bluuebunny/crossref_metadata_2025_split huggingface dataset:
“It's Not an Acting Job … Don't Underestimate What a Simulated Patient Does”: A Qualitative Study Exploring the Perspectives of Simulated Patients in Health Professions Education
Authors: Pritchard Shane A. , Denning Tracy , Keating Jennifer L. , Blackstock Felicity C. , Nestel Debra 
Published: November 2019

Introduction
Simulated patients (SPs) are individuals who have learned to realistically portray patient roles in health professional education. Program recommendations are increasing for simulation programs, and as key stakeholders, SPs' perspectives seem underrepresented. The aim of the study was to explore the experiences, perspectives, and practices of SPs to gain insights on topics of importance to SPs and inform program recommendations.

Methods
An interpretivist research paradigm and qualitative design were adopted. Eighteen SPs participated in 2 focus groups that were audio recorded, transcribed, and deidentified. Three researchers completed inductive thematic analysis. Institutional ethical approval was obtained.

Results
Three themes represented the different elements of SP practice: becoming and being a SP, preparing for a SP role, and performing a SP role. Simulated patients identify as educated specialists with unique responsibilities and attributes. Simulated patients are committed to representing the perspectives of real patients, while simultaneously supporting learners and educators. Simulated patients can feel unprepared to perform a role but have innovated responsive strategies.

Conclusions
Simulated patients considered 3 primary aspects to their practice and shared ways that they might be well supported. Simulated patients represent a community of practice, characterized by mutual engagement, joint enterprise, and a shared repertoire. Ongoing SP input in SP programs may benefit SPs and lead to higher-quality educational experiences for learners.
Comparison of a Behavioral Versus an Educational Weight Management Intervention After Renal Transplantation: A Randomized Controlled Trial
Authors: Schmid-Mohler Gabriela , Zala Patrizia , Graf Nicole , Witschi Patrick , Mueller Thomas F. , Peter Wüthrich Rudolf , Huber Laura , Fehr Thomas , Spirig Rebecca 
Published: November 2019

Background.
In the first year following renal transplantation, preventing weight gain to minimize overweight or obesity is particularly important. The aim of this study is to test the effect of an 8-month behavioral intervention BMI and physical activity.

Methods.
This randomized controlled study included 123 adult kidney or kidney-pancreas recipients. Patients were randomized to usual (1 educational session, then weight self-monitoring) and intervention care (usual care plus 7–8 counseling sessions). Alongside weight, body composition, and physical activity, satisfaction and perceptions regarding care were measured at weeks 2–6 (baseline), then at months 8 and 12.

Results.
Both groups reported comparably high satisfaction. The intervention group (IG) reported more chronic care-related activities. In patients with BMIs ≥ 18.5, mean weight gain (from baseline) was unexpectedly low in both groups: at month 8, +0.04 kg/m2 in IG patients and +0.14 kg/m2 in the control group (P = 0.590), and respectively, +0.03 kg/m2 and +0.19 kg/m2 at month 12 (P = 0.454). Both groups were physically active, walking averages of 10 807 (IG) and 11 093 (control group) steps per day at month 8 (P = 0.823), and respectively 9773 and 11 217 at month 12 (P = 0.195).

Conclusions.
The behavioral intervention had high patient acceptance and supported patients in maintaining their weight, but had no superior effect on a single educational session. Further research is needed to assess patient weight gain risk profiles to stratify the intervention.
‘Excess anxiety’ and ‘less anxiety’: both depend on vestibular function
Authors: Brandt Thomas , Dieterich Marianne 
Published: November 2019

Purpose of review
To present evidence of a functional interrelation between the vestibular and the anxiety systems based on a complex reciprocally organized network. The review focuses on the differential effects of various vestibular disorders, on psychiatric comorbidity, and on anxiety related to vertigo.

