GigaByte (Hong Kong, China)最新文献_第6页

Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo 刚果民主共和国金沙萨市基孔肯雅流行后地区伊蚊(双翅目:库蚊科)昆虫学采集数据

GigaByte (Hong Kong, China) Pub Date : 2023-11-08 DOI: 10.46471/gigabyte.96

Victoire Nsabatien, Josue Zanga, Fiacre Agossa, Nono Mvuama, Maxwell Bamba, Osée Mansiangi, Leon Mbashi, Vanessa Mvudi, Glodie Diza, Dorcas Kantin, Narcisse Basosila, Hyacinthe Lukoki, Arsene Bokulu, Christelle Bosulu, Erick Bukaka, Jonas Nagahuedi, Jean Claude Palata, Emery Metelo

{"title":"Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo","authors":"Victoire Nsabatien, Josue Zanga, Fiacre Agossa, Nono Mvuama, Maxwell Bamba, Osée Mansiangi, Leon Mbashi, Vanessa Mvudi, Glodie Diza, Dorcas Kantin, Narcisse Basosila, Hyacinthe Lukoki, Arsene Bokulu, Christelle Bosulu, Erick Bukaka, Jonas Nagahuedi, Jean Claude Palata, Emery Metelo","doi":"10.46471/gigabyte.96","DOIUrl":"https://doi.org/10.46471/gigabyte.96","url":null,"abstract":"Arbovirus epidemics (chikungunya, dengue, West Nile fever, yellow fever and zika) are a growing threat in African areas where Aedes (Stegomyia) aegypti (Linnaeus, 1762) and Aedes albopictus (Skuse, 1895) are present. The lack of comprehensive sampling of these two vectors limits our understanding of their propagation dynamics in areas at risk of arboviruses. Here, we collected 6,943 observations (both larval and human capture) of Ae. aegypti and Ae. albopictus between 2020 and 2022. The study was carried out in the Vallee de la Funa, a post-epidemic zone in the city of Kinshasa, Democratic Republic of Congo. Our results provide important information for future basic and advanced studies on the ecology and phenology of these vectors, as well as on vector dynamics after a post-epidemic period. The data from this study are published in the public domain as the Darwin Core Archive in the Global Biodiversity Information Facility.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"8 14","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135391259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome assembly and annotation of the Brown-Spotted Pit viper Protobothrops mucrosquamatus 棕斑蝮蛇(Protobothrops mucrosquamatus)基因组组装与注释

GigaByte (Hong Kong, China) Pub Date : 2023-11-07 DOI: 10.46471/gigabyte.97

Xiaotong Niu, Haorong Lu, Minhui Shi, Shiqing Wang, Yajie Zhou, Huan Liu

引用次数: 0

Spatial patterns associated with the distribution of immature stages of Aedes aegypti in three dengue high-risk municipalities of Southwestern Colombia. 哥伦比亚西南部三个登革热高危城市埃及伊蚊未成熟期分布的空间格局。

GigaByte (Hong Kong, China) Pub Date : 2023-10-27 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.95

Cristina Sánchez Gutierrez, Erika Santamaría, Carlos Andrés Morales, María Camila Lesmes, Horacio Cadena, Alvaro Avila-Diaz, Patricia Fuya, Catalina Marceló-Díaz

{"title":"Spatial patterns associated with the distribution of immature stages of Aedes aegypti in three dengue high-risk municipalities of Southwestern Colombia.","authors":"Cristina Sánchez Gutierrez, Erika Santamaría, Carlos Andrés Morales, María Camila Lesmes, Horacio Cadena, Alvaro Avila-Diaz, Patricia Fuya, Catalina Marceló-Díaz","doi":"10.46471/gigabyte.95","DOIUrl":"10.46471/gigabyte.95","url":null,"abstract":"Aedes aegypti mosquitoes are the main vector of human arbovirosis in tropical and subtropical areas. Their adaptation to urban and rural environments generates infestations inside households. Therefore, entomological surveillance associated with spatio-temporal analysis is an innovative approach for vector control and dengue management. Here, our main aim was to inspect immature pupal stages in households belonging to municipalities at high risk of dengue in Cauca, Colombia, by implementing entomological indices and relating how they influence adult mosquitos' density. We provide novel data for the geographical distribution of 3,806 immature pupal stages of Ae. aegypti. We also report entomological indices and spatial characterization. Our results suggest that, for Ae. aegypti species, pupal productivity generates high densities of adult mosquitos in neighbouring households, evidencing seasonal behaviour. Our dataset is essential as it provides an innovative strategy for mitigating vector-borne diseases using vector spatial patterns. It also delineates the association between these vector spatial patterns, entomological indicators, and breeding sites in high-risk neighbourhoods.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte95"},"PeriodicalIF":0.0,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10620433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71489644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome assembly of the bearded iris, Iris pallida Lam. 苍白鸢尾的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2023-10-05 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.94

