Scientific Data最新文献_第10页

Chromosome-level genome assembly of a critically endangered species Leuciscus chuanchicus.

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-15 DOI: 10.1038/s41597-025-04787-2

Qi Wang, Qi Zhou, Hongyan Liu, Jiongtang Li, Yanliang Jiang

{"title":"Chromosome-level genome assembly of a critically endangered species Leuciscus chuanchicus.","authors":"Qi Wang, Qi Zhou, Hongyan Liu, Jiongtang Li, Yanliang Jiang","doi":"10.1038/s41597-025-04787-2","DOIUrl":"10.1038/s41597-025-04787-2","url":null,"abstract":"Leuciscus chuanchicus, a critically endangered cyprinid endemic in the Yellow River, represents an evolutionary significant lineage within Leuciscinae. However, conservation efforts for this species have been hindered by the lack of genetic and genomic resources. Here we reported a high-quality chromosome-level genome of L. chuanchicus by combining Illumina reads, PacBio HiFi long reads and Hi-C data. The assembled genome size was 1.16 Gb, with a contig N50 size of 31,116,631 bp and a scaffold N50 size of 43,855,677 bp. The resulting 130 scaffolds were further clustered and ordered into 25 chromosomes based on the Hi-C data, representing 97.84% of the assembled sequences. The genome contained 60.36% repetitive sequences and 35,014 noncoding RNAs. A total of 31,196 protein-coding genes were predicted, of which 28,323 (90.79%) were functionally annotated. The BUSCO and OMArk revealed 97.6% and 91.28% completion rates, respectively. This study assembled a high-quality genome of L. chuanchicus, and provided fundamental genomic resources for investigating the molecular mechanism and evolution of the Leuciscinae.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"441"},"PeriodicalIF":5.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11910599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

B(RAIN)²-BRAIN integrated Resource for Anatomy and Intracranial Neurophysiology.

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-15 DOI: 10.1038/s41597-025-04784-5

Amirreza Alijanpourotaghsara, Koorosh Mirpour, Jeong Woo Choi, Krishna Kanth Chitta, Ahmed Shalaby, Misque Boswell, Sahil Chilukuri, Samantha L Cohen, Ryan Byon, Mohsen Benam, Saar Kariv, Jeon Lee, Dominique Duncan, Nader Pouratian

{"title":"B(RAIN)2-BRAIN integrated Resource for Anatomy and Intracranial Neurophysiology.","authors":"Amirreza Alijanpourotaghsara, Koorosh Mirpour, Jeong Woo Choi, Krishna Kanth Chitta, Ahmed Shalaby, Misque Boswell, Sahil Chilukuri, Samantha L Cohen, Ryan Byon, Mohsen Benam, Saar Kariv, Jeon Lee, Dominique Duncan, Nader Pouratian","doi":"10.1038/s41597-025-04784-5","DOIUrl":"10.1038/s41597-025-04784-5","url":null,"abstract":"The Brain Integrated Resource for Human Anatomy and Intracranial Neurophysiology (B(RAIN)2) is a multi-center data resource that provides standardized imaging and intracranial neurophysiological data from patients who have undergone deep brain stimulation (DBS) implantation with intracranial electroencephalography (iEEG) recordings. The database includes patients' electrophysiological recordings from the cerebral cortex and deeper brain structures, alongside high-resolution neurological imaging scans taken at preoperative, intraoperative, and postoperative stages. The data are systematically organized using the Brain Imaging Data Structure (BIDS) format for imaging data and iEEG-BIDS for intracranial electrophysiological recordings. This standardized structure facilitates data integration, sharing, and analysis across research institutions. Additionally, the database features detailed metadata, such as diagnostic information and neurological assessment scores, providing a comprehensive profile of each patient's data.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"442"},"PeriodicalIF":5.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11910653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Electromyographic typing gesture classification dataset for neurotechnological human-machine interfaces.

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-15 DOI: 10.1038/s41597-025-04763-w

Jonathan Eby, Moshe Beutel, David Koivisto, Idan Achituve, Ethan Fetaya, José Zariffa

{"title":"Electromyographic typing gesture classification dataset for neurotechnological human-machine interfaces.","authors":"Jonathan Eby, Moshe Beutel, David Koivisto, Idan Achituve, Ethan Fetaya, José Zariffa","doi":"10.1038/s41597-025-04763-w","DOIUrl":"10.1038/s41597-025-04763-w","url":null,"abstract":"Neurotechnological interfaces have the potential to create new forms of human-machine interactions, by allowing devices to interact directly with neurological signals instead of via intermediates such as keystrokes. Surface electromyography (sEMG) has been used extensively in myoelectric control systems, which use bioelectric activity recorded from muscles during contractions to classify actions. This technology has been used primarily for rehabilitation applications. In order to support the development of myoelectric interfaces for a broader range of human-machine interactions, we present an sEMG dataset obtained during key presses in a typing task. This fine-grained classification dataset consists of 16-channel bilateral sEMG recordings and key logs, collected from 19 individuals in two sessions on different days. We report baseline results on intra-session, inter-session and inter-subject evaluations. Our baseline results show that within-session accuracy is relatively high, even with simple learning models. However, the results on between-session and between-participant are much lower, showing that generalizing between sessions and individuals is an open challenge.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"440"},"PeriodicalIF":5.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level haplotype-resolved genome assembly of bread wheat's wild relative Aegilops mutica.

