julilili42/papers huggingface dataset:
The Functional Movement Screen as an injury prediction tool for German physical education and exercise science students: a prospective cohort-study
2021-06-24

Abstract Background Several studies have evaluated the applicability of the Functional Movement Screen (FMS) as a screening tool for injury prediction. However, only few studies investigate gender differences for FMS as a screening tool for female and male college students. Objective To evaluate gender differences in FMS single items and the overall score. In addition, the applicability of FMS as a diagnostic tool for injury prevention of German exercise students will be investigated. Method N = 99 college students performed an FMS at the beginning of the semester. Injuries were recorded for the entire term. Gender differences of FMS single items were assessed using the Mann-Whitney-U-Test. Differences in injury prediction were calculated using logistic regression. If the model was statistically significant, diagnostic accuracy was calculated using receiver operating characteristic (ROC) curves and the area under the curve (AUC). The Youden index was used to identify a cut-off score. 2 × 2 contingency tables, sensitivity and specifity, positive/negative predictive values, and likelihood ratios were assessed. Results There were significant gender differences for Deep Squat, Shoulder Mobility, Trunk Stability Push Up, and Active Straight Leg Raise. The logistic regression showed that the composite score was statistically significant in clarifying the model for females (p = 0.005, RN 2 = 0.14), but not for males (p = 0.18, RN 2 = 0.04). The ROC curve indicated acceptable injury prediction in females (AUC: 0.66, p = 0.02) and poor injury prediction in males (AUC: 0.40, p = 0.19). The cut-off score of ≤ 16 for females resulted in a sensitivity of 63 % and specificity of 54 %. No cut-off score was calculated for males. Conclusion Females performed better on flexibility items, while males scored higher on strength exercises. Results of the study indicate low predictive accuracy. Therefore, no solid recommendation can be made for the use of the FMS as an injury screening tool for either female or male German exercise science students.
Failure to show robust noun-referent associations in German-learning infants
2021-06-24

Work with the looking-while-listening paradigm suggested that six-month-old English-learning infants associated several common nouns with pictures of their referents. This was evidenced by systematic fixations towards the named target picture (while one distractor picture was present). However, Norwegian-learning infants did not systematically fixate the target pictures until they were 8- to 9-months old, suggesting a cross-linguistic difference in the onset of noun comprehension. Moreover, their success in this task appeared to be modulated by aspects of stimulus pairing, specifically frequency differences between target and distractor: High (resp. low) frequent targets attracted more fixations if they were paired with low (resp. high) frequent distractors. In the present eye-tracking study, we tested 42 monolingual German-learning infants aged six to 14 months by means of a looking-while-listening paradigm. Infants saw two pictures side-by-side on a screen, whilst an unfamiliar male talker named one of both. Overall, infants did not fixate the target picture more than the distractor picture. In line with previous results, infants’ performance on the task was higher when the target and distractor word differed within their word frequency operationalized by the parental rating of word exposure. Therefore, our results further emphasize cross-linguistic differences in early word learning and strengthen the view that infants might use extra-linguistic cues within the stimulus pairing, such as frequency imbalance, to disambiguate between two potential referents.
Designing non-equilibrium states of quantum matter through stochastic\\n resetting
2021-06-25

We consider closed quantum many-body systems subject to stochastic resetting.\\nThis means that their unitary time evolution is interrupted by resets at\\nrandomly selected times. When a reset takes place the system is reinitialized\\nto a state chosen from a set of reset states conditionally on the outcome of a\\nmeasurement taken immediately before resetting. We construct analytically the\\nresulting non-equilibrium stationary state, thereby establishing an explicit\\nconnection between quantum quenches in closed systems and the emergent open\\nsystem dynamics induced by stochastic resetting. We discuss as an application\\nthe paradigmatic transverse-field quantum Ising chain. We show that signatures\\nof its ground-state quantum phase transition are visible in the steady state of\\nthe reset dynamics as a sharp crossover. Our findings show that a controlled\\nstochastic resetting dynamics allows to design non-equilibrium stationary\\nstates of quantum many-body systems, where uncontrolled dissipation and heating\\ncan be prevented. These states can thus be created on demand and exploited,\\ne.g., as a resource for quantum enhanced sensing on quantum simulator\\nplatforms.\\n
Animal Welfare Attitudes: Effects of Gender and Diet in University Samples from 22 Countries
2021-06-25