Recent findings
Episodic vertigo syndromes such as vestibular migraine, vestibular paroxysmia, and Menière's disease are associated with a significant increase of psychiatric comorbidity, in particular anxiety/phobic disorders and depression. Chronic unilateral and bilateral vestibulopathy (BVP) do not exhibit a higher than normal psychiatric comorbidity. Anxiety related to the vertigo symptoms is also increased in episodic structural vestibular disorders but not in patients with chronic unilateral or bilateral loss of vestibular function. The lack of vertigo-related anxiety in BVP is a novel finding. Several studies have revealed special features related to anxiety in patients suffering from BVP: despite objectively impaired postural balance with frequent falls, they usually do not complain about fear of falling; they do not report an increased susceptibility to fear of heights; they do not have an increased psychiatric comorbidity; and they do not report increased anxiety related to the perceived vertigo. Subtle or moderate vestibular stimulation (by galvanic currents or use of a swing) may have beneficial effects on stress or mood state in healthy adults, and promote sleep in humans and rodents. The intimate structural and functional linkage of the vestibular and anxiety systems includes numerous nuclei, provincial and connector hubs, the thalamocortical network, and the cerebellum with many neural transmitter systems.

Summary
The different involvement of emotional processes and anxiety – to the extent of ‘excess anxiety’ or ‘less anxiety’ – in structural vestibular disorders may be due to the specific dysfunction and whether the system activity is excited or diminished. Both psychiatric comorbidity and vertigo-related anxiety are maximal with excitation and minimal with loss of peripheral vestibular function.
Substance use disorders in people with intellectual disability
Authors: Didden Robert , VanDerNagel Joanne , Delforterie Monique , van Duijvenbode Neomi 
Published: November 2019

Purpose of review
To provide an overview of studies on substance use and substance use disorder (SUD) in individuals with mild intellectual disability or borderline intellectual functioning (MID–BIF).

Recent findings
Many individuals with MID–BIF use tobacco, alcohol, and drugs. On average, rates of substance use and SUD are similar to or even higher than those in peers with average intelligence. Individuals with MID–BIF are overrepresented in (forensic) addiction care. Several instruments are now available for the assessment of SUD and its risk factors in this target group. Prevention and intervention programs have been shown feasible and with promising outcomes, although the evidence base is still small. Professionals in addiction care and intellectual disability care facilities show deficiencies in skills in addressing SUD in clients with MID–BIF.

Summary
Research in this area is still in its infancy, though an increasing number of studies show promising outcomes regarding case identification, assessment, and treatment of SUD in intellectual disability. Policy and practice should be adapted to the characteristics of individuals with MID–BIF.
Psychological treatment strategies for challenging behaviours in neurodevelopmental disorders: what lies beyond a purely behavioural approach?
Authors: Woodcock Kate A. , Blackwell Siobhán 
Published: November 2019

Purpose of review
Challenging behaviour shown by individuals with neurodevelopmental disorders (NDDs) has a major negative impact. There is robust evidence for the efficacy of treatments based on applied behaviour analysis. However, such approaches are limited in important ways – providing only part of the whole solution. We reviewed the literature to provide an overview of recent progress in psychological treatments for challenging behaviour and how these advance the field beyond a purely behavioural approach.

Recent finding
We identified 1029 articles via a systematic search and screened for those implementing a psychological intervention with individuals with NDD (or caregivers) and measuring the potential impact on challenging behaviour. Of the 69 included studies published since 2018, more than 50% implemented a purely behavioural intervention. Other studies could generally be categorized as implementing parent training, meditation, skill training or technology-assisted interventions.

Summary
Greater consideration of the interplay between behavioural and nonbehavioural intervention components; systematic approaches to personalization when going beyond the behavioural model; mental health and broad social communication needs; and models that include cognitive and emotional pathways to challenging behaviour; is needed to advance the field. Furthermore, technology should not be overlooked as an important potential facilitator of intervention efforts.
Molecular Evolution of the Sex Peptide Network in Drosophila
Authors: McGeary Meaghan K. , Findlay Geoffrey D. 
Published: November 2019

