chunks_stream.jsonl

{"text": "We have compared genomes of Alteromonas macleodii \"deep ecotype\" isolates from two deep Mediterranean sites and two surface samples from the Aegean and the English Channel. A total of nine different genomes were analyzed. They belong to five clonal frames (CFs) that differ among them by approximately 30,000 single-nucleotide polymorphisms (SNPs) over their core genomes. Two of the CFs contain three strains each with nearly identical genomes (~100 SNPs over the core genome). One of the CFs had representatives that were isolated from samples taken more than 1,000 km away, 2,500 m deeper, and 5 years apart. These data mark the longest proven persistence of a CF in nature (outside of clinical settings). We have found evidence for frequent recombination events between or within CFs and even with the distantly related A. macleodii surface ecotype. The different CFs had different flexible genomic islands. They can be classified into two groups; one type is additive, that is, containing different numbers of gene cassettes, and is very variable in short time periods (they often varied even within a single CF). The other type was more stable and produced the complete replacement of a genomic fragment by another with different genes. Although this type was more conserved within each CF, we found examples of recombination among distantly related CFs including English Channel and Mediterranean isolates.\n\nGenomic diversity of \"deep ecotype\" Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames.", "token_count": 358, "char_count": 1528, "word_count": 235, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:19.689273", "source": {"split": "train_shard_00002", "doc_id": 656}, "chunk_id": "train_shard_00002_656_0", "global_id": 13600}
{"text": "Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly <i>Pseudomonas</i> species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.\n\nGut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua.", "token_count": 416, "char_count": 1784, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["gut", "ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:20.315190", "source": {"split": "train_shard_00002", "doc_id": 657}, "chunk_id": "train_shard_00002_657_0", "global_id": 13601}
{"text": "Enterohemorrhagic and enteropathogenic <i>Escherichia coli</i> are gastrointestinal pathogens that disrupt the intestinal microvilli to form attaching and effacing (A/E) lesions on infected cells and cause diarrhea. This pathomorphological trait is encoded within the pathogenicity island locus of enterocyte effacement (LEE). The LEE houses a type 3 secretion system (T3SS), which upon assembly bridges the bacterial cytosol to that of the host and enables the bacterium to traffic dozens of effectors into the host where they hijack regulatory and signal transduction pathways and contribute to bacterial colonization and disease. Owing to the importance of the LEE to EHEC and EPEC pathogenesis, much of the research on these pathogens has centered on its regulation. To date, over 40 proteinaceous factors have been identified that control the LEE at various hierarchical levels of gene expression. In contrast, RNA-based regulatory mechanisms that converge on the LEE have only just begun to be unraveled. In this minireview, we highlight major breakthroughs in small RNAs (sRNAs)-dependent regulation of the LEE, with an emphasis on their mechanisms of action and/or LEE-encoded targets.\n\nThe Tip of the Iceberg: On the Roles of Regulatory Small RNAs in the Virulence of Enterohemorrhagic and Enteropathogenic <i>Escherichia coli</i>.", "token_count": 353, "char_count": 1340, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6531, "quality_score": 0.8265, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:20.894786", "source": {"split": "train_shard_00002", "doc_id": 658}, "chunk_id": "train_shard_00002_658_0", "global_id": 13602}
{"text": "About 2,500 papers dated 2014-2016 were recovered by searching the PubMed database for <i>Streptomyces</i>, which are the richest known source of antibiotics. This review integrates around 100 of these papers in sections dealing with evolution, ecology, pathogenicity, growth and development, stress responses and secondary metabolism, gene expression, and technical advances. Genomic approaches have greatly accelerated progress. For example, it has been definitively shown that interspecies recombination of conserved genes has occurred during evolution, in addition to exchanges of some of the tens of thousands of non-conserved accessory genes. The closeness of the association of <i>Streptomyces</i> with plants, fungi, and insects has become clear and is reflected in the importance of regulators of cellulose and chitin utilisation in overall <i>Streptomyces</i> biology. Interestingly, endogenous cellulose-like glycans are also proving important in hyphal growth and in the clumping that affects industrial fermentations. Nucleotide secondary messengers, including cyclic di-GMP, have been shown to provide key input into developmental processes such as germination and reproductive growth, while late morphological changes during sporulation involve control by phosphorylation. The discovery that nitric oxide is produced endogenously puts a new face on speculative models in which regulatory Wbl proteins (peculiar to actinobacteria) respond to nitric oxide produced in stressful physiological transitions. Some dramatic insights have come from a new model system for <i>Streptomyces</i> developmental biology, <i>Streptomyces venezuelae</i>, including molecular evidence of very close interplay in each of two pairs of regulatory proteins. An extra dimension has been added to the many complexities of the regulation of secondary metabolism by findings of regulatory crosstalk within and between pathways, and even between species, mediated by end products", "token_count": 466, "char_count": 1968, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism", "fermentation"], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:21.540851", "source": {"split": "train_shard_00002", "doc_id": 659}, "chunk_id": "train_shard_00002_659_0", "global_id": 13603}
{"text": "Among many outcomes from the application of chromosome immunoprecipitation sequencing (ChIP-seq) analysis and other methods based on \"next-generation sequencing\" has been the finding that 21% of <i>Streptomyces</i> mRNA species lack leader sequences and conventional ribosome binding sites. Further technical advances now emerging should lead to continued acceleration of knowledge, and more effective exploitation, of these astonishing and critically important organisms.\n\nRecent advances in understanding <i>Streptomyces</i>.", "token_count": 123, "char_count": 527, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8769, "quality_score": 0.9385, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:21.919650", "source": {"split": "train_shard_00002", "doc_id": 659}, "chunk_id": "train_shard_00002_659_1", "global_id": 13604}
