bluuebunny/crossref_metadata_2025_split huggingface dataset:
A High-Reliability Organization Framework for Health Care: A Multiyear Implementation Strategy and Associated Outcomes
Authors: Sculli Gary L. , Pendley-Louis Robin , Neily Julia , Anderson Timothy M. , Isaacks David B. , Knowles Regina , Young-Xu Yinong , Gunnar William 
Published: October 2020

Objectives
Applying high-reliability organization (HRO) principles to health care is complex. No consensus exists as to an effective framework for HRO implementation or the direct impact of adoption.

Methods
The Veterans Health Administration (VHA) National Center for Patient Safety established the high-reliability hospital (HRH) model for HRO adoption and piloted HRH in collaboration with the Truman VA Medical Center (Truman) during a 3-year intervention period (January 1, 2016–December 31, 2018). High-reliability hospital components are as follows: annual patient safety (PS) assessment, annual PS culture survey, annual root cause analysis training, daily leadership walk-arounds, monthly PS forum, annual processes standardization review, Just Culture training, unit-based Clinical Team Training, unit-based continuous improvement projects, and annual Clinical Team Training simulation education. The impact of HRH was examined using a PS Culture Survey, PS event reporting, and quality outcomes of standardized mortality rate and complication rate.

Results
Truman internally improved PS culture and PS event reporting rates resulting in outcomes better than all VHA facilities (All VHA; P < 0.001 and P < 0.001, respectively). Low-harm PS event reporting increased (P < 0.001); however, serious safety event rate remained unchanged versus All VHA. Significant improvement in Truman standardized mortality rate and complication rate versus All VHA occurred immediately and were sustained through intervention (slopes, P < 0.001 and P < 0.020; respectively).

Conclusions
High-reliability hospital is an effective framework for HRO implementation and will be applied to 18 additional VHA sites. Based on these results, the expected outcome will be improved PS culture and overall PS event reporting. The impact of HRH on serious safety event rate and quality measures requires further study.
COVID-19 Susceptibility and Outcomes Among People Living With HIV in San Francisco
Authors: Sachdev Darpun , Mara Elise , Hsu Ling , Scheer Susan , Rutherford George , Enanoria Wayne , Gandhi Monica 
Published: October 2020

Introduction:
Studies to examine whether HIV predisposes to a higher incidence of COVID-19 or more severe disease are accumulating. Initial studies from New York City suggested more severe disease among people living with HIV (PLWH), but this was during a time when hospitals were over-capacity and health systems stretched. This report presents the incidence and outcomes among PLWH with COVID-19 in San Francisco over the first 6 months of the pandemic.

Methods:
Community transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first reported in San Francisco on March 5, 2020. This report examines the match of the San Francisco Department of Public Health COVID-19 testing database and the San Francisco Department of Public Health HIV Surveillance case registry from March 24, 2020, to September 3, 2020.

Results:
Among 4252 COVID-19 tests performed among PLWH, 4.5% (N = 193) were positive for COVID-19, compared with a 3.5% (N = 9626) positivity rate among the 272,555 people without HIV tested for COVID-19 (P < 0.001). The mean age of those infected with HIV/COVID-19 was 48 years (20–76), 38.9% White, 38.3% Latinx, 11.9% Black, and 91.2% were men. Only 54.6% of coinfected PLWH were housed, with the remainder marginally housed. The rate of severe illness with COVID-19 was not increased among PLWH.

Discussion:
In San Francisco, susceptibility to COVID-19 was increased among PLWH over the first 6 months of the pandemic, although clinical outcomes were similar to those without HIV. Homelessness and higher rates of congregate living situations among PLWH likely accounted for this disparity. Special efforts to house patients with marginal housing during the COVID-19 pandemic are needed.
Clinical application of non-coding RNAs in sepsis
Authors: Iro Mildred A. , Soundara Pandi Sudha Priya 
Published: October 2020

Purpose of review
Studies indicating that non-coding RNAs (ncRNAs) play a regulatory role in sepsis are increasing rapidly. This present review summarizes recent publications on the role of microRNAs and long non-coding RNAs (lncRNAs) in sepsis.

