Showing papers by "Brigham Young University published in 2020"

SciPy 1.0: fundamental algorithms for scientific computing in Python.

Abstract: SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

Author Correction: SciPy 1.0: fundamental algorithms for scientific computing in Python.

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Carbon release through abrupt permafrost thaw

Abstract: The permafrost zone is expected to be a substantial carbon source to the atmosphere, yet large-scale models currently only simulate gradual changes in seasonally thawed soil. Abrupt thaw will probably occur in <20% of the permafrost zone but could affect half of permafrost carbon through collapsing ground, rapid erosion and landslides. Here, we synthesize the best available information and develop inventory models to simulate abrupt thaw impacts on permafrost carbon balance. Emissions across 2.5 million km2 of abrupt thaw could provide a similar climate feedback as gradual thaw emissions from the entire 18 million km2 permafrost region under the warming projection of Representative Concentration Pathway 8.5. While models forecast that gradual thaw may lead to net ecosystem carbon uptake under projections of Representative Concentration Pathway 4.5, abrupt thaw emissions are likely to offset this potential carbon sink. Active hillslope erosional features will occupy 3% of abrupt thaw terrain by 2300 but emit one-third of abrupt thaw carbon losses. Thaw lakes and wetlands are methane hot spots but their carbon release is partially offset by slowly regrowing vegetation. After considering abrupt thaw stabilization, lake drainage and soil carbon uptake by vegetation regrowth, we conclude that models considering only gradual permafrost thaw are substantially underestimating carbon emissions from thawing permafrost. Analyses of inventory models under two climate change projection scenarios suggest that carbon emissions from abrupt thaw of permafrost through ground collapse, erosion and landslides could contribute significantly to the overall permafrost carbon balance.

Outdoor air pollution and cancer: An overview of the current evidence and public health recommendations.

Abstract: Outdoor air pollution is a major contributor to the burden of disease worldwide. Most of the global population resides in places where air pollution levels, because of emissions from industry, power generation, transportation, and domestic burning, considerably exceed the World Health Organization's health-based air-quality guidelines. Outdoor air pollution poses an urgent worldwide public health challenge because it is ubiquitous and has numerous serious adverse human health effects, including cancer. Currently, there is substantial evidence from studies of humans and experimental animals as well as mechanistic evidence to support a causal link between outdoor (ambient) air pollution, and especially particulate matter (PM) in outdoor air, with lung cancer incidence and mortality. It is estimated that hundreds of thousands of lung cancer deaths annually worldwide are attributable to PM air pollution. Epidemiological evidence on outdoor air pollution and the risk of other types of cancer, such as bladder cancer or breast cancer, is more limited. Outdoor air pollution may also be associated with poorer cancer survival, although further research is needed. This report presents an overview of outdoor air pollutants, sources, and global levels, as well as a description of epidemiological evidence linking outdoor air pollution with cancer incidence and mortality. Biological mechanisms of air pollution-derived carcinogenesis are also described. This report concludes by summarizing public health/policy recommendations, including multilevel interventions aimed at individual, community, and regional scales. Specific roles for medical and health care communities with regard to prevention and advocacy and recommendations for further research are also described.

Practical guide for curve fitting in x-ray photoelectron spectroscopy

Abstract: The use of peak fitting to extract information from x-ray photoelectron spectroscopy (XPS) data is of growing use and importance. Due to increased instrument accessibility and reliability, the use of XPS instrumentation has significantly increased around the world. However, the increased use has not been matched by the expertise of the new users, and the erroneous application of curve fitting has contributed to ambiguity and confusion in parts of the literature. This guide discusses the physics and chemistry involved in generating XPS spectra, describes good practices for peak fitting, and provides examples of appropriate use along with tools for avoiding mistakes.

Dense sampling of bird diversity increases power of comparative genomics.

Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Faculty readiness for online crisis teaching: transitioning to online teaching during the COVID-19 pandemic

Abstract: This mixed-methods study was designed to measure and elaborate constructs of faculty online readiness from pre- COVID-19 pandemic literature. Bringing together the validation of a scale to measure ...

