Showing papers by "Brigham Young University published in 2021"

Social Isolation and Loneliness Among San Francisco Bay Area Older Adults During the COVID-19 Shelter-in-Place Orders.

Abstract: BACKGROUND/OBJECTIVES: Physical distancing during the COVID-19 pandemic may have unintended, detrimental effects on social isolation and loneliness among older adults. Our objectives were to investigate (1) experiences of social isolation and loneliness during shelter-in-place orders, and (2) unmet health needs related to changes in social interactions. DESIGN: Mixed-methods longitudinal phone-based survey administered every 2 weeks. SETTING: Two community sites and an academic geriatrics outpatient clinical practice. PARTICIPANTS: A total of 151 community-dwelling older adults. MEASUREMENTS: We measured social isolation using a six-item modified Duke Social Support Index, social interaction subscale, that included assessments of video-based and Internet-based socializing. Measures of loneliness included self-reported worsened loneliness due to the COVID-19 pandemic and loneliness severity based on the three-item University of California, Los Angeles (UCLA) Loneliness Scale. Participants were invited to share open-ended comments about their social experiences. RESULTS: Participants were on average aged 75 years (standard deviation = 10), 50% had hearing or vision impairment, 64% lived alone, and 26% had difficulty bathing. Participants reported social isolation in 40% of interviews, 76% reported minimal video-based socializing, and 42% minimal Internet-based socializing. Socially isolated participants reported difficulty finding help with functional needs including bathing (20% vs 55%; P = .04). More than half (54%) of the participants reported worsened loneliness due to COVID-19 that was associated with worsened depression (62% vs 9%; P < .001) and anxiety (57% vs 9%; P < .001). Rates of loneliness improved on average by time since shelter-in-place orders (4-6 weeks: 46% vs 13-15 weeks: 27%; P = .009), however, loneliness persisted or worsened for a subgroup of participants. Open-ended responses revealed challenges faced by the subgroup experiencing persistent loneliness including poor emotional coping and discomfort with new technologies. CONCLUSION: Many older adults are adjusting to COVID-19 restrictions since the start of shelter-in-place orders. Additional steps are critically needed to address the psychological suffering and unmet medical needs of those with persistent loneliness or barriers to technology-based social interaction.

The emerging landscape of single-molecule protein sequencing technologies

Abstract: Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics. This Perspective describes new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell proteomics.

A megastudy of text-based nudges encouraging patients to get vaccinated at an upcoming doctor's appointment

Abstract: Many Americans fail to get life-saving vaccines each year, and the availability of a vaccine for COVID-19 makes the challenge of encouraging vaccination more urgent than ever. We present a large field experiment (N = 47,306) testing 19 nudges delivered to patients via text message and designed to boost adoption of the influenza vaccine. Our findings suggest that text messages sent prior to a primary care visit can boost vaccination rates by an average of 5%. Overall, interventions performed better when they were 1) framed as reminders to get flu shots that were already reserved for the patient and 2) congruent with the sort of communications patients expected to receive from their healthcare provider (i.e., not surprising, casual, or interactive). The best-performing intervention in our study reminded patients twice to get their flu shot at their upcoming doctor's appointment and indicated it was reserved for them. This successful script could be used as a template for campaigns to encourage the adoption of life-saving vaccines, including against COVID-19.

Practical guides for x-ray photoelectron spectroscopy (XPS): Interpreting the carbon 1s spectrum

Abstract: The carbon 1s photoelectron spectrum is the most widely fit and analyzed narrow scan in the x-ray photoelectron spectroscopy (XPS) literature. It is, therefore, critically important to adopt well-established protocols based on best practices for its analysis, since results of these efforts affect research outcomes in a wide range of different application areas across materials science. Unfortunately, much XPS peak fitting in the scientific literature is inaccurate. In this guide, we describe and explain the most common problems associated with C 1s narrow scan analysis in the XPS literature. We then provide an overview of rules, principles, and considerations that, taken together, should guide the approach to the analysis of C 1s spectra. We propose that following this approach should result in (1) the avoidance of common problems and (2) the extraction of reliable, reproducible, and meaningful information from experimental data.

Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell

Abstract: We report on the combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer for greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions for more effective MS analysis of multiply charged peptides, resulting in an average of 1056 protein groups identified from single HeLa cells without MS1-level feature matching. This is 2.3 times more identifications than without FAIMS and a far greater level of proteome coverage for single mammalian cells than has been previously reported for a label-free study. Differential analysis of single microdissected motor neurons and interneurons from human spinal tissue indicated a similar level of proteome coverage, and the two subpopulations of cells were readily differentiated based on single-cell label-free quantification.

Machine learning for alloys

Abstract: Alloy modelling has a history of machine-learning-like approaches, preceding the tide of data-science-inspired work. The dawn of computational databases has made the integration of analysis, prediction and discovery the key theme in accelerated alloy research. Advances in machine-learning methods and enhanced data generation have created a fertile ground for computational materials science. Pairing machine learning and alloys has proven to be particularly instrumental in pushing progress in a wide variety of materials, including metallic glasses, high-entropy alloys, shape-memory alloys, magnets, superalloys, catalysts and structural materials. This Review examines the present state of machine-learning-driven alloy research, discusses the approaches and applications in the field and summarizes theoretical predictions and experimental validations. We foresee that the partnership between machine learning and alloys will lead to the design of new and improved systems. Machine learning is enabling a metallurgical renaissance. This Review discusses recent progress in representations, descriptors and interatomic potentials, overviewing metallic glasses, high-entropy alloys, superalloys and shape-memory alloys, magnets and catalysts, and the prediction of mechanical and thermal properties.

In an era of uncertainty: Impact of COVID-19 on dental education.

Abstract: Purpose/objectives The coronavirus disease 2019 (COVID-19) pandemic arguably represents the worst public health crisis of the 21st century. However, no empirical study currently exists in the literature that examines the impact of the COVID-19 pandemic on dental education. This study evaluated the impact of COVID-19 on dental education and dental students' experience. Methods An anonymous online survey was administrated to professional dental students that focused on their experiences related to COVID-19. The survey included questions about student demographics, protocols for school reopening and student perceptions of institutional responses, student concerns, and psychological impacts. Results Among the 145 respondents, 92.4% were pre-doctoral dental students and 7.6% were orthodontic residents; 48.2% were female and 12.6% students lived alone during the school closure due to the pandemic. Students' age ranged from 23 to 39 years. Younger students expressed more concerns about their emotional health (P = 0.01). In terms of the school's overall response to COVID-19, 73.1% students thought it was effective. The majority (83%) of students believed that social distancing in school can minimize the development of COVID-19. In general, students felt that clinical education suffered after transitioning to online but responded more positively about adjustments to other online curricular components. Conclusions The COVID-19 pandemic significantly impacted dental education. Our findings indicate that students are experiencing increased levels of stress and feel their clinical education has suffered. Most students appear comfortable with technology adaptations for didactic curriculum and favor masks, social distancing, and liberal use of sanitizers.

Representation and participation across 20 years of plant genome sequencing.

Abstract: The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic data from an increasingly diverse set of taxa provides unprecedented potential to better understand the genome biology and evolution of land plants. Here we provide a contemporary view of land plant genomics, including analyses on assembly quality, taxonomic distribution of sequenced species and national participation. We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of study species. We identify numerous disconnects between the native range of focal species and the national affiliation of the researchers studying them, which we argue are rooted in colonialism-both past and present. Luckily, falling sequencing costs, widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps and empower a more global plant genomics community.

Adaptive immunity induces mutualism between commensal eukaryotes.

Abstract: Pathogenic fungi reside in the intestinal microbiota but rarely cause disease. Little is known about the interactions between fungi and the immune system that promote commensalism. Here we investigate the role of adaptive immunity in promoting mutual interactions between fungi and host. We find that potentially pathogenic Candida species induce and are targeted by intestinal immunoglobulin A (IgA) responses. Focused studies on Candida albicans reveal that the pathogenic hyphal morphotype, which is specialized for adhesion and invasion, is preferentially targeted and suppressed by intestinal IgA responses. IgA from mice and humans directly targets hyphal-enriched cell-surface adhesins. Although typically required for pathogenesis, C. albicans hyphae are less fit for gut colonization1,2 and we show that immune selection against hyphae improves the competitive fitness of C. albicans. C. albicans exacerbates intestinal colitis3 and we demonstrate that hyphae and an IgA-targeted adhesin exacerbate intestinal damage. Finally, using a clinically relevant vaccine to induce an adhesin-specific immune response protects mice from C. albicans-associated damage during colitis. Together, our findings show that adaptive immunity suppresses harmful fungal effectors, with benefits to both C. albicans and its host. Thus, IgA uniquely uncouples colonization from pathogenesis in commensal fungi to promote homeostasis. Studies of mouse and human IgA responses against Candida albicans and other common fungal species show that host adaptive immunity selects for fungal effectors that promote commensalism and prevent intestinal disease.

