery for dapsone as a potential treatment of acne: preparation, characterization and", "token_count": 165, "char_count": 721, "word_count": 105, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:52.902784", "source": {"split": "train_shard_00000", "doc_id": 3049}, "chunk_id": "train_shard_00000_3049_0", "global_id": 3366}
{"text": "The liver is the primary organ for the metabolic degradation of xenobiotics. Transmembrane transport proteins from the ABC and the SLC families mediate the uptake of endogenous compounds and xenobiotics into the hepatocyte as well as their elimination from the cells. Multiple processes are involved. The uptake of xenobiotics in hepatocytes is mediated by organic anion transporting polypeptides (OATPs) and by organic anion and cation transporters (OATs and OCTs). The elimination of drugs and metabolites from the liver cell back to the bloodstream is accomplished mainly by multidrug resistance-associated protein 3 (MRP3) and MRP4, while the elimination towards the biliary canaliculi is mediated by several different transporters (MRP2, BCRP, MDR1 and MATE1). Since bile acids and their salts are toxic detergents for hepatocytes, they have to be eliminated efficiently. This task is accomplished by the bile salt export pump BSEP. Two further transporters, MDR3 and ATP8B1 are involved in the proper constitution of bile. All these transporters can be influenced, mainly inhibited by a number of drugs, but also by metabolites from endogenous compounds such as estrogens. Additionally, rare monogenetic diseases exist which can be explained by absence of function or dysfunction of specific hepatic transporters, such as progressive familial intrahepatic cholestasis type 2 by genetic modifications in BSEP that lead to a loss of transporter function. Functional impairment of other transporters by genetics or by drugs also leads to liver injury, a potentially life-threatening disease that is still not fully understood. Hence, the interplay between drugs and hepatic transporters is multiple, and the knowledge of this interplay helps in understanding the etiology and molecular mechanisms behind some forms of (drug-induced) liver injury.\n\nDrugs and hepatic transporters: A review.", "token_count": 474, "char_count": 1892, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5986, "quality_score": 0.7993, "entities": {"genes": ["MATE1", "MDR3", "MRP3", "MRP2", "MRP4", "MDR1"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:53.548276", "source": {"split": "train_shard_00000", "doc_id": 3050}, "chunk_id": "train_shard_00000_3050_0", "global_id": 3367}
{"text": "The purpose of this study was to assess the potential effects of polysaccharides from edible mushroom Grifola frondosa (GFP) on lipid metabolic disorders and gut microbiota dysbiosis, and elucidate their possible regulatory mechanisms on lipid and cholesterol metabolism in high-fat diet (HFD)-exacerbated hyperlipidemic and hypercholesterolemic rats. Results showed that oral administration of GFP markedly alleviated dyslipidaemia through decreasing the serum levels of total triglycerides, total cholesterol, and free fatty acids, and significantly suppressing hepatic lipid accumulation and steatosis. Besides, the excretion of fecal bile acids was also promoted by oral administration of GFP. Metagenomic analysis revealed that GFP supplementation (400 mg kg-1 day-1) resulted in significant structure changes on gut microbiota in HFD-fed rats, in particular modulating the relative abundance of functionally relevant microbial phylotypes compared with the HFD group. Key microbial phylotypes responding to GFP intervention were identified to strongly correlate with the lipid metabolism disorder associated parameters using the correlation network based on Spearman's correlation coefficient. Serum and hepatic lipid profiles were found positively correlated with Clostridium-XVIII, Butyricicoccus and Turicibacter, but negatively correlated with Helicobater, Intestinimonas, Barnesiella, Parasutterella, Ruminococcus and Flavonifracter. Moreover, GFP treatment (400 mg kg-1 day-1) regulated the mRNA expression levels of the genes responsible for hepatic lipid and cholesterol metabolism. Oral supplementation of GFP markedly increased the mRNA expression of cholesterol 7α-hydroxylase (CYP7A1) and bile salt export pump (BSEP), suggesting an enhancement of bile acid (BA) synthesis and excretion from the liver", "token_count": 473, "char_count": 1818, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["gut", "acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:54.569809", "source": {"split": "train_shard_00000", "doc_id": 3051}, "chunk_id": "train_shard_00000_3051_0", "global_id": 3368}
{"text": "These findings illustrated that GFP could ameliorate lipid metabolic disorders through modulating specific gut microbial phylotypes and regulating hepatic lipid and cholesterol metabolism related genes, and therefore could be used as a potential functional food ingredient for the prevention or treatment of hyperlipidemia.\n\nGrifola frondosa polysaccharides ameliorate lipid metabolic disorders and gut microbiota dysbiosis in high-fat diet fed rats.", "token_count": 114, "char_count": 450, "word_count": 59, "semantic_coherence": 1, "information_density": 0.8305, "quality_score": 0.9153, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["gut", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:54.937230", "source": {"split": "train_shard_00000", "doc_id": 3051}, "chunk_id": "train_shard_00000_3051_1", "global_id": 3369}
