Research papers

World Health Organization 2020 guidelines on physical activity and sedentary behaviour

Fiona Bull, Salih S Al-Ansari, Stuart Biddle, Katja Borodulin, Matthew P. Buman, Greet Cardon, Catherine Carty, Jean‐Philipp…

Objectives To describe new WHO 2020 guidelines on physical activity and sedentary behaviour. Methods The guidelines were developed in accordance with WHO protocols. An expert Guideline Development Group reviewed evidence to assess associations between physical activity and sedentary behaviour for an agreed set of health outcomes and population groups. The assessment used and systematically updated recent relevant systematic reviews; new primary reviews addressed additional health outcomes or subpopulations. Results The new guidelines address children, adolescents, adults, older adults and include new specific recommendations for pregnant and postpartum women and people living with chronic conditions or disability. All adults should undertake 150–300 min of moderate-intensity, or 75–150 min of vigorous-intensity physical activity, or some equivalent combination of moderate-intensity and vigorous-intensity aerobic physical activity, per week. Among children and adolescents, an average of 60 min/day of moderate-to-vigorous intensity aerobic physical activity across the week provides health benefits. The guidelines recommend regular muscle-strengthening activity for all age groups. Additionally, reducing sedentary behaviours is recommended across all age groups and abilities, although evidence was insufficient to quantify a sedentary behaviour threshold. Conclusion These 2020 WHO guidelines update previous WHO recommendations released in 2010. They reaffirm messages that some physical activity is better than none, that more physical activity is better for optimal health outcomes and provide a new recommendation on reducing sedentary behaviours. These guidelines highlight the importance of regularly undertaking both aerobic and muscle strengthening activities and for the first time, there are specific recommendations for specific populations including for pregnant and postpartum women and people living with chronic conditions or disability. These guidelines should be used to inform national health policies aligned with the WHO Global Action Plan on Physical Activity 2018–2030 and to strengthen surveillance systems that track progress towards national and global targets.

Computational Analysis on Numerical Simulation of Internal Flow Physics for Pump as Turbine in Renewable Small Hydro Energy Generation

Jianguo Du, Daniel Adu, Emmanuel Acheaw, Shakir Hafeez, Eric Ofosu Antw

Energy contributes significantly in almost all aspects of human life as well as economic activities and plays a crucial role in the infrastructural development of a county to alleviate poverty. Generating energy from a renewable source such as small hydropower through the application of pump operating as a turbine mode called Pump as Turbine is one of the best alternatives to provide clean and inexpensive energy. Using Pump as Turbine helps in generating reasonably priced hydroelectric power for communities in underdeveloped counties. This study investigates the effects of internal flow behaviour and performance of Pump as Turbine under different rotational speed and flow rate. The rotational speed is an essential physical parameter as it affects the Pump as Turbine operation. A model-specific speed centrifugal pump model with head 32 (m), flow rate of 12.5 (m3/h) and the rotational speed of 2900 rpm, has been selected for the study. Numerical simulations have been conducted using the k-ω turbulence model to solve three-dimensional (3D) equations. The pump mode experimental data were used to confirm the results for better analysis. The results predicted that vortex and turbulent kinetic energy increase per rotational speed increase. Also, at the higher rotational speed, very high recirculation of flow is detected at the blade suction chamber, although the pressure side has a smooth flow. This study provides beneficial information which will serve as a reference to help improve PAT performance along with selecting PAT for a small hydropower site. Future works will consider the impact of blade thickness and cavitation in Pump as Turbine.

Floral Biology and Pollination Efficiency in Yam (Dioscorea spp.)

Jean M. Mondo, Paterne A. Agre, Alex Edemodu, Patrick Adebola, Robert Asiedu, M. O. Akoroda, Asrat Asfaw

Yam (Dioscorea spp.) is a monocotyledonous herbaceous vine cultivated for its starchy underground or aerial tubers in the tropics and subtropics. It is an allogamous and polyploid species that reproduces by both sexual and asexual mechanisms. However, many of the landrace cultivars, including most of the popular varieties, reproduce exclusively by vegetative propagation (planting the tubers). These varieties are either sterile or produce sparse and irregular flowering with high flower abortion rate, low fruit and seed set. Production of crossbreed seeds for genetic improvement and for maintaining genetic diversity in yams is, therefore, mainly achieved through natural or managed pollination. Flowering in yam is mostly dioecious and, in some instances, monoecious. Flowering asynchrony, sticky nature of the pollen grains, and cross incompatibility are among the challenges in making genetic progress in yam breeding. There are many limitations in basic and applied knowledge of yam flower biology and pollination. This paper, therefore, reviews the flowering biology, pollination, and methods of improving pollination efficiency in yam breeding programs.