{"text": "N-Acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N-acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spectral library retrieving N-acyl lipid patterns from 2,700 public datasets, identifying 851 N-acyl lipids that were detected 356,542 times. 777 are not documented in lipid structural databases, with 18% of these derived from short-chain fatty acids and found in the digestive tract and other organs. Their levels varied with diet and microbial colonization and in people living with diabetes. We used the library to link microbial N-acyl lipids, including histamine and polyamine conjugates, to HIV status and cognitive impairment. This resource will enhance the annotation of these compounds in future studies to further the understanding of their roles in health and disease and to highlight the value of large-scale untargeted metabolomics data for metabolite discovery.\n\nThe microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids.", "token_count": 267, "char_count": 1094, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:22.473857", "source": {"split": "train_shard_00002", "doc_id": 660}, "chunk_id": "train_shard_00002_660_0", "global_id": 13605}
{"text": "<h4>Background</h4>Immunoglobulin (Ig)A proteases of Haemophilus influenzae are highly specific endopeptidases that cleave the hinge region of human IgA1 and also mediate invasion and trafficking in human respiratory epithelial cells, facilitating persistence of H. influenzae. Little is known about the expression of IgA proteases in clinical settings of H. influenzae infection.<h4>Methods</h4>We identified and characterized IgA protease genes in H. influenzae and studied their expression and proteolytic specificity, in vitro and in vivo in 169 independent strains of H. influenzae collected longitudinally over 10 years from adults with chronic obstructive pulmonary disease.<h4>Results</h4>The H. influenzae pangenome has 2 alleles of IgA protease genes; all strains have igaA, and 40% of strains have igaB. Each allele has 2 variants with differing proteolytic specificities for human IgA1. A total of 88% of 169 strains express IgA protease activity. Expression of the 4 forms of IgA protease varies among strains. Based on the presence of IgA1 fragments in sputum samples, each of the different forms of IgA protease is selectively expressed in the human airways during infection.<h4>Conclusions</h4>Four variants of IgA proteases are variably expressed by H. influenzae during infection of the human airways.\n\nExpression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary Disease.", "token_count": 415, "char_count": 1453, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5317, "quality_score": 0.7659, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:23.095480", "source": {"split": "train_shard_00002", "doc_id": 661}, "chunk_id": "train_shard_00002_661_0", "global_id": 13606}
{"text": "Defining bacterial species and understanding the relative cohesiveness of different components of their genomes remains a fundamental problem in microbiology. Bacterial species tend to be comprised of both a set of core and dispensable genes, with the sum of these two components forming the species pan-genome. The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear. Here we demonstrate, through the analysis of 96 genome sequences derived from two closely related sympatric sister species of pathogenic bacteria (Campylobacter coli and C. jejuni), that their pan-genome is indeed finite and that there are unique and cohesive features to each of their genomes defining their genomic identity. The two species have a similar pan-genome size; however, C. coli has acquired a larger core genome and each species has evolved a number of species-specific core genes, possibly reflecting different adaptive strategies. Genome-wide assessment of the level of lateral gene transfer within and between the two sister species, as well as within the core and non-core genes, demonstrates a resistance to interspecies recombination in the core genome of the two species and therefore provides persuasive support for the core genome hypothesis for bacterial species.\n\nEvolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.", "token_count": 310, "char_count": 1447, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5488, "quality_score": 0.7744, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:23.667799", "source": {"split": "train_shard_00002", "doc_id": 662}, "chunk_id": "train_shard_00002_662_0", "global_id": 13607}
{"text": "Soft rot of onion disks inoculated with the yeast Kluyveromyces marxianus var. marxianus increased significantly (P = 0.01) as temperature increased from 10 to 30 C. Rot was not evident in onion disks inoculated with the yeast and incubated for 12 days at 2 C. A temperature of 2 C or less during transit and storage of bulbs will reduce damage caused by the yeast. The amount of soft rot caused by seven isolates of K. m. var. marxianus from the Walla Walla Valley of southeastern Washington and northeastern Oregon did not vary significantly (P = 0.05) when tested on onion disks. A strain of the bacterium Erwinia carotovora subsp. carotovora from onion produced significantly (P = 0.01) more soft rot in onion than K. m. var. marxianus at 25 and 15 C, whereas K. m. var. marxianus produced significantly more soft rot in onion than a strain of E. c. subsp. carotovora from potato. Resistance to K. m. var. marxianus was not evident in 25 onion cultivars grown in the Pacific Northwest.\n\nYeast soft rot of onion in the Walla Walla Valley of Washington and Oregon.", "token_count": 317, "char_count": 1066, "word_count": 187, "semantic_coherence": 1, "information_density": 0.4652, "quality_score": 0.7326, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["temperature"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:24.222981", "source": {"split": "train_shard_00002", "doc_id": 663}, "chunk_id": "train_shard_00002_663_0", "global_id": 13608}
{"text": "Cellobiose, the last product in cellulose degradation, is converted into two molecules of glucose by a beta-glucosidase. S. cerevisiae does posses the structural gene for a beta-glucosidase, but it is very poorly expressed; we thus decided to isolate and characterize that of Kluyveromyces fragilis. We constructed in E. coli HB101 strain a genomic library of the Kluyveromyces fragilis Y610 strain (ATCC 12424), a yeast able to grow on cellobiose and which constitutively produces the beta-glucosidase. The structural gene for beta-glucosidase was identified by its expression in E. coli. The initial isolated cosmid KF1 contained an insert of 35 Kb and by successive subcloning the insert size was reduced to 3.5 Kb (KF4). This cloned beta-glucosidase gene introduced in S. cerevisiae by transformation is expressed at a level of about 500 times that of K. fragilis. We checked by Southern hybridization that the high expression level was not due to a rearrangement of K. fragilis DNA during the cloning experiments. Nevertheless to obtain yeast transformants able to grow on cellobiose a yeast strain whose permeability to sugar is increased must be used and this last point is discussed.\n\nCloning and expression of the structural gene for beta-glucosidase of Kluyveromyces fragilis in Escherichia coli and Saccharomyces cerevisiae.", "token_count": 364, "char_count": 1335, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5707, "quality_score": 0.7854, "entities": {"genes": ["KF1", "KF4", "HB101"], "proteins": [], "pathways": [], "organisms": ["kluyveromyces", "yeast", "saccharomyces"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:24.804701", "source": {"split": "train_shard_00002", "doc_id": 664}, "chunk_id": "train_shard_00002_664_0", "global_id": 13609}
