Open research Europe最新文献

{"title":"Optimisation of pipes with constant diameter using the heuristic optimality criterion.","authors":"David Blacher, Michael Harasek","doi":"10.12688/openreseurope.15943.2","DOIUrl":"https://doi.org/10.12688/openreseurope.15943.2","url":null,"abstract":"<p><strong>Background: </strong>Minimising internal pressure drop in pipes is crucial for energy efficiency of fluid flow applications. Numerous computational optimisation tools that are capable of modifying flow geometries to reduce the pressure drop have been developed. Among these is a comparably simple heuristic optimisation al- gorithm which mimics erosion and sedimentation processes based on the shear stress in the vicinity of the domain boundaries. Although this method succeeds in modifying flow geometries for reduced pressure drop, it allows the fluid domain to widen during the reshaping process. Therefore, a reported reduction of pressure drop is not only caused by an improvement of the flow path, but also by an increase in the domain width. However, pipes with a constant circular diameter are favoured in many applications because they can be easily manufactured.</p><p><strong>Methods: </strong>Here we combine the heuristic optimisation approach with a novel geometrical constraint that maintains constant average diameter throughout the reshaping process. To our knowledge, this is the first application of a diameter-preserving constraint to the heuristic optimality criterion, enabling assessment of pressure drop reduction achieved solely through flow path modification without diameter dilation effects. We determined the applicability of the new algorithm for 2D channel and 3D pipe ge- ometries, conducting numerical simulations using the Lattice Boltzmann method with Reynolds numbers ranging from 40 to 500.</p><p><strong>Results: </strong>For the novel constant diameter constraint, the method successfully derived improved shapes across most tested Reynolds numbers while maintaining the initial average diameter. Notably, shapes derived at <i>Re</i> = 40 unexpectedly outperformed those derived at higher Reynolds numbers across all tested flow conditions, suggesting that low-Re geometries may capture fundamental flow features beneficial across wider Reynolds number ranges.</p><p><strong>Conclusions: </strong>This finding suggests applicability to higher Reynolds number flows, potentially even at turbulent industrial flows to be investigated in fu- ture research.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"3 ","pages":"156"},"PeriodicalIF":0.0,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13146464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147847119","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}

{"title":"Cell motility influences microfluidics capturing in scRNA-seq.","authors":"Lara López-Escobar, Ana M Nascimento, Tomás Gomes, Luis Graça, Luisa M Figueiredo","doi":"10.12688/openreseurope.19781.2","DOIUrl":"https://doi.org/10.12688/openreseurope.19781.2","url":null,"abstract":"<p><p>Microfluidic isolation methods for single-cell RNA sequencing (scRNA-seq) have primarily been designed for immotile cells, with limited consideration for motile cells, such as those with flagella or cilia. By studying the encapsulation efficiency of the flagellated <i>Trypanosoma brucei</i> using the 10x Genomics platform, we found that maintaining parasites at room temperature results in a low encapsulation yield. We implemented a rapid cooling method to 0°C prior to encapsulation, which reduced parasite motility and prevented undesired transcriptomic changes. This allowed for a representative scRNA-seq dataset, avoiding the disproportionate loss of the most motile forms. This study highlights the challenges of using motile cells in microfluidic systems and the biases caused by losing specific subpopulations, emphasizing the need for optimized protocols for non-standard mammalian cells.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"154"},"PeriodicalIF":0.0,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13069381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147679208","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}