Cognitive-behavioural reflective training for improving critical thinking disposition of nursing students

Godwin C. Abiogu, Moses Onyemaechi Ede, John J. Agah, Felix Okechukwu Ugwuozor, Maduka L. Nweke, Nneka Nwosu, Ogechi Nnamani…

BACKGROUND/OBJECTIVE: The importance of critical thinking in improving treatment practices in, for instance, the nursing profession, cannot be overemphasized. Despite this importance, empirical studies have shown that helping strategies to train learners on critical thinking disposition are needed. Given this knowledge gap, this study investigated the impacts of cognitive-behavioral reflective training for improving the critical thinking disposition of nursing students. METHOD: Of all the students screened, a total of 167 participants were assigned to the treatment group and waitlisted control group. A researchers-developed training program aimed at improving critical thinking disposition was delivered in English language by therapists. RESULTS: Repeated-measures ANOVA showed that there was no significant difference between the critical thinking disposition of nursing students in the treatment and control groups as measured by CTDI-M at the posttest. At the posttreatment and follow-up measures, there were consistently improved impacts of CBRT on the critical thinking disposition of nursing students in Nigeria as measured by CTDI-M. CONCLUSION: Following the results, we concluded that cognitive-behavioral reflective training was beneficial and had sustained improvement in enhancing the critical thinking disposition of nursing students.

Monkeypox Virus in Nigeria: Infection Biology, Epidemiology, and Evolution

Emmanuel Alakunle, Ugo Moens, Godwin Nchinda, Malachy Ifeanyi Okeke

Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), which is a member of orthopoxvirus genus. The reemergence of MPXV in 2017 (at Bayelsa state) after 39 years of no reported case in Nigeria, and the export of travelers' monkeypox (MPX) from Nigeria to other parts of the world, in 2018 and 2019, respectively, have raised concern that MPXV may have emerged to occupy the ecological and immunological niche vacated by smallpox virus. This review X-rays the current state of knowledge pertaining the infection biology, epidemiology, and evolution of MPXV in Nigeria and worldwide, especially with regard to the human, cellular, and viral factors that modulate the virus transmission dynamics, infection, and its maintenance in nature. This paper also elucidates the role of recombination, gene loss and gene gain in MPXV evolution, chronicles the role of signaling in MPXV infection, and reviews the current therapeutic options available for the treatment and prevention of MPX. Additionally, genome-wide phylogenetic analysis was undertaken, and we show that MPXV isolates from recent 2017 outbreak in Nigeria were monophyletic with the isolate exported to Israel from Nigeria but do not share the most recent common ancestor with isolates obtained from earlier outbreaks, in 1971 and 1978, respectively. Finally, the review highlighted gaps in knowledge particularly the non-identification of a definitive reservoir host animal for MPXV and proposed future research endeavors to address the unresolved questions.

Physics in Africa

Rabia Salihu Sa’id, Ibiyinka Fuwape, Alain M. Dikandé, J. Mimouni, Francis Hasford, Delia A. Haynes, Irvy Ma Gledhill, Georg…