{"text": "Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts. In the present study, host-pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. These observations suggest that the utilization of metabolites such as arginine by intracellular MAP might affect host NO production. Our dual RNA-seq data can provide novel insights by capturing the global transcriptome with higher resolution, especially in MAP, thus enabling a more systematic understanding of host-pathogen interactions.\n\nDelineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis.", "token_count": 426, "char_count": 1818, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": {"genes": ["NOS2"], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:25.431677", "source": {"split": "train_shard_00002", "doc_id": 665}, "chunk_id": "train_shard_00002_665_0", "global_id": 13610}
{"text": "Kluyveromyces fragilis immobilized in calcium alginate gel was compared to Saccharomyces cerevisiae coimmobilized with beta-galactosidase, for continuous ethanol production from whey permeate in packed-bed-type columns. Four different whey concentrations were studied, equivalent to 4.5, 10, 15, and 20% lactose, respectively. In all cases the coimmobilized preparation produced more ethanol than K. fragilis. The study went on for more than 5 weeks. K. fragilis showed a decline in activity after 20 days, while the coimmobilized preparation was stableduring the entrire investigation. Under experimental conditions theoretical yields of ethanol were obtained from 4.5 and 10% lactose substrates with the coimmobilized system. Using 15% lactose substrate, theoretical yields were only obtained when a galactose-adapted immobilized S. cerevisiae column was run in series with the coimmobilized column. Then a maximum of 71 g/L ethanol was produced with a productivity of 2.5 g/L h. The coimmobilized column alone gave a maximum ethanol concentration of 52 g/L with a productivity of 4.5 g/L h, whereas immobolized K. fragilis only produced 13 g/L ethanol with a productivity of 1.1 g/L h. It was not possible to obtain theoretical yields of ethanol from the highest substrate concentration.\n\nComparison between immobilized Kluyveromyces fragilis and Saccharomyces cerevisiae coimmobilized with beta-galactosidase, with respect to continuous ethanol production from concentrated whey permeate.", "token_count": 405, "char_count": 1492, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5381, "quality_score": 0.769, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["kluyveromyces", "saccharomyces"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:26.049205", "source": {"split": "train_shard_00002", "doc_id": 666}, "chunk_id": "train_shard_00002_666_0", "global_id": 13611}
{"text": "Streptococcus oralis, a commensal species of the human oral cavity, belongs to the Mitis group of streptococci, which includes one of the major human pathogens as well, S. pneumoniae. We report here the first complete genome sequence of this species. S. oralis Uo5, a high-level penicillin- and multiple-antibiotic-resistant isolate from Hungary, is competent for genetic transformation under laboratory conditions. Comparative and functional genomics of Uo5 will be important in understanding the evolution of pathogenesis among Mitis streptococci and their potential to engage in interspecies gene transfer.\n\nGenome of Streptococcus oralis strain Uo5.", "token_count": 167, "char_count": 653, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7717, "quality_score": 0.8859, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:26.489747", "source": {"split": "train_shard_00002", "doc_id": 667}, "chunk_id": "train_shard_00002_667_0", "global_id": 13612}
{"text": "The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation. We show that this phylogenetic correlation indeed leads to many false discoveries and propose phylogenetic linear regression as a powerful solution. To apply this method across the bacterial tree of life, where most species have not been experimentally phenotyped, we use metagenomes from hundreds of people to quantify each species' prevalence in and specificity for the gut microbiome. This analysis reveals thousands of genes potentially involved in adaptation to the gut across species, including many novel candidates as well as processes known to contribute to fitness of gut bacteria, such as acid tolerance in Bacteroidetes and sporulation in Firmicutes. We also find microbial genes associated with a preference for the gut over other body sites, which are significantly enriched for genes linked to fitness in an in vivo competition experiment. Finally, we identify gene families associated with higher prevalence in patients with Crohn's disease, including Proteobacterial genes involved in conjugation and fimbria regulation, processes previously linked to inflammation. These gene targets may represent new avenues for modulating host colonization and disease. Our strategy of combining metagenomics with phylogenetic modeling is general and can be used to identify genes associated with adaptation to any environment.\n\nPhylogeny-corrected identification of microbial gene families relevant to human gut colonization.", "token_count": 419, "char_count": 2084, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5728, "quality_score": 0.7864, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "acid", "ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:27.111195", "source": {"split": "train_shard_00002", "doc_id": 668}, "chunk_id": "train_shard_00002_668_0", "global_id": 13613}
{"text": "<h4>Background</h4>Efficient natural transformation in Neisseria requires the presence of short DNA uptake sequences (DUSs). Doubts remain whether DUSs propagate by pure selfish molecular drive or are selected for 'safe sex' among conspecifics.<h4>Results</h4>Six neisserial genomes were aligned to identify gene conversion fragments, DUS distribution, spacing, and conservation. We found a strong link between recombination and DUS: DUS spacing matches the size of conversion fragments; genomes with shorter conversion fragments have more DUSs and more conserved DUSs; and conversion fragments are enriched in DUSs. Many recent and singly occurring DUSs exhibit too high divergence with homologous sequences in other genomes to have arisen by point mutation, suggesting their appearance by recombination. DUSs are over-represented in the core genome, under-represented in regions under diversification, and absent in both recently acquired genes and recently lost core genes. This suggests that DUSs are implicated in genome stability rather than in generating adaptive variation. DUS elements are most frequent in the permissive locations of the core genome but are themselves highly conserved, undergoing mutation selection balance and/or molecular drive. Similar preliminary results were found for the functionally analogous uptake signal sequence in Pasteurellaceae.<h4>Conclusion</h4>As do many other pathogens, Neisseria and Pasteurellaceae have hyperdynamic genomes that generate deleterious mutations by intrachromosomal recombination and by transient hypermutation. The results presented here suggest that transformation in Neisseria and Pasteurellaceae allows them to counteract the deleterious effects of genome instability in the core genome. Thus, rather than promoting hypervariation, bacterial sex could be regenerative.\n\nThe impact of the neisserial DNA uptake sequences on genome evolution and stability.", "token_count": 447, "char_count": 1922, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:27.752391", "source": {"split": "train_shard_00002", "doc_id": 669}, "chunk_id": "train_shard_00002_669_0", "global_id": 13614}
