bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest
Authors: Collin François‐David , Durif Ghislain , Raynal Louis , Lombaert Eric , Gautier Mathieu , Vitalis Renaud , Marin Jean‐Michel , Estoup Arnaud 
Published: May 2021

AbstractSimulation‐based methods such as approximate Bayesian computation (ABC) are well‐adapted to the analysis of complex scenarios of populations and species genetic history. In this context, supervised machine learning (SML) methods provide attractive statistical solutions to conduct efficient inferences about scenario choice and parameter estimation. The Random Forest methodology (RF) is a powerful ensemble of SML algorithms used for classification or regression problems. Random Forest allows conducting inferences at a low computational cost, without preliminary selection of the relevant components of the ABC summary statistics, and bypassing the derivation of ABC tolerance levels. We have implemented a set of RF algorithms to process inferences using simulated data sets generated from an extended version of the population genetic simulator implemented in DIYABC v2.1.0. The resulting computer package, named DIYABC Random Forest v1.0, integrates two functionalities into a user‐friendly interface: the simulation under custom evolutionary scenarios of different types of molecular data (microsatellites, DNA sequences or SNPs) and RF treatments including statistical tools to evaluate the power and accuracy of inferences. We illustrate the functionalities of DIYABC Random Forest v1.0 for both scenario choice and parameter estimation through the analysis of pseudo‐observed and real data sets corresponding to pool‐sequencing and individual‐sequencing SNP data sets. Because of the properties inherent to the implemented RF methods and the large feature vector (including various summary statistics and their linear combinations) available for SNP data, DIYABC Random Forest v1.0 can efficiently contribute to the analysis of large SNP data sets to make inferences about complex population genetic histories.
Large pulmonary sclerosing pneumocytoma in a young female: A rare lung tumor
Authors: Kang Do Kyun , Kang Min Kyun , Heo Woon , Hwang Youn‐Ho , Kim Ji Yeon 
Published: May 2021

AbstractWe report a case of a 28‐year‐old female who presented with a solid mass lesion in the right middle lobe (RML). A chest computed tomography (CT) scan showed a 3.5 cm sized round and solid mass between the medial and lateral segment of the RML. The patient underwent a percutaneous lung biopsy with CT scan guidance and pathological examination showed pulmonary sclerosing pneumocytoma. RML lobectomy was performed for definitive treatment. Here, we describe this rare lung disease which presented as a large homogeneous lesion. Pulmonary sclerosing pneumocytoma should be considered in the differential diagnosis of solitary lung tumor, even if the patient is young.
Do Stronger Wise‐Thinking Dispositions Facilitate Auditors' Objective Evaluation of Evidence When Assessing and Addressing Fraud Risk?*
Authors: Brewster Billy E. , Johanns Alex J. , Peecher Mark E. , Solomon Ira 
Published: May 2021

ABSTRACTThe objective evaluation of evidence is imperative for audit effectiveness and the proper exercise of professional skepticism. However, numerous studies suggest that auditors fail to evaluate evidence objectively when assessing or addressing the risk of material misstatement due to fraud. We develop theory to predict that auditors do evaluate evidence objectively but only when they have stronger wise‐thinking dispositions (WTDs), a construct that is new to the audit literature. We define WTDs as the tendency of individuals to naturally engage in the balanced revision of beliefs and doubts about target phenomena by thinking openly and reflectively about evidence. We report prediction‐consistent results from two experiments that measure the strength of participants' WTDs and manipulate whether the underlying evidence is less or more indicative of fraud. The experimental results also document that auditors vary considerably in WTD strength and collectively demonstrate the reproducibility of audit judgment‐quality benefits of stronger WTDs. We further validate the WTD construct in auditing using confirmatory bi‐factor analyses to show that it has one higher‐order general factor along with several subfactors. Overall, our theory and results advance the literature by identifying WTDs as a determinant of auditors' ability to objectively evaluate evidence. In addition, our findings have implications for standard setters and audit firms as quality control standards and audit working paper review processes might benefit from revisions that take into account that auditors do not objectively evaluate evidence unless they have stronger WTDs.
Considerable mortality and morbidity in neonates born below 500 gram
Authors: Goeral Katharina , Fuiko Renate , Binder Julia , Lindtner Claudia , Jernej Raphaela , Rittenschober‐Boehm Judith , Klebermass‐Schrehof Katrin , Berger Angelika , Grill Agnes 
Published: May 2021