Africa tends to be isolated and sometimes forgotten when it comes to scientific research and in particular physics. But the region has great potential, being home to the youngest population in the world, and despite a variety of issues, there has been steady, albeit uneven progress towards establishing a scientific infrastructure. Ten African researchers discuss the diverse challenges and opportunities faced by physicists across the continent. Ten African researchers discuss the varied challenges and opportunities faced by physicists across the continent. Rabia Salihu Sa’id is a full professor of Atmospheric Physics at Bayero University, Kano, in Nigeria. She holds a PhD, MSc and BSc in Physics and an MSc in Environment and Development, and is an expert in the effects of dust aerosols on climate and air quality measurements. In 2015, she received the OWSD (Organization for Women in Science for the Developing World)/ TWAS (The World Academy of Sciences)/Elsevier Foundation Award for Early Career (Physics), which rewards and encourages women working and living in developing countries who are in the early stages of their scientific careers, having often overcome great challenges to achieve research excellence. Ibiyinka Fuwape has been a professor of physics at the Federal University of Technology, Akure, Nigeria since 1989. She is currently the Vice Chancellor of the Michael and Cecilia Ibru University, Agbarha-Otor, Delta State, Nigeria. Her research interests include theory of chaos and application of nonlinear dynamics in coupled oscillator systems, neuronal systems, and lower and upper atmospheric research. She is an alumna of the Schlumberger Faculty of the Future Fellowship programme. Alain Moise Dikandé (full professor in physics) is Head of the Physics Department, Faculty of Science, University of Buea, Cameroon. He is an Alexander von Humboldt Fellow in the ‘Experienced Researchers’ Category, a Senior Associate of the Abdus Salam International Centre for Theoretical Physics (ICTP, Trieste, Italy), guest editor of the special issue of the Journal of the Optical Society of America (JOSA A and B): Optics in Africa and member of the editorial board of Journal of Optics. Jamal Mimouni is an Algerian astrophysicist, who received his higher education between Algiers University and the United States (PhD in Particle Physics in 1985, University of Pennsylvania). He is the head of a graduate programme in astrophysics at Constantine 1 University in Algeria, and the President of the African Astronomical Society. He is an active participant in the debate on science and society in the Arab-Muslim World. Francis Hasford is the Head of Medical Physics at the University of Ghana and Ghana Atomic Energy Commission, Secretary General of the Federation of African Medical Physics Organizations, expert medical physicist for the International Atomic Energy Agency and member of the IOMP (International Organization for Medical Physics) Web Sub-committee. He received his PhD from the University of Ghana and is an associate of the International Centre for Theoretical Physics. He is the recipient of the 2016 International Union of Pure and Applied Physics (IUPAP)/IOMP Young Scientist Award in Medical Physics. Delia Haynes did her PhD at Trinity Hall at the University of Cambridge, followed by a postdoctoral fellowship with the Pfizer Institute for Pharmaceutical Materials Science, also at Cambridge. She has been at Stellenbosch University since 2007, where she is now a professor in the Department of Chemistry and Polymer Science. Delia is the chair of the Steering Committee to form the African Crystallographic Association. Irvy (Igle) Gledhill spent time at the University of California, Los Angeles and Stanford before moving to the Council for Scientific and Industrial Research in South Africa, her home country. She is now Visiting Professor of Flow Physics at the University of the Witwatersrand. She is a past president of the South African Institute of Physics and a Vice-President of the Network of African Science Academies. She edits . George Amolo is a professor of physics and Director of the School of Physics and Earth Science, The Technical University of Kenya, Nairobi, and a research associate in Computational Modelling and Materials Science with the Kenya Education Network (KENET). He received his PhD from the University of the Witwatersrand, South Africa, and worked in the University of Eldoret and Moi University, Eldoret, Kenya, before moving to the Technical University of Kenya in 2016. Omololu Akin-Ojo received his BSc and MSc Physics degrees from the University of Ibadan, and his PhD from the University of Delaware (USA). Following two postdoctoral stints at Boston University and the Abdus Salam International Centre for Theoretical Physics (ICTP) Trieste, Italy, he returned to Africa — first to Nigeria and now Rwanda as Director of the East African Institute for Fundamental Research , a physics training and research hub. His main research interest is in condensed matter physics and its applications for African development and advancement. Nashwa Eassa is an associate professor of physics and the Dean of the Deanship of Scientific Research at Al Neelain University. She undertook a postdoctoral fellowship in the Nanophotonics group at Nelson Mandela Metropolitan University (NMMU), South Africa. She holds a PhD in physics from NMMU and Master of Science in material physics and nanotechnology from Linköping University, Sweden.

Array programming with NumPy

Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, J…

Abstract Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves 1 and in the first imaging of a black hole 2 . Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis.

A Review of the Biology and Control of Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), with Special Reference to Biological Control Using Entomopathogenic Fungi

Ibrahim Sani, Siti Izera Ismail, Sumaiyah Abdullah, Johari Jalinas, Syari Jamian, Norsazilawati Saad

Whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), consists of genetically diverse species known to cause significant destruction in several crops around the world. Nymphs and adults of B. tabaci cause damage to plants during feeding, and they can act as a virus vector, thus causing significant yield loss to crops in the tropical and subtropical regions. Chemical pesticides are widely used to control B. tabaci due to their immediate action, but this approach has several drawbacks including food safety issues, insecticide resistance, environmental pollution, and the effect on non-target organisms. A biological control agent using entomopathogenic fungi (EPF) has therefore been developed as an alternative against the conventional use of chemical pesticides in an integrated pest management (IPM) system to effectively control B. tabaci. It is apparent from this review that species of hyphomycetes fungi are the most common EPF used to effectively control B. tabaci, with the second instar being the most susceptible stage of infection. Therefore, this review article focuses specifically on the control of B. tabaci with special emphasis on the use of EPF as biological control agents and their integration in IPM.