{"text": "To investigate the effects of geniposidic acid( GPA) on hepato-enteric circulation in cholestasis rats,and to explore the mechanism based on the sirtuin 1( Sirt1)-farnesol X receptor( FXR) pathway,sixty SD rats were randomly divided into 6 groups:blank control group,ANIT model group,ursodeoxycholic acid group( 100 mg·kg~(-1)·d-1 UDCA),and GPA high,medium and low( 100,50 and 25 mg·kg~(-1)·d-1) dosage groups,10 rats in each group. Corresponding drugs were intragastrically( ig) administered for10 days. After administration on day 8,all rats except blank rats were administered with 65 mg·kg~(-1)α-naphthalene isothiocyanate( ANIT) once. After the last administration,the serum levels of alanine aminotransferase( ALT),glutamine oxalacetate aminotransferase( AST),gamma-glutamyltransferase( γ-GGT),alkaline phosphatase( ALP),total bilirubin( TB) and total bile acid( TBA)were measured,and the mRNA transcription levels of Sirt1,FXR,multidrug resistant associated protein 2( MRP2),bile salt export pump( BSEP),sodium taurocholate contractible polypeptide( NTCP) in liver and apical sodium bile acid transporter( ASBT),ileum bile acid binding protein( IBABP) in ileum were detected by reverse transcription-polymerase chain reaction( RT-PCR). The protein expression levels of Sirt1,FXR and NTCP were detected by Western blot; the expression of MRP2,BSEP in liver and ASBT,IBABP in ileum were determined by immunofluorescence three staining", "token_count": 478, "char_count": 1439, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": {"genes": ["MRP2"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:55.563347", "source": {"split": "train_shard_00000", "doc_id": 3052}, "chunk_id": "train_shard_00000_3052_0", "global_id": 3370}
{"text": "Primary rat hepatocytes were cultured in vitro to investigate the inhibitory effect of GPA on a potent and selective Sirt1 inhibitor( EX 527),and the mRNA and protein expression levels of Sirt1 and FXR were detected by RT-PCR and Western blot. GPA significantly decreased the levels of ALT,AST,γ-GGT,ALP,TB,TBA in serum( P<0.01) and improved the pathological damage of liver tissues in ANIT-induced cholestasis rats; significantly increased the mRNA and protein expression levels of Sirt1,FXR,MRP2,BSEP,NTCP in liver and ASBT,IBABP in ileum( P< 0.01). In vitro primary hepatocytes experiment indicated that the gene and protein expression levels of FXR and Sirt1 were noticeably improved by GPA in primary hepatocytes inhibited by EX-527( P<0.01). It was found that the improvement of GPA was in a dose-dependent manner. GPA could improve bile acid hepatointestinal circulation and play a liver protection and cholagogu role in cholestasis rats induced by ANIT.The mechanism may be that GPA activated FXR by regulating Sirt1,a key regulator of oxidative stress injury,and then the activated FXR could regulate protein of bile acid hepato-enteric circulation.\n\n[Effect of geniposidic acid on hepato-enteric circulation in cholestasis rats through Sirt1-FXR signaling pathway].", "token_count": 372, "char_count": 1275, "word_count": 185, "semantic_coherence": 1, "information_density": 0.5405, "quality_score": 0.7703, "entities": {"genes": ["MRP2"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:56.122316", "source": {"split": "train_shard_00000", "doc_id": 3052}, "chunk_id": "train_shard_00000_3052_1", "global_id": 3371}
{"text": "The Autotransporter IcsA Promotes Shigella flexneri Biofilm Formation in the Presence of Bile Salts.", "token_count": 31, "char_count": 100, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:56.472362", "source": {"split": "train_shard_00000", "doc_id": 3053}, "chunk_id": "train_shard_00000_3053_0", "global_id": 3372}
{"text": "Extended multi-locus sequence typing (eMLST) methods have become popular in the field of genomic epidemiology. Before eMLST methods can be applied in epidemiological investigations, the selection of a suitable scheme is critical. The core genome scheme (cgMLST) has become the most popular eMLST approach for strain typing in the epidemiological domain. In addition to strain typing, many public health researchers and clinical microbiologists wish to investigate which genes cause genetic differences between compared strains. Therefore, a tool that can be used to extract canonical genes with an eMLST scheme would be particularly useful. In this study, we present cano-eMLST, a well-designed program that applies a feature-selection methodology to create a canonical locus combination with discriminatory power by traversing a genetic relatedness tree based on a user-selected scheme. The cano-eMLST program is provided mainly to help infectious disease laboratory researchers identify potential factors related to bacterial pathogenesis. The core program (tree-traversing approach) of cano-eMLST is implemented in Perl and Python. All the necessary dependencies and environmental settings are provided in the encapsulated version (VirtualBox or VMware) and self-installation version (all use source code and libraries).\n\nThe Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial Strains.", "token_count": 329, "char_count": 1508, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:57.022946", "source": {"split": "train_shard_00000", "doc_id": 3054}, "chunk_id": "train_shard_00000_3054_0", "global_id": 3373}
{"text": "Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of Pseudomonas aeruginosa strain PA34. We obtained the complete genome of PA34 utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The susceptibility to heavy metals and cytotoxicity was determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 genomic islands (GIs) were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (AAC(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.\n\nAccessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34.", "token_count": 445, "char_count": 1754, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": {"genes": ["PA34"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:57.633972", "source": {"split": "train_shard_00000", "doc_id": 3055}, "chunk_id": "train_shard_00000_3055_0", "global_id": 3374}
