bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scene wheels: Measuring perception and memory of real-world scenes with a continuous stimulus space
Authors: Son Gaeun , Walther Dirk B. , Mack Michael L. 
Published: October 2020

AbstractPrecisely characterizing mental representations of visual experiences requires careful control of experimental stimuli. Recent work leveraging such stimulus control has led to important insights; however, these findings are constrained to simple visual properties like colour and line orientation. There remains a critical methodological barrier to characterizing perceptual and mnemonic representations of realistic visual experiences. Here, we introduce a novel method to systematically control visual properties of natural scene stimuli. Using generative adversarial networks (GAN), a state-of-art deep learning technique for creating highly realistic synthetic images, we generated scene wheels in which continuously changing visual properties smoothly transition between meaningful realistic scenes. To validate the efficacy of scene wheels, we conducted two behavioral experiments that assess perceptual and mnemonic representations attained from the scene wheels. In the perceptual validation experiment, we tested whether the continuous transition of scene images along the wheel is reflected in human perceptual similarity judgment. The perceived similarity of the scene images correspondingly decreased as distances between the images increase on the wheel. In the memory experiment, participants reconstructed to-be-remembered scenes from the scene wheels. Reconstruction errors for these scenes resemble error distributions observed in prior studies using simple stimulus properties. Importantly, perceptual similarity judgment and memory precision varied systematically with scene wheel radius. These findings suggest our novel approach offers a window into the mental representations of naturalistic visual experiences.
Soluble Spike DNA vaccine provides long-term protective immunity against SAR-CoV-2 in mice and nonhuman primates
Authors: Seo Yong Bok , Suh You Suk , Ryu Ji In , Jang Hwanhee , Oh Hanseul , Koo Bon-Sang , Seo Sang-Hwan , Hong Jung Joo , Song Manki , Kim Sung-Joo , Sung Young Chul 
Published: October 2020

SummaryThe unprecedented and rapid spread of SARS-CoV-2 has motivated the need for a rapidly producible and scalable vaccine. Here, we developed a synthetic soluble SARS-CoV-2 spike (S) DNA-based vaccine candidate, GX-19. In mice, immunization with GX-19 elicited not only S-specific systemic and pulmonary antibody responses but also Th1-biased T cell responses in a dose-dependent manner. GX-19 vaccinated nonhuman primate seroconverted rapidly and exhibited detectable neutralizing antibody response as well as multifunctional CD4+ and CD8+ T cell responses. Notably, when the immunized nonhuman primates were challenged at 10 weeks after the last vaccination with GX-19, they did not develop fever and reduced viral loads in contrast to non-vaccinated primates as a control. These findings indicate that GX-19 vaccination provides durable protective immune response and also support further development of GX-19 as a vaccine candidate for SARS-CoV-2 in human clinical trials.
Practice modifies the response to errors during a novel motor sequence learning task
Authors: Rachaveti Dhanush , Ranganathan Rajiv , SKM Varadhan 
Published: October 2020

AbstractThe occurrence of an error when performing a motor sequence causes an immediate reduction in speed on subsequent trials, which is referred to as post-error slowing. However, understanding how post-error slowing changes with practice has been difficult because it requires extended practice on a novel sequence task. To address this issue, we examined post-error slowing in a novel glove-based typing task that participants performed for 15 consecutive days. Speed and accuracy improved from the early to middle stages of practice, but did not show any further improvements between middle and late stage of practice. However, when we analyzed the response to errors, we found that participants decreased both the magnitude and duration of post-error slowing with practice, even after there were no detectable improvements in overall task performance. These results indicate that learning not only improves overall task performance but also modifies the ability to respond to errors.
Novel metric for hyperbolic phylogenetic tree embeddings
Authors: Matsumoto Hirotaka , Mimori Takahiro , Fukunaga Tsukasa 
Published: October 2020

Advances in experimental technologies such as DNA sequencing have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods.The demo code is attached as a supplementary file in a compiled jupyter notebook. The code used for analyses is available on GitHub athttps://github.com/hmatsu1226/HyPhyTree.
Health conditions and the risk of home injury in French adults: Results from a prospective study of the MAVIE cohort
Authors: Rojas Castro Madelyn Yiseth , Avalos Marta , Contrand Benjamin , Dupuy Marion , Sztal-Kutas Catherine , Orriols Ludivine , Lagarde Emmanuel 
Published: October 2020