The Effectiveness of Multimedia Instructional Learning Packages in Enhancing Secondary School Students’ Attitudes toward Biology

Bukola Omowumi Akinbadewa, Olaniyi Alaba Sofowora

The study investigated the effectiveness of multimedia learning packages in improving the attitudes of students toward learning Biology in secondary schools. The study employed a quantitative and qualitative research approach. The population for the study consisted of all students offering Biology as a subject in the senior secondary schools in Ibadan North Local Government Area of Nigeria, from where a sample of 80 students was randomly selected from three secondary schools and assigned to three groups (one control and two experimental groups). Two multimedia instructional learning packages (MILP) were designed for the study. The topic treated was Cell Division, and the study lasted for six weeks. The packages and all instruments used were validated for content and construct validity, and reliability test was also done. The results showed that multimedia instructional packages used in teaching and learning Biology in secondary schools enhanced better students’ engagements and positive attitudes toward learning. It was concluded that students developed positive attitudes toward learning Biology after using the packages and that multimedia instructional packages are an interesting and creative method of teaching, learning, and enhancing positive attitudes towards learning among secondary school students.

Molecular Biology and Epidemiology of Neurotropic Viruses

Abba Musa Abdullahi, Shah T Sarmast, Romil Singh

Neurotropic viruses are those viruses that can cause central nervous system (CNS) diseases with both neuroinvasive and neurovirulence properties. It comprises a wide range of viruses, including herpes simplex virus, poliovirus, enteroviruses, parechovirus, West Nile virus, Japanese encephalitis virus, measles, and mumps viruses among others. Some of these viruses are highly neuroinvasive and neurovirulent, while others are weakly neuroinvasive and neurovirulent. Moreover, some of them, like herpes simplex viruses, are highly neuroinvasive but weakly neurovirulent for the peripheral nervous system and highly neurovirulent but weakly neuroinvasive for the central nervous system. All these disparities are a result of differences in their genomic constitution, associated vectors, geographical region, and environmental factors. Therefore, a successful intervention will be almost impossible without a clear understanding of the molecular biology and epidemiology of these viruses. Thus, we conducted a review of the published studies on the molecular biology and epidemiology of the common neurotropic viruses to make the viral genetic makeup more understandable for targeted intervention and provide the morbidity and mortality data of the different neurotropic viruses for more serious action.

Characterization of complex fluvio–deltaic deposits in Northeast China using multi-modal machine learning fusion

Cyril D. Boateng, Li‐Yun Fu, Sylvester K. Danuor

Due to the lack of petroleum resources, stratigraphic reservoirs have become an important source of future discoveries. We describe a methodology for predicting reservoir sands from complex reservoir seismic data. Data analysis involves a bio-integrated framework called multi-modal machine learning fusion (MMMLF) based on neural networks. First, acoustic-related seismic attributes from post-stack seismic data were used to characterize the reservoirs. They enhanced the understanding of the structure and spatial distribution of petrophysical properties of lithostratigraphic reservoirs. The attributes were then classified as varied modal inputs into a central fusion engine for prediction. We applied the method to a dataset from Northeast China. Using seismic attributes and rock physics relationships as input data, MMMLF was performed to predict the spatial distribution of lithology in the Upper Guantao substrata. Despite the large scattering in the acoustic-related data properties, the proposed MMMLF methodology predicted the distribution of lithological properties through the gamma ray logs. Moreover, complex stratigraphic traps such as braided fluvial sandstones in the fluvio-deltaic deposits were delineated. These findings can have significant implications for future exploration and production in Northeast China and similar petroleum provinces around the world.

Dementia prevention, intervention, and care: 2020 report of the Lancet Commission

Gill Livingston, Jonathan Huntley, Andrew Sommerlad, David Ames, Clive Ballard, Sube Banerjee, Carol Brayne, Alistair Burns,…

ENHANCING STUDENTS' ATTITUDE AND ACHIEVEMENT IN BIOLOGY THROUGH INNOVATIVE STRATEGIES

Martha Ijok Adibe Njoku, Chinwe Nwagbo

In this research, the impact of peer tutoring and group tutoring led to team learning approaches on the attitude of the students towards and achievement in biology. The thesis had been motivated by four research questions and six null hypotheses. The research had used a quasi-experimental method. In particular, the design of the un-equivalent control group. The sample size was 182 SS 1 students from the four sampled government senior high schools in Port-Harcourt metropolis, River State, Nigeria in four intact classrooms. Two of the classes were exposed to peer tutoring while the remaining two were exposed to peer-led team learning strategies. Biology Attitudinal Scale (BAS), and Biology Achievement Test (BAT) were data collection instruments. BAS construct validity was developed using factor analysis, while BAT material validity was calculated using the specification table. Reliability for BAS and BAT was obtained using formula 20 (K-R 20) from Cronbach Alpha and Kudar-Richardson. Mean and the standard deviation was used to answer the study questions while Covariance analysis (ANCOVA) was used to evaluate the hypotheses at 0.05 significance point. The findings showed that peer-led team learning approach is better than peer tutoring in enhancing the attitude and achievement of the students in biology. The implications of the findings were highlighted and recommendations made.

