cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24901782.v1
title: CULTURE AND SEQUENCE OF AIRWAY COMMENSAL BACTERIA UNDERPINNING THE MICROBIAL-MUCOSAL COMPLEX

description: https://www.biorxiv.org/content/10.1101/2022.09.08.507073v1<br>Lung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide<sup>1</sup><sup>-</sup><sup>4</sup>. Microbial communities at the airway mucosal barrier are conserved and highly ordered<sup>5</sup>, reflecting symbiosis and co-evolution with human host factors<sup>6</sup>. Freed of selection to digest nutrients for the host, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species, identifying abundant novel organisms within the genera <i>Streptococcus, Pauljensenia, Neisseria</i> and <i>Gemella</i>. Bacterial genomes were enriched for genes encoding antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. RNA-targeting CRISPR elements in some taxa suggest the potential to prevent or treat specific viral infections. Homologues of human <i>RO60</i> present in <i>Neisseria</i> spp. provide a possible respiratory primer for autoimmunity in systemic lupus erythematosus (SLE) and Sjögren syndrome. We interpret the structure and biogeography of airway microbial communities from clinical surveys in the context of whole-genome content, identifying features of airway dysbiosis that may presage breakdown of homeostasis during acute attacks of asthma and chronic obstructive pulmonary disease (COPD). We match the gene content of isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.
DOI: 10.34740/kaggle/dsv/7367330
title: tmdb movies data
DOI: 10.5281/zenodo.10457996
title: Data from: Identification of Loci Associated with Resistance to Banana Xanthomonas Wilt (Xanthomonas vasicola pv. musacearum) Using DArTSeq SNPs and Continuous Mapping

description: Banana Xanthomonas wilt, caused by Xanthomonas vasicola pv. musacearum (Xvm), is a devastating disease that results in total yield loss of affected plants. Resistance to the disease is limited in Musa acuminata, but it has been identified so far in the zebrina subspecies. This study identified markers associated with tolerance to Xvm in Monyet, a tetraploid banana from the zebrina subspecies which was identified to be partially resistant to the bacterium. We used a triploid progeny of 135 F1 hybrids resulting from a cross between Monyet (Xvm partially resistant) and Kokopo (diploid and Xvm susceptible). The F1 hybrids were screened in pots for resistance to Xvm. Genotyping was done by DArTSeq.  

This page makes available the raw sequence data from DArTSeq (the 8 files named raw_sequence) and the phenotyping data.
DOI: 10.5281/zenodo.10457997
title: Data from: Identification of Loci Associated with Resistance to Banana Xanthomonas Wilt (Xanthomonas vasicola pv. musacearum) Using DArTSeq SNPs and Continuous Mapping

description: Banana Xanthomonas wilt, caused by Xanthomonas vasicola pv. musacearum (Xvm), is a devastating disease that results in total yield loss of affected plants. Resistance to the disease is limited in Musa acuminata, but it has been identified so far in the zebrina subspecies. This study identified markers associated with tolerance to Xvm in Monyet, a tetraploid banana from the zebrina subspecies which was identified to be partially resistant to the bacterium. We used a triploid progeny of 135 F1 hybrids resulting from a cross between Monyet (Xvm partially resistant) and Kokopo (diploid and Xvm susceptible). The F1 hybrids were screened in pots for resistance to Xvm. Genotyping was done by DArTSeq.  

This page makes available the raw sequence data from DArTSeq (the 8 files named raw_sequence) and the phenotyping data.
DOI: 10.6084/m9.figshare.24966216.v1
title: Soil chemical property data

description: Soil chemical properties at each sampling point.
DOI: 10.6084/m9.figshare.24901788
title: Genomic attributes of airway commensal bacteria 2023

description: https://www.biorxiv.org/content/10.1101/2022.09.08.507073v1<br>Lung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide<sup>1</sup><sup>-</sup><sup>4</sup>. Microbial communities at the airway mucosal barrier are conserved and highly ordered<sup>5</sup>, reflecting symbiosis and co-evolution with human host factors<sup>6</sup>. Freed of selection to digest nutrients for the host, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species, identifying abundant novel organisms within the genera <i>Streptococcus, Pauljensenia, Neisseria</i> and <i>Gemella</i>. Bacterial genomes were enriched for genes encoding antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. RNA-targeting CRISPR elements in some taxa suggest the potential to prevent or treat specific viral infections. Homologues of human <i>RO60</i> present in <i>Neisseria</i> spp. provide a possible respiratory primer for autoimmunity in systemic lupus erythematosus (SLE) and Sjögren syndrome. We interpret the structure and biogeography of airway microbial communities from clinical surveys in the context of whole-genome content, identifying features of airway dysbiosis that may presage breakdown of homeostasis during acute attacks of asthma and chronic obstructive pulmonary disease (COPD). We match the gene content of isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.<br>
DOI: 10.6084/m9.figshare.24966216
title: Soil chemical property data