Influences on Attitudes regarding Potential COVID-19 Vaccination in the United States

Abstract: The COVID-19 pandemic continues to ravage the world, with the United States being highly affected. A vaccine provides the best hope for a permanent solution to controlling the pandemic. However, to be effective, a vaccine must be accepted and used by a large majority of the population. The aim of this study was to understand the attitudes towards and obstacles facing vaccination with a potential COVID-19 vaccine. To measure these attitudes a survey was administered to 316 respondents across the United States by a survey corporation. Structural equation modeling was used to analyze the relationships of several factors with attitudes toward potential COVID-19 vaccination. Prior vaccine usage and attitudes predicted attitudes towards COVID-19 vaccination. Assessment of the severity of COVID-19 for the United States was also predictive. Approximately 68% of all respondents were supportive of being vaccinated for COVID-19, but side effects, efficacy and length of testing remained concerns. Longer testing, increased efficacy and development in the United States were significantly associated with increased vaccine acceptance. Messages promoting COVID-19 vaccination should seek to alleviate the concerns of those who are already vaccine-hesitant. Messaging directed at the benefits of vaccination for the United States as a country would address the second predictive factor. Enough time should be taken to allay concerns about both short- and long-term side effects before a vaccine is released.

Society of Critical Care Medicine's International Consensus Conference on Prediction and Identification of Long-Term Impairments After Critical Illness.

Abstract: Background: After critical illness, new or worsening impairments in physical, cognitive, and/or mental health function are common among patients who have survived. Who should be screened for long-term impairments, what tools to use, and when remain unclear. Objectives: Provide pragmatic recommendations to clinicians caring for adult survivors of critical illness related to screening for postdischarge impairments. Participants: Thirty-one international experts in risk-stratification and assessment of survivors of critical illness, including practitioners involved in the Society of Critical Care Medicine’s Thrive Post-ICU Collaboratives, survivors of critical illness, and clinical researchers. Design: Society of Critical Care Medicine consensus conference on post-intensive care syndrome prediction and assessment, held in Dallas, in May 2019. A systematic search of PubMed and the Cochrane Library was conducted in 2018 and updated in 2019 to complete an original systematic review and to identify pre-existing systematic reviews. Meeting Outcomes: We concluded that existing tools are insufficient to reliably predict post-intensive care syndrome. We identified factors before (e.g., frailty, preexisting functional impairments), during (e.g., duration of delirium, sepsis, acute respiratory distress syndrome), and after (e.g., early symptoms of anxiety, depression, or post-traumatic stress disorder) critical illness that can be used to identify patients at high-risk for cognitive, mental health, and physical impairments after critical illness in whom screening is recommended. We recommend serial assessments, beginning within 2–4 weeks of hospital discharge, using the following screening tools: Montreal Cognitive Assessment test; Hospital Anxiety and Depression Scale; Impact of Event Scale-Revised (post-traumatic stress disorder); 6-minute walk; and/or the EuroQol-5D-5L, a health-related quality of life measure (physical function). Conclusions: Beginning with an assessment of a patient’s pre-ICU functional abilities at ICU admission, clinicians have a care coordination strategy to identify and manage impairments across the continuum. As hospital discharge approaches, clinicians should use brief, standardized assessments and compare these results to patient’s pre-ICU functional abilities (“functional reconciliation”). We recommend serial assessments for post-intensive care syndrome-related problems continue within 2–4 weeks of hospital discharge, be prioritized among high-risk patients, using the identified screening tools to prompt referrals for services and/or more detailed assessments.

3D Printed Microfluidics

Abstract: Traditional microfabrication techniques suffer from several disadvantages, including the inability to create truly three-dimensional (3D) architectures, expensive and time-consuming processes when changing device designs, and difficulty in transitioning from prototyping fabrication to bulk manufacturing. 3D printing is an emerging technique that could overcome these disadvantages. While most 3D printed fluidic devices and features to date have been on the millifluidic size scale, some truly microfluidic devices have been shown. Currently, stereolithography is the most promising approach for routine creation of microfluidic structures, but several approaches under development also have potential. Microfluidic 3D printing is still in an early stage, similar to where polydimethylsiloxane was two decades ago. With additional work to advance printer hardware and software control, expand and improve resin and printing material selections, and realize additional applications for 3D printed devices, we foresee 3D printing becoming the dominant microfluidic fabrication method.

Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution.

