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Articles 1 - 30 of 245

Full-Text Articles in Physical Sciences and Mathematics

Physical Models Of Living Systems Prologue: A Breakthrough On Hiv, Philip C. Nelson Nov 2021

Physical Models Of Living Systems Prologue: A Breakthrough On Hiv, Philip C. Nelson

Department of Physics Papers

No abstract provided.


Poliomyelitis Virus Vs Smallpox: An Ordinary Differential Equation Model Comparison, Kate Mcgough Nov 2021

Poliomyelitis Virus Vs Smallpox: An Ordinary Differential Equation Model Comparison, Kate Mcgough

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Characterizing Long Covid: Deep Phenotype Of A Complex Condition [Preprint], Rachel R. Deer, Feifan Liu, Melissa Haendel, Peter N. Robinson Jun 2021

Characterizing Long Covid: Deep Phenotype Of A Complex Condition [Preprint], Rachel R. Deer, Feifan Liu, Melissa Haendel, Peter N. Robinson

University of Massachusetts Medical School Faculty Publications

Importance Since late 2019, the novel coronavirus SARS-CoV-2 has given rise to a global pandemic and introduced many health challenges with economic, social, and political consequences. In addition to a complex acute presentation that can affect multiple organ systems, there is mounting evidence of various persistent long-term sequelae. The worldwide scientific community is characterizing a diverse range of seemingly common long-term outcomes associated with SARS-CoV-2 infection, but the underlying assumptions in these studies vary widely making comparisons difficult. Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 infection (PASC or “long COVID”), but they are difficult to integrate ...


Covid-19: A One Health Issue, Karen Gruszynski Jun 2021

Covid-19: A One Health Issue, Karen Gruszynski

Cumberland Mountain Naturalist

COVID-19 has very rapidly become part of modern societal lexicon as the disease highlights the importance understanding zoonotic diseases and the impact they can have on human life. With a 177million human cases and 3.82million deaths globally at the time of this publication, the "One Health" nature of the disease has had a lasting impact across the planet. As the disease spread rapidly, it highlighted the dissemination of information through social media and other sources. With this in mind, Dr. Gary Vroegindewey, Director for One Health at LMU-CVM, put forth the idea to have students collect and summarize information ...


Report Of The National Institutes Of Health Sars-Cov-2 Antiviral Therapeutics Summit, Matthew D. Hall, James M. Anderson, Celia A. Schiffer, Anthony J. Conley, Mindy I. Davis Jun 2021

Report Of The National Institutes Of Health Sars-Cov-2 Antiviral Therapeutics Summit, Matthew D. Hall, James M. Anderson, Celia A. Schiffer, Anthony J. Conley, Mindy I. Davis

COVID-19 Publications by UMass Chan Authors

The NIH Virtual SARS-CoV-2 Antiviral Summit, held on November 6, 2020, was organized to provide an overview on the status and challenges in developing antiviral therapeutics for COVID-19, including combinations of antivirals. Scientific experts from the public and private sectors convened virtually during a live videocast to discuss SARS-CoV-2 targets for drug discovery as well as the preclinical tools needed to develop and evaluate effective small molecule antivirals. The goals of the Summit were to review the current state of the science, identify unmet research needs, share insights and lessons learned from treating other infectious diseases, identify opportunities for public-private ...


Spring 2021 May 2021

Spring 2021

Scientia

From the Dean: A Decade of Purpose and Progress; Lab Notes: Alumna Wins Gordon Bell Special Prize, New Scholarships, Vaccination Site Volunteers; Women in Science Lecture, National Institutes of Health Grants, "Unequal Cities" Research; All Hands on Deck: Inspired pandemic approaches showcase interdisciplinary acumen in action; Unlocking Potential: Christopher Beasley thinks psychology is key to academic transformation for the formerly incarcerated; Puzzle Master: Bridget Tenner goes to pieces solving problems in cutting-edge mathematics


Lexicographic Sensitivity Functions For Nonsmooth Models In Mathematical Biology, Matthew D. Ackley May 2021

Lexicographic Sensitivity Functions For Nonsmooth Models In Mathematical Biology, Matthew D. Ackley

Electronic Theses and Dissertations

Systems of ordinary differential equations (ODEs) may be used to model a wide variety of real-world phenomena in biology and engineering. Classical sensitivity theory is well-established and concerns itself with quantifying the responsiveness of such models to changes in parameter values. By performing a sensitivity analysis, a variety of insights can be gained into a model (and hence, the real-world system that it represents); in particular, the information gained can uncover a system's most important aspects, for use in design, control or optimization of the system. However, while the results of such analysis are desirable, the approach that classical ...


