Scientific Data最新文献_第2页

Dynamic key vascular anatomy dataset for D2 lymph node dissection during laparoscopic gastric cancer surgery. 腹腔镜胃癌手术中D2淋巴结清扫的动态关键血管解剖数据集。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-29 DOI: 10.1038/s41597-025-05255-7

Longfei Gou, Haolin Wu, Chang Chen, Jiayu Lai, Hua Yang, Yuqing Qiu, Boer Su, Hongyu Wang, Bingyu Zhao, Xin Ye, Jinming Li, Xiaobing Bao, Guoxin Li, Jiang Yu, Yanfeng Hu, Qi Dou, Hao Chen

{"title":"Dynamic key vascular anatomy dataset for D2 lymph node dissection during laparoscopic gastric cancer surgery.","authors":"Longfei Gou, Haolin Wu, Chang Chen, Jiayu Lai, Hua Yang, Yuqing Qiu, Boer Su, Hongyu Wang, Bingyu Zhao, Xin Ye, Jinming Li, Xiaobing Bao, Guoxin Li, Jiang Yu, Yanfeng Hu, Qi Dou, Hao Chen","doi":"10.1038/s41597-025-05255-7","DOIUrl":"https://doi.org/10.1038/s41597-025-05255-7","url":null,"abstract":"Gastric cancer (GC) is the fifth most common malignant tumor worldwide. Surgical resection remains the primary treatment for GC, with laparoscopic surgery recommended by several international guidelines. Due to complex perigastric vessels, standard D2 lymph node dissection (LND) in laparoscopic GC (LapGC) surgery is challenging. Careful dissection is required to expose, dissect, and ligate vessels without injury, ensuring radical LND. Computer vision has the potential to assist in the identification of key vessels during LapGC surgery, thereby reducing the risk of vascular injury. However, existing publicly available surgical anatomy datasets mainly focus on organ segmentation and simple surgeries. To address the clinical challenges and research needs outlined above, we present the LapGC Key Vascular Anatomy Dataset (LapGC-KVAD-30). This dataset was extracted from thirty complete surgical videos and contains annotations for fifteen types of key vessels across eight D2 LND scenes. The LapGC-KVAD-30 uniquely contains 5303 frames that showcase the dynamic process of key vessels from initial appearance to full exposure (or ligation), providing essential information for effective and safe LND.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"903"},"PeriodicalIF":5.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improving data sharing and knowledge transfer via the Neuroelectrophysiology Analysis Ontology (NEAO). 通过神经电生理分析本体（NEAO）改进数据共享和知识转移。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-29 DOI: 10.1038/s41597-025-05213-3

Cristiano A Köhler, Sonja Grün, Michael Denker

{"title":"Improving data sharing and knowledge transfer via the Neuroelectrophysiology Analysis Ontology (NEAO).","authors":"Cristiano A Köhler, Sonja Grün, Michael Denker","doi":"10.1038/s41597-025-05213-3","DOIUrl":"https://doi.org/10.1038/s41597-025-05213-3","url":null,"abstract":"Describing the analysis of data from electrophysiology experiments investigating the function of neural systems is challenging. On the one hand, data can be analyzed by distinct methods with similar purposes, such as different algorithms to estimate the spectral power content of a measured time series. On the other hand, different software codes can implement the same analysis algorithm, while adopting different names to identify functions and parameters. These ambiguities complicate reporting analysis results, e.g., in a manuscript or on a scientific platform. Here, we illustrate how an ontology to describe the analysis process can assist in improving clarity, rigour and comprehensibility by complementing, simplifying and classifying the details of the implementation. We implemented the Neuroelectrophysiology Analysis Ontology (NEAO) to define a vocabulary and to standardize the descriptions of processes for neuroelectrophysiology data analysis. Real-world examples demonstrate how NEAO can annotate provenance information describing an analysis. Based on such provenance, we detail how it supports querying information (e.g., using knowledge graphs) that enable researchers to find, understand and reuse analysis results.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"907"},"PeriodicalIF":5.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144180416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level genome assembly of Paracoccus marginatus based on PacBio and Hi-C technologies. 基于PacBio和Hi-C技术的边缘副球菌染色体水平基因组组装。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-29 DOI: 10.1038/s41597-025-04944-7

Jiufeng Wei, Jinying Xue, Xuejie Shen, Gaoxiang Zhang, Qing Zhao, Yunyun Lu, Minmin Niu, Wei Ji