{"text": "The objective of this case-control study, conducted in a large Italian university hospital over a 12-month period, was to evaluate the risk factors associated with the emergence of azole resistant oral candidosis in 64 Human Immunodeficiency Virus (HIV) infected patients. A swab was obtained from each patient by brushing candidal lesions. Candida albicans was isolated in 41 patients (64%), Candida glabrata in ten (16%), Candida krusei in five (8%), Candida kefyr in two (3%), Candida tropicalis in two (3%), and Candida lipolytica and Candida guilliermondii in one case, respectively. Two patients suffered a double infection i.e. C. albicans+C. krusei and C. albicans+C. glabrata, respectively. Candida species were tested in vitro for their susceptibility to ketoconazole, fluconazole, itraconazole and amphotericin B. MICs of the four antifungal drugs were obtained for each yeast using a microdilution broth method developed in our laboratory. Twenty four (37%) of the isolated strains were resistant both to itraconazole and fluconazole, five (8%) to fluconazole alone, and two (3%) to ketoconazole alone, while none of the isolated strains was resistant to amphotericin B. Patients with oral candidosis caused by a strain resistant to one or more azole drug were compared to control patients with azole-susceptible oral candidosis. On univariate analysis, more than five episodes of oral candidosis in the last year (P = 0.01), previous use of azole therapy (P = 0.001), C2-3 category of HIV infection (P = 0.01) and low number of circulating CD4+ T-cells (P = 0.03) were significantly associated with an increased risk for the development of azole resistance. However, previous use of azole therapy was the only factor selected by a stepwise logistic regression analysis which was independently associated with the isolation of azole resistant strains (P = 0.003)", "token_count": 518, "char_count": 1874, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5505, "quality_score": 0.7753, "entities": {"genes": ["CD4"], "proteins": [], "pathways": [], "organisms": ["yeast"], "conditions": ["ph"]}, "biobert_ready": false, "timestamp": "2025-11-01T07:07:28.417306", "source": {"split": "train_shard_00002", "doc_id": 670}, "chunk_id": "train_shard_00002_670_0", "global_id": 13615}
{"text": "Our findings indicate that, in view of the potential risk for the emergence and selection of azole resistant strains of Candida in patients with AIDS, it is important to carefully choose the antifungal drug for the therapy of mild fungal infections after evaluation of the in-vitro susceptibility of the isolated strains.\n\nAnalysis of the risk factors associated with the emergence of azole resistant oral candidosis in the course of HIV infection.", "token_count": 98, "char_count": 448, "word_count": 71, "semantic_coherence": 1, "information_density": 0.662, "quality_score": 0.831, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:28.837730", "source": {"split": "train_shard_00002", "doc_id": 670}, "chunk_id": "train_shard_00002_670_1", "global_id": 13616}
{"text": "<i>Background and Objective</i>: <i>Vibrio cholerae</i> continues to emerge as a dangerous pathogen because of increasing resistance to a number of antibiotics. This paper provides a solution to emerging antibiotic resistance by introducing novel proteins as vaccine candidates against cholera. <i>Materials and Methods</i>: <i>Vibrio cholerae</i> genome versatility is a hurdle for developing a vaccine to combat diarrhoeal infection, so its core gene information was used to determine a potential vaccine candidate. Whole genome sequence data of more than 100 <i>Vibrio cholerae</i> strains were used simultaneously to get core genome information. The VacSol pipeline based on reverse vaccinology was selected to address the problem of safe, cheap, temperature-stable, and effective vaccine candidates which can be used for vaccine development against <i>Vibrio cholerae</i>. VacSol screens vaccine candidates using integrated, well-known, and robust algorithms/tools for proteome analysis. The proteomes of the pathogens were initially screened to predict homology using BLASTp. Proteomes that are non-homologous to humans are then subjected to a predictor for localization. Helicer predicts transmembrane helices for the protein. Proteins failing to comply with the set parameters were filtered at each step, and finally, 11 proteins were filtered as vaccine candidates. <i>Results</i>: This selected group of vaccine candidates consists of proteins from almost all structural parts of <i>Vibrio cholerae</i>. Their blast results show that this filtered group includes flagellin A protein, a protein from the Zn transporter system, a lipocarrier outer membrane protein, a peptidoglycan-associated protein, a DNA-binding protein, a chemotaxis protein, a tRNA Pseuriudine synthase A, and two selected proteins, which were beta lactamases. The last two uncharacterized proteins possess 100% similarity to <i>V. albensis</i> and <i>Enterobacter</i>, respectively. Tertiary structure and active site determination show a large number of pockets on each protein", "token_count": 510, "char_count": 2059, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.805, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["temperature"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:29.501889", "source": {"split": "train_shard_00002", "doc_id": 671}, "chunk_id": "train_shard_00002_671_0", "global_id": 13617}
{"text": "<i>Conclusions</i>: The most interesting finding of this study is that 10 proteins out of 11 filtered proteins are introduced as novel potential vaccine candidates. These novel vaccine candidates can result in the development of cost-effective and broad-spectrum vaccines which can be used in countries where cholera is a major contributor to diarrheal disease.\n\nPreliminary Work Towards Finding Proteins as Potential Vaccine Candidates for <i>Vibrio cholerae</i> Pakistani Isolates through Reverse Vaccinology.", "token_count": 128, "char_count": 511, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:29.943017", "source": {"split": "train_shard_00002", "doc_id": 671}, "chunk_id": "train_shard_00002_671_1", "global_id": 13618}
