Showing papers by "University of Nebraska–Lincoln published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Psychology for Musicians : Understanding and Acquiring the Skills

Abstract: PART I: MUSICAL LEARNING 1. Science and Musical Skills 2. Development 3. Motivation 4. Practice SECTION II: MUSICAL SKILLS 5. Expression and Interpretation 6. Reading or Listening and Remembering 7. Composition and Improvisation 8. Managing Performance Anxiety SECTION III: MUSICAL ROLES 9. The Performer 10. The Teacher 11. The Listener 12. The User

The Color of COVID-19: Structural Racism and the Disproportionate Impact of the Pandemic on Older Black and Latinx Adults

Abstract: Objectives The aim of this evidence-based theoretically informed article was to provide an overview of how and why the COVID-19 outbreak is particularly detrimental for the health of older Black and Latinx adults. Methods We draw upon current events, academic literature, and numerous data sources to illustrate how biopsychosocial factors place older adults at higher risk for COVID-19 relative to younger adults, and how structural racism magnifies these risks for black and Latinx adults across the life course. Results We identify 3 proximate mechanisms through which structural racism operates as a fundamental cause of racial/ethnic inequalities in COVID-19 burden among older adults: (a) risk of exposure, (b) weathering processes, and (c) health care access and quality. Discussion While the ongoing COVID-19 pandemic is an unprecedented crisis, the racial/ethnic health inequalities among older adults it has exposed are longstanding and deeply rooted in structural racism within American society. This knowledge presents both challenges and opportunities for researchers and policymakers as they seek to address the needs of older adults. It is imperative that federal, state, and local governments collect and release comprehensive data on the number of confirmed COVID-19 cases and deaths by race/ethnicity and age to better gauge the impact of the outbreak across minority communities. We conclude with a discussion of incremental steps to be taken to lessen the disproportionate burden of COVID-19 among older Black and Latinx adults, as well as the need for transformative actions that address structural racism in order to achieve population health equity.

Prevalence of Clinical and Subclinical Myocarditis in Competitive Athletes With Recent SARS-CoV-2 Infection: Results From the Big Ten COVID-19 Cardiac Registry.

Abstract: Importance Myocarditis is a leading cause of sudden death in competitive athletes Myocardial inflammation is known to occur with SARS-CoV-2 Different screening approaches for detection of myocarditis have been reported The Big Ten Conference requires comprehensive cardiac testing including cardiac magnetic resonance (CMR) imaging for all athletes with COVID-19, allowing comparison of screening approaches Objective To determine the prevalence of myocarditis in athletes with COVID-19 and compare screening strategies for safe return to play Design, Setting, and Participants Big Ten COVID-19 Cardiac Registry principal investigators were surveyed for aggregate observational data from March 1, 2020, through December 15, 2020, on athletes with COVID-19 For athletes with myocarditis, presence of cardiac symptoms and details of cardiac testing were recorded Myocarditis was categorized as clinical or subclinical based on the presence of cardiac symptoms and CMR findings Subclinical myocarditis classified as probable or possible myocarditis based on other testing abnormalities Myocarditis prevalence across universities was determined The utility of different screening strategies was evaluated Exposures SARS-CoV-2 by polymerase chain reaction testing Main Outcome and Measure Myocarditis via cardiovascular diagnostic testing Results Representing 13 universities, cardiovascular testing was performed in 1597 athletes (964 men [604%]) Thirty-seven (including 27 men) were diagnosed with COVID-19 myocarditis (overall 23%; range per program, 0%-76%); 9 had clinical myocarditis and 28 had subclinical myocarditis If cardiac testing was based on cardiac symptoms alone, only 5 athletes would have been detected (detected prevalence, 031%) Cardiac magnetic resonance imaging for all athletes yielded a 74-fold increase in detection of myocarditis (clinical and subclinical) Follow-up CMR imaging performed in 27 (730%) demonstrated resolution of T2 elevation in all (100%) and late gadolinium enhancement in 11 (407%) Conclusions and Relevance In this cohort study of 1597 US competitive athletes with CMR screening after COVID-19 infection, 37 athletes (23%) were diagnosed with clinical and subclinical myocarditis Variability was observed in prevalence across universities, and testing protocols were closely tied to the detection of myocarditis Variable ascertainment and unknown implications of CMR findings underscore the need for standardized timing and interpretation of cardiac testing These unique CMR imaging data provide a more complete understanding of the prevalence of clinical and subclinical myocarditis in college athletes after COVID-19 infection The role of CMR in routine screening for athletes safe return to play should be explored further