Media Analysis Of Coverage Of Environmental Issues In The Midst Of A Pandemic, Alexandria N. Miller, Lucia A. Bolles Apr 2021

Media Analysis Of Coverage Of Environmental Issues In The Midst Of A Pandemic, Alexandria N. Miller, Lucia A. Bolles

Thinking Matters Symposium

This research aimed to answer the question “has the coronavirus impacted the print media’s coverage of important environmental issues?” The research analyzed 2 different print newspapers - The New York Times and the Wall Street Journal - to determine if there was a change in coverage of environmental news as the coronavirus spread in the US. Data for stories published in the first four days of every month from March through September was compiled for 2019 and 2020. Our findings showed a 78.85% decrease in coverage of environmental issues between 2019 and 2020 when stories related to the coronavirus pandemic ...


P14: Emerging Role Of Pharmacists In Treatment And Vaccination For Covid-19, Dwaynie Bacon Jr, Man Ha, Dr. Mandal Apr 2021

P14: Emerging Role Of Pharmacists In Treatment And Vaccination For Covid-19, Dwaynie Bacon Jr, Man Ha, Dr. Mandal

Annual Research Symposium

No abstract provided.


Simulated Contact Tracing Of Covid-19 Propagation At Kutztown University For Fall 2020, Dale E. Parson Apr 2021

Simulated Contact Tracing Of Covid-19 Propagation At Kutztown University For Fall 2020, Dale E. Parson

Computer Science and Information Technology Faculty

From mid-May through August 2020 the author designed, built, revised, and analyzed resulting data from two simulation programs for virtual contact tracing of COVID-19 infection propagation at Kutztown University in the fall 2020 semester. The first was command-line driven and non-graphical, with results distributed to faculty and administrators on May 28. The second was a three-dimensional interactive graphical simulation, distributed to faculty, administrators, and the public as a narrated video via YouTube on July 16. The algorithm is an adaptation of spreading activation as used in theoretical psychology and artificial intelligence research since the 1970s. It propagates discrete, probable infections ...


Flattening The Curve: The Effects Of Intervention Strategies During Covid-19, Kelly A. Reagan, Rachel J. Pryor, Gonzalo M. Bearman, David M. Chan Mar 2021

Flattening The Curve: The Effects Of Intervention Strategies During Covid-19, Kelly A. Reagan, Rachel J. Pryor, Gonzalo M. Bearman, David M. Chan

Spora: A Journal of Biomathematics

COVID-19 has plagued countries worldwide due to its infectious nature. Social distancing and the use of personal protective equipment (PPE) are two main strategies employed to prevent its spread. A SIR model with a time-dependent transmission rate is implemented to examine the effect of social distancing and PPE use in hospitals. These strategies’ effect on the size and timing of the peak number of infectious individuals are examined as well as the total number of individuals infected by the epidemic. The effect on the epidemic of when social distancing is relaxed is also examined. Overall, social distancing was shown to ...


Gene Expression In Tonsils In Swine Following Infection With Porcine Reproductive And Respiratory Syndrome Virus, Qian Dong, Joan K. Lunney, Kyu-Sang Lim, Yet Nguyen, Andrew S. Hess, Hamid Beiki, Raymond R. R. Rowland, Kristen Walker, James M. Reecy, Christopher K. Tuggle, Jack C. M. Dekkers Feb 2021

Gene Expression In Tonsils In Swine Following Infection With Porcine Reproductive And Respiratory Syndrome Virus, Qian Dong, Joan K. Lunney, Kyu-Sang Lim, Yet Nguyen, Andrew S. Hess, Hamid Beiki, Raymond R. R. Rowland, Kristen Walker, James M. Reecy, Christopher K. Tuggle, Jack C. M. Dekkers

Animal Science Publications

Background: Porcine reproductive and respiratory syndrome (PRRS) is a threat to pig production worldwide. Our objective was to understand mechanisms of persistence of PRRS virus (PRRSV) in tonsil. Transcriptome data from tonsil samples collected at 42 days post infection (dpi) were generated by RNA-seq and NanoString on 51 pigs that were selected to contrast the two PRRSV isolates used, NVSL and KS06, high and low tonsil viral level at 42 dpi, and the favorable and unfavorable genotypes at a genetic marker (WUR) for the putative PRRSV resistance gene GBP5.

Results: The number of differentially expressed genes (DEGs) differed markedly between ...


