bluuebunny/crossref_metadata_2025_split huggingface dataset:
Segmental duplications and their variation in a complete human genome
Authors: Vollger Mitchell R. , Guitart Xavi , Dishuck Philip C. , Mercuri Ludovica , Harvey William T. , Gershman Ariel , Diekhans Mark , Sulovari Arvis , Munson Katherine M. , Lewis Alexandra M. , Hoekzema Kendra , Porubsky David , Li Ruiyang , Nurk Sergey , Koren Sergey , Miga Karen H. , Phillippy Adam M. , Timp Winston , Ventura Mario , Eichler Evan E. 
Published: May 2021

ABSTRACTDespite their importance in disease and evolution, highly identical segmental duplications (SDs) have been among the last regions of the human reference genome (GRCh38) to be finished. Based on a complete telomere-to-telomere human genome (T2T-CHM13), we present the first comprehensive view of human SD organization. SDs account for nearly one-third of the additional sequence increasing the genome-wide estimate from 5.4% to 7.0% (218 Mbp). An analysis of 266 human genomes shows that 91% of the new T2T-CHM13 SD sequence (68.3 Mbp) better represents human copy number. We find that SDs show increased single-nucleotide variation diversity when compared to unique regions; we characterize methylation signatures that correlate with duplicate gene transcription and predict 182 novel protein-coding gene candidates. We find that 63% (35.11/55.7 Mbp) of acrocentric chromosomes consist of SDs distinct from rDNA and satellite sequences. Acrocentric SDs are 1.75-fold longer (p=0.00034) than other SDs, are frequently shared with autosomal pericentromeric regions, and are heteromorphic among human chromosomes. Comparing long-read assemblies from other human (n=12) and nonhuman primate (n=5) genomes, we use the T2T-CHM13 genome to systematically reconstruct the evolution and structural haplotype diversity of biomedically relevant (LPA, SMN) and duplicated genes (TBC1D3, SRGAP2C, ARHGAP11B) important in the expansion of the human frontal cortex. The analysis reveals unprecedented patterns of structural heterozygosity and massive evolutionary differences in SD organization between humans and their closest living relatives.
Additive and epistatic effects influence spectral tuning in molluscan retinochrome opsin
Authors: Smedley G. Dalton , McElroy Kyle E. , Serb Jeanne M. 
Published: May 2021

AbstractThe relationship between genotype and phenotype is nontrivial due to often complex molecular pathways that make it difficult to unambiguously relate phenotypes to specific genotypes. Photopigments, an opsin apoprotein bound to a light-absorbing chromophore, present an opportunity to directly relate the amino acid sequence to an absorbance peak phenotype (λmax). We examined this relationship by conducting a series of site-directed mutagenesis experiments of retinochrome, a non-visual opsin, from two closely related species: the common bay scallop, Argopecten irradians, and the king scallop, Pecten maximus. Using protein folding models, we identified three amino acid sites of likely functional importance and expressed mutated retinochrome proteins in vitro. Our results show that the mutation of amino acids lining the opsin binding pocket are responsible for fine spectral tuning, or small changes in the λmax of these light sensitive proteins Most mutations caused a blue shift regardless of the retinochrome background, with shifts ranging from a 12 nm blue shift to a 5 nm red shift from the wild-type λmax. These mutations do not show an additive effect, but rather suggests the presence of epistatic interactions. This work highlights the importance of binding pocket shape in the evolution of spectral tuning and builds on our ability to relate genotypic changes to phenotypes in an emerging model for opsin functional analysis.Author summarySite-directed mutagenesis determined that spectral tuning in retinochrome is not solely additive, but is influenced by intra-molecular epistasis.
An investigation of the credibility of and confidence in audit value: evidence from a developing country
Authors: Akther Taslima , Xu Fengju 
Published: May 2021

