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pmcid large_stringlengths 8 11 | pmid large_stringlengths 0 9 | authors large_stringlengths 0 33.4k | title large_stringlengths 0 2.49k | publication_date large_stringlengths 10 10 | keywords large_stringlengths 0 17k | abstract large_stringlengths 0 122k | text large_stringlengths 9 8.39M |
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PMC10000013 | Sayan Chatterjee,Lakshmi Vineela Nalla,Monika Sharma,Nishant Sharma,Aditya A. Singh,Fehmina Mushtaque Malim,Manasi Ghatage,Mohd Mukarram,Abhijeet Pawar,Nidhi Parihar,Neha Arya,Amit Khairnar | Association of COVID-19 with Comorbidities: An Update | 27-02-2023 | COVID-19,comorbidity,diabetes,cancer,Parkinson’s disease,cardiovascular disease | Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) which was identified in Wuhan, China in December 2019 and jeopardized human lives. It spreads at an unprecedented rate worldwide, with serious and still-unfolding health conditions and economic ramifications. Based ... | Association of COVID-19 with Comorbidities: An Update
Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) which was identified in Wuhan, China in December 2019 and jeopardized human lives. It spreads at an unprecedented rate worldwide, with serious and still-unfoldi... | |
PMC10000025 | Qi Min,Lu Yang,Yu Wang,Yili Liu,Mingfeng Jiang | Transcriptome-Based Evaluation of Optimal Reference Genes for Quantitative Real-Time PCR in Yak Stomach throughout the Growth Cycle | 03-03-2023 | yak,stomach,transcriptome-wide,reference gene,RT-qPCR | Simple Summary The stomach is one of the primary sites for the digestion and absorption of nutrients. Quantifying related gene expression patterns using quantitative real-time PCR (RT-qPCR) is conducive to further understanding the molecular mechanisms underlying nutrition metabolism in the yak stomach. The authenticit... | Transcriptome-Based Evaluation of Optimal Reference Genes for Quantitative Real-Time PCR in Yak Stomach throughout the Growth Cycle
The stomach is one of the primary sites for the digestion and absorption of nutrients. Quantifying related gene expression patterns using quantitative real-time PCR (RT-qPCR) is conducive... | |
PMC10000032 | Maria Brockmann,Christoph Leineweber,Tom Hellebuyck,An Martel,Frank Pasmans,Michaela Gentil,Elisabeth Müller,Rachel E. Marschang | Establishment of a Real-Time PCR Assay for the Detection of Devriesea agamarum in Lizards | 28-02-2023 | Devriesea agamarum,polymerase chain reaction,Uromastyx sp.,Pogona vitticeps,bearded dragon,lizard,reptile,cheilitis,dermatitis | Simple Summary Bacterial infections can play an important role in dermatitis in lizards. The bacterial species Devriesea (D.) agamarum is a known cause of dermatitis, cheilitis and even fatal disease in lizards. Disease has most often been reported in Uromastyx species, but other lizards may also be affected. However, ... | Establishment of a Real-Time PCR Assay for the Detection of Devriesea agamarum in Lizards
Bacterial infections can play an important role in dermatitis in lizards. The bacterial species Devriesea (D.) agamarum is a known cause of dermatitis, cheilitis and even fatal disease in lizards. Disease has most often been repo... | |
PMC10000039 | Neelam A. Topno,Veerbhan Kesarwani,Sandeep Kumar Kushwaha,Sarwar Azam,Mohammad Kadivella,Ravi Kumar Gandham,Subeer S. Majumdar | Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds | 28-02-2023 | milk fat,whole-genome sequencing,SNPs,genomic variation,variant calling,indigenous breeds | Highlights What are the main findings? Differentially expressed milk fat QTL genes explored with whole genome se-quencing for variant analysis. Identified non-synonymous SNPs for hub and bottleneck QTL genes associated with milk fat traits. What is the implication of the main finding? Identified differential pattern(s)... | Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds
What are the main findings? Differentially expressed milk fat QTL genes explored with whole genome se-quencing for variant analysis. Identified non-synonymous SNPs for hub and bottleneck QTL genes associated with milk fat trai... | |
PMC10000040 | Yue Sun,Yanze Yu,Jinhao Guo,Linqiang Zhong,Minghai Zhang | Alterations in Fecal Microbiota Linked to Environment and Sex in Red Deer (Cervus elaphus) | 04-03-2023 | cervidae,KEGG,fecal microbiota,16s rRNA | Simple Summary The gut microbiota forms a complex microecosystem in vertebrates and is affected by various factors. Wild and captive red deer currently live in the same region but have vastly different diets. In this study, the 16S rRNA sequencing technology was performed to evaluate variations in the fecal microbiota ... | Alterations in Fecal Microbiota Linked to Environment and Sex in Red Deer (Cervus elaphus)