{"title":"Exploring MAR perceptions in Kosovo - disparities in knowledge about MAR among young people.","authors":"Vera Dimitrievska, Jana Meloska, Virginie Rozée, Manon Vialle, Kristien Hens, Joke Struyf, Anna De Bayas Sanchez, Michaela Fuller Fuller, Francisco Güell, María López-Toribio, José Miguel Carrasco","doi":"10.12688/openreseurope.18974.5","DOIUrl":"10.12688/openreseurope.18974.5","url":null,"abstract":"<p><p>Research on knowledge and perception about (in) fertility and Medically Assisted Reproduction (MAR) techniques among young people in Kosovo is lacking. Part of the European Project's B ²-InF's team conducted a qualitative study in Kosovo with young adults (18-30) in 2021 assessing perceptions and views related to MAR and information provided by the MAR clinics in Kosovo. Main objective of this study is to explore perceptions about motherhood/fatherhood and to understand (in) fertility issues among young people in Kosovo. It is focused to delve more into MAR knowledge and techniques of young people in Kosovo and in general. Fifteen interviews with young people living in Kosovo were conducted between June and July 2021. A total of 3 themes emerged during the qualitative analysis and were grouped in three main theme levels. The first level, perceptions about motherhood and fatherhood among young people in Kosovo is about different views of young people, desires about becoming parents, and what is their personal attitude towards parenting. The second, analyzing how (in) fertility is perceived by young people from a gendered perspective. The third, MAR perceptions and new techniques that are prevailing in the global sense as different access opportunities are present. The findings from our interviews demonstrated that parenthood is still gender related. Male (in) fertility is often considered a taboo among the young people in Kosovo. A substantial amount of lack of knowledge was found in relation to MAR techniques, highlighting the importance of detailed information about the whole process of MAR treatments.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"20"},"PeriodicalIF":0.0,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12906643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146208215","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}

{"title":"Automated Execution of Data Pipelines based on Configuration Files.","authors":"Károly Bósa, Paul Heinzlreiter","doi":"10.12688/openreseurope.21019.2","DOIUrl":"10.12688/openreseurope.21019.2","url":null,"abstract":"<p><strong>Background: </strong>Data preparation is a fundamental aspect of data engineering, a prerequisite for later tasks such as data visualization, reporting, and training machine learning models. Despite the recurring patterns in data transformation processes, the specific steps often vary depending on the project context, data sources, and application domain.</p><p><strong>Methods: </strong>To address these challenges, this paper presents a flexible and extensible framework that enables the coordinated execution of modular data processing steps defined in a configuration file. By adopting a declarative, configuration-driven approach, the framework promotes modular, step-by-step development while substantially improving code reuse, maintainability, and adaptability. The framework also supports basic iterative execution constructs, such as loops and limited recursion, within the data pipeline definitions to accommodate more complex workflows.</p><p><strong>Results: </strong>By enabling the reuse of existing code snippets, the framework shifts development efforts toward enhancing and refining a shared code base, rather than repeatedly creating project-specific, disposable implementations. The long-term benefits of this approach become increasingly apparent as the system evolves. As more generalized modules and functions are developed, they can reduce duplication and improve maintainability without sacrificing flexibility.</p><p><strong>Conclusions: </strong>To assess the effectiveness of the framework, we apply cyclomatic complexity as a metric, demonstrating how the proposed approach impacts the development effort across some relatively simple, real-world data engineering scenarios.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"291"},"PeriodicalIF":0.0,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12784049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145954177","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}

{"title":"ERGA-BGE reference genome of <i>Lewinskya acuminata,</i> a common epiphytic Mediterranean moss with disjunct populations in California and Ethiopia.","authors":"Pablo Aguado-Ramsay, Francisco Lara, Isabel Draper, Maria Conejero, Astrid Böhne, Rita Monteiro, Thomas Marcussen, Torsten H Struck, Rebekah A Oomen, Alice Moussy, Corinne Cruaud, Karine Labadie, Lola Demirdjian, Emilie Téodori, Patrick Wincker, Pedro H Oliveira, Jean-Marc Aury, Chiara Bortoluzzi","doi":"10.12688/openreseurope.21670.2","DOIUrl":"10.12688/openreseurope.21670.2","url":null,"abstract":"<p><p>The reference genome of <i>Lewinskya acuminata</i> (H. Philib.) F. Lara, Garilleti & Goffinet will enable phylogenomic, biogeographic, and evolutionary studies within the <i>Orthotrichaceae</i> and related bryophyte lineages at a depth previously inaccessible. This species of moss is among the most representative of the Mediterranean epiphytic communities and can be readily identified by its long-acuminate leaves, fusiform capsules with a vestigial exostome, a well-developed endostome of six broad segments, and a dark, puckered peristome mouth when dry. The entirety of the genome sequence was assembled into 6 contiguous chromosomal pseudomolecules, while the mitochondrial and chloroplastic genomes were assembled, respectively, as a single contig of 104,820 bp and two contigs of 123,029 bp and 122,994 bp. This chromosome-level assembly encompasses 0.25 Gb, composed of 51 contigs and 13 scaffolds, with contig and scaffold N50 values of 11.5 Mb and 40.8 Mb, respectively.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"357"},"PeriodicalIF":0.0,"publicationDate":"2026-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12873536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146144856","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}

