bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA barcoding of fungal specimens using PacBio long‐read high‐throughput sequencing
Authors: Runnel Kadri , Abarenkov Kessy , Copoț Ovidiu , Mikryukov Vladimir , Kõljalg Urmas , Saar Irja , Tedersoo Leho 
Published: June 2022

AbstractMolecular methods are increasingly used to identify species that lack conspicuous macro‐ or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long‐read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population‐level studies.
Accelerated epigenetic aging in newborns with Down syndrome
Authors: Xu Keren , Li Shaobo , Muskens Ivo S. , Elliott Natalina , Myint Swe Swe , Pandey Priyatama , Hansen Helen M. , Morimoto Libby M. , Kang Alice Y. , Ma Xiaomei , Metayer Catherine , Mueller Beth A. , Roberts Irene , Walsh Kyle M. , Horvath Steve , Wiemels Joseph L. , de Smith Adam J. 
Published: June 2022

AbstractAccelerated aging is a hallmark of Down syndrome (DS), with adults experiencing early‐onset Alzheimer's disease and premature aging of the skin, hair, and immune and endocrine systems. Accelerated epigenetic aging has been found in the blood and brain tissue of adults with DS but when premature aging in DS begins remains unknown. We investigated whether accelerated aging in DS is already detectable in blood at birth. We assessed the association between age acceleration and DS using five epigenetic clocks in 346 newborns with DS and 567 newborns without DS using Illumina MethylationEPIC DNA methylation array data. We compared two epigenetic aging clocks (DNAmSkinBloodClock and pan‐tissue DNAmAge) and three epigenetic gestational age clocks (Haftorn, Knight, and Bohlin) between DS and non‐DS newborns using linear regression adjusting for observed age, sex, batch, deconvoluted blood cell proportions, and genetic ancestry. Targeted sequencing of GATA1 was performed in a subset of 184 newborns with DS to identify somatic mutations associated with transient abnormal myelopoiesis. DS was significantly associated with increased DNAmSkinBloodClock (effect estimate = 0.2442, p < 0.0001), with an epigenetic age acceleration of 244 days in newborns with DS after adjusting for potential confounding factors (95% confidence interval: 196–292 days). We also found evidence of epigenetic age acceleration associated with somatic GATA1 mutations among newborns with DS (p = 0.015). DS was not associated with epigenetic gestational age acceleration. We demonstrate that accelerated epigenetic aging in the blood of DS patients begins prenatally, with implications for the pathophysiology of immunosenescence and other aging‐related traits in DS.
Investigating the cost‐effectiveness of three cessation interventions on a national scale using the Economics of Smoking in Pregnancy (ESIP) decision analytical model
Authors: Jones Matthew , Smith Murray , Lewis Sarah , Parrott Steve , Coleman Tim 
Published: June 2022

AbstractAimTo measure the cost‐effectiveness of adding text message (TMB), exercise (EB) and abstinent‐contingent financial incentive‐based (CFIB) stop smoking interventions to standard smoking cessation support for pregnant women in England.DesignModelling cost‐effectiveness outcomes by separately adding three cessation interventions to standard cessation care offered to pregnant women in England. English National Health Service Stop Smoking Services (NHS SSS) statistics from 2019 to 2020 were used for estimating the base quit rate. Intervention effectiveness and cost data for interventions were taken from trial reports. Cost‐effectiveness was derived using the economics of smoking in pregnancy (ESIP) model from a health service and personal social services perspective. Interventions were compared with each other as well as against standard cessation care.SettingEnglish NHS SSS.Participants/casesA total of 13 799 pregnant women who accessed NHS SSS. Interventions and comparator; comparator: standard stop smoking support comprising behavioural intervention and an offer of nicotine replacement therapy (NRT). Three additive interventions were TMB, EB and CFIB.MeasurementsIncremental cost‐effectiveness ratios per quality‐adjusted life‐years gained for both mothers and offspring over their life‐times; return on investment (ROI); and cost‐effectiveness acceptability curves (CEACs).FindingsThe addition of any of the interventions compared with standard care alone was preferred, but only significant for the addition of CFIB, with the CEAC suggesting an at least 90% chance of being favoured to standard care alone. When compared against each other CFIB appeared to yield the largest returns, but this was not significant. The estimated ROI for CFIB was £2 [95% confidence interval (CI) = £1–3] in health‐care savings for every £1 spent by the NHS on the cessation intervention.ConclusionsFor a health system which currently provides behavioural support and an offer of nicotine replacement therapy as standard stop smoking support for pregnant women, the greatest economic gains would be provided by operating an abstinent‐contingent financial incentives scheme alongside this.
Morphology of female reproductive system of Mediterranean flatheaded peachborer, Capnodis tenebrionis (Linnaeus, 1761) (Coleoptera: Buprestidae)
Authors: Özyurt Koçakoğlu Nurcan , Çağlar Üzeyir , Candan Selami 
Published: June 2022

