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OrthReg:a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation

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Zoological Research 2020年第4期41卷 471-475页

作者： Yun-Fei Ma Cui-Ping Huang Fang-Ru Lu Jin-Xiu Li Xu-Man Han adeniyi cadeola Yun Gao Jia-Kun Deng Hai-Bing Xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China University of Chinese Academy of Sciences Beijing100049China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Yunnan UniversityKunmingYunnan 650091China Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province School of Life SciencesYunnan UniversityKunmingYunnan 650091China

DEAR EDITOR,Cis-regulatory elements play an important role in the development of traits and disease in organisms(Ma et al.,2020;Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements(ENCODE)(Davis et al., 2018) and Functional Annotation of Animal Genomes(FAANG)(FAANG Consortium et al., 2015)offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms.

关键词： species. traits regulatory

Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences

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Zoological Research 2020年第1期41卷 51-60页

作者： Xi-Yao Ma Tiao Ning adeniyi cadeola Jie Li Ali Esmailizadeh Jacqueline KLichoti Bernard RAgwanda Jainagul Isakova Almaz AAldashev Shi-Fang Wu He-Qun Liu Najmudinov Tojiddin Abdulloevich Manilova Elena Afanasevna Khudoidodov Behruz Ibrohimovich Rahamon Akinyele Moshood Adedokun Sunday Charles Olaogun Oscar JSanke Godwin FMangbon Xi Chen Wei-Kang Yang Zhe Wang Min-Sheng Peng Sheila COmmeh Yan Li Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan UniversityKunmingYunnan 650091China Agriculture College Kunming UniversityKunmingYunnan 650214China Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province Kunming UniversityKunmingYunnan 650214China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsGermplasm Bank of Wild SpeciesKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Sino-Africa Joint Research Center Chinese Academy of SciencesKunmingYunnan 650223China Department of Animal Science Faculty of AgricultureShahid Bahonar University of KermanKerman PB 76169-133Iran State Department of Livestock Ministry of Agriculture Livestock and FisheriesNairobi 00100Kenya Department of Zoology National Museums of KenyaNairobi 00100Kenya Institute of Molecular Biology and Medicine Bishkek 720040Kyrgyzstan E.N.Pavlovsky Institute of Zoology and Parasitology Academy of Sciences of Republic of TajikistanDushanbe 734025Tajikistan Department of Veterinary Medicine University of IbadanIbadan 200284Nigeria Taraba State Ministry of Agriculture and Natural Resources Jalingo 660221Nigeria Division of Veterinary Office Serti 663101Nigeria Research Center for Ecology and Environment of Central Asia Chinese Academy of SciencesUrumqiXinjiang 830011China Key Laboratory of Biogeography and Bioresource in Arid Land Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiang 830011China Department of Physiology Hebei Medical UniversityShijiazhuangHebei 050017China Hebei Key Laboratory of Animal Science Hebei Medical UniversityShijiazhuangHebei 050017China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China Animal Biotechnology Group Institute of Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairob

Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in ***,domestication histories of these two lineages remain *** therefore compared several population characteristics between these two lineages based on global sampling,which included 171 sequences obtained in this study(including Middle Asian,East Asian,and African samples)plus 536 published sequences(including European,Asian,and African samples).The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop(D-loop)sequences,*** Clade I lineage experienced an increase in population size more than 8000 years ago and shows a complex haplotype *** contrast,the population size of the Clade II lineage has remained relatively constant,with a simpler haplotype *** the distribution of the two lineages was almost equal across the Eurasian mainland,they still presented discernible but complex geographic bias in most parts of Africa,which are known as their domestication *** from sub-Saharan Africa tended to descend from the Clade I lineage,whereas the Clade II lineage was dominant along the East and North coasts of ***,the migration routes inferred from diversity decay suggested different expansion across China between the two ***,these differences indicated non-simultaneous domestication of the two lineages,which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa,respectively.