description: Soil chemical properties at each sampling point.
DOI: 10.6084/m9.figshare.24966216.v2
title: Soil chemical property data

description: Soil chemical properties at each sampling point.
DOI: 10.21227/d5rq-ba62
title: EAF-U Dataset

description: EAF-U Datasets include six underwater image sets from UIEB, EUVP, UCCS, UIQS, and Seathru. R615 contains 615 real underwater images and their corresponding reference images from UIEBD. U300 contains 300 underwater images from UCCS. E329 contains unpaired underwater images from EUVP. U60 contains 60 challenging underwater images from UIEBD. U500 contains 500 underwater images from UIQS. Seathru contains 889 underwater images.
DOI: 10.6084/m9.figshare.24958362
title: 炎症因子，免疫细胞，代谢组学下载链接

description: The download address of some data
DOI: 10.6084/m9.figshare.24958362.v1
title: 炎症因子，免疫细胞，代谢组学下载链接

description: The download address of some data
DOI: 10.5281/zenodo.10467895
title: Data
DOI: 10.5281/zenodo.10467941
title: Data
DOI: 10.5281/zenodo.10467894
title: Data
DOI: 10.5281/zenodo.10472756
title: Data
DOI: 10.5281/zenodo.10472771
title: Data
DOI: 10.6084/m9.figshare.24720152
title: Do sperm and lubricants <i>gel</i> well with each other? A systematic review

description: Vaginal lubricants are commonly used to aid sexual pleasure and/or to help combat vaginal dryness and dyspareunia. Several studies have reported their impact on sperm function, however there are no published guidelines to help healthcare professionals and couples select a vaginal lubricant that is ‘sperm-safe’. To address this, we conducted a literature search using both PubMed and Scopus to identify and appraise manuscripts that reported the impact of lubricants on sperm function. We did not restrict the literature search by year of publication, and we only included manuscripts that looked at the impact of vaginal lubricants on human sperm. The quality of the eligible studies was assessed using the Björndahl et al., (2016) checklist for semen analysis, as most of the studies reported the findings of a basic semen analysis. A total of 24 articles were eligible for analysis with a total of 35 vaginal lubricants (that were available to buy over the counter) being included, 2 of which studied the effect of vaginal lubricants on sperm function <i>in vivo,</i> and 22 being conducted <i>in vitro</i>. KY Jelly, PreSeed and Astroglide were most studied, with most manuscripts focussing on their impact on sperm motility. A paucity of data on most lubricants combined with methodological variations between studies and limited/no reporting on pregnancy outcomes means greater efforts are required before an evidence-based guideline can be published.
DOI: 10.6084/m9.figshare.24720152.v1
title: Do sperm and lubricants <i>gel</i> well with each other? A systematic review

description: Vaginal lubricants are commonly used to aid sexual pleasure and/or to help combat vaginal dryness and dyspareunia. Several studies have reported their impact on sperm function, however there are no published guidelines to help healthcare professionals and couples select a vaginal lubricant that is ‘sperm-safe’. To address this, we conducted a literature search using both PubMed and Scopus to identify and appraise manuscripts that reported the impact of lubricants on sperm function. We did not restrict the literature search by year of publication, and we only included manuscripts that looked at the impact of vaginal lubricants on human sperm. The quality of the eligible studies was assessed using the Björndahl et al., (2016) checklist for semen analysis, as most of the studies reported the findings of a basic semen analysis. A total of 24 articles were eligible for analysis with a total of 35 vaginal lubricants (that were available to buy over the counter) being included, 2 of which studied the effect of vaginal lubricants on sperm function <i>in vivo,</i> and 22 being conducted <i>in vitro</i>. KY Jelly, PreSeed and Astroglide were most studied, with most manuscripts focussing on their impact on sperm motility. A paucity of data on most lubricants combined with methodological variations between studies and limited/no reporting on pregnancy outcomes means greater efforts are required before an evidence-based guideline can be published.
DOI: 10.5281/zenodo.10472889
title: Dataset from: Automatic deforestation driver attribution using deep learning on satellite imagery