Long-Term Dynamics Of The Kidney Disease Epidemic Among Hiv-Infected Individuals, Heather Gudaz, Henry A. Ogu, Elissa J. Schwartz Feb 2021

Long-Term Dynamics Of The Kidney Disease Epidemic Among Hiv-Infected Individuals, Heather Gudaz, Henry A. Ogu, Elissa J. Schwartz

Spora: A Journal of Biomathematics

One of many risks facing HIV+ individuals is the development of kidney dysfunction and end stage kidney disease (ESKD). A differential equation-based mathematical model was developed to assess the impact of antiretroviral therapy on the progression to kidney disease and on reducing mortality due to kidney failure. Analytical and numerical predictions of long-term HIV+ ESKD prevalence show that therapy can lead to either extremely low levels of disease prevalence or increased prevalence, depending on drug efficacy levels and mechanisms of action. Maintenance of HIV+ ESKD prevalence below one individual is possible with sufficient efficacy (e.g., 99%) against the progression ...


Data For "Arch_Covid_Crowding_Vc", Wayne Freimund, Zachary D. Miller Jan 2021

Data For "Arch_Covid_Crowding_Vc", Wayne Freimund, Zachary D. Miller

Browse all Datasets

Monitoring of visitor use in Arches National Park to assess social distancing behaviors of visitors during the COVID-19 pandemic.


Computing For Numeracy: How Safe Is Your Covid-19 Social Bubble?, Charles Connor Jan 2021

Computing For Numeracy: How Safe Is Your Covid-19 Social Bubble?, Charles Connor

Numeracy

The COVID-19 pandemic has led many people to form social bubbles. These social bubbles are small groups of people who interact with one another but restrict interactions with the outside world. The assumption in forming social bubbles is that risk of infection and severe outcomes, like hospitalization, are reduced. How effective are social bubbles? A Bayesian event tree is developed to calculate the probabilities of specific outcomes, like hospitalization, using example rates of infection in the greater community and example prior functions describing the effectiveness of isolation by members of the social bubble. The probabilities are solved for two contrasting ...


Use Of Lymesim 2.0 To Assess The Potential For Single And Integrated Management Methods To Control Blacklegged Ticks (Ixodes Scapularis; Acari: Ixodidae) And Transmission Of Lyme Disease Spirochetes, Shravani Chitineni, Elizabeth R. Gleim, Holly D. Gaff Jan 2021

Use Of Lymesim 2.0 To Assess The Potential For Single And Integrated Management Methods To Control Blacklegged Ticks (Ixodes Scapularis; Acari: Ixodidae) And Transmission Of Lyme Disease Spirochetes, Shravani Chitineni, Elizabeth R. Gleim, Holly D. Gaff

Undergraduate Honors Theses

Annual Lyme disease cases continue to rise in the U.S. making it the most reported vector-borne illness in the country. The pathogen (Borrelia burgdorferi) and primary vector (Ixodes scapularis; blacklegged tick) dynamics of Lyme disease are complicated by the multitude of vertebrate hosts and varying environmental factors, making models an ideal tool for exploring disease dynamics in a time- and cost-effective way. In the current study, LYMESIM 2.0, a mechanistic model, was used to explore the effectiveness of three commonly used tick control methods: habitat-targeted acaricide (spraying), rodent-targeted acaricide (bait boxes), and white-tailed deer targeted acaricide (4-poster devices ...


Current And Time‐Lagged Effects Of Climate On Innate Immunity In Two Sympatric Snake Species, Lucia L. Combrink, Anne M. Bronikowski, David A. W. Miller, Amanda M. Sparkman Jan 2021

Current And Time‐Lagged Effects Of Climate On Innate Immunity In Two Sympatric Snake Species, Lucia L. Combrink, Anne M. Bronikowski, David A. W. Miller, Amanda M. Sparkman

Ecology, Evolution and Organismal Biology Publications

  1. Changing environments result in alterations at all levels of biological organization, from genetics to physiology to demography. The increasing frequency of droughts worldwide is associated with higher temperatures and reduced precipitation that can impact population persistence via effects on individual immune function and survival.
  2. We examined the effects of annual climate variation on immunity in two sympatric species of garter snakes from four populations in California over a seven‐year period that included the record‐breaking drought.
  3. We examined three indices of innate immunity: bactericidal competence (BC), natural antibodies (NABs), and complement‐mediated lysis (CL).
  4. Precipitation was the only climatic ...