PurposeThis study aims to investigate the factors that enhance the credibility of and confidence in audit value.Design/methodology/approachData were collected from 254 institutional investors through a questionnaire survey and were analyzed using partial least squares structural equation modelling (PLS-SEM).FindingsThe findings reveal that the two influential predictors of enhanced credibility and confidence are perceived auditor independence and improved auditor communication. Factors related to auditor–client affiliation, such as restrictions on providing non-audit services, mandatory auditor rotation and the presence of effective audit committees, are identified as creating the perceived independence. Improved auditor communication is linked with improving the audit report and ensuring audit education, thus creating more sophisticated users who better understand the scope and purpose of an audit. Furthermore, independent audit oversight acts as a moderator in the relationship between perceived auditor independence, improved auditor communication and enhanced credibility. Enhanced credibility can lead to greater confidence in audit value.Originality/valueIn the wake of the global financial crisis and loss of confidence in the role of auditors, this study investigates the factors that can enhance the credibility of and confidence in audit value, especially in a non-Anglo-American setting. This study is unique in terms of methodological development, as it uses a higher-order Type II reflective–formative model using PLS-SEM.
Near-field scattering from PEC wedge excited by electric dipole in lossy medium
Authors: Öztürk Hülya , Yegin Korkut 
Published: May 2021

Purpose
The purpose of this paper is to derive the dyadic representations of Green’s function in lossy medium because of the electric current dipole source radiating in close proximity of a PEC wedge and to reveal the effect of conductivity on the scattered electric field.

Design/methodology/approach
By using the scalarization procedure, the paraxial fields are obtained first and then scalar Green’s functions are used to derive asymptotic forms of the dyadic Green’s functions. The problem is also analyzed by the image theory and analytical derivations are compared. However, analytically calculated results are validated with FEKO, a commercially available numerical electromagnetic field solver.

Findings
The results indicate that excellent agreement is observed between analytical and numerical results. Moreover, it is found that the presence of conductivity introduces a reduction in scattered electric fields.

Originality/value
Asymptotically derived forms presented in this study can be used to calculate field distributions in the paraxial region of a wedge in a lossy medium.
Individual and situational predictors of intention to hire gay male and ultra-orthodox male job applicants
Authors: Brender-Ilan Yael , Kay Avi 
Published: May 2021

PurposeThis paper examines personal and situational factors that may contribute to biases in hiring decisions at the workplace, focusing on willingness to hire male gay or male Jewish ultra-Orthodox Jewish job candidates.Design/methodology/approach942 Jewish participants in Israel responded to an anonymous online questionnaire regarding a scenario addressing the possible employments of two male applicants: a homosexual and an ultra-Orthodox Jew. A variety of statistical tools, including regression analysis were performed to test hypotheses.FindingsFindings show that social dominance orientation, conservatism, gender and religiosity as well as frequency of contact with the “unlike other” impacted on hiring intention of the participants. These relationships varied in strength and direction with regard to the two applicant types in question.Practical implicationsThe explication of the phenomenon in question has both important theoretical and practical importance in a world where – concurrently – there exists increasing contact among individuals from different backgrounds and (perhaps not coincidently) increased signs of wariness of and discrimination toward those unlike ourselves. In light of economic costs related to discrimination – not to mention the personal costs to those discriminated against – organizations must better understand the dynamics of the phenomenon in question.Originality/valueThis is one of the first empirical examinations of the relative impact of personal and situational factors on hiring bias. In addition, it is the first study of its kind in Israel focusing on the mechanisms behind hiring bias toward gay males and ultra-orthodox males.
Does quality of governance contribute to the heterogeneity in happiness levels across MENA countries?
Authors: Youssef Jamile , Diab Sara 
Published: May 2021