AbstractSuccessful reproduction depends on interactions between numerous proteins beyond those involved directly in gamete fusion. While such reproductive proteins evolve in response to sexual selection pressures, how networks of interacting proteins arise and evolve as reproductive phenotypes change remains an open question. Here, we investigated the molecular evolution of the “sex peptide network” of Drosophila melanogaster, a functionally well-characterized reproductive protein network. In this species, the peptide hormone sex peptide (SP) and its interacting proteins cause major changes in female physiology and behavior after mating. In contrast, females of more distantly related Drosophila species do not respond to SP. In spite of these phenotypic differences, we detected orthologs of all network proteins across 22 diverse Drosophila species and found evidence that most orthologs likely function in reproduction throughout the genus. Within SP-responsive species, we detected the recurrent, adaptive evolution of several network proteins, consistent with sexual selection acting to continually refine network function. We also found some evidence for adaptive evolution of several proteins along two specific phylogenetic lineages that correspond with increased expression of the SP receptor in female reproductive tracts or increased sperm length, respectively. Finally, we used gene expression profiling to examine the likely degree of functional conservation of the paralogs of an SP network protein that arose via gene duplication. Our results suggest a dynamic history for the SP network in which network members arose before the onset of robust SP-mediated responses and then were shaped by both purifying and positive selection.
Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study
Authors: Rode Julie , Pelletier Agnès , Fumey Julien , Rode Stéphane , Cabanat Anne-Lise , Ouvrard Anne , Chaix Bastien , White Bradley , Harnden Matthew , Xuan Nguyen Thi , Vereshagin Alexander , Casane Didier 
Published: November 2019

AbstractSnow leopards (Panthera uncia) are a keystone species of Central Asia’s high mountain ecosystem. The species is listed as vulnerable and is elusive, preventing accurate population assessments that could inform conservation actions. Non-invasive genetic monitoring conducted by citizen scientists offers avenues to provide key data on this species that would otherwise be inaccessible. From 2011 to 2015, OSI-Panthera citizen science expeditions tracked signs of presence of snow leopards along transects in the main valleys and crests of the Sarychat-Ertash State Reserve (Kyrgyzstan). Scat samples were genotyped at seven autosomal microsatellite loci and at a X/Y locus for sex identification, which allowed estimating a minimum of 11 individuals present in the reserve from 2011 to 2015. The genetic recapture of 7 of these individuals enabled diachronic monitoring, providing indications of individuals’ movements throughout the reserve. We found putative family relationships between several individuals. Our results demonstrate the potential of this citizen science program to get a precise description of a snow leopard population through time.
A deep learning-based model of normal histology
Authors: Sing Tobias , Hoefling Holger , Hossain Imtiaz , Boisclair Julie , Doelemeyer Arno , Flandre Thierry , Piaia Alessandro , Romanet Vincent , Santarossa Gianluca , Saravanan Chandrassegar , Sutter Esther , Turner Oliver , Wuersch Kuno , Moulin Pierre 
Published: November 2019

AbstractDeep learning models have been applied on various tissues in order to recognize malignancies. However, these models focus on relatively narrow tissue context or well-defined pathologies. Here, instead of focusing on pathologies, we introduce models characterizing the diversity of normal tissues. We obtained 1,690 slides with rat tissue samples from the control groups of six preclinical toxicology studies, on which tissue regions were outlined and annotated by pathologists into 46 different tissue classes. From these annotated regions, we sampled small patches of 224 × 224 pixels at six different levels of magnification. Using four studies as training set and two studies as test set, we trained VGG-16, ResNet-50, and Inception-v3 networks separately at each of these magnification levels. Among these models, Inception-v3 consistently outperformed the other networks and attained accuracies up to 83.4% (top-3 accuracy: 96.3%). Further analysis showed that most tissue confusions occurred within clusters of histologically similar tissues. Investigation of the embedding layer using the UMAP method revealed not only pronounced clusters corresponding to the individual tissues, but also subclusters corresponding to histologically meaningful structures that had neither been annotated nor trained for. This suggests that the histological representation learned by the normal histology network could also be used to flag abnormal tissue as outliers in the embedding space without a need to explicitly train for specific types of abnormalities. Finally, we found that models trained on rat tissues can be used on non-human primate and minipig tissues with minimal retraining.Author contributionT.S. and H.H. contributed equally to this work.Significance statementLike many other scientific disciplines, histopathology has been profoundly impacted by recent advances in machine learning with deep neural networks. In this field, most deep learning models reported in the literature are trained on pathologies in specific tissues/contexts. Here, we aim to establish a model of normal tissues as a foundation for future models of histopathology. We build models that are specific to histopathology images and we show that their embeddings are better feature vectors for describing the underlying images than those of off-the shelf CNN models. Therefore, our models could be useful for transfer learning to improve the accuracy of other histopathology models.
Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury
Authors: Renthal William , Tochitsky Ivan , Yang Lite , Cheng Yung-Chih , Li Emmy , Kawaguchi Riki , Geschwind Daniel H. , Woolf Clifford J. 
Published: November 2019

