arXiv - QuanBio - Other Quantitative Biology最新文献

{"title":"Alternatives to the statistical mass confusion of testing for no-effect","authors":"Josh L. Morgan","doi":"arxiv-2407.07114","DOIUrl":"https://doi.org/arxiv-2407.07114","url":null,"abstract":"Statisticians and researchers have argued about the merits of effect size\u0000estimation relative to hypothesis testing for decades. Cell biology has largely\u0000avoided this debate and is now in a quantitation crisis. In experimental cell\u0000biology, statistical analysis has grown to mean testing the null hypothesis\u0000that there was no experimental effect. This weak form of hypothesis testing\u0000neglects effect size, is universally misinterpreted, and is disastrously prone\u0000to error when combined with high-throughput cell biology. The first part of the\u0000solution proposed here is to limit statistical hypothesis testing to the small\u0000subset of experiments where a biologically meaningful null hypotheses can be\u0000defined prior to the experiment. The second part of the solution is to make\u0000confidence intervals the default statistic in cell biology.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141588648","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 unpaved road towards efficient selective breeding in insects for food and feed","authors":"Laura Skrubbeltrang Hansen, Stine Frey Laursen, Simon Bahrndorff, Jesper Givskov Sørensen, Goutam Sahana, Torsten Nygaard Kristensen, Hanne Marie Nielsen","doi":"arxiv-2406.16364","DOIUrl":"https://doi.org/arxiv-2406.16364","url":null,"abstract":"Insect production for food and feed presents a promising supplement to ensure\u0000food safety and address the adverse impacts of agriculture on climate and\u0000environment in the future. However, optimisation is required for insect\u0000production to realise its full potential. This can be by targeted improvement\u0000of traits of interest through selective breeding, an approach which has so far\u0000been underexplored and underutilised in insect farming. Here we present a\u0000comprehensive review of the selective breeding framework in the context of\u0000insect production. We systematically evaluate adjustments of selective breeding\u0000techniques to the realm of insects and highlight the essential components\u0000integral to the breeding process. The discussion covers every step of a\u0000conventional breeding scheme, such as formulation of breeding objectives,\u0000phenotyping, estimation of genetic parameters and breeding values, selection of\u0000appropriate breeding strategies, and mitigation of issues associated with\u0000genetic diversity depletion and inbreeding. This review combines knowledge from\u0000diverse disciplines, bridging the gap between animal breeding, quantitative\u0000genetics, evolutionary biology, and entomology, offering an integrated view of\u0000the insect breeding research area and uniting knowledge which has previously\u0000remained scattered across diverse fields of expertise.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141505129","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":"Effectiveness of ChatGPT in explaining complex medical reports to patients","authors":"Mengxuan Sun, Ehud Reiter, Anne E Kiltie, George Ramsay, Lisa Duncan, Peter Murchie, Rosalind Adam","doi":"arxiv-2406.15963","DOIUrl":"https://doi.org/arxiv-2406.15963","url":null,"abstract":"Electronic health records contain detailed information about the medical\u0000condition of patients, but they are difficult for patients to understand even\u0000if they have access to them. We explore whether ChatGPT (GPT 4) can help\u0000explain multidisciplinary team (MDT) reports to colorectal and prostate cancer\u0000patients. These reports are written in dense medical language and assume\u0000clinical knowledge, so they are a good test of the ability of ChatGPT to\u0000explain complex medical reports to patients. We asked clinicians and lay people\u0000(not patients) to review explanations and responses of ChatGPT. We also ran\u0000three focus groups (including cancer patients, caregivers, computer scientists,\u0000and clinicians) to discuss output of ChatGPT. Our studies highlighted issues\u0000with inaccurate information, inappropriate language, limited personalization,\u0000AI distrust, and challenges integrating large language models (LLMs) into\u0000clinical workflow. These issues will need to be resolved before LLMs can be\u0000used to explain complex personal medical information to patients.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141505132","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":"Computing in the Life Sciences: From Early Algorithms to Modern AI","authors":"Samuel A. Donkor, Matthew E. Walsh, Alexander J. Titus","doi":"arxiv-2406.12108","DOIUrl":"https://doi.org/arxiv-2406.12108","url":null,"abstract":"Computing in the life sciences has undergone a transformative evolution, from\u0000early computational models in the 1950s to the applications of artificial\u0000intelligence (AI) and machine learning (ML) seen today. This paper highlights\u0000key milestones and technological advancements through the historical\u0000development of computing in the life sciences. The discussion includes the\u0000inception of computational models for biological processes, the advent of\u0000bioinformatics tools, and the integration of AI/ML in modern life sciences\u0000research. Attention is given to AI-enabled tools used in the life sciences,\u0000such as scientific large language models and bio-AI tools, examining their\u0000capabilities, limitations, and impact to biological risk. This paper seeks to\u0000clarify and establish essential terminology and concepts to ensure informed\u0000decision-making and effective communication across disciplines.