{"text": "Non-typhoidal Salmonella (NTS) bacteremia is a significant cause of morbidity and mortality worldwide. It is considered to be an emerging and neglected tropical disease in Africa. We studied this in two tertiary hospitals-Al Farwaniya and Al Amiri-in Kuwait, a subtropical country, from April 2013-May 2016. NTS bacteremia was present in 30 of 53,860 (0.75%) and 31 of 290,36 (1.33%) blood cultures in the two hospitals respectively. In Al Farwaniya hospital, one-third of the patients were from some tropical developing countries of Asia. About 66% of all patients (40/61) had diarrhea, and of these, 65% had the corresponding blood serovar isolated from stool culture. A few patients had Salmonella cultured from urine. Patients were either young or old. Most of the patients had co-morbidities affecting the immune system. Two patients each died in both hospitals. The number of different serovars cultured in each hospital was 13, and most infections were due to S. Enteritidis (all sequence type [ST]) 11) and S. Typhimurium (all ST19) except in a subgroup of expatriate patients from tropical developing countries in Al Farwaniya hospital. About a quarter of the isolates were multidrug-resistant. Most patients were treated with a cephalosporin with or without other antibiotics. S. Enteritidis and S. Typhimurium isolates were typed by pulsed field-gel electrophoresis (PFGE) and a selected number of isolates were whole-genome sequenced. Up to four different clades were present by PFGE in either species. Whole-genome sequenced isolates showed antibiotic-resistance genes that showed phenotypic correlation, and in some cases, phenotypes showed absence of specific genes. Whole-genome sequenced isolates showed presence of genes that contributed to blood-stream infection. Phylogeny by core genome analysis showed a close relationship with S. Typhimurium and S. Enteritidis from other parts of the world", "token_count": 520, "char_count": 1913, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5544, "quality_score": 0.7772, "entities": {"genes": ["ST19"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:14:58.266526", "source": {"split": "train_shard_00000", "doc_id": 3056}, "chunk_id": "train_shard_00000_3056_0", "global_id": 3375}
{"text": "The uniqueness of our study included the finding of a low prevalence of infection, mortality and multidrug-resistance, a relatively high prevalence of gastrointestinal infection in patients, and the characterization of selected isolates of S. Typhimurium and S. Enteritidis serovars by whole-genome sequencing that shed light on phylogeny, virulence and resistance. Similarities with studies from developing countries especially Africa included infection in patients with co-morbidities affecting the immune system, predominance of S. Typhimurium and S. Enteritidis serovars and presence of drug-resistance in isolates.\n\nNon-typhoidal Salmonella blood stream infection in Kuwait: Clinical and microbiological characteristics.", "token_count": 171, "char_count": 725, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:58.697346", "source": {"split": "train_shard_00000", "doc_id": 3056}, "chunk_id": "train_shard_00000_3056_1", "global_id": 3376}
{"text": "The bile salt export pump (BSEP, ABCB11) mediates bile acid efflux from hepatocytes into bile. Although the inhibition of BSEP has been implicated as an important mechanism of drug-induced liver injury (DILI), liver injury caused by BSEP-inhibiting drugs is rarely reproduced in experimental animals, probably due to species differences in bile acid composition between humans and rodents. In this study, we tested whether supplementation with chenodeoxycholic acid (CDCA) sodium, a hydrophobic bile salt, could sensitize rats to liver injury caused by a BSEP-inhibiting drug. A potent BSEP inhibitor, ketoconazole (KTZ), which is associated with clinical DILI, was intragastrically administered simultaneously with CDCA at a nontoxic dose once a day for 3 days. Plasma transaminase levels significantly increased in rats receiving CDCA+KTZ, whereas neither treatment with CDCA alone, KTZ alone nor a combination of CDCA and miconazole, a safe analog to KTZ, induced liver injury. In CDCA+KTZ-treated rats, most bile acid species in the liver significantly increased compared with treatment with vehicle or CDCA alone, suggesting that KTZ administration inhibited bile acid excretion. Furthermore, hepatic mRNA expression levels of a bile acid synthesis enzyme, Cyp7a1, and a basolateral bile salt influx transporter, Ntcp, decreased, whereas a canalicular phosphatidylcholine flippase, Mdr2, increased in the CDCA+KTZ group to compensate for hepatic bile acid accumulation. In conclusion, we found that oral CDCA supplementation predisposed rats to KTZ-induced liver injury due to the hepatic accumulation of bile acids. This method may be useful for assessing the potential of BSEP-inhibiting drugs inducing liver injury in vivo.\n\nExperimental Evidence of Liver Injury by BSEP-Inhibiting Drugs With a Bile Salt Supplementation in Rats.", "token_count": 493, "char_count": 1837, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7943, "entities": {"genes": ["ABCB11"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:59.316586", "source": {"split": "train_shard_00000", "doc_id": 3057}, "chunk_id": "train_shard_00000_3057_0", "global_id": 3377}
{"text": "Pregnancy is associated with progressive hypercholanemia, hypercholesterolemia, and hypertriglyceridemia, which can result in metabolic disease in susceptible women. Gut signals modify hepatic homeostatic pathways, linking intestinal content to metabolic activity. We sought to identify whether enteric endocrine signals contribute to raised serum bile acids observed in human and murine pregnancies, by measuring fibroblast growth factor (FGF) 19/15 protein and mRNA levels, and 7α-hydroxy-4-cholesten-3-one. Terminal ileal farnesoid X receptor (FXR)-mediated gene expression and apical sodium bile acid transporter (ASBT) protein concentration were measured by qPCR and western blotting. Shotgun whole-genome sequencing and ultra-performance liquid chromatography tandem mass spectrometry were used to determine the cecal microbiome and metabonome. Targeted and untargeted pathway analyses were performed to predict the systemic effects of the altered metagenome and metabolite profiles. Dietary CA supplementation was used to determine whether the observed