关键词： Donkey lineage Domestication history Population Expansion

Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

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Zoological Research 2021年第4期42卷 450-460页

作者： Lin Zeng He-Qun Liu Xiao-Long Tu Chang-Mian Ji Xiao Gou Ali Esmailizadeh Sheng Wang Ming-Shan Wang Ming-Cheng Wang Xiao-Long Li Hadi Charati adeniyi cadeola Rahamon Akinyele Moshood Adedokun Olatunbosun Oladipo Sunday Charles Olaogun Oscar JSanke Mangbon Godwin F Sheila Cecily Ommeh Bernard Agwanda Jacqueline Kasiiti Lichoti Jian-Lin Han Hong-Kun Zheng Chang-Fa Wang Ya-Ping Zhang Laurent A.F.Frantz Dong-Dong Wu State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouHainan 571101China College of Animal Science and Technology Yunnan Agricultural UniversityKunmingYunnan 650201China Department of Animal Science Faculty of AgricultureShahid Bahonar University of KermanKermanPB 76169-133Iran Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China Sino-Africa Joint Research Center Chinese Academy of SciencesKunmingYunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China Institute of Three-River-Source National Park Chinese Academy of SciencesXiningQinghai 810008China School of Biological and Chemical Sciences Queen Mary University of LondonLondon E14NSUK Department of Genetics Albert Einstein College of MedicineBronxNew YorkNY 10461USA Annoroad Gene Tech.(Beijing)Co. Ltd.Beijing 100176China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsGermplasm Bank of Wild SpeciesKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Department of Veterinary Medicine University of IbadanIbadan 200284Nigeria Federal College of Animal Health and Production Technology Moor-PlantationIbadan 234102Nigeria Taraba State Ministry of Agriculture and Natural Resources Jalingo 660221Nigeria Division of Veterinary Office Serti 663101Nigeria Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi 62000-00200Kenya Department of Zoology National Museums of KenyaNairobi 40658-00100Kenya State Department of Livestock Ministry of AgricultureLivestockFisheries and IrrigationN

Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan ***,the kiang,a closely related equid species,also inhabits this *** reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan ***,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has *** assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in *** Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high *** addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan *** findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.

关键词： Kiang Donkey High altitude Adaptation Selection

Thermochemical co-conversion of biomass-plastic waste to biochar:a review

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Green Chemical Engineering 2024年第1期5卷 31-49页

作者： Adewale George adeniyi Kingsley O.Iwuozor Ebuka Chizitere Emenike Oluwaseun J.Ajala Samuel Ogunniyi Kabir B.Muritala Department of Chemical Engineering Faculty of Engineering and TechnologyUniversity of IlorinIlorinP.M.B.1515Nigeria Department of Chemical Engineering Landmark UniversityOmu-AranKwara StateP.M.B.1001Nigeria Department of Pure and Industrial Chemistry Nnamdi Azikiwe UniversityAwkaP.M.B.5025Nigeria Department of Chemistry Federal University of TechnologyBosso CampusMinnaNiger StateP.M.B.65Nigeria

Biomass and plastics are two of the most common municipal solid wastes globally that have continuously placed a burden on the *** is therefore important that they are properly *** coconversion offers a valuable opportunity to recycle biomass and plastics simultaneously into biochar,which reduces the time and cost of recycling them individually while producing a material with a wide range of *** study is a review of published literature that discusses the thermochemical co-processing of biomass and plastic wastes into *** was observed that co-pyrolysis and co-hydrothermal carbonization are the most commonly utilized technologies for this *** characteristics of different biomass and plastics that have been thermochemically converted into biochar were *** properties of the resulting biochar are affected by the feedstock composition,pre-treatment and blending ratio,the reactor’s configuration,reaction temperature,and the presence of a *** studies found that treating the feedstocks separately resulted in a lower yield of biochar than processing them *** biochar created by this procedure has been used as a soil additive and as an adsorbent for water *** perspectives and suggestions,such as the necessity for some technical advancement,biochar’s economic benefits,improved government participation,and raised social awareness,were also *** factors have the potential to propel this field of study to great horizons.

关键词： Biomass Co-pyrolysis Plastic Thermochemical process Valorization

A Study of EM Algorithm as an Imputation Method: A Model-Based Simulation Study with Application to a Synthetic Compositional Data

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Open Journal of Modelling and Simulation 2024年第2期12卷 33-42页

作者： Yisa adeniyi Abolade Yichuan Zhao Department of Mathematics and Statistics Georgia State University Atlanta Georgia USA