ABSTRACTBackgroundHome injury (HI) is a significant cause of mortality and morbidity in adults of all ages. Health conditions significantly impact HI among old adults, but little is known for other adults.Study designProspective cohort studyObjectiveWe assessed the associations between health-related factors and HI’s risk in a French study, the MAVIE cohort.MethodsPoisson mixed models were fitted using health-related data information (diseases, treatments, and disabilities) at baseline and the number of injuries prospectively recorded during the follow-up, adjusting for significant socio-demographics and exposure to a range of home activities. Attributable fractions (AFs) were estimated based on RR estimations measured in the fully adjusted models.ResultsA total of 6,146 dwelling adults aged 15 or more were followed up for 5.1 years on average. Vertigo or dizziness (RR=2.36, 95% CI 1.06 to 5.01) and sciatica or back pain (RR=1.49, 95% CI 1.08 to 2.05) were independently associated with an increased risk of HI. These two groups of conditions showed the most significant associations among people aged 15 to 49, whereas musculoskeletal diseases other than rachialgias and arthropathies were the most significant health-related risk factor in people aged 50 and more. Sciatica or back pain represented the highest-burden of HIs in overall adults (8%) and among people aged 15 to 49 (12%).ConclusionOur results suggest that adults with musculoskeletal disorders and vertigo or dizziness symptoms have a higher risk of HI, regardless of age.
Olig3 acts as a master regulator of cerebellar development
Authors: Lowenstein Elijah D. , Rusanova Aleksandra , Stelzer Jonas , Hernaiz-Llorens Marc , Schroer Adrian E. , Epifanova Ekaterina , Bladt Francesca , Isik Eser Göksu , Jia Shiqi , Tarabykin Victor , Hernandez-Miranda Luis R. 
Published: October 2020

AbstractThe mature cerebellum controls motor skill precision and participates in other sophisticated brain functions that include learning, cognition and speech. Different types of GABAergic and glutamatergic cerebellar neurons originate in temporal order from two progenitor niches, the ventricular zone and rhombic lip, which express the transcription factors Ptf1a and Atoh1, respectively. However, the molecular machinery required to specify the distinct neuronal types emanating from these progenitor zones is still unclear. Here, we uncover the transcription factor Olig3 as a major determinant in generating the earliest neuronal derivatives emanating from both progenitor zones. In the rhombic lip, Olig3 regulates progenitor cell proliferation. In the ventricular zone, Olig3 safeguards Purkinje cell specification by curtailing the expression of Pax2, a transcription factor that we found to impose an inhibitory interneuron identity. Our work thus defines Olig3 as a key factor in cerebellar development.
Conduction velocity along the local axons of parvalbumin interneurons correlates with the degree of axonal myelination
Authors: Micheva Kristina D. , Kiraly Marianna , Perez Marc M. , Madison Daniel V. 
Published: October 2020

AbstractParvalbumin-containing (PV+) basket cells in mammalian neocortex are fast-spiking interneurons that regulate the activity of local neuronal circuits in multiple ways. Even though PV+ basket cells are locally projecting interneurons, their axons are myelinated. Can this myelination contribute in any significant way to the speed of action potential propagation along such short axons? We used dual whole cell recordings of synaptically connected PV+ interneurons and their postsynaptic target in acutely-prepared neocortical slices from adult mice to measure the amplitude and latency of single presynaptic action potential-evoked inhibitory postsynaptic currents (IPSCs). These same neurons were then imaged with immunofluorescent array tomography, the synaptic contacts between them identified and a precise map of the connections was generated, with the exact axonal length and extent of myelin coverage. Our results support that myelination of PV+ basket cells significantly increases conduction velocity, and does so to a degree that can be physiologically relevant.
What is the evidence for transmission of COVID-19 by children in schools? A living systematic review
Authors: Xu Wei , Li Xue , Dozier Marshall , He Yazhou , Kirolos Amir , Lang Zhongyu , Mathews Catherine , Siegfried Nandi , Theodoratou Evropi 
Published: October 2020