alterations could be overcome by intestinal bile acids functioning as FXR agonists. Human and murine pregnancy were associated with reduced intestinal FXR signaling, with lower FGF19/15 and resultant increased hepatic bile acid synthesis. Terminal ileal ASBT protein was reduced in murine pregnancy. Cecal bile acid conjugation was reduced in pregnancy because of elevated bile salt hydrolase-producing Bacteroidetes. CA supplementation induced intestinal FXR signaling, which was not abrogated by pregnancy, with strikingly similar changes to the microbiota and metabonome as identified in pregnancy. Conclusion: The altered intestinal microbiota of pregnancy enhance bile acid deconjugation, reducing ileal bile acid uptake and lowering FXR induction in enterocytes. This exacerbates the effects mediated by reduced bile acid uptake transporters in pregnancy", "token_count": 489, "char_count": 1920, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5952, "quality_score": 0.7976, "entities": {"genes": ["FGF19"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:14:59.941092", "source": {"split": "train_shard_00000", "doc_id": 3058}, "chunk_id": "train_shard_00000_3058_0", "global_id": 3378}
{"text": "Thus, in pregnant women and mice, there is reduced FGF19/15-mediated hepatic repression of hepatic bile acid synthesis, resulting in hypercholanemia.\n\nEnhanced Microbial Bile Acid Deconjugation and Impaired Ileal Uptake in Pregnancy Repress Intestinal Regulation of Bile Acid Synthesis.", "token_count": 92, "char_count": 286, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": {"genes": ["FGF19"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:00.304790", "source": {"split": "train_shard_00000", "doc_id": 3058}, "chunk_id": "train_shard_00000_3058_1", "global_id": 3379}
{"text": "Two experiments, 1 in vitro and 1 in vivo study, were conducted to analyze probiotic species characteristics and survival in the intestine of broiler birds. The in vitro study characterized the effect of bile salt supplementation and pH on the proliferation of Lactobacillus reuteri, Pediococcus acidilactici, Bifidobacterium animalis, and Enterococcus faecium. L. reuteri and P. acidilactici growth was maximal when the media was supplemented with 1.0% bile salt, whereas B. animalis and E. faecium growth was maximal when the media was supplemented with 0.5% bile salt. Altering the pH between 2.5 and 5.8 did not significantly (P > 0.05) alter the proliferation of L. reuteri and B. animalis. Decreasing the pH from 5.8 to 2.0 decreased P. acidilactici growth, whereas it increased the E. faecium proliferation. The in vivo study quantified the concentration of L. reuteri, P. acidilactici, B. animalis, E. faecium, and L. salivarius in different intestinal sections from birds supplemented with and without synbiotic containing the above 5 bacteria species. Birds were supplemented with and without synbiotic for 18 d, after which all birds were fed the same basal diet with no synbiotic. At 72 h of feeding, the basal diet with no synbiotics, when the probiotic species in the feed is expected not to confound the recovery of probiotic species from the intestine, intestinal contents were collected. L. reuteri, P. acidilactici, E. faecium, and L. salivarius were below detectable amount in the control group. L. reuteri concentration expressed as copy numbers/g and as percentage of total bacteria was highest in the jejunum and ileum, respectively. E. faecium concentration was highest in the ileum. The copy number of P. acidilactici increased at the duodenum and plateaued after duodenum. L. salivarius concentration was highest in the jejunum", "token_count": 514, "char_count": 1852, "word_count": 288, "semantic_coherence": 1, "information_density": 0.4792, "quality_score": 0.7396, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:15:00.915482", "source": {"split": "train_shard_00000", "doc_id": 3059}, "chunk_id": "train_shard_00000_3059_0", "global_id": 3380}
{"text": "It can be concluded that real-time PCR can be applied to quantify the concentrations of probiotic species in the intestine and probiotic species differ in their ability to colonize different sections of the intestine.\n\nIn vitro characterization and analysis of probiotic species in the chicken intestine by real-time polymerase chain reaction.", "token_count": 79, "char_count": 343, "word_count": 51, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:01.280208", "source": {"split": "train_shard_00000", "doc_id": 3059}, "chunk_id": "train_shard_00000_3059_1", "global_id": 3381}
{"text": "Gastrointestinal (GI) infection is one of the most common types of infectious diseases. Application of probiotic strains in the control of such infections represents a promising approach. In this study, Lactobacillus fermentum strain 4-17 was isolated from kashkineh, an Iranian cereal fermented food, and identified by sequencing its 16S rRNA gene using universal primers. Its probiotic features, including resistance to acid, bile tolerance, antibacterial activity, resistance to intestinal and gastric juices, and hydrophobicity were evaluated. The ability of this strain to adhere to human intestinal cells as well as the anti-adhesive effect of L. fermentum strain 4-17 against E. coli isolated from patients with urinary tract infection was investigated. L. fermentum strain 4-17 was capable of surviving at various conditions such as low pH values, bile salts exposure, and GI tract environment. It showed 43% cell hydrophobicity. The adhesion level of L. fermentum strain 4-17 to human colon adenocarcinoma Caco-2 cells was 8.5% which was also confirmed by scanning electron microscopy (SEM). Furthermore, this strain showed appropriate anti-adhesive properties (including competition, inhibition and replacement properties) against human pathogenic bacteria. These data suggest that L. fermentum strain 4-17 could be examined further for its useful effects and introduced as a novel candidate probiotic to control GI infection disease.\n\nEvaluation of adherence and anti-infective properties of probiotic Lactobacillus fermentum strain 4-17 against Escherichia coli causing urinary tract infection in humans.", "token_count": 412, "char_count": 1616, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6228, "quality_score": 0.8114, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:01.878015", "source": {"split": "train_shard_00000", "doc_id": 3060}, "chunk_id": "train_shard_00000_3060_0", "global_id": 3382}