Recent findings
MicroRNAs (miRNAs) and lncRNAs are being identified as potential sepsis biomarkers and therapeutic targets. Experimental studies have examined the biological mechanisms that might underpin the regulatory role of these ncRNAs in sepsis.

Summary
Clinical applications of miRNAs and lncRNAs in sepsis are on the horizon. These data could lead to the identification of novel treatments or indeed support the repurposing of existing drugs for sepsis. Validation of the findings from these preliminary studies and crucially integration of multiomics datasets will undoubtedly revolutionize the clinical management of sepsis.
Do the Benefits of Educational Attainment for Late-life Cognition Differ by Racial/Ethnic Group?
Authors: Eng Chloe W. , Glymour Medellena Maria , Gilsanz Paola , Mungas Dan M. , Mayeda Elizabeth R. , Meyer Oanh L. , Whitmer Rachel A. 
Published: October 2020

Introduction:
Educational attainment is associated with late-life cognitive performance and dementia; few studies have examined diverse racial/ethnic groups to assess whether the association differs by race/ethnicity.

Methods:
We investigated whether the association between educational attainment and cognition differed between White, Black, Asian, and Latino participants in the Kaiser Healthy Aging and Diverse Life Experiences study (n=1348). Covariate-adjusted multivariable linear regression models examined domains of verbal episodic memory, semantic memory, and executive functioning.

Results:
We observed significant effect heterogeneity by race/ethnicity only for verbal episodic memory (P=0.0198), for which any schooling between high school and college was beneficial for White, Asian, and Black participants, but not Latino participants. We found no evidence of heterogeneity for semantic memory or executive function.

Discussion:
With the exception of Latino performance on verbal episodic memory, more education consistently predicted better cognitive scores to a similar extent across racial/ethnic groups, despite likely heterogenous educational and social experiences.
Using Test Positivity and Reported Case Rates to Estimate State-Level COVID-19 Prevalence and Seroprevalence in the United States
Authors: Chiu Weihsueh A. , Ndeffo-Mbah Martial L. 
Published: October 2020

AbstractAccurate estimates of infection prevalence and seroprevalence are essential for evaluating and informing public health responses needed to address the ongoing spread of COVID-19 in the United States. A data-driven Bayesian single parameter semi-empirical model was developed and used to evaluate state-level prevalence and seroprevalence of COVID-19 using daily reported cases and test positivity ratios. COVID-19 prevalence is well-approximated by the geometric mean of the positivity rate and the reported case rate. As of December 8, 2020, we estimate nation-wide a prevalence of 1.4% [Credible Interval (CrI): 0.8%-1.9%] and a seroprevalence of 11.1% [CrI: 10.1%-12.2%], with state-level prevalence ranging from 0.3% [CrI: 0.2%-0.4%] in Maine to 3.0% [CrI: 1.1%-5.7%] in Pennsylvania, and seroprevalence from 1.4% [CrI: 1.0%-2.0%] in Maine to 22% [CrI: 18%-27%] in New York. The use of this simple and easy-to-communicate model will improve the ability to make public health decisions that effectively respond to the ongoing pandemic.Biographical Sketch of AuthorsDr. Weihsueh A. Chiu, is a professor of environmental health sciences at Texas A&M University. He is an expert in data-driven Bayesian modeling of public health related dynamical systems. Dr. Martial L. Ndeffo-Mbah, is an Assistant Professor of Epidemiology at Texas A&M University. He is an expert in mathematical and computational modeling of infectious diseases.Summary LineRelying on reported cases and test positivity rates individually can result in incorrect inferences as to the spread of COVID-19, and public health decision-making can be improved by instead using their geometric mean as a measure of COVID-19 prevalence and transmission.
Safely Reopening K-12 Schools During the COVID-19 Pandemic
Authors: Shelley Courtney D. , Chadwick Philippa S. , Manore Carrie , Del Valle Sara Y. 
Published: October 2020

