arXiv - QuanBio - Other Quantitative Biology最新文献

{"title":"Large deviation principles and evolutionary multiple structure alignment of non-coding RNA","authors":"Brandon Legried","doi":"arxiv-2405.14904","DOIUrl":"https://doi.org/arxiv-2405.14904","url":null,"abstract":"Non-coding RNA are functional molecules that are not translated into\u0000proteins. Their function comes as important regulators of biological function.\u0000Because they are not translated, they need not be as stable as other types of\u0000RNA. The TKF91 Structure Tree from Holmes 2004 is a probability model that\u0000effectively describes correlated substitution, insertion, and deletion of base\u0000pairs, and found to have some worth in understanding dynamic folding patterns.\u0000In this paper, we provide a new probabilistic analysis of the TKF91 Structure\u0000Tree. Large deviation principles on stem lengths, helix lengths, and tree size\u0000are proved. Additionally, we give a new alignment procedure that constructs\u0000accurate sequence and structural alignments for sequences with low identity for\u0000a dense enough phylogeny.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"237 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141171147","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":"Petri nets in modelling glucose regulating processes in the liver","authors":"Kamila Barylska, Anna Gogolińska","doi":"arxiv-2405.11009","DOIUrl":"https://doi.org/arxiv-2405.11009","url":null,"abstract":"Diabetes is a chronic condition, considered one of the civilization diseases,\u0000that is characterized by sustained high blood sugar levels. There is no doubt\u0000that more and more people is going to suffer from diabetes, hence it is crucial\u0000to understand better its biological foundations. The essential processes\u0000related to the control of glucose levels in the blood are: glycolysis (process\u0000of breaking down of glucose) and glucose synthesis, both taking place in the\u0000liver. The glycolysis occurs during feeding and it is stimulated by insulin. On\u0000the other hand, the glucose synthesis arises during fasting and it is\u0000stimulated by glucagon. In the paper we present a Petri net model of glycolysis\u0000and glucose synthesis in the liver. The model is created based on medical\u0000literature. Standard Petri nets techniques are used to analyse the properties\u0000of the model: traps, reachability graphs, tokens dynamics, deadlocks analysis.\u0000The results are described in the paper. Our analysis shows that the model\u0000captures the interactions between different enzymes and substances, which is\u0000consistent with the biological processes occurring during fasting and feeding.\u0000The model constitutes the first element of our long-time goal to create the\u0000whole body model of the glucose regulation in a healthy human and a person with\u0000diabetes.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141148767","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":"Simplicity within biological complexity","authors":"Natasa Przulj, Noel Malod-Dognin","doi":"arxiv-2405.09595","DOIUrl":"https://doi.org/arxiv-2405.09595","url":null,"abstract":"Heterogeneous, interconnected, systems-level, molecular data have become\u0000increasingly available and key in precision medicine. We need to utilize them\u0000to better stratify patients into risk groups, discover new biomarkers and\u0000targets, repurpose known and discover new drugs to personalize medical\u0000treatment. Existing methodologies are limited and a paradigm shift is needed to\u0000achieve quantitative and qualitative breakthroughs. In this perspective paper,\u0000we survey the literature and argue for the development of a comprehensive,\u0000general framework for embedding of multi-scale molecular network data that\u0000would enable their explainable exploitation in precision medicine in linear\u0000time. Network embedding methods map nodes to points in low-dimensional space,\u0000so that proximity in the learned space reflects the network's topology-function\u0000relationships. They have recently achieved unprecedented performance on hard\u0000problems of utilizing few omic data in various biomedical applications.\u0000However, research thus far has been limited to special variants of the problems\u0000and data, with the performance depending on the underlying topology-function\u0000network biology hypotheses, the biomedical applications and evaluation metrics.