PurposeHappiness levels differ among the Middle East and North African (MENA) countries and follow a downtrend, making such heterogeneity a popular topic to investigate. The paper aims to study the contribution of governance quality on the heterogeneity in happiness levels across MENA countries while controlling for demographic and socioeconomic variables.Design/methodology/approachThe paper applies panel random-effects regression analysis on three samples: full sample, rich and poor subsamples, using data from 20 MENA countries over the 2007–2017 period.FindingsThe empirical results for the full sample conclude that better technical quality of governance increases happiness in the region. Furthermore, findings suggest that political stability and absence of violence matters for people's happiness only in rich countries. Whereas, control of corruption is positively associated with happiness level in the full sample and poor subsample. Across all three samples, voice and accountability has no impact on happiness.Research limitations/implicationsA possible limitation of the paper is using an index for happiness based on a subjective weight distribution. Therefore, researchers are encouraged to implement a novel method using data envelopment analysis.Practical implicationsThis paper includes implications for policymakers in the MENA region. Governments should strengthen existing laws and create a comprehensive database of laws, fight corruption and prioritize raising income.Originality/valueThis paper is the first to categorize MENA countries into rich and poor to analyze how governance quality contributes to the heterogeneity in happiness levels.
An explanatory model of authentic leadership, flourishing and work–family balance of nurses in French hospitals
Authors: Chevalier Séverine , Coillot Hélène , Colombat Philippe , Bosselut Grégoire , Guilbert Laure , Fouquereau Evelyne 
Published: May 2021

PurposeThis study aims to investigate the relationship between a positive leadership style [i.e. authentic leadership (AL)] and nurses’ psychological health (i.e. nurses’ flourishing and satisfaction with work–family balance), including psychological capital (PsyCap) as a mediational variable.Design/methodology/approachA cross-sectional study was conducted with a self-report questionnaire including 1,076 nurses from public and private hospitals in France.FindingsStructural equation modeling results revealed that AL is related to nurses’ flourishing and satisfaction with work–family balance and that PsyCap acted as a partial mediator between this leadership style and positive outcomes.Practical implicationsThis research indicated that hospitals can enhance nurses’ psychological health not only in their work but also in their lives in general by improving leaders’ authentic management style and developing PsyCap (e.g. staffing, training and development).Originality/valueAn original feature of this paper concerns its focus on the mediating role of PsyCap in the relationship between AL and these positive outcomes. Moreover, this study underlined the influence of leadership style on nurses’ psychological health beyond occupational health. The research makes a valuable contribution to the existing AL literature by establishing a new explanatory model of AL and nurses’ psychological health in the French context. It also highlights the interest in developing this leadership style in health-care settings.
The day the clock stopped. Primitive states of unintegration, multidimensional working through and the birth of the analytical subject
Authors: de Rienzo Antonio 
Published: May 2021

AbstractThis paper is based on one idea and built around one clinical experience that helped me to broaden my comprehension of it. The idea, underlying the work of several authors, is that when the analytic field is saturated with primitive and unintegrated mental contents, the analyst’s somatic countertransference is a precious indicator of a deep, dissociated form of communication. The clinical experience concerns the difficult elaboration of a complex, multifaceted countertransference that took place during the early stages of the analysis of a sensitive patient who used to communicate in a very dissociated way and that I found hard to contain. This experience, closely described in the article, led me to formulate the clinical idea that the transference field may be made of distinct layers (psychoid, affective, verbal), and that each one of them may potentially convey dissociated, even contrasting bits of information. The corollary of this is that the analyst should be ready to accept contrasting sensations, feelings and thoughts at the same time, as they might be the basic ingredients of a complex reverie. The analyst could find himself/herself in front of his/her own internal unelaborated multiplicity before a symbolic image may emerge to link the scattered pieces of the experience. Nevertheless, the heart of this paper is not about suggesting an idea, but in the sharing of a complex working through, which fostered the birth of a new, more human relational perspective: the capacity of being together in time, in a transitional space where there is neither total separation nor fusion.
Trichomoniasis and adverse birth outcomes: a systematic review and meta‐analysis
Authors: Van Gerwen OT , Craig‐Kuhn MC , Jones AT , Schroeder JA , Deaver J , Buekens P , Kissinger PJ , Muzny CA 
Published: May 2021