AbstractData evaluating mortality and morbidity in infants born ≤500 g are scarce and show wide variability. To support counselling and decision‐making, we analysed neurodevelopmental outcome in all neonates ≤500 g birth weight.Retrospective analysis including preterm infants with a birth weight ≤500 g and a gestational age >22 weeks born at a single tertiary perinatal centre between 2010 and 2017.Of 59 live births, 88% received standard care. Birth weight ranged from 318 to 500 g and gestational age from 23 to 29 weeks. 56% of neonates were born ≤3rd percentile and 42% of treated infants survived. Neurodevelopmental outcome was available in 91% of patients and was evaluated using Bayley Scales of Infant Development at two years. 50% showed a favourable mental development (normal or mild impairment), 75% a favourable motor development and 45% a favourable outcome in both outcome subcategories. When additionally considering visual and hearing disability and, or, cerebral palsy level ≥2 according to the Gross Motor Function Classification System 35% had a good neurodevelopmental outcome.Survival rate was 37% for all live births and 42% for infants with standard care. More than one‐third of survivors showed no significant neurodevelopmental impairment at two years.
The road to zero nosocomial infections in neonates—a narrative review
Authors: Jansen Sophie J. , Lopriore Enrico , van der Beek Martha T. , Veldkamp Karin Ellen , Steggerda Sylke J. , Bekker Vincent 
Published: May 2021

AbstractAimNosocomial infections (NI) in neonates are associated with prolonged hospitalisation, adverse neurodevelopmental outcome and high mortality. Over the past decade, numerous prevention strategies have resulted in significant reductions in NI rates. In this review, we aim to provide an overview of current NI rates from large, geographically defined cohorts.MethodsPubMed, Web of Science, EMBASE and Cochrane Library were searched for evidence regarding epidemiology and prevention of NI in neonates. Extracted studies were synthesised in a narrative form with experiential reflection.ResultsDespite the abundance of geographically defined incidence proportions, an epidemiological overview of NI is difficult to provide, given the lack of consensus definition for neonatal NI and different baseline populations being compared. Successful prevention efforts have focused on implementing evidence‐based practices while eliminating outdated strategies. The most promising model for reduction in infection rates is based on quality improvement (QI) collaboratives and benchmarking, involving identification and implementation of best practices, selection of measurable outcomes and fostering a sense of community and transparency.ConclusionThe preventative rather than curative approach forms the new paradigm for reducing the burden of neonatal infections. Despite progress achieved, continued work towards improved prevention practices is required in the strive towards zero NIs.
Extensive microbiological respiratory tract specimen characterization in critically ill COVID‐19 patients
Authors: Thomsen Kim , Pedersen Henrik Planck , Iversen Susanne , Wiese Lothar , Fuursted Kurt , Nielsen Henrik Vedel , Christensen Jens Jørgen Elmer , Nielsen Xiaohui Chen 
Published: May 2021