Robert E Bruccoleri, Edward J Oakeley, Ann Marie E Faust, Marc Altorfer, Sophie Dessus-Babus, David Burckhardt, Mevion Oertli, Ulrike Naumann, Frank Petersen, Joanne Wong

{"title":"Genome assembly of the bearded iris, Iris pallida Lam.","authors":"Robert E Bruccoleri, Edward J Oakeley, Ann Marie E Faust, Marc Altorfer, Sophie Dessus-Babus, David Burckhardt, Mevion Oertli, Ulrike Naumann, Frank Petersen, Joanne Wong","doi":"10.46471/gigabyte.94","DOIUrl":"10.46471/gigabyte.94","url":null,"abstract":"Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest in irises lies in the secondary metabolites present in their rhizomes. The Dalmatian Iris (Iris pallida Lam.) is an ornamental plant that also produces secondary metabolites with potential value to the fragrance and pharmaceutical industries. In addition to providing base notes for the fragrance industry, iris tissues and extracts possess antioxidant, anti-inflammatory and immunomodulatory effects. However, study of these secondary metabolites has been hampered by a lack of genomic information, requiring difficult extraction and analysis techniques. Here, we report the genome sequence of Iris pallida Lam., generated with Pacific Bioscience long-read sequencing, resulting in a 10.04-Gbp assembly with a scaffold N50 of 14.34 Mbp and 91.8% complete BUSCOs. This reference genome will allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte94"},"PeriodicalIF":0.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41222110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The genome assembly and annotation of the Oriental rat snake Ptyas mucosa. 东方大鼠蛇Ptyas粘膜的基因组组装与注释。

GigaByte (Hong Kong, China) Pub Date : 2023-09-20 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.92

Jiangang Wang, Shiqing Wang, Song Huang, Qing Wang, Tianming Lan, Ming Jiang, Haitao Wu, Yuxiang Yuan

引用次数: 0

A database of restriction maps to expand the utility of bacterial artificial chromosomes. 一个限制性图谱数据库，以扩大细菌人工染色体的实用性。

GigaByte (Hong Kong, China) Pub Date : 2023-09-20 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.93

Eamon Winden, Alejandro Vasquez-Echeverri, Susana Calle-Castañeda, Yumin Lian, Juan Pablo Hernandez Ortiz, David C Schwartz

引用次数: 0

ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R. ensemblQueryR：在R中对Ensembl LD API端点进行快速、灵活、高吞吐量的查询。

GigaByte (Hong Kong, China) Pub Date : 2023-09-14 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.91

Aine Fairbrother-Browne, Sonia García-Ruiz, Regina Hertfelder Reynolds, Mina Ryten, Alan Hodgkinson

{"title":"ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R.","authors":"Aine Fairbrother-Browne, Sonia García-Ruiz, Regina Hertfelder Reynolds, Mina Ryten, Alan Hodgkinson","doi":"10.46471/gigabyte.91","DOIUrl":"10.46471/gigabyte.91","url":null,"abstract":"We present ensemblQueryR, an R package for querying Ensembl linkage disequilibrium (LD) endpoints. This package is flexible, fast and user-friendly, and optimised for high-throughput querying. ensemblQueryR uses functions that are intuitive and amenable to custom code integration, familiar R object types as inputs and outputs as well as providing parallelisation functionality. For each Ensembl LD endpoint, ensemblQueryR provides two functions, permitting both single- and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate improved computational performance of ensemblQueryR over an exisiting tool in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through Docker and singularity images, making this tool widely accessible to the scientific community.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10507293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41153439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome assembly and annotation of the Sharp-nosed Pit Viper Deinagkistrodon acutus based on next-generation sequencing data. 基于新一代测序数据的尖吻蝮基因组组装和注释。