Compositional data, such as relative information, is a crucial aspect of machine learning and other related fields. It is typically recorded as closed data or sums to a constant, like 100%. The statistical linear model is the most used technique for identifying hidden relationships between underlying random variables of interest. However, data quality is a significant challenge in machine learning, especially when missing data is present. The linear regression model is a commonly used statistical modeling technique used in various applications to find relationships between variables of interest. When estimating linear regression parameters which are useful for things like future prediction and partial effects analysis of independent variables, maximum likelihood estimation (MLE) is the method of choice. However, many datasets contain missing observations, which can lead to costly and time-consuming data recovery. To address this issue, the expectation-maximization (EM) algorithm has been suggested as a solution for situations including missing data. The EM algorithm repeatedly finds the best estimates of parameters in statistical models that depend on variables or data that have not been observed. This is called maximum likelihood or maximum a posteriori (MAP). Using the present estimate as input, the expectation (E) step constructs a log-likelihood function. Finding the parameters that maximize the anticipated log-likelihood, as determined in the E step, is the job of the maximization (M) phase. This study looked at how well the EM algorithm worked on a made-up compositional dataset with missing observations. It used both the robust least square version and ordinary least square regression techniques. The efficacy of the EM algorithm was compared with two alternative imputation techniques, k-Nearest Neighbor (k-NN) and mean imputation (), in terms of Aitchison distances and covariance.

关键词： Compositional Data Linear Regression Model Least Square Method Robust Least Square Method Synthetic Data Aitchison Distance Maximum Likelihood Estimation Expectation-Maximization Algorithm k-Nearest Neighbor and Mean imputation

Smart contract applications in the built environment: How prepared are Nigerian construction stakeholders?

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Frontiers of Engineering Management 2024年第1期11卷 50-61页

作者： Andrew EBEKOZIEN Clinton AIGBAVBOA Samuel adeniyi ADEKUNLE Mohamad Shaharudin SAMSURIJAN John ALIU Bernard Martins ARTHUR-AIDOO Godpower Chinyeru AMADI Department of Construction Management and Quantity Surveying University of JohannesburgJohannesburg 2006South Africa School of Social Sciences Universiti Sains MalaysiaGelugor11800 USM PenangMalaysia Department of Quantity Surveying Auchi PolytechnicAuchiNigeria Institute for Resilient Infrastructure Systems College of EngineeringUniversity of GeorgiaAthensGA 30602USA Department of Building Technology Faculty of Built EnvironmentAccra Technical UniversityAccraGhana Nigerian Institute of Management Port HarcourtNigeria

Studies have demonstrated that advanced technology,such as smart contract applications,can enhance both pre-and post-contract administration within the built environment *** contract technology,exemplifying blockchain technologies,has the potential to improve transparency,trust,and the security of data transactions within this ***,there is a dearth of academic literature concerning smart contract applications within the construction industries of developing countries,with a specific focus on ***,this study seeks to explore the relevance of smart contract technology and address the challenges impeding its adoption,offering strategies to mitigate the obstacles faced by smart contract *** investigate the stakeholders,this research conducted 14 virtual interview sessions to achieve data *** interviewees encompassed project management practitioners,senior management personnel from construction companies,experts in construction dispute resolution,professionals in construction software,and representatives from government construction *** data obtained from these interviews underwent thorough analysis employing a thematic *** study duly recognizes the significance of smart contract applications within the *** the 12 identified barriers,issues such as identity theft and data leakage,communication and synchronization challenges,high computational expenses,lack of driving impetus,excessive electricity consumption,intricate implementation processes,absence of a universally applicable legal framework,and the lack of a localized legal framework were recurrent impediments affecting the adoption of smart contract applications within the *** study also delves into comprehensive measures to mitigate these *** conclusion,this study critically evaluates the relevance of smart contract applications within the built environment,with a specific focus on promoting their *** may serve

关键词： built environment industry digitalization Nigeria smart contract technological revolution

Understanding the impact of HIV on mpox transmission in the MSM population: A mathematical modeling study

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Infectious Disease Modelling 2024年第4期9卷 1117-1137页

作者： Andrew Omame Qing Han Sarafa A.Iyaniwura adeniyi Ebenezer Nicola L.Bragazzi Xiaoying Wang Jude D.Kong Woldegebriel A.Woldegerima Abdus Salam School of Mathematical Sciences Government College UniversityLahorePakistan Laboratory for Industrial and Applied Mathematics(LIAM) Department of Mathematics and StatisticsYork UniversityTorontoOntarioCanada Africa-Canada Artificial Intelligence and Data Innovation Consortium(ACADIC) Canada Theoretical Biology and Biophysics Theoretical DivisionLos Alamos National LaboratoryLos AlamosNM87545USA Postgraduate School of Public Health Department of Health Sciences(DISSAL)University of Genoa16126GenoaItaly United Nations Educational Scientific and Cultural Organization(UNESCO)Health Anthropology Biosphere and Healing SystemsUniversity of Genoa16126GenoaItaly Department of Food and Drugs University of Parma43125ParmaItaly Department of Mathematics Trent University PeterboroughOntarioCanada Artificial Intelligence&Mathematical Modeling Lab(AIMM Lab) Dalla Lana School of Public HealthUniversity of Toronto155 College St Room 500TorontoONM5T 3M7Canada Department of Mathematics University of TorontoOntarioCanada Global South Artificial Intelligence for Pandemic and Epidemic Preparedness and Response Network(AI4PEP) Canada Department of Mathematics Federal University of TechnologyOwerriNigeria