\u0000The availability of multi-omic data, modern graph embedding paradigms and\u0000compute power call for a creation and training of efficient, explainable and\u0000controllable models, having no potentially dangerous, unexpected behaviour,\u0000that make a qualitative breakthrough. We propose to develop a general,\u0000comprehensive embedding framework for multi-omic network data, from models to\u0000efficient and scalable software implementation, and to apply it to biomedical\u0000informatics. It will lead to a paradigm shift in computational and biomedical\u0000understanding of data and diseases that will open up ways to solving some of\u0000the major bottlenecks in precision medicine and other domains.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141062658","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":"Rooting of thornless blackberry cuttings as induced by the extract of white willow (Salix alba L.) shoots collected in different times","authors":"Kocher Omer Salih, Aram Akram Mohammed, Ibrahim Maaroof Noori","doi":"arxiv-2405.08849","DOIUrl":"https://doi.org/arxiv-2405.08849","url":null,"abstract":"The aqueous extract of Salix spp contains many compounds which may act as\u0000root-promoting agents in cuttings. S. alba is a deciduous tree containing\u0000variable phytochemicals which are variable throughout the year. So, in this\u0000study, one- and two-year-old shoots of S. alba were collected on the 15th of\u0000each month in the year 2022, extracted in 2% ethanol at 9 g.L-1, and placed in\u0000a water bath at 35 {deg}C, then they applied to thornless blackberry cuttings\u0000for 1.5 hr. The results explained that the highest rooting percentage (66.67%)\u0000was obtained in the cuttings soaked in the extract of willow shoots collected\u0000on 15th of January. They were not significantly different from control\u0000cuttings, but they were different from the cuttings soaked in the extract of\u0000willow shoots collected on 15th of August and October (33.33%). The majority of\u0000other shoot and root traits were high in the cuttings soaked in the extract of\u0000willow shoots collected on 15th of December. The willow shoots collected on\u000015th of January contained the lowest total phenols (51.4 {mu}g.mL-1) and total\u0000flavonoids (29.07 {mu}g.mL-1). Moreover, the highest total phenols (57\u0000{mu}g.mL-1) and IAA (365.17 {mu}g.mL-1) were recorded in the willow shoots\u0000collected on 15th of March, however each total flavonoids (44.96 {mu}g.mL-1)\u0000and salicylic acid (492.61 {mu}g.mL-1) were the highest in the willow shoots\u0000collected on 15th of April. Generally, based on rooting percentage, it is\u0000advisable to collect willow shoots on 15th of January and February for\u0000extraction and application to the thornless blackberry cuttings.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141062696","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":"Characterization of mood and emotion regulation in females with PMS/PMDD using near-infrared spectroscopy to assess prefrontal cerebral blood flow and the mood questionnaire","authors":"Makiko Aoki, Masato Suzuki, Satoshi Suzuki, Kosuke Oiwa, Yoshitaka Maeda, Hisayo Okayama","doi":"arxiv-2405.06457","DOIUrl":"https://doi.org/arxiv-2405.06457","url":null,"abstract":"Many sexually mature women experience premenstrual syndrome (PMS) or\u0000premenstrual dysphoric mood disorder (PMDD). Current approaches for managing\u0000PMS and PMDD rely on daily mental condition recording, which many discontinue\u0000due to its impracticality. Hence, there's a critical need for a simple,\u0000objective method to monitor mental symptoms. One of the principal symptoms of\u0000PMDD is a dysfunction in emotional regulation, which has been demonstrated\u0000through brain-function imaging measurements to involve hyperactivity in the\u0000amygdala and a decrease in functionality in the prefrontal cortex (PFC).\u0000However, most research has been focused on PMDD, leaving a gap in understanding\u0000of PMS. Near-infrared spectroscopy (NIRS) measures brain activity by\u0000spectroscopically determining the amount of hemoglobin in the blood vessels.\u0000This study aimed to characterize the emotional regulation function in PMS. We\u0000measured brain activity in the PFC region using NIRS when participants were\u0000presented with emotion-inducing pictures. Furthermore, moods highly associated\u0000with emotions were assessed through questionnaires. Forty-six participants were\u0000categorized into non-PMS, PMS, and PMDD groups based on the gynecologist's\u0000diagnosis. POMS2 scores revealed higher negative mood and lower positive mood\u0000in the follicular phase for the PMS group, while the PMDD group exhibited\u0000heightened negative mood during the luteal phase. NIRS results showed reduced\u0000emotional expression in the PMS group during both phases, while no significant\u0000differences were observed in the PMDD group compared to non-PMS. It was found\u0000that there are differences in the distribution of mood during the luteal and\u0000follicular phase and in cerebral blood flow responses to emotional stimuli\u0000between PMS and PMDD. These findings suggest the potential for providing\u0000individuals with awareness of PMS or PMDD through scores on the POMS2 and NIRS\u0000measurements.