{"title":"\"You give everything the child requires to attend school\": Exploring caregiver involvement in children's education in Ghana.","authors":"Esinam Ami Avornyo, Richard Appiah, Elisabetta Aurino, Sharon Wolf","doi":"10.12688/openreseurope.20510.2","DOIUrl":"https://doi.org/10.12688/openreseurope.20510.2","url":null,"abstract":"<p><p>Background Parents' and other primary caregivers' involvement in children's education is a key determinant of children's academic outcomes and a major goal of education systems worldwide. However, the current literature lacks a broad understanding of what formal educational involvement means for parents in West African settings, and the factors that drive or limit their involvement. Understanding caregivers' perspectives and the factors that drive their involvement is essential for developing effective policies and interventions. Methods We conducted focus group discussions with 132 caregivers from rural and peri-urban communities in three regions of Ghana. Participants were purposively recruited and data were analyzed using thematic analysis. Results Caregivers primarily viewed their role as providing basic needs and school materials. However, caregivers with higher education discussed supporting their children's homework. Caregivers' involvements were constrained by four types of barriers: social and economic, caregiver and family, educational system, and child-level factors. Conclusion Our findings can inform culturally responsive education policies and interventions in Ghana and other similar low-resource settings.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"283"},"PeriodicalIF":0.0,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12989055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147470502","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}

{"title":"Genome wide association study of vaginal microbiota genetic diversity in French women.","authors":"Samuel Alizon, Claire Bernat, Vanina Boué, Sophie Grasset, Soraya Groc, Tsukushi Kamiya, Massilva Rahmoun, Christian Selinger, Nicolas Tessandier, Marine Bonneau, Vincent Foulongne, Christelle Graf, Jacques Reynes, Michel Segondy, Vincent Tribout, Jacques Ravel, Nathalie Boulle, Carmen Lia Murall, Vincent Pedergnana, Jean-François Deleuze","doi":"10.12688/openreseurope.20462.2","DOIUrl":"https://doi.org/10.12688/openreseurope.20462.2","url":null,"abstract":"<p><strong>Background: </strong>The composition of the vaginal microbiota is known to be highly structured into five main community state types (CSTs) that are found in all human populations. Several associations between perceived ethnicity and the type of community have been reported but analyses of human genetic data, especially genome wide association studies (GWAS), remain limited and mostly rely on phenotypic traits rather than microbial DNA data.</p><p><strong>Methods: </strong>Analysing genotyping data from in 168 women from the PAPCLEAR cohort study in France, we perform a GWAS looking for human genetic polymorphisms associated with vaginal microbiota community composition. For the latter, we use Simpson diversity and community state type (CST) as summary statistics to summarise 16S RNA metabarcoding data.</p><p><strong>Results: </strong>We show that inverse Simpson diversity is the trait related to the vaginal microbiota that is best explained by the human genome. Furthermore, we identify several genomic regions associated with variations in this trait and show that the covariates associated with vaginal microbiota composition do not correlate with these genetic variants.</p><p><strong>Conclusion: </strong>This is one of the first GWAS to use microbial genetic data instead of symptoms to characterise the vaginal microbiota. However, it remains limited because of the size of our cohort and our results call for more powered studies in terms of participants and genome coverage.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"186"},"PeriodicalIF":0.0,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13003221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147500912","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}