AbstractCapnodis tenebrionis causes damage in many species of Rosaceae. The present study investigates on the morphology of the female reproductive system of C. tenebrionis. The female reproductive system of C. tenebrionis has a pair of ovaries, lateral oviducts, a common oviduct, spermatheca, and bursa copulatrix. Each ovary in C. tenebrionis consists of approximately 24 telotrophic meroistic type ovarioles. The ovarioles of C. tenebrionis have four regions (terminal filament, tropharium, vitellarium, and pedicel). Tropharium have trophocytes, young oocytes, and prefollicular cells. Vitellarium consists of previtellogenic, vitellogenic, and choriogenic oocytes. Previtellogenic oocyte is surrounded by cylindrical epithelial cells. Its ooplasm is homogeneous and basophilic. In vitellogenic oocyte, there are intercellular spaces between monolayered follicle cells. Its ooplasm has yolk granules and lipid droplets. Choriogenic oocyte are surrounded by chorion and single‐layered cylindrical cells. There are yolk granules and lipid droplets in its ooplasm which is asidophilic. In C. tenebrionis female, spermatheca and bursa copulatrix wall is surrounded by thin cuticular intima, monolayer epithelial, glandular cells, and muscle layer. Spermatheca lumen contains a large number of spermatozoa. Bursa copulatrix lumen is filled with secretory material. This study may be useful in terms of the morphology of mature female reproductive organs of Buprestidae and other coleopteran species.
Everybody hurts (sometimes): The role of victim category accessibility in prosocial responses towards victimized outgroups
Authors: Sharvit Keren , Kremer‐Sharon Shira 
Published: June 2022

AbstractCollective victimization can lead to competitiveness and reduced willingness to act on behalf of other victimized groups, but in some cases increases prosocial responses. We propose the concept of victim category accessibility (VCA) as one explanation for different reactions to victimization. Assuming that ‘victims’ is one among many categories into which individuals classify themselves and others, high VCA should increase the common categorization of ingroup and outgroup members as victims and increase prosocial responses towards victimized outgroups. Conversely, low VCA should increase the difficulty of identifying commonalities between ingroup and outgroup victims and reduce prosocial responses. In three studies, we develop a novel measure of VCA based on the Indirect Category Accessibility Task and demonstrate its association with willingness to act on behalf of victimized outgroups, but not ingroup members, beyond self‐reported beliefs about victimization. The findings suggest a key role for VCA in understanding prosocial responses towards victimized outgroups.
Tracking a multitude of abilities as they develop
Authors: Bolsinova Maria , Brinkhuis Matthieu J. S. , Hofman Abe D. , Maris Gunter 
Published: June 2022