引用次数: 0

Remediating toxic elements with sunflower, hemp, castor bean, & bamboo: an open dataset of harmonized variables. 用向日葵、大麻、蓖麻豆和竹子修复有毒元素：一个协调变量的开放数据集。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-29 DOI: 10.1038/s41597-025-05239-7

Hyunji Ha, Ken G Sweat, Kendra D Conrow, Richard S Haney, Thomas M Cahill, David S LeBauer, Maxwell C K Leung

引用次数: 0

A curated benchmark dataset for molecular identification based on genome skimming. 基于基因组略读的分子鉴定基准数据集。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-29 DOI: 10.1038/s41597-025-05230-2

Renata C Asprino, Liming Cai, Yujing Yan, Peter J Flynn, Lucas C Marinho, Xiaoshan Duan, Christiane Anderson, Goia M Lyra, Charles C Davis, Bruno A S de Medeiros

{"title":"A curated benchmark dataset for molecular identification based on genome skimming.","authors":"Renata C Asprino, Liming Cai, Yujing Yan, Peter J Flynn, Lucas C Marinho, Xiaoshan Duan, Christiane Anderson, Goia M Lyra, Charles C Davis, Bruno A S de Medeiros","doi":"10.1038/s41597-025-05230-2","DOIUrl":"https://doi.org/10.1038/s41597-025-05230-2","url":null,"abstract":"Genome skimming is a promising sequencing strategy for DNA-based taxonomic identification. However, the lack of standardized datasets for benchmarking genome skimming tools presents a challenge in comparing new methods to existing ones. As part of the development of varKoder, a new tool for DNA-based identification, we curated four datasets designed for comparing molecular identification tools using low-coverage genomes. These datasets comprise vast phylogenetic and taxonomic diversity from closely related species to all taxa currently represented on NCBI SRA. One of them consists of novel sequences from taxonomically verified samples in the plant clade Malpighiales, while the other three datasets compile publicly available data. All include raw genome skim sequences to enable comprehensive testing and validation of a variety molecular species identification methods. We also provide the two-dimensional graphical representations of genomic data used in varKoder. These datasets represent a reliable resource for researchers to assess the accuracy, efficiency, and robustness of new tools to varKoder and other methods in a consistent and reproducible manner.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"906"},"PeriodicalIF":5.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus). 金倒钩（Barbodes semifasciolatus）染色体水平基因组组装的单倍型解析。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-29 DOI: 10.1038/s41597-025-05178-3

Weitao Chen, Chao Li, Rong Yang, Yuefei Li, Baosheng Wu, Jie Li

{"title":"Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus).","authors":"Weitao Chen, Chao Li, Rong Yang, Yuefei Li, Baosheng Wu, Jie Li","doi":"10.1038/s41597-025-05178-3","DOIUrl":"https://doi.org/10.1038/s41597-025-05178-3","url":null,"abstract":"The gold barb (Barbodes semifasciolatus), a member of the Cyprinidae family, exhibits remarkable adaptability to highly acidic environments, making it an ideal model for studying extreme environmental adaptation. However, its genome has not been previously characterized. To address this, we assembled a high-quality chromosome-scale genome for B. semifasciolatus using High-Fidelity (HiFi) sequencing and Hi-C technology. The resulting haplotype-resolved assemblies, spanning 776 Mb and 779 Mb across 25 chromosomes, achieved genome coverages of 99.5% and 99.7%, respectively, and included four gap-free chromosomes. Genome quality assessment using BUSCO indicated a high completeness score of 98.2% for haplotype1 and 98.3% for haplotype2, further validated by strong synteny with the zebrafish (Danio rerio), confirming the assembly's integrity and continuity. Through integration of full-length transcriptome data, RNA sequencing, and homology-based annotation, we identified 26,057 protein-coding genes with 2,087 pseudogenes in haplotype 2, and 25,622 protein-coding genes with 2,101 pseudogenes in haplotype 1. This high-resolution genome assembly is a crucial resource for advancing research in the Cyprinidae, particularly for understanding adaptive evolution in extreme environments.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"902"},"PeriodicalIF":5.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SorpVision: A Comprehensive Dataset for Cementitious Sorptivity Analysis Powered by Computer Vision. SorpVision：一个基于计算机视觉的胶凝吸附分析综合数据集。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-29 DOI: 10.1038/s41597-025-05185-4