GigaByte (Hong Kong, China) Pub Date : 2023-09-04 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.88

Xinyu Wang, Lirong Liu, Wenbiao Zhu, Shiqing Wang, Minhui Shi, Shuhui Yang, Haorong Lu, Jun Cao

引用次数: 0

Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies. 小号图：可视化遗传关联研究中等位基因频率与效应大小之间的关系。

GigaByte (Hong Kong, China) Pub Date : 2023-09-01 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.89

Lucia Corte, Lathan Liou, Paul F O'Reilly, Judit García-González

{"title":"Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies.","authors":"Lucia Corte, Lathan Liou, Paul F O'Reilly, Judit García-González","doi":"10.46471/gigabyte.89","DOIUrl":"10.46471/gigabyte.89","url":null,"abstract":"Recent advances in genome-wide association and sequencing studies have shown that the genetic architecture of complex traits and diseases involves a combination of rare and common genetic variants distributed throughout the genome. One way to better understand this architecture is to visualize genetic associations across a wide range of allele frequencies. However, there is currently no standardized or consistent graphical representation for effectively illustrating these results. Here we propose a standardized approach for visualizing the effect size of risk variants across the allele frequency spectrum. The proposed plots have a distinctive trumpet shape: with the majority of variants having high frequency and small effects, and a small number of variants having lower frequency and larger effects. To demonstrate the utility of trumpet plots in illustrating the relationship between the number of variants, their frequency, and the magnitude of their effects in shaping the genetic architecture of complex traits and diseases, we generated trumpet plots for more than one hundred traits in the UK Biobank. To facilitate their broader use, we developed an R package, 'TrumpetPlots' (available at the Comprehensive R Archive Network) and R Shiny application, 'Shiny Trumpets' (available at https://juditgg.shinyapps.io/shinytrumpets/) that allows users to explore these results and submit their own data.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte89"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10268544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

aws-s3-integrity-check: an open-source bash tool to verify the integrity of a dataset stored on Amazon S3. aws-s3-integrity-check：一款开源 bash 工具，用于验证存储在亚马逊 S3 上的数据集的完整性。

GigaByte (Hong Kong, China) Pub Date : 2023-08-23 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.87

Sonia García-Ruiz, Regina Hertfelder Reynolds, Melissa Grant-Peters, Emil Karl Gustavsson, Aine Fairbrother-Browne, Zhongbo Chen, Jonathan William Brenton, Mina Ryten

{"title":"aws-s3-integrity-check: an open-source bash tool to verify the integrity of a dataset stored on Amazon S3.","authors":"Sonia García-Ruiz, Regina Hertfelder Reynolds, Melissa Grant-Peters, Emil Karl Gustavsson, Aine Fairbrother-Browne, Zhongbo Chen, Jonathan William Brenton, Mina Ryten","doi":"10.46471/gigabyte.87","DOIUrl":"10.46471/gigabyte.87","url":null,"abstract":"Amazon Simple Storage Service (Amazon S3) is a widely used platform for storing large biomedical datasets. Unintended data alterations can occur during data writing and transmission, altering the original content and generating unexpected results. However, no open-source and easy-to-use tool exists to verify end-to-end data integrity. Here, we present aws-s3-integrity-check, a user-friendly, lightweight, and reliable bash tool to verify the integrity of a dataset stored in an Amazon S3 bucket. Using this tool, we only needed ∼114 min to verify the integrity of 1,045 records ranging between 5 bytes and 10 gigabytes and occupying ∼935 gigabytes of the Amazon S3 cloud. Our aws-s3-integrity-check tool also provides file-by-file on-screen and log-file-based information about the status of each integrity check. To our knowledge, this tool is the only open-source one that allows verifying the integrity of a dataset uploaded to the Amazon S3 Storage quickly, reliably, and efficiently. The tool is freely available for download and use at https://github.com/SoniaRuiz/aws-s3-integrity-check and https://hub.docker.com/r/soniaruiz/aws-s3-integrity-check.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte87"},"PeriodicalIF":0.0,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10448181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10165035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0