{"title":"Mechanical Self-replication","authors":"Ralph P. Lano","doi":"arxiv-2407.14556","DOIUrl":"https://doi.org/arxiv-2407.14556","url":null,"abstract":"This study presents a theoretical model for a self-replicating mechanical\u0000system inspired by biological processes within living cells and supported by\u0000computer simulations. The model decomposes self-replication into core\u0000components, each of which is executed by a single machine constructed from a\u0000set of basic block types. Key functionalities such as sorting, copying, and\u0000building, are demonstrated. The model provides valuable insights into the\u0000constraints of self-replicating systems. The discussion also addresses the\u0000spatial and timing behavior of the system, as well as its efficiency and\u0000complexity. This work provides a foundational framework for future studies on\u0000self-replicating mechanisms and their information-processing applications.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"47 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774446","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}
Belinda Neo, Dale Tilbrook, Noel Nannup, Alison Daly, Eleanor Dunlop, John Jacky, Carol Michie, Cindy Prior, Brad Farrant, Carrington C. J. Shepherd, Lucinda J. Black
{"title":"Quantifying vitamin D intake among Aboriginal and Torres Strait Islander peoples in Australia","authors":"Belinda Neo, Dale Tilbrook, Noel Nannup, Alison Daly, Eleanor Dunlop, John Jacky, Carol Michie, Cindy Prior, Brad Farrant, Carrington C. J. Shepherd, Lucinda J. Black","doi":"arxiv-2407.13797","DOIUrl":"https://doi.org/arxiv-2407.13797","url":null,"abstract":"Background/Objective: Vitamin D deficiency (serum 25-hydroxyvitamin D\u0000[25(OH)D] concentration <50 nmol/L) is prevalent among Aboriginal and Torres\u0000Strait Islander peoples in Australia. Alternative to sun exposure (the primary\u0000source of vitamin D), vitamin D can also be obtained from food (e.g., fish,\u0000eggs, and meat) and supplements. However, vitamin D intake among Aboriginal and\u0000Torres Strait Islander peoples is currently unknown. We aimed to provide the\u0000first quantification of vitamin D intake using nationally representative data\u0000from Aboriginal and Torres Strait Islander peoples. Methods: We used food\u0000consumption data collected in the 2012-2013 National Aboriginal and Torres\u0000Strait Islander Nutrition and Physical Activity Survey (n = 4,109) and vitamin\u0000D food composition data to quantify mean absolute vitamin D intake by sex, age\u0000group, and remoteness of location. Differences in mean vitamin D intake between\u0000sexes and between remoteness of location were assessed using the 95% confidence\u0000interval (95% CI). Results: The mean (standard deviation (SD)) vitamin D intake\u0000among Aboriginal and Torres Strait Islander peoples was 2.9 (3.0) {mu}g/day.\u0000Males had a statistically significantly higher mean (SD) [95% CI] vitamin D\u0000intake (3.2 (3.1) [3.0-3.4] {mu}g/day) than females (2.6 (2.7) [2.4-2.7]\u0000{mu}g/day). There were no statistically significant differences between mean\u0000(SD) [95% CI] vitamin D intake in non-remote (2.9 (2.2) [2.7-3.1] {mu}g/day)\u0000and remote areas (2.8 (4.8) [2.6-3.0] {mu}g/day). Conclusions: Vitamin D\u0000intake among Aboriginal and Torres Strait Islander peoples is low. Food-based\u0000public health strategies could be developed to promote higher vitamin D intake\u0000among this population.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141738505","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}
Trevor Reckell, Beckett Sterner, Petar Jevtić, Reggie Davidrajuh
{"title":"A Numerical Comparison of Petri Net and Ordinary Differential Equation SIR Component Models","authors":"Trevor Reckell, Beckett Sterner, Petar Jevtić, Reggie Davidrajuh","doi":"arxiv-2407.10019","DOIUrl":"https://doi.org/arxiv-2407.10019","url":null,"abstract":"Petri nets are a promising modeling framework for epidemiology, including the\u0000spread of disease across populations or within an individual. In particular,\u0000the Susceptible-Infectious-Recovered (SIR) compartment model is foundational\u0000for population epidemiological modeling and has been implemented in several\u0000prior Petri net studies. However, the SIR model is generally stated as a system\u0000of ordinary differential equations (ODEs) with continuous time and variables,\u0000while Petri nets are discrete event simulations. To our knowledge, no prior\u0000study has investigated the numerical equivalence of Petri net SIR models to the\u0000classical ODE formulation. We introduce crucial numerical techniques for\u0000implementing SIR models in the GPenSim package for Petri net simulations. We\u0000show that these techniques are critical for Petri net SIR models and show a\u0000relative root mean squared error of less than 1% compared to ODE simulations\u0000for biologically relevant parameter ranges. We conclude that Petri nets provide\u0000a valid framework for modeling SIR-type dynamics using biologically relevant\u0000parameter values provided that the other PN structures we outline are also\u0000implemented.