Animal Welfare Attitudes (AWA) are defined as human attitudes towards the welfare of animals in different dimensions and settings. Demographic factors, such as age and gender are associated with AWA. The aim of this study was to assess gender differences among university students in a large convenience sample from twenty-two nations in AWA. A total of 7914 people participated in the study (5155 women, 2711 men, 48 diverse). Participants completed a questionnaire that collected demographic data, typical diet and responses to the Composite Respect for Animals Scale Short version (CRAS-S). In addition, we used a measure of gender empowerment from the Human Development Report. The largest variance in AWA was explained by diet, followed by country and gender. In terms of diet, 6385 participants reported to be omnivores, 296 as pescatarian, 637 ate a vegetarian diet and 434 were vegans (n = 162 without answer). Diet was related with CRAS-S scores; people with a vegan diet scored higher in AWA than omnivores. Women scored significantly higher on AWA than men. Furthermore, gender differences in AWA increased as gender inequality decreased.
The ARCA Registry: A Collaborative Global Platform for Advancing Trial Readiness in Autosomal Recessive Cerebellar Ataxias
2021-06-25

Autosomal recessive cerebellar ataxias (ARCAs) form an ultrarare yet expanding group of neurodegenerative multisystemic diseases affecting the cerebellum and other neurological or non-neurological systems. With the advent of targeted therapies for ARCAs, disease registries have become a precious source of real-world quantitative and qualitative data complementing knowledge from preclinical studies and clinical trials. Here, we review the ARCA Registry , a global collaborative multicenter platform (&amp;gt;15 countries, &amp;gt;30 sites) with the overarching goal to advance trial readiness in ARCAs. It presents a good clinical practice (GCP)- and general data protection regulation (GDPR)-compliant professional-reported registry for multicenter web-based capture of cross-center standardized longitudinal data. Modular electronic case report forms (eCRFs) with core, extended, and optional datasets allow data capture tailored to the participating site's variable interests and resources. The eCRFs cover all key data elements required by regulatory authorities [European Medicines Agency (EMA)] and the European Rare Disease (ERD) platform. They capture genotype, phenotype, and progression and include demographic data, biomarkers, comorbidity, medication, magnetic resonance imaging (MRI), and longitudinal clinician- or patient-reported ratings of ataxia severity, non-ataxia features, disease stage, activities of daily living, and (mental) health status. Moreover, they are aligned to major autosomal-dominant spinocerebellar ataxia (SCA) and sporadic ataxia (SPORTAX) registries in the field, thus allowing for joint and comparative analyses not only across ARCAs but also with SCAs and sporadic ataxias. The registry is at the core of a systematic multi-component ARCA database cluster with a linked biobank and an evolving study database for digital outcome measures. Currently, the registry contains more than 800 patients with almost 1,500 visits representing all ages and disease stages; 65% of patients with established genetic diagnoses capture all the main ARCA genes, and 35% with unsolved diagnoses are targets for advanced next-generation sequencing. The ARCA Registry serves as the backbone of many major European and transatlantic consortia, such as PREPARE, PROSPAX, and the Ataxia Global Initiative, with additional data input from SPORTAX. It has thus become the largest global trial-readiness registry in the ARCA field.
The highly conserved FOXJ1 target CFAP161 is dispensable for motile ciliary function in mouse and Xenopus
2021-06-25