Charting a path between firm-specific incentives and human capital-based competitive advantage

Abstract: Research Summary Scholars have long recognized the theoretical and practical implications of firm‐specific human capital. However, we highlight that firm‐specific incentives (i.e., worker incentives that provide more utility to workers in the focal firm than similar incentives available at other employers) provide an important pathway to competitive advantages that has not been comprehensively examined in the extant organizational research. We address this gap by (a) defining firm‐specific incentives and showing why they are different from incentive conceptualizations and typologies in the extant literature, (b) articulating potential origins of firm‐specific incentives, and (c) formally proposing the conditions under which firm‐specific incentives facilitate human capital‐based competitive advantages. In so doing, we develop a cohesive theoretical framework of incentive‐based competitive advantage that integrates across multiple literatures. Managerial Summary Just as companies differentiate their products by creating unique value for customers, they also create unique value for their employees. Some companies do this by offering employee incentives, perks, and benefits that are highly unique to the company and difficult for other companies to imitate. These unique incentives, perks, and benefits can help these companies to attract, motivate, and retain top talent at a financial discount and, accordingly, can help these companies realize competitive advantages over their rivals.

Effects of Salinity Stress on Chloroplast Structure and Function.

Abstract: Salinity is a growing problem affecting soils and agriculture in many parts of the world. The presence of salt in plant cells disrupts many basic metabolic processes, contributing to severe negative effects on plant development and growth. This review focuses on the effects of salinity on chloroplasts, including the structures and function of these organelles. Chloroplasts house various important biochemical reactions, including photosynthesis, most of which are considered essential for plant survival. Salinity can affect these reactions in a number of ways, for example, by changing the chloroplast size, number, lamellar organization, lipid and starch accumulation, and interfering with cross-membrane transportation. Research has shown that maintenance of the normal chloroplast physiology is necessary for the survival of the entire plant. Many plant species have evolved different mechanisms to withstand the harmful effects of salt-induced toxicity on their chloroplasts and its machinery. The differences depend on the plant species and growth stage and can be quite different between salt-sensitive (glycophyte) and salt-tolerant (halophyte) plants. Salt stress tolerance is a complex trait, and many aspects of salt tolerance in plants are not entirely clear yet. In this review, we discuss the different mechanisms of salt stress tolerance in plants with a special focus on chloroplast structure and its functions, including the underlying differences between glycophytes and halophytes.

Stakeholder Identification and Salience After 20 Years: Progress, Problems, and Prospects

Abstract: To contribute to the continuing challenge of explaining how managers identify stakeholders and assess their salience, in this article, we chronicle the history, assess the impact, and evaluate the ...

A Multisite Preregistered Paradigmatic Test of the Ego-Depletion Effect:

Abstract: We conducted a preregistered multilaboratory project (k = 36; N = 3,531) to assess the size and robustness of ego-depletion effects using a novel replication method, termed the paradigmatic replication approach. Each laboratory implemented one of two procedures that was intended to manipulate self-control and tested performance on a subsequent measure of self-control. Confirmatory tests found a nonsignificant result (d = 0.06). Confirmatory Bayesian meta-analyses using an informed-prior hypothesis (δ = 0.30, SD = 0.15) found that the data were 4 times more likely under the null than the alternative hypothesis. Hence, preregistered analyses did not find evidence for a depletion effect. Exploratory analyses on the full sample (i.e., ignoring exclusion criteria) found a statistically significant effect (d = 0.08); Bayesian analyses showed that the data were about equally likely under the null and informed-prior hypotheses. Exploratory moderator tests suggested that the depletion effect was larger for participants who reported more fatigue but was not moderated by trait self-control, willpower beliefs, or action orientation.