BackgroundTrichomoniasis commonly affects women of childbearing age and has been linked to several adverse birth outcomes.ObjectiveTo elucidate the association between trichomoniasis in pregnant women and adverse birth outcomes, including preterm delivery, prelabour rupture of membranes and low birthweight.Search strategyMEDLINE, EMBASE andClinicalTrials.govwere systematically searched in December 2020 without time or language restrictions.Selection criteriaOriginal research studies were included if they assessed at least one of the specified adverse birth outcomes in pregnant women with laboratory‐diagnosed trichomoniasis.Data collection and analysisEstimates from included articles were either extracted or calculated and then pooled to produce a combined estimate of the association of trichomoniasis with each adverse birth outcome using the random effects model. Heterogeneity was assessed using theI2statistic and Cochran'sQtest.Main resultsLiterature search produced 1658 publications after removal of duplicates (n = 770), with five additional publications identified by hand search. After screening titles and abstracts for relevance, full text of 84 studies was reviewed and 19 met inclusion criteria for meta‐analysis. Significant associations were found between trichomoniasis and preterm delivery (OR 1.27; 95% CI 1.08–1.50), prelabour rupture of membranes (OR 1.87; 95% CI 1.53–2.29) and low birthweight (OR 2.12; 95% CI 1.15–3.91).ConclusionsTrichomoniasis in pregnant women is associated with preterm delivery, prelabour rupture of membranes and low birthweight. Rigorous studies are needed to determine the impact of universal trichomoniasis screening and treatment during pregnancy on reducing perinatal morbidity.Tweetable abstractThis systematic review and meta‐analysis found that in the setting of pregnancy, trichomoniasis is significantly associated with multiple adverse birth outcomes, including preterm delivery, low birthweight, and prelabour rupture of membranes.
Elucidating the relationship between nutrition indices and coronary artery calcification in patients undergoing maintenance hemodialysis
Authors: Huang Yingzi , Ge Yongchun , Li Furong , Zhang Chuanzhen , Zhang Zhaoyong , Xu Na , Wang Rui , Wu Shun , Geng Xin , Quan Yongqiang , Ren Hongqi 
Published: May 2021

AbstractCardiovascular diseases (CVD) are common in maintenance hemodialysis (MHD) patients, and vascular calcification is associated with the incidence of CVD. Malnourished MHD patients are particularly prone to CVD events. Thus far, there is no clear explanation for the relationship of nutrition status with vascular calcification; therefore, we investigated the relationship between malnutrition and vascular calcification. One hundred thirty‐one patients underwent laboratory testing, assessment of vascular calcification, modified quantitative subjective global assessment (MQSGA), bioelectrical impedance analysis (BIA), and anthropometric measurements. The patients were divided into two groups based on the presence or absence of coronary artery calcification (CAC), and nutritional statuses were compared between the two groups. The MQSGA score was higher in the CAC group (mean 10.9 ± 1.81) than in the no‐CAC group (mean 10.2 ± 1.51); in addition, the mean phase angle (PA) value was significantly lower in the CAC group than in the no‐CAC group. Stratification according to CAC score showed that age, Kt/V, incidence of valve calcification, incidence of abdominal aortic calcification, MQSGA score, and blood cell mass were related to the severity of CAC. In addition, quartile analysis revealed that MQSGA score and PA value were related to the incidence and severity of vascular calcification. Binary regression analysis showed that MQSGA score, age, hemoglobin level, and high‐density lipoprotein level were independent risk factors for dialysis‐related CAC. Patients on MHD who exhibited malnutrition were more likely to have vascular calcification, especially CAC. Namely, the higher the MQSGA score, the lower the PA, and the more likely the occurrence of CAC.
Evaluating Instream Restoration Effectiveness in Reducing Nitrogen Export from an Urban Catchment with a Data‐Model Approach
Authors: Lin Laurence , Reisinger Alexander J. , Rosi Emma J. , Groffman Peter M. , Band Lawrence E. 
Published: May 2021