Abstract: Biological tissues exhibit complex spatial heterogeneity that directs the functions of multicellular organisms. Quantifying protein expression is essential for elucidating processes within complex biological assemblies. Imaging mass spectrometry (IMS) is a powerful emerging tool for mapping the spatial distribution of metabolites and lipids across tissue surfaces, but technical challenges have limited the application of IMS to the analysis of proteomes. Methods for probing the spatial distribution of the proteome have generally relied on the use of labels and/or antibodies, which limits multiplexing and requires a priori knowledge of protein targets. Past efforts to make spatially resolved proteome measurements across tissues have had limited spatial resolution and proteome coverage and have relied on manual workflows. Here, we demonstrate an automated approach to imaging that utilizes label-free nanoproteomics to analyze tissue voxels, generating quantitative cell-type-specific images for >2000 proteins with 100-µm spatial resolution across mouse uterine tissue sections preparing for blastocyst implantation.

Social Network Analysis of COVID-19 Sentiments: Application of Artificial Intelligence.

Abstract: Background: The coronavirus disease (COVID-19) pandemic led to substantial public discussion. Understanding these discussions can help institutions, governments, and individuals navigate the pandemic. Objective: The aim of this study is to analyze discussions on Twitter related to COVID-19 and to investigate the sentiments toward COVID-19. Methods: This study applied machine learning methods in the field of artificial intelligence to analyze data collected from Twitter. Using tweets originating exclusively in the United States and written in English during the 1-month period from March 20 to April 19, 2020, the study examined COVID-19–related discussions. Social network and sentiment analyses were also conducted to determine the social network of dominant topics and whether the tweets expressed positive, neutral, or negative sentiments. Geographic analysis of the tweets was also conducted. Results: There were a total of 14,180,603 likes, 863,411 replies, 3,087,812 retweets, and 641,381 mentions in tweets during the study timeframe. Out of 902,138 tweets analyzed, sentiment analysis classified 434,254 (48.2%) tweets as having a positive sentiment, 187,042 (20.7%) as neutral, and 280,842 (31.1%) as negative. The study identified 5 dominant themes among COVID-19–related tweets: health care environment, emotional support, business economy, social change, and psychological stress. Alaska, Wyoming, New Mexico, Pennsylvania, and Florida were the states expressing the most negative sentiment while Vermont, North Dakota, Utah, Colorado, Tennessee, and North Carolina conveyed the most positive sentiment. Conclusions: This study identified 5 prevalent themes of COVID-19 discussion with sentiments ranging from positive to negative. These themes and sentiments can clarify the public’s response to COVID-19 and help officials navigate the pandemic.

Quantifying sources of variability in infancy research using the infant-directed-speech preference

Abstract: Psychological scientists have become increasingly concerned with issues related to methodology and replicability, and infancy researchers in particular face specific challenges related to replicability: For example, high-powered studies are difficult to conduct, testing conditions vary across labs, and different labs have access to different infant populations. Addressing these concerns, we report on a large-scale, multisite study aimed at (a) assessing the overall replicability of a single theoretically important phenomenon and (b) examining methodological, cultural, and developmental moderators. We focus on infants’ preference for infant-directed speech (IDS) over adult-directed speech (ADS). Stimuli of mothers speaking to their infants and to an adult in North American English were created using seminaturalistic laboratory-based audio recordings. Infants’ relative preference for IDS and ADS was assessed across 67 laboratories in North America, Europe, Australia, and Asia using the three common methods for measuring infants’ discrimination (head-turn preference, central fixation, and eye tracking). The overall meta-analytic effect size (Cohen’s d) was 0.35, 95% confidence interval = [0.29, 0.42], which was reliably above zero but smaller than the meta-analytic mean computed from previous literature (0.67). The IDS preference was significantly stronger in older children, in those children for whom the stimuli matched their native language and dialect, and in data from labs using the head-turn preference procedure. Together, these findings replicate the IDS preference but suggest that its magnitude is modulated by development, native-language experience, and testing procedure.

Large-scale mapping of cortical alterations in 22q11.2 deletion syndrome: Convergence with idiopathic psychosis and effects of deletion size.