COVID-19 lockdown: Impact on college students' lives.

Abstract: Objective: In light of COVID-19, leaders issued stay-at-home orders, including closure of higher-education schools. Most students left campus, likely impacting their employment and social network. Leaders are making decisions about opening universities and modality of instruction. Understanding students' psychological, physiological, academic, and financial responses to the shut-down and reopening of campuses can help leaders make informed decisions. Participants: 654 students from a large western university enrolled during the pandemic shutdown. Methods: Students were invited via email to complete an online survey. Results: Students reported stress, depression, loneliness, lack of motivation, difficulty focusing on schoolwork, restless sleep, appetite changes, job loss concerns, and difficulties coping. Most wanted to return to campus and felt social/physical distancing was effective but were mixed in terms of testing or masks. Conclusions: Moving to remote learning created physical and psychological stress. Students want to return to campus but do not want to take risk-reducing measures.

Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing

Abstract: The first insect genome (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 insect species representing 20 orders. In this study, we analyzed the most-contiguous assembly for each species and provide a "state of the field" perspective, emphasizing taxonomic representation, assembly quality, gene completeness, and sequencing technologies. Relative to species richness, genomic efforts have been biased towards four orders (Diptera, Hymenoptera, Collembola, and Phasmatodea), Coleoptera are underrepresented, and 11 orders still lack a publicly available genome assembly. The average insect genome assembly is 439.2 megabases in length with 87.5% of single-copy benchmarking genes intact. Most notable has been the impact of long-read sequencing; assemblies that incorporate long-reads are ∼48x more contiguous than those that do not. We offer four recommendations as we collectively continue building insect genome resources: (1) seek better integration between independent research groups and consortia, (2) balance future sampling between filling taxonomic gaps and generating data for targeted questions, (3) take advantage of long read sequencing technologies, and (4) expand and improve gene annotations.

The Emerging Science of Virtue.

Abstract: Numerous scholars have claimed that positive ethical traits such as virtues are important in human psychology and behavior. Psychologists have begun to test these claims. The scores of studies on v...

Lowering the transmission and spread of human coronavirus.

Abstract: The emergence of the severe acute respiratory syndrome coronavirus 2 pandemic has created an unprecedented healthcare, social, and economic disaster. Wearing of masks and social distancing can significantly decrease transmission and spread, however, due to circumstances such as medical or dental intervention and personal choice these practices have not been universally adopted. Additional strategies are required to lessen transmission. Nasal rinses and mouthwashes, which directly impact the major sites of reception and transmission of human coronaviruses (HCoV), may provide an additional level of protection against the virus. Common over-the-counter nasal rinses and mouthwashes/gargles were tested for their ability to inactivate high concentrations of HCoV using contact times of 30 s, 1 min, and 2 min. Reductions in titers were measured by using the tissue culture infectious dose 50 (TCID50 ) assay. A 1% baby shampoo nasal rinse solution inactivated HCoV greater than 99.9% with a 2-min contact time. Several over-the-counter mouthwash/gargle products including Listerine and Listerine-like products were highly effective at inactivating infectious virus with greater than 99.9% even with a 30-s contact time. In the current manuscript we have demonstrated that several commonly available healthcare products have significant virucidal properties with respect to HCoV.

Impact of the COVID-19 Pandemic on Loneliness and Social Isolation: A Multi-Country Study.

Abstract: The COVID-19 global pandemic and subsequent public health social measures have challenged our social and economic life, with increasing concerns around potentially rising levels of social isolation and loneliness. This paper is based on cross-sectional online survey data (available in 10 languages, from 2 June to 16 November 2020) with 20,398 respondents from 101 different countries. It aims to help increase our understanding of the global risk factors that are associated with social isolation and loneliness, irrespective of culture or country, to support evidence-based policy, services and public health interventions. We found the prevalence of severe loneliness was 21% during COVID-19 with 6% retrospectively reporting severe loneliness prior to the pandemic. A fifth were defined as isolated based on their usual connections, with 13% reporting a substantial increase in isolation during COVID-19. Personal finances and mental health were overarching and consistently cross-cutting predictors of loneliness and social isolation, both before and during the pandemic. With the likelihood of future waves of COVID-19 and related restrictions, it must be a public health priority to address the root causes of loneliness and social isolation and, in particular, address the needs of specific groups such as carers or those living alone.