{"text": "Phospholipase C (PLC) enzymes are essential in regulating several important cellular functions in eukaryotes, including yeasts. In this study, PCR was used to identify a gene encoding PLC activity in Candida albicans, using oligonucleotide primers complementary to sequences encoding highly conserved amino acid regions within the X domains of previously characterized eukaryotic phospholipase C genes. The nucleotide sequence of the C. albicans gene, CAPLC1 (2997 bp), was determined from a recombinant clone containing C. albicans 132A genomic DNA; it encoded a polypeptide of 1099 amino acids with a predicted molecular mass of 124.6 kDa. The deduced amino acid sequence of this polypeptide (CAPLC1) exhibited many of the features common to previously characterized PLCs, including specific X and Y catalytic domains. The CAPLC1 protein also exhibited several unique features, including a novel stretch of 18-19 amino acid residues within the X domain and an unusually long N-terminus which did not contain a recognizable EF-hand Ca(2+)-binding domain. An overall amino acid homology of more than 27% with PLCs previously characterized from Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that the CAPLC1 protein is a delta-form of phosphoinositide-specific PLC (PI-PLC). PLC activity was detected in cell-free extracts of both yeast and hyphal forms of C. albicans 132A following 7 h and 24 h growth using the PLC-specific substrate p-nitrophenylphosphorylcholine (p-NPPC). In addition, CAPLC1 mRNA was detected by reverse transcriptase PCR in both yeast and hyphal forms of C. albicans 132A at the same time intervals. Expression of CAPLC1 activity was also detected in extracts of Escherichia coli DH5 alpha harbouring plasmids which contained portions of the CAPLC1 gene lacking sequences encoding part of the N-terminus", "token_count": 514, "char_count": 1844, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5904, "quality_score": 0.7952, "entities": {"genes": ["DH5", "CAPLC1"], "proteins": [], "pathways": [], "organisms": ["yeast", "saccharomyces"], "conditions": ["acid", "ph"]}, "biobert_ready": false, "timestamp": "2025-11-01T07:07:30.607492", "source": {"split": "train_shard_00002", "doc_id": 672}, "chunk_id": "train_shard_00002_672_0", "global_id": 13619}
{"text": "Southern hybridization and PCR analyses revealed that all C. albicans and Candida dubliniensis isolates examined possessed sequences homologous to CAPLC1. Sequences related to CAPLC1 were detected in some but not all isolates of Candida tropicalis, Candida glabrata and Candida parapsilosis tested, but not in the isolates of Candida krusei, Candida kefyr, Candida guillermondii and Candida lusitaniae examined. This paper reports the first description of the cloning and sequencing of a PLC gene from a pathogenic yeast species.\n\nGenetic characterization of a phospholipase C gene from Candida albicans: presence of homologous sequences in Candida species other than Candida albicans.", "token_count": 179, "char_count": 685, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8163, "entities": {"genes": ["CAPLC1"], "proteins": [], "pathways": [], "organisms": ["yeast"], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:31.060686", "source": {"split": "train_shard_00002", "doc_id": 672}, "chunk_id": "train_shard_00002_672_1", "global_id": 13620}
{"text": "<h4>Background</h4>Public Health England (PHE) holds a collection of Shigella flexneri Type strains isolated between 1949 and 1972 representing 15 established serotypes and one provisional type, E1037. In this study, the genomes of all 16 PHE Type strains were sequenced using the Illumina HiSeq platform. The relationship between core genome phylogeny and serotype was examined.<h4>Results</h4>The most common target gene for the detection of Shigella species in clinical PCR assays, ipaH, was detected in all genomes. The type-specific target genes were correctly identified in each genome sequence. In contrast to the S. flexneri in serotype 5 strain described by Sun et al. (2012), the two PHE serotype 5 Type strains possessed an additional oac gene and were differentiated by the presence (serotype 5b) or absence (serotype 5a) of gtrX. The somatic antigen structure and phylogenetic relationship were broadly congruent for strains expressing serotype specific antigens III, IV and V, but not for those expressing I and II. The whole genome phylogenies of the 15 isolates sequenced showed that the serotype 6 Type Strain was phylogenetically distinct from the other S. flexneri serotypes sequenced. The provisional serotype E1037 fell within the serotype 4 clade, being most closely related to the Serotype 4a Type Strain.<h4>Conclusions</h4>The S. flexneri genome sequences were used to evaluate phylogenetic relationships between Type strains and validate genotypic and phenotypic assays. The analysis confirmed that the PHE S. flexneri Type strains are phenotypically and genotypically distinct. Novel variants will continue to be added to this archive.\n\nDraft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence.", "token_count": 496, "char_count": 1848, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5809, "quality_score": 0.7904, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:31.708769", "source": {"split": "train_shard_00002", "doc_id": 673}, "chunk_id": "train_shard_00002_673_0", "global_id": 13621}
{"text": "Genome: ASM5205707v1\n\nASM5205707v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:32.075392", "source": {"split": "train_shard_00002", "doc_id": 674}, "chunk_id": "train_shard_00002_674_0", "global_id": 13622}
{"text": "{\"uid\": \"29576111\", \"rsuid\": \"\", \"gbuid\": \"76762418\", \"assemblyaccession\": \"GCA_052057075.1\", \"lastmajorreleaseaccession\": \"GCA_052057075.1\", \"latestaccession\": \"\", \"chainid\": \"52057075\", \"assemblyname\": \"ASM5205707v1\", \"ucscname\": \"\", \"ensemblname\": \"\", \"taxid\": \"4911\", \"organism\": \"Kluyveromyces marxianus (budding yeasts & allies)\", \"speciestaxid\": \"4911\", \"speciesname\": \"Kluyveromyces marxianus\", \"assemblytype\": \"haploid\", \"assemblystatus\": \"Contig\", \"assemblystatussort\": 6, \"wgs\": \"JBPVIK01\", \"gb_bioprojects\": [{\"bioprojectaccn\": \"PRJNA1295373\", \"bioprojectid\": 1295373}], \"gb_projects\": [], \"rs_bioprojects\": [], \"rs_projects\": [], \"biosampleaccn\": \"SAMN50166912\", \"biosampleid\": \"50166912\", \"biosource\": {\"infraspecieslist\": [{\"sub_type\": \"strain\", \"sub_value\": \"YZC-01\"}], \"sex\": \"\", \"isolate\": \"\"}, \"coverage\": \"287.92\", \"partialgenomerepresentation\": \"false\", \"primary\": \"76762408\", \"assemblydescription\": \"\", \"releaselevel\": \"Major\", \"releasetype\": \"Major\", \"asmreleasedate_genbank\": \"2025/08/15 00:00\", \"asmreleasedate_refseq\": \"1/01/01 00:00\", \"seqreleasedate\": \"2025/08/15 00:00\", \"asmupdatedate\": \"2025/08/15 00:00\", \"submissiondate\": \"2025/08/15 00:00\", \"lastupdatedate\": \"2025/08/15 00:00\", \"submitterorganization\": \"University of Science and Technology Beijing\", \"refseq_category\": \"na\", \"anomalouslist\": [], \"exclfromrefseq\": [], \"propertylist\": [\"full-genome-representation\", \"latest\", \"latest_genbank\", \"wgs\"], \"fromtype\": \"\", \"synonym\": {\"genbank\": \"GCA_052057075.1\", \"refseq\": \"\", \"similarity\": \"\"}, \"contign50\": 1248555, \"scaffoldn50\": 