Abstract Cilia are protrusions of the cell surface and composed of hundreds of proteins many of which are evolutionary and functionally well conserved. In cells assembling motile cilia the expression of numerous ciliary components is under the control of the transcription factor FOXJ1. Here, we analyse the evolutionary conserved FOXJ1 target CFAP161 in Xenopus and mouse. In both species Cfap161 expression correlates with the presence of motile cilia and depends on FOXJ1. Tagged CFAP161 localises to the basal bodies of multiciliated cells of the Xenopus larval epidermis, and in mice CFAP161 protein localises to the axoneme. Surprisingly, disruption of the Cfap161 gene in both species did not lead to motile cilia-related phenotypes, which contrasts with the conserved expression in cells carrying motile cilia and high sequence conservation. In mice mutation of Cfap161 stabilised the mutant mRNA making genetic compensation triggered by mRNA decay unlikely. However, genes related to microtubules and cilia, microtubule motor activity and inner dyneins were dysregulated, which might buffer the Cfap161 mutation.
Controlling Site‐Directed RNA Editing by Chemically Induced Dimerization
2021-06-25

Abstract Various RNA‐targeting approaches have been engineered to modify specific sites on endogenous transcripts, breaking new ground for a variety of basic research tools and promising clinical applications in the future. Here, we combine site‐directed adenosine‐to‐inosine RNA editing with chemically induced dimerization. Specifically, we achieve tight and dose‐dependent control of the editing reaction with gibberellic acid, and obtain editing yields up to 20 % and 44 % in the endogenous STAT1 and GAPDH transcript in cell culture. Furthermore, the disease‐relevant MECP2 R106Q mutation was repaired with editing yields up to 42 %. The introduced principle will enable new applications where temporal or spatiotemporal control of an RNA‐targeting mechanism is desired.
Middle Pleistocene Homo behavior and culture at 140,000 to 120,000 years ago and interactions with Homo sapiens
2021-06-25

Middle Pleistocene Homo in the Levant Our understanding of the origin, distribution, and evolution of early humans and their close relatives has been greatly refined by recent new information. Adding to this trend, Hershkovitz et al. have uncovered evidence of a previously unknown archaic Homo population, the “Nesher Ramla Homo ” (see the Perspective by Mirazon Lahr). The authors present comprehensive qualitative and quantitative analyses of fossilized remains from a site in Israel dated to 140,000 to 120,000 years ago indicating the presence of a previously unrecognized group of hominins representing the last surviving populations of Middle Pleistocene Homo in Europe, southwest Asia, and Africa. In a companion paper, Zaidner et al. present the radiometric ages, stone tool assemblages, faunal assemblages, and other behavioral and environmental data associated with these fossils. This evidence shows that these hominins had fully mastered technology that until only recently was linked to either Homo sapiens or Neanderthals. Nesher Ramla Homo was an efficient hunter of large and small game, used wood for fuel, cooked or roasted meat, and maintained fires. These findings provide archaeological support for cultural interactions between different human lineages during the Middle Paleolithic, suggesting that admixture between Middle Pleistocene Homo and H. sapiens had already occurred by this time. Science , abh3169 and abh3020, this issue p. 1424 and p. 1429 ; see also abj3077, p. 1395
Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes
2021-06-25

As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome.
Diagnosing pediatric mitochondrial disease: lessons from 2,000 exomes
2021-06-25

