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Introduction To The Special Issue On Reproducibility In Neuroimaging, Russell A. Poldrack, Kirstie Whitaker, David N. Kennedy 2019 Stanford University

Introduction To The Special Issue On Reproducibility In Neuroimaging, Russell A. Poldrack, Kirstie Whitaker, David N. Kennedy

Open Access Articles

The last decade has seen increasing attention to the problem of scientific reproducibility, across a broad range of scientific fields (Camerer et al., 2016;Morrison, 2014;Open Science Collaboration, 2015). Within the field of neuroimaging, there has been a particular focus on issues of analytic variability (Bowring et al., 2019;Carp, 2012) statistical power (Button et al., 2013;Poldrack et al., 2017), and test-retest reliability (Bennett and Miller, 2013), all of which have raised alarms regarding the potential for irreproducible results. In addition, failed replications (Boekel et al., 2015;Dinga et al., 2019) and meta-analytic null results (Müller et al ...


#37 - Quantifying Precursors To Algal Blooms In Lake Sidney Lanier, Dakota Boncore 2019 University of North Georgia

#37 - Quantifying Precursors To Algal Blooms In Lake Sidney Lanier, Dakota Boncore

Georgia Undergraduate Research Conference (GURC)

Quantifying Precursors to Algal Blooms in Lake Sidney Lanier

Authors: D.Boncore, M. Flood

Department of Biology, University of North Geogia, Gainesville GA

Lake Sidney Lanier is a 38,000 acre reservoir on the Chestatee River that provides flood control, recreation and fresh water for Atlanta and Gainesville, among other municipalities. The lake is situated in an area that is rapidly growing and many of the smaller coves are affected by the development on their shores and from the creeks feed into the coves. The Flat Creek branch of Lake Sidney Lanier drains runoff from a section of Gainesville that ...


Prevalence Of Malaria Reported During Summer And Winter At A Tertiary Care Hospital In Karachi, Pakistan, Fazal M. Arain, Aisha Memon, Roohi Jamal, Ahmed Raheem Buksh, Mohammad Asim Beg 2019 Aga Khan University

Prevalence Of Malaria Reported During Summer And Winter At A Tertiary Care Hospital In Karachi, Pakistan, Fazal M. Arain, Aisha Memon, Roohi Jamal, Ahmed Raheem Buksh, Mohammad Asim Beg

Department of Biological & Biomedical Sciences

This study was designed to determine the prevalence and type of malaria cases that presented throughout the year 2014 in a tertiary care hospital in Karachi, Pakistan. A total of 1099 cases, (377 females, 722 males) were reported. Plasmodium vivax (P. vivax) was discovered in 93.7% cases compared to 6.3% Plasmodium falciparum (P. falciparum). Based on the highest and lowest weather temperatures, in summer (June, July and August) and in winter (December, January and February) were differentiated. The number of cases were greater during summer months compared to winter. Interestingly, the ratio of P. falciparum to P. vivax ...


Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold 2019 University of Massachusetts Amherst

Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold

Doctoral Dissertations

Soils serve as massive carbon sinks, but their ability to continue this ecological service is contingent on how the resident soil microbial community will respond to the ongoing climate crisis. One key dimension of the microbial response to warming is its carbon use efficiency (CUE), or the fraction of carbon taken up by an organism which is allocated to growth rather than respiration. However, the scientific community is still in the early stages of understanding the drivers, consequences - and even accurate measurements of - CUE. In this dissertation, I first quantified the variability of CUE and its responsiveness to temperature and ...


A Belmont Report For Animals?, Hope Ferdowsian, L. Syd M. Johnson, Jane Johnson, Andrew Fenton, Adam Shriver, John Gluck 2019 University of Pennsylvania

A Belmont Report For Animals?, Hope Ferdowsian, L. Syd M. Johnson, Jane Johnson, Andrew Fenton, Adam Shriver, John Gluck

John P. Gluck, PhD

Human and animal research both operate within established standards. In the United States, criticism of the human research environment and recorded abuses of human research subjects served as the impetus for the establishment of the National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research, and the resulting Belmont Report. The Belmont Report established key ethical principles to which human research should adhere: respect for autonomy, obligations to beneficence and justice, and special protections for vulnerable individuals and populations. While current guidelines appropriately aim to protect the individual interests of human participants in research, no similar, comprehensive ...


