Research ideas and outcomes最新文献

{"title":"Interplay of hypoxia and host cells in the translocation, invasion and dissemination of Taenia solium in neurocysticercosis","authors":"Eunice Ayerakwa, Isawumi Abiola","doi":"10.3897/rio.10.e124177","DOIUrl":"https://doi.org/10.3897/rio.10.e124177","url":null,"abstract":"Neurocysticercosis, caused by the invasion of the central nervous system (CNS) by Taenia solium larvae, poses a significant global health burden. Despite its prevalence and severe neurological consequences, understanding of the molecular and signalling pathways facilitating parasite dissemination and CNS invasion is limited. The lack of comprehensive knowledge of host-parasite interactions and associated proteins involved in T. solium infection hinders the development of targeted interventions to mitigate its ability to cross the epithelia barrier. This is complicated by reduced oxygen availability in the intestine, a phenomenon called hypoxia. Hypoxia can result in epithelial barrier disruption and cell damage, thereby promoting the translocation and dissemination of T. solium. This study aims to establish the role of hypoxia in T. solium invasion and disseminated infections. The effect of hypoxia on the migration, viability and morphological characteristics of T. solium would be determined using transwell invasion assays, flow cytometry and microscopy. T. solium oncosphere development and dissemination under hypoxic and normoxic conditions will be monitored using animal models. Also, host-parasite transcriptome and proteome profiling will be performed to determine pathways triggered under hypoxic conditions. It is expected that hypoxia would promote the invasion and dissemination of T. solium by enhancing epithelial and endothelial cell permeability. , hypoxia will induce the expression of binding and adhesion proteins and other virulence markers such as enolase, serpin, and glutathione transferases that are involved in host invasion. Understanding the role of hypoxia in the translocation mechanism of T. solium can be leveraged to provide insights into host tissues dissemination and the development of appropriate interventions.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"26 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140982955","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}

{"title":"Raising the Neanderthal (molecules) from the dead: a proposal for in vivo resurrection of Neanderthal haemoglobin for the investigation of biochemical adaptations for cold tolerance","authors":"Katherine McLean","doi":"10.3897/rio.10.e107983","DOIUrl":"https://doi.org/10.3897/rio.10.e107983","url":null,"abstract":"Since the first discoveries of Neanderthal fossils, their derived characteristics, such as increased robusticity, have engaged researchers. Adaptation to cold environments has been hypothesised to explain such traits and this hypothesis has driven the majority of discourse. This proposal seeks to examine this hypothesis and locate evidence of Neanderthals being physiologically adapted to cold at the biomolecular level. Haemoglobin is a biomolecule that has been previously demonstrated to adapt to cold in some species, driven by the inhibition of the protein’s function by low temperatures. Neanderthal haemoglobin is extinct; however, using pre-sequenced genomic data, I propose to resurrect Neanderthal haemoglobin so I can examine the consequences of lowered temperature on its function. This project could potentially detect signs of cold adaptation in the Neanderthal globin genes and provide empirical evidence for the cold adaptation hypothesis.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"122 21","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140985455","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}

{"title":"Probing Genetics and Environmental Factors underlying Uterine Fibroid Tumorigenesis in Ghana, West Africa","authors":"Tosin Senbadejo, Isawumi Abiola, Lily Paemka","doi":"10.3897/rio.10.e116907","DOIUrl":"https://doi.org/10.3897/rio.10.e116907","url":null,"abstract":"Uterine fibroid (UF) is the most prevalent benign tumour that affects millions of women globally, with a high incidence of 70% amongst women of reproductive age. UF has been associated with various complications, such as recurrent surgeries, infertility, anemia and pregnancy loss. Notably, women of African descent often experience more severe symptoms and complications. Although hormones, growth factors, and genetic alterations are widely associated with UF, the precise mechanism underlying its pathogenesis is not fully understood. Recent evidence suggests altered microbiota may serve as a potential risk factor for UF development. Altered microbiota can contribute to tumorigenesis via epigenetic changes to host cells or toxic effects from invasion. The lack of curative-drug treatment poses significant challenges to patients with UF. Patients often undergo surgeries that require the removal of the uterus or tumour, which can negatively impact fertility. Furthermore, uterine fibroids’ diagnosis relies on expensive imaging technologies such as ultrasound, which may not be readily available in developing countries. Moreso, diagnosis is often conducted only after patients’ symptoms become severe. Although late presentation may contribute to severe symptoms and complications among women with UF in Africa, other factors that influence severity and increase incidence in this population remain unknown. A comprehensive assessment of UF predisposing factors in high-risk populations such as Ghana could give better insights into disease pathogenesis. Hence, this study aims to assess: UF-associated demographic factors, the role of uterine microbiota dysbiosis on UF tumorigenesis; and molecular markers associated with UF in the Ghanaian population. Epidemiological data and clinical samples (tissues, blood and cervico-vaginal swabs) will be obtained. The characterization of samples will involve metagenomics, whole genome sequencing, functional validation of SNPs and SNP genotyping. The association of risk alleles with disease phenotypes will be assessed via regression analysis using PLINK v.1.9. The findings will provide information on potential disease markers that can be explored for better management strategies for UF in high-risk populations.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":" 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140992326","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}