Recently, the Urnings algorithm (Bolsinova et al.,  2022, J. R. Stat. Soc. Ser. C Appl. Statistics, 71, 91) has been proposed that allows for tracking the development of abilities of the learners and the difficulties of the items in adaptive learning systems. It is a simple and scalable algorithm which is suited for large‐scale applications in which large streams of data are coming into the system and on‐the‐fly updating is needed. Compared to alternatives like the Elo rating system and its extensions, the Urnings rating system allows the uncertainty of the ratings to be evaluated and accounts for adaptive item selection which, if not corrected for, may distort the ratings. In this paper we extend the Urnings algorithm to allow for both between‐item and within‐item multidimensionality. This allows for tracking the development of interrelated abilities both at the individual and the population level. We present formal derivations of the multidimensional Urnings algorithm, illustrate its properties in simulations, and present an application to data from an adaptive learning system for primary school mathematics called Math Garden.
Economic incentives for the wildlife trade and costs of epidemics compared across individual, national, and global scales
Authors: de Wit Luz A. , Fisher Brendan , Naidoo Robin , Ricketts Taylor H. 
Published: June 2022

AbstractThe wildlife trade drives biodiversity loss and zoonotic disease emergence, and the health and economic impacts of COVID‐19 have sparked discussions over stricter regulation of the wildlife trade. Yet regulation for conservation and health purposes is at odds with the economic incentives provided by this multibillion‐dollar industry. To understand why the wildlife trade persists despite associated biodiversity and global health threats, we used a benefit–cost approach using simple calculations to compare the economic benefits of the wildlife trade at the individual, national, and global scales to the costs of COVID‐19, severe acute respiratory syndrome (SARS), and Ebola disease across scenarios of epidemic frequency. For COVID‐19, benefits of the wildlife trade outweigh costs at individual scales, but costs far exceed benefits at national and global scales, particularly if epidemics were to become frequent. For SARS and Ebola, benefits outweigh costs at all scales, except if Ebola‐like epidemics were to become frequent. The wildlife trade produces net benefits for people who depend on wildlife for food and income but incurs net costs on stakeholders at larger scales from increased epidemic risk. While our analysis omits a variety of costs and benefits that are difficult to quantify and contrast, our analysis is meant to illustrate the distributional outcomes across stakeholder groups that could result from increased wildlife trade regulation. Importantly, the feasibility of trade regulatory policies will depend on how these benefits and costs compare across groups and would therefore need to involve accessible and attractive alternative sources of food and livelihoods for those who depend on the wildlife trade.
Are covered bonds different from securitization bonds? A comparative analysis of credit spreads
Authors: Correia Mafalda C. , Pinto João M. 
Published: June 2022

AbstractThis study compares credit spreads and pricing determinants of securitization vis‐à‐vis covered bonds. Our analysis reveals that although ratings are the most important pricing determinant for asset‐backed securities (ABS) and mortgage‐backed securities (MBS) investors place relatively more importance on contractual, macroeconomic and banks' characteristics rather than ratings in pricing covered bonds. We find evidence of a mispricing effect in structured finance markets: ABS and MBS have higher credit spreads than similarly rated public‐covered bonds and mortgage‐covered bonds and security prices reflect information beyond credit ratings. We find no evidence of borrowing costs affecting banks' choice between securitization and covered bonds.
Phenotypic and molecular responses of copepods to UV radiation stress in a clear versus a glacially turbid lake
Authors: Tartarotti Barbara , Sommaruga Ruben , Saul Nadine 
Published: June 2022

Abstract

Zooplankton are exposed to multiple environmental stressors in alpine lakes. However, phenotypic and molecular responses of copepods to different environmental conditions, including ultraviolet radiation (UVR), are still not fully understood. Here, we tested whether gene expression patterns vary within the same species, Cyclops abyssorum tatricus, but in populations from different environments (a clear vs. a glacially turbid lake) when exposed to UVR. Moreover, we wanted to examine potential seasonal variation (summer vs. autumn) in copepod gene expression.

We measured photoprotective compounds (mycosporine‐like amino acids and carotenoids) and antioxidant capacities in two copepod populations and studied gene expression of heat shock proteins (hsps) as indicator of stress after UVR exposure in the laboratory.

