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The R Journal (June 2020) 12(1): Complete Issue, The R Foundation

The R Journal

Editorial, Michael J. Kane

Contributed Research Articles

gk: An R Package for the g-and-k and Generalised g-and-h Distributions, Dennis Prangle

NlinTS: An R Package for Causality Detection in Time Series, Youssef Hmamouche

Mapping Smoothed Spatial Effect Estimates from Individual-Level Data: MapGAM, Lu Bai, Daniel L. Gillen, Scott M. Bartell, and Verónica M. Vieira

mudfold: An R Package for Nonparametric IRT Modelling of Unfolding Processes, Spyros E. Balafas, Wim P. Krijnen, Wendy J. Post, and Ernst C. Wit

tsmp: An R Package for Time Series with Matrix Profile, Francisco Bischoff and Pedro Pereira Rodrigues

Individual-Level Modelling of Infectious Disease Data: EpiILM, …

2020 O'Callahan Society Newsletter, O'Callahan Society, College Of The Holy Cross

O'Callahan Society Newsletters

This annual newsletter of the O'Callahan Society includes articles about the Class of 2020 virtual Commencement and includes excerpts from a speech by Dr. Anthony Fauci '62, the USS Thresher Memorial, Midshipman 1/C Benjamin Chiacchia, commemoration of the 75th anniversary of the bombing of the USS Franklin, unit news, alumni news, the 2019 annual meeting, retirement of Captain Larry G. McCullen as Commander of the Holy Cross NROTC Unit, ongoing O'Callahan Society programs, publications, and a list of alumni buried in Arlington National Cemetery.

2019 Annual Dinner, which highlighted 1968 - a pivotal year in the Vietnam War when public …

Cartography Of Opportunistic Pathogens And Antibiotic Resistance Genes In A Tertiary Hospital Environment, Kern Rei Chng, Chenhao Li, Denis Bertrand, Amanda Hui Qi Ng, Junmei Samantha Kwah, Hwee Meng Low, Chengxuan Tong, Maanasa Natrajan, Michael Hongjie Zhang, Licheng Xu, Karrie Kwan Ki Ko, Eliza Xin Pei Ho, Tamar V. Av-Shalom, Jeanette Woon Pei Teo, Chiea Chuen Khor

Journal Articles

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic …

Evidence Of Pathogen-Induced Immunogenetic Selection Across The Large Geographic Range Of A Wild Seabird, Hila Levy, Stephen R. Fiddaman, Julianna A. Vianna, Daly Noll, Gemma Clucas, Jasmine K. H. Sidhu, Michael J. Polito, Charles A. Bost, Richard A. Phillips, Sarah Crofts, Gary D. Miller, Pierre Pistorius, Francesco Bonnadonna, Celine Le Bohec, Andres Barbosa, Phil Trathan, Andrea Raya Rey, Laurent A. F. Frantz, Tom Hart, Adrian L. Smith

Faculty Publications

Over evolutionary time, pathogen challenge shapes the immunepheno type of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between ''different clades. Inthis study, we examine the …

These 5 Habits Can Make Public Transportation Safer During Covid-19, Haley Herfurth

Browse All News

No abstract provided.

Artificial Intelligence-Powered Search Tools And Resources In The Fight Against Covid-19., Larry J Kricka, Sergei Polevikov, Jason Y Park, Paolo Fortina, Sergio Bernardini, Daniel Satchkov, Valentin Kolesov, Maxim Grishkov

Department of Cancer Biology Faculty Papers

Emerging technologies are set to play an important role in our response to the COVID-19 pandemic. This paper explores three prominent initiatives: COVID-19 focused datasets (e.g., CORD-19); Artificial intelligence-powered search tools (e.g., WellAI, SciSight); and contact tracing based on mobile communication technology. We believe that increasing awareness of these tools will be important in future research into the disease, COVID-19, and the virus, SARS-CoV-2.

