GigaByte (Hong Kong, China)最新文献_第7页

A dataset and template for assessing the ecological status of marine sediments and waters, based on microbial taxa. 根据微生物类群评估海洋沉积物和水域生态状况的数据集和模板。

GigaByte (Hong Kong, China) Pub Date : 2023-08-14 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.86

Angel Borja

引用次数: 0

Digitizing the Culicidae collection of Naturalis Biodiversity Center, with a special focus on the former Bonne-Wepster subcollection. 将纳洛利斯生物多样性中心的蝇科动物藏品数字化，特别关注前 Bonne-Wepster 子藏品。

GigaByte (Hong Kong, China) Pub Date : 2023-07-18 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.85

Pasquale Ciliberti, Astrid Roquas, Becky Desjardins, Bibiche Berkholst, Frank Loggen, Menno Hooft, Gideon Gijswijt, Dick de Graaff

{"title":"Digitizing the Culicidae collection of Naturalis Biodiversity Center, with a special focus on the former Bonne-Wepster subcollection.","authors":"Pasquale Ciliberti, Astrid Roquas, Becky Desjardins, Bibiche Berkholst, Frank Loggen, Menno Hooft, Gideon Gijswijt, Dick de Graaff","doi":"10.46471/gigabyte.85","DOIUrl":"10.46471/gigabyte.85","url":null,"abstract":"Natural history collections contain a wealth of information on species diversity, distribution and ecology. However, due to historical and practical constraints, this valuable information is not always available to researchers. Our project aimed at unlocking data handwritten in notebooks owned by Johanna Bonne-Wepster, a Culicidae researcher. These handwritten notes refer to specimens labeled with a number only. The notebooks were scanned and entered into a Google spreadsheet. The specimens were provided with a unique identifier, labeled with the information from the notebooks and the data exported to the Global Biodiversity Information Facility. In addition, the type specimens were photographed. Besides Johanna Bonne-Wepster's collection, mosquitoes from the former Rijksmuseum van Natuurlijk Historie collection and the former Zoölogisch Museum Amsterdam Nederland collection were digitized. All specimens are now housed at the Naturalis Biodiversity Center museum in Leiden. This paper describes the efforts to mobilize this data and the problems we encountered.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte85"},"PeriodicalIF":0.0,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10355122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10208256","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 hybrid grapevine Vitis 'Chambourcin'. 杂交葡萄藤'Chambourcin'的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2023-07-03 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.84

Sagar Patel, Zachary N Harris, Jason P Londo, Allison Miller, Anne Fennell

引用次数: 0

Anopheles sampling collections in the health districts of Korhogo (Côte d'Ivoire) and Diébougou (Burkina Faso) between 2016 and 2018. 2016 年至 2018 年期间在科霍戈（科特迪瓦）和迪布古（布基纳法索）卫生区采集的疟蚊样本。

GigaByte (Hong Kong, China) Pub Date : 2023-06-30 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.83

Paul Taconet, Barnabas Zogo, Dieudonné Diloma Soma, Ludovic P Ahoua Alou, Karine Mouline, Roch Kounbobr Dabiré, Alphonsine Amanan Koffi, Cédric Pennetier, Nicolas Moiroux

{"title":"Anopheles sampling collections in the health districts of Korhogo (Côte d'Ivoire) and Diébougou (Burkina Faso) between 2016 and 2018.","authors":"Paul Taconet, Barnabas Zogo, Dieudonné Diloma Soma, Ludovic P Ahoua Alou, Karine Mouline, Roch Kounbobr Dabiré, Alphonsine Amanan Koffi, Cédric Pennetier, Nicolas Moiroux","doi":"10.46471/gigabyte.83","DOIUrl":"10.46471/gigabyte.83","url":null,"abstract":"Characterizing the entomological profile of malaria transmission at fine spatiotemporal scales is essential for developing and implementing effective vector control strategies. Here, we present a fine-grained dataset of Anopheles mosquitoes (Diptera: Culicidae) collected in 55 villages of the rural districts of Korhogo (Northern Côte d'Ivoire) and Diébougou (South-West Burkina Faso) between 2016 and 2018. In the framework of a randomized controlled trial, Anopheles mosquitoes were periodically collected by Human Landing Catches experts inside and outside households, and analyzed individually to identify the genus and, for a subsample, species, insecticide resistance genetic mutations, Plasmodium falciparum infection, and parity status. More than 3,000 collection sessions were carried out, achieving about 45,000 h of sampling efforts. Over 60,000 Anopheles were collected (mainly A. gambiae s.s., A. coluzzii, and A. funestus). The dataset is published as a Darwin Core archive in the Global Biodiversity Information Facility, comprising four files: events, occurrences, mosquito characterizations, and environmental data.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte83"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10318348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9803417","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 many-banded krait, Bungarus multicinctus. 多带石龙子（Bungarus multicinctus）的基因组组装和注释。