Incorporating New Technologies Into Toxicity Testing And Risk Assessment: Moving From 21st Century Vision To A Data-Driven Framework, Russell S. Thomas, Martin A. Philbert, Scott Auerbach, Barbara A. Wetmore, Michael J. Devito, Ila Cote, J. Craig Rowlands, Maurice Whelan, Sean M. Hays, Melvin E. Andersen, M.E. (Bette) Meek, Lawrence W. Reiter, Jason C. Lambert, Harvey J. Clewell III, Martin L. Stephens, Q. Jay Zhao, Scott C. Wesselkamper, Lynn Flowers, Edward W. Carney, Tim P. Pastoor, Dan D. Petersen, Carole L. Yauk, Andy Nong 2019 The Hamner Institutes for Health Sciences

Incorporating New Technologies Into Toxicity Testing And Risk Assessment: Moving From 21st Century Vision To A Data-Driven Framework, Russell S. Thomas, Martin A. Philbert, Scott Auerbach, Barbara A. Wetmore, Michael J. Devito, Ila Cote, J. Craig Rowlands, Maurice Whelan, Sean M. Hays, Melvin E. Andersen, M.E. (Bette) Meek, Lawrence W. Reiter, Jason C. Lambert, Harvey J. Clewell Iii, Martin L. Stephens, Q. Jay Zhao, Scott C. Wesselkamper, Lynn Flowers, Edward W. Carney, Tim P. Pastoor, Dan D. Petersen, Carole L. Yauk, Andy Nong

Martin Stephens, PhD

Based on existing data and previous work, a series of studies is proposed as a basis toward a pragmatic early step in transforming toxicity testing. These studies were assembled into a data-driven framework that invokes successive tiers of testing with margin of exposure (MOE) as the primary metric. The first tier of the framework integrates data from high-throughput in vitro assays, in vitro-to-in vivo extrapolation (IVIVE) pharmacokinetic modeling, and exposure modeling. The in vitro assays are used to separate chemicals based on their relative selectivity in interacting with biological targets and identify the concentration at which these interactions ...


Beyond The 3rs: Expanding The Use Of Human-Relevant Replacement Methods In Biomedical Research, Kathrin Herrmann, Francesca Pistollato, Martin L. Stephens 2019 Johns Hopkins Bloomberg School of Public Health

Beyond The 3rs: Expanding The Use Of Human-Relevant Replacement Methods In Biomedical Research, Kathrin Herrmann, Francesca Pistollato, Martin L. Stephens

Martin Stephens, PhD

This year marks the 60th anniversary of Russell and Burch’s pioneering book, The Principles of Humane Experimental Technique. Their 3Rs framework has helped to inspire humane and scientific progress in experimental technique. However, it is time to update its strategic application. The 21st century has already seen the development of promising, high-tech non-animal models, such as organs-on-a-chip and computational approaches that, in our view, will replace animals as the default option in biomedical experimentation. How fast this transition will take place will depend on the pace at which these new models are optimized to reflect the biology of humans ...


Accelerating The Development Of 21st-Century Toxicology: Outcome Of A Human Toxicology Project Consortium Workshop, Martin L. Stephens, Craig Barrow, Melvin E. Andersen, Kim Boekelheide, Paul L. Carmichael, Michael P. Holsapple, Mark Lafranconi 2019 The Humane Society of the United States

Accelerating The Development Of 21st-Century Toxicology: Outcome Of A Human Toxicology Project Consortium Workshop, Martin L. Stephens, Craig Barrow, Melvin E. Andersen, Kim Boekelheide, Paul L. Carmichael, Michael P. Holsapple, Mark Lafranconi

Martin Stephens, PhD

The U.S. National Research Council (NRC) report on “Toxicity Testing in the 21st century” calls for a fundamental shift in the way that chemicals are tested for human health effects and evaluated in risk assessments. The new approach would move toward in vitro methods, typically using human cells in a high-throughput context. The in vitro methods would be designed to detect significant perturbations to “toxicity pathways,” i.e., key biological pathways that, when sufficiently perturbed, lead to adverse health outcomes. To explore progress on the report’s implementation, the Human Toxicology Project Consortium hosted a workshop on 9–10 ...


