cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23827839
title: Ringwidth.xlsx

description: These are the raw data of tree ring width of B. maximowicziana trees grown in Naie and Furano in central Hokkaido from 2000 to 2016.
DOI: 10.6084/m9.figshare.23827839.v1
title: Ringwidth.xlsx

description: These are the raw data of tree ring width of B. maximowicziana trees grown in Naie and Furano in central Hokkaido from 2000 to 2016.
DOI: 10.5281/zenodo.7980862
title: MI dataset( Digononta)

description: the Digononta images in MI dataset
DOI: 10.5281/zenodo.7980861
title: MI dataset( Digononta)

description: the Digononta images in MI dataset
DOI: 10.6084/m9.figshare.23827912
title: Epigenetic aging in cows is accelerated by milk production

description: DNA methylation has proven to be the most promising age-predictive biomarker in mammals resulting in the emergence of ‘epigenetic clocks’ that describe the relationship between methylation levels and age. Using Targeted bisulfite Sequencing, we evaluated blood DNA-methylation data from 96 domesticated cows (<i>Bos Taurus</i>) of which 88 were adults and 8 were calves. This allowed us to measure DNA methylation across three thousand regions in the genome that were conserved across mammals. The significant association of age with the changes in DNA methylation enabled us to construct an epigenetic clock that predicts the age of cows to within nine months. We also investigated whether factors exist that moderate the association between epigenetic age and actual age and found that milk production levels significantly increase the rate of epigenetic ageing, suggesting that the stress of excessive milk production might be accelerating epigenetic ageing in cows.
DOI: 10.6084/m9.figshare.23827912.v1
title: Epigenetic aging in cows is accelerated by milk production

description: DNA methylation has proven to be the most promising age-predictive biomarker in mammals resulting in the emergence of ‘epigenetic clocks’ that describe the relationship between methylation levels and age. Using Targeted bisulfite Sequencing, we evaluated blood DNA-methylation data from 96 domesticated cows (<i>Bos Taurus</i>) of which 88 were adults and 8 were calves. This allowed us to measure DNA methylation across three thousand regions in the genome that were conserved across mammals. The significant association of age with the changes in DNA methylation enabled us to construct an epigenetic clock that predicts the age of cows to within nine months. We also investigated whether factors exist that moderate the association between epigenetic age and actual age and found that milk production levels significantly increase the rate of epigenetic ageing, suggesting that the stress of excessive milk production might be accelerating epigenetic ageing in cows.
DOI: 10.14457/tu.the.2022.473
title: ระดับเสียงบริเวณโดยรอบถนนข้าวสาร แขวงตลาดยอด เขตพระนครและการตอบสนองของประชาชนในชุมชนพื้นที่ใกล้เคียง

