bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the influence of BMI on the outcome after total knee arthroplasty
Authors: Wang Huan , Qiong Ma , Ma Baoan 
Published: May 2021

Background:
A meta-analysis of published cohort studies was used to evaluate differences in outcome measures after total knee arthroplasty (TKA) among thinnish, normal, overweight, obese, and morbidly obese patients.

Materials and methods:
Manual retrieval of the results of patients with different body mass index (BMI) in primary TKA from the self-built Chinese and English databases such as PubMed, EMBASE, Cochrane, Sinomed, CnKI, Wanfang, and Vip from November 2020 was performed. Include retrospective or prospective cohort studies, according to the World Health Organization BMI packet primary TKA special surgical hospital in New York, the knee joint function assessment used in patients with knee scoring criteria (HSS) or the knee society score (KSS) as well as the operation time, intraoperative blood transfusion volume, length of hospital stay, postoperative complications of literature, literature including repeat, system evaluation, meta-analysis, case report, BMI groups not strictly and outcome indicators of incomplete documents. After independent literature screening, data extraction, and quality evaluation by 2 researchers, meta-analysis was carried out with Revman5.4 software. In the end, 20 literatures were included.

Results:
The preoperative score decreased with the increase of BMI in each group, while the postoperative knee joint function score in the normal group, overweight group, obese group, and in the morbidly obese group were all higher than that before the surgery (P<0.00001), and the changes were more obvious in the morbidly obese group. The length of stay in the normal group was the shortest, followed by the overweight and obese group. The operative time and intraoperative blood transfusion showed that the thinnish group was less than the normal group, while the overweight and the obese group was higher than the normal group. Finally, postoperative complications in the other groups were all higher than the normal group, with significant differences. We can see the preoperative knee function score decreased with the increase of BMI, the operation time, intraoperative blood transfusion volume, length of hospital stay, presents the opposite trend, the postoperative complications in each group were higher than in normal group, here also pay special attention to thinnish group compared with normal group complications increase.

Conclusion:
The present meta-analysis demonstrated that BMI higher than normal can affect intraoperative risk of TKA and postoperative recovery, and increase the risk of complications.
Genomics of aging: The role of sirtuin and metabolic health
Authors: Wysocki Kenneth , Seibert Diane 
Published: May 2021

ABSTRACT
Healthy aging is not the result of a single factor. Genes, dietary choices/options, exercise, and environmental exposures all play a role. A family of seven nicotinamide adenine dinucleotide (NAD)–dependent sirtuin proteins are very involved in various metabolic functions, such as glucose and fat regulation, and polymorphisms in these genes have been associated with the development of obesity, type 2 diabetes, cancer, cardiovascular disease, and longevity. Nutraceuticals (i.e., resveratrol, quercetin, kaempferol, and curcumin) and other therapies (i.e., synthetic sirtuin-activating compounds, NAD, nicotinamide mononucleotide) are all being explored as in potential therapies in the sirtuin pathway and point to promising treatments to promote metabolic health and reduce obesity and age-related disease. For the clinician looking to reduce the risk of age-related metabolic disorders, evidence points to these supplements and appropriate food choices as the next generation of pharmaceutical grade therapies continue to be researched for human use.
Rethinking DNP education: Just another mountain to climb
Authors: Beauchesne Michelle A. 
Published: May 2021

ABSTRACT
The World Health Organization designated 2020 as the International Year of the Nurse and Midwife in celebration of the 200th birthday of Florence Nightingale, the founder of modern nursing. This article considers the future of nurse practitioner education in light of nursing history. First, a brief overview describes the progression of nursing education since the founding of the Nightingale School in 1860. Then, current challenges in NP education are discussed. Potential solutions to these issues are presented.
Wastewater-based estimation of the effective reproductive number of SARS-CoV-2
Authors: Huisman Jana S. , Scire Jérémie , Caduff Lea , Fernandez-Cassi Xavier , Ganesanandamoorthy Pravin , Kull Anina , Scheidegger Andreas , Stachler Elyse , Boehm Alexandria B. , Hughes Bridgette , Knudson Alisha , Topol Aaron , Wigginton Krista R. , Wolfe Marlene K. , Kohn Tamar , Ort Christoph , Stadler Tanja , Julian Timothy R. 
Published: May 2021

AbstractBackgroundThe effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These estimates are temporarily biased when clinical testing or reporting strategies change.ObjectivesWe show that the dynamics of SARS-CoV-2 RNA in wastewater can be used to estimate Re in near real-time, independent of clinical data and without the associated biases.MethodsWe collected longitudinal measurements of SARS-CoV-2 RNA in wastewater in Zurich, CH, and San Jose (CA), USA. We combined this data with information on the temporal dynamics of shedding (the shedding load distribution) to estimate a time series proportional to the daily COVID-19 infection incidence. We estimated a wastewater-based Re from this incidence.ResultsThe method to estimate Re from wastewater works robustly on data from two different countries and two wastewater matrices. The resulting estimates are as similar to the Re estimates from case report data as Re estimates based on observed cases, hospitalizations, and deaths are among each other. We further provide details on the effect of sampling frequency and the shedding load distribution on the ability to infer Re.DiscussionTo our knowledge, this is the first time Re has been estimated from wastewater. This method provides a low cost, rapid, and independent way to inform SARS-CoV-2 monitoring during the ongoing pandemic and is applicable to future wastewater-based epidemiology targeting other pathogens.
Original antigenic sin responses to heterologous Betacoronavirus spike proteins are observed in mice following intramuscular administration, but are not apparent in children following SARS-CoV-2 infection
Authors: Lapp Stacey A. , Edara Venkata Viswanadh , Lu Austin , Lai Lilin , Hussaini Laila , Chahroudi Ann , Anderson Larry J. , Suthar Mehul S. , Anderson Evan J. , Rostad Christina A. 
Published: May 2021

AbstractBackgroundThe effects of pre-existing endemic human coronavirus (HCoV) immunity on SARS-CoV-2 serologic and clinical responses are incompletely understood.ObjectivesWe sought to determine the effects of prior exposure to HCoV Betacoronavirus HKU1 spike protein on serologic responses to SARS-CoV-2 spike protein after intramuscular administration in mice. We also sought to understand the baseline seroprevalence of HKU1 spike antibodies in healthy children and to measure their correlation with SARS-CoV-2 binding and neutralizing antibodies in children hospitalized with acute coronavirus disease 2019 (COVID-19) or multisystem inflammatory syndrome (MIS-C).MethodsGroups of 5 mice were injected intramuscularly with two doses of alum-adjuvanted HKU1 spike followed by SARS-CoV-2 spike; or the reciprocal regimen of SARS-Cov-2 spike followed by HKU1 spike. Sera collected 21 days following each injection was analyzed for IgG antibodies to HKU1 spike, SARS-CoV-2 spike, and SARS-CoV-2 neutralization. Sera from children hospitalized with acute COVID-19, MIS-C or healthy controls (n=14 per group) were analyzed for these same antibodies.ResultsMice primed with SARS-CoV-2 spike and boosted with HKU1 spike developed high titers of SARS-CoV-2 binding and neutralizing antibodies; however, mice primed with HKU1 spike and boosted with SARS-CoV-2 spike were unable to mount neutralizing antibodies to SARS-CoV-2. HKU1 spike antibodies were detected in all children with acute COVID-19, MIS-C, and healthy controls. Although children with MIS-C had significantly higher HKU1 spike titers than healthy children (GMT 37239 vs. 7551, P=0.012), these titers correlated positively with both SARS-CoV-2 binding (r=0.7577, P<0.001) and neutralizing (r=0.6201, P=0.001) antibodies.ConclusionsPrior murine exposure to HKU1 spike protein completely impeded the development of neutralizing antibodies to SARS-CoV-2, consistent with original antigenic sin. In contrast, the presence of HKU1 spike IgG antibodies in children with acute COVID-19 or MIS-C was not associated with diminished neutralizing antibody responses to SARS-CoV-2.
Single-tube collection and nucleic acid analysis of clinical samples: a rapid approach for SARS-CoV-2 saliva testing
Authors: Cole Kyle H. , Bouin Alexis , Ruiz Caila , Semler Bert L. , Inlay Matthew A. , Lupták Andrej 
Published: May 2021

AbstractThe SARS-CoV-2 pandemic has brought to light the need for expedient diagnostic testing. Cost and availability of large-scale testing capacity has led to a lag in turnaround time and hindered contact tracing efforts, resulting in a further spread of SARS-CoV-2. To increase the speed and frequency of testing, we developed a cost-effective single-tube approach for collection, denaturation, and analysis of clinical samples. The approach utilizes 1 µL microbiological inoculation loops to collect saliva, sodium dodecyl sulfate (SDS) to inactivate and release viral genomic RNA, and a diagnostic reaction mix containing polysorbate 80 (Tween 80). In the same tube, the SDS-denatured clinical samples are introduced to the mixtures containing all components for nucleic acids detection and Tween 80 micelles to absorb the SDS and allow enzymatic reactions to proceed, obviating the need for further handling of the samples. The samples can be collected by the tested individuals, further decreasing the need for trained personnel to administer the test. We validated this single-tube sample- to-assay method with RT-qPCR and RT-LAMP and discovered little-to-no difference between Tween- and SDS-containing reaction mixtures, compared to CDC-approved reagents. This approach significantly reduces the logistical burden of traditional large-scale testing and provides a method of deployable point-of-care diagnostics to increase testing frequency.
Modular effects of gene promoters and chromatin environments on noise in gene expression
Authors: Zhao Siqi , Pincus Zachary , Cohen Barak A 
Published: May 2021

AbstractGenetically identical cells growing in the same environment can have large differences in gene expression. Both locally actingcis-regulatory sequences (CRS) and the regional properties of chromosomal environments influence the noisiness of a gene’s expression. Whether or not local CRS and regional chromosomal environments act independently on noise, or whether they interact in complex ways is unknown. To address this question, we measured the expression mean and noise of reporter genes driven by different CRS at multiple chromosomal locations. While a strong power law relationship between mean expression and noise explains ~60% of noise for diverse promoters across chromosomal locations, modeling the residual mean-independent noise suggests that chromosomal environments have strong effects on expression noise by influencing how quickly genes transition from their inactive states to their active states and that the effects of local CRS and regional chromatin on noise are largely independent. Our results support a modular genome in which regional chromatin modifies the inherent relationship between the mean and noise of expression regardless of the identity of the promoter sequence.
Best practices for analyzing imputed genotypes from low-pass sequencing in dogs
Authors: Buckley Reuben M. , Harris Alex C. , Wang Guo-Dong , Whitaker D. Thad , Zhang Ya-Ping , Ostrander Elaine A. 
Published: May 2021

AbstractAlthough DNA array-based approaches for genome wide association studies (GWAS) permit the collection of thousands of low-cost genotypes, it is often at the expense of resolution and completeness, as SNP chip technologies are ultimately limited by SNPs chosen during array development. An alternative low-cost approach is low-pass whole genome sequencing (WGS) followed by imputation. Rather than relying on high levels of genotype confidence at a set of select loci, low-pass WGS and imputation relies on the combined information from millions of randomly sampled low confidence genotypes. To investigate low-pass WGS and imputation in the dog, we assessed accuracy and performance by downsampling 97 high-coverage (>15x) WGS datasets from 51 different breeds to approximately 1x coverage, simulating low-pass WGS. Using a reference panel of 676 dogs from 91 breeds, genotypes were imputed from the downsampled data and compared to a truth set of genotypes generated from high coverage WGS. Using our truth set, we optimized a variant quality filtering strategy that retained approximately 80% of 14M imputed sites and lowered the imputation error rate from 3.0% to 1.5%. Seven million sites remained with a MAF > 5% and an average imputation quality score of 0.95. Finally, we simulated the impact of imputation errors on outcomes for case-control GWAS, where small effect sizes were most impacted and medium to large effect sizes were minorly impacted. These analyses provide best practice guidelines for study design and data post-processing of low-pass WGS imputed genotypes in dogs.
Genetic and ecomorphological divergence between sympatricAstyanaxmorphs from Central America
Authors: Garita-Alvarado Carlos A. , Garduño-Sánchez Marco , Barluenga Marta , Ornelas-García C. Patricia 
Published: May 2021

AbstractEcological and morphological divergence within populations can be a signal of adaptive divergence, which can maintain intraspecific polymorphisms and promote ecological speciation in the event of reproductive isolation. Here, we evaluate correlations among morphology, trophic ecology, and genetic differentiation between two divergent morphs (elongate and deep-body) of the fish genusAstyanaxin the San Juan River basin in Central America, to infer the putative evolutionary mechanism shaping this system. We collected the two morphs from three water bodies and analyzed: 1) the correlation between body shape and the shape of the premaxilla, a relevant trophic structure, 2) the trophic level and niche width of each morph, 3) the correspondence between trophic level and body and premaxillary shape, and 4) the genetic differentiation between morphs using mitochondrial and nuclear markers. We found a strong correlation between the body and premaxillary shape of the morphs. The elongate-body morph had a streamlined body, a premaxilla with acuter angles and a narrower ascending process, and a higher trophic level, characteristic of species with predatorial habits. By contrast, the deep-body morph had a higher body depth, a premaxilla with less acute angles, and a broader trophic niche, suggesting generalist habits. Despite the strong correlation between morphological and ecological divergence, the morphs showed limited genetic differentiation, supporting the idea that morphs may be undergoing incipient ecological speciation, although alternative scenarios such as stable polymorphism or plasticity should also be considered. This study provides evidence about the role of ecological factors in the diversification processes inAstyanax.
VirusTaxo: Taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment
Authors: Raju Rajan Saha , Nahid Abdullah Al , Shuvo Preonath , Islam Rashedul 
Published: May 2021

AbstractTaxonomic classification of viruses is a multi-class hierarchical classification problem, as taxonomic ranks (e.g., order, family and genus) of viruses are hierarchically structured and have multiple classes in each rank. Classification of biological sequences which are hierarchically structured with multiple classes is challenging. Here we developed a machine learning architecture, VirusTaxo, using a multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach and accurately assigns the order, family and genus of a virus from the genome sequence. The average accuracies of VirusTaxo for DNA viruses are 99% (order), 98% (family) and 95% (genus) and for RNA viruses 97% (order), 96% (family) and 82% (genus). VirusTaxo can be used to detect taxonomy of novel viruses using full length genome or contig sequences.AvailabilityOnline version of VirusTaxo is available athttps://omics-lab.com/virustaxo/.
Watching Death in the Gerbil Cochlea Using Optical Coherence Tomography
Authors: Cho Nam Hyun , Wang Haobing , Puria Sunil 
Published: May 2021

AbstractBecause it is difficult to directly observe the morphology of the living cochlea, our ability to infer the mechanical functioning of the living ear has been limited. Nearly all of our knowledge about cochlear morphology comes from postmortem tissue that was fixed and processed using procedures that possibly distort the structures and fluid spaces of the organ of Corti. In this study, optical coherence tomography was employed to obtain in vivo and postmortem micron-scale volumetric images of the high-frequency hook region of the gerbil cochlea through the round-window membrane. The anatomical structures and fluid spaces of the organ of Corti were segmented and quantified in vivo and over a 90-minute postmortem period. The results show that some aspects of the organ of Corti are significantly altered over the course of death, such as the volumes of the fluid spaces, whereas the dimensions of other features change very little. We postulate that the fluid space of the outer tunnel and its surrounding tectal cells form a resonant structure that can affect the motion of the reticular lamina and thereby have a profound effect on outer-hair-cell transduction and thus cochlear amplification. In addition, the in vivo fluid pressure of the inner spiral sulcus is postulated to effectively inflate the connected sub-tectorial gap between the tectorial membrane and the reticular lamina. This gap height decreases after death, which is hypothesized to reduce and disrupt hair-cell transduction
An inexpensive, high-precision, modular spherical treadmill setup optimized forDrosophilaexperiments
Authors: Loesche Frank , Reiser Michael B. 
Published: May 2021

ABSTRACTTo pursue a more mechanistic understanding of the neural control of behavior, many neuroethologists study animal behavior in controlled laboratory environments. One popular approach is to measure the movements of restrained animals while presenting controlled sensory stimulation. This approach is especially powerful when applied to genetic model organisms, such asDrosophila melanogaster,where modern genetic tools enable unprecedented access to the nervous system for activity monitoring or targeted manipulation. While there is a long history of measuring the behavior of body- and head-fixed insects walking on an air-supported ball, the methods typically require complex setups with many custom components. Here we present a compact, simplified setup for these experiments that achieves high-performance at low cost.The simplified setup combines existing hardware and software solutions with new component designs. We replaced expensive optomechanical and custom machined components with off-the-shelf and 3D-printed parts. We built the system around an inexpensive camera that achieves 180 Hz imaging and use an inexpensive tablet computer for presenting view-angle-corrected stimuli updated through a local network. We quantify the performance of the integrated system and characterize the visually guided behavior of flies in response to a range of visual stimuli. The improved system is thoroughly documented. This publication is accompanied by CAD files, parts lists, source code, and step-by-step instructions for setting up the system and analyzing behavioral data. We detail a complete ~$.300 system, including a cold-anesthesia tethering stage, that is ideal for hands-on teaching laboratories. This represents a nearly 50-fold cost reduction as compared to a typical system used in research laboratories, yet is fully featured and yields excellent performance.We report the current state of this system, which started with a one-day teaching lab for which we built seven parallel setups and continues towards a setup in our lab for larger-scale analysis of visual-motor behavior in flies. Because of the simplicity, compactness, and low cost of this system, we believe that high-performance measurements of tethered insect behavior should now be widely accessible and suitable for integration into many systems. This access enables broad opportunities for comparative work across labs, species, and behavioral paradigms.
PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis
Authors: Ashuach Tal , Reidenbach Daniel A. , Gayoso Adam , Yosef Nir 
Published: May 2021

AbstractSingle-cell ATAC sequencing (scATAC-seq) is a powerful and increasingly popular technique to explore the regulatory landscape of heterogeneous cellular populations. However, the high noise levels, degree of sparsity, and scale of the generated data make its analysis challenging. Here we present PeakVI, a probabilistic framework that leverages deep neural networks to analyze scATAC-seq data. PeakVI fits an informative latent space that preserves biological heterogeneity while correcting batch effects and accounting for technical effects such as library size and region-specific biases. Additionally, PeakVI provides a technique for identifying differential accessibility at a single region resolution, which can be used for cell-type annotation as well as identification of key cis-regulatory elements. We use public datasets to demonstrate that PeakVI is scalable, stable, robust to low-quality data, and outperforms current analysis methods on a range of critical analysis tasks. PeakVI is publicly available and implemented in the scvi-tools framework: https://docs.scvi-tools.org/.