SummaryPrimary somatosensory neurons are specialized to transmit specific types of sensory information through differences in cell size, myelination, and the expression of distinct receptors and ion channels, which together define their transcriptional and functional identity. By transcriptionally profiling sensory ganglia at single-cell resolution, we find that different somatosensory neuronal subtypes undergo a remarkably consistent and dramatic transcriptional response to peripheral nerve injury that both promotes axonal regeneration and suppresses cell identity. Successful axonal regeneration leads to a restoration of neuronal cell identity and the deactivation of the growth program. This injury-induced transcriptional reprogramming requires Atf3, a transcription factor which is induced rapidly after injury and is necessary for axonal regeneration and functional recovery. While Atf3 and other injury-induced transcription factors are known for their role in reprogramming cell fate, their function in mature neurons is likely to facilitate major adaptive changes in cell function in response to damaging environmental stimuli.
RsQTL: correlation of expressed SNVs with splicing using RNA-sequencing data
Authors: Sein Justin , Spurr Liam F. , Bousounis Pavlos , Prashant N M , Liu Hongyu , Alomran Nawaf , Bernot Jimmy , Ibeawuchi Helen , Reece-Stremtan Dacian , Horvath Anelia 
Published: November 2019

SummaryRsQTL is a tool for identification of splicing quantitative trait loci (sQTLs) from RNA-sequencing (RNA-seq) data by correlating the variant allele fraction at expressed SNV loci in the transcriptome (VAFRNA) with the proportion of molecules spanning local exon-exon junctions at loci with differential intron excision (percent spliced in, PSI). We exemplify the method on sets of RNA-seq data from human tissues obtained though the Genotype-Tissue Expression Project (GTEx). RsQTL does not require matched DNA and can identify a subset of expressed sQTL loci. Due to the dynamic nature of VAFRNA, RsQTL is applicable for the assessment of conditional and dynamic variation-splicing relationships.Availability and implementationhttps://github.com/HorvathLab/RsQTL.Contacthorvatha@gwu.edu or jsein@gwmail.gwu.eduSupplementary InformationRsQTL_Supplementary_Data.zip
Effective downregulation of BCR-ABL tumorigenicity by RNA targeted CRISPR-Cas13a
Authors: Singh Aditya , Bhatia Prateek 
Published: November 2019