description: Direct drivers of deforestation in Indonesia from 2012-2019.
DOI: 10.5281/zenodo.10472890
title: Dataset from: Automatic deforestation driver attribution using deep learning on satellite imagery

description: Direct drivers of deforestation in Indonesia from 2012-2019.
DOI: 10.6084/m9.figshare.24864243.v1
title: A large dataset for VEP based brain-computer interfaces employing narrow band code modulation and frequency-phase modulation

description: Brain-computer interfaces (BCIs) realize the information transmission between the brain and the external world. Visual evoked potential (VEP) based BCIs have gained widespread attention in the field of multi-instruction interaction attributed to their high information transfer rate (ITR). However, improving the ITR and the practicability is challenging for existing VEP based BCIs due to factors such as the encoding efficiency and the calibration time. Therefore, to address this issue, this study proposed a new encoding method employing narrow band random sequences and provided a large dataset for VEP based brain-computer interfaces. Narrow band random sequences are random sequences with a specific frequency band. The dataset encompasses three paradigms that employ three kinds of encoding sequences: narrow band sequences with a frequency band of 15~25 Hz (NBRS-15), narrow band random sequences with a frequency band of 8~16 Hz (NBRS-8), and sequences utilizing joint frequency-phase modulation method with a frequency range of 8-15.8 Hz (JFPM-8). The dataset includes 59-channel electroencephalogram data for 100 subjects, and the quality of the dataset is validated through quantitative analyses on EEG characteristics and classification performance. The proposed dataset is recommended for the development of classification algorithms for VEP based BCIs, and for exploring the potential of code-modulated VEP based BCIs employing narrow band random sequences.
DOI: 10.6084/m9.figshare.24559633.v1
title: Sr-Nd-Hf data.xlsx

description: The Sr-Nd-Hf isotopes and rare earth elements of 68 samples in IODP Site U1477 from the offshore Zambezi mouth.
DOI: 10.6084/m9.figshare.24966327
title: <b>的完整线粒体基因组</b><b><i>Yunleon longicorpus</i></b><b> Yang, 1986 (Neuroptera, Myrmeleontidae) and its phylogenetic implications</b>

description: 为探究<i>长蜥</i>在蝽科中的位置，以蝗科（Myrmeleontidae<i>白芷（Balmes birmanus</i>为外群，利用18个物种的13个蛋白编码基因（PCGs）序列构建系统发育树; 进一步探讨<i>Yunleon</i>和<i>Epacanthaclisis</i>属的分类在部落水平上，我们利用 <i>考克斯1</i> Nemoleontini、Megistopini、Acanthoplectrini、Dendroleontini、Haplogleniini和Ascalaphini中27个物种的cox1序列来构建NCBI中线粒体基因组序列所缺乏的系统发育树。PhyloSuite v.1.2.3 Zhang et al.， 202013个PCG的核苷酸序列（无终止密码子）在MEGA7.0中通过肌肉对齐（Kumar等人，2016）。使用 PhyloSuite v.1.2.3 连接基因比对（Zhang 等人，2020）。使用 AICc 和 BIC 在 PhyloSuite v.1.2.3 中使用 PartitionFinder2 选择最大似然 （ML） 和贝叶斯推理 （BI） 系统发育分析的分区方案;最大似然 （ML） 和贝叶斯推理 （BI） 系统发育分析的核苷酸替换模型由 PhyloSuite v.1.2.3 中的 ModelFinder 估计（Zhang 等人，2020）。在PhyloSuite v.1.2.3中，IQ-TREE在超快引导（UFB）近似方法下重建了ML分析，重复次数为10000次。MrBayes 在 PhyloSuite v.1.2.3 中用 4 条链重建了 BI 分析。独立运行2,000,000代，每1,000代采样一次。前 25% 的树木因烧毁而被丢弃。这些树在 FigTree v1.4.3 （Rambaut & Drummond 2016）
DOI: 10.6084/m9.figshare.24966327.v1
title: <b>的完整线粒体基因组</b><b><i>Yunleon longicorpus</i></b><b> Yang, 1986 (Neuroptera, Myrmeleontidae) and its phylogenetic implications</b>