Review of Particle Physics

Particle Data Group, P. Żyła, R.M. Barnett, J. Beringer, O. I. Dahl, D. A. Dwyer, D. E. Groom, C -J Lin, K. S. Lugovsky, E. …

Abstract The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,324 new measurements from 878 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on High Energy Soft QCD and Diffraction and one on the Determination of CKM Angles from B Hadrons. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 98 review articles. Volume 2 consists of the Particle Listings and contains also 22 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print and as a web version optimized for use on phones as well as an Android app.

A Mathematical Theory of Evidence

Glenn Shafer

Both in science and in practical affairs we reason by combining facts only inconclusively supported by evidence. Building on an abstract understanding of this process of combination, this book constructs a new theory of epistemic probability. The theory draws on the work of A. P. Dempster but diverges from Depster's viewpoint by identifying his as epistemic probabilities and taking his rule for combining upper and lower as fundamental. The book opens with a critique of the well-known Bayesian theory of epistemic probability. It then proceeds to develop an alternative to the additive set functions and the rule of conditioning of the Bayesian theory: set functions that need only be what Choquet called monotone of order of infinity. and Dempster's rule for combining such set functions. This rule, together with the idea of weights of evidence, leads to both an extensive new theory and a better understanding of the Bayesian theory. The book concludes with a brief treatment of statistical inference and a discussion of the limitations of epistemic probability. Appendices contain mathematical proofs, which are relatively elementary and seldom depend on mathematics more advanced that the binomial theorem.

Comparative Effect of Cooperative Learning on Students’ Performance in Mechanics Concepts: A Case of Two Secondary Schools in Berekum Municipality, Ghana

Eric Appiah-Twumasi, Victor Antwi, Ishmael Kwesi Anderson, Nelly Adjoa Sakyi-Hagan

The study sought to establish differences in the effect of cooperative learning strategy with and without the instructional manual on the Senior High School students’ performance in Mechanics concepts in Physics in the Berekum Municipality, Ghana. The research design employed in this study was the experimental using the pretest and posttest equivalent control group design. A sample of 93 SHS 2 students, drawn from two intact classes was used. An instrument known as Mechanics Concepts Test (MCT) was employed in data gathering. Mean score, standard deviation; t-test, mean gain and effect size analysis were used to answer the research questions, while the independent sample t-test was used to test a hypothesis. The results revealed that students taught using the cooperative learning strategy with the instructional manual performed significantly better in the Mechanics Concepts Test (MCT) than those taught using the cooperative learning strategy only. Therefore, it is recommended that physics teachers should use the cooperative learning strategy along with the instructional manual in order to enhance the performance of students in secondary schools.

A close look at the biology of SARS-CoV-2, and the potential influence of weather conditions and seasons on COVID-19 case spread

Kamoru A. Adedokun, Ayodeji Oluwadare Olarinmoye, Jelili Olaide Mustapha, Ramat T. Kamorudeen

BACKGROUND: There is sufficient epidemiological and biological evidence of increased human susceptibility to viral pathogens such as Middle East respiratory syndrome coronavirus, respiratory syncytial virus, human metapneumovirus and influenza virus, in cold weather. The pattern of outbreak of the coronavirus disease 2019 (COVID-19) in China during the flu season is further proof that meteorological conditions may potentially influence the susceptibility of human populations to coronaviruses, a situation that may become increasingly evident as the current global pandemic of COVID-19 unfolds. MAIN BODY: A very rapid spread and high mortality rates have characterized the COVID-19 pandemic in countries north of the equator where air temperatures have been seasonally low. It is unclear if the currently high rates of COVID-19 infections in countries of the northern hemisphere will wane during the summer months, or if fewer people overall will become infected with COVID-19 in countries south of the equator where warmer weather conditions prevail through most of the year. However, apart from the influence of seasons, evidence based on the structural biology and biochemical properties of many enveloped viruses similar to the novel severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 (aetiology of COVID-19), support the higher likelihood of the latter of the two outcomes. Other factors that may potentially impact the rate of virus spread include the effectiveness of infection control practices, individual and herd immunity, and emergency preparedness levels of countries. CONCLUSION: This report highlights the potential influence of weather conditions, seasons and non-climatological factors on the geographical spread of cases of COVID-19 across the globe.