GigaByte (Hong Kong, China) Pub Date : 2023-06-29 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.82

Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Tianming Lan, Shuhui Yang, Song Huang

引用次数: 0

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). 皇冠珍珠 V2：欧洲淡水珍珠贻贝 Margaritifera margaritifera (Linnaeus, 1758) 的改进基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2023-05-15 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.81

André Gomes-Dos-Santos, Manuel Lopes-Lima, André M Machado, Thomas Forest, Guillaume Achaz, Amílcar Teixeira, Vincent Prié, L Filipe C Castro, Elsa Froufe

{"title":"The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758).","authors":"André Gomes-Dos-Santos, Manuel Lopes-Lima, André M Machado, Thomas Forest, Guillaume Achaz, Amílcar Teixeira, Vincent Prié, L Filipe C Castro, Elsa Froufe","doi":"10.46471/gigabyte.81","DOIUrl":"10.46471/gigabyte.81","url":null,"abstract":"Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species' unique biological and evolutionary features, helping promote its conservation.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte81"},"PeriodicalIF":0.0,"publicationDate":"2023-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10189783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9862369","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

Mycobacterial metabolic model development for drug target identification. 用于药物靶点鉴定的分枝杆菌代谢模型开发。

GigaByte (Hong Kong, China) Pub Date : 2023-04-30 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.80

Bridget P Bannerman, Alexandru Oarga, Jorge Júlvez

{"title":"Mycobacterial metabolic model development for drug target identification.","authors":"Bridget P Bannerman, Alexandru Oarga, Jorge Júlvez","doi":"10.46471/gigabyte.80","DOIUrl":"10.46471/gigabyte.80","url":null,"abstract":"Antibiotic resistance is increasing at an alarming rate, and three related mycobacteria are sources of widespread infections in humans. According to the World Health Organization, Mycobacterium leprae, which causes leprosy, is still endemic in tropical countries; Mycobacterium tuberculosis is the second leading infectious killer worldwide after COVID-19; and Mycobacteroides abscessus, a group of non-tuberculous mycobacteria, causes lung infections and other healthcare-associated infections in humans. Due to the rise in resistance to common antibacterial drugs, it is critical that we develop alternatives to traditional treatment procedures. Furthermore, an understanding of the biochemical mechanisms underlying pathogenic evolution is important for the treatment and management of these diseases. In this study, metabolic models have been developed for two bacterial pathogens, M. leprae and My. abscessus, and a new computational tool has been used to identify potential drug targets, which are referred to as bottleneck reactions. The genes, reactions, and pathways in each of these organisms have been highlighted; the potential drug targets can be further explored as broad-spectrum antibacterials and the unique drug targets for each pathogen are significant for precision medicine initiatives. The models and associated datasets described in this paper are available in GigaDB, Biomodels, and PatMeDB repositories.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte80"},"PeriodicalIF":0.0,"publicationDate":"2023-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10154535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9433054","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 first genome assembly of the amphibian nematode parasite (Aplectana chamaeleonis). 两栖动物线虫寄生虫（Aplectana chamaeleonis）的首次基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2023-03-27 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.79

Lei Han, Tianlu Liu, Fengping He, Zhijun Hou

引用次数: 0

Genome assembly of the deep-sea coral Lophelia pertusa. 深海珊瑚 Lophelia pertusa 的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2023-03-16 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.78

Santiago Herrera, Erik E Cordes

引用次数: 0

PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects. PhysiCOOL：用于模型校准和优化模式化项目的通用框架。

GigaByte (Hong Kong, China) Pub Date : 2023-02-28 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.77

Inês G Gonçalves, David A Hormuth, Sandhya Prabhakaran, Caleb M Phillips, José Manuel García-Aznar

{"title":"PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects.","authors":"Inês G Gonçalves, David A Hormuth, Sandhya Prabhakaran, Caleb M Phillips, José Manuel García-Aznar","doi":"10.46471/gigabyte.77","DOIUrl":"10.46471/gigabyte.77","url":null,"abstract":"In silico models of biological systems are usually very complex and rely on a large number of parameters describing physical and biological properties that require validation. As such, parameter space exploration is an essential component of computational model development to fully characterize and validate simulation results. Experimental data may also be used to constrain parameter space (or enable model calibration) to enhance the biological relevance of model parameters. One widely used computational platform in the mathematical biology community is PhysiCell, which provides a standardized approach to agent-based models of biological phenomena at different time and spatial scales. Nonetheless, one limitation of PhysiCell is the lack of a generalized approach for parameter space exploration and calibration that can be run without high-performance computing access. Here, we present PhysiCOOL, an open-source Python library tailored to create standardized calibration and optimization routines for PhysiCell models.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte77"},"PeriodicalIF":0.0,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10027115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9164410","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