Vitamin D Status Is Not Associated With Cognitive Or Motor Function In Pre-School Ugandan Children, Agnes M. Mutua, Margaret Nampijja, Alison M. Elliott, John M. Pettifor, Thomas N. Williams, Amina Abubakar, Emily L. Webb, Sarah H. Atkinson

Institute for Human Development, East Africa

Vitamin D deficiency is common worldwide and young children are among the most affected groups. Animal studies suggest a key role for vitamin D in brain development. However, studies investigating the effects of vitamin D on neurobehavioural outcomes in children are inconclusive and evidence is limited in sub-Saharan Africa. We evaluated the effect of vitamin D status on cognitive and motor outcomes using prospective data from the Entebbe Mother and Baby Study birth cohort. We analysed data from 302 Ugandan children with 25-hydroxyvitamin D (25(OH)D) measurements below five years and developmental measures at five years of age. We used multivariable …

Relationships Of P16 Immunohistochemistry And Other Biomarkers With Diagnoses Of Cervical Abnormalities: Implications For Last Terminology, Philip E. Castle, Rachael Adcock, Jack Cuzick, Nicolas Wentzensen, Norah E. Torrez-Martinez, Salina M. Torres, Mark H. Stoler, Brigitte M. Ronnett, Nancy E. Joste, Teresa M. Darragh, Patti E. Gravitt, Mark Schiffman, William C. Hunt, Walter K. Kinney, Cosette M. Wheeler

Pathology Research and Scholarship

CONTEXT.—: Lower Anogenital Squamous Terminology (LAST) standardization recommended p16

OBJECTIVE.—: To describe the relationships of p16 IHC and other biomarkers associated with cervical cancer risk with biopsy diagnoses.

DESIGN.—: A statewide, stratified sample of cervical biopsies diagnosed by community pathologists (CPs), including 1512 CIN2, underwent a consensus, expert pathologist panel (EP) review (without p16 IHC results), p16 IHC interpretation by a third pathology group, and human papillomavirus (HPV) genotyping, results of which were grouped hierarchically according to cancer risk. Antecedent cytologic interpretations were also available.

RESULTS.—: Biopsies were more likely to test p16 IHC positive with increasing severity of CP …

Editorial, Michael J. Kane

The R Journal

Onbehalf of the editorial board, I am pleased to present Volume 12, Issue 1 of the R Journal and mysecond issue as the Editor in Chief. Since the last issue Simon Urbanek has joined the editorial board and we have made a few structural changes. First, the R Foundation has approved the R Journal having Associate Editors. This change will allow us to address the increase in submission volume. The addition of the new AE positions should help alleviate some of the workload the editors have been dealing with and will result in shorter turn-around times for submissions. Second, complete …

Individual-Level Modelling Of Infectious Disease Data: Epiilm, Vineetha Warriyar, Waleed Almutiry, Rob Deardon

The R Journal

In this article we introduce the R package EpiILM, which provides tools for simulation from, and inference for, discrete-time individual-level models of infectious disease transmission proposed by Deardon et al. (2010). The inference is set in a Bayesian framework and is carried out via Metropolis Hastings Markov chain Monte Carlo (MCMC). For its fast implementation, key functions are coded in Fortran. Both spatial and contact network models are implemented in the package and can be set in either susceptible-infected (SI) or susceptible-infected-removed (SIR) compartmental frameworks. Use of the package is demonstrated through examples involving both simulated and real data.

Risk Perception, Behavioural Response To Covid-19, And The Mediating Role Of Information Sources In Zambia, Byrne Kaulu, Edna Kabala, Rosemary Mapoma, Christopher Munyonzwe

Southern African Journal of Policy and Development

The role of information sources in mediating the relationship between behavioural responses to COVID-19 and its determinants has hardly been studied. This study fills the knowledge gap with a focus on Zambia, a middle-income country. Data was collected using an online questionnaire. The key independent variables were risk perception of COVID-19, risk perception of the health care system (local and global), and risk perception of the big five global health problems (HIV/AIDS, cancer, injury from road traffic accidents, influenza, and diabetes). Risk perception of the health care system was measured by looking at whether or not the respondents trust the …

Urban Planning: Post Pandemic America, Tess Houseman

City and Regional Planning

Today’s urban planners have little to no experience dealing with pandemics as the modern focus in the field has turned away from infectious disease and public health and realigned itself with modest, long-term, encompassing health goals. Considering this, this analysis will focus on two historical case studies of past pandemics and what took place in their planning aftermath. The information garnered will then be used to hypothesize what new changes to state general plan guidelines may be warranted to mitigate the impacts of future pandemics.