The gut microbiota forms a complex microecosystem in vertebrates and is affected by various factors. Wild and captive red deer currently live in the same region but have vastly different diets. In this study, the 16S rRNA sequen... | |
PMC10000043 | "Asmaa Sadat,Alshimaa M. M. Farag,Driss Elhanafi,Amal Awad,Ehab Kotb Elmahallawy,Noorah Alsowayeh,Ma(...TRUNCATED) | "Immunological and Oxidative Biomarkers in Bovine Serum from Healthy, Clinical, and Sub-Clinical Mas(...TRUNCATED) | 01-03-2023 | mastitis,E. coli,S. aureus,oxidative/antioxidant molecules,APP,inflammatory cytokines | "Simple Summary Establishing reliable biomarkers of udder bacterial infection and its bovine immune (...TRUNCATED) | "Immunological and Oxidative Biomarkers in Bovine Serum from Healthy, Clinical, and Sub-Clinical Mas(...TRUNCATED) | |
PMC10000048 | Duy Ngoc Do,Prashanth Suravajhala | Editorial: Role of Non-Coding RNAs in Animals | 23-02-2023 | "Editorial: Role of Non-Coding RNAs in Animals\n\nThe importance of non-coding RNAs (ncRNAs), such a(...TRUNCATED) | |||
PMC10000050 | "Rosa Marchetti,Valerio Faeti,Maurizio Gallo,Massimo Pindo,Davide Bochicchio,Luca Buttazzoni,Giacint(...TRUNCATED) | Protein Content in the Diet Influences Growth and Diarrhea in Weaning Piglets | 22-02-2023 | piglet,post-weaning diarrhea,dietary protein,fecal microbiota,feces composition | "Simple Summary Weaning (that is, removal from the sow) and the following two months are the riskies(...TRUNCATED) | "Protein Content in the Diet Influences Growth and Diarrhea in Weaning Piglets\n\nWeaning (that is, (...TRUNCATED) | |
PMC10000055 | Xin Yang,Xuemei Wu,Shuang Huang,Qian Yao,Xi Chen,Junke Song,Yingying Fan,Guanghui Zhao | "C3a/C3aR Affects the Propagation of Cryptosporidium parvum in the Ileum Tissues of Mice by Regulati(...TRUNCATED) | 24-02-2023 | "Cryptosporidium parvum,C3a/C3aR signaling,propagation,intestinal barrier function,cell proliferatio(...TRUNCATED) | "Simple Summary The complement system plays important roles in both innate and adaptive immunity. Th(...TRUNCATED) | "C3a/C3aR Affects the Propagation of Cryptosporidium parvum in the Ileum Tissues of Mice by Regulati(...TRUNCATED) | |
PMC10000059 | Maria Irene Pacini,Maurizio Mazzei,Micaela Sgorbini,Rossella D’Alfonso,Roberto Amerigo Papini | "A One-Year Retrospective Analysis of Viral and Parasitological Agents in Wildlife Animals Admitted (...TRUNCATED) | 04-03-2023 | wildlife,central Italy,viruses,helminths,protozoa,interspecies transmission,zoonotic pathogen | "Simple Summary In recent decades, wildlife populations in Italy have continued to expand, and some (...TRUNCATED) | "A One-Year Retrospective Analysis of Viral and Parasitological Agents in Wildlife Animals Admitted (...TRUNCATED) |
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LitScan EPMC Subset
This dataset is a subset of afg1/epmc-oa-subset, which itself comes from the Europe PMC open access subset of about 5.9 million articles.
Here, we take the ~960 parquet files from the full OA subset and join them against a list of PMCIDs for articles found by LitScan, which should discuss ncRNA for the ~9.6 million IDs searched from RNAcentral. The result is a collection of just over 1 million open access fulltext articles ostensibly about ncRNA.
The primary use case for this is pre-finetuning on domain specific text. This idea of domain adaptation is similar to what NVIDIA have done with their ChipNeMo model.
We are planning to finetune some models on this dataset, probably TinyLlama, since it is quite quick to train. These will be useful for e.g. generating embeddings for RAG, or further downstream finetuning on tasks like summarisation.
Limitations
The epmc-oa-subset parquet files are parsed from JATS, which does not always go entirely to plan. As a result, there are likely to be some articles with missing text, or strange tags left in. These should be quite rare, but I can't guarantee they're not in there.
LitScan itself also has some limitations, namely that there is quite a high false positive rate for those RNA IDs that are a bit generic. This means that while most of the articles in this dataset should be focused on RNA, there will be a significant minority that are about all sorts of other things, including but not limited to: concrete, female mice, recurrent neural networks. This is a very tricky problem to solve!
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