bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resisted adduction sit-up test (RASUT) as a screening tool for pelvic versus hip pathology
Authors: Galano Gregory J , Tyler Timothy F , Stubbs Trevor , Ashraf Ali , Roberts Michael , McHugh Malachy P , Zoland Mark P , Nicholas Stephen J 
Published: November 2021

ABSTRACT
Groin pain is a common symptom in hip and pelvic pathology and differentiating between the two remains a challenge. The purpose of this study was to examine whether a test combining resisted adduction with a sit-up (RASUT) differentiates between pelvic and hip pathology. The RASUT was performed on 160 patients with complaints of hip or groin pain who subsequently had their diagnosis confirmed by magnetic resonance imaging (MRI) or surgery. Patients were categorized as having pelvic pathology (athletic pubalgia or other) or hip pathology (intra-articular or other). Athletic pubalgia was defined as any condition involving the disruption of the pubic aponeurotic plate. Sensitivity, specificity, positive predictive accuracy, negative predictive accuracy and diagnostic odds ratios were computed. Seventy-one patients had pelvic pathology (40 athletic pubalgia), 81 had hip pathology and 8 had both. The RASUT was effective in differentiating pelvic from hip pathology; 50 of 77 patients with a positive RASUT had pelvic pathology versus 29 of 83 patients with a negative test (P &lt; 0.001). RASUT was diagnostic for athletic pubalgia (diagnostic odds ratio 6.08, P &lt; 0.001); 35 of 45 patients with athletic pubalgia had a positive RASUT (78% sensitivity) and 73 of 83 patients with a negative RASUT did not have athletic pubalgia (88% negative predictive accuracy). The RASUT can be used to differentiate pelvic from hip pathology and to identify patients without athletic pubalgia. This is a valuable screening tool in the armamentarium of the sports medicine clinician.
Bacterial Communities of Lab and Field Northern House Mosquitoes (Diptera: Culicidae) Throughout Diapause
Authors: Didion Elise M , Doyle Megan , Benoit Joshua B 
Published: November 2021

Abstract
Diapause is a hormonally driven response which is triggered by environmental cues that signal impending adverse conditions and prompts metabolic, developmental, and behavioral changes to allow survival until the return of favorable conditions. Microbial symbionts have been shown to influence the metabolism, development, and behavior of their host organisms, all of which are common diapause-associated characteristics. Surveys of bacterial components in relation to diapause have been examined in few systems, of which the species are usually inactive during dormancy, such as eggs or pupae. This is specifically intriguing as adult female diapause in Culex pipiens (Diptera: Culicidae) can last between 4 and 7 mo and females remain mobile within their hibernacula. Furthermore, it is unknown how microbiota changes associated with prolonged dormancy are different between the lab and field for insect systems. This study aims to characterize how the microbiota of C. pipiens changes throughout diapause under both field and lab settings when provided identical food and water resources. Based on these studies, C. pipiens microbiota shifts as diapause progresses and there are considerable differences between field and lab individuals even when provided the same carbohydrate and water sources. Specific bacterial communities have more association with different periods of diapause, field and lab rearing conditions, and nutritional reserve levels. These studies highlight that diapausing mosquito microbiota studies ideally should occur in field mesocosms and at multiple locations, to increase applicability to wild C. pipiens as prolonged exposure to artificial rearing conditions could impact metrics related to diapause-microbiome interactions. Additionally, these findings suggest that it would be worthwhile to establish if the microbiota shift during diapause impacts host physiology and whether this shift is critical to diapause success.
Are pharmacists well equipped to deal with global health emergencies? Burnout during COVID-19
Authors: Al-Haqan Asmaa , Alenezi Farah , Al-Mutairi Shriefa , Al-Taweel Dalal 
Published: November 2021

Abstract

Objectives
This study aimed to evaluate and assess the burnout effect among pharmacists during COVID-19 pandemic in Kuwait.

Methods
A cross-sectional study using an online self-administered questionnaire was conducted from September 2020 to January 2021. The questionnaire included demographic questions as well as items from the Copenhagen Burnout Inventory (CBI) to assess burnout in three domains: personal burnout, work-related burnout and client-related burnout. Descriptive statistics, correlations and comparative analysis were performed.