Vanquishing Viruses Is A Blazer Tradition, Haley Herfurth

Browse All News

No abstract provided.

Human Rights And Global Health Emergencies Preparedness, Andrea Boggio

History and Social Sciences Faculty Journal Articles

The spread of infectious disease is always ranked high as a global threat. It features prominently among the list of urgent health challenges for the next decade, issued in early January 2020 by WHO. The emergence of the 2019 Novel Coronavirus (COVID-19) in the Hubei Province in China, is a reminder of global health vulnerabilities.

Quercetin And Vitamin C: An Experimental, Synergistic Therapy For The Prevention And Treatment Of Sars-Cov-2 Related Disease (Covid-19), Ruben Manuel Luciano Colunga Biancatelli, Max Berrill, John D. Catravas, Paul Ellis Marik

Bioelectrics Publications

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) represents an emergent global threat which is straining worldwide healthcare capacity. As of May 27th, the disease caused by SARS-CoV-2 (COVID-19) has resulted in more than 340,000 deaths worldwide, with 100,000 deaths in the US alone. It is imperative to study and develop pharmacological treatments suitable for the prevention and treatment of COVID-19. Ascorbic acid is a crucial vitamin necessary for the correct functioning of the immune system. It plays a role in stress response and has shown promising results when administered to the critically ill. Quercetin is a well-known flavonoid whose antiviral properties …

Palliative Care Challenges And Strategies For The Management Amid Covid-19 Pandemic In India: Perspectives Of Palliative Care Nurses, Cancer Patients, And Caregivers, Radhika Pai, Malathi Nayak, N. Sangeetha

Open Access archive

The WHO selected 2020 to recognize the work of nurses and midwives because it is the bicentenary of the birth of the founder of modern nursing, Florence Nightingale. It has been demonstrated amply now as the nurses are the largest sector of health-care workers in every country, playing a pivotal role in response to the novel coronavirus (COVID-19) pandemic worldwide. Every day, nurses are working tirelessly by leaving their homes to assist the sick, allay community fears, and address concerns. This article is written by interviewing the staff nurses working in the wards/outpatient departments of a reputed palliative care center …

Antibiotic Prescription Practices In Primary Care In Low- And Middle-Income Countries: A Systematic Review And Meta-Analysis, Giorgia Sulis, Pierrick Adam, Vaidehi Nafade, Genevieve Gore

Open Access archive

Background The widespread use of antibiotics plays a major role in the development and spread of antimicrobial resistance. However, important knowledge gaps still exist regarding the extent of their use in low- and middle-income countries (LMICs), particularly at the primary care level. We performed a systematic review and meta-analysis of studies conducted in primary care in LMICs to estimate the prevalence of antibiotic prescriptions as well as the proportion of such prescriptions that are inappropriate. Methods and findings We searched PubMed, Embase, Global Health, and CENTRAL for articles published between 1 January 2010 and 4 April 2019 without language restrictions. …

A Germline Mutation In The Pot1 Gene Is A Candidate For Familial Non-Medullary Thyroid Cancer, Aayushi Srivastava, Beiping Miao, Diamanto Skopelitou, Varun Kumar

Open Access archive

Non-medullary thyroid cancer (NMTC) is a common endocrine malignancy with a genetic basis that has yet to be unequivocally established. In a recent whole-genome sequencing study of five families with occurrence of NMTCs, we shortlisted promising variants with the help of bioinformatics tools. Here, we report in silico analyses and in vitro experiments on a novel germline variant (p.V29L) in the highly conserved oligonucleotide/oligosaccharide binding domain of the Protection of Telomeres 1 (POT1) gene in one of the families. The results showed a reduction in telomere-bound POT1 levels in the mutant protein as compared to its wild-type counterpart. HEK293T cells …

The Genesis Of Sars-Cov-2 Virus And The Origin Of The Covid-19 Pandemic, Alan L. Gillen

Faculty Publications and Presentations

The current outbreak of the 2019 novel coronavirus (SARS-CoV-2, fig. 1), causing a respiratory-tract illness, first started in Wuhan, China, and has been escalating worldwide. The official disease name became known as COVID-19 in mid-spring 2020. It shares some characteristics of the SARS virus of 2002–3. Early on, with many cases in Wuhan, China, it was reported that the outbreak had some association with animal markets, which indicated that there was animal-to-person transmission. Like SARS-CoV-1, the suspected animal source of the virus is bats. We have not seen this virus before, and our bodies were not ready for this, nor …