description: การศึกษาเชิงพรรณนามีวัตถุประสงค์เพื่อวัดระดับเสียงในสิ่งแวดล้อม จัดทำแผนที่เส้นเสียง และศึกษาปัจจัยที่มีความสัมพันธ์ต่อการตอบสนองของประชาชนกับระดับเสียงบริเวณถนนข้าวสาร โดยรวบรวมข้อมูลจากการตรวจวัดเสียง จัดทำแผนที่เส้นเสียงด้วยโปรแกรม SURFER รวมถึงใช้แบบสัมภาษณ์ กลุ่มตัวอย่าง 165 ครัวเรือน วิเคราะห์ข้อมูลด้วยร้อยละ ค่าเฉลี่ย ส่วนเบี่ยงเบนมาตรฐาน Pearson Chi-Square , Fisher’s Exact Test ที่ระดับนัยสำคัญ 5%ผลการวิจัยพบว่า จากการวัดระดับเสียงเฉลี่ยนอกอาคาร จำนวน 168 จุดที่กระจายอยู่ในพื้นที่ที่ศึกษาทั้งที่ถนนข้าวสารและชุมชนทั้ง 4 แห่ง มีค่าระดับเสียงเฉลี่ย 55.5 – 102.7 เดซิเบลเอ ระดับเสียงเฉลี่ย สูงกว่า 90 เดซิเบลเอ จำนวน 110 จุด จากแผนที่เส้นเสียงที่จัดทำขึ้นครอบคลุมทั้ง 4 ชุมชนนั้น เห็นได้ชัดเจนว่า 2 ชุมชนที่ตั้งอยู่สองข้างทางของถนนข้าวสารเป็นพื้นที่ที่มีระดับเสียงสูงกว่าอีก 2 ชุมชน ที่ตั้งอยู่ที่หัวและท้ายของถนน ส่วนผลจากการวัดระดับเสียงรบกวนซึ่งเป็นการวัดระดับเสียงเฉลี่ย 24 ชั่วโมง เป็นอาคารที่พักอาศัยจำนวน 8 แห่ง พบว่า 7 แห่ง มีระดับเสียงที่เป็นเสียงรบกวนตามกฎหมาย ทั้งในวันหยุดและวันธรรมดา มี 1 แห่ง ที่มีระดับเสียงต่ำกว่าเกณฑ์เสียงรบกวนตามกฎหมาย อนึ่ง ผลจากการวัดระดับเสียงสูงสุด ณ ขณะใดขณะหนึ่ง บริเวณที่พักอาศัยทั้ง 8 แห่งดังกล่าว พบว่ามีระดับเสียงสูงสุดระหว่าง 55.1 – 98.0 เดซิเบลเอ นอกจากนี้ การศึกษาตอบสนองของประชาชนต่อเสียงรบกวน พบว่าการเปิดเพลงหรือการแสดงดนตรีสดบริเวณถนนข้าวสารเป็นมลภาวะทางเสียงให้แก่ผู้อยู่อาศัยในชุมชนถึงร้อยละ 56.4 โดยมีความรำคาญระดับปานกลางร้อยละ 26.9 รบกวนการพักผ่อน ร้อยละ 35.8 โดยเป็นการรบกวนการพักผ่อนระดับปานกลางร้อยละ 44.1 และพบว่าความถี่ของการรบกวน คือ รบกวนในทุกวัน ร้อยละ 50 โดยมีระยะเวลาการรบกวน ในช่วงเวลา 18.00-24.00 น. ถึงร้อยละ 74.1 ผลจากการศึกษานี้แสดงให้เห็นว่ามาตรการควบคุมมลภาวะทางเสียงต่อชุมชนยังไม่เพียงพอ จำเป็นต้องดำเนินมาตรการป้องกันเสียงรบกวนโดยการควบคุมที่แหล่งกำเนิดอย่างมีประสิทธิภาพยิ่งขึ้น
DOI: 10.6084/m9.figshare.23812830.v29
title: Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiratio

description: Regridding Global CMIP6 GCMs dataset(0.5 degree)Historical dataset:14 CMIP6 GCMs (1850-2014)Future dataset: 14CMIP6 GCMs and 4 SSP scenarios (2015-2100)Composition of dataset: Average temperature, Maximum temperature, Minimum temperature, Windspeed, Relative humidity, Solar radiationIf you are using our codes and dataset, please use the following references:Song, Y.H., Chung, E.S., Shahid, S., Kim, Y.J., Kim, D.K. 2023. Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiration. Scientific Data.<br>
DOI: 10.5281/zenodo.8210047
title: Accurate TCR-pMHC Interaction Prediction Using a BERT-based Transfer Learning Method

description: The training data of TCR-BERT and pMHC-BERT and the healthy TCR dataset. For the complete training and testing code of TABR-BERT, see Freshwind-Bioinformatics/TABR-BERT: TABR-BERT: an Accurate and Robust BERT-based Transfer Learning Model for TCR-pMHC Interaction Prediction (github.com).
DOI: 10.5281/zenodo.8210046
title: Accurate TCR-pMHC Interaction Prediction Using a BERT-based Transfer Learning Method

description: The training data of TCR-BERT and pMHC-BERT and the healthy TCR dataset. For the complete training and testing code of TABR-BERT, see Freshwind-Bioinformatics/TABR-BERT: TABR-BERT: an Accurate and Robust BERT-based Transfer Learning Model for TCR-pMHC Interaction Prediction (github.com).
DOI: 10.5281/zenodo.8209788
title: VHE test

description: Test dataset
DOI: 10.5281/zenodo.8209787
title: VHE test

description: Test dataset
DOI: 10.5281/zenodo.8210254
title: ScRAPv20230731: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