Machine-learned interatomic potentials for alloys and alloy phase diagrams

Abstract: We introduce machine-learned potentials for Ag-Pd to describe the energy of alloy configurations over a wide range of compositions We compare two different approaches Moment tensor potentials (MTPs) are polynomial-like functions of interatomic distances and angles The Gaussian approximation potential (GAP) framework uses kernel regression, and we use the smooth overlap of atomic position (SOAP) representation of atomic neighborhoods that consist of a complete set of rotational and permutational invariants provided by the power spectrum of the spherical Fourier transform of the neighbor density Both types of potentials give excellent accuracy for a wide range of compositions, competitive with the accuracy of cluster expansion, a benchmark for this system While both models are able to describe small deformations away from the lattice positions, SOAP-GAP excels at transferability as shown by sensible transformation paths between configurations, and MTP allows, due to its lower computational cost, the calculation of compositional phase diagrams Given the fact that both methods perform nearly as well as cluster expansion but yield off-lattice models, we expect them to open new avenues in computational materials modeling for alloys

Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling.

Abstract: Recent advances in sample preparation and analysis have enabled direct profiling of protein expression in single mammalian cells and other trace samples. Several techniques to prepare and analyze low-input samples employ custom fluidics for nanoliter sample processing and manual sample injection onto a specialized separation column. While being effective, these highly specialized systems require significant expertise to fabricate and operate, which has greatly limited implementation in most proteomic laboratories. Here, we report a fully automated platform termed autoPOTS (automated preparation in one pot for trace samples) that uses only commercially available instrumentation for sample processing and analysis. An unmodified, low-cost commercial robotic pipetting platform was utilized for one-pot sample preparation. We used low-volume 384-well plates and periodically added water or buffer to the microwells to compensate for limited evaporation during sample incubation. Prepared samples were analyzed directly from the well plate with a commercial autosampler that was modified with a 10-port valve for compatibility with 30 μm i.d. nanoLC columns. We used autoPOTS to analyze 1-500 HeLa cells and observed only a moderate reduction in peptide coverage for 150 cells and a 24% reduction in coverage for single cells compared to our previously developed nanoPOTS platform. To evaluate clinical feasibility, we identified an average of 1095 protein groups from ∼130 sorted B or T lymphocytes. We anticipate that the straightforward implementation of autoPOTS will make it an attractive option for low-input and single-cell proteomics in many laboratories.

MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

Abstract: Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software. MCMICRO is a modular and open-source computational pipeline for transforming highly multiplexed whole-slide images of tissues into single-cell data. MCMICRO is versatile and can be used with CODEX, mxIF, CyCIF, mIHC and H&E staining data.

Male adiposity, sperm parameters and reproductive hormones: An updated systematic review and collaborative meta-analysis.

Abstract: The present updated systematic review and meta-analysis aims to summarize the evidence from published studies with low risk for any important bias (based on methodological quality assessment) investigating the potential associations of adiposity with sperm quality and reproductive hormones. We conducted a systematic search of the literature published in MEDLINE-PubMed and EMBASE through June 2019. Based on the criteria in our review, 169 eligible publications were used for data abstraction. Finally, 60 articles were included in the qualitative analysis and 28 in the quantitative analysis. Our systematic review results indicated that overweight and/or obesity were associated with low semen quality parameters (i.e., semen volume, sperm count and concentration, sperm vitality and normal morphology) and some specific reproductive hormones (e.g., inhibin B, total testosterone and sex hormone-binding globulin). Overweight and/or obesity were also positively associated with high estradiol concentrations. Meta-analysis indicated that overweight and/or obesity categories were associated with lower sperm quality (i.e., semen volume, sperm count and concentration, sperm vitality, total motility and normal morphology), and underweight category was likewise associated with low sperm normal morphology. In conclusion, our results suggest that maintaining a healthy body weight is important for increasing sperm quality parameters and potentially male fertility.