Key findings
A total of 277 completed responses were received. The overall mean (SD) score for the respondents’ burnout was 52.8 (19.1). The mean (SD) burnout scores for the three CBI domains (personal, work-related and client-related) were 56.6 (21.7), 53.9 (21.4) and 47.0 (23.8), respectively. It was found that younger age, female, Kuwaiti, Kuwait University graduates and less experienced participants had higher personal, work-related, client-related burnout scores. Personal and work-related scores were more strongly correlated (r = 0.81); in comparison with their correlation with the client-related score (r ≈ 0.55).

Conclusions
High burnout scores for pharmacists in Kuwait on a personal, work-related and client-related level during the COVID-19 pandemic were found. Strategies for early identification of burnout and recognition of modifiable factors that affect pharmacists’ work in Kuwait are needed to promote pharmacists’ psychological well-being.
Measuring Skin Color: Consistency, Comparability, and Meaningfulness of Rating Scale Scores and Handheld Device Readings
Authors: Gordon Rachel A , Branigan Amelia R , Khan Mariya Adnan , Nunez Johanna G 
Published: November 2021

Abstract
As US society continues to diversify and calls for better measurements of racialized appearance increase, survey researchers need guidance about effective strategies for assessing skin color in field research. This study examined the consistency, comparability, and meaningfulness of the two most widely used skin tone rating scales (Massey–Martin and PERLA) and two portable and inexpensive handheld devices for skin color measurement (Nix colorimeter and Labby spectrophotometer). We collected data in person using these four instruments from forty-six college students selected to reflect a wide range of skin tones across four racial-ethnic groups (Asian, Black, Latinx, White). These college students, five study staff, and 459 adults from an online sample also rated forty stock photos, again selected for skin tone diversity. Our results—based on data collected under controlled conditions—demonstrate high consistency across raters and readings. The Massey–Martin and PERLA scale scores were highly linearly related to each other, although PERLA better differentiated among people with the lightest skin tones. The Nix and Labby darkness-to-lightness (L*) readings were likewise linearly related to each other and to the Massey–Martin and PERLA scores, in addition to showing expected variation within and between race ethnicities. In addition, darker Massey–Martin and PERLA ratings correlated with online raters’ expectations that a photographed person experienced greater discrimination. In contrast, the redness (a*) and yellowness (b*) undertones were highest in the mid-range of the rating scale scores and demonstrated greater overlap across race-ethnicities. Overall, each instrument showed sufficient consistency, comparability, and meaningfulness for use in field surveys when implemented soundly (e.g., not requiring memorization). However, PERLA might be preferred to Massey–Martin in studies representing individuals with the lightest skin tones, and handheld devices may be preferred to rating scales to reduce measurement error when studies could gather only a single rating.
A Rescaling Bootstrap Approach For Imputed Survey Data
Authors: Mashreghi Zeinab , Deng Huiqi 
Published: November 2021

Abstract
Imputation is usually used to deal with item nonresponse in surveys. Treating the imputed values as true observations may obviously lead to serious underestimation of the variance of point estimators. In this article, we propose a new bootstrap method under the rescaling bootstrap approach for estimating the variance of an imputed estimator obtained after applying deterministic regression or random hot-deck imputation. A novel technique is used to rescale the original data set through solving certain systems of linear equations. The proposed procedure can handle unequal response probabilities and large sampling fractions. Some simulation studies are conducted to show the great performance of the proposed method in terms of relative bias, relative efficiency, and coverage probability, for both population mean and median.
Modelling multiwavelength emission of Ultra-luminous X-ray Sources accreting above the Eddington limit
Authors: Ambrosi E , Zampieri L , Pintore F , Wolter A 
Published: November 2021