description: <strong><em>Saccharomyces cerevisiae </em>Reference Assembly Panel (ScRAP) v20230731 </strong>&gt; The haplotype-resolved and/or collapsed T2T genome assemblies for 142 <em>S. cerevisiae</em> strains isolated from diverse geographical and ecological niches.
description: Citation: Samuel O'Donnell, Jia-Xing Yue, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stephane Delmas, Fabien Dutreux, Teo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer, Gianni Liti, Gilles Fischer. (2023) Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae. Nature Genetics, (doi: https://doi.org/10.1038/s41588-023-01459-y) https://www.nature.com/articles/s41588-023-01459-y Alternative download source: https://www.evomicslab.org/db/ScRAPdb/ Funding: This work was supported by the Agence Nationale de la Recherche ANR-16-CE12-0019 (to G.L., J.S. and G.F.) and ANR-18-CE12-0004 (to G.L. and G.F.). This work was also partially supported by the ANR-15-IDEX-01 (to G.L.), Fondation pour la Recherche Médicale (EQU202003010413 to G.L.), the European Research Council (ERC Consolidator Grant 772505 to J.S.), the Guangdong Basic and Applied Basic Research Foundation (2019A1515110762 to J.-X.Y.), Guangdong Pearl River Talents Program (2019QN01Y183 to J.-X.Y.), and National Natural Science Foundation of China (32070592 to J.-X.Y.). J.S. is a Fellow of the University of Strasbourg Institute for Advanced Study (USIAS) and a member of the Institut Universitaire de France.
DOI: 10.5281/zenodo.8210253
title: ScRAPv20230731: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

description: <strong><em>Saccharomyces cerevisiae </em>Reference Assembly Panel (ScRAP) v20230731 </strong>&gt; The haplotype-resolved and/or collapsed T2T genome assemblies for 142 <em>S. cerevisiae</em> strains isolated from diverse geographical and ecological niches.
description: Citation: Samuel O'Donnell, Jia-Xing Yue, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stephane Delmas, Fabien Dutreux, Teo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer, Gianni Liti, Gilles Fischer. (2023) Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae. Nature Genetics, (doi: https://doi.org/10.1038/s41588-023-01459-y) https://www.nature.com/articles/s41588-023-01459-y Alternative download source: https://www.evomicslab.org/db/ScRAPdb/ Funding: This work was supported by the Agence Nationale de la Recherche ANR-16-CE12-0019 (to G.L., J.S. and G.F.) and ANR-18-CE12-0004 (to G.L. and G.F.). This work was also partially supported by the ANR-15-IDEX-01 (to G.L.), Fondation pour la Recherche Médicale (EQU202003010413 to G.L.), the European Research Council (ERC Consolidator Grant 772505 to J.S.), the Guangdong Basic and Applied Basic Research Foundation (2019A1515110762 to J.-X.Y.), Guangdong Pearl River Talents Program (2019QN01Y183 to J.-X.Y.), and National Natural Science Foundation of China (32070592 to J.-X.Y.). J.S. is a Fellow of the University of Strasbourg Institute for Advanced Study (USIAS) and a member of the Institut Universitaire de France.
DOI: 10.5281/zenodo.8082181
title: Dataset of moment coordinate transformations

description: The dataset used to generate the results in "Moment tracking and their coordinate transformations for macroparticles with an application to plasmas around black holes", available as a preprint at https://arxiv.org/abs/2308.01276 PhaseSpaceData contains the data used to generate figure 5. SchwarzschildResults contains the data used to generate figure 7a and figure 8a. KruskalSzekeresResults contains the data used to generate figure 7b and 8b.
DOI: 10.5281/zenodo.8082180
title: Dataset of moment coordinate transformations

description: The dataset used to generate the results in "Moment tracking and their coordinate transformations for macroparticles with an application to plasmas around black holes", available as a preprint at https://arxiv.org/abs/2308.01276 PhaseSpaceData contains the data used to generate figure 5. SchwarzschildResults contains the data used to generate figure 7a and figure 8a. KruskalSzekeresResults contains the data used to generate figure 7b and 8b.
DOI: 10.5281/zenodo.8210464
title: Reproducing surface water isoscapes of δ18O and δ2H across China: A machine learning approach

description: This dataset support this submission.
DOI: 10.5281/zenodo.8210463
title: Reproducing surface water isoscapes of δ18O and δ2H across China: A machine learning approach