AbstractMicrobial co‐infections may contribute to the pulmonary deterioration in COVID‐19 patients needing intensive care treatment. The present study portrays the extent of co‐infections in COVID‐19 ICU patients. Conventional culture, molecular detections for atypical aetiologies, QiaStat‐Dx® respiratory panel V2 detecting 21 respiratory pathogens and ribosomal DNA genes 16S/18S amplicon‐based microbiome analyses were performed on respiratory samples from 34 COVID‐19 patients admitted to the ICU. Potential pathogens were detected in seven patients (21%) by culturing, in four patients (12%) by microbiome analysis and in one patient (3%) by respiratory panel. Among 20 patients receiving antibiotics prior to ICU admission, fungi (3 Candida albicans, 1 C. tropicalis, 1 C. dubliniensis) were cultured in 5 (15%) endotracheal aspirates. Among 14 patients who were antibiotic‐naive at ICU admission, two patients (6%) had bacterial respiratory pathogens (Staphylococcus aureus, Streptococcus pseudopneumoniae) cultured in their endotracheal aspirates. Microbiome analysis recognized four potential respiratory pathogens (3 Haemophilus influenza, 1 Fusobacterium necrophorum) isolated in samples from four other patients (12%). QiaStat‐Dx® respiratory panel V2 detected adenovirus in one patient (3%). The prevalence of pulmonary microbial co‐infections is modest among COVID‐19 patients upon admission to ICU. Microbiome analysis complements conventional microbial diagnostics in characterization of respiratory co‐infections.
Constructionist co‐design: A dual approach to curriculum and professional development
Authors: Kelter Jacob , Peel Amanda , Bain Connor , Anton Gabriella , Dabholkar Sugat , Horn Michael S. , Wilensky Uri 
Published: May 2021

AbstractThis paper reports on the first iteration of the Computational Thinking Summer Institute, a month‐long programme in which high school teachers co‐designed computationally enhanced mathematics and science curricula with researchers. The co‐design process itself was a constructionist learning experience for teachers resulting in constructionist curricula to be used in their own classrooms. We present three case studies to illustrate different ways teachers and researchers divided the labour of co‐design and the implications of these different co‐design styles for teacher learning and classroom enactment. Specifically, some teachers programmed their own computational tools, while others helped to conceptualise them but left the construction to their co‐design partners. Results indicate that constructionist co‐design is a promising dual approach to curriculum and professional development but that sometimes these two goals are in tension. Most teachers gained considerable confidence and skills in computational thinking, but sometimes the pressure to finish curriculum development during the institute led teachers to leave construction of computational tools to their co‐design partners, limiting their own opportunities for computational learning.
Practitioner notesWhat is already known about this topic?

Computational tools can support constructionist science and math learning by making powerful ideas tangible.
Supporting teachers to learn computational thinking and to use constructionist pedagogies is challenging.
What this paper adds?

Constructionist co‐design is a promising approach to simultaneously support curriculum development and professional development, but there are tensions to navigate in trying to accomplish both goals simultaneously.
Implications for practice and/or policy

Designers of professional development should consider constructionist co‐design as an approach but should be aware of potential tensions and prepare for them.
Translational research in action: The use of technology to disseminate information to parents during the COVID‐19 pandemic
Authors: Laxton Debra , Cooper Linda , Younie Sarah 
Published: May 2021

AbstractThis paper addresses the research problem of how to reach, engage and support parents in home‐educating young children during the first national COVID‐19 lockdown in England (March–June 2020), which was addressed through using technology. An internet‐mediated research (IMR) approach is used to investigate the effectiveness of using technology and translational research as strategies for disseminating a rapidly produced digital guide, for promoting play‐based learning at home, to parents. Lockdown with the closure of early years provision led to parents finding themselves isolated at home with young children. Early years educators were managing a unique set of circumstances where communication with families, including those ‘harder‐to‐reach’ was contextually problematic. Qualitative data using IMR captured online interactions by unobtrusive and obtrusive methods; unsolicited emails and social media comments and questionnaire responses. Conventional content analysis identified emerging themes of access, availability, reliability and readability. Analysis showed a combination of factors impacted on the speed and scale of sharing and downloading the digital guide. First, being digitally ready as platforms were already used by early years educators and Local Authorities. Second, the professional drive of Local Authorities and early years educators to support families during the crisis and third, the availability of an easily accessible online resource seen as valuable in improving play‐based learning at home.
Practitioner notesWhat is already known about this topic?

There are high levels of digital readiness in the United Kingdom.
Technology is one method used by early years settings to communicate with parents.
Parental engagement is challenging.
What this paper adds?