Simulating Bacterial Growth, Competition, And Resistance With Agent-Based Models And Laboratory Experiments, Anne E. Yust, Davida S. Smyth 2019 The New School

Simulating Bacterial Growth, Competition, And Resistance With Agent-Based Models And Laboratory Experiments, Anne E. Yust, Davida S. Smyth

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Integrating Mathematics And Biology In The Classroom: A Compendium Of Case Studies And Labs, Becky Sanft, Anne Walter 2019 University of North Carolina at Asheville

Integrating Mathematics And Biology In The Classroom: A Compendium Of Case Studies And Labs, Becky Sanft, Anne Walter

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


A Belmont Report For Animals?, Hope Ferdowsian, L. Syd M. Johnson, Jane Johnson, Andrew Fenton, Adam Shriver, John Gluck 2019 University of Pennsylvania

A Belmont Report For Animals?, Hope Ferdowsian, L. Syd M. Johnson, Jane Johnson, Andrew Fenton, Adam Shriver, John Gluck

Professional Science Research Ethics Collection

Human and animal research both operate within established standards. In the United States, criticism of the human research environment and recorded abuses of human research subjects served as the impetus for the establishment of the National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research, and the resulting Belmont Report. The Belmont Report established key ethical principles to which human research should adhere: respect for autonomy, obligations to beneficence and justice, and special protections for vulnerable individuals and populations. While current guidelines appropriately aim to protect the individual interests of human participants in research, no similar, comprehensive ...


Considering Aspects Of The 3rs Principles Within Experimental Animal Biology, Lynne U. Sneddon, Lewis G. Halsey, Nic R. Bury 2019 University of Liverpool

Considering Aspects Of The 3rs Principles Within Experimental Animal Biology, Lynne U. Sneddon, Lewis G. Halsey, Nic R. Bury

Lynne Sneddon, PhD

The 3Rs – Replacement, Reduction and Refinement – are embedded into the legislation and guidelines governing the ethics of animal use in experiments. Here, we consider the advantages of adopting key aspects of the 3Rs into experimental biology, represented mainly by the fields of animal behaviour, neurobiology, physiology, toxicology and biomechanics. Replacing protected animals with less sentient forms or species, cells, tissues or computer modelling approaches has been broadly successful. However, many studies investigate specific models that exhibit a particular adaptation, or a species that is a target for conservation, such that their replacement is inappropriate. Regardless of the species used, refining ...


Excess No Stabilizes The Luminal Domain Of Stim2 In A Cys-Specific Manner Thereby Regulating Basal Calcium Homeostasis And Store-Operated Calcium Entry, Matthew Novello 2019 The University of Western Ontario

Excess No Stabilizes The Luminal Domain Of Stim2 In A Cys-Specific Manner Thereby Regulating Basal Calcium Homeostasis And Store-Operated Calcium Entry, Matthew Novello

Electronic Thesis and Dissertation Repository

Stromal-interaction molecule 2 (STIM2) is an endoplasmic reticulum (ER) membrane-inserted Ca2+-sensing protein which, together with the plasma membrane Ca2+ channel Orai1, regulates basal Ca2+ homeostasis and store-operated Ca2+ entry (SOCE). Recent evidence suggests that S-nitrosylation, which is the covalent attachment of a nitric oxide (NO) moiety to a cysteine thiol, can attenuate the function of the paralog STIM1 protein. Compared to STIM1, STIM2 also functions as a basal Ca2+ homeostatic feedback regulator. Therefore, the objective of my study was to evaluate the susceptibility of STIM2 to S-nitrosylation and the effects that this ...


The Animal Research Controversy: Protest, Process & Public Policy, Andrew N. Rowan, Franklin M. Loew, Joan C. Weer 2019 Tufts University

The Animal Research Controversy: Protest, Process & Public Policy, Andrew N. Rowan, Franklin M. Loew, Joan C. Weer

Andrew N. Rowan, DPhil

The controversy today regarding the use of animals in research appears on the surface to be a strongly polarized struggle between the scientific community and the animal protection movement. However, there is a wide range of opinions and philosophies on both sides. Mistrust between the factions has blossomed while communication has withered. Through the 1960s, 1970s and early 1980s, the animal movement grew in numbers and financial resources, and developed much greater public recognition and political clout. The research community paid relatively little attention to the animal movement for much of this period but, alarmed by several public relations coups ...


The Photo Quiz: A Look Back And A Look Forward, Erik Munson, Alexander J. McAdam 2019 Marquette University

The Photo Quiz: A Look Back And A Look Forward, Erik Munson, Alexander J. Mcadam

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.