Challenges and Solutions for Cellular Based V2X Communications

Abstract: A wide variety of works have been conducted in vehicle-to-everything (V2X) communications to enable a variety of applications for road safety, traffic efficiency and passenger infotainment. Although dedicated short-range communications (DSRC) based V2X is already in the deployment phase, cellular based V2X is gaining more interest in academia and industry most recently. This article surveys the existing work and challenges on LTE and 5G to support efficient V2X communications. First, we present the motivations for cellular based V2X communications. Second, we summarize the LTE V2X architecture and operating scenarios being considered. Third, we discuss the challenges in existing LTE for supporting V2X communications such as physical layer structure, synchronization, multimedia broadcast multicast services (MBMS), resource allocation, security and survey the recent solutions to these challenges. We further discuss the challenges and possible solutions for 5G based vehicular communications. Finally, we discuss the open research issues and possible research directions in cellular based vehicular communications.

A unified vegetation index for quantifying the terrestrial biosphere.

Abstract: Empirical vegetation indices derived from spectral reflectance data are widely used in remote sensing of the biosphere, as they represent robust proxies for canopy structure, leaf pigment content, and, subsequently, plant photosynthetic potential. Here, we generalize the broad family of commonly used vegetation indices by exploiting all higher-order relations between the spectral channels involved. This results in a higher sensitivity to vegetation biophysical and physiological parameters. The presented nonlinear generalization of the celebrated normalized difference vegetation index (NDVI) consistently improves accuracy in monitoring key parameters, such as leaf area index, gross primary productivity, and sun-induced chlorophyll fluorescence. Results suggest that the statistical approach maximally exploits the spectral information and addresses long-standing problems in satellite Earth Observation of the terrestrial biosphere. The nonlinear NDVI will allow more accurate measures of terrestrial carbon source/sink dynamics and potentials for stabilizing atmospheric CO2 and mitigating global climate change.

Electron and photon reconstruction and identification with the CMS experiment at the CERN LHC

Abstract: The performance is presented of the reconstruction and identification algorithms for electrons and photons with the CMS experiment at the LHC. The reported results are based on proton-proton collision data collected at a center-of-mass energy of 13 TeV and recorded in 2016-2018, corresponding to an integrated luminosity of 136 fb$^{-1}$. Results obtained from lead-lead collision data collected at $\sqrt{s_\mathrm{NN}}=$ 5.02 TeV are also presented. Innovative techniques are used to reconstruct the electron and photon signals in the detector and to optimize the energy resolution. Events with electrons and photons in the final state are used to measure the energy resolution and energy scale uncertainty in the recorded events. The measured energy resolution for electrons produced in Z boson decays in proton-proton collision data ranges from 2 to 5%, depending on electron pseudorapidity and energy loss through bremsstrahlung in the detector material. The energy scale in the same range of energies is measured with an uncertainty smaller than 0.1 (0.3)% in the barrel (endcap) region in proton-proton collisions and better than 1 (3)% in the barrel (endcap) region in heavy ion collisions. The timing resolution for electrons from Z boson decays with the full 2016-2018 proton-proton collision data set is measured to be 200 ps.

Energy-efficient design for mmWave-enabled NOMA-UAV networks

Abstract: Owing to the recent advances of non-orthogonal multiple access (NOMA) and millimeter-wave (mmWave), these two technologies are combined in unmanned aerial vehicle (UAV) networks in this paper.However, energy efficiency has become a significant metric for UAVs owning to their limited energy.Thus, we aim to maximize the energy efficiency for mmWave-enabled NOMA-UAV networks by optimizing the UAV placement, hybrid precoding and power allocation.However, the optimization problem is complicated and intractable, which is decomposed into several sub-problems.First, we solve the UAV placement problem by approximating it into a convex one.Then, the hybrid precoding with user clustering is performed to better reap the multi-antenna gain. Particularly, three schemes are proposed, where the cluster head selection algorithm is adopted while considering different equivalent channels of users.Finally, the power allocation is optimized to maximize the energy efficiency, which is converted to convex and solved via an iterative algorithm.Simulation results are provided to evaluate the performance of the proposedschemes.