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"45 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140938471","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":"Vector-borne threats: Sustainable approaches to their diagnosis and treatment","authors":"Areesha Naveed, Ayesha Haidar, Rameen Atique, Arshi Saeed, Bushra Anwar, Ambreen Talib, Uzma Bilal, Javeria Sharif, Ayesha Nadeem, Ayesha Muazzam, Abdul Samad","doi":"arxiv-2405.06718","DOIUrl":"https://doi.org/arxiv-2405.06718","url":null,"abstract":"Arbovirus is a vital, life-threatening disease worldwide and continues to be\u0000a significant problem while the world is dealing with the major coronavirus\u0000(COVID-19) pandemic. Vectors, mostly mosquitoes and ticks, transmit this\u0000disease. Dengue fever, chikungunya, and Zika viruses are the major threats\u0000because of their high incidence, public health burden, and clinically\u0000significant disease spectrum. These vector-borne disease causes one-fourth of\u0000annual deaths, leading to various infectious diseases. The arbovirus represents\u0000eight different families and 14 genera; most viruses belong to the family\u0000Bunyaviridae, and some also belong to Togaviridae, Reoviridae, and\u0000Flaviviridae. The arbovirus disease was isolated first in tropical and\u0000subtropical regions of South America and Africa and has high significance\u0000because of suitable environmental conditions for virus transmission and vector\u0000expansion. Its transmission cycle ranges from simple to highly complex. DENV is\u0000the most prevalent, results in febrile illness, and has transmission in 128\u0000different countries. CHIKV causes infection in asymptomatic people, and the\u0000problems include nephritis, arthritis, myelitis, and acute encephalopathy.\u0000ZIKV-infected 80% of people are asymptomatic and may cause rashes, myalgia,\u0000fever, headache, and conjunctivitis. Vaccines for DENV are not clinically\u0000available; it is a primary arboviral infection in the world nowadays. The\u0000exposure of arbovirus diseases continues to be a global health problem\u0000regardless of continuing efforts. This review article will overview major\u0000arbovirus diseases and their diagnosis, treatment, and prevention strategies.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"139 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140938472","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 miscalibration of the honeybee odometer","authors":"Laura Luebbert, Lior Pachter","doi":"arxiv-2405.12998","DOIUrl":"https://doi.org/arxiv-2405.12998","url":null,"abstract":"We examine a series of articles on honeybee odometry and navigation published\u0000between 1996 and 2010, and find inconsistencies in results, duplicated figures,\u0000indications of data manipulation, and incorrect calculations. This suggests\u0000that redoing the experiments in question is warranted.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141148718","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 design specification for Critical Illness Digital Twins to cure sepsis: responding to the National Academies of Sciences, Engineering and Medicine Report: Foundational Research Gaps and Future Directions for Digital Twins","authors":"Gary An, Chase Cockrell","doi":"arxiv-2405.05301","DOIUrl":"https://doi.org/arxiv-2405.05301","url":null,"abstract":"On December 15, 2023, The National Academies of Sciences, Engineering and\u0000Medicine (NASEM) released a report entitled: Foundational Research Gaps and\u0000Future Directions for Digital Twins. The ostensible purpose of this report was\u0000to bring some structure to the burgeoning field of digital twins by providing a\u0000working definition and a series of research challenges that need to be\u0000addressed to allow this technology to fulfill its full potential. In the work\u0000presented herein we focus on five specific findings from the NASEM Report: 1)\u0000definition of a Digital Twin, 2) using fit-for-purpose guidance, 3) developing\u0000novel approaches to Verification, Validation and Uncertainty Quantification\u0000(VVUQ) of Digital Twins, 4) incorporating control as an explicit purpose for a\u0000Digital Twin and 5) using a Digital Twin to guide data collection and sensor\u0000development, and describe how these findings are addressed through the design\u0000specifications for a Critical Illness Digital Twin (CIDT) aimed at curing\u0000sepsis.