{"text": "The sequencing of over a thousand Saccharomyces cerevisiae genomes revealed a complex pangenome. Over one third of the discovered genes are not present in the S. cerevisiae core genome but instead are often restricted to a subset of yeast isolates and thus may be important for adaptation to specific environmental niches. We refer to these genes as \"pan-genes,\" being part of the pangenome but not the core genome. Here, we describe the evolutionary journey and characterisation of a novel pan-gene, originally named hypothetical (HYPO) open-reading frame. Phylogenetic analysis reveals that HYPO has been predominantly retained in S. cerevisiae strains associated with brewing but has been repeatedly lost in most other fungal species during evolution. There is also evidence that HYPO was horizontally transferred at least once, from S. cerevisiae to Saccharomyces paradoxus. The phylogenetic analysis of HYPO exemplifies the complexity and intricacy of evolutionary trajectories of genes within the S. cerevisiae pangenome. To examine possible functions for Hypo, we overexpressed a HYPO-GFP fusion protein in both S. cerevisiae and Saccharomyces pastorianus. The protein localised to the plasma membrane where it accumulated initially in distinct foci. Time-lapse fluorescent imaging revealed that when cells are grown in wort, Hypo-gfp fluorescence spreads throughout the membrane during cell growth. The overexpression of Hypo-gfp in S. cerevisiae or S. pastorianus strains did not significantly alter cell growth in medium-containing glucose, maltose, maltotriose, or wort at different concentrations.\n\nEvolutionary journey and characterisation of a novel pan-gene associated with beer strains of Saccharomyces cerevisiae.", "token_count": 448, "char_count": 1730, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6032, "quality_score": 0.8016, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["yeast", "saccharomyces"], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:02.490669", "source": {"split": "train_shard_00000", "doc_id": 3061}, "chunk_id": "train_shard_00000_3061_0", "global_id": 3383}
{"text": "Pasteurella multocida is a heterogeneous bacterium, which has the capacity to cause disease in a wide range of host species and is also recognized as an important zoonotic pathogen. Two sequential deaths in captive fur seals occurred at Sea World, Australia during December 2017. A fibrinosuppurative bronchopneumonia in a Subantarctic fur seal (Arctocephalus tropicalis) resulted in death within 24 h of nonspecific signs of illness, whereas a septic peritonitis in a New Zealand fur seal (Arctocephalus forsteri) resulted in death within 12 h of clinical presentation. The cases happened within three days in two different pool locations, although both had previously been housed in the same area. A total of six Pasteurella multocida isolates were obtained from several internal organs at necropsy in both cases and were subjected to whole genome sequencing and phylogenomic analysis. In-silico typing of the isolates revealed that all belonged to Multi-Locus Sequence Type 7 and carried lipopolysaccharide outer core biosynthesis loci Type 3. Phylogenomic analysis of the isolates confirmed that the isolates were near identical at the core genome level, suggesting acquisition from a common source. The results also revealed the presence of within host and across animal diversity of P. multocida isolates for the first time even in a clearly connected outbreak.\n\nNovel insights into pasteurellosis in captive pinnipeds.", "token_count": 352, "char_count": 1425, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8233, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:03.042426", "source": {"split": "train_shard_00000", "doc_id": 3062}, "chunk_id": "train_shard_00000_3062_0", "global_id": 3384}
{"text": "Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.\n\nCulture-enriched human gut microbiomes reveal core and accessory resistance genes.", "token_count": 200, "char_count": 923, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8228, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:03.475566", "source": {"split": "train_shard_00000", "doc_id": 3063}, "chunk_id": "train_shard_00000_3063_0", "global_id": 3385}
{"text": "An inability to standardize the bioinformatic data produced by whole-genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, United Kingdom, using Ridom SeqSphere software for core genome multilocus sequence typing (cgMLST) analysis of whole-genome sequencing data. The phylogenetics of tuberculosis in Wales have not previously been studied. Sixty-six\n\nPhylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole-Genome Sequencing Data.", "token_count": 175, "char_count": 641, "word_count": 90, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:03.906493", "source": {"split": "train_shard_00000", "doc_id": 3064}, "chunk_id": "train_shard_00000_3064_0", "global_id": 3386}