{"title":"Sharing data, caring for collections. Open data on collection agents affiliated with the Museum für Naturkunde Berlin","authors":"Sabine von Mering, Erik Stolze, Katja Kaiser, Mareike Petersen","doi":"10.3897/rio.10.e118851","DOIUrl":"https://doi.org/10.3897/rio.10.e118851","url":null,"abstract":"Linked open data on collection agents contribute to increased discoverability, accessibility and transparency of natural history collections. Despite major efforts to digitise and open up museum and university object collections, related information is often stored in internal resources. This paper describes a project conducted at the Museum für Naturkunde Berlin (MfN) contributing to its collection disclosure and development initiatives. Information on historical collectors and other collection agents was transferred from the internal MfN collector wiki to Wikidata. For a total of 600 collection agents, existing Wikidata items were enriched or new items created.\u0000 Special emphasis was put on linking these people to the Museum, to document their affiliation with the MfN, its collection and its archive. Within the project, an open participatory approach was taken. Several Wikidata edit-a-thons were organised to test this collaborative and innovative format for possible future application by the Museum. By opening up institutional silos and openly sharing data on agents connected to museum holdings, these data become more widely accessible and reusable, for example, as a resource for transdisciplinary provenance research.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":" 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140998702","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}

{"title":"Knowledge re-integration in real-world laboratories to transform cities and communities: report on workshop designs","authors":"Marie Neumann, Franziska Ehnert","doi":"10.3897/rio.10.e124018","DOIUrl":"https://doi.org/10.3897/rio.10.e124018","url":null,"abstract":"How can we re-integrate knowledge generated in real-world laboratories (RWLs) into societal practice? In the RWL “Dresden – City of the Future 2030+”, the re-integration of knowledge was central to the research design. In this Workshop Report, we focus on facilitation methods for knowledge re-integration into societal practice. This is to guide transdisciplinary research practice and help researchers in designing and facilitating such research processes. We conceptualise knowledge re-integration, based on the current literature. Further, we describe our facilitation methods (two workshop formats) to document and reflect on our experiences. A self-reflective evaluation is conducted with the help of evaluation criteria synthesised from the literature on transdisciplinary research (TDR). Our reflections confirm that the facilitation of exchange with the target group/target context can greatly enhance the transferability of knowledge gained in TDR settings. In our conclusion, we highlight the importance of facilitators and knowledge brokers, as well as co-creation with local stakeholders to reach out to the target group.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":" 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140691050","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}

{"title":"The Chemistry Development Kit in 2024: improving cheminformatics research","authors":"E. Willighagen, Marc Teunis, Alyanne De Haan","doi":"10.3897/rio.10.e124884","DOIUrl":"https://doi.org/10.3897/rio.10.e124884","url":null,"abstract":"Cheminformatics is the research field that deals with information about chemical systems. This includes the chemical structure which is used in computational chemistry where quantum chemistry is too complex. The Chemistry Development Kit (CDK) was one of the first Open Science libraries in chemistry, co-founded in The Netherlands. The source code goes as far back as 1997 and has been maintained for more than 25 years. The CDK is used by many tools in drug discovery, computational toxicology, and bioinformatics. This project will develop improvements to the core library and update tools using the CDK to use the latest release.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":" 14","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140691217","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}

{"title":"Why and how did LifeWatch emerge?","authors":"Wouter Los","doi":"10.3897/rio.10.e121892","DOIUrl":"https://doi.org/10.3897/rio.10.e121892","url":null,"abstract":"The original vision on what later became LifeWatch ERIC started about a quarter of a century ago in 1996. In those days, the promise of digital technologies entered biodiversity and ecosystem research. Not only by digitiing relevant information, but also with applications to process such data. While several (inter)national initiatives embarked on specific topics, there was also an idea that the upcoming view on grid computing provided attractive solutions for federated data sources, together with a strong computing capacity. This paper presents the history from conception to early actions, until actual preparations towards a research infrastructure on the European scale.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":" 84","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140692364","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}