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Abstract: Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

Lakes in the era of global change: moving beyond single-lake thinking in maintaining biodiversity and ecosystem services.

Abstract: The Anthropocene presents formidable threats to freshwater ecosystems. Lakes are especially vulnerable and important at the same time. They cover only a small area worldwide but harbour high levels of biodiversity and contribute disproportionately to ecosystem services. Lakes differ with respect to their general type (e.g. land-locked, drainage, floodplain and large lakes) and position in the landscape (e.g. highland versus lowland lakes), which contribute to the dynamics of these systems. Lakes should be generally viewed as 'meta-systems', whereby biodiversity is strongly affected by species dispersal, and ecosystem dynamics are contributed by the flow of matter and substances among locations in a broader waterscape context. Lake connectivity in the waterscape and position in the landscape determine the degree to which a lake is prone to invasion by non-native species and accumulation of harmful substances. Highly connected lakes low in the landscape accumulate nutrients and pollutants originating from ecosystems higher in the landscape. The monitoring and restoration of lake biodiversity and ecosystem services should consider the fact that a high degree of dynamism is present at local, regional and global scales. However, local and regional monitoring may be plagued by the unpredictability of ecological phenomena, hindering adaptive management of lakes. Although monitoring data are increasingly becoming available to study responses of lakes to global change, we still lack suitable integration of models for entire waterscapes. Research across disciplinary boundaries is needed to address the challenges that lakes face in the Anthropocene because they may play an increasingly important role in harbouring unique aquatic biota as well as providing ecosystem goods and services in the future.

Reconstruction of ancient microbial genomes from the human gut.

Abstract: Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces. Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.

The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice

Abstract: Extibacter muris is a newly described mouse gut bacterium which metabolizes cholic acid (CA) to deoxycholic acid (DCA) via 7α-dehydroxylation. Although bile acids influence metabolic and inflammatory responses, few in vivo models exist for studying their metabolism and impact on the host. Mice were colonized from birth with the simplified community Oligo-MM12 with or without E. muris. As the metabolism of bile acids is known to affect lipid homeostasis, mice were fed either a low- or high-fat diet for eight weeks before sampling and analyses targeting the gut and liver. Multiple Oligo-MM12 strains were capable of deconjugating primary bile acids in vitro. E. muris produced DCA from CA either as pure compound or in mouse bile. This production was inducible by CA in vitro. Ursodeoxycholic, chenodeoxycholic, and β-muricholic acid were not metabolized under the conditions tested. All gnotobiotic mice were stably colonized with E. muris, which showed higher relative abundances after HF diet feeding. The presence of E. muris had minor, diet-dependent effects on Oligo-MM12 communities. The secondary bile acids DCA and surprisingly LCA and their taurine conjugates were detected exclusively in E. muris-colonized mice. E. muris colonization did not influence body weight, white adipose tissue mass, liver histopathology, hepatic aspartate aminotransferase, or blood levels of cholesterol, insulin, and paralytic peptide (PP). However, proteomics revealed shifts in hepatic pathways involved in amino acid, glucose, lipid, energy, and drug metabolism in E. muris-colonized mice. Liver fatty acid composition was substantially altered by dietary fat but not by E. muris.In summary, E. muris stably colonized the gut of mice harboring a simplified community and produced secondary bile acids, which affected proteomes in the liver. This new gnotobiotic mouse model can now be used to study the pathophysiological role of secondary bile acids in vivo.

Infectious Diseases Society of America Position Paper: Recommended Revisions to the National Severe Sepsis and Septic Shock Early Management Bundle (SEP-1) Sepsis Quality Measure.