1248555, \"annotrpturl\": \"\", \"ftppath_genbank\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/052/057/075/GCA_052057075.1_ASM5205707v1\", \"ftppath_refseq\": \"\", \"ftppath_assembly_rpt\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/052/057/075/GCA_052057075.1_ASM5205707v1/GCA_052057075.1_ASM5205707v1_assembly_report.txt\", \"ftppath_stats_rpt\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/052/057/075/GCA_052057075.1_ASM5205707v1/GCA_052057075.1_ASM5205707v1_assembly_stats.txt\", \"ftppath_regions_rpt\": \"\", \"busco\": {\"refseqannotationrelease\": \"\", \"buscolineage\": \"\", \"buscover\": \"\", \"complete\": \"\", \"singlecopy\": \"\", \"duplicated\": \"\", \"fragmented\": \"\", \"missing\": \"\", \"totalcount\": \"\"}, \"sortorder\": \"5C6X91959987514440520570759800\", \"meta\": \" <Stats> <Stat category=\\\"alt_loci_count\\\" sequence_tag=\\\"all\\\">0</Stat> <Stat category=\\\"chromosome_count\\\" sequence_tag=\\\"all\\\">0</Stat> <Stat category=\\\"contig_count\\\" sequence_tag=\\\"all\\\">11</Stat> <Stat category=\\\"contig_l50\\\" sequence_tag=\\\"all\\\">4</Stat> <Stat category=\\\"contig_n50\\\" sequence_tag=\\\"all\\\">1248555</Stat> <Stat category=\\\"non_chromosome_replicon_count\\\" sequence_tag=\\\"all\\\">0</Stat> <Stat category=\\\"replicon_count\\\" sequence_tag=\\\"all\\\">0</Stat> <Stat category=\\\"scaffold_count\\\" sequence_tag=\\\"all\\\">11</Stat> <Stat category=\\\"scaffold_count\\\" sequence_tag=\\\"placed\\\">0</Stat> <Stat category=\\\"scaffold_count\\\" sequence_tag=\\\"unlocalized\\\">0</Stat> <Stat category=\\\"scaffold_count\\\" sequence_tag=\\\"unplaced\\\">11</Stat> <Stat category=\\\"scaffold_l50\\\" sequence_tag=\\\"all\\\">4</Stat> <Stat category=\\\"scaffold_n50\\\" sequence_tag=\\\"all\\\">1248555</Stat> <Stat category=\\\"total_length\\\" sequence_tag=\\\"all\\\">10674396</Stat> <Stat category=\\\"ungapped_length\\\" sequence_tag=\\\"all\\\">10674396</Stat> </Stats> <FtpSites>   <FtpPath type=\\\"Assembly_rpt\\\">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/052/057/075/GCA_052057075.1_ASM5205707v1/GCA_052057075.1_ASM5205707v1_assembly_report.txt</FtpPath>   <FtpPath type=\\\"GenBank\\\">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/052/057/075/GCA_052057075.1_ASM5205707v1</FtpPath>   <FtpPath type=\\\"Stats_rpt\\\">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/052/057/075/GCA_052057075.1_ASM5205707v1/GCA_052057075.1_ASM5205707v1_assembly_stats.txt</FtpPath> </FtpSites> <assembly-level>1</assembly-level> <assembly-status>Contig</assembly-status> <representative-status>na</representative-status> <submitter-organization>University of Science and Technology Beijing</submitter-organization>    \"}", "token_count": 1859, "char_count": 4045, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6974, "quality_score": 0.8487, "entities": {"genes": ["JBPVIK01", "PRJNA1295373", "SAMN50166912"], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": []}, "biobert_ready": false, "timestamp": "2025-11-01T07:07:32.706214", "source": {"split": "train_shard_00002", "doc_id": 674}, "chunk_id": "train_shard_00002_674_1", "global_id": 13623}
{"text": "Genome: ASM4656278v1\n\nASM4656278v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:33.074965", "source": {"split": "train_shard_00002", "doc_id": 675}, "chunk_id": "train_shard_00002_675_0", "global_id": 13624}
{"text": "{\"uid\": \"26135151\", \"rsuid\": \"\", \"gbuid\": \"67942538\", \"assemblyaccession\": \"GCA_046562785.1\", \"lastmajorreleaseaccession\": \"GCA_046562785.1\", \"latestaccession\": \"\", \"chainid\": \"46562785\", \"assemblyname\": \"ASM4656278v1\", \"ucscname\": \"\", \"ensemblname\": \"\", \"taxid\": \"4911\", \"organism\": \"Kluyveromyces marxianus (budding yeasts & allies)\", \"speciestaxid\": \"4911\", \"speciesname\": \"Kluyveromyces marxianus\", \"assemblytype\": \"haploid\", \"assemblystatus\": \"Contig\", \"assemblystatussort\": 6, \"wgs\": \"JBJBSF01\", \"gb_bioprojects\": [{\"bioprojectaccn\": \"PRJNA957743\", \"bioprojectid\": 957743}], \"gb_projects\": [], \"rs_bioprojects\": [], \"rs_projects\": [], \"biosampleaccn\": \"SAMN34262491\", \"biosampleid\": \"34262491\", \"biosource\": {\"infraspecieslist\": [{\"sub_type\": \"strain\", \"sub_value\": \"Y1190\"}], \"sex\": \"\", \"isolate\": \"\"}, \"coverage\": \"547\", \"partialgenomerepresentation\": \"false\", \"primary\": \"67942418\", \"assemblydescription\": \"\", \"releaselevel\": \"Major\", \"releasetype\": \"Major\", \"asmreleasedate_genbank\": \"2025/01/08 00:00\", \"asmreleasedate_refseq\": \"1/01/01 00:00\", \"seqreleasedate\": \"2025/01/08 00:00\", \"asmupdatedate\": \"2025/01/08 00:00\", \"submissiondate\": \"2025/01/08 00:00\", \"lastupdatedate\": \"2025/01/08 00:00\", \"submitterorganization\": \"Concordia University\", \"refseq_category\": \"na\", \"anomalouslist\": [], \"exclfromrefseq\": [], \"propertylist\": [\"full-genome-representation\", \"has-mitochondrion\", \"latest\", \"latest_genbank\", \"wgs\"], \"fromtype\": \"\", \"synonym\": {\"genbank\": \"GCA_046562785.1\", \"refseq\": \"\", \"similarity\": \"\"}, \"contign50\": 1590052, \"scaffoldn50\": 1590052, \"annotrpturl\": \"\", \"ftppath_genbank\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/046/562/785/GCA_046562785.1_ASM4656278v1\", \"ftppath_refseq\": \"\", \"ftppath_assembly_rpt\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/046/562/785/GCA_046562785.1_ASM4656278v1/GCA_046562785.1_ASM4656278v1_assembly_report.txt\", \"ftppath_stats_rpt\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/046/562/785/GCA_046562785.1_ASM4656278v1/GCA_046562785.1_ASM4656278v1_assembly_stats.txt\", \"ftppath_regions_rpt\": \"\", \"busco\": {\"refseqannotationrelease\": \"\", \"buscolineage\": \"\", \"buscover\": \"\", \"complete\": \"\", \"singlecopy\": \"\", \"duplicated\": \"\", \"fragmented\": \"\", \"missing\": \"\", \"totalcount\": \"\"}, \"sortorder\": \"5C6X91959984099470465627859800\", \"meta\": \" <Stats> <Stat category=\\\"alt_loci_count\\\" sequence_tag=\\\"all\\\">0</Stat> <Stat category=\\\"chromosome_count\\\" sequence_tag=\\\"all\\\">0</Stat> <Stat category=\\\"contig_count\\\" sequence_tag=\\\"all\\\">10</Stat> <Stat category=\\\"contig_l50\\\" sequence_tag=\\\"all\\\">4</Stat> <Stat category=\\\"contig_n50\\\" sequence_tag=\\\"all\\\">1590052</Stat> <Stat category=\\\"non_chromosome_replicon_count\\\" sequence_tag=\\\"all\\\">1</Stat> <Stat category=\\\"replicon_count\\\" sequence_tag=\\\"all\\\">1</Stat> <Stat category=\\\"scaffold_count\\\" sequence_tag=\\\"all\\\">10</Stat> <Stat category=\\\"scaffold_count\\\" sequence_tag=\\\"placed\\\">1</Stat> <Stat category=\\\"scaffold_count\\\" sequence_tag=\\\"unlocalized\\\">0</Stat> <Stat category=\\\"scaffold_count\\\" sequence_tag=\\\"unplaced\\\">9</Stat> <Stat category=\\\"scaffold_l50\\\" sequence_tag=\\\"all\\\">4</Stat> <Stat category=\\\"scaffold_n50\\\" sequence_tag=\\\"all\\\">1590052</Stat> <Stat category=\\\"total_length\\\" sequence_tag=\\\"all\\\">10951256</Stat> <Stat category=\\\"ungapped_length\\\" sequence_tag=\\\"all\\\">10951256</Stat> </Stats> <FtpSites>   <FtpPath type=\\\"Assembly_rpt\\\">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/046/562/785/GCA_046562785.1_ASM4656278v1/GCA_046562785.1_ASM4656278v1_assembly_report.txt</FtpPath>   <FtpPath type=\\\"GenBank\\\">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/046/562/785/GCA_046562785.1_ASM4656278v1</FtpPath>   <FtpPath type=\\\"Stats_rpt\\\">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/046/562/785/GCA_046562785.1_ASM4656278v1/GCA_046562785.1_ASM4656278v1_assembly_stats.txt</FtpPath> </FtpSites> <assembly-level>1</assembly-level> <assembly-status>Contig</assembly-status> <representative-status>na</representative-status> <submitter-organization>Concordia University</submitter-organization>    \"}", "token_count": 1856, "char_count": 4011, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7104, "quality_score": 0.8552, "entities": {"genes": ["SAMN34262491", "JBJBSF01", "PRJNA957743"], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": []}, "biobert_ready": false, "timestamp": "2025-11-01T07:07:33.703432", "source": {"split": "train_shard_00002", "doc_id": 675}, "chunk_id": "train_shard_00002_675_1", "global_id": 13625}