ABSTRACTEarly school closures were a consistent, nationwide response to the COVID-19 pandemic in mid-March due to the role that children play in spreading influenza. This left us with limited understanding of COVID-19 transmission in children until several states reopened schools for the 2020-2021 school year. While early school closures were likely beneficial in protecting children in the initial stages of the pandemic in the U.S., long-term closures pose significant cumulative effects in children who rely on schools for instruction and additional social services, and for parents who need to balance work and childcare obligations. Reopening schools safely is a high priority for many interested stakeholders.Proposed in-person school reopening plans include traditional, 100% school capacity, five days per week instruction, hybrid scenarios with reduced in-person instruction and virtual learning, and various reduced school capacity schedules with non-pharmaceutical interventions in place. To assess the potential impacts of different reopening plans, we created a modified SIR-type transmission model that captures multiple known pathways of COVID-19 transmission in a 100,000-person community.Our results show that plans that utilize consecutive days in school and divide students into separated smaller cohorts who attend school together, as well as plans that emphasize distance learning, are better able to suppress disease spread and reduce risk from an introduced infective into the community. Plans with more consecutive school days are protective for both the schoolchildren and surrounding community by acting to separate the larger intermixing population into smaller intermixing subpopulations. The “Five-Day Switch” plan, which separates students into two cohorts, each of whom attend in-person learning for five consecutive days followed by five days of distance learning, best captures these protective attributes. All modeled plans assumed initially disease-free communities and that children’s interactions with the community are greatly reduced during instructional days, both for in-person and distance learning.
A virulence associated siderophore importer causes antimicrobial efflux inKlebsiella pneumoniae
Authors: Farzand Robeena , Rajakumar Kumar , Barer Michael R , Freestone Primrose P E , Mukamolova Galina V , Oggioni Marco R , O’Hare Helen M 
Published: October 2020

AbstractThe accessory genome of many pathogenic bacteria includes ABC transporters that scavenge metal by siderophore uptake and ABC transporters that contribute to antimicrobial resistance by multidrug efflux. There are mechanistic and recently recognised structural similarities between siderophore importer proteins and efflux pumps. Here we investigated the influence of siderophore importer YbtPQ on antimicrobial resistance ofKlebsiella pneumoniae. YbtPQ is encoded in the yersiniabactin cluster in a prevalent mobile genetic element ICEKp, and is also common in pathogenicity islands ofEscherichia coliandYersiniaspecies, where yersiniabactin enhances virulence. Deletion of ICEKp increased the sensitivity ofK. pneumoniaeto all antimicrobials tested. The mechanism was dependent on the yersiniabactin importer YbtPQ and involved antimicrobial efflux, since it was affected by the inhibitor reserpine. The element ICEKp is naturally highly mobile, indeed the accessory genome ofK. pneumoniaeis recognised as a reservoir of genes for the emergence of hospital outbreak strains and for transfer to other Gram-negative pathogens. Introduction of ICEKp, or a plasmid encoding YbtPQ, toE. colidecreased its sensitivity to a broad range of antimicrobials. Thus, a confirmed siderophore importer, on a rapidly evolving and highly mobile element capable of interspecies transfer, may have a secondary function exporting antimicrobials.
Plasmodesmata-localized proteins and reactive oxygen species orchestrate light-induced rapid systemic signaling in Arabidopsis
Authors: Fichman Yosef , Myers Ronald J. , Grant DeAna G. , Mittler Ron 
Published: October 2020