{"title":"A lab-centric, workflow-based data management system for environmental DNA research","authors":"Alex Borisenko, Robert G. Young, Robert Hanner","doi":"10.3897/rio.10.e120483","DOIUrl":"https://doi.org/10.3897/rio.10.e120483","url":null,"abstract":"The adoption of environmental DNA approaches as a standard tool for biodiversity monitoring leads to the increase in the number of eDNA-based species occurrence records; however, considerable disparity remains in the nature and quality of associated information, much of it unpublished and/or poorly parametrised. A robust system for tracking biological materials from their point of origin through laboratory analyses is required to connect inferred taxon occurrences with analytical history and provenance data. The bulk of eDNA research is currently driven by small-scale operations where the tasks of digitisation, organisation and cross-referencing field records with laboratory analytical data and biomaterial sample location, are often performed manually and disconnected.\u0000 We present an integrative, full-stack data management solution that provides a structured ontological concept, a minimalist data schema for eDNA research and a software application prototype designed to facilitate real-time digitisation, parsing, annotation and archival of eDNA data. The system tracks the provenance and analytical history of biological samples through a structured hierarchy of events, linked with associated digital file attachment archives, such as images and raw sequence files, and with inferred taxonomic occurrence records. The data entry process is compartmentalised and incorporated into the corresponding stages of standard operations used in fieldwork, biological collection management and laboratory analysis. Resulting data records can be integrated into various output formats required for large-scale analytics, publication and/or submission to global data aggregators. The prototype is implemented on the Microsoft 365 platform as a relational database (Access) linked to cloud-based data tables (SharePoint) and a set of associated data conversion spreadsheets (Excel). The system is designed primarily around the data management needs of small research labs; however, it is scalable to larger institutions and inter-institutional academic networks.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"138 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140369261","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}

{"title":"Development of a field diagnostic tool for Schistosoma mansoni Praziquantel resistant markers in selected endemic communities","authors":"Maame Ekua Acquah, F. Aboagye, Yvonne Ashong, Lydia Mosi","doi":"10.3897/rio.10.e120899","DOIUrl":"https://doi.org/10.3897/rio.10.e120899","url":null,"abstract":"Schistosomiasis is a neglected tropical disease that affects more than 200 million people and 45% of infections have been shown to occur in school-aged children. A large percentage of the disease burden lies in Africa. In 2012, the WHO outlined a roadmap for the elimination of schistosomiasis by 2020; however, this was not achieved. Treatment for schistosomiasis is by the use of Praziquantel, a drug in use for over 30 years and there is a concern for emerging drug resistance. There are several species of the genus Schistosoma causing infection in humans. For this study, Schistosoma mansoni which causes intestinal schistosomiasis will be investigated. There are reports of lowering cure rates and suboptimal response to praziquantel following several cycles of mass drug administration (MDA). Praziquantel resistance has also been reported in some countries and laboratory-bred schistosome experiments. To address the concerns of resistance, this study aims to employ a two-part approach to assess the prevalence of S. mansoni. praziquantel resistance amongst school-aged children in schistosomiasis endemic communities in Ghana and develop a diagnostic tool to aid in field assessment of infections. To achieve this, the study will attempt to answer the following research questions: 1. Is there developing S. mansoni praziquantel resistance in communities that have undergone several mass drug administrations? 2. Is there an interplay between intermediate host exposure to praziquantel and the development of praziquantel drug resistance in the definitive host?","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":" 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140212104","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}

{"title":"Report on the Marine Imaging Workshop 2022","authors":"Catherine Borremans, Jennifer M. Durden, T. Schoening, Emma J. Curtis, Luther Adams, Alexandra Branzan Albu, A. Arnaubec, S. Ayata, Reshma Baburaj, Corinne Bassin, Miriam Beck, Katharine Bigham, Rachel Boschen-Rose, Chad Collett, Matteo Contini, Paulo Correa, C. Domínguez-Carrió, Gautier Dreyfus, Graeme Duncan, Maxime Ferrera, Valentin Foulon, A. Friedman, Santosh Gaikwad, Chloe Game, Adriana GAYTÁN-CABALLERO, Fanny Girard, Michela Giusti, Mélissa Hanafi-Portier, Kerry Howell, Iryna Hulevata, Kiamuke Itiowe, Chris Jackett, Jan Jansen, Clarissa Karthäuser, K. Katija, Maxime Kernec, Gabriel Kim, Marcelo Kitahara, Daniel Langenkämper, Tim Langlois, Nadine Lanteri, Claude Jianping Li, Qi-Ran Li, Pierre-Olivier Liabot, Dhugal Lindsay, Ali Loulidi, Y. Marcon, Simone Marini, Ashley Marranzino, M. Massot-Campos, M. Matabos, Lénaick Menot, B. Moreno, Marcus Morrissey, D. Nakath, T. Nattkemper, Monika Neufeld, M. Obst, Karine Olu, Alexa Parimbelli, F. Pasotti, Dominique Pelletier, Margaux Perhirin, Nils Piechaud, O","doi":"10.3897/rio.10.e119782","DOIUrl":"https://doi.org/10.3897/rio.10.e119782","url":null,"abstract":"Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and quantity of data collected from images. The 4th Marine Imaging Workshop was organised from 3-6 October 2022 in Brest (France) in a hybrid mode. More than a hundred participants were welcomed in person and about 80 people attended the online sessions. The workshop was organised in a single plenary session of presentations followed by discussion sessions. These were based on dynamic polls and open questions that allowed recording of the imaging community’s current and future ideas. In addition, a whole day was dedicated to practical sessions on image analysis, data standardisation and communication tools. The format of this edition allowed the participation of a wider community, including lower-income countries, early career scientists, all working on laboratory, benthic and pelagic imaging.\u0000 This article summarises the topics addressed during the workshop, particularly the outcomes of the discussion sessions for future reference and to make the workshop results available to the open public.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"34 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140234247","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}