ABSTRACTBackgroundIt is of paramount importance to understand the transmission of SARS-CoV-2 in schools, which could support the decision-making about educational facilities closure or re-opening with effective prevention and control measures in place.MethodsWe conducted a systematic review and meta-analysis to investigate the extent of SARS-CoV-2 transmission in schools. We performed risk of bias evaluation of all included studies using the Newcastle-Ottawa Scale (NOS).Results2,178 articles were retrieved and 11 studies were included. Five cohort studies reported a combined 22 student and 21 staff index cases that exposed 3,345 contacts with 18 transmissions [overall infection attack rate (IAR): 0.08% (95% CI: 0.00%–0.86%)]. IARs for students and school staff were 0.15% (95% CI: 0.00%–0.93%) and 0.70% (95% CI: 0.00%–3.56%) respectively. Six cross-sectional studies reported 639 SARS-CoV-2 positive cases in 6,682 study participants tested [overall SARS-CoV-2 positivity rate: 8.00% (95% CI: 2.17%–16.95%)]. SARS-CoV-2 positivity rate was estimated to be 8.74% (95% CI: 2.34%–18.53%) among students, compared to 13.68% (95% CI: 1.68%–33.89%) among school staff. Gender differences were not found for secondary infection (OR: 1.44, 95% CI: 0.50-4.14, P= 0.49) and SARS-CoV-2 positivity (OR: 0.90, 95% CI: 0.72-1.13, P= 0.36) in schools. Fever, cough, dyspnea, ageusia, anosmia, rhinitis, sore throat, headache, myalgia, asthenia, and diarrhoea were all associated with the detection of SARS-CoV-2 antibodies (based on two studies). Overall, study quality was judged to be poor with risk of performance and attrition bias, limiting the confidence in the results.ConclusionsThere is limited high-quality evidence available to quantify the extent of SARS-CoV-2 transmission in schools or to compare it to community transmission. Emerging evidence suggests lower IAR and SARS-CoV-2 positivity rate in students compared to school staff. Future prospective and adequately controlled cohort studies are necessary to confirm this finding.
Increased brain volume from higher cereal and lower coffee intake: Shared genetic determinants and impacts on cognition and metabolism
Authors: Kang Jujiao , Jia Tianye , Jiao Zeyu , Shen Chun , Xie Chao , Cheng Wei , Sahakian Barbara J , Waxman David , Feng Jianfeng 
Published: October 2020

AbstractIt is unclear how different diets may affect human brain development and if genetic and environmental factors play a part. We investigated diet effects in the UK Biobank data from 18,879 healthy adults and discovered anti-correlated brain-wide grey matter volume (GMV)-association patterns between coffee and cereal intake, coincidence with their anti-correlated genetic constructs. The Mendelian randomisation approach further indicated a causal effect of higher coffee intake on reduced total GMV, which is likely through regulating the expression of genes responsible for synaptic development in the brain. The identified genetic factors may further affect people’s lifestyle habits and body/blood fat levels through the mediation of cereal/coffee intake, and the brain-wide expression pattern of gene CPLX3, a dedicated marker of subplate neurons that regulate cortical development and plasticity, may underlie the shared GMV-association patterns among the coffee/cereal intake and cognitive functions. All the main findings were successfully replicated in the newly-released independent UK Biobank data from 16,412 healthy adults. Our findings thus revealed that high-cereal and low-coffee diets shared similar brain and genetic constructs, leading to long-term beneficial associations regarding cognitive, BMI and other metabolic measures. This study has important implications for public health, especially during the pandemic, given the poorer outcomes of COVID-19 patients with greater BMIs.Significance statementWe investigated diet effects on the brain structure and its genetic constructs using the UK Biobank data and discovered a causal effect of higher coffee intake on reduced total grey matter volume (GMV) and replicable anti-correlated brain-wide association GMV patterns between cereal and coffee intake. Further, the high-cereal and low-coffee diets shared similar brain and genetic constructs, leading to long-term beneficial associations regarding cognitive, BMI, and other metabolic indicators. Our study has important implications for public health, especially during the pandemic, given the poorer outcomes of COVID-19 patients with greater BMIs.
Evaluating Short-term Forecast among Different Epidemiological Models under a Bayesian Framework
Authors: Li Qiwei , Bedi Tejasv , Xiao Guanghua , Xie Yang 
Published: October 2020

AbstractForecasting of COVID-19 daily confirmed cases has been one of the several challenges posed on the governments and health sectors on a global scale. To facilitate informed public health decisions, the concerned parties rely on short-term daily projections generated via predictive modeling. We calibrate stochastic variants of growth models and the standard SIR model into one Bayesian framework to evaluate their short-term forecasts. In summary, it was noted that none of the models proved to be golden standards across all the regions in their entirety, while all outperformed ARIMA in a predictive capacity as well as in terms of interpretability.
Native structure of flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries
Authors: Kawamoto Akihiro , Miyata Tomoko , Makino Fumiaki , Kinoshita Miki , Minamino Tohru , Imada Katsumi , Kato Takayuki , Namba Keiichi 
Published: October 2020