AbstractSystemic signaling and systemic acquired acclimation (SAA) are key to the survival of plants during episodes of abiotic stress. These processes depend on a continuous chain of cell-to-cell signaling events that extends from the initial tissue that senses the stress (local tissue) to the entire plant (systemic tissues). Among the different systemic signaling molecules and processes thought to be involved in this cell-to-cell signaling mechanism are reactive oxygen species (ROS), calcium, electric and hydraulic signals. How these different signals and processes are interlinked, and how they transmit the systemic signal all the way from the local tissue to the entire plant, remain however largely unknown. Here, studying the systemic response ofArabidopsis thalianato a local treatment of excess light stress, we report that respiratory burst oxidase homolog D (RBOHD)-generated ROS enhance cell-to-cell transport and plasmodesmata (PD) pore size in a process that depends on the function of PD-localized proteins (PDLPs) 1 and 5, promoting the cell-to-cell transport of systemic signals during responses to light stress. We further identify aquaporins, and several different calcium-permeable channels, belonging to the glutamate receptor-like, mechanosensitive small conductance-like, and cyclic nucleotide-gated families, as involved in this process, but determine that their function is primarily required for the maintenance of the signal in each cell along the path of the systemic signal, as well as for the establishment of acclimation at the local and systemic tissues. PD and RBOHD-generated ROS orchestrate therefore light stress-induced rapid cell-to-cell spread of systemic signals in Arabidopsis.One-sentence summaryRespiratory burst oxidase homolog D-generated reactive oxygen species enhance cell-to-cell transport and plasmodesmata (PD) pore size in a process that depends on the function of the PD-localized proteins (PDLPs) 1 and 5, promoting the cell-to-cell transport of rapid systemic signals during the response of Arabidopsis to excess light stress.
Circadian fluctuations in glucocorticoid level predict perceptual discrimination sensitivity
Authors: Obleser Jonas , Kreitewolf Jens , Vielhauer Ricarda , Lindner Fanny , David Carolin , Oster Henrik , Tune Sarah 
Published: October 2020

SummarySlow neurobiological rhythms, such as the circadian secretion of glucocorticoid (GC) hormones, modulate a wide variety of body functions. Whether and how such endocrine fluctuations also exert an influence on perceptual abilities is largely uncharted. Here, we show that phasic, moderate increases in GC availability prove beneficial to auditory discrimination. In an age-varying sample of N = 68 healthy human participants, we characterise the covariation of saliva cortisol with perceptual sensitivity in an auditory pitch-discrimination task at five time points across the sleep--wake cycle. First, momentary saliva cortisol levels were captured well by the time relative to wake-up and overall sleep duration. Second, within individuals, higher cortisol level just prior to behavioural testing predicted better pitch discrimination ability, expressed as a steepened psychometric curve. This effect of glucocorticoids held under a set of statistical control models. Our results pave the way for more in-depth studies on neuroendocrinological determinants of sensory encoding and perception.
Breeding Program Optimization for Genomic Selection in Winter Wheat
Authors: Calvert Megan , Evers Byron , Wang Xu , Fritz Allan , Poland Jesse 
Published: October 2020

AbstractDeveloping methodologies in the fields of phenomics and genomic prediction have the potential to increase the production of crop species by accelerating germplasm improvement. The integration of these technologies into germplasm improvement and breeding programs requires evidence that there will be a direct economic benefit to the program. We determined a basic set of parameters, such as prediction accuracy greater than 0.3, the ability to genotype over 7 lines for the cost of one phenotypic evaluation, and heritability levels below 0.4, at which the use of genomic selection would be of economic benefit in terms of genetic gain and operational costs to the Kansas State University (KSU) winter wheat breeding program. The breeding program was then examined to determine whether the parameters benefitting genomic selection were observed or achievable in a practical sense. Our results show that the KSU winter wheat breeding program is at a decision point with regards to their primary means of selection. A few operational changes to increase prediction accuracy would place the program in the parameter space where genomic selection is expected to outpace the current phenotypic selection methodology at a parity of the operation cost and would be of greatest benefit to the program.
Prevalence of Mild Cognitive Impairment in the Lothian Birth Cohort 1936
Authors: Welstead Miles , Luciano Michelle , Muniz-Terrera Graciela , Taylor Adele M. , Russ Tom C. 
Published: October 2020