Abstract: The Centers for Medicare & Medicaid Services' Severe Sepsis and Septic Shock Early Management Bundle (SEP-1) measure has appropriately established sepsis as a national priority. However, the Infectious Diseases Society of America (IDSA and five additional endorsing societies) is concerned about SEP-1's potential to drive antibiotic overuse because it does not account for the high rate of sepsis overdiagnosis and encourages aggressive antibiotics for all patients with possible sepsis, regardless of the certainty of diagnosis or severity of illness. IDSA is also concerned that SEP-1's complex "time zero" definition is not evidence-based and is prone to inter-observer variation. In this position paper, IDSA outlines several recommendations aimed at reducing the risk of unintended consequences of SEP-1 while maintaining focus on its evidence-based elements. IDSA's core recommendation is to limit SEP-1 to septic shock, for which the evidence supporting the benefit of immediate antibiotics is greatest. Prompt empiric antibiotics are often appropriate for suspected sepsis without shock, but IDSA believes there is too much heterogeneity and difficulty defining this population, uncertainty about the presence of infection, and insufficient data on the necessity of immediate antibiotics to support a mandatory treatment standard for all patients in this category. IDSA believes guidance on managing possible sepsis without shock is more appropriate for guidelines that can delineate the strengths and limitations of supporting evidence and allow clinicians discretion in applying specific recommendations to individual patients. Removing sepsis without shock from SEP-1 will mitigate the risk of unnecessary antibiotic prescribing for noninfectious syndromes, simplify data abstraction, increase measure reliability, and focus attention on the population most likely to benefit from immediate empiric broad-spectrum antibiotics.

Yogurt, cultured fermented milk, and health: a systematic review.

Abstract: Consumption of yogurt and other fermented products is associated with improved health outcomes. Although dairy consumption is included in most dietary guidelines, there have been few specific recommendations for yogurt and cultured dairy products. A qualitative systematic review was conducted to determine the effect of consumption of fermented milk products on gastrointestinal and cardiovascular health, cancer risk, weight management, diabetes and metabolic health, and bone density using PRISMA guidelines. English language papers in PubMed were searched, with no date restrictions. In total, 1057 abstracts were screened, of which 602 were excluded owing to lack of appropriate controls, potential biases, and experimental design issues. The remaining 455 papers were independently reviewed by both authors and 108 studies were included in the final review. The authors met regularly to concur, through consensus, on relevance, methods, findings, quality, and conclusions. The included studies were published between 1979 and 2017. From the 108 included studies, 76 reported a favorable outcome of fermented milks on health and 67 of these were considered to be positive or neutral quality according to the Academy of Nutrition and Dietetics’ Quality Criteria Checklist. Of the 32 remaining studies, the study outcomes were either not significant (28) or unfavorable (4), and most studies (18) were of neutral quality. A causal relationship exists between lactose digestion and tolerance and yogurt consumption, and consistent associations exist between fermented milk consumption and reduced risk of breast and colorectal cancer and type 2 diabetes, improved weight maintenance, and improved cardiovascular, bone, and gastrointestinal health. Further, an association exists between prostate cancer occurrence and dairy product consumption in general, with no difference between fermented and unfermented products. This article argues that yogurt and other fermented milk products provide favorable health outcomes beyond the milk from which these products are made and that consumption of these products should be encouraged as part of national dietary guidelines. Systematic review registration: PROSPERO registration no. CRD42017068953.

Universal DNA methylation age across mammalian tissues

Abstract: Aging is often perceived as a degenerative process caused by random accrual of cellular damage over time. In spite of this, age can be accurately estimated by epigenetic clocks based on DNA methylation profiles from almost any tissue of the body. Since such pan-tissue epigenetic clocks have been successfully developed for several different species, it is difficult to ignore the likelihood that a defined and shared mechanism instead, underlies the aging process. To address this, we generated 10,000 methylation arrays, each profiling up to 37,000 cytosines in highly-conserved stretches of DNA, from over 59 tissue-types derived from 128 mammalian species. From these, we identified and characterized specific cytosines, whose methylation levels change with age across mammalian species. Genes associated with these cytosines are greatly enriched in mammalian developmental processes and implicated in age-associated diseases. From the methylation profiles of these age-related cytosines, we successfully constructed three highly accurate universal mammalian clocks for eutherians, and one universal clock for marsupials. The universal clocks for eutherians are similarly accurate for estimating ages (r>0.96) of any mammalian species and tissue with a single mathematical formula. Collectively, these new observations support the notion that aging is indeed evolutionarily conserved and coupled to developmental processes across all mammalian species - a notion that was long-debated without the benefit of this new and compelling evidence.