AbstractThe bacterial flagellar MS ring is a transmembrane complex acting as the core of the flagellar motor. It not only acts as the template for rod and C ring assembly but also houses the type III protein export gate for assembly of the rod, hook and filament. The cytoplasmic C ring, involved in torque generation and rotation switch, is directly attached to the MS ring, and a symmetry mismatch between 26-fold MS ring and 34-fold C ring had been a long puzzle as to whether this would play some role in motor function. Although this puzzle seemed to have been resolved by the recent high-resolution structure of the MS ring with 33-fold symmetry with a variation from 32-fold to 35-fold because the C ring also shows a similar symmetry variation, it still remained ambiguous whether their symmetries are matched in the native motor structure. Here we show that the native MS ring structure formed by full-length FliF is 34-fold with no symmetry variation whereas the C ring has a small symmetry variation, indicating a flexibility in C ring assembly to generate small symmetry mismatches. We also show two conformations of FliF in part of its periplasmic region to form the 34-subunit ring with 23-fold and 11-fold subsymmetries in the inner and middle M ring, respectively, to accommodate the export gate at the center of the M ring.
What Treatment Outcomes Matter Most? A Q-study of Outcome Priority Profiles Among Youth with Lived Experience of Depression
Authors: Krause K. R. , Edbrooke-Childs J. , Bear H. A. , Calderón A. , Wolpert M. 
Published: October 2020

AbstractObjectiveOver the past years, interest in youth perspectives on what constitutes an important outcome in the treatment of depression has been growing, but limited attention has been given to heterogeneity in outcome priorities and minority viewpoints. These are important to consider for person-centered outcome tracking in clinical practice, or when conducting clinical trials targeting specific populations. This study used Q-methodology to identify outcome priority profiles among youth with lived experience of service use for depression.MethodA purposive sample of 28 youth (aged 16–21 years) rank-ordered 35 outcomes by importance and completed brief semi-structured interviews eliciting their sorting rationales. By-person principal component analysis was used to identify outcome priority profiles based on all Q-sort configurations. Priority profiles were described and interpreted with reference to the qualitative interview data.ResultsFour distinct outcome priority profiles were identified: “symptom reduction and enhanced well-being”; “improved coping and self-management”; “better understanding past and present”; and “less interference with daily life”. All four profiles prioritized outcomes related to improved mood and affect over other outcome concepts. Beyond these core outcomes, profiles differed in the level of importance assigned to learning practical coping skills, processing experiences, finding safe ways to articulate emotions, and reduced interference of depression with life and identity.ConclusionAs part of a person-centered approach to care delivery, care providers should routinely engage young people in conversation and shared decision-making about the types of change they would like to prioritize and track during treatment, beyond a common core of consensus outcomes.
Methods for detection of clusters of observations with an outlying correlation coefficient value
Authors: Desmet Lieven , Venet David , Trotta Laura , Burzykowski Tomasz , Buyse Marc 
Published: October 2020

AbstractMultivariate datasets with a clustered structure are the natural framework for, e.g., multicentre clinical trials. We propose a number of methods aimed at detecting clusters with outlying correlation coefficients. While the methods can be used in a variety of settings, we focus mainly on their application to central statistical monitoring of clinical trials. In particular, we consider the issue of detecting centers (or other clusters of patients such as regions) with outlying correlation coefficients for bivariate data in a multicenter clinical trial. It appears that, in that context, the proposed methods perform well, as we show by using a simulation study and a number of real life datasets.
Evaluation of statistical methods used in the analysis of interrupted time series studies: a simulation study
Authors: Turner Simon L , Forbes Andrew B , Karahalios Amalia , Taljaard Monica , McKenzie Joanne E 
Published: October 2020

AbstractInterrupted time series (ITS) studies are frequently used to evaluate the effects of population-level interventions or exposures. To our knowledge, no studies have compared the performance of different statistical methods for this design. We simulated data to compare the performance of a set of statistical methods under a range of scenarios which included different level and slope changes, varying lengths of series and magnitudes of autocorrelation. We also examined the performance of the Durbin-Watson (DW) test for detecting autocorrelation. All methods yielded unbiased estimates of the level and slope changes over all scenarios. The magnitude of autocorrelation was underestimated by all methods, however, restricted maximum likelihood (REML) yielded the least biased estimates. Underestimation of autocorrelation led to standard errors that were too small and coverage less than the nominal 95%. All methods performed better with longer time series, except for ordinary least squares (OLS) in the presence of autocorrelation and Newey-West for high values of autocorrelation. The DW test for the presence of autocorrelation performed poorly except for long series and large autocorrelation. From the methods evaluated, OLS was the preferred method in series with fewer than 12 points, while in longer series, REML was preferred. The DW test should not be relied upon to detect autocorrelation, except when the series is long. Care is needed when interpreting results from all methods, given confidence intervals will generally be too narrow. Further research is required to develop better performing methods for ITS, especially for short series.