The recent mpox outbreak(in 2022e2023)has different clinical and epidemiological features compared with previous outbreaks of the *** this outbreak,sexual contact was believed to be the primary transmission route of the *** addition,the community of men having sex with men(MSM)was disproportionately affected by the *** population is also disproportionately affected by HIV *** that both diseases can be transmitted sexually,the endemicity of HIV,and the high sexual behavior associated with the MSM community,it is essential to understand the effect of the two diseases spreading simultaneously in an MSM ***,we aim to understand the potential effects of HIV on an mpox outbreak in the MSM *** develop a mechanistic mathematical model of HIV and mpox *** model incorporates the dynamics of both diseases and considers HIV treatment with antiretroviral therapy(ART).In addition,we consider a potential scenario where HIV infection increases susceptibility to mpox,and investigate the potential impact of this mechanism on mpox *** analysis shows that HIV can facilitate the spread of mpox in an MSM population,and that HIV treatment with ART may not be sufficient to control the spread of mpox in the ***,we showed that a moderate use of condoms or reduction in sexual contact in the population combined with ART is beneficial in controlling mpox *** on our analysis,it is evident that effective control of HIV,specifically through substantial ART use,moderate condom compliance,and reduction in sexual contact,is imperative for curtailing the transmission of mpox in an MSM population and mitigating the compounding impact of these intertwined epidemics.

关键词： HIV-mpox co-infection Infectious disease modeling Invasion reproduction number Control reproduction number sensitivity analysis MSM

Detection of Partial and Extended Blockages: A Case Study of Edible Oil Pipeline System

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Journal of Minerals and Materials Characterization and Engineering 2024年第3期12卷 204-223页

作者： Babatunde Victor Omidiji Ayodele Abeeb Daniyan adeniyi Taiwo Kunle Michael Oluwasegun Department of Mechanical Engineering Obafemi Awolowo University Ile-Ife Nigeria Department of Materials Science and Engineering Obafemi Awolowo University Ile-Ife Nigeria Department of Mechanical Engineering First Technical University Ibadan Nigeria Department of Mechanical Engineering University of Manitoba Manitoba Canada

This work focuses on the development and implementation of a simulation-based approach for the detection of partial and extended blockages within an edible oil pipeline system. Blockages, whether partial or extended, pose a significant operational and safety risks. This study employs computational fluid dynamics (CFD) simulations to model the flow behaviour of edible oil through pipeline under varying conditions. It leverages advanced computational fluid dynamics (CFD) simulations to analyze pressure, velocity, and temperature variations along the pipeline. By simulating scenarios with different blockage characteristics, there is establishment of distinctive patterns indicative of partial and extended obstructions. Through extensive analysis of simulation data, sensing element, and monitoring system, processing signal input and response output, the system can accurately pinpoint the location and severity of blockages, providing crucial insights for timely intervention. The detection system represents a significant advancement in pipeline monitoring technology, offering a proactive and accurate approach to identify blockages and mitigate potential risks and ensure the uninterrupted flow of edible oil, thereby enabling timely intervention and maintenance.

关键词： Computational Fluid Dynamics (CFD) Simulations Pipeline Blockages

Does External Debt Promote Human Longevity in Developing Countries?Evidence from West African Countries

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Fudan Journal of the Humanities and Social Sciences 2023年第2期16卷 213-237页

作者： Samson adeniyi Aladejare Department of Economics Federal University WukariWukariNigeria

This study assessed the impact of external debt on longevity in developing countries,particularly in West Africa,from 1981 to *** was proxied by life expectancy at birth,while the study evaluated effects from external debt from the perspective of sustainability,liquidity,and ***,outcomes from macroeconomic volatility were controlled through inflation and exchange rate ***,the robustness of inferences was ensured by using estimated outcomes from the cross-sectional augmented autoregressive distributed lag(CS-ARDL),dynamic common correlated effects(DCCE),and the Driscoll–Kraay(D–K)***,the study showed that unsustainable,illiquid,and insolvent external debt and macroeconomic volatility shorten longevity mainly in the long-term in West African ***,longevity will decline when weak external debt management promotes poverty in developing countries.

关键词： External debt Life expectancy Quality of life Development West Africa