A translational research strategy (to share research‐informed‐knowledge with stakeholders) and internet‐mediated research (to gather data from stakeholders) combine effectively for use within the early years sector to disseminate research knowledge to parents and support home learning environments.
The high levels of technology readiness of early years educators and parents in England provides opportunities for disseminating information and improving home learning environments.
Accessing and sharing documents online may involve parents but is insufficient to engage.
Implications for practice and/or policy

Early years settings need to be more proactive in engaging with parents online.
Technology provides opportunities to develop interaction and the sharing of information with parents.
Digital media should be used as additional communication strategies and should not replace the fundamental importance of face‐to‐face‐interaction.
Transplant‐associated thrombotic microangiopathy and immune haematological complications following intestine‐containing organ transplantation: experience from over 100 consecutive cases
Authors: Thomas Will , Foukaneli Theodora , Cosgrove Joyce , Massey Dunecan , Woodward Jeremy , Middleton Stephen , Besser Martin , Russell Neil , Amin Irum , Butler Andrew , Sharkey Lisa 
Published: May 2021

SummaryDescriptions of passenger lymphocyte syndrome (PLS), immune cytopenias and transplant‐associated thrombotic microangiopathy (TA‐TMA) after intestine‐containing transplants remain scarce. We describe our centre’s experience of these complications from 2007 to 2019. Ninety‐six patients received 103 transplants. PLS occurred in 9 (9%) patients (median 12 days post‐transplant); all due to ABO antibodies. There were 31 minor ABO mismatch transplants. No patient required change in immunosuppression. Immune cytopenias (excluding PLS) occurred in six patients at an incidence of 1·7/100 patient years; three immune haemolysis, one immune thrombocytopenia, one acquired Glanzmann’s and one immune neutropenia; 50% occurred with other cytopenias. All cases eventually responded to treatment, with a median of four treatments (range 1–8) and 5/6 were treated with rituximab. One patient with immune haemolysis required bortezomib. Complications were common in patients with immune cytopenias; 4/6 with infection needing intravenous antibiotics and 3/6 with venous thromboembolism. In 3/6 cases, a secondary cause for the immune cytopenia was evident. Switching from tacrolimus to ciclosporin was not necessary. There were five cases of transplant‐associated thrombotic microangiopathy (TA‐TMA; 1·5/100 patient years) requiring calcineurin inhibitor withdrawal; two cases associated with acute rejection. Two cases were managed with plasma exchange, one with plasma infusions and one with eculizumab. Further research in this patient group is required.
A universal anti‐Xa assay for rivaroxaban, apixaban, and edoxaban measurements: method validation, diagnostic accuracy and external validation
Authors: Willekens Guido , Studt Jan‐Dirk , Mendez Adriana , Alberio Lorenzo , Fontana Pierre , Wuillemin Walter A. , Schmidt Adrian , Graf Lukas , Gerber Bernhard , Bovet Cedric , Sauter Thomas C. , Nagler Michael 
Published: May 2021

SummaryA universal anti‐Xa assay for the determination of rivaroxaban, apixaban and edoxaban drug concentrations would simplify laboratory procedures and facilitate widespread implementation. Following two pilot studies analysing spiked samples and material from 698 patients, we conducted a prospective multicentre cross‐sectional study, including 867 patients treated with rivaroxaban, apixaban or edoxaban in clinical practice to comprehensively evaluate a simple, readily available anti‐Xa assay that would accurately measure drug concentrations and correctly predict relevant levels in clinical practice. Anti‐Xa activity was measured by an assay calibrated with low‐molecular‐weight heparin (LMWH) in addition to ultra‐high performance liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). As an external validation, LMWH‐calibrated anti‐Xa activity was also determined in nine external laboratories. The LMWH‐calibrated anti‐Xa activity correlated strongly with rivaroxaban, apixaban or edoxaban drug levels [rs = 0·98, 95% confidence interval (CI) 0·98–0·98]. The sensitivity for the clinically relevant cut‐off levels of 30, 50 and 100 µg/l was 96·2% (95% CI 94·4–97·4), 96·4% (95% CI 94·4–97·7) and 96·7% (95% CI 94·3–98·1) respectively. Concordant results were obtained in the external validation study. In conclusion, a universal, LMWH‐calibrated anti‐Xa assay accurately measured rivaroxaban, apixaban and edoxaban concentrations and correctly predicted relevant drug concentrations in clinical practice.
Zinc attenuates ferroptosis and promotes functional recovery in contusion spinal cord injury by activating Nrf2/GPX4 defense pathway
Authors: Ge Ming‐hao , Tian He , Mao Liang , Li Dao‐yong , Lin Jia‐quan , Hu Heng‐shuo , Huang Shuo‐cheng , Zhang Chuan‐jie , Mei Xi‐fan 
Published: May 2021