Comorbidity and its Impact on Patients with COVID-19

Adekunle Sanyaolu, Chuku Okorie, Aleksandra Marinkovic, Risha Patidar, Kokab Younis, Priyank Desai, Zaheeda Hosein, Inderbir…

Denoising Diffusion Probabilistic Models

Ho, Jonathan, Ajay N. Jain, Pieter Abbeel

DiffuCpG 1. Introduction In this study, we used a generative AI diffusion model to address missing methylation data. We trained the model with Whole-Genome Bisulfite Sequencing data from 26 acute myeloid leukemia samples and validated it with Reduced Representation Bisulfite Sequencing data from 93 myelodysplastic syndrome and 13 normal samples. Additional testing included data from the Illumina 450k methylation array and Single-Cell Reduced Representation Bisulfite Sequencing on HepG2 cells. Our model, DiffuCpG, outperformed previous methods by integrating a broader range of genomic features, utilizing both short- and long-range interactions without increasing input complexity. It demonstrated superior accuracy, scalability, and versatility across various tissues, diseases, and technologies, providing predictions in both binary and continuous methylation states. In this repository, we deposit the code used to build the diffusion models along with necessary example datasets to train and test a diffusion model for methylation imputation purposes. Docker Usage Install Docker Install Docker using the following link:https://docs.docker.com/engine/install/Recommended system specs: Debian 12 bookworm with 16GB RAM or more.Make sure you have the latest Nvidia GPU driver installed and docker can access your Nvidia GPU. Run Docker images with Tissue-specific Models docker pull yay135/diffucpg_tssUse our example to generate input samples with Hi-C matrix and CIS (Confidence Interval Cross Sample) data.docker run -it yay135/diffucpg_tssthenpython generate_train_test_samples.py The tissue-specific models (pytorch) are for CD34+ cells, GBM and BRCA, they are stored in folders named "model*" in the image. Run the Tissue specific modelsdocker run -it yay135/diffucpg_tssthenpython batch_run.py Run Docker images Example Models docker pull yay135/diffucpgIf you do not have a GPU enabled system, pull a CPU-only imagedocker pull yay135/diffucpg_cpuprepare your input data directory, use the following command to print a example input data directorydocker run --rm yay135/diffucpg -e trueassume your data directory name is "input_data"in windowsdocker run --gpus all -v .\input_data\:/data --rm yay135/diffucpgin unix or linuxdocker run --gpus all -v ./input_data:/data --rm yay135/diffucpg Other docker options -d or --device : select which cuda device to run with, default is 0-m or --mingcpg : scan your methyl array, limit only imputing windows with at least m non-missing methyl values, default is m=10-o or --overlap : set number of impute epochs, shift window locations between epochs, get mean imputed values for each CpG location, default is 2example:docker run --gpus all -v ./input_data:/data --rm yay135/diffucpg -d 1 -m 5 -o 3use cuda device 1, min number of non-missing methyl values in a window is 5, overlap epochs 3 The following tutorials are for non-docker usages. 2. Data and Models Example datasets are available for download using "gdown.sh". The example datasets only contain WGBS methylation data. The model is the DDPM diffusion model, the repository contains a complete implementation for 1-dimensional input. Please refer to https://arxiv.org/abs/2006.11239 and https://huggingface.co/blog/annotated-diffusion for more details. 3. How to use 3.1 System Requirements The number of steps in the diffusion process is set to 2000. Imputing a sample requires 2000 steps. Gpu acceleration is preferred. 16GB of RAM is required. The code is fully tested and operational on the following platform: Distributor ID: DebianDescription: Debian GNU/Linux 12 (bookworm)Release: 12Codename: bookworm 3.2 Clone the Current Project Run the following command to clone the project.git clone https://github.com/yay135/DiffuCpG.git 3.4 Configure Environment Make sure you have the following software installed in your system:Python 3.9+Pytorch 2.0.1+ 3.4 Run Training and Testing python run.pyThe script will download necessary data and install dependencies automatically. 4 Data and Script Details 4.1 RAW Data The methylation arrays downloaded are in the folder "raw", each file is a methylation array. The first 2 columns are "chromosome" and "location". The assembly used for mapping in our project is the "GRCH37 primary assembly". It is also downloaded automatically. The rest of the columns in each file are methylation levels(required) and other biological data (optional) you wish to incorporate to enhance the model. These files in the raw folder are the initial inputs for pipeline,if you wish to use your own data, it must be configured as such before running the pipeline. 4.2 Generate Sample Use script "generate_samples.py" to generate samples for training and testing.The model can not directly read and impute a methylation array file. Instead, each methylation array is divided into windows, each window is 1kb (1000 base pairs) in length, and each training testing sample is generated from a window. Each sample contains at least 5 channels. the first 4 is the sequence one-hot encoding, the 5th is the methylation data. If a base pair location is not a CpG location, the methylation data value for it is "-1". If a CpG's methylation data is missing or waiting for imputaion, its value is also "-1". Other biological data can be added as extra channels. Check out example raw files in the folder "raw" to form your own datasets for training and testing sample generation.For each raw file in the "raw" folder, the first 3 columns are chr, loc, and methylation.The rest of the columns are treated as additional channels and will be added to each sample during generation. '-d' or '--folder': specify raw data folder'-i' or '--index' : which column in a raw file is the methylation array'-t' or '--tol' : how many missing methylation value is tolerated(we recommend 0 for generating training samples and -1 for generating testing samples, 0 will force the script to only select from windows with no missings, -1 will tolerate missing as much as possible.)'-c' or '--chr' : limit which chromosome to use, default is "chr#" to use all chromosomes'-w' or '--winsize' : what window size to use, default is 1000 '-m' or '--mincpg': force generate from window to have a minimum number of CpGs, default is 10 '-n' or '--nsample': number of samples to generate per chromosome '-p' or '--output': samples output folder, default is "out" Use script "generate_samples_concat.py" to generate samples from long-range interacting windows such as Hi-C interactions or computed correlation.Check out the example long range file in the folder "data" to form your own long-range interacting windows for sample generation and concatenation. 4.3 Training Script Use diffusion.py to train and test a DDPM model using the generated samples'-t' or '--train_folder' : the folder containing the training samples'-f' or '--model_folder' : the model folder, will be created if it does not exist'-w' or '--win_size' : window size of each sample, default is 1000'-c' or '--channel': channel size of each sample'-d' or '--cuda_device' : if you have multiple cuda gpus, select which gpu to use, default is 0"-e" or "--epoch" : how many epochs for training, default is 2000"-s" or "--earlystop" : whether to use "early stopping" during training, default is False"-p" or "--patience" : patience for early stopping, default is 10 4.4 Imputation Use diffusion_inpainting.py to perform imputation on generated samples.'-t' or '--test_folder' : the folder containing samples for imputation'-o' or '--out_folder': imputed output folder name, default="inpainting_out"'-w' or '--win_size' : window size of each sample, default is 1000'-c' or '--channel': channel size of each sample'-d' or '--cuda_device' : if you have multiple cuda gpus, select which gpu to use, default is 0 Team If you have any questions or concerns about the project, please contact the following team member: Fengyao Yan fxy134@miami.edu