Abstract: The 22q11.2 deletion (22q11DS) is a common chromosomal microdeletion and a potent risk factor for psychotic illness. Prior studies reported widespread cortical changes in 22q11DS, but were generally underpowered to characterize neuroanatomic abnormalities associated with psychosis in 22q11DS, and/or neuroanatomic effects of variability in deletion size. To address these issues, we developed the ENIGMA (Enhancing Neuro Imaging Genetics Through Meta-Analysis) 22q11.2 Working Group, representing the largest analysis of brain structural alterations in 22q11DS to date. The imaging data were collected from 10 centers worldwide, including 474 subjects with 22q11DS (age = 18.2 ± 8.6; 46.9% female) and 315 typically developing, matched controls (age = 18.0 ± 9.2; 45.9% female). Compared to controls, 22q11DS individuals showed thicker cortical gray matter overall (left/right hemispheres: Cohen’s d = 0.61/0.65), but focal thickness reduction in temporal and cingulate cortex. Cortical surface area (SA), however, showed pervasive reductions in 22q11DS (left/right hemispheres: d = −1.01/−1.02). 22q11DS cases vs. controls were classified with 93.8% accuracy based on these neuroanatomic patterns. Comparison of 22q11DS-psychosis to idiopathic schizophrenia (ENIGMA-Schizophrenia Working Group) revealed significant convergence of affected brain regions, particularly in fronto-temporal cortex. Finally, cortical SA was significantly greater in 22q11DS cases with smaller 1.5 Mb deletions, relative to those with typical 3 Mb deletions. We found a robust neuroanatomic signature of 22q11DS, and the first evidence that deletion size impacts brain structure. Psychotic illness in this highly penetrant deletion was associated with similar neuroanatomic abnormalities to idiopathic schizophrenia. These consistent cross-site findings highlight the homogeneity of this single genetic etiology, and support the suitability of 22q11DS as a biological model of schizophrenia.

Microfluidics: Innovations in Materials and Their Fabrication and Functionalization.

Abstract: Microfluidics is a growing field of study because these devices offer novel and versatile approaches for addressing a range of scientific problems. Microfluidics have been used in separations, cell analysis, and microreactors, to illustrate a few applications. Microfluidics have been defined in terms of microliter volumes or micrometer dimensions of channels. For this review, we utilize the latter definition, where microfluidic channels range from 1-1000 µm in width or height. Microfluidic devices are fabricated in a host of ways, with a large variety of materials. Indeed, device material can affect flow, absorptivity, biocompatibility, and function of microfluidic components.

Thinking beyond Zoom: Using Asynchronous Video to Maintain Connection and Engagement during the COVID-19 Pandemic.

Abstract: The COVID-19 pandemic forced colleges and universities to move all in-person courses to a remote or online learning format. As a result, many faculty, including teacher educators, opted to transition their courses to live synchronous web meetings using web conferencing tools like Zoom. Despite benefits of synchronous communication, there are constraints with the use and overuse of synchronous live meetings (which many teacher educators ended up experiencing during the pandemic). In this paper, we describe the experiences of how four different faculty, at four different universities, used asynchronous video to maintain connection and engagement during the COVID-19 pandemic. We conclude with implications for practice and future research.

Improved Single-Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry.

Abstract: Single-cell proteomics can provide unique insights into biological processes by resolving heterogeneity that is obscured by bulk measurements. Gains in the overall sensitivity and proteome coverage...

Kinetostatic and Dynamic Modeling of Flexure-Based Compliant Mechanisms: A Survey

Abstract: Flexure-based compliant mechanisms are becoming increasingly promising in precision engineering, robotics, and other applications due to the excellent advantages of no friction, no backlash, no wear, and minimal requirement of assembly. Because compliant mechanisms have inherent coupling of kinematic-mechanical behaviors with large deflections and/or complex serial-parallel configurations, the kinetostatic and dynamic analyses are challenging in comparison to their rigid-body counterparts. To address these challenges, a variety of techniques have been reported in a growing stream of publications. This paper surveys and compares the conceptual ideas, key advances, and applicable scopes, and open problems of the state-of-the-art kinetostatic and dynamic modeling methods for compliant mechanisms in terms of small and large deflections. Future challenges are discussed and new opportunities for extended study are highlighted as well. The presented review provides a guide on how to select suitable modeling approaches for those engaged in the field of compliant mechanisms.

Measuring the predictability of life outcomes with a scientific mass collaboration.

Abstract: How predictable are life trajectories? We investigated this question with a scientific mass collaboration using the common task method; 160 teams built predictive models for six life outcomes using data from the Fragile Families and Child Wellbeing Study, a high-quality birth cohort study. Despite using a rich dataset and applying machine-learning methods optimized for prediction, the best predictions were not very accurate and were only slightly better than those from a simple benchmark model. Within each outcome, prediction error was strongly associated with the family being predicted and weakly associated with the technique used to generate the prediction. Overall, these results suggest practical limits to the predictability of life outcomes in some settings and illustrate the value of mass collaborations in the social sciences.