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-13 DOI: 10.1038/s41597-025-04737-y

Surbhi Grewal, Cai-Yun Yang, Ksenia Krasheninnikova, Joanna Collins, Jonathan M D Wood, Stephen Ashling, Duncan Scholefield, Gemy G Kaithakottil, David Swarbreck, Eric Yao, Taner Z Sen, Ian P King, Julie King

引用次数: 0

A 1 km monthly dataset of historical and future climate changes over China.

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-13 DOI: 10.1038/s41597-025-04761-y

Xiaofei Hu, Shaolin Shi, Borui Zhou, Jian Ni

{"title":"A 1 km monthly dataset of historical and future climate changes over China.","authors":"Xiaofei Hu, Shaolin Shi, Borui Zhou, Jian Ni","doi":"10.1038/s41597-025-04761-y","DOIUrl":"10.1038/s41597-025-04761-y","url":null,"abstract":"High-resolution climate data are important for understanding the impacts of climate change on multiple sectors worldwide. In this study, based on the latest released meteorological records during 1991-2020 and the recently updated general circulation models (GCMs), we established a 30-year averaged 0.01° (≈1 km) dataset of 5 basic climate variables and 23 bioclimatic variables, using ANUSPLIN software, delta correction (DC) downscaling, and cubic spline resampling method. Each variable contained monthly gridded historical data during 1991-2020 and bias-corrected future data over three periods (2021-2040, 2041-2070, 2071-2100), three scenarios (SSP1-2.6, SSP2-4.5, and SSP5-8.5) and 10 GCMs (including an ensemble model). The historical interpolations generated by the ANUSPLIIN software showed a good fit (above 0.91) with observations. The DC correction improved the accuracy of most GCM original simulations, reducing the bias by 0.69%-58.63%. This new dataset therefore demonstrates reliable data quality, and further provides high-resolution and bias-corrected long-term averaged historical and future climate data across China for ecological and climate impact studies.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"436"},"PeriodicalIF":5.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level genome assembly of the spangled emperor, Lethrinus nebulosus (Forsskål 1775).

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-13 DOI: 10.1038/s41597-025-04690-w

Lara Parata, Liam Anstiss, Emma de Jong, Adrianne Doran, Richard J Edwards, Stephen J Newman, Samuel D Payet, Craig L Skepper, Corey B Wakefield, Shannon Corrigan

{"title":"Chromosome-level genome assembly of the spangled emperor, Lethrinus nebulosus (Forsskål 1775).","authors":"Lara Parata, Liam Anstiss, Emma de Jong, Adrianne Doran, Richard J Edwards, Stephen J Newman, Samuel D Payet, Craig L Skepper, Corey B Wakefield, Shannon Corrigan","doi":"10.1038/s41597-025-04690-w","DOIUrl":"10.1038/s41597-025-04690-w","url":null,"abstract":"Spangled emperor, Lethrinus nebulosus (Forsskål 1775), is a tropical marine fish of economic and cultural importance throughout the Indo-West Pacific. It is one of the most targeted recreational fishes in the Gascoyne Coast Bioregion of Western Australia where it serves as an indicator species for recreational fishing. Here, we present a highly accurate, near-gapless, chromosome-level, haplotype-phased reference genome assembly of L. nebulosus (Lethrinus nebulosus (Spangled Emperor) genome, fLetNeb1.1; PRJNA1074345), the first for the species and the first high-quality genome representative of the family Lethrinidae. The 1.09 Gb genome was assembled from PacBio HiFi and Dovetail Omni-C proximity ligation sequencing data. The contig N50 is 21-24 Mbp and BUSCO completeness greater than 99%. A preliminary gene annotation identified 24,583 genes with the predicted transcriptome achieving a BUSCO completeness score of 99.1% This resource will facilitate genomic studies to inform the sustainable management of L. nebulosus and other Lethrinids.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"435"},"PeriodicalIF":5.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TCMEval-SDT: a benchmark dataset for syndrome differentiation thought of traditional Chinese medicine.