The Biology of Lactoferrin, an Iron-Binding Protein That Can Help Defend Against Viruses and Bacteria

Douglas B. Kell, Eugene L. Heyden, Etheresia Pretorius

Lactoferrin is a nutrient classically found in mammalian milk. It binds iron and is transferred via a variety of receptors into and between cells, serum, bile, and cerebrospinal fluid. It has important immunological properties, and is both antibacterial and antiviral. In particular, there is evidence that it can bind to at least some of the receptors used by coronaviruses and thereby block their entry. Of importance are Heparan Sulfate Proteoglycans (HSPGs) and the host receptor angiotensin-converting enzyme 2 (ACE2), as based on other activities lactoferrin might prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from attaching to the host cells. Lactoferrin (and more specifically enteric-coated LF because of increased bioavailability) may consequently be of preventive and therapeutic value during the present COVID-19 pandemic.

Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility

Melissa Arons, Kelly M Hatfield, Sujan Reddy, Anne Kimball, Allison James, Jesica R. Jacobs, Joanne Taylor, Kevin B. Spicer,…

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can spread rapidly within skilled nursing facilities. After identification of a case of Covid-19 in a skilled nursing facility, we assessed transmission and evaluated the adequacy of symptom-based screening to identify infections in residents. METHODS: We conducted two serial point-prevalence surveys, 1 week apart, in which assenting residents of the facility underwent nasopharyngeal and oropharyngeal testing for SARS-CoV-2, including real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), viral culture, and sequencing. Symptoms that had been present during the preceding 14 days were recorded. Asymptomatic residents who tested positive were reassessed 7 days later. Residents with SARS-CoV-2 infection were categorized as symptomatic with typical symptoms (fever, cough, or shortness of breath), symptomatic with only atypical symptoms, presymptomatic, or asymptomatic. RESULTS: Twenty-three days after the first positive test result in a resident at this skilled nursing facility, 57 of 89 residents (64%) tested positive for SARS-CoV-2. Among 76 residents who participated in point-prevalence surveys, 48 (63%) tested positive. Of these 48 residents, 27 (56%) were asymptomatic at the time of testing; 24 subsequently developed symptoms (median time to onset, 4 days). Samples from these 24 presymptomatic residents had a median rRT-PCR cycle threshold value of 23.1, and viable virus was recovered from 17 residents. As of April 3, of the 57 residents with SARS-CoV-2 infection, 11 had been hospitalized (3 in the intensive care unit) and 15 had died (mortality, 26%). Of the 34 residents whose specimens were sequenced, 27 (79%) had sequences that fit into two clusters with a difference of one nucleotide. CONCLUSIONS: Rapid and widespread transmission of SARS-CoV-2 was demonstrated in this skilled nursing facility. More than half of residents with positive test results were asymptomatic at the time of testing and most likely contributed to transmission. Infection-control strategies focused solely on symptomatic residents were not sufficient to prevent transmission after SARS-CoV-2 introduction into this facility.