ABSTRACT
We model the multiwavelength properties of binaries accreting at super-critical rates with the aim to better understand the observational properties of Ultra-luminous X-ray Sources (ULXs). We calculate an extended grid of binary systems which evolve through Roche Lobe Overflow and undergo case A mass transfer from massive donors (up to 25 ${\rm M}_{\odot } \,$) on to massive black holes (BHs) (up to 100 ${\rm M}_{\odot } \,$). Angular momentum loss with the ejection of mass through an outflow is incorporated. We apply our super-Eddington accretion model to these systems, computing their evolutionary tracks on the colour–magnitude diagram (CMD) for the Johnson and Hubble Space Telescope photometric systems. We found that the tracks occupy specific positions on the CMD depending on the evolutionary stage of the donor and of the binary. Moreover, their shapes are similar, regardless the BH mass. More massive BHs lead to more luminous tracks. We additionally compute their optical-through-X-ray spectral energy distribution considering the effects of a Comptonizing corona that surrounds the innermost regions of the disc. We apply our model to four ULXs: NGC 4559 X-7, NGC 5204 X-1, Holmberg II X-1, and NGC 5907 ULX-2. We found that accretion on to BHs with mass in the range of 35–55 ${\rm M}_{\odot }$ is consistent with to the observational properties of these sources. We finally explore and discuss the possibility to extend our model also to ULXs powered by accreting pulsars (PULXs).
Radio and X-ray spectral properties of gamma-ray bursts and pulsar wind nebulae
Authors: Zhu Bo-Tao , Lu Fang-Wu , Zhou Bing , Fang Jun , Zhang Li 
Published: November 2021

ABSTRACT
Both gamma-ray bursts (GRBs) and pulsar wind nebula (PWNe) are energetic outflows that are produced in powerful high-energy astrophysical environments. Based on the correlations between the radio luminosity LR and X-ray luminosity LX as well as between the multiband spectral slope αRX and radio flux FR for compiled GRB and PWN samples, the radio and X-ray spectral properties are statistically investigated. The results show that (1) the correlations between LR and LX are consistent for GRBs and PWNe, within the uncertainties; and (2) for the whole sample, FR is related to αRX, and GRBs have lower αRX than PWNe. It may be concluded that GRBs and PWNe have the same or similar particle acceleration mechanisms and radiation processes, i.e. synchrotron radiation, to produce the radio-to-X-ray band emission.
Angular clustering properties of the DESI QSO target selection using DR9 Legacy Imaging Surveys
Authors: Chaussidon Edmond , Yèche Christophe , Palanque-Delabrouille Nathalie , de Mattia Arnaud , Myers Adam D , Rezaie Mehdi , Ross Ashley J , Seo Hee-Jong , Brooks David , Gaztañaga Enrique , Kehoe Robert , Levi Michael E , Newman Jeffrey A , Tarlé Gregory , Zhang Kai 
Published: November 2021

ABSTRACT
The quasar target selection for the upcoming survey of the Dark Energy Spectroscopic Instrument (DESI) will be fixed for the next 5 yr. The aim of this work is to validate the quasar selection by studying the impact of imaging systematics as well as stellar and galactic contaminants, and to develop a procedure to mitigate them. Density fluctuations of quasar targets are found to be related to photometric properties such as seeing and depth of the Data Release 9 of the DESI Legacy Imaging Surveys. To model this complex relation, we explore machine learning algorithms (random forest and multilayer perceptron) as an alternative to the standard linear regression. Splitting the footprint of the Legacy Imaging Surveys into three regions according to photometric properties, we perform an independent analysis in each region, validating our method using extended Baryon Oscillation Spectroscopic Survey (eBOSS) EZ-mocks. The mitigation procedure is tested by comparing the angular correlation of the corrected target selection on each photometric region to the angular correlation function obtained using quasars from the Sloan Digital Sky Survey (SDSS) Data Release 16. With our procedure, we recover a similar level of correlation between DESI quasar targets and SDSS quasars in two-thirds of the total footprint and we show that the excess of correlation in the remaining area is due to a stellar contamination that should be removed with DESI spectroscopic data. We derive the Limber parameters in our three imaging regions and compare them to previous measurements from SDSS and the 2dF QSO Redshift Survey.
Spatio-temporal bands of coronal bright points and their relation to solar torsional oscillations
Authors: Tsinamdzgvrishvili Tamar , Chargeishvili B B , Shergelashvili Bidzina M , Mghebrishvili Irakli 
Published: November 2021

ABSTRACT
Using automatic processing of daily fits files from SOHO_EIT, we studied the temporal evolution of the latitudinal distribution of bright coronal points from 1995 to 2020. The study revealed homogeneous and inhomogeneous components of the latitudinal distribution. The homogeneous component has cyclical variations with a significant phase shift compared to the number of sunspots. The residual inhomogeneous component manifests itself as migration of the centre of increased density from high to low latitudes. The bands of the residual density of coronal bright points (CBP) reflect solar torsional oscillations. It should be associated with the strengthening of the local alpha-omega dynamo. However, the cyclical nature of the number of CBP is explained by the diffusion of large-scale magnetic fluxes.
The impact of primordial binary on the dynamical evolution of intermediate massive star clusters
Authors: Wang Long , Tanikawa Ataru , Fujii Michiko S 
Published: November 2021