AbstractAimTo induce BCR-ABL gene silencing using CRISPR Cas13a.BackgroundCML is a clonal myeloproliferative disorder of pluripotent stem cells driven by a reciprocal translocation between chromosome 9 and 22, forming a BCR-ABL fusion gene. Tyrosinekinase inhibitor drugs like imatinib are the mainstay of treatment and cases resistant to these drugs have a poor prognosis in the absence of a compatible stem-cell donor. However, with rapid advancements in gene-editing technologies, most studies are now focusing on developing a translational model targeting single-gene disorders with a prospective permanent cure.ObjectiveTo explore the potential application of the RNA targeting CRISPR-Cas13a system for effective knockdown of BCR-ABL fusion transcript in a CML cell line, K562.MethodCRISPR Cas13a crRNA was designed specific to the chimeric BCR-ABL gene and the system was transfected as a two-plasmid system into a CML cell line, K562. The effects were enumerated by evaluating the expression levels of downstream genes dependent on the expression of the BCR-ABL gene. Also, next-generation sequencing was used to ascertain the effects of CRISPR on the gene.ResultsThe CRISPR system was successfully able to lower the expression of downstream genes (pCRKL and pCRK) dependent on the activated BCR-ABL kinase signal by up-to 4.3 folds. The viability of the CRISPR treated cells were also significantly lowered by 373.83-fold (p-value= 0.000891196). The time-dependent kinetics also highlighted the significant in-vitro suppressive activity to last up to 8 weeks (p-value: 0.025). As per the cDNA sequencing data from Oxford MinION next-generation sequencer, the CRISPR treated cells show 62.37% suspected cleaved reads.ConclusionThese preliminary results highlight an excellent potential application of RNA targeting CRISPRs in Haematological neoplasms like CML and should pave way for further research in this direction.
Rapid Recalibration of Peri-Personal Space; Psychophysical, Electrophysiological, and Neural Network Modeling Evidence
Authors: Noel Jean-Paul , Bertoni Tommaso , Terrebonne Emily , Pellencin Elisa , Herbelin Bruno , Cascio Carissa , Blanke Olaf , Magosso Elisa , Wallace Mark T. , Serino Andrea 
Published: November 2019

AbstractInteractions between individuals and the environment are mediated by the body and occur within the peri-personal space (PPS) – the space surrounding the body. The multisensory encoding of this space plastically adapts to different bodily constraints and stimuli features. However, these remapping effects have only been demonstrated on the time-scale of days, hours, or minutes. Yet, if PPS mediates human-environment interactions in an adaptive manner, its representation should be altered by sensory history on trial-to-trial timescale. Here we test this idea first via a visuo-tactile reaction time paradigm in augmented reality where participants are asked to respond as fast as possible to touch, as visual object approach them. Results demonstrate that reaction times to touch are facilitated as a function of visual proximity, and the sigmoidal function describing this facilitation shifts closer to the body if the immediately precedent trial had indexed a smaller visuo-tactile disparity (i.e., positive serial dependency). Next, we derive the electroencephalographic correlates of PPS and demonstrate that this measure is equally shaped by recent sensory history. Finally, we demonstrate that a validated neural network model of PPS is able to account for the present results via a simple Hebbian plasticity rule. The present findings suggest that PPS encoding remaps on a very rapid time-scale and is sensitive to recent sensory history.
ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules
Authors: Ludwig Marcus , Nothias Louis-Félix , Dührkop Kai , Koester Irina , Fleischauer Markus , Hoffmann Martin A. , Petras Daniel , Vargas Fernando , Morsy Mustafa , Aluwihare Lihini , Dorrestein Pieter C. , Böcker Sebastian 
Published: November 2019

1AbstractThe confident high-throughput identification of small molecules remains one of the most challenging tasks in mass spectrometry-based metabolomics. SIRIUS has become a powerful tool for the interpretation of tandem mass spectra, and shows outstanding performance for identifying the molecular formula of a query compound, being the first step of structure identification. Nevertheless, the identification of both molecular formulas for large compounds above 500 Daltons and novelmolecular formulasremains highly challenging. Here, we present ZODIAC, a network-based algorithm for thede novoestimation of molecular formulas. ZODIAC reranks SIRIUS’ molecular formula candidates, combining fragmentation tree computation with Bayesian statistics using Gibbs sampling. Through careful algorithm engineering, ZODIAC’s Gibbs sampling is very swift in practice. ZODIAC decreases incorrect annotations 16.2-fold on a challenging plant extract dataset with most compounds above 700 Dalton; we then show improvements on four additional, diverse datasets. Our analysis led to the discovery of compounds with novel molecular formulas such as C24H47BrNO8P which, as of today, is not present in any publicly available molecular structure databases.