Determinants of depression among nursing students in Cameroon: a cross-sectional analysis

Tsi Njim, Clarence Mbanga, Dave Mouemba, Haman Makebe, Louise Toukam, Belmond Kika, Isabelle Mulango

Abstract Background Nursing students are highly susceptible to depression given the heavy workload and clinical demands of the curriculum. Depression has negative impacts on their health and academic performance. This study aimed to determine the determinants of depression amongst nursing students in the English-speaking regions of Cameroon. Methods A cross-sectional analysis of 447 nursing students recruited from a combination of state-owned and private nursing institutions in the English-speaking regions of Cameroon from January – April 2018 was carried out. Independent correlates of depression were determined using multivariable regression analysis, with the level of significance set at 95%. Results The overall prevalence of depression (Patient Health Questionnaire - 9 > 4) and major depressive disorder (Patient Health Questionnaire - 9 > 9) in these students was 69.57 and 26.40% respectively. Independent correlates of depression were found to be: total Oldenburg Burnout Inventory score (aOR: 1.18; 95% CI: 1.11, 1.25; p value < 0.01); level of studies (aOR: 0.72; 95% CI: 0.55, 0.94; p value = 0.02) and occurrence of a life-changing crises (aOR: 2.13; 95% CI: 1.28, 3.55, p value < 0.01). Conclusion The prevalence of depression amongst nursing students in Cameroon is high. Determinants proposed in this study require further assessment to facilitate early identification and management of depression in this high-risk group, in order to limit the negative effects linked with the condition.

Worldwide Prevalence and Burden of Functional Gastrointestinal Disorders, Results of Rome Foundation Global Study

Ami D. Sperber, Shrikant I. Bangdiwala, Douglas A. Drossman, Uday C. Ghoshal, Magnus Simrén, Jan Tack, William E. Whitehead,…

BACKGROUND & AIMS: Although functional gastrointestinal disorders (FGIDs), now called disorders of gut-brain interaction, have major economic effects on health care systems and adversely affect quality of life, little is known about their global prevalence and distribution. We investigated the prevalence of and factors associated with 22 FGIDs, in 33 countries on 6 continents. METHODS: Data were collected via the Internet in 24 countries, personal interviews in 7 countries, and both in 2 countries, using the Rome IV diagnostic questionnaire, Rome III irritable bowel syndrome questions, and 80 items to identify variables associated with FGIDs. Data collection methods differed for Internet and household groups, so data analyses were conducted and reported separately. RESULTS: Among the 73,076 adult respondents (49.5% women), diagnostic criteria were met for at least 1 FGID by 40.3% persons who completed the Internet surveys (95% confidence interval [CI], 39.9-40.7) and 20.7% of persons who completed the household surveys (95% CI, 20.2-21.3). FGIDs were more prevalent among women than men, based on responses to the Internet survey (odds ratio, 1.7; 95% CI, 1.6-1.7) and household survey (odds ratio, 1.3; 95% CI, 1.3-1.4). FGIDs were associated with lower quality of life and more frequent doctor visits. Proportions of subjects with irritable bowel syndrome were lower when the Rome IV criteria were used, compared with the Rome III criteria, in the Internet survey (4.1% vs 10.1%) and household survey (1.5% vs 3.5%). CONCLUSIONS: In a large-scale multinational study, we found that more than 40% of persons worldwide have FGIDs, which affect quality of life and health care use. Although the absolute prevalence was higher among Internet respondents, similar trends and relative distributions were found in people who completed Internet vs personal interviews.

Journal of Universal Computer Science

Arto Salomaa, Cristian S. Calude, Hermann Maurer

Almost all researchers in computer science have access to Internet by now: with some 2 million Internet nodes at the time of writing an estimated 30 million people can connect to Internet, many of them directly from their desk. Internet has become an increasingly powerful information, communication