ABSTRACT
Observations found that star clusters contain a large fraction of binaries. Tight binaries are an important heating source that influences the long-term dynamical evolution of star clusters. However, due to the limitation of N-body tool, previous theoretical modelling for globular clusters (GCs) by using direct N-body simulations has not investigated how a large fraction of primordial binaries affect their long-term evolution. In this work, by using the high-performance N-body code, petar, we carry out star-by-star models for intermediate massive GCs (N = 100 000) with the primordial binary fraction varying from 0 to 1. We find that when a stellar-mass black hole (BH) subsystem exists, the structural evolution of GCs (core and half-mass radii) only depends on the properties of massive primordial binaries, because they affect the number of BH binaries (BBHs), which dominate the binary heating process. Low-mass binaries including double white dwarf binaries (BWDs) have almost no influence on the dynamics. Meanwhile, only gravitational wave mergers from BBHs are strongly affected by dynamical interactions, while low-mass mergers from BWDs show no difference in the isolated environment (field) and in GCs. Low-mass binaries become important only after most BHs escape and the core collapse of light stars occurs. Our result suggests that for N-body modelling of GCs with a BH subsystem dominating binary heating, it is not necessary to include low-mass binaries. These binaries can be studied separately by using standalone binary stellar evolution codes. This way can significantly reduce the computing cost.
GenBank
Authors: Sayers Eric W , Cavanaugh Mark , Clark Karen , Pruitt Kim D , Schoch Conrad L , Sherry Stephen T , Karsch-Mizrachi Ilene 
Published: November 2021

Abstract
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 15.3 trillion base pairs from over 2.5 billion nucleotide sequences for 504 000 formally described species. Recent updates include resources for data from the SARS-CoV-2 virus, including a SARS-CoV-2 landing page, NCBI Datasets, NCBI Virus and the Submission Portal. We also discuss upcoming changes to GI identifiers, a new data management interface for BioProject, and advice for providing contextual metadata in submissions.
OUHP: an optimized universal hairpin primer system for cost-effective and high-throughput RT-qPCR-based quantification of microRNA (miRNA) expression
Authors: He Fang , Ni Na , Wang Hao , Zeng Zongyue , Zhao Piao , Shi Deyao , Xia Yinglin , Chen Connie , Hu Daniel A , Qin Kevin H , Wagstaff William , Qin David , Hendren-Santiago Bryce , Ho Sherwin H , Haydon Rex C , Luu Hue H , Reid Russell R , Shen Le , Gan Hua , Fan Jiaming , He Tong-Chuan 
Published: November 2021

Abstract
MicroRNAs (miRNAs or miRs) are single-stranded, ∼22-nucleotide noncoding RNAs that regulate many cellular processes. While numerous miRNA quantification technologies are available, a recent analysis of 12 commercial platforms revealed high variations in reproducibility, sensitivity, accuracy, specificity and concordance within and/or between platforms. Here, we developed a universal hairpin primer (UHP) system that negates the use of miRNA-specific hairpin primers (MsHPs) for quantitative reverse transcription PCR (RT-qPCR)-based miRNA quantification. Specifically, we analyzed four UHPs that share the same hairpin structure but are anchored with two, three, four and six degenerate nucleotides at 3′-ends (namely UHP2, UHP3, UHP4 and UHP6), and found that the four UHPs yielded robust RT products and quantified miRNAs with high efficiency. UHP-based RT-qPCR miRNA quantification was not affected by long transcripts. By analyzing 14 miRNAs, we demonstrated that UHP4 closely mimicked MsHPs in miRNA quantification. Fine-tuning experiments identified an optimized UHP (OUHP) mix with a molar composition of UHP2:UHP4:UHP6 = 8:1:1, which closely recapitulated MsHPs in miRNA quantification. Using synthetic LET7 isomiRs, we demonstrated that the OUHP-based qPCR system exhibited high specificity and sensitivity. Collectively, our results demonstrate that the OUHP system can serve as a reliable and cost-effective surrogate of MsHPs for RT-qPCR-based miRNA quantification for basic research and precision medicine.
VID22counteracts G-quadruplex-induced genome instability
Authors: Galati Elena , Bosio Maria C , Novarina Daniele , Chiara Matteo , Bernini Giulia M , Mozzarelli Alessandro M , García-Rubio Maria L , Gómez-González Belén , Aguilera Andrés , Carzaniga Thomas , Todisco Marco , Bellini Tommaso , Nava Giulia M , Frigè Gianmaria , Sertic Sarah , Horner David S , Baryshnikova Anastasia , Manzari Caterina , D’Erchia Anna M , Pesole Graziano , Brown Grant W , Muzi-Falconi Marco , Lazzaro Federico 
Published: November 2021