Development Of Environmental Metabarcoding Analysis For Use In Ecological Studies Of Aquatic Fungal And Oomycete Communities Using Nanopore Sequencing, Douglas Bennett Jan 2021

Development Of Environmental Metabarcoding Analysis For Use In Ecological Studies Of Aquatic Fungal And Oomycete Communities Using Nanopore Sequencing, Douglas Bennett

All Master's Theses

One of several factors contributing to amphibian decline are organisms called water molds (oomycetes), which parasitize and kill amphibian and fish eggs, larvae, and occasionally adults. Amphibian decline is one of the most difficult issues facing ecologists and conservationists to date; half of amphibian species are in severe decline and one third of amphibian species are facing extinction, threatening the stability of ecosystems globally. Multiple oomycete species are known to cause the disease saprolegniasis and contribute to amphibian decline; however, the full range of species involved is not presently known. This study evaluated the Oxford Nanopore minION DNA sequencer (R9 ...


Spatio-Temporal Modelling Of Tick Life-Stage Count Data With Spatially Varying Coefficients, Thabo Lephoto, Henry Mwambi, Oliver Bodhlyera, Holly Gaff Jan 2021

Spatio-Temporal Modelling Of Tick Life-Stage Count Data With Spatially Varying Coefficients, Thabo Lephoto, Henry Mwambi, Oliver Bodhlyera, Holly Gaff

Biological Sciences Faculty Publications

There is a vast amount of geo-referenced data in many fields of study including ecological studies. Geo-referencing is usually by point referencing; that is, latitudes and longitudes or by areal referencing, which includes districts, counties, states, provinces and other administrative units. The availability of large geo-referenced datasets for modelling has necessitated the development and application of spatial statistical methods. However, spatial varying coefficients models exploring the abundance of tick counts remain limited. In this study we used data that was collected and prepared by researchers in the Department of Biological Sciences from the Old Dominion University, Virginia, USA. We modelled ...


Kynurenic Acid May Underlie Sex-Specific Immune Responses To Covid-19, Yuping Cai, Daniel J. Kim, Takehiro Takahashi, David I. Broadhurst, Hong Yan, Shuangge Ma, Nicholas J. W. Rattray, Arnau Casanovas-Massana, Benjamin Israelow, Jon Klein, Carolina Lucas, Tianyang Mao, Adam J. Moore, M. Catherine Muenker, Ji Eun Oh, Julio Silva, Patrick Wong, Albert I. Ko, Sajid A. Khan, Akiko Iwasaki, Caroline H. Johnson, Yale Impact Research Team Jan 2021

Kynurenic Acid May Underlie Sex-Specific Immune Responses To Covid-19, Yuping Cai, Daniel J. Kim, Takehiro Takahashi, David I. Broadhurst, Hong Yan, Shuangge Ma, Nicholas J. W. Rattray, Arnau Casanovas-Massana, Benjamin Israelow, Jon Klein, Carolina Lucas, Tianyang Mao, Adam J. Moore, M. Catherine Muenker, Ji Eun Oh, Julio Silva, Patrick Wong, Albert I. Ko, Sajid A. Khan, Akiko Iwasaki, Caroline H. Johnson, Yale Impact Research Team

Research outputs 2014 to 2021

Coronavirus disease 2019 (COVID-19) has poorer clinical outcomes in males than in females, and immune responses underlie these sex-related differences. Because immune responses are, in part, regulated by metabolites, we examined the serum metabolomes of COVID-19 patients. In male patients, kynurenic acid (KA) and a high KA–to–kynurenine (K) ratio (KA:K) positively correlated with age and with inflammatory cytokines and chemokines and negatively correlated with T cell responses. Males that clinically deteriorated had a higher KA:K than those that stabilized. KA inhibits glutamate release, and glutamate abundance was lower in patients that clinically deteriorated and correlated with ...


Physical Models Of Living Systems 2nd Ed, New Chapter: Demographic Variation In Epidemic Spread, Philip C. Nelson Dec 2020

Physical Models Of Living Systems 2nd Ed, New Chapter: Demographic Variation In Epidemic Spread, Philip C. Nelson

Department of Physics Papers

This chapter extends the first edition of Physical Models of Living Systems (WH Freeman 2015). This preliminary version is made freely available as-is in the hope that it will be useful.


The Values And Limitations Of Mathematical Modelling To Covid-19 In The World: A Follow Up Report, Yuanji Tang, Sherry Tang, Shixia Wang Dec 2020

The Values And Limitations Of Mathematical Modelling To Covid-19 In The World: A Follow Up Report, Yuanji Tang, Sherry Tang, Shixia Wang

COVID-19 Publications by UMass Chan Authors

We previously described a mathematical model to simulate the course of the COVID-19 pandemic and try to predict how this outbreak might evolve in the following two months when the pandemic cases will drop significantly. Our original paper prepared in March 2020 analyzed the outbreaks of COVID-19 in the US and its selected states to identify the rise, peak, and decrease of cases within a given geographic population, as well as a rough calculation of accumulated total cases in this population from the beginning to the end of June 2020. The current report will describe how well the later actual ...