ABSTRACTBackgroundThe Lothian Birth Cohort 1936 (LBC1936) is a highly-phenotyped longitudinal study of cognitive and brain ageing. Given its substantial clinical importance, we derived an indicator of mild cognitive impairment (MCI) as well as amnestic and non-amnestic subtypes at three time points.MethodsMCI status was derived at three waves of the LBC1936 at ages 76 (n=567), 79 (n=441), and 82 years (n=341). A general MCI category was derived as well as amnestic MCI (aMCI) and non-amnestic MCI (naMCI). A comparison was made between MCI derivations using normative data from the LBC1936 cohort versus the general UK population.ResultsMCI rates showed a proportional increase at each wave between 76 and 82 years from 15% to 18%. Rates of MCI subtypes also showed a proportional increase over time: aMCI 4% to 6%; naMCI 12% to 16%. Higher rates of MCI were found when using the LBC1936 normative data to derive MCI classification rather than UK-wide norms.ConclusionsWe found that MCI and aMCI rates in the LBC1936 were consistent with previous research. However, naMCI rates were higher than expected. Future LBC1936 research should assess the predictive factors associated with MCI prevalence to validate previous findings and identify novel risk factors.
BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
Authors: Fan Jeremy , Huang Steven , Chorlton Samuel D 
Published: October 2020

AbstractBackgroundAs the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification in a fast and accurate manner are needed. Existing tools were either designed for short-read data (eg. Centrifuge) or take days to analyse modern sequencer outputs (eg. MetaMaps).ResultsWe present BugSeq, a novel, highly accurate metagenomic classifier for nanopore reads. BugSeq (F1=0.91-0.95) offers better read classification than MetaMaps (F1=0.89-0.94) in a fraction of the time. BugSeq significantly improves on the accuracy of Centrifuge (F1=0.79-0.93) while offering competitive run times. We apply BugSeq to metagenomic sequencing of 41 samples from patients with lower respiratory tract infections and show that it produces greater concordance with microbiological culture and qPCR compared with “What’s In My Pot” analysis.ConclusionBugSeq is deployed to the cloud for easy and scalable long-read metagenomic analyses. BugSeq is freely available for non-commercial use athttps://bugseq.com/free.Contactsam@bugseq.com
In VivoValidation of Bimolecular Fluorescence Complementation (BiFC) to Investigate Aggregate Formation in Amyotrophic Lateral Sclerosis (ALS)
Authors: Don Emily K , Maschirow Alina , Radford Rowan A W , Scherer Natalie M , Vidal-Itriago Andres , Hogan Alison , Maurel Cindy , Formella Isabel , Stoddart Jack J , Hall Thomas E , Lee Albert , Shi Bingyang , Cole Nicholas J , Laird Angela S , Badrock Andrew P , Chung Roger S , Morsch Marco 
Published: October 2020

AbstractAmyotrophic lateral sclerosis (ALS) is a form of motor neuron disease (MND) that is characterized by the progressive loss of motor neurons within the spinal cord, brainstem and motor cortex. Although ALS clinically manifests as a heterogeneous disease, with varying disease onset and survival, a unifying feature is the presence of ubiquitinated cytoplasmic protein inclusion aggregates containing TDP-43. However, the precise mechanisms linking protein inclusions and aggregation to neuronal loss are currently poorly understood.Bimolecular Fluorescence Complementation (BiFC) takes advantage the association of fluorophore fragments (non-fluorescent on their own) that are attached to an aggregation prone protein of interest. Interaction of the proteins of interest allows for the fluorescent reporter protein to fold into its native state and emit a fluorescent signal. Here, we combined the power of BiFC with the advantages of the zebrafish system to validate, optimize and visualize of the formation of ALS-linked aggregates in real time in a vertebrate model. We further providein vivovalidation of the selectivity of this technique and demonstrate reduced spontaneous self-assembly of the non-fluorescent fragmentsin vivoby introducing a fluorophore mutation. Additionally, we report preliminary findings on the dynamic aggregation of the ALS-linked hallmark proteins Fus and TDP-43 in their corresponding nuclear and cytoplasmic compartments using BiFC.Overall, our data demonstrates the suitability of this BiFC approach to study and characterize ALS-linked aggregate formationin vivo. Importantly, the same principle can be applied in the context of other neurodegenerative diseases and has therefore critical implications to advance our understanding of pathologies that underlie aberrant protein aggregation.