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141505130","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":"Mining comorbidities: a brief survey","authors":"Giovanna Maria Dimitri","doi":"arxiv-2406.10696","DOIUrl":"https://doi.org/arxiv-2406.10696","url":null,"abstract":"In this manuscript we will present a brief overview of the comorbidity\u0000concept. We will start by laying its foundations and its definitions and then\u0000describing the role that machine learning can hold in mining and defining it.\u0000The purpose of this short survey is to present a brief overview of the\u0000definition of comorbidity as a concept, and showing some of the latest\u0000applications and potentialities for the application of natural language\u0000processing and text mining techniques.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141505131","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":"Experimental Measurement of Assembly Indices are Required to Determine The Threshold for Life","authors":"Sara I. Walker, Cole Mathis, Stuart Marshall, Leroy Cronin","doi":"arxiv-2406.06826","DOIUrl":"https://doi.org/arxiv-2406.06826","url":null,"abstract":"Assembly Theory (AT) was developed to help distinguish living from non-living\u0000systems. The theory is simple as it posits that the amount of selection or\u0000Assembly is a function of the number of complex objects where their complexity\u0000can be objectively determined using assembly indices. The assembly index of a\u0000given object relates to the number of recursive joining operations required to\u0000build that object and can be not only rigorously defined mathematically but can\u0000be experimentally measured. In pervious work we outlined the theoretical basis,\u0000but also extensive experimental measurements that demonstrated the predictive\u0000power of AT. These measurements showed that is a threshold in assembly indices\u0000for organic molecules whereby abiotic chemical systems could not randomly\u0000produce molecules with an assembly index greater or equal than 15. In a recent\u0000paper by Hazen et al [1] the authors not only confused the concept of AT with\u0000the algorithms used to calculate assembly indices, but also attempted to\u0000falsify AT by calculating theoretical assembly indices for objects made from\u0000inorganic building blocks. A fundamental misunderstanding made by the authors\u0000is that the threshold is a requirement of the theory, rather than experimental\u0000observation. This means that exploration of inorganic assembly indices\u0000similarly requires an experimental observation, correlated with the theoretical\u0000calculations. Then and only then can the exploration of complex inorganic\u0000molecules be done using AT and the threshold for living systems, as expressed\u0000with such building blocks, be determined. Since Hazen et al.[1] present no\u0000experimental measurements of assembly theory, their analysis is not\u0000falsifiable.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141505134","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 Vertebrate Breed Ontology: Towards Effective Breed Data Standardization","authors":"Kathleen R. MullenUniversity of Colorado Anschutz Medical Campus, Imke TammenUniversity of Sydney, Nicolas A. MatentzogluSemanticly Ltd, Marius MatherUniversity of Sydney, Christopher J. MungallLawrence Berkeley National Laboratory, Melissa A. HaendelUniversity of North Carolina at Chapel Hill, Frank W. NicholasUniversity of Sydney, Sabrina ToroUniversity of North Carolina at Chapel Hill, the Vertebrate Breed Ontology Consortium","doi":"arxiv-2406.02623","DOIUrl":"https://doi.org/arxiv-2406.02623","url":null,"abstract":"Background: Limited universally adopted data standards in veterinary science\u0000hinders data interoperability and therefore integration and comparison; this\u0000ultimately impedes application of existing information-based tools to support\u0000advancement in veterinary diagnostics, treatments, and precision medicine. Objectives: Creation of a Vertebrate Breed Ontology (VBO) as a single,\u0000coherent logic-based standard for documenting breed names in animal health,\u0000production and research-related records will improve data use capabilities in\u0000veterinary and comparative medicine. Animals: No live animals were used in this study. Methods: A list of breed names and related information was compiled from\u0000relevant sources, organizations, communities, and experts using manual and\u0000computational approaches to create VBO. Each breed is represented by a VBO term\u0000that includes all provenance and the breed's related information as metadata.\u0000VBO terms are classified using description logic to allow computational\u0000applications and Artificial Intelligence-readiness. Results: VBO is an open, community-driven ontology representing over 19,000\u0000livestock and companion animal breeds covering 41 species. Breeds are\u0000classified based on community and expert conventions (e.g., horse breed, cattle\u0000breed). This classification is supported by relations to the breeds' genus and\u0000species indicated by NCBI Taxonomy terms. Relationships between VBO terms, e.g.\u0000relating breeds to their foundation stock, provide additional context to\u0000support advanced data analytics. VBO term metadata includes common names and\u0000synonyms, breed identifiers or codes, and attributed cross-references to other\u0000databases. Conclusion and clinical importance: Veterinary data interoperability and\u0000computability can be enhanced by the adoption of VBO as a source of standard\u0000breed names in databases and veterinary electronic health records.