description: This dataset support this submission.
DOI: 10.6084/m9.figshare.23812830.v30
title: Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiratio

description: Regridding Global CMIP6 GCMs dataset(0.5 degree)Historical dataset:14 CMIP6 GCMs (1850-2014)Future dataset: 14CMIP6 GCMs and 4 SSP scenarios (2015-2100)Composition of dataset: Average temperature, Maximum temperature, Minimum temperature, Windspeed, Relative humidity, Solar radiationIf you are using our codes and dataset, please use the following references:Song, Y.H., Chung, E.S., Shahid, S., Kim, Y.J., Kim, D.K. 2023. Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiration. Scientific Data.<br>
DOI: 10.6084/m9.figshare.23827968
title: Test1

description: It is a dataset for test
DOI: 10.6084/m9.figshare.23827968.v1
title: Test

description: It is a dataset for test
DOI: 10.6084/m9.figshare.23827968.v2
title: Test1

description: It is a dataset for test
DOI: 10.25345/c5rv0d999
title: MassIVE MSV000092578 - Multi-Protease Investigation of Arabidopsis Thaliana Cell Culture Mitochondria
title: The aim of this project is to deeply map the proteome of mitochondria from the model plant Arabidopsis thaliana. For this purpose, mitochondria were isolated from Arabidopsis cell cultures, their proteins extracted and processed using SP3 digestion. To achieve high sequence coverage, the proteins were digested with a total of six different proteases and measured using sensitive timsTOF Pro hardware and TIMS fractionation.
DOI: 10.25345/c5n29ph5x
title: MassIVE MSV000092579 - Quantitative proteomic profiling of HCC1954 cells treated with a CDK12 degrader
title: HCC1954 cells growing at 80% confluency in a 10-cm dish were treated with (R)-2-(4-(9-ethyl-6-(((6-(furan-3-yl)pyridin-3-yl)methyl)amino)-9H-purin-2-yl)morpholin-3-yl)ethan-1-ol (a CDK12 degrader) at 300 nM (0.5% in DMSO) or DMSO as a control for 2 hours. Each was carried out in triplicates. The cells were disrupted in a lysis buffer containing 2% SDS, 2 mM MgCl2, 50 mM triethylammonium bicarbonate, 1x HALT phosphatase and protease inhibitors (ThermoFisher Scientific, Waltham, MA) using Bioruptor Sonicator (Diagenode, Denville, NJ). Proteins were recovered and proteolyzed with trypsin on S-trap columns (PROTIFI, Fairport, NY). The resultant peptides were labeled with 6-plex TMT isobaric reagents (triplicates for 2 conditions), mixed altogether, subfractionated by basic reversed phase high performance liquid chromatography, and analyzed by LC-MS/MS (ThermoFisher, Q-Exactive). The LC-MS/MS data were processed by using Proteome Discoverer v2.4.
DOI: 10.6084/m9.figshare.23827986
title: Supplementary Material for: A heterozygous variant of FGF13 caused X-linked developmental and epileptic encephalopathy 90 in a Chinese family

description: Developmental and epileptic encephalopathy (DEE) refers to a group of severe epilepsy encephalopathy and development disorders, and its typical clinical features include seizures, drug resistance, and developmental delay or regression. To date, limited studies have reported DEEs driven by FGF13. Here, we reported a girl with DEE90 caused by variant of FGF13. Her electroencephalography (EEG) showed discontinuous hypsarrhythmia, and a heterozygous nonsynonymous variant in FGF13 [NM_004114.4: c.5C&gt;G, p.(Ala2Gly)] was identified from the proband. The variant was not reported in public databases such as gnomAD and Exome Aggregation Consortium (ExAC), and predicted to be damaging to proteins and classified as likely pathogenic (LP) according to the ACMG guidelines. The seizure was finally controlled by a combination of ACTH + zonisamide (10 mg/kg.d) + levetiracetam (52 mg/kg.d) + clonazepam (0.7 mg/kg.d).
DOI: 10.6084/m9.figshare.23827986.v1
title: Supplementary Material for: A heterozygous variant of FGF13 caused X-linked developmental and epileptic encephalopathy 90 in a Chinese family

