julilili42/papers huggingface dataset:
The Kids Obesity Prevention Program: Cluster Randomized Controlled Trial to Evaluate a Serious Game for the Prevention and Treatment of Childhood Obesity
2019-12-16

Background Health games provide opportunities for the treatment and prevention of childhood obesity. We developed a motion-controlled serious game for children that addresses 3 core topics of nutrition, physical activity, and stress coping. It is the first serious game that extensively targets the dietary energy density principle (DED-P) in relation to nutrition. The game is intended to provide an additional educational component for the prevention and treatment of obesity in children. Objective The Kids Obesity Prevention study aimed to evaluate the newly developed game and to evaluate how well children are able to understand and apply the DED-P. Methods This cluster randomized controlled trial collected data from 82 primary school children aged 9 to 12 years and their parents at baseline (T0), at 2 weeks after study commencement (T1), and at the 4-week follow-up (T2). The dropout rate was 3.6%. The intervention group (IG) played the game within 2 weeks (2 sessions with different game modules). One part of the game involves selection of food with the lower energy density when presented with a pair of foods. This allows assessment of whether the children have understood the DED-P and whether they can apply it to unknown foods under time pressure. The control group (CG) received a brochure about the food pyramid concept and physical activity. The primary outcome was the gain in knowledge (nutrition and stress coping) and measured with a pretested questionnaire. The secondary outcomes were the maintenance of knowledge, application of the DED-P, feelings during game play, game acceptance, and behavioral measures (physical activity, media consumption, and dietary intake). Results The knowledge score ranging from 0 to 100 increased from T0 (IG: 53 [SD 10], CG: 50 [SD 11]) to T1 (IG: 69 [SD 11], CG: 52 [SD 12]) in IG versus CG (P&lt;.001). At T2, the knowledge score of IG remained at the same level as that of T1. Game data showed that after DED-P education, the classification under time pressure of unknown versus known food pairs according to their DED category was similar (hit rate around 70%). Overall, 95% of the children liked the game very much or much. No group changes were observed at the behavioral level. Conclusions The Kids Obesity Prevention program sustainably increased knowledge in the areas of nutrition and stress coping, and children were able to apply the DED-P. Trial Registration ClinicalTrials.gov NCT02551978; https://clinicaltrials.gov/ct2/show/NCT02551978
An open-source multiple-bioreactor system for replicable gas-fermentation experiments: Nitrate feed results in stochastic inhibition events, but improves ethanol production ofClostridium ljungdahliiwith CO2and H2
2019-12-16

Abstract The pH-value in fermentation broth has a large impact on the metabolic flux and growth behavior of acetogens. A decreasing pH level throughout time due to undissociated acetic acid accumulation is anticipated under uncontrolled pH conditions such as in bottle experiment. As a result, the impact of changes in the metabolism ( e.g ., due to a genetic modification) might remain unclear or even unrevealed. In contrast, pH-controlled conditions can be easily achieved in commercially available bioreactors. However, their acquisition is costly and their operation is time consuming, and therefore the experiment is often limited to a single bioreactor run. Here, we present a self-built, relatively cheap, and easy to handle open-source multiple-bioreactor system (MBS) consisting of six pH-controlled bioreactors at a 1-L scale. The functionality of the MBS was tested in three experiments by cultivating the acetogen Clostridium ljungdahlii with CO 2 and H 2 at steady-state conditions (=chemostat). The experiments were addressing the questions: (1) does the MBS provide replicable data for gas-fermentation experiments?; (2) does feeding acetate alter the production rate of ethanol; and (3) does feeding nitrate influence the product spectrum under controlled pH conditions with CO 2 and H 2 ? We applied four different periods in each experiment ranging from pH 6.0 to pH 4.5. Our data show high reproducibility for gas-fermentation experiments with C. ljungdahlii , using the MBS. We found that feeding acetate did not improve ethanol production, but rather impaired growth and reduced acetate production. Using nitrate as sole N-source, on the other hand, enhanced biomass production even at a low pH. However, we observed differences in growth, acetate, and ethanol production rates between triplicate bioreactors (n=3). We explained the different performances because of stochastic inhibition events, which we observed through the accumulation of nitrite, and which led to complete crashes at different operating times. One of these bioreactors recovered after the crash and showed enhanced ethanol production rates while simultaneously producing less acetate. The MBS offers a great opportunity to perform bench-scale bioreactor experiments at steady-state conditions with replicates, which is especially attractive for academia.
Evidence-Based Decision Aid for Patients With Parkinson Disease: Protocol for Interview Study, Online Survey, and Two Randomized Controlled Trials (Preprint)
2019-12-16

<sec> <title>BACKGROUND</title> Shared decision making is particularly important in situations with different treatment alternatives. For the treatment of idiopathic Parkinson disease, both pharmacological and surgical approaches can be applied. </sec> <sec> <title>OBJECTIVE</title> In this research project, a series of studies will be conducted to investigate how decision aids for patients with idiopathic Parkinson disease should be designed in order to support the decision-making process. </sec> <sec> <title>METHