bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of Error in Interpretive Pathology
Authors: Packer Matthew D C , Ravinsky Esther , Azordegan Nazila 
Published: October 2021

Abstract

Objectives
To demonstrate how the educational presentation and targeted review of cases with discrepant interpretive findings between pathologists can raise awareness for specific diagnostic errors through identification of common overarching patterns of error in interpretive pathology.

Methods
We performed a review of 147 surgical pathology and cytopathology cases of discordances from 23 PowerPoint presentations presented between 2010 and 2017. Pathologists and pathology residents, blinded from the official interpretations, were presented each case and surveyed for their own diagnostic assessments. Survey results were compared with the final/correct interpretations of the signing pathologists.

Results
Of the 134 cases with available survey results, there were 87 (64.9%) for which most survey respondents proposed a diagnostic interpretation concordant with the final/correct diagnosis. There were 37 (27.6%) cases for which most survey responses were either wholly or partially discordant with the final/correct diagnosis. For 10 (7.5%) cases, there were equal numbers of concordant and discordant survey responses.

Conclusions
Our analyses of the cases with frequent erroneous diagnoses reveal common patterns of error that are widely applicable and outline specific error-prone interpretive tendencies. Greater awareness for these tendencies, highlighted by presentation of discordant cases, can improve the quality of diagnostic pathology services.
Factors Associated With Not Having a Healthcare Visit in the Past Year Among US Adults With Hypertension: Data From NHANES 2013–2018
Authors: Akinyelure Oluwasegun P , Hubbard Demetria , Sakhuja Swati , Hardy Shakia T , Oparil Suzanne , Cherrington Andrea L , Reynolds Kristi , Wozniak Gregory , Muntner Paul 
Published: September 2021

Abstract

Background
Not having a healthcare visit in the past year has been associated with a higher likelihood of uncontrolled blood pressure (BP) among individuals with hypertension.

Methods
We examined factors associated with not having a healthcare visit in the past year among US adults with hypertension using data from the US National Health and Nutrition Examination Survey 2013–2018 (n = 5,985). Hypertension was defined as systolic BP (SBP) ≥140 mm Hg, diastolic BP (DBP) ≥90 mm Hg, or antihypertensive medication use. Having a healthcare visit in the past year was self-reported.

Results
Overall, 7.0% of US adults with hypertension reported not having a healthcare visit in the past year. Those without vs. with a healthcare visit in the past year were less likely to be aware they had hypertension (45.0% vs. 83.9%), to be taking antihypertensive medication (36.7% vs. 91.4%, among those who were aware they had hypertension), and to have controlled BP (SBP/DBP &lt;140/90 mm Hg; 9.1% vs. 51.7%). After multivariable adjustment, not having a healthcare visit in the past year was more common among US adults without health insurance (prevalence ratio [PR]: 2.22; 95% confidence interval [CI] 1.68–2.95), without a usual source of healthcare (PR: 5.65; 95% CI 4.16–7.67), who smoked cigarettes (PR: 1.34; 95% CI 1.02–1.77), and with heavy vs. no alcohol consumption (PR: 1.55; 95% CI 1.16–2.08). Also, not having a healthcare visit in the past year was more common among those without diabetes or a history of atherosclerotic cardiovascular disease, and those not taking a statin.

Conclusions
Interventions should be considered to ensure all adults with hypertension have annual healthcare visits.
Attenuation of Myocardial Fibrosis Using Molecular Hydrogen by Inhibiting the TGF-β Signaling Pathway in Spontaneous Hypertensive Rats
Authors: Liu Libo , Shi Qian , Liu Xiaohong , Li Yanmin , Li Xiuchang 
Published: October 2021

Abstract

BACKGROUND
Previous studies have shown that hydrogen can antagonize the fibrosis of various organs. We investigated whether hydrogen-rich saline (HRS) can attenuate myocardial fibrosis in spontaneously hypertensive rats (SHRs) and clarified the mechanisms involved.

METHODS
We examined the effect of HRS and pirfenidone (PFD) on myocardial fibrosis in SHR. Systolic blood pressure, left ventricular mass index (LVMI), and heart weight index (HWI) were measured, Masson trichrome staining was performed. We assessed the role of superoxide dismutase (SOD), malondialdehyde (MDA), Alpha-smooth muscle actin (α-SMA), collagen I, collagen III, and tissue inhibitors of metalloproteinases (TIMPs) in myocardium. We detected the concentrations of procollagen type-I C-terminal propeptide (PICP), procollagen type-III N-terminal propeptide (PIIINP), and angiotensin II (Ang II) in rat serum. Furthermore, the relative protein levels of the transforming growth factor beta (TGF-β)/Smad pathway were tested.

RESULTS
We discovered that HRS decreases LVMI (P &lt; 0.05) and HWI (P &lt; 0.05) in vivo. Compared with model group, HRS decreases the level of collagen volume fraction (P &lt; 0.0001), collagen I (P &lt; 0.001), and collagen III (P &lt; 0.001) in myocardium, and Ang II (P &lt; 0.05), PICP (P &lt; 0.001), and PIIINP (P &lt; 0.05) in serum. In addition, HRS downregulates the expression of MDA (P &lt; 0.01), α-SMA (P &lt; 0.05), and TIMPs (P &lt; 0.05), and increased SOD (P &lt; 0.05). Furthermore, HRS downregulated the expression levels of TGF-β1 (P &lt; 0.0001), Smad3 (P &lt; 0.0001), and Smad2/3 (P &lt; 0.001), but had no effect on Smad7 expression (P &gt; 0.05). PFD had similar effect compared with HRS and control group.

CONCLUSIONS
HRS reduced oxidative stress and improved myocardial collagen content, which may be related to inhibition of the TGF-β signaling pathway. This suggests that HRS is an effective therapeutic strategy for myocardial fibrosis.
Does developmental environment affect sexual conflict? An experimental test in the seed beetle
Authors: Zhang Zhuzhi , Head Megan L 
Published: October 2021

AbstractSexual conflict and sexually antagonistic coevolution are driven by differences in reproductive interests between the sexes. There have been numerous studies focused on how both the social and physical environment that individuals experience as adults, or where mating occurs, mediate the intensity of sexual conflict. However, how the physical environment that juveniles experience, mediates their later mating interactions, is still poorly understood. In seed beetles, Callosobruchus maculatus, water is an important resource that can impact fitness and reproduction. Here, we manipulated the water content of beans that beetles were reared in and explored how this environmental variation affects mating interactions and subsequent male and female fitness. We measured the mass of ejaculate transferred, mating behavior, female fecundity, and offspring production as well as male and female lifespan. We found that males reared in wet environments transferred a larger ejaculate to females, but only when females were reared in dry environments. We also found that females mated to males reared in dry environments laid more eggs than those mated to males from wet environments. Additionally, eggs laid by females reared in dry conditions had greater survival when they had mated to males reared in dry than wet environments. Overall, however, there were no treatment effects on the number of adult offspring females produced nor male or female adult lifespan, thus it is difficult to determine the evolutionary implications of these results. Our research provides evidence for the importance of developmental environment for determining the expression of adult mating and fitness traits.
Post-fledging behavioral ecology of migratory songbirds: how do fledgling activity rates vary across species?
Authors: Jones Todd M , Ward Michael P 
Published: October 2021

AbstractDespite a large literature on the ontogeny of animal behavior, our understanding of behavioral development in young songbirds remains relatively poor. This is particularly true for the post-fledging period, where it is often difficult to follow and observe small, freely moving fledglings for extended periods of time. Fortunately, technological advances have enabled more robust examinations of songbird post-fledging behaviors. To provide greater insight into fledgling developmental and behavioral ecology, we used automated radio-telemetry systems to document post-fledging activity rates of juveniles across 9 songbird species of east-central Illinois, USA. Specifically, we sought to examine differences in the ontogeny of activity rates across species, and compare activity rates to intrinsic (e.g. morphological traits, age) and extrinsic (e.g. predation risk, brood size) factors that have the potential to influence fledgling behavior. While post-fledging activity rates differed by species, our findings show remarkable similarities in the ontogeny of fledgling activity across the avian community; all species exhibited a steady increase in activity rates with post-fledging age, with rates leveling off roughly 3 to 4 weeks post-fledging. These general patterns mirrored rates of post-fledging mortality (primarily due to predation) across the period, including the presence or absence of a post-fledging bottleneck, in which species with bottlenecks exhibit slight declines in activity rates during the first few days out of the nest. Alongside fledgling age and mortality risk, our findings also suggest that juvenile wing development and brood size at fledging mediate fledgling activity rates within and across species.
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics
Authors: Murphy Alan E , Schilder Brian M , Skene Nathan G 
Published: September 2021

Abstract

Motivation
Genome-wide association studies (GWAS) summary statistics have popularized and accelerated genetic research. However, a lack of standardization of the file formats used has proven problematic when running secondary analysis tools or performing meta-analysis studies.

Results
To address this issue, we have developed MungeSumstats, a Bioconductor R package for the standardization and quality control of GWAS summary statistics. MungeSumstats can handle the most common summary statistic formats, including variant call format (VCF) producing a reformatted, standardized, tabular summary statistic file, VCF or R native data object.

Availability and implementation
MungeSumstats is available on Bioconductor (v 3.13) and can also be found on Github at: https://neurogenomics.github.io/MungeSumstats.

Supplementary information
Supplementary data are available at Bioinformatics online.
RCytoGPS: an R package for reading and visualizing cytogenetics data
Authors: Abrams Zachary B , Tally Dwayne G , Abruzzo Lynne V , Coombes Kevin R 
Published: September 2021

Abstract

Summary
Cytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology.

Availability and implementation
Freely available at https://CRAN.R-project.org/package=RCytoGPS. The code for the underlying CytoGPS software can be found at https://github.com/i2-wustl/CytoGPS
EZH2 knockout in oral cavity basal epithelia causes more invasive squamous cell carcinomas
Authors: Baquero Jorge , Tang Xiao-Han , Scognamiglio Theresa , Gudas Lorraine J 
Published: October 2021

Abstract
Oral squamous cell carcinoma (oral SCC) is an aggressive disease and despite intensive treatments, 5-year survival rates for patients have remained low in the last 20 years. Enhancer of zeste homolog 2 (EZH2), part of polycomb repressive complex 2 (PRC2), is highly expressed in human oral SCC samples and cell lines and has been associated with greater epithelia-to-mesenchymal transition (EMT), invasion and metastasis. Here, we developed a tamoxifen-regulated, transgenic mouse line (KcEZH2) in which EZH2 is selectively knocked out (KO) in some tongue epithelial basal stem cells (SCs) in adult mice. EZH2 KO SCs do not show the H3K27me3 mark, as assessed by double-label immunofluorescence. We used this mouse line to assess EZH2 actions during oral tumorigenesis with our immunocompetent 4-nitroquinoline 1-oxide model of oral SCC. We report that higher percentages of mice with invasive SCCs and high-grade neoplastic lesions are observed in mice containing EZH2 KO SCs (KcEZH2-2TΔ and KcEZH2-5TΔ mice). Moreover, EZH2 expression does not correlate with the expression of markers of invasive SCCs. Finally, EZH2 KO cells that are E-cadherin+ are present at invasion fronts infiltrating underlying muscle tissue. Our findings indicate that the knockout of EZH2 in basal SCs of tongue epithelia results in more aggressive carcinomas, and this should be considered when targeting EZH2 as a therapeutic strategy.
Therapeutic Emergency Use Authorizations (EUAs) During Pandemics: Double-edged Swords
Authors: Bhimraj Adarsh , Morgan Rebecca L , Shumaker Amy Hirsch , Lavergne Valery , Baden Lindsey , Cheng Vincent Chi-Chung , Edwards Kathryn M , Gandhi Rajesh T , Gallagher Jason C , Muller William J , O’Horo John C , Shoham Shmuel , Wollins Dana Swartzberg , Falck-Ytter Yngve 
Published: October 2021

Abstract
Given the urgent need for treatments during the coronavirus disease 2019 pandemic, the US Food and Drug Administration issued emergency use authorizations (EUAs) for multiple therapies. In several instances, however, these EUAs were issued before sufficient evidence of a given therapy’s efficacy and safety were available, potentially promoting ineffective or even harmful therapies and undermining the generation of definitive evidence. We describe the strengths and weaknesses of the different therapeutic EUAs issued during this pandemic. We also contrast them to the vaccine EUAs and suggest a framework and criteria for an evidence-based, trustworthy, and publicly transparent therapeutic EUA process for future pandemics.
Modeling Temperature-Dependent Development Rate in Insects and Implications of Experimental Design
Authors: Régnier Baptiste , Legrand Judith , Rebaudo François 
Published: October 2021

Abstract
Characterizing the temperature-dependent development rate requires empirical data acquired by rearing individuals at different temperatures. Many mathematical models can be fitted to empirical data, making model comparison a mandatory step, yet model selection practices widely vary. We present guidelines for model selection using statistical criteria and the assessment of biological relevance of fits, exemplified throughout a Lepidoptera pest dataset. We also used in silico experiments to explore how experimental design and species attributes impact estimation accuracy of biological traits. Our results suggested that the uncertainty in model predictions was mostly determined by the rearing effort and the variance in development times of individuals. We found that a higher number of tested temperatures instead of a higher sample size per temperature may lead to more accurate estimations of model parameters. Our simulations suggested that an inappropriate model choice can lead to biased estimated values of biological traits (defined as attributes of temperature dependent development rate, i.e., optimal temperature for development and critical thresholds), highlighting the need for standardized model selection methods. Therefore, our results have direct implications for future studies on the temperature-dependent development rate of insects.
A new dissection-specific hybrid stent graft for patients with DeBakey type I aortic dissection
Authors: Charchyan Eduard , Breshenkov Denis , Belov Yuriy 
Published: October 2021

Abstract

OBJECTIVES
We present our first experience of using a new dissection-specific hybrid stent graft (SG) (the ‘Soft Elephant Trunk’) in the frozen elephant trunk technique, in patients with non-acute DeBakey type I aortic dissection.

METHODS
Between September 2016 and February 2021, patients with non-acute DeBakey type I aortic dissection underwent the frozen elephant trunk procedure at our centre using 3 SG types: group Z used stiff, distal Z-shaped nitinol SGs (E-Vita, Medtronic); group R used a stiff, ring-shaped nitinol SG (Thoraflex); and group S used a soft, distal dissection-specific SG. Predictors of distal SG-induced new entry were analysed. End points were hospital- and midterm-follow-up results.

RESULTS
The study comprised 109 patients with 46 (42.2%), 22 (20.2%) and 41 (37.6%) patients in groups Z, R and S, respectively. No significant differences were found in early outcomes. Freedom from distal SG-induced new entry was comparable in groups Z, R and S (68.9% vs 92.9% vs 100%, log-rank = 0.14). There was no significant difference in follow-up between the groups. Four-year survival rates were 80.44%, 71.59% and 95.06% in groups Z, R and S, respectively. On multivariable analysis, the presence of connective tissue disorders [hazard ratio (HR) = 5.62, P = 0.11] and SG diameter (HR = 1.37, P = 0.034) were strong predictors of distal SG-induced new entry.

CONCLUSIONS
Dissection-specific hybrid SG with a soft distal end is effective in patients with non-acute DeBakey type I aortic dissection. Compared to non-soft distal SGs, this can reduce the incidence of distal complications. Long-term outcomes are necessary to determine the potential advantages and disadvantages of the new prosthesis.
Can nudging only get you so far? Testing for nudge combination effects
Authors: Howley Peter , Ocean Neel 
Published: October 2021

AbstractThere is an emerging body of evidence to suggest that nudges can motivate behaviour change. The question as to whether using nudges in tandem ‘crowds out’ the marginal effectiveness of each one has attracted little attention. Using a randomised survey experiment consisting of 1,800 farmers, we tested the impact of two nudge interventions (injunctive norm and social signalling) when used individually in isolation and also when used in combination. Our findings are indicative of limited crowd out effects and more generally suggest that there may be scope for employing non-monetary interventions in combination when it comes to encouraging technology uptake.
The importance of including density in multiparameter asymptotic linearized direct waveform inversion: a case study from the Eastern Nankai Trough
Authors: Farshad Milad , Chauris Hervé , Noble Mark 
Published: October 2021

SUMMARY
Iterative least-squares reverse time migration (LSRTM) is the state-of-the-art linearized waveform inversion method to obtain quantitative subsurface parameters. The main drawback of such an iterative imaging scheme is the significant computational expense of many modelling/adjoint cycles through iterations. In the context of the extended domain, an interesting alternative to LSRTM is the asymptotic linearized direct waveform inversion, providing quantitative results with only a single iteration. This approach was first proposed for constant-density acoustics and recently extended to the variable-density case. The former is based on the application of the asymptotic inverse Born operator, whereas the latter has two more extra steps: building an angle-dependent response of the asymptotic inverse Born operator and then solving a weighted least-squares approach for simultaneous inversion of two acoustic parameters. To examine the importance of accounting for density variations, we compare constant- and variable-density linearized direct waveform inversion techniques applied to a marine real data set from the Eastern Nankai Trough, offshore Japan. The inversion results confirm the efficiency of the asymptotic linearized direct waveform inversion in estimating quantitative parameters within a single iteration. The variable-density direct inversion yields subsurface images that (1) exhibit a superior resolution and (2) better reconstruct the field data than does the constant-density approach, even if the data set does not contain large enough surface offset to fully decompose velocity and density perturbations.
Graph neural network based hydraulic turbine data stream prediction
Authors: Li Ning , Ren Jing , Zhou Xin , Li Jun , Xue Chen 
Published: October 2021

Abstract
As a kind of green energy with mature technology, hydropower energy is more and more widely used in our real life. As the core equipment of a hydropower station, hydraulic turbine units will experience varying degrees of vibration and aging during the process of power generation. Due to the complex internal structure and the interaction between different components, the analysis and prediction of the relevant operating data of the water turbine unit has important application value. This paper proposes a graph neural network framework for multivariate data stream prediction. In this method, a graph learning module is designed to automatically extract the one-way relationship between different components of the turbine unit. In addition, the mix-hop propagation layer and expansion layer are designed to capture the spatial and temporal correlations in hydraulic turbine data stream. Experiments show that the proposed method has higher accuracy comparing with the existing methods.
Vision impairment and self-reported anxiety and depression in older adults in Nigeria: evidence from a cross-sectional survey in Kogi State
Authors: Gascoyne Ben , Jolley Emma , Penzin Selben , Ogundimu Kola , Owoeye Foluso , Schmidt Elena 
Published: October 2021

Abstract

Background
More than 2 billion people are thought to be living with some form of vision impairment worldwide. Yet relatively little is known about the wider impacts of vision loss on individual health and well-being, particularly in low- and middle-income countries (LMICs). This study estimated the associations between all-cause vision impairment and self-reported symptoms of anxiety and depression among older adults in Kogi State, Nigeria.

Methods
Individual eyes were examined according to the standard Rapid Assessment of Avoidable Blindness methodology, and anxiety and depression were assessed using the Washington Group Short Set on Functioning–Enhanced. The associations were estimated using multivariable logistic regression models, adding two- and three-way interaction terms to test whether these differed for gender subgroups and with age.

Results
Overall, symptoms of either anxiety or depression, or both, were worse among people with severe visual impairment or blindness compared with those with no impairment (OR=2.72, 95% CI 1.86 to 3.99). Higher levels of anxiety and/or depression were observed among men with severe visual impairment and blindness compared with women, and this gender gap appeared to widen as people got older.

Conclusions
These findings suggest a substantial mental health burden among people with vision impairment in LMICs, particularly older men, underscoring the importance of targeted policies and programmes addressing the preventable causes of vision impairment and blindness.