AbstractAimSpinal cord injury (SCI) involves multiple pathological processes. Ferroptosis has been shown to play a critical role in the injury process. We wanted to explore whether zinc can inhibit ferroptosis, reduce inflammation, and then exert a neuroprotective effect.MethodsThe Alice method was used to establish a spinal cord injury model. The Basso Mouse Scale (BMS), Nissl staining, hematoxylin‐eosin staining, and immunofluorescence analysis were used to investigate the protective effect of zinc on neurons on spinal cord neurons and the recovery of motor function. The regulation of the nuclear factor E2/heme oxygenase‐1 (NRF2/HO‐1) pathway was assessed, the levels of essential ferroptosis proteins were measured, and the changes in mitochondria were confirmed by transmission electron microscopy and 5,5′,6,6′‐tetrachloro‐1,1′,3,3′‐tetraethyl‐imidacarbocyanine iodide (JC‐1) staining. In vitro experiments using VSC4.1 (spinal cord anterior horn motor neuroma cell line), 4‐hydroxynonenal (4HNE), reactive oxygen species (ROS), superoxide dismutase (SOD), malondialdehyde (MDA), glutathione (GSH), lipid peroxides, and finally the levels of inflammatory factors were detected to assess the effect of zinc.ResultsZinc reversed behavioral and structural changes after SCI. Zinc increased the expression of NRF2/HO‐1, thereby increasing the content of glutathione peroxidase 4 (GPX4), SOD, and GHS and reducing the levels of lipid peroxides, MDA, and ROS. Zinc also rescued injured mitochondria and effectively reduced spinal cord injury and the levels of inflammatory factors, and the NRF2 inhibitor Brusatol reversed the effects of zinc.ConclusionZinc promoted the degradation of oxidative stress products and lipid peroxides through the NRF2/HO‐1 and GPX4 signaling pathways to inhibit ferroptosis in neurons.
Incidence, risk factors, and long‐term outcomes associated with antibody‐mediated rejection — The long‐term Deterioration of Kidney Allograft Function (DeKAF) prospective cohort study
Authors: Hart Allyson , Schladt David P. , Matas Arthur J. , Itzler Robbin , Israni Ajay K. , Kasiske Bertram L. 
Published: May 2021

AbstractMajor gaps remain in our understanding of antibody‐mediated rejection (AMR) after kidney transplant. We examined the incidence, risk factors, response to treatment, and effects on outcomes of AMR at seven transplant programs in the long‐term Deterioration of Kidney Allograft Function prospective study cohort. Among 3131 kidney recipients, there were 194 observed AMR cases (6.2%) during (mean ± SD) 4.85 ± 1.86 years of follow‐up. Time to AMR was 0.97 ± 1.17 (median, 0.48) years. Risk factors for AMR included younger recipient age, human leukocyte antigen DR mismatches, panel‐reactive antibody >0%, positive T‐ or B‐cell cross‐match, and delayed graft function. Compared with no AMR, the adjusted time‐dependent hazard ratio for death‐censored graft failure is 10.1 (95% confidence interval, 6.5‐15.7) for all AMR patients, 4.0 (2.5, 9.1) for early AMR (<90 days after transplant), and 24.0 (14.0‐41.1) for late AMR (≥90 days after transplant). Patients were treated with different therapeutic combinations. Of 194 kidney transplant recipients with AMR, 50 (25.8%) did not respond to treatment, defined as second AMR within 100 days or no improvement in estimated glomerular filtration rate by 42 days. Long‐term outcomes after AMR are poor, regardless of the initial response to treatment. Better prevention and new therapeutic strategies are needed to improve long‐term allograft survival.