Nih Funding For Research Underlying New Cancer Therapies, Ekaterina Galkina Cleary, Fred D. Ledley

Natural & Applied Sciences Faculty Publications

Contemporary discovery and development of cancer drugs are based on the model that investments in basic biomedical science will provide insights that can be translated into new cures. In the USA, basic research is primarily funded by the National Institutes of Health (NIH),1 which allocates half of its research budget to basic science,2 with smaller amounts contributed by philanthropy, academics, or industry.1 Basic science is formally defined as the “systematic study directed toward fuller knowledge or understanding of the fundamental aspects of phenomena and observable facts without specific application towards processes or products in mind”.3 However, science is often useinspired,4 …

Sensitivity And Specificity Of Cerebrospinal Fluid Glucose Measurement By An Amperometric Glucometer, Ahmed S. Alkhalifah, Khalid A. Alqatari, Abdullah A. Alkhalifa, Baneen A. Akakah, Zainab S. Alobaid

Saudi Medical Journal

Objectives: To provide more data regarding the role of an amperometric glucometer in diagnosing meningitis. Methods: This is a prospective study conducted at the Pediatric and Neonatology Department, Qatif Central Hospital, Qatif, Saudi Arabia between March 2017 and September 2018. We measured glucose concentrations in cerebrospinal fluid (CSF) and blood using a central laboratory and amperometric glucometer (AG). We compared CSF/blood glucose ratios obtained in a central laboratory from clinical bedside examination with a glucometer, and calculated the sensitivity and specificity for detecting cases of meningitis. Results: A total of 101 patients with clinical suspicion of meningitis were recruited for …

Promoting Healthy Movement Behaviours Among Children During The Covid-19 Pandemic, Hongyan Guan, Anthony D. Okely, Nicolas Aguilar-Farias, Borja Del Pozo Cruz, Catherine E. Draper, Asmaa El Hamdouchi, Alex A. Florindo, Alejandra Jáuregui, Peter T. Katzmarzyk, Anna Kontsevaya, Marie Löf, Wonsoon Park, John J. Reilly, Deepika Sharma, Mark S. Tremblay, Sanne L.C. Veldman

Population and Public Health Science Faculty Publications

No abstract provided.

Labrad : Vol 46, Issue 2 - June 2020, Aga Khan University Hospital, Karachi

LABRAD - Departments of Pathology & Laboratory Medicine and Radiology Archives

• Pathophysiology of Lung Injury in Context with Novel Coronavirus 2019
• Imaging in COVID-19 Pandemic: Salient Features
• Qualitative Real-Time RT-PCR For Detection of SARS-Cov-2 RNA
• Coagulopathy and Anticoagulants in COVID-19
• AKUH Blood Bank During SARS-COV-2 Outbreak
• Significance of COVID-19 Whole Genome Sequencing
• Convalescent Plasma Therapy for COVID-19
• COVID-19: An Alarm Bell for Healthcare System in Pakistan!
• Emergency Online Undergraduate Medial Education During COVID 19
• Adopting Virtual Teaching During the Pandemic-An Overview of the Utility of ‘Microsoft Teams’ from an Educator’s Perspectiv
• The Best of the Recent Past
• Polaroid

Genetic Counseling And Preventive Medicine In Bosnia And Herzegovina, Philip C. Aka

California Western International Law Journal

No abstract provided.

Effects Of Vitamin D Deficiency On Neurobehavioural Outcomes In Children: A Systematic Review, Agnes M. Mutua, Reagan M. Mogire, Alison M. Elliott, Thomas N. Williams, Emily L. Webb, Amina Abubakar, Sarah H. Atkinson

Institute for Human Development, East Africa

Introduction: Vitamin D plays an important role in brain development in experimental studies; however, the effect of vitamin D deficiency on child development remains inadequately characterized. We aimed to estimate the effects of vitamin D deficiency on neurobehavioural outcomes in children up to 18 years of age.