Hossein Kabir, Jordan Wu, Sunav Dahal, Tony Joo, Nishant Garg

{"title":"SorpVision: A Comprehensive Dataset for Cementitious Sorptivity Analysis Powered by Computer Vision.","authors":"Hossein Kabir, Jordan Wu, Sunav Dahal, Tony Joo, Nishant Garg","doi":"10.1038/s41597-025-05185-4","DOIUrl":"https://doi.org/10.1038/s41597-025-05185-4","url":null,"abstract":"As the construction industry advances toward more efficient methods for assessing durability, the need for automated sorptivity evaluation has become increasingly critical. Consequently, this study introduces SorpVision, a dataset of 7,384 images (5,000 real and 2,384 synthetic) designed to support our custom computer vision-based framework for automated sorptivity evaluation in cementitious materials. Traditional methods, such as ASTM C1585, depend on manual weighing, which is time-consuming and limits measurement intervals. SorpVision, combined with a cost-effective USB camera setup and a robust vision algorithm, facilitates real-time water level detection in cementitious systems. The framework, trained using 1,440 data points from pastes with water-to-cement (w/c) ratios of 0.4-0.8 and curing durations of 1-7 days, achieves high predictive accuracy for initial and secondary sorptivities (R2 > 0.9 for cement pastes). Moreover, it generalizes well to mortar and concrete, yielding R2 values of 0.96 and 0.87 for initial sorptivity and 0.74 and 0.65 for secondary sorptivity, respectively. SorpVision offers an accurate, data-driven foundation for scalable, automated durability evaluations, supporting sustainable infrastructure development.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"904"},"PeriodicalIF":5.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A benchmark dataset for class-wise segmentation of construction and demolition waste in cluttered environments. 一个在杂乱环境中分类分割建筑和拆除垃圾的基准数据集。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-28 DOI: 10.1038/s41597-025-05243-x

Diani Sirimewan, Sanuwani Dayarathna, Sudharshan Raman, Yu Bai, Mehrdad Arashpour

{"title":"A benchmark dataset for class-wise segmentation of construction and demolition waste in cluttered environments.","authors":"Diani Sirimewan, Sanuwani Dayarathna, Sudharshan Raman, Yu Bai, Mehrdad Arashpour","doi":"10.1038/s41597-025-05243-x","DOIUrl":"10.1038/s41597-025-05243-x","url":null,"abstract":"Efficient management of construction and demolition waste (CDW) is essential for enhancing resource recovery. The lack of publicly available, high-quality datasets for waste recognition limits the development and adoption of automated waste handling solutions. To facilitate data sharing and reuse, this study introduces 'CDW-Seg', a benchmark dataset for class-wise segmentation of CDW. The dataset comprises high-resolution images captured at authentic construction sites, featuring skip bins filled with a diverse mixture of CDW materials in-the-wild. It includes 5,413 manually annotated objects across ten categories: concrete, fill dirt, timber, hard plastic, soft plastic, steel, fabric, cardboard, plasterboard, and the skip bin, representing a total of 2,492,021,189 pixels. Each object was meticulously annotated through semantic segmentation, providing reliable ground-truth labels. To demonstrate the applicability of the dataset, an adapter-based fine-tuning approach was implemented using a hierarchical Vision Transformer, ensuring computational efficiency suitable for deployment in automated waste handling scenarios. The CDW-Seg has been made publicly accessible to promote data sharing, facilitate further research, and support the development of automated solutions for resource recovery.","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"885"},"PeriodicalIF":5.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120074/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174719","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

Correction: Chromosome-level Haploid Assembly of Cannabis sativa L. cv. Pink Pepper. 更正：大麻（Cannabis sativa L. cv.）染色体水平单倍体组装。粉红胡椒。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-28 DOI: 10.1038/s41597-025-05259-3

Byeong-Ryeol Ryu, Gyeong-Ju Gim, Ye-Rim Shin, Min-Ji Kang, Min-Jun Kim, Tae-Hyung Kwon, Young-Seok Lim, Sang-Hyuck Park, Jung-Dae Lim

引用次数: 0

GODEEEP-hydro: Historical and projected power system ready hydropower data for the United States. godeep -hydro：美国历史和预测的电力系统水电数据。

IF 5.8 2区综合性期刊

Scientific Data Pub Date : 2025-05-28 DOI: 10.1038/s41597-025-05097-3

Cameron Bracken, Youngjun Son, Daniel Broman, Nathalie Voisin

引用次数: 0