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-13 DOI: 10.1038/s41597-025-04772-9

Zhe Wang, Meng Hao, Suyuan Peng, Yuyan Huang, Yiwei Lu, Keyu Yao, Xiaolin Yang, Yan Zhu

{"title":"TCMEval-SDT: a benchmark dataset for syndrome differentiation thought of traditional Chinese medicine.","authors":"Zhe Wang, Meng Hao, Suyuan Peng, Yuyan Huang, Yiwei Lu, Keyu Yao, Xiaolin Yang, Yan Zhu","doi":"10.1038/s41597-025-04772-9","DOIUrl":"10.1038/s41597-025-04772-9","url":null,"abstract":"This paper presents a large publicly available benchmark dataset (TCMEval-SDT) for the thought process involved in syndrome differentiation in traditional Chinese medicine (TCM). The dataset consists of 300 TCM syndrome diagnosis cases sourced from the internet, classical Chinese medical texts, and medical records from hospitals, with metadata adhering to the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. Each case has been annotated and curated by TCM experts and includes medical record ID, clinical data, explanatory summary, TCM syndrome, clinical information, and TCM pathogenesis, to support algorithms or models in emulating the diagnostic process of TCM clinicians. To provide a comprehensive description of the TCM syndrome diagnosis process, we summarize the diagnosis into four steps: (1) clinical information extraction, (2) TCM pathogenesis reasoning, (3) TCM syndrome reasoning, and (4) explanatory summary. We have also established validation criteria to evaluate their ability in TCM clinical diagnosis using this dataset. To facilitate research and evaluation in syndrome diagnosis of TCM, the TCMEval-SDT dataset is made publicly available under the CC-BY 4.0 license.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"437"},"PeriodicalIF":5.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dual Radar: A Multi-modal Dataset with Dual 4D Radar for Autononous Driving.

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-13 DOI: 10.1038/s41597-025-04698-2

Xinyu Zhang, Li Wang, Jian Chen, Cheng Fang, Guangqi Yang, Yichen Wang, Lei Yang, Ziying Song, Lin Liu, Xiaofei Zhang, Bin Xu, Zhiwei Li, Qingshan Yang, Jun Li, Zhenlin Zhang, Weida Wang, Shuzhi Sam Ge

{"title":"Dual Radar: A Multi-modal Dataset with Dual 4D Radar for Autononous Driving.","authors":"Xinyu Zhang, Li Wang, Jian Chen, Cheng Fang, Guangqi Yang, Yichen Wang, Lei Yang, Ziying Song, Lin Liu, Xiaofei Zhang, Bin Xu, Zhiwei Li, Qingshan Yang, Jun Li, Zhenlin Zhang, Weida Wang, Shuzhi Sam Ge","doi":"10.1038/s41597-025-04698-2","DOIUrl":"10.1038/s41597-025-04698-2","url":null,"abstract":"4D radar has higher point cloud density and precise vertical resolution than conventional 3D radar, making it promising for adverse scenarios in the environmental perception of autonomous driving. However, 4D radar is more noisy than LiDAR and requires different filtering strategies that affect the point cloud density and noise level. Comparative analyses of different point cloud densities and noise levels are still lacking, mainly because the available datasets use only one type of 4D radar, making it difficult to compare different 4D radars in the same scenario. We introduce a novel large-scale multi-modal dataset that captures both types of 4D radar, consisting of 151 sequences, most of which are 20 seconds long and contain 10,007 synchronized and annotated frames. Our dataset captures a variety of challenging driving scenarios, including multiple road conditions, weather conditions, different lighting intensities and periods. It supports 3D object detection and tracking as well as multi-modal tasks. We experimentally validate the dataset, providing valuable insights for studying different types of 4D radar.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"439"},"PeriodicalIF":5.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A global urban tree leaf area index dataset for urban climate modeling.

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-12 DOI: 10.1038/s41597-025-04729-y

Wenzong Dong, Hua Yuan, Wanyi Lin, Zhuo Liu, Jiayi Xiang, Zhongwang Wei, Lu Li, Qingliang Li, Yongjiu Dai

{"title":"A global urban tree leaf area index dataset for urban climate modeling.","authors":"Wenzong Dong, Hua Yuan, Wanyi Lin, Zhuo Liu, Jiayi Xiang, Zhongwang Wei, Lu Li, Qingliang Li, Yongjiu Dai","doi":"10.1038/s41597-025-04729-y","DOIUrl":"10.1038/s41597-025-04729-y","url":null,"abstract":"Urban trees are recognized for mitigating urban thermal stress, therefore incorporating their effects is crucial for urban climate research. However, due to the limitation of remote sensing, the LAI in urban areas is generally masked (e.g., MODIS), which in turn limits its application in Urban Canopy Models (UCMs). To address this gap, we developed a high-resolution (500 m) and long-time-series (2000-2022) urban tree LAI dataset derived through the Random Forest model trained with MODIS LAI data, with the help of meteorological variables and tree height datasets. The results show that our dataset has high accuracy when validated against site reference maps, with R of 0.85 and RMSE of 1.03 m2/m2. Compared to reprocessed MODIS LAI, our modeled LAI exhibits an RMSE ranging from 0.36 to 0.64 m2/m2 and an R ranging from 0.89 to 0.97 globally. This dataset provides a reasonable representation of urban tree LAI in terms of magnitude and seasonal changes, thereby potentially enhancing its applications in UCMs and urban climate studies.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"426"},"PeriodicalIF":5.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A chromosomal-level genome assembly of Begonia fimbristipula (Begoniaceae).

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-03-12 DOI: 10.1038/s41597-025-04768-5

Tian-Wen Xiao, Zheng-Feng Wang, Hai-Fei Yan

引用次数: 0