Abstract Background The spectrum of mitochondrial disease is genetically and phenotypically diverse, resulting from pathogenic variants in over 400 genes, with aerobic energy metabolism defects as a common denominator. Such heterogeneity poses a significant challenge in making an accurate diagnosis, critical for precision medicine. Methods In an international collaboration initiated by the European Network for Mitochondrial Diseases (GENOMIT) we recruited 2,023 pediatric patients at 11 specialist referral centers between October 2010 and January 2021, accumulating exome sequencing and HPO-encoded phenotype data. An exome-wide search for variants in known and potential novel disease genes, complemented by functional studies, followed ACMG guidelines. Results 1,109 cases (55%) received a molecular diagnosis, of which one fifth have potential disease-modifying treatments (236/1,109, 21%). Functional studies enabled diagnostic uplift from 36% to 55% and discovery of 62 novel disease genes. Pathogenic variants were identified within genes encoding mitochondrial proteins or RNAs in 801 cases (72%), while, given extensive phenotype overlap, the remainder involved proteins targeted to other cellular compartments. To delineate genotype-phenotype associations, our data was complemented with registry and literature data to develop “GENOMITexplorer”, an open access resource detailing patient- (n=3,940), gene- (n=427), and variant-level (n=1,492) associations (prokischlab.github.io/GENOMITexplorer/). Conclusions Reaching a molecular diagnosis was essential for implementation of precision medicine and clinical trial eligibility, underlining the need for genome-wide screening given inability to accurately define mitochondrial diseases clinically. Key to diagnostic success were functional studies, encouraging early acquisition of patient- derived tissues and routine integration of high-throughput functional data to improve patient care by uplifting diagnostic rate.
Lipofection with Synthetic mRNA as a Simple Method for T-Cell Immunomonitoring
2021-06-25

The quantification of T-cell immune responses is crucial for the monitoring of natural and treatment-induced immunity, as well as for the validation of new immunotherapeutic approaches. The present study presents a simple method based on lipofection of synthetic mRNA in mononuclear cells as a method to determine in vitro T-cell responses. We compared several commercially available transfection reagents for their potential to transfect mRNA into human peripheral blood mononuclear cells and murine splenocytes. We also investigated the impact of RNA modifications in improving this method. Our results demonstrate that antigen-specific T-cell immunomonitoring can be easily and quickly performed by simple lipofection of antigen-coding mRNA in complex immune cell populations. Thus, our work discloses a convenient solution for the in vitro monitoring of natural or therapy-induced T-cell immune responses.
Simulation of laser-induced retinal thermal injuries for non-uniform irradiance profiles and the applicability of the laser safety standard
2021-06-25

Significance: A validated biophysical computer model simulating retinal thermal damage thresholds is used to investigate elongated retinal images. The International Commission on Non-Ionizing Radiation Protection Guideline and the laser safety standard IEC 60825-1:2014 include a method for averaging non-uniform extended sources, however, there are no studies that have examined the applicability in detail. Our study represents a method that can also support future research in the field of eye safety. Aim: As there is currently no experimental data available for non-uniform irradiance profiles, the calculation procedure given in the laser safety standard is derived from symmetric retinal images. We aim to verify this calculation procedure for such profiles on the retina in the thermal hazard regime. Approach: A three-dimensional computer model, which solves the heat transfer equation and the Arrhenius equation describing the denaturation of the proteins in the retina, is used to simulate the threshold values for the retinal thermal injury. Three different non-uniform irradiance profiles, elliptical Gaussian, elliptical top-hat, and rectangular top-hat distributions, are investigated for a wavelength of 530 nm. The profiles are varied in their sizes and simulated for different single-pulse durations. By applying the laser safety standard, the maximum allowed energies are calculated and divided by the corresponding threshold values to obtain the reduction factor (RF) which is a crucial parameter. Results: Due to the thermal behavior in the retinal tissues, the Gaussian irradiance profiles yield larger threshold values than both top-hat profiles. Furthermore, the ratio between the threshold values and the maximum allowed energies are found to be the lowest for the Gaussian profiles. Conclusion: The simulated retinal thermal injury thresholds for the three investigated non-uniform irradiance profiles show larger RFs than the minimum RF found for symmetric profiles. This supports the applicability of the evaluation scheme of the laser safety standard for non-uniform retinal images.
Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae
2021-06-25