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141719309","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":"Automated and Continuous Chronotyping from a Calendar using Machine Learning","authors":"Pratiik Kaushik, Koorosh Askari, Saksham Gupta, Rahul Mohan, Kris Skrinak, Royan Kamyar, Benjamin Smarr","doi":"arxiv-2407.06478","DOIUrl":"https://doi.org/arxiv-2407.06478","url":null,"abstract":"Objectives: Chronotypes -- comparisons of individuals' circadian phase\u0000relative to others -- can contextualize mental health risk assessments, and\u0000support detection of social jet lag, which can hamper mental health and\u0000cognition. Existing ways of determining chronotypes, such as Dim Light\u0000Melatonin Onset (DLMO) or the Morningness-Eveningness Questionnaire (MEQ), are\u0000limited by being discrete in time and time-intensive to update, rarely\u0000capturing real-world variability over time. Chronotyping users based on living\u0000schedules, as in daily planner apps, might augment existing methods by\u0000assessing chronotype and social jet lag continuously and at scale. Developing\u0000this functionality would require a novel tool to translate between digital\u0000schedules and chronotypes. Here we use a supervised binary classifier to assess\u0000the feasibility of this approach. Methods: In this study, 1,460 registered\u0000users from the Owaves app opted in to filled out the MEQ survey. Of those, 142\u0000met the eligibility criteria for data analysis. We used multimodal app data to\u0000assess the classification of individuals identified as morning and evening\u0000types from MEQ data, basing the classifier on app time series data. This\u0000includes daily timing for 8 main lifestyle activity categories (exercise,\u0000sleep, social interactions, meal times, relaxation, work, play, and\u0000miscellaneous) as defined in the app. Results: The novel chronotyping tool was\u0000able to predict the morningness and eveningness of its users with an ROC AUC of\u00000.70. Conclusion: Our findings support the feasibility of chronotype\u0000classification from multimodal, real-world app data. We highlight challenges to\u0000applying binary labels to complex, multimodal behaviors. Our findings suggest a\u0000potential for real-time monitoring to support future, prospective mental health\u0000research.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566350","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}
Ghita Ghislat, Saiveth Hernandez-Hernandez, Chayanit Piwajanusorn, Pedro J. Ballester
{"title":"Challenges with the application and adoption of artificial intelligence for drug discovery","authors":"Ghita Ghislat, Saiveth Hernandez-Hernandez, Chayanit Piwajanusorn, Pedro J. Ballester","doi":"arxiv-2407.05150","DOIUrl":"https://doi.org/arxiv-2407.05150","url":null,"abstract":"Artificial intelligence (AI) is exhibiting tremendous potential to reduce the\u0000massive costs and long timescales of drug discovery. There are however\u0000important challenges limiting the impact and scope of AI models. Typically,\u0000these models are evaluated on benchmarks that are unlikely to anticipate their\u0000prospective performance, which inadvertently misguides their development.\u0000Indeed, while all the developed models excel in a selected benchmark, only a\u0000small proportion of them are ultimately reported to have prospective value\u0000(e.g. by discovering potent and innovative drug leads for a therapeutic\u0000target). Here we discuss a range of data issues (bias, inconsistency, skewness,\u0000irrelevance, small size, high dimensionality), how they challenge AI models and\u0000which issue-specific mitigations have been effective. Next, we point out the\u0000challenges faced by uncertainty quantification techniques aimed at enhancing\u0000these AI models. We also discuss how conceptual errors, unrealistic benchmarks\u0000and performance misestimation can confound the evaluation of models and thus\u0000their development. Lastly, we explain how human bias, whether from AI experts\u0000or drug discovery experts, constitutes another challenge that can be alleviated\u0000with prospective studies.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566349","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}
Styliani-Christina Fragkouli, Dhwani Solanki, Leyla J Castro, Fotis E Psomopoulos, Núria Queralt-Rosinach, Davide Cirillo, Lisa C Crossman