description: 为探究<i>长蜥</i>在蝽科中的位置，以蝗科（Myrmeleontidae<i>白芷（Balmes birmanus</i>为外群，利用18个物种的13个蛋白编码基因（PCGs）序列构建系统发育树; 进一步探讨<i>Yunleon</i>和<i>Epacanthaclisis</i>属的分类在部落水平上，我们利用 <i>考克斯1</i> Nemoleontini、Megistopini、Acanthoplectrini、Dendroleontini、Haplogleniini和Ascalaphini中27个物种的cox1序列来构建NCBI中线粒体基因组序列所缺乏的系统发育树。PhyloSuite v.1.2.3 Zhang et al.， 202013个PCG的核苷酸序列（无终止密码子）在MEGA7.0中通过肌肉对齐（Kumar等人，2016）。使用 PhyloSuite v.1.2.3 连接基因比对（Zhang 等人，2020）。使用 AICc 和 BIC 在 PhyloSuite v.1.2.3 中使用 PartitionFinder2 选择最大似然 （ML） 和贝叶斯推理 （BI） 系统发育分析的分区方案;最大似然 （ML） 和贝叶斯推理 （BI） 系统发育分析的核苷酸替换模型由 PhyloSuite v.1.2.3 中的 ModelFinder 估计（Zhang 等人，2020）。在PhyloSuite v.1.2.3中，IQ-TREE在超快引导（UFB）近似方法下重建了ML分析，重复次数为10000次。MrBayes 在 PhyloSuite v.1.2.3 中用 4 条链重建了 BI 分析。独立运行2,000,000代，每1,000代采样一次。前 25% 的树木因烧毁而被丢弃。这些树在 FigTree v1.4.3 （Rambaut & Drummond 2016）
DOI: 10.34740/kaggle/dsv/7367614
title: Mobile phone activity in Milan
DOI: 10.5281/zenodo.10472559
title: Significant Deep (200-2000 cm) Soil Water Use Does Not Compensate Drought Stress Effect on Photosynthesis in Dryland Tree Plantations

description: A database describing deep soil water uptake in plantations on the Loess Plateau
DOI: 10.6084/m9.figshare.24560584
title: Sentiment Analysis Test Dataset Created from Two COVID-19 Surveys: National Institutes of Health (NIH) and Stanford University

description: Two COVID-19 surveys were used to create the <b>test dataset</b>, both collected by teams from the National Institutes of Health (NIH) and Stanford University. The collected data were intended to assess the general topics experienced by participants during the pandemic lockdown. The test dataset comprises a total of 1,000 randomly chosen sentences, with 500 sentences selected from each survey. Each set was annotated by three separate and independent annotators. The annotators were instructed to assess the polarity of each sentence on a scale of -1 (negative), 0 (neutral), or 1 (positive). We then followed a three-step procedure to determine the final labels. First, if all three annotators agreed on a label (full agreement), that label was accepted. Second, if two out of the three agreed on a label (partial agreement), that label was also accepted. Third, if there was no agreement, the label was set as neutral (no agreement).
DOI: 10.6084/m9.figshare.24560584.v1
title: Sentiment Analysis Test Dataset Created from Two COVID-19 Surveys: National Institute of Health (NIH) and Stanford University

description: Two COVID-19 surveys were used to create the <b>test dataset</b>, both collected by teams from the National Institute of Health (NIH) and Stanford University. The collected data were intended to assess the general topics experienced by participants during the pandemic lockdown. The test dataset comprises a total of 1,000 randomly chosen sentences, with 500 sentences selected from each survey. Each set was annotated by three separate and independent annotators. The annotators were instructed to assess the polarity of each sentence on a scale of -1 (negative), 0 (neutral), or 1 (positive). We then followed a three-step procedure to determine the final labels. First, if all three annotators agreed on a label (full agreement), that label was accepted. Second, if two out of the three agreed on a label (partial agreement), that label was also accepted. Third, if there was no agreement, the label was set as neutral (no agreement).
DOI: 10.5517/ccdc.csd.cc292tt1
title: CCDC 2117883: Experimental Crystal Structure Determination

description: Related Article: Xinling Cao, Yinggang Duan, Kaihong Lv, Zihan Lu, Yihua Chen, Shengjiao Yan|2022|Green Synth. Cat.|4|321|doi:10.1016/j.gresc.2022.10.014
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.8005267
title: Rat1 promotes premature transcription termination at R-loops

description: Rough Data from Merida-Cerro et al. Rat1 promotes premature transcription termination at R-loops
DOI: 10.5281/zenodo.10362342
title: Rat1 promotes premature transcription termination at R-loops

description: Rough Data from Merida-Cerro et al.