Sulfolobaceae family, comprising diverse thermoacidophilic and aerobic sulfur-metabolizing Archaea from various geographical locations, offers an ideal opportunity to infer the evolutionary dynamics across the members of this family. Comparative pan-genomics coupled with evolutionary analyses has revealed asymmetric genome evolution within the Sulfolobaceae family. The trend of genome streamlining followed by periods of differential gene gains resulted in an overall genome expansion in some species of this family, whereas there was reduction in others. Among the core genes, both Sulfolobus islandicus and Saccharolobus solfataricus showed a considerable fraction of positively selected genes and also higher frequencies of gene acquisition. In contrast, Sulfolobus acidocaldarius genomes experienced substantial amount of gene loss and strong purifying selection as manifested by relatively lower genome size and higher genome conservation. Central carbohydrate metabolism and sulfur metabolism coevolved with the genome diversification pattern of this archaeal family. The autotrophic CO 2 fixation with three significant positively selected enzymes from S. islandicus and S. solfataricus was found to be more imperative than heterotrophic CO 2 fixation for Sulfolobaceae . Overall, our analysis provides an insight into the interplay of various genomic adaptation strategies including gene gain–loss, mutation, and selection influencing genome diversification of Sulfolobaceae at various taxonomic levels and geographical locations.
Interpretable gender classification from retinal fundus images using BagNets
2021-06-25

Abstract Deep neural networks (DNNs) are able to predict a person’s gender from retinal fundus images with high accuracy, even though this task is usually considered hardly possible by ophthalmologists. Therefore, it has been an open question which features allow reliable discrimination between male and female fundus images. To study this question, we used a particular DNN architecture called BagNet, which extracts local features from small image patches and then averages the class evidence across all patches. The BagNet performed on par with the more sophisticated Inception-v3 model, showing that the gender information can be read out from local features alone. BagNets also naturally provide saliency maps, which we used to highlight the most informative patches in fundus images. We found that most evidence was provided by patches from the optic disc and the macula, with patches from the optic disc providing mostly male and patches from the macula providing mostly female evidence. Although further research is needed to clarify the exact nature of this evidence, our results suggest that there are localized structural differences in fundus images between genders. Overall, we believe that BagNets may provide a compelling alternative to the standard DNN architectures also in other medical image analysis tasks, as they do not require post-hoc explainability methods.
Impairment of episodic memory in genetic frontotemporal dementia: A GENFI study.
2021-06-25

IntroductionWe aimed to assess episodic memory in genetic frontotemporal dementia (FTD) with the Free and Cued Selective Reminding Test (FCSRT).MethodsThe FCSRT was administered in 417 presymptomatic and symptomatic mutation carriers (181 chromosome 9 open reading frame 72 [<i>C9orf72</i>], 163 progranulin [<i>GRN</i>], and 73 microtubule-associated protein tau [<i>MAPT</i>]) and 290 controls. Group differences and correlations with other neuropsychological tests were examined. We performed voxel-based morphometry to investigate the underlying neural substrates of the FCSRT.ResultsAll symptomatic mutation carrier groups and presymptomatic <i>MAPT</i> mutation carriers performed significantly worse on all FCSRT scores compared to controls. In the presymptomatic <i>C9orf72</i> group, deficits were found on all scores except for the delayed total recall task, while no deficits were found in presymptomatic <i>GRN</i> mutation carriers. Performance on the FCSRT correlated with executive function, particularly in <i>C9orf72</i> mutation carriers, but also with memory and naming tasks in the <i>MAPT</i> group. FCSRT performance also correlated with gray matter volumes of frontal, temporal, and subcortical regions in <i>C9orf72</i> and <i>GRN</i>, but mainly temporal areas in <i>MAPT</i> mutation carriers.DiscussionThe FCSRT detects presymptomatic deficits in <i>C9orf72</i>- and <i>MAPT</i>-associated FTD and provides important insight into the underlying cause of memory impairment in different forms of FTD.