{"title":"Synthetic data: How could it be used for infectious disease research?","authors":"Styliani-Christina Fragkouli, Dhwani Solanki, Leyla J Castro, Fotis E Psomopoulos, Núria Queralt-Rosinach, Davide Cirillo, Lisa C Crossman","doi":"arxiv-2407.06211","DOIUrl":"https://doi.org/arxiv-2407.06211","url":null,"abstract":"Over the last three to five years, it has become possible to generate machine\u0000learning synthetic data for healthcare-related uses. However, concerns have\u0000been raised about potential negative factors associated with the possibilities\u0000of artificial dataset generation. These include the potential misuse of\u0000generative artificial intelligence (AI) in fields such as cybercrime, the use\u0000of deepfakes and fake news to deceive or manipulate, and displacement of human\u0000jobs across various market sectors. Here, we consider both current and future positive advances and possibilities\u0000with synthetic datasets. Synthetic data offers significant benefits,\u0000particularly in data privacy, research, in balancing datasets and reducing bias\u0000in machine learning models. Generative AI is an artificial intelligence genre\u0000capable of creating text, images, video or other data using generative models.\u0000The recent explosion of interest in GenAI was heralded by the invention and\u0000speedy move to use of large language models (LLM). These computational models\u0000are able to achieve general-purpose language generation and other natural\u0000language processing tasks and are based on transformer architectures, which\u0000made an evolutionary leap from previous neural network architectures. Fuelled by the advent of improved GenAI techniques and wide scale usage, this\u0000is surely the time to consider how synthetic data can be used to advance\u0000infectious disease research. In this commentary we aim to create an overview of\u0000the current and future position of synthetic data in infectious disease\u0000research.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566351","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}
T Yahaya, KA Sani, E Oladele, E Yawa, M Musa, M Abubakar, R Sulaiman, M Bilyaminu
{"title":"Cement Dust Exposure and Risk of Hyperglycemia and Overweight among Artisans and Residents Close to a Cement Factory in Sokoto, Nigeria","authors":"T Yahaya, KA Sani, E Oladele, E Yawa, M Musa, M Abubakar, R Sulaiman, M Bilyaminu","doi":"arxiv-2407.00420","DOIUrl":"https://doi.org/arxiv-2407.00420","url":null,"abstract":"The potential health risks of cement dust exposure are increasingly raising\u0000concern worldwide as the cement industry expands in response to rising cement\u0000demand. This necessitates the need to determine the nature of the risks in\u0000order to develop appropriate measures. This study determined the effects of\u0000cement dust exposure on the weight and blood glucose levels of people residing\u0000or working around a cement company in Sokoto, Nigeria. Demographic information\u0000was obtained using questionnaires from 72 participants, which included age,\u0000gender, educational level, exposure hours, occupation, and lifestyle. The blood\u0000glucose levels and body mass index (BMI) were measured using a Fine Test\u0000glucometer and a mechanical scale, respectively. The results showed that most\u0000of the people living or working around the cement company were middle-aged men\u0000(31-40; 42.06%) with a primary (33.33%) or secondary (45.83%) school education.\u0000It showed that 30 (41.69%) of the participants were overweight while 5 (6.94%)\u0000were obese. Additionally, 52.78% of the participants were diabetic while 31.94%\u0000were prediabetic. Participants that were exposed for long hours (> 15 hours per\u0000day) were the most diabetic (20% of the participants), followed by smokers\u0000(15%), and artisans (7%). It can be concluded that exposure to cement dust from\u0000the company increased the risk of overweight, obesity, and hyperglycemia among\u0000the participants. These health risks were worsened by daily long hours of\u0000exposure, smoking, and artisanal pollutant exposure. Human settlements and\u0000artisans should not be located near the cement company, and the company should\u0000minimize pollutant emissions.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141505128","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":"Machine Learning Models for Dengue Forecasting in Singapore","authors":"Zi Iun Lai, Wai Kit Fung, Enquan Chew","doi":"arxiv-2407.00332","DOIUrl":"https://doi.org/arxiv-2407.00332","url":null,"abstract":"With emerging prevalence beyond traditionally endemic regions, the global\u0000burden of dengue disease is forecasted to be one of the fastest growing. With\u0000limited direct treatment or vaccination currently available, prevention through\u0000vector control is widely believed to be the most effective form of managing\u0000outbreaks. This study examines traditional state space models (moving average,\u0000autoregressive, ARIMA, SARIMA), supervised learning techniques (XGBoost, SVM,\u0000KNN) and deep networks (LSTM, CNN, ConvLSTM) for forecasting weekly dengue\u0000cases in Singapore. Meteorological data and search engine trends were included\u0000as features for ML techniques. Forecasts using CNNs yielded lowest RMSE in\u0000weekly cases in 2019.