AbstractGenome instability is a condition characterized by the accumulation of genetic alterations and is a hallmark of cancer cells. To uncover new genes and cellular pathways affecting endogenous DNA damage and genome integrity, we exploited a Synthetic Genetic Array (SGA)-based screen in yeast. Among the positive genes, we identified VID22, reported to be involved in DNA double-strand break repair. vid22Δ cells exhibit increased levels of endogenous DNA damage, chronic DNA damage response activation and accumulate DNA aberrations in sequences displaying high probabilities of forming G-quadruplexes (G4-DNA). If not resolved, these DNA secondary structures can block the progression of both DNA and RNA polymerases and correlate with chromosome fragile sites. Vid22 binds to and protects DNA at G4-containing regions both in vitro and in vivo. Loss of VID22 causes an increase in gross chromosomal rearrangement (GCR) events dependent on G-quadruplex forming sequences. Moreover, the absence of Vid22 causes defects in the correct maintenance of G4-DNA rich elements, such as telomeres and mtDNA, and hypersensitivity to the G4-stabilizing ligand TMPyP4. We thus propose that Vid22 is directly involved in genome integrity maintenance as a novel regulator of G4 metabolism.
Decoding the effects of synonymous variants
Authors: Zeng Zishuo , Aptekmann Ariel A , Bromberg Yana 
Published: November 2021

Abstract
Synonymous single nucleotide variants (sSNVs) are common in the human genome but are often overlooked. However, sSNVs can have significant biological impact and may lead to disease. Existing computational methods for evaluating the effect of sSNVs suffer from the lack of gold-standard training/evaluation data and exhibit over-reliance on sequence conservation signals. We developed synVep (synonymous Variant effect predictor), a machine learning-based method that overcomes both of these limitations. Our training data was a combination of variants reported by gnomAD (observed) and those unreported, but possible in the human genome (generated). We used positive-unlabeled learning to purify the generated variant set of any likely unobservable variants. We then trained two sequential extreme gradient boosting models to identify subsets of the remaining variants putatively enriched and depleted in effect. Our method attained 90% precision/recall on a previously unseen set of variants. Furthermore, although synVep does not explicitly use conservation, its scores correlated with evolutionary distances between orthologs in cross-species variation analysis. synVep was also able to differentiate pathogenic vs. benign variants, as well as splice-site disrupting variants (SDV) vs. non-SDVs. Thus, synVep provides an important improvement in annotation of sSNVs, allowing users to focus on variants that most likely harbor effects.
SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions
Authors: Torrens-Fontanals Mariona , Peralta-García Alejandro , Talarico Carmine , Guixà-González Ramon , Giorgino Toni , Selent Jana 
Published: November 2021

Abstract
SCoV2-MD (www.scov2-md.org) is a new online resource that systematically organizes atomistic simulations of the SARS-CoV-2 proteome. The database includes simulations produced by leading groups using molecular dynamics (MD) methods to investigate the structure-dynamics-function relationships of viral proteins. SCoV2-MD cross-references the molecular data with the pandemic evolution by tracking all available variants sequenced during the pandemic and deposited in the GISAID resource. SCoV2-MD enables the interactive analysis of the deposited trajectories through a web interface, which enables users to search by viral protein, isolate, phylogenetic attributes, or specific point mutation. Each mutation can then be analyzed interactively combining static (e.g. a variety of amino acid substitution penalties) and dynamic (time-dependent data derived from the dynamics of the local geometry) scores. Dynamic scores can be computed on the basis of nine non-covalent interaction types, including steric properties, solvent accessibility, hydrogen bonding, and other types of chemical interactions. Where available, experimental data such as antibody escape and change in binding affinities from deep mutational scanning experiments are also made available. All metrics can be combined to build predefined or custom scores to interrogate the impact of evolving variants on protein structure and function.