{"text": "Genome: ASM4364731v1\n\nASM4364731v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:34.072830", "source": {"split": "train_shard_00002", "doc_id": 676}, "chunk_id": "train_shard_00002_676_0", "global_id": 13626}
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{"text": "Genome: ASM3632132v1\n\nASM3632132v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:36.057304", "source": {"split": "train_shard_00002", "doc_id": 678}, "chunk_id": "train_shard_00002_678_0", "global_id": 13630}
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{"text": "Genome: ASM2987366v1\n\nASM2987366v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:42.080797", "source": {"split": "train_shard_00002", "doc_id": 684}, "chunk_id": "train_shard_00002_684_0", "global_id": 13642}
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{"text": "Genome: ASM2987369v1\n\nASM2987369v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:43.138176", "source": {"split": "train_shard_00002", "doc_id": 685}, "chunk_id": "train_shard_00002_685_0", "global_id": 13644}
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{"text": "Genome: ASM2987365v1\n\nASM2987365v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:45.113307", "source": {"split": "train_shard_00002", "doc_id": 687}, "chunk_id": "train_shard_00002_687_0", "global_id": 13648}
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{"text": "Genome: ASM2876858v1\n\nASM2876858v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:46.108364", "source": {"split": "train_shard_00002", "doc_id": 688}, "chunk_id": "train_shard_00002_688_0", "global_id": 13650}
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{"text": "Genome: ERR4757804_bin.1_CONCOCT_v1.1_MAG\n\nERR4757804_bin.1_CONCOCT_v1.1_MAG", "token_count": 51, "char_count": 76, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:47.117696", "source": {"split": "train_shard_00002", "doc_id": 689}, "chunk_id": "train_shard_00002_689_0", "global_id": 13652}
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{"text": "Genome: ASM2241465v1\n\nASM2241465v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:48.117890", "source": {"split": "train_shard_00002", "doc_id": 690}, "chunk_id": "train_shard_00002_690_0", "global_id": 13654}
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{"text": "Genome: ASM2101442v1\n\nASM2101442v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:49.106371", "source": {"split": "train_shard_00002", "doc_id": 691}, "chunk_id": "train_shard_00002_691_0", "global_id": 13656}
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{"text": "Genome: ASM2101439v1\n\nASM2101439v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:50.096204", "source": {"split": "train_shard_00002", "doc_id": 692}, "chunk_id": "train_shard_00002_692_0", "global_id": 13658}
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{"text": "Genome: ASM1662610v1\n\nASM1662610v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:52.101240", "source": {"split": "train_shard_00002", "doc_id": 694}, "chunk_id": "train_shard_00002_694_0", "global_id": 13662}
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{"text": "Genome: ASM1662595v1\n\nASM1662595v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:53.140841", "source": {"split": "train_shard_00002", "doc_id": 695}, "chunk_id": "train_shard_00002_695_0", "global_id": 13664}
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{"text": "Genome: ASM1658427v1\n\nASM1658427v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:54.184161", "source": {"split": "train_shard_00002", "doc_id": 696}, "chunk_id": "train_shard_00002_696_0", "global_id": 13666}
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{"text": "Genome: ASM1658416v1\n\nASM1658416v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:55.235066", "source": {"split": "train_shard_00002", "doc_id": 697}, "chunk_id": "train_shard_00002_697_0", "global_id": 13668}
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{"text": "Genome: 100656_19_assem\n\n100656_19_assem", "token_count": 28, "char_count": 40, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:56.224549", "source": {"split": "train_shard_00002", "doc_id": 698}, "chunk_id": "train_shard_00002_698_0", "global_id": 13670}
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{"text": "Genome: ASM185444v2\n\nASM185444v2", "token_count": 25, "char_count": 32, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:57.220678", "source": {"split": "train_shard_00002", "doc_id": 699}, "chunk_id": "train_shard_00002_699_0", "global_id": 13672}
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{"text": "Genome: ASM800026v1\n\nASM800026v1", "token_count": 25, "char_count": 32, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:58.233726", "source": {"split": "train_shard_00002", "doc_id": 700}, "chunk_id": "train_shard_00002_700_0", "global_id": 13674}
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{"text": "Genome: ASM304615v1\n\nASM304615v1", "token_count": 25, "char_count": 32, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:07:59.600206", "source": {"split": "train_shard_00002", "doc_id": 701}, "chunk_id": "train_shard_00002_701_0", "global_id": 13676}
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{"text": "Genome: ASM235661v1\n\nASM235661v1", "token_count": 25, "char_count": 32, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:08:00.596598", "source": {"split": "train_shard_00002", "doc_id": 702}, "chunk_id": "train_shard_00002_702_0", "global_id": 13678}
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{"text": "Genome: ASM185444v1\n\nASM185444v1", "token_count": 25, "char_count": 32, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:08:01.596389", "source": {"split": "train_shard_00002", "doc_id": 703}, "chunk_id": "train_shard_00002_703_0", "global_id": 13680}
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{"text": "Genome: KmarxUFS1.0\n\nKmarxUFS1.0", "token_count": 21, "char_count": 32, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:08:02.603121", "source": {"split": "train_shard_00002", "doc_id": 704}, "chunk_id": "train_shard_00002_704_0", "global_id": 13682}
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{"text": "Genome: KM02\n\nKM02", "token_count": 13, "char_count": 18, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": ["KM02"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:08:07.700934", "source": {"split": "train_shard_00002", "doc_id": 709}, "chunk_id": "train_shard_00002_709_0", "global_id": 13692}