{"text": "Listeria monocytogenes is sporadically detected on a range of ready to eat fresh produce lines, such as spinach and rocket, and is a threat to public health. However, little is known about the diversity of L. monocytogenes present on fresh produce and their potential pathogenicity. In this work, fifteen Listeria monocytogenes isolates from the UK fresh produce supply chain were characterised using whole genome sequencing (WGS). Additionally, isolates were characterised based on their ability to form biofilm. Whole genome sequencing data was used to determine the sequence type of isolates based on multi-locus sequence typing (MLST), construct a core single nucleotide polymorphism (SNP) phylogeny and determine the presence of virulence and resistance associated genes. MLST revealed 9 distinct sequence types (STs) spanning 2 lineages (I & II) with one isolate belonging to the ST6 subtype, strains from which have been recently implicated in two large, food-associated L. monocytogenes outbreaks in South Africa and across Europe. Although most of the 15 isolates were different, comparison of core genome SNPs showed 4 pairs of 'indistinguishable' strains (<5 SNPs difference). Virulence profiling revealed that some isolates completely lacked the Listeria pathogenicity island-3 (LIPI-3) amongst other virulence factors. Investigation of the inlA gene showed that no strains in this study contained a premature stop codon (PMSC), an indicator of attenuated virulence. Assessment of biofilm production showed that isolates found in the fresh produce supply chain differ in their ability to form biofilm. This trait is considered important for L. monocytogenes to persist in environments associated with food production and processing. Overall the work indicates that a genetically diverse range of L. monocytogenes strains is present in the UK fresh produce supply chain and the virulence profiles found suggests that at least some of the strains are capable of causing human illness. Interestingly, the presence of some genetically indistinguishable isolates within the 15 isolates examined suggests that cross-contamination in the fresh produce environment does occur", "token_count": 504, "char_count": 2179, "word_count": 320, "semantic_coherence": 1, "information_density": 0.5625, "quality_score": 0.7812, "entities": {"genes": ["ST6"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:04.550500", "source": {"split": "train_shard_00000", "doc_id": 3065}, "chunk_id": "train_shard_00000_3065_0", "global_id": 3387}
{"text": "These findings have useful implications in terms of food safety and for informing microbial surveillance programmes in the UK fresh produce supply chain.\n\nListeria monocytogenes isolates from ready to eat plant produce are diverse and have virulence potential.", "token_count": 55, "char_count": 260, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:04.923409", "source": {"split": "train_shard_00000", "doc_id": 3065}, "chunk_id": "train_shard_00000_3065_1", "global_id": 3388}
{"text": "Illnesses caused by Shiga toxin-producing Escherichia coli (STECs) can be life threatening, such as hemolytic uremic syndrome (HUS). The STECs most frequently identified by USDA's Microbiological Data Program (MDP) carried toxin gene subtypes stx1a and/or stx2a. Here we described the genome sequences of 331 STECs isolated from foods regulated by the FDA 2010-2017, and determined their genomic identity, serotype, sequence type, virulence potential, and prevalence of antimicrobial resistance. Isolates were selected from the MDP archive, routine food testing by FDA field labs (ORA), and food testing by a contract company. Only 276 (83%) strains were confirmed as STECs by in silico analysis. Foods from which STECs were recovered included cilantro (6%), spinach (25%), lettuce (11%), and flour (9%). Phylogenetic analysis using core genome MLST revealed these STEC genomes were highly variable, with some clustering associated with ST types and serotypes. We detected 95 different sequence types (ST); several ST were previously associated with HUS: ST21 and ST29 (O26:H11), ST11 (O157:H7), ST33 (O91:H14), ST17 (O103:H2), and ST16 (O111:H-). in silico virulome analyses showed ~ 51% of these strains were potentially pathogenic [besides stx gene they also carried eae (25%) or 26% saa (26%)]. Virulence gene prevalence was also determined: stx1 only (19%); stx2 only (66%); and stx1/sxt2 (15%). Our data form a new WGS dataset that can be used to support food safety investigations and monitor the recurrence/emergence of E. coli in foods.", "token_count": 488, "char_count": 1545, "word_count": 232, "semantic_coherence": 1, "information_density": 0.7328, "quality_score": 0.8664, "entities": {"genes": ["ST29", "ST33", "ST17", "ST21", "ST16", "ST11"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:05.574454", "source": {"split": "train_shard_00000", "doc_id": 3066}, "chunk_id": "train_shard_00000_3066_0", "global_id": 3389}
{"text": "Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017.", "token_count": 47, "char_count": 138, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:05.948552", "source": {"split": "train_shard_00000", "doc_id": 3066}, "chunk_id": "train_shard_00000_3066_1", "global_id": 3390}
{"text": "Critical illness is associated with a disturbed regulation of gastrointestinal hormones resulting in functional and metabolic anomalies. Fibroblast growth factor 19 (FGF19) is an ileum-derived metabolic hormone induced by bile salts upon gallbladder emptying after enteral nutrient stimulation. Our aim was to study the nutrient-stimulated FGF19 response in 24 patients admitted to the intensive care unit (ICU) compared with 12 healthy controls. All subjects received intraduodenal high-lipid nutrient infusion for 120 minutes. Blood was collected every 30 minutes until 1 hour after infusion, and gallbladder emptying was studied by ultrasound. Serum levels of bile salts and FGF19 were assessed. ICU patients had significantly higher fasting bile salt serum levels compared with controls, whereas FGF19 serum levels were similar. In both groups, nutrient infusion elicited substantial bile salt elevations (P < 0.001), peaking at 90 minutes, albeit with a significantly lower peak in the ICU patients (P = 0.029). In controls, FGF19 was significantly elevated relative to baseline from 120 minutes onward (P < 0.001). In ICU patients, the FGF19 response was blunted, as reflected by significantly lower FGF19 elevations at 120, 150, and 180 minutes (P < 0.05) and significantly lower area under the curve (AUC) values compared with controls (P < 0.001). Gallbladder dysmotility was associated with the impaired FGF19 response in critical illness. The gallbladder ejection fraction correlated positively with FGF19 AUC values (ρ = +0.34, P = 0.045). In 10 of 24 ICU patients, gallbladder emptying was disturbed. These patients had significantly lower FGF19 AUC values (P < 0.001)", "token_count": 499, "char_count": 1681, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5635, "quality_score": 0.7817, "entities": {"genes": ["FGF19"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:06.572976", "source": {"split": "train_shard_00000", "doc_id": 3067}, "chunk_id": "train_shard_00000_3067_0", "global_id": 3391}