Methods: We searched PubMed, EMBASE, PsycINFO, Scopus, Cochrane Library, Web of Science and Open Grey for published studies up to 10th January 2020. We included all studies that assessed the effects of maternal or child vitamin D status or vitamin D supplementation on neurobehavioural outcomes in children. Study findings were synthesized qualitatively as …

Efficacy Of Bezlotoxumab In Participants Receiving Metronidazole, Vancomycin, Or Fidaxomicin For Treatment Of Clostridioides (Clostridium) Difficile Infection, Erik R. Dubberke, Dale N. Gerding, Ciarán P. Kelly, Kevin W. Garey, Galia Rahav, Audrey Mosley, Robert Tipping, Mary Beth Dorr

Open Access Publications

Background: In phase 3 MODIFY I/II trials, bezlotoxumab significantly reduced recurrence of

Methods: In MODIFY I/II (NCT01241552/NCT01513239), participants received a single infusion of bezlotoxumab (10 mg/kg) or placebo during anti-CDI treatment. Using pooled data from MODIFY I/II, initial clinical cure (ICC) and rCDI were assessed in metronidazole-, vancomycin-, and fidaxomicin-treated subgroups.

Results: Of 1554 participants in MODIFY I/II, 753 (48.5%) received metronidazole, 745 (47.9%) vancomycin, and 56 (3.6%) fidaxomicin. Fewer participants receiving metronidazole had a prior CDI episode in the previous 6 months (12.9%) or ≥1 risk factor for rCDI (66.0%) vs participants receiving vancomycin (41.2% and 83.6%, respectively) and …

A Case Of Pott's Disease: Typical Presentation Of An Uncommon Disease In The United States, Neha Patel, Ravi Patel, Marek Krysztofiak, K V. Sundaresh

West Florida Division GME Research Day 2020

Pott’s disease (PD), also known as tuberculosis spondylitis, is a rare disease of the spine which is typically caused by extraspinal infection. The basic lesion in Pott's disease is a combination of osteomyelitis and arthritis, usually affecting more than one vertebra. The anterior aspect of the vertebral body adjacent to the subchondral plate is commonly involved. Spinal TB can include any of the following: progressive bone destruction leading to vertebral collapse and kyphosis, cold abscess formation (due to extension of infection into adjacent ligaments and soft tissues), spinal canal narrowing by abscesses, granulation tissue or direct dural invasionresulting in spinal …

Pasteurella Multocida Bacteremia Secondary To Multiple Cat Scratches, Charles Boadu, Andrea Hernandez, Bassem Zeidan, John T. Young, Johnathan Frunzi

West Florida Division GME Research Day 2020

Pasteurella multocida(P. multocida)is part of the normal gastrointestinal and upper respiratory flora of domestic and wild animals such as dogs, cats, rabbits, opossums, boars, tigers, lions and horses ^{(1, 2)}. Transmission of P. multocidais usually through scratches and bites leading to infections of the soft tissue and skin ^(3,4). P. multocida bacteremia is rare, but occurs in individuals with major risk factors including chronic pulmonary disease, diabetes mellitus, end state renal disease (ESRD), and an immunocompromised state ^(3,4). Non traumatic infections of P. multocida in immunocompromised individuals,are more likely to require care in the intensive care unit …

Ada News - 06/01/2020, American Dental Association, Publishing Division

ADA News

Established in 1970 as the official newspaper of the American Dental Association, the ADA News serves practicing dentists and others allied to the dental profession in the U.S. and internationally. It is the No. 1 source of news and information about the many benefits and services the ADA delivers to members daily as well as timely information on scientific, social, political and economic developments affecting dentistry and health care.

2020-June-01-Etsu Health Internal Medicine Resident Physician Class Of 2020, University Marketing And Communication, East Tennessee State University

ETSU News

ETSU Health Internal Medicine held its 2020 graduation at the Veterans Administration campus Gazebo on Saturday, May 30.  Due to the current COVID-19 social distancing guidelines, the event was recorded for friends and family to view. 

Twenty-one residents completed their three-year program as required by the ACGME, which will allow these individuals to become Board Certified in Internal Medicine as a field of practice.  They may also continue their education through additional training fellowships within the areas of: cardiology, gastroenterology, rheumatology, endocrinology, oncology, infectious diseases and pulmonology. 

The Department of Internal Medicine congratulates these outstanding individuals for their efforts and …