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{"text": "Genome: KM02r2\n\nKM02r2", "token_count": 17, "char_count": 22, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:08:08.688887", "source": {"split": "train_shard_00002", "doc_id": 710}, "chunk_id": "train_shard_00002_710_0", "global_id": 13694}
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{"text": "Genome: ASM74778v1\n\nASM74778v1", "token_count": 23, "char_count": 30, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-11-01T07:08:09.678360", "source": {"split": "train_shard_00002", "doc_id": 711}, "chunk_id": "train_shard_00002_711_0", "global_id": 13696}
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{"text": "Cellular responses to maladaptive environmental changes—stresses—allow for organismal adaptation to diverse and dynamic conditions. Across the tree of life, cells upregulate a highly conserved transcriptional program in response to so-called proteotoxic stresses such as heat shock. Correspondingly, in eukaryotes, these stresses induce the formation of biomolecular condensates, clusters of mRNA and protein which are referred to as stress granules under severe stress. However, major questions remain about this stress-induced response. How conserved is the condensation response relative to the transcriptional response? How does it vary across environmental niches, and to what extent does it correspond with the conserved transcriptional response? To answer these fundamental questions, we studied the growth, transcriptional, and condensation heat-induced stress responses in three fungal species adapted to thrive in different thermal environments: cryophilic S. kudriavzevii, mesophilic S. cerevisiae, and thermotolerant K. marxianus. Here we show that transcriptional heat shock responses track each species’ evolved temperature range of growth. Further, orthologous proteins—including poly(A)-binding protein, Pab1, a core marker of stress granules—form condensates in vivo at temperatures systematically tuned to the temperature at which the organisms activate the transcriptional heat shock response and slow their growth. In vitro, purified Pab1 from each species condenses autonomously at niche-specific temperatures. Homologous mutations in Pab1 cause similar shifts in relative condensation temperature across species, and crucially, mutations which suppress condensation in vitro also reduce fitness during heat stress. Our findings indicate that stress-induced protein condensation is adaptive, conserved, integrated with the growth and transcriptional responses, and tuned to features of the cellular and organismal environment to initiate at niche-specific levels.\n\nAn adaptive biomolecular condensation response is conserved across environmentally divergent species", "token_count": 463, "char_count": 2086, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus"], "conditions": ["ph", "temperature"]}, "biobert_ready": true, "timestamp": "2025-11-01T07:08:10.955495", "source": {"split": "train_shard_00002", "doc_id": 712}, "chunk_id": "train_shard_00002_712_0", "global_id": 13698}
{"text": "{\"uid\": \"200234499\", \"accession\": \"GSE234499\", \"gds\": \"\", \"title\": \"An adaptive biomolecular condensation response is conserved across environmentally divergent species\", \"summary\": \"Cellular responses to maladaptive environmental changes\\u2014stresses\\u2014allow for organismal adaptation to diverse and dynamic conditions. Across the tree of life, cells upregulate a highly conserved transcriptional program in response to so-called proteotoxic stresses such as heat shock. Correspondingly, in eukaryotes, these stresses induce the formation of biomolecular condensates, clusters of mRNA and protein which are referred to as stress granules under severe stress. However, major questions remain about this stress-induced response. How conserved is the condensation response relative to the transcriptional response? How does it vary across environmental niches, and to what extent does it correspond with the conserved transcriptional response? To answer these fundamental questions, we studied the growth, transcriptional, and condensation heat-induced stress responses in three fungal species adapted to thrive in different thermal environments: cryophilic S. kudriavzevii, mesophilic S. cerevisiae, and thermotolerant K. marxianus. Here we show that transcriptional heat shock responses track each species\\u2019 evolved temperature range of growth. Further, orthologous proteins\\u2014including poly(A)-binding protein, Pab1, a core marker of stress granules\\u2014form condensates in vivo at temperatures systematically tuned to the temperature at which the organisms activate the transcriptional heat shock response and slow their growth. In vitro, purified Pab1 from each species condenses autonomously at niche-specific temperatures. Homologous mutations in Pab1 cause similar shifts in relative condensation temperature across species, and crucially, mutations which suppress condensation in vitro also reduce fitness during heat stress. Our findings indicate that stress-induced protein condensation is adaptive, conserved, integrated with the growth and transcriptional responses, and tuned to features of the cellular and organismal environment to initiate at niche-specific levels.\", \"gpl\": \"27812;29573;33472\", \"gse\": \"234499\", \"taxon\": \"Kluyveromyces marxianus; Saccharomyces cerevisiae; Saccharomyces kudriavzevii\", \"entrytype\": \"GSE\", \"gdstype\": \"Expression profiling by high throughput sequencing\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2023/07/31\", \"suppfile\": \"TSV\", \"samples\": [{\"accession\": \"GSM7469738\", \"title\": \"Kmarx_37C_BR2\"}, {\"accession\": \"GSM7469735\", \"title\": \"Scer_40C_BR1\"}, {\"accession\": \"GSM7469730\", \"title\": \"Skud_24C_BR2\"}, {\"accession\": \"GSM7469733\", \"title\": \"Scer_33C_BR1\"}, {\"accession\": \"GSM7469736\", \"title\": \"Scer_40C_BR2\"}, {\"accession\": \"GSM7469739\", \"title\": \"Kmarx_46C_BR1\"}, {\"accession\": \"GSM7469731\", \"title\": \"Skud_31C_BR1\"}, {\"accession\": \"GSM7469740\", \"title\": \"Kmarx_46C_BR2\"}, {\"accession\": \"GSM7469734\", \"title\": \"Scer_33C_BR2\"}, {\"accession\": \"GSM7469737\", \"title\": \"Kmarx_37C_BR1\"}, {\"accession\": \"GSM7469729\", \"title\": \"Skud_24C_BR1\"}, {\"accession\": \"GSM7469732\", \"title\": \"Skud_31C_BR2\"}], \"relations\": [], \"extrelations\": [], \"n_samples\": 12, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [\"38605014\"], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE234nnn/GSE234499/\", \"geo2r\": \"no\", \"bioproject\": \"PRJNA981544\"}", "token_count": 1160, "char_count": 3477, "word_count": 383, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8211, "entities": {"genes": ["GSE234499", "GSM7469732", "PRJNA981544", "GSM7469738", "GSM7469731", "GSM7469734", "GSM7469737", "GSM7469736", "GSM7469730", "GSM7469733"], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "saccharomyces"], "conditions": ["ph", "temperature"]}, "biobert_ready": false, "timestamp": "2025-11-01T07:08:11.612404", "source": {"split": "train_shard_00002", "doc_id": 712}, "chunk_id": "train_shard_00002_712_1", "global_id": 13699}