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140938252","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 and validation of a short form of the medication literacy scale for Chinese College Students","authors":"Chen ZhenzhenCollege of Science, Minzu University of China, Beijing, ChinaSchool of Nursing, China Medical University, Shenyang, Liaoning Province, China, Ren JiabaoCollege of Science, Minzu University of China, Beijing, ChinaSchool of Nursing, China Medical University, Shenyang, Liaoning Province, China, Duan TingyuHebei Institute of Communications, Hebei, China, Chen KeDepartment of Social Science and Humanities, Harbin Medical University, Harbin, Heilongjiang Province, China, Hou RuyiSchool of Journalism and Communication, Renmin University of China, Beijing, China, Li YimiaoSchool of Journalism and Communication, Renmin University of China, Beijing, China, Zeng LeixiaoSchool of Journalism and Communication, Renmin University of China, Beijing, China, Meng XiaoxuanTianjin Medical University, Tianjin, China, Wu YiboSchool of Public Health, Peking University, Beijing, China, Liu YuSchool of Nursing, China Medical University, Shenyang, Liaoning Province, China","doi":"arxiv-2405.02853","DOIUrl":"https://doi.org/arxiv-2405.02853","url":null,"abstract":"Medication literacy is integral to health literacy, pivotal for medication\u0000safety and adherence. It denotes an individual's capacity to discern,\u0000comprehend, and convey medication-related information. Existing scales,\u0000however, are time-consuming and predominantly cater to patients and community\u0000dwellers, necessitating a more succinct instrument. This study presents the\u0000development of a brief Medication Literacy Scale (MLS-14) utilizing classical\u0000test theory (CTT) and item response theory (IRT), targeting a college student\u0000demographic. The MLS-14's abbreviated version, a 6-item scale (MLS-SF), was\u0000distilled through CTT and IRT methodologies, engaging 2431 Chinese college\u0000students to scrutinize its psychometric properties. The MLS-SF demonstrated a\u0000Cronbach's {alpha} of 0.765, with three extracted factors via exploratory\u0000factor analysis, accounting for 66% of the cumulative variance. All items\u0000exhibited factor loadings above 0.5. The scale's three-factor structure was\u0000substantiated through confirmatory factor analysis with satisfactory fit\u0000indices (chi2/df=5.11, RMSEA=0.063, GFI=0.990, AGFI=0.966, NFI=0.984,\u0000IFI=0.987, CFI=0.987). IRT modeling confirmed reasonable discrimination and\u0000location parameters for all items, free of differential item functioning (DIF)\u0000by gender. Except for items 4 and 10, the remaining items were informative at\u0000medium theta levels, indicating their utility in assessing medication literacy\u0000efficiently. The developed 6-item Medication Literacy Short Form (MLS-SF)\u0000proves to be a reliable and valid instrument for the expedited evaluation of\u0000college students' medication literacy, offering a valuable addition to the\u0000arsenal of health literacy assessment tools.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"44 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140888915","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 Convergence of AI and Synthetic Biology: The Looming Deluge","authors":"Cindy Vindman, Benjamin Trump, Christopher Cummings, Madison Smith, Alexander J. Titus, Ken Oye, Valentina Prado, Eyup Turmus, Igor Linkov","doi":"arxiv-2404.18973","DOIUrl":"https://doi.org/arxiv-2404.18973","url":null,"abstract":"The convergence of artificial intelligence (AI) and synthetic biology is\u0000rapidly accelerating the pace of biological discovery and engineering. AI\u0000techniques, such as large language models and biological design tools, are\u0000enabling the automated design, build, test, and learning cycles for engineered\u0000biological systems. This convergence promises to democratize synthetic biology\u0000and unlock novel applications across domains from medicine to environmental\u0000sustainability. However, it also poses significant risks around reliability,\u0000dual use, and governance. The opacity of AI models, the deskilling of\u0000workforces, and the outdated nature of current regulatory frameworks present\u0000challenges in ensuring responsible development. Urgent attention is needed to\u0000update governance structures, integrate human oversight into increasingly\u0000automated workflows, and foster a culture of responsibility among the growing\u0000community of bioengineers. Only by proactively addressing these issues can we\u0000realize the transformative potential of AI-driven synthetic biology while\u0000mitigating its risks.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"88 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140828439","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}