{"text": "Gallbladder emptying and the FGF19 response were respectively disturbed or absent in patients receiving norepinephrine. Conclusion: The nutrient-stimulated FGF19 response is impaired in ICU patients, which is mechanistically linked to gallbladder dysmotility in critical illness. This may contribute to disturbed liver metabolism in these patients and has potential as a nutritional biomarker.\n\nGallbladder Dyskinesia Is Associated With an Impaired Postprandial Fibroblast Growth Factor 19 Response in Critically Ill Patients.", "token_count": 138, "char_count": 526, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7536, "quality_score": 0.8768, "entities": {"genes": ["FGF19"], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:06.987873", "source": {"split": "train_shard_00000", "doc_id": 3067}, "chunk_id": "train_shard_00000_3067_1", "global_id": 3392}
{"text": "Biliary lipids consist mainly of bile salts, phospholipids and cholesterol, which form mixed micelles and vesicles. Bile salts play various physiological roles but have damaging effects on cell membranes due to their detergent properties. The cytotoxicity of bile salts on hepatocytes leads to liver injuries and is largely determined by the bile salt species, the concentrations of bile salts, phospholipids and cholesterol, and the lipid composition of cell membranes. In bile, monomers and simple micelles of bile salts coexist with mixed micelles and vesicles in dynamic equilibrium, and contribute to the cytotoxicity on hepatocytes. The ATP-binding cassette (ABC) transporter family members, ABCB11, ABCB4 and ABCG5/ABCG8, mediate the biliary secretion of bile salts, phospholipids and cholesterol, respectively. Mutations in ABCB4 result in severe cholestatic diseases, and the biliary phospholipids are necessary for the attenuation of bile salt cytotoxicity. On the other hand, cholesterol reverses the cytoprotective effects of phospholipids against bile salts. In addition, phosphatidylethanolamine N-methyltransferase increases the cell resistance to bile salts by changing the phospholipid composition and structures of the apical membranes. In this review, we focus on the molecular mechanisms for the protection of hepatocytes against bile salt cytotoxicity. Further understanding of these mechanisms will help to develop new therapeutic strategies for cholestatic liver diseases.\n\nMolecular Mechanisms for Protection of Hepatocytes against Bile Salt Cytotoxicity.", "token_count": 411, "char_count": 1579, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5253, "quality_score": 0.7627, "entities": {"genes": ["ABCG8", "ABCB4", "ABCG5", "ABCB11"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:07.581659", "source": {"split": "train_shard_00000", "doc_id": 3068}, "chunk_id": "train_shard_00000_3068_0", "global_id": 3393}
{"text": "From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium (VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized.\n\nWGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome.", "token_count": 178, "char_count": 636, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7108, "quality_score": 0.8554, "entities": {"genes": ["ST80"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:08.016094", "source": {"split": "train_shard_00000", "doc_id": 3069}, "chunk_id": "train_shard_00000_3069_0", "global_id": 3394}
{"text": "In total, 95 Acinetobacter baumannii isolates recovered from patients from two hospitals in Cochabamba, Bolivia were studied. The presence of class D and B β-lactamases was investigated using polymerase chain reaction, and antimicrobial susceptibility testing was performed by agar dilution and broth microdilution. The resistance rate to carbapenems was 53.7%. All carbapenem-resistant A. baumannii (CRAb, n=51) and four carbapenem-susceptible isolates were further analysed by whole-genome sequencing. The resulting genome assemblies were used to identify the acquired resistome, and core genome multi-locus sequence typing (cgMLST) was used to determine their molecular epidemiology. All but one of the CRAb isolates (n=50) belonged to international clone (IC) 7 and they clustered into five sequence types; on cgMLST, they were found to be separated by ≥40 alleles. All CRAb isolates carried bla\n\nAcinetobacter baumannii analysis by core genome multi-locus sequence typing in two hospitals in Bolivia: endemicity of international clone 7 isolates (CC25).", "token_count": 292, "char_count": 1058, "word_count": 149, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": {"genes": ["CC25"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:08.552710", "source": {"split": "train_shard_00000", "doc_id": 3070}, "chunk_id": "train_shard_00000_3070_0", "global_id": 3395}