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"57 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141513144","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 behavior of pomegranate (Punica granatum L.) hardwood cuttings in relation to genotype and irrigation frequency","authors":"Kocher Omer Salih, Aram Akram Mohammed, Jamal Mahmood Faraj, Anwar Mohammed Raouf, Nawroz Abdul-Razzak Tahir","doi":"arxiv-2407.00408","DOIUrl":"https://doi.org/arxiv-2407.00408","url":null,"abstract":"The study was conducted to determine the best irrigation frequency for\u0000rooting hardwood cuttings of some pomegranate genotypes that are cultivated in\u0000Halabja province, Kurdistan Region, Iraq. The hardwood cuttings were collected\u0000from 11 genotypes, which were 'Salakhani Trsh' (G1), 'Salakhani Mekhosh' (G2),\u0000'Amriki' (G3), 'Twekl Sury Trsh' (G4), 'Twekl Astury Naw Spy' (G5), 'Hanara\u0000Sherina' (G6), 'Kawa Hanary Sherin' (G7), 'Kawa Hanary Trsh' (G8), 'Malesay\u0000Twekl Asture' (G9), 'Malesay Twekl Tank' (G10), and 'Sura Hanary Trsh' (G11).\u0000The genotypes were subjected to irrigation applications by 1-day, 2-day, 7-day,\u0000or 10-day frequencies. Among pomegranates, G11, G6, and G7 produced 95, 90, and\u000083% rooting percentages, which were significantly higher than the rest of other\u0000genotypes. The lowest rooting percentages (28, 36, 38, and 40%) were found in\u0000G1, G5, G3, and G10, respectively. The effect of irrigation frequencies on the\u0000genotypes confirmed that a 7-day frequency was the best irrigation frequency to\u0000achieve the maximum rooting percentages (93, 86, 80, 73, 53, and 40%) in G6,\u0000G9, G2, G4, G3, and G1, respectively. In contrast, the minimum rooting\u0000percentage (20%) was recorded in G3 with a 1-day frequency and in G1 with\u000010-day frequency. In this study, it was found that the cuttings of G11, G6, and\u0000G7 had the best ability to form roots, and irrigation with a 7-day frequency\u0000was the best for the cuttings of all the 11 pomegranate genotypes investigated.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"163 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141513143","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":"Comparative Evaluation of the Proximate and Cytogenotoxicity of Ash and Rice Chips Used as Mango Fruit Artificial Ripening Agents in Birnin Kebbi, Nigeria","authors":"CD Obadiah, TO Yahaya, AA Aliero, M Abdulkareem","doi":"arxiv-2408.01425","DOIUrl":"https://doi.org/arxiv-2408.01425","url":null,"abstract":"The high demand for mango (Mangifera indica L.) fruits has led sellers to\u0000employ ripening agents. However, concerns are growing regarding the potential\u0000toxicities of induced ripening, emphasizing the need for scientific\u0000investigation. Samples of artificially and naturally ripened mangoes were\u0000analyzed for proximate composition using standard protocols. Cytogenotoxicity\u0000was then assessed using the Allium cepa L. toxicity test. Twenty (20)A. cepa\u0000(onion) bulbs were used, with 5 ripened naturally, 5 with wood ash, 5 with\u0000herbaceous ash, and 5 with rice chips, all grown over tap water for five days.\u0000The root tips of the bulbs were assayed and examined for chromosomal\u0000aberrations. The results revealed a significant (P<0.05) increase in moisture,\u0000protein, and ash content of mangoes as ripening agents were introduced. Mangoes\u0000ripened with wood ash exhibited the highest moisture content (81%), while those\u0000ripened with rice chips had the highest protein (0.5%) and ash content (1.5%).\u0000Naturally ripened mangoes displayed the highest fat (0.0095%) and fiber\u0000(11.46%) contents. The A. cepa toxicity test indicated significant (p<0.05)\u0000differences in the root growth of mangoes ripened with various agents. Wood ash\u0000resulted in the highest root growth (2.62cm), while herbaceous ash had the\u0000least (2.18%). Chromosomal aberrations, including sticky, vagrant, and laggard\u0000abnormalities, were observed in all agents, with herbaceous ash exhibiting the\u0000highest and rice chips the least. The obtained results suggest that induced\u0000ripening of the fruits could induce toxicities, highlighting the necessity for\u0000public awareness regarding the potential dangers posed by these agents.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141933083","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}