{"title":"ERGA-BGE reference genome of the Azores Bullfinch - <i>Pyrrhula murina</i> Godman, 1866: an IUCN Vulnerable Species endemic to a single island in the Azores Archipelago (Portugal).","authors":"Ricardo Jorge Lopes, Astrid Böhne, Thomas Marcussen, Rebekah A Oomen, Torsten Hugo Struck, Laura Aguilera, Marta Gut, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler S Alioto, Rita Monteiro","doi":"10.12688/openreseurope.20666.3","DOIUrl":"https://doi.org/10.12688/openreseurope.20666.3","url":null,"abstract":"<p><p><i>The reference genome of Pyrrhula murina</i>'s reference genome will substantially enhance the current monitoring of genetic diversity and population viability and will allow us to understand the effective population size trends throughout time and recent bottlenecks and population expansions. A total of 42 contiguous chromosomal pseudomolecules were assembled from the genome sequence, using ONT, HI-C and Illumina data. This chromosome-level assembly encompasses 1.2 Gb, composed of 65 contigs and 60 scaffolds, with contig and scaffold N50 values of 65 Mb and 76 Mb, respectively.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"210"},"PeriodicalIF":0.0,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12982980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147470533","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}

{"title":"A Translator at Work: Samuel ben Judah of Marseilles's Translation Notes on Alexander's <i>De Anima</i>.","authors":"Hanna Paulmann","doi":"10.12688/openreseurope.20551.2","DOIUrl":"10.12688/openreseurope.20551.2","url":null,"abstract":"<p><strong>Background: </strong>Samuel ben Judah of Marseilles's mid-fourteenth-century Hebrew translation of Alexander of Aphrodisias's <i>De anima</i>, made from Isḥaq ibn Ḥunayn's ninth-century Arabic translation of the original Greek, survives in four manuscripts. Three of these contain Samuel's notes on his translation, which disclose a wealth of information concerning textual problems he faced, editorial decisions he took, and his understanding of the text and its arguments.</p><p><strong>Methods: </strong>The present paper analyses these notes, which have never been studied before, according to philosophical and philological methods.</p><p><strong>Results: </strong>My analysis shows that Samuel is a philosophically engaged translator who approaches Alexander's text with a text-critical attitude that enables him to render it in a more coherent and accessible form than that found in the Arabic manuscript that served as his source. Thus, this paper deepens our understanding of Samuel's activity as a translator.</p><p><strong>Conclusions: </strong>These results shows that we should take translators seriously as philosophical agents in their own right and compels us to study manuscripts that contain translations to find and explore the translators' own voices within or next to their works.</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"306"},"PeriodicalIF":0.0,"publicationDate":"2026-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12639282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589644","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}

{"title":"ERGA-BGE Chromosome-Level Genome of <i>Patella rustica</i> Linnaeus, 1758: a Resource to Investigate Responses to Global Warming in the intertidal.","authors":"Rui Faria, Rocío Nieto Vilela, Fernando P Lima, Rita Monteiro, Astrid Böhne, Thomas Marcussen, Torsten H Struck, Rebekah A Oomen, Marta Gut, Laura Aguilera, Tyler Alioto, Francisco Câmara Ferreira, Jèssica Gómez-Garrido, Fernando Cruz, Anna Lazar, Leanne Haggerty, Fergal Martin, Tom Brown","doi":"10.12688/openreseurope.21608.2","DOIUrl":"https://doi.org/10.12688/openreseurope.21608.2","url":null,"abstract":"<p><p>The reference genome of <i>Patella rustica</i> Linnaeus, 1758 (Gastropoda, Patellidae) will offer a unique opportunity to understand how intertidal organisms respond to the effects of global warming, contributing to improve our predictions about the impact of climate change on the maintenance and diversification of marine biodiversity. A total of 9 contiguous chromosomal pseudomolecules were assembled from the genome sequence, made up from Oxford Nanopore Technologies (ONT) long-reads, WGS and Chromatin-Conformation-Capture (Hi-C) short-read sequences. This chromosome-level assembly encompasses 719 Mb, composed of 157 contigs and 24 scaffolds, with contig and scaffold N50 values of 8.52 Mb and 83.6 Mb, respectively, and assembly and annotation BUSCO completeness of 97.7% and 96.5%, respectively. The production of this genome assembly and annotation was coordinated and supported by the European Reference Genome Atlas (ERGA) and Biodiversity Genomics Europe project (BGE).</p>","PeriodicalId":74359,"journal":{"name":"Open research Europe","volume":"5 ","pages":"350"},"PeriodicalIF":0.0,"publicationDate":"2026-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12982983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147470542","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}