AbstractUrbanization increases stormwater runoff into streams, resulting in channel erosion, and increases in sediment and nutrient delivery to receiving water bodies. Stream restoration is widely used as a Best Management Practice to stabilize banks and reduce sediment and nutrient loads. While most instream nutrient retention measurements are often limited to low flow conditions, most of the nutrient load is mobilized at high stream flows in urban settings. We, therefore, use a process‐based stream ecosystem model in conjunction with measurements at low flows and focus on estimation of stream nitrogen retention over the full streamflow distribution. The model provides a theoretical framework to evaluate the geomorphic, hydrologic, and ecological factors that are manipulated by stream restoration, and drive nitrogen retention. We set a model for a pool‐riffle sequence restored stream (190 m) in Baltimore County, Maryland and calibrated the model to the in situ measured primary production (Nash–Sutcliffe model efficiency coefficient [NSE] NSE = 0.89), respiration (NSE = 0.74), and nitrate uptake lengths (R2 = 0.88). At the daily scale, simulations showed low nitrogen retention during high flows due to high transport rates, mobilization of stored hyporheic nitrogen, and scouring of periphyton biomass. This result underscores the need to reduce contributing watershed runoff flashiness to promote aquatic nutrient cycling and retention. At monthly and yearly time scale, model predicted a higher percent reduction in summer than in winter and estimated 5.7%–9.5% of annual nitrate reductions. While the model was tested in a pool‐riffle sequence restoration design, the approach can be adapted to evaluate a range of channel restoration design characteristics, and the effects of upland watershed restoration to mitigate stormwater loading through both restored and unrestored streams.
Genetic associations for two biological age measures point to distinct aging phenotypes
Authors: Kuo Chia‐Ling , Pilling Luke C. , Liu Zuyun , Atkins Janice L. , Levine Morgan E. 
Published: May 2021

AbstractBiological age measures outperform chronological age in predicting various aging outcomes, yet little is known regarding genetic predisposition. We performed genome‐wide association scans of two age‐adjusted biological age measures (PhenoAgeAcceleration and BioAgeAcceleration), estimated from clinical biochemistry markers (Levine et al., 2018; Levine, 2013) in European‐descent participants from UK Biobank. The strongest signals were found in the APOE gene, tagged by the two major protein‐coding SNPs, PhenoAgeAccel—rs429358 (APOE e4 determinant) (p = 1.50 × 10−72); BioAgeAccel—rs7412 (APOE e2 determinant) (p = 3.16 × 10−60). Interestingly, we observed inverse APOE e2 and e4 associations and unique pathway enrichments when comparing the two biological age measures. Genes associated with BioAgeAccel were enriched in lipid related pathways, while genes associated with PhenoAgeAccel showed enrichment for immune system, cell function, and carbohydrate homeostasis pathways, suggesting the two measures capture different aging domains. Our study reaffirms that aging patterns are heterogeneous across individuals, and the manner in which a person ages may be partly attributed to genetic predisposition.
The important role of non‐covalent drug‐protein interactions in drug hypersensitivity reactions
Authors: Pichler Werner J. 
Published: May 2021

AbstractDrug hypersensitivity reactions (DHR) are heterogeneous and unusual immune reactions with rather unique clinical presentations. Accumulating evidence indicates that certain non‐covalent drug‐protein interactions are able to elicit exclusively effector functions of antibody reactions or complete T‐cell reactions which contribute substantially to DHR. Here, we discuss three key interactions; (a) mimicry: whereby soluble, non‐covalent drug‐protein complexes (“fake antigens”) mimic covalent drug‐protein adducts; (b) increased antibody affinity: for example, in quinine‐type immune thrombocytopenia where the drug gets trapped between antibody and membrane‐bound glycoprotein; and (c) p‐i‐stimulation: where naïve and memory T cells are activated by direct binding of drugs to the human leukocyte antigen and/or T‐cell receptors. This transient drug‐immune receptor interaction initiates a polyclonal T‐cell response with mild‐to‐severe DHR symptoms. Notable complications arising from p‐i DHR can include viral reactivations, autoimmunity, and multiple drug hypersensitivity. In conclusion, DHR is characterized by abnormal immune stimulation driven by non‐covalent drug‐protein interactions. This contrasts DHR from “normal” immunity, which relies on antigen‐formation by covalent hapten‐protein adducts and predominantly results in asymptomatic immunity.