Compared with the copepod population from the clear lake, the population from the turbid lake showed lower mycosporine‐like amino acid, but higher carotenoid concentrations that decreased over the season. Antioxidant capacities (both lipophilic and hydrophilic) were higher in autumn than in summer. The hsp60 and hsp90 genes were constitutively expressed, regardless of habitat origin and season, while hsp70 was upregulated after exposure to UVR (up to 2.8‐fold change). We observed stronger upregulation of hsp70 gene expression in autumn for the turbid and summer for the clear lake, with highest gene expression 24 hr post‐UVR exposure (up to 10.2‐fold change in the turbid and 3.9‐fold in the clear lake).

We show how variation in phenotypic traits modulates hsp gene expression patterns, specifically hsp70 gene expression. Rapidly induced defences against cellular stress may improve survival in harsh environments such as alpine lakes, especially since these sensitive ecosystems may experience further changes in the future.
Exploring motivations and resistances for implementing shared decision‐making in clinical practice: A systematic review based on a structure–process–outcome model
Authors: Tang Changhai , Wang Anqi , Yan Jingjing 
Published: June 2022

AbstractObjectiveShared decision‐making (SDM) as a multicollaborative approach is vital for facilitating patient‐centred care. Considering the limited clinical practice, we attempted to synthesize the motivations and resistances, and investigate their mutual relationships for advancing the implementation of SDM.MethodsA comprehensive systematic review using Preferred Reporting Items for Systematic Review and Meta‐Analysis guidelines was performed. ‘Shared decision making’ was searched as the mesh term through PubMed, Web of Science and EBSCO from 2000 to 2021, and the quality of literature was appraised using the QualSyst Tool. Motivations and resistances were categorized based on content analysis and the ‘structure–process–outcome’ model.ResultsFrom 8319 potential citations, 105 were included, comprising 53 qualitative studies (the average quality score is 0.92) and 52 quantitative studies (the average quality score is 0.95). A total of 42 categories of factors were identified into 11 themes and further grouped into three dimensions: structure, process and outcome. The structure dimension comprised six themes (71.43%), the process dimension contained four themes (11.01%) and the outcome dimension covered only one theme. Across all categories, decision‐making time and patients' decision preparedness in the process dimension were the most reported, followed by physicians' communication skills and health care environment in the structure dimension. Analysis of implementation of SDM among various types of diseases showed that more influencing factors were extracted from chronic diseases and unspecified disease decisions.ConclusionsThe major determinants for the implementation of SDM are focused on the structural dimension, which challenges the health systems of both developed and low‐ and middle‐income countries. Furthermore, we consider it important to understand more about the interactions among the factors to take integrated measures to address the problems and to ensure the effectiveness of implementing SDM.Patient or Public ContributionPatients, healthcare professionals and other stakeholders articulated their perspectives on the implementation of SDM actively, and these were adopted and analysed in this study. However, the above‐mentioned individuals were not directly involved in the process of this study. Protocol was registered on PROSPERO (CRD42021259309).
Predictors and outcomes of dose reduction of methotrexate and cyclosporin graft‐versus‐host disease prophylaxis following allogeneic haemopoietic cell transplantation
Authors: Ramanan Radha , Lim Andrew B. M. , Tan Joanne L. C. , Barmanray Rahul D. , Mason Kate , Collins Jenny , Hillman Matthew , Szer Jeff , Bajel Ashish , Ritchie David 
Published: June 2022