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548530","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":"Free-ranging dogs quickly learn to recognize a rewarding person","authors":"Srijaya Nandi, Mousumi Chakraborty, Aesha Lahiri, Hindolii Gope, Sujata Khan Bhaduri, Anindita Bhadra","doi":"arxiv-2405.19936","DOIUrl":"https://doi.org/arxiv-2405.19936","url":null,"abstract":"Individual human recognition is important for species that live in close\u0000proximity to humans. Numerous studies on domesticated species and urban-adapted\u0000birds have highlighted this ability. One such species which is heavily reliant\u0000on humans is the free-ranging dog. Very little knowledge exists on the amount\u0000of time taken by free-ranging dogs to learn and remember individual humans. Due\u0000to their territorial nature, they have a high probability of encountering the\u0000same people multiple times on the streets. Being able to distinguish individual\u0000humans might be helpful in making decisions regarding people from whom to beg\u0000for food or social reward. We investigated if free-ranging dogs are capable of\u0000identifying the person rewarding them and the amount of time required for them\u0000to learn it. We conducted field trials on randomly selected adult free-ranging\u0000dogs in West Bengal, India. On Day 1, a choice test was conducted. The\u0000experimenter chosen did not provide reward while the other experimenter\u0000provided a piece of boiled chicken followed by petting. The person giving\u0000reward on Day 1 served as the correct choice on four subsequent days of\u0000training. Day 6 was the test day when none of the experimenters had a reward.\u0000We analyzed the choice made by the dogs, the time taken to approach during the\u0000choice tests, and the socialization index, which was calculated based on the\u0000intensity of affiliative behaviour shown towards the experimenters. The dogs\u0000made correct choices at a significantly higher rate on the fifth and sixth\u0000days, as compared to Day 2, suggesting learning. This is the first study aiming\u0000to understand the time taken for individual human recognition in free-ranging\u0000dogs and can serve as the scaffold for future studies to understand the\u0000dog-human relationship in open environments, like urban ecosystems.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"63 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141193426","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":"Biodiversity data standards for the organization and dissemination of complex research projects and digital twins: a guide","authors":"Carrie Andrew, Sharif Islam, Claus Weiland, Dag Endresen","doi":"arxiv-2405.19857","DOIUrl":"https://doi.org/arxiv-2405.19857","url":null,"abstract":"Biodiversity data are substantially increasing, spurred by technological\u0000advances and community (citizen) science initiatives. To integrate data is,\u0000likewise, becoming more commonplace. Open science promotes open sharing and\u0000data usage. Data standardization is an instrument for the organization and\u0000integration of biodiversity data, which is required for complex research\u0000projects and digital twins. However, just like with an actual instrument, there\u0000is a learning curve to understanding the data standards field. Here we provide\u0000a guide, for data providers and data users, on the logistics of compiling and\u0000utilizing biodiversity data. We emphasize data standards, because they are\u0000integral to data integration. Three primary avenues for compiling biodiversity\u0000data are compared, explaining the importance of research infrastructures for\u0000coordinated long-term data aggregation. We exemplify the Biodiversity Digital\u0000Twin (BioDT) as a case study. Four approaches to data standardization are\u0000presented in terms of the balance between practical constraints and the\u0000advancement of the data standards field. We aim for this paper to guide and\u0000raise awareness of the existing issues related to data standardization, and\u0000especially how data standards are key to data interoperability, i.e., machine\u0000accessibility. The future is promising for computational biodiversity\u0000advancements, such as with the BioDT project, but it rests upon the shoulders\u0000of machine actionability and readability, and that requires data standards for\u0000computational communication.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"88 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141193496","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":"Observation of Significant Photosynthesis in Garden Cress and Cyanobacteria under Simulated Illumination from a K Dwarf Star","authors":"Iva Vilović, Dirk Schulze-Makuch, René Heller","doi":"arxiv-2405.19180","DOIUrl":"https://doi.org/arxiv-2405.19180","url":null,"abstract":"Stars with about 45 to 80% the mass of the Sun, so-called K dwarf stars, have\u0000previously been proposed as optimal host stars in the search for habitable\u0000extrasolar worlds. These stars are abundant, have stable luminosities over\u0000billions of years longer than Sun-like stars, and offer favorable space\u0000environmental conditions. So far, the theoretical and experimental focus on\u0000exoplanet habitability has been on even less massive, though potentially less\u0000hospitable red dwarf stars. Here we present the first experimental data on the\u0000responses of photosynthetic organisms to a simulated K dwarf spectrum. We find\u0000that garden cress Lepidium sativum under K-dwarf radiation exhibits comparable\u0000growth and photosynthetic efficiency as under solar illumination on Earth. The\u0000cyanobacterium Chroococcidiopsis sp. CCMEE 029 exhibits significantly higher\u0000photosynthetic efficiency and culture growth under K dwarf radiation compared\u0000to solar conditions. Our findings of the affirmative responses of these two\u0000photosynthetic organisms to K dwarf radiation suggest that exoplanets in the\u0000habitable zones around such stars deserve high priority in the search for\u0000extrasolar life.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"181 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141193153","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}