Applying Immuno-Epidemiology Principles To Violence, Anna H. Sisk, Nina H. Fefferman, Judy Day, Patricia Bamwine Nov 2020

Applying Immuno-Epidemiology Principles To Violence, Anna H. Sisk, Nina H. Fefferman, Judy Day, Patricia Bamwine

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


The Effect Of Fcgammariia Polymorphisms On Dengue Outbreak Severity, Leah Darwin, Richard V. Clarke Nov 2020

The Effect Of Fcgammariia Polymorphisms On Dengue Outbreak Severity, Leah Darwin, Richard V. Clarke

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Modeling And Preparedness: The Transmission Dynamics Of Covid-19 Outbreak In Provinces Of Ecuador, Carlos E. Bustamante Orellana, Jordy Cevallos-Chavez, Cesar Montalvo, Jeff Sulliavan, Edwin Michael, Anuj Mubayi Nov 2020

Modeling And Preparedness: The Transmission Dynamics Of Covid-19 Outbreak In Provinces Of Ecuador, Carlos E. Bustamante Orellana, Jordy Cevallos-Chavez, Cesar Montalvo, Jeff Sulliavan, Edwin Michael, Anuj Mubayi

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


In Silico Modelling For The Treatment Of Gastric Cancer, Leonardo F. Martinez, Diana Gamboa, Paul A. Valle Nov 2020

In Silico Modelling For The Treatment Of Gastric Cancer, Leonardo F. Martinez, Diana Gamboa, Paul A. Valle

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Biophysical And Stable Isotopic Profiles Of The Salmon Louse Lepeophtheirus Salmonis (Krøyer, 1837), Emma Taccardi Aug 2020

Biophysical And Stable Isotopic Profiles Of The Salmon Louse Lepeophtheirus Salmonis (Krøyer, 1837), Emma Taccardi

Electronic Theses and Dissertations

The salmon louse Lepeophtheirus salmonis is a parasitic copepod that infects wild and farmed salmonids throughout the northern hemisphere. L. salmonis represents the largest economic hurdle of the Atlantic salmon (Salmo salar) industry, with an estimated annual cost of nearly $1 billion globally due to production losses and anti-parasitic control measures. Salmon farming in Maine has existed for decades and is a critical economic driver, yet the region is underrepresented in global sea lice research. The aim of this work was to examine parasites in the context of animal trophic transfer and characterize physiological condition by quantifying the flow of ...


Remdesivir For The Treatment Of Covid-19 - Preliminary Report, John H. Beigel, Robert W. Finberg, Actt-1 Study Group Members May 2020

Remdesivir For The Treatment Of Covid-19 - Preliminary Report, John H. Beigel, Robert W. Finberg, Actt-1 Study Group Members

COVID-19 Publications by UMass Chan Authors

BACKGROUND: Although several therapeutic agents have been evaluated for the treatment of coronavirus disease 2019 (Covid-19), none have yet been shown to be efficacious.

METHODS: We conducted a double-blind, randomized, placebo-controlled trial of intravenous remdesivir in adults hospitalized with Covid-19 with evidence of lower respiratory tract involvement. Patients were randomly assigned to receive either remdesivir (200 mg loading dose on day 1, followed by 100 mg daily for up to 9 additional days) or placebo for up to 10 days. The primary outcome was the time to recovery, defined by either discharge from the hospital or hospitalization for infection-control purposes ...


Modeling Vaccination Strategies To Control White-Nose Syndrome In Little Brown Bat Colonies, Eva Cornwell, David Elzinga, Shelby R. Stowe, Alex Capaldi May 2020

Modeling Vaccination Strategies To Control White-Nose Syndrome In Little Brown Bat Colonies, Eva Cornwell, David Elzinga, Shelby R. Stowe, Alex Capaldi

Biology and Medicine Through Mathematics Conference

No abstract provided.


Mathematical Modeling Of The Car T-Cell Therapy, Emek Kose, Elizabeth Zollinger, Samantha Elliott May 2020

Mathematical Modeling Of The Car T-Cell Therapy, Emek Kose, Elizabeth Zollinger, Samantha Elliott

Biology and Medicine Through Mathematics Conference

No abstract provided.