AbstractBackgroundConcern regarding dose‐related toxicities of methotrexate (MTX) and cyclosporin (CYA) graft‐versus‐host disease (GVHD) prophylaxis occasionally leads to dose alterations post allogeneic haemopoietic cell transplant (alloHCT).AimsTo clarify causes of MTX and CYA dose alteration and assess impact on patient outcomes, including GVHD, relapse, non‐relapse mortality (NRM) and overall survival (OS).MethodsAnalysis of retrospective data was performed in a single tertiary centre of patients who underwent alloHCT for any indication and who received GVHD prophylaxis with CYA and MTX between the years 2011 and 2015. Univariate analysis was conducted using the log‐rank test for OS and using competing risk regression for NRM, relapse and GVHD. Fisher exact tests were used to determine if an association existed between each of the pre‐transplant variables and MTX alteration. Multivariate models for OS and NRM were constructed using Cox proportional hazards modelling and competing risk regression respectively.ResultsFifty‐four (28%) of 196 had MTX alterations and 61/187 (33%) had CYA alterations. Reasons for MTX alteration included mucositis, renal or liver impairment, fluid overload and sepsis. Causes of CYA alteration were numerous, but most commonly due to acute kidney impairment. MTX alteration was associated with inferior OS (hazard ratio 2.4; P = <0.001) and higher NRM (odds ratio (OR) 4.6; P < 0.001) at 6 years post‐landmark. CYA alteration was associated with greater NRM (OR 2.7; P = 0.0137) at 6 years. GVHD rates were unaffected by dose alteration.ConclusionsOur findings suggest dose alteration in MTX and CYA GVHD prophylaxis is associated with adverse survival outcomes in alloHCT, without a significant impact on GVHD rates.
Professional values and ethical sensitivities of student nurses during the COVID‐19 pandemic
Authors: Ayaz‐Alkaya Sultan , Akca Ayşegül 
Published: June 2022

AbstractBackgroundProfessional values in nursing are the foundation of ethical practice affecting patient care quality.AimThe purpose of the present study was to evaluate the development of professional values and ethical sensitivities among new nurses during the COVID‐19 pandemic.MethodsA prospective observational study with a pre‐test and post‐test design was used. The sample constituted students (n = 302). The Nurses Professional Values Scale‐Revised and Modified Moral Sensitivity Questionnaire for Student Nurses were used for collecting data.ResultsProfessional values post‐test mean scores of participants were significantly higher than the pre‐test scores (p < 0.001). No significant difference was determined between the pre‐test and post‐test mean scores of ethical sensitivity (p > 0.05).ConclusionThe current study concluded that the professional values of newly graduated nurses developed during the COVID‐19 pandemic, but there was no change in ethical sensitivities.Implications for nursing and health policyThis study provides one of the first pieces of evidence for nursing educators and managers to assess the professional values and ethical sensitivities of newly qualified nurses who may have been affected both during and after the outbreak. Newly qualified nurses should are valued members of the health care institutions, and orientation programmes should be implemented to improve their perceptions of the profession.
What can analysis of 47 million job advertisements tell us about how opportunities for homeworking are evolving in the United Kingdom?
Authors: Darby Julia , McIntyre Stuart , Roy Graeme 
Published: June 2022

AbstractUsing an extensive database of job adverts, we investigate the extent to which homeworking is likely to continue. We track how advertisement language has evolved to indicate homeworking opportunities and how the characteristics of jobs offering these opportunities have changed, including a greater degree of polarisation in opportunity by salary.
TGA factors promote plant root growth by modulating redox homeostasis or response
Authors: Hu Xiaochen , Yang Liyun , Ren Mengfei , Liu Lin , Fu Jing , Cui Hongchang 
Published: June 2022

AbstractTo identify novel regulators of stem cell renewal, we mined an existing but little explored cell type‐specific transcriptome dataset for the Arabidopsis root. A member of the TGA family of transcription factors, TGA8, was found to be specifically expressed in the quiescent center (QC). Mutation in TGA8 caused a subtle root growth phenotype, suggesting functional redundancy with other TGA members. Using a promoter::HGFP transgenic approach, we showed that all TGA factors were expressed in the root, albeit at different levels and with distinct spatial patterns. Mutant analyses revealed that all TGA factors examined contribute to root growth by promoting stem cell renewal, meristem activity, and cell elongation. Combining transcriptome analyses, histochemical assays, and physiological tests, we demonstrated that functional redundancy exists among members of clades II and V or those in clades I and III. These two groups of TGA factors act differently, however, as their mutants responded to oxidative stress differently and quantitative reverse transcription polymerase chain reaction assays showed they regulate different sets of genes that are involved in redox homeostasis. Our study has thus uncovered a previously unrecognized broad role and a mechanistic explanation for TGA factors in root growth and development.