A Comparison Of Lung Function Values Among A Scuba Diver Population And In Comparison To A Non-Diver Population, Gabriel C. Hutson, Jeremy D. Rentsch, Erin M. Eaton 2019 Francis Marion University

A Comparison Of Lung Function Values Among A Scuba Diver Population And In Comparison To A Non-Diver Population, Gabriel C. Hutson, Jeremy D. Rentsch, Erin M. Eaton

Journal of the South Carolina Academy of Science

The purpose of this study was to investigate possible correlations between lung function values (PEF, IRV, ERV, and FVC) among a diver population, as well as in comparison to a non-diver population. Independent variables for both populations were biological sex, age, and weekly physical activity. Independent variables for the diver population were dive tenure, number of logged dives, certification level, and gas mixture used. A spirometry test was conducted to collect lung function values of both populations. Data from this study suggest a statistically significant relationship between diver and non-diver sex and FVC, diver age and ERV, diver sex and ...


Acute Toxicity Testing Without Animals: More Scientific And Less Of A Gamble, Gillian R. Langley 2019 British Union for the Abolition of Vivisection

Acute Toxicity Testing Without Animals: More Scientific And Less Of A Gamble, Gillian R. Langley

Gill Langley, PhD

In this report, we argue specifically that acute toxicity data should not be sought from animal tests. The underlying principle of such tests on rats and mice is that the results can be effectively extrapolated to humans. In fact, after nearly 80 years of use of these tests, the predictivity of rodent data for human acute toxic effects has been disputed but never proven.


Publication Reform To Safeguard Wildlife From Researcher Harm, Kate A. Field, Paul C. Paquet, Kyle A. Artelle, Gilbert Proulx, Ryan K. Brook, Chris T. Darimont 2019 University of Victoria

Publication Reform To Safeguard Wildlife From Researcher Harm, Kate A. Field, Paul C. Paquet, Kyle A. Artelle, Gilbert Proulx, Ryan K. Brook, Chris T. Darimont

Chris Darimont, PhD

Despite abundant focus on responsible care of laboratory animals, we argue that inattention to the maltreatment of wildlife constitutes an ethical blind spot in contemporary animal research. We begin by reviewing significant shortcomings in legal and institutional oversight, arguing for the relatively rapid and transformational potential of editorial oversight at journals in preventing harm to vertebrates studied in the field and outside the direct supervision of institutions. Straightforward changes to animal care policies in journals, which our analysis of 206 journals suggests are either absent (34%), weak, incoherent, or neglected by researchers, could provide a practical, effective, and rapidly imposed ...


Spatial And Temporal Variation In The Diet Composition Of Zooplankton In Mission Bay, Bryanna Paulson 2019 University of San Diego

Spatial And Temporal Variation In The Diet Composition Of Zooplankton In Mission Bay, Bryanna Paulson

Theses

Analyses of quantitative data on zooplankton diets are vital for understanding the drivers of zooplankton abundance within an ecosystem. Such analyses also provide insight into trophic pathways within the lower planktonic food web, which support populations of higher trophic level species. This study used carbon and nitrogen stable isotope ratios of size-fractionated plankton in Mission Bay, San Diego, CA to examine the spatial and temporal variation in zooplankton trophic ecology and determine potential environmental drivers of zooplankton community structure. Carbon stable isotopes reflect primary production sources in an organism’s diet, and nitrogen stable isotope ratios can be used to ...


Ipsc Based Gene Correction And Disease Model Of A New Class Of Lgmd Due To Poglut1 Mutation, Jose Ortiz-Vitali 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Ipsc Based Gene Correction And Disease Model Of A New Class Of Lgmd Due To Poglut1 Mutation, Jose Ortiz-Vitali

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Recently, a novel class of muscular dystrophy has been discovered in a family due to autosomal recessive missense mutation in POGLUT1. Mutation of this enzyme leads to decreased O-glucosyltransferase activity and impaired Notch signaling, the pathways important for skeletal muscle stem cell (satellite cells) quiescence and activation. We hypothesize that reduced POGLUT1 activity and impaired Notch signaling is causative of this limb girdle muscular dystrophy through dysfunction of muscle stem cells and myogenic progenitors.

To test this, we have used iPSCs for disease modeling and rescue experiments. Using a CRISPR based gene targeting method, we aimed to correct the point ...


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