Rat1 promotes premature transcription termination at R-loops
DOI: 10.5281/zenodo.8005266
title: Rat1 promotes premature transcription termination at R-loops

description: Rough Data from Merida-Cerro et al.


Rat1 promotes premature transcription termination at R-loops
DOI: 10.6084/m9.figshare.24966435
title: Supplementary Material for: Health-related complications during follow-up and their impact on blood cancer survivors – results from the ‘Aftercare in Blood Cancer Survivors’ (ABC) study

description: Introduction Blood cancer survivors are at increased risk for medical complications. 
Methods Our questionnaire-based study involved 1,551 blood cancer survivors with a ≥3-year interval since the last intense treatment. Its goal was to quantify health-related complications during follow-up and assess their impact on the patients’ lives.
Results 20.4% of responding survivors reported a disease relapse, most often in indolent lymphomas. Second primary malignancies occurred in 14.1%, primarily in lymphoma and allogeneic transplantation survivors. The most frequent malignancy was basal cell carcinoma of the skin, but myeloid malignancies, melanoma, bladder, head-and-neck, and thyroid cancer also appeared disproportionately frequent. An increased infection rate was reported by 43.7%, most often after allogeneic transplantation. New cardiovascular diseases were reported by 30.2%, with a high rate of thromboembolic events in multiple myeloma and myeloproliferative diseases. Polyneuropathies were reported by 39.1%, most often by survivors with a history of multiple myeloma or aggressive lymphoma. Disease relapse was perceived as the highest burden, followed by second primary malignancy, increased infection frequency, and polyneuropathy. In each area investigated, the range of perceived severities was wide.
Conclusions Health-related complications are frequent during blood cancer follow-up, with significant repercussions on the patients’ lives.
DOI: 10.6084/m9.figshare.24966435.v1
title: Supplementary Material for: Health-related complications during follow-up and their impact on blood cancer survivors – results from the ‘Aftercare in Blood Cancer Survivors’ (ABC) study

description: Introduction Blood cancer survivors are at increased risk for medical complications. 
Methods Our questionnaire-based study involved 1,551 blood cancer survivors with a ≥3-year interval since the last intense treatment. Its goal was to quantify health-related complications during follow-up and assess their impact on the patients’ lives.
Results 20.4% of responding survivors reported a disease relapse, most often in indolent lymphomas. Second primary malignancies occurred in 14.1%, primarily in lymphoma and allogeneic transplantation survivors. The most frequent malignancy was basal cell carcinoma of the skin, but myeloid malignancies, melanoma, bladder, head-and-neck, and thyroid cancer also appeared disproportionately frequent. An increased infection rate was reported by 43.7%, most often after allogeneic transplantation. New cardiovascular diseases were reported by 30.2%, with a high rate of thromboembolic events in multiple myeloma and myeloproliferative diseases. Polyneuropathies were reported by 39.1%, most often by survivors with a history of multiple myeloma or aggressive lymphoma. Disease relapse was perceived as the highest burden, followed by second primary malignancy, increased infection frequency, and polyneuropathy. In each area investigated, the range of perceived severities was wide.
Conclusions Health-related complications are frequent during blood cancer follow-up, with significant repercussions on the patients’ lives.
DOI: 10.6084/m9.figshare.24966192
title: Soil chemical properties at each sampling point

description: Soil chemical properties at each sampling point
DOI: 10.6084/m9.figshare.24966192.v1
title: Soil chemical properties at each sampling point

description: Soil chemical properties at each sampling point
DOI: 10.5281/zenodo.7761649
title: Exploiting the potential of urban DAS grids: Ambient-noise subsurface imaging using joint Rayleigh and Love waves

description: Ambient-noise cross-correlation functions used in this study.
DOI: 10.5281/zenodo.7761648
title: Exploiting the potential of urban DAS grids: Ambient-noise subsurface imaging using joint Rayleigh and Love waves

description: Ambient-noise cross-correlation functions used in this study.

This work can be found at GitHub: https://github.com/NickJi98/DAS_Love_wave_2024_SRL.git
DOI: 10.5281/zenodo.7761930
title: Exploiting the potential of urban DAS grids: Ambient-noise subsurface imaging using joint Rayleigh and Love waves

description: Ambient-noise cross-correlation functions used in this study.

This work can be found at GitHub: https://github.com/NickJi98/DAS_Love_wave_2024_SRL.git