description: Developmental and epileptic encephalopathy (DEE) refers to a group of severe epilepsy encephalopathy and development disorders, and its typical clinical features include seizures, drug resistance, and developmental delay or regression. To date, limited studies have reported DEEs driven by FGF13. Here, we reported a girl with DEE90 caused by variant of FGF13. Her electroencephalography (EEG) showed discontinuous hypsarrhythmia, and a heterozygous nonsynonymous variant in FGF13 [NM_004114.4: c.5C&gt;G, p.(Ala2Gly)] was identified from the proband. The variant was not reported in public databases such as gnomAD and Exome Aggregation Consortium (ExAC), and predicted to be damaging to proteins and classified as likely pathogenic (LP) according to the ACMG guidelines. The seizure was finally controlled by a combination of ACTH + zonisamide (10 mg/kg.d) + levetiracetam (52 mg/kg.d) + clonazepam (0.7 mg/kg.d).
DOI: 10.25345/c5h98zq1s
title: MassIVE MSV000092580 - MALDI-TOF MS analysis of Burkholderia pseudomallei and closely related species isolated from soils and water in Khon Kaen, Thailand
title: supplementary data of raw spectrum data of MALDI-TOF MS
DOI: 10.5281/zenodo.8210291
title: Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts

description: Sequencing reads were assembled using the genome assembler pipeline Shovill v1.1.0. Briefly, the Shovill pipeline included read trimming using Trimmomatic v0.39, de novo assembly with SPAdes v3.15.5 and genome polishing with Pilon v1.24. After the pipeline, additional polishing was performed by mapping the reads back to the contigs with BWA v0.7.17 and sorting the resulting SAM/BAM files using SAMtools v1.15.1. Pilon v1.24 was then used to correct bases, fix mis-assemblies and fill gaps. The reformat.sh script from the Bbmap package v38.76 (-minlength=1000) was used to filter out contigs less than 1000bp. The draft genome assemblies were then annotated with Bakta v1.7.0. Single nucleotide polymorphism (SNP) detection between WT (WTref) and SS (SSref) samples were then performed using snippy v4.6.0, where both WT and SS samples were inputted as the reference genome in turn. A subset of the snippy output files are uploaded here and contain all variants found.
DOI: 10.5281/zenodo.8210290
title: Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts

description: Sequencing reads were assembled using the genome assembler pipeline Shovill v1.1.0. Briefly, the Shovill pipeline included read trimming using Trimmomatic v0.39, de novo assembly with SPAdes v3.15.5 and genome polishing with Pilon v1.24. After the pipeline, additional polishing was performed by mapping the reads back to the contigs with BWA v0.7.17 and sorting the resulting SAM/BAM files using SAMtools v1.15.1. Pilon v1.24 was then used to correct bases, fix mis-assemblies and fill gaps. The reformat.sh script from the Bbmap package v38.76 (-minlength=1000) was used to filter out contigs less than 1000bp. The draft genome assemblies were then annotated with Bakta v1.7.0. Single nucleotide polymorphism (SNP) detection between WT (WTref) and SS (SSref) samples were then performed using snippy v4.6.0, where both WT and SS samples were inputted as the reference genome in turn. A subset of the snippy output files are uploaded here and contain all variants found.
DOI: 10.21227/s0yz-en95
title: Telugu Conversational Dataset for Sarcasm Detection

description: Sentiment analysis, which aims to identify the positive or negative tone of a given text, has seen a surge in interest over the past two decades, making it one of the most studied areas of study in the fields of Natural Language Processing and Information Extraction. Due to the ambiguous nature of sarcasm, however, sarcasm detection is an essential part of sentiment analysis. The task becomes exceedingly challenging when applied to a language with a more intricate morphology and a lack of available resources, such as Telugu. Collecting appropriate and well-annotated corpora is the main challenge in this area of study. In this work, we developed a Telugu dataset of 10,000 conversations, of which 5,000 are sarcastic, and the remaining 5,000 are not. Sarcastic conversations have been collected from various television comedy shows like Jabardasth, Extra Jabardasth, Pataas, etc., and various internet resources. At the same time, non-sarcastic conversations are collected from serials, movies, and celebrity interviews. Three experts, who are teachers and practitioners, have annotated the collected dataset.
DOI: 10.25625/hfgjwn/xyqee3
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