{"text": "Anthrax, caused by Bacillus anthracis, is a severe zoonosis with a great impact on both human and animal health. In the present study, we identified the phylogenetic relationships among 16 Japanese strains of B. anthracis, including eight bovine strains, two equine strains, five swine strains, and one former vaccine strain, using in silico canonical single nucleotide polymorphism (canSNP) and core genome SNP analyses. The results of our in silico canSNP analysis suggest that these 16 Japanese strains could be divided into four lineages: i) one equine strain in A.Br.Ames, ii) one equine and six bovine strains in A.Br.001/002, iii) five swine and one bovine strain in A.Br.Aust94, and iv) one bovine and one vaccine strain in A.Br.008/011. A comparison with non-Japanese B. anthracis strains revealed a total of 3787 SNPs identified from the whole genome sequences of the Japanese strains; these SNP data were subjected to a phylogenetic analysis using the maximum parsimony (MP) method. Our core genome SNP analysis was also able to detect differences of a few chromosomal SNPs across clonal strains from the same cases that had different storage and passage histories. Additionally, our whole genome SNP analysis clearly indicated that the Japanese swine anthrax cases of 1982 were caused by at least three independent strains; however, their phylogeny revealed no clear relationship with swine strains from other countries. The bovine strain belonging to the A.Br.008/011 lineage differed from a former Japanese vaccine strain by only 12 SNPs. Together with the phylogenic results and epidemiological circumstances, the diversity of strains reveals that the B. anthracis available in Japan probably resulted from multiple relatively recent import events, rather than reflecting the persistence of a more ancient ecologically established group.\n\nComparative genomics and phylogenetic analysis of Bacillus anthracis strains isolated from domestic animals in Japan.", "token_count": 509, "char_count": 1971, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5642, "quality_score": 0.7821, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:09.181504", "source": {"split": "train_shard_00000", "doc_id": 3071}, "chunk_id": "train_shard_00000_3071_0", "global_id": 3396}
{"text": "Corynebacterium pseudotuberculosis is the etiologic agent of veterinary relevance diseases, such as caseous lymphadenitis, affecting different animal species causing damage to the global agribusiness. So far, there are no completely effective treatment methods to overcome the impacts caused by this pathogen. Several genomes of the species are deposited on public databases, allowing the execution of studies related to the pan-genomic approach. In this study, we used an integrated in silico workflow to prospect novel putative targets using the core genome, a set of shared genes among 65 C. pseudotuberculosis strains. Subsequently, through RNA-Seq data of the same abiotic stresses in two strains, we selected only induced genes to compose the reverse vaccinology workflow based in two different strategies. Our results predicted six probable antigens in both analysis, which indicates that they have a strong potential to be used in further studies as vaccine targets against this bacterium.\n\nPrediction of new vaccine targets in the core genome of Corynebacterium pseudotuberculosis through omics approaches and reverse vaccinology.", "token_count": 253, "char_count": 1139, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:09.648029", "source": {"split": "train_shard_00000", "doc_id": 3072}, "chunk_id": "train_shard_00000_3072_0", "global_id": 3397}
{"text": "Yeasts are extremely useful, not only for fermentation but also for a wide spectrum of fuel and chemical productions. We analyzed the overall metabolic turnover and transcript dynamics in glycolysis and the TCA cycle, revealing the difference in adaptive pyruvate metabolic response between a Crabtree-negative species, Kluyveromyces marxianus, and a Crabtree-positive species, Saccharomyces cerevisiae, during aerobic growth. Pyruvate metabolism was inclined toward ethanol production under aerobic conditions in S. cerevisiae, while increased transcript abundances of the genes involved in ethanol metabolism and those encoding pyruvate dehydrogenase were seen in K. marxianus, indicating the augmentation of acetyl-CoA synthesis. Furthermore, different metabolic turnover in the TCA cycle was observed in the two species: malate and fumarate production in S. cerevisiae was higher than in K. marxianus, irrespective of aeration; however, fluxes of both the reductive and oxidative TCA cycles were enhanced in K. marxianus by aeration, implying both the cycles contribute to efficient electron flux without producing ethanol. Additionally, decreased hexokinase activity under aerobic conditions is expected to be important for maintenance of suitable carbon flux. These findings demonstrate differences in the key metabolic trait of yeasts employing respiration or fermentation, and provide important insight into the metabolic engineering of yeasts.\n\nIncreased flux in acetyl-CoA synthetic pathway and TCA cycle of Kluyveromyces marxianus under respiratory conditions.", "token_count": 385, "char_count": 1571, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8107, "entities": {"genes": [], "proteins": [], "pathways": ["glycolysis", "metabolism", "fermentation", "respiration"], "organisms": ["marxianus", "kluyveromyces", "yeast", "saccharomyces"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:10.235110", "source": {"split": "train_shard_00000", "doc_id": 3073}, "chunk_id": "train_shard_00000_3073_0", "global_id": 3398}
{"text": "High-temperature fermentation is desirable for the industrial production of ethanol, which requires thermotolerant yeast strains. However, yeast thermotolerance is a complicated quantitative trait. The understanding of genetic basis behind high-temperature fermentation performance is still limited. Quantitative trait locus (QTL) mapping by pooled-segregant whole genome sequencing has been proved to be a powerful and reliable approach to identify the loci, genes and single nucleotide polymorphism (SNP) variants linked to quantitative traits of yeast.\n\nQTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast.", "token_count": 152, "char_count": 671, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7209, "quality_score": 0.8605, "entities": {"genes": [], "proteins": [], "pathways": ["fermentation"], "organisms": ["yeast"], "conditions": ["ph", "temperature"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:15:10.652169", "source": {"split": "train_shard_00000", "doc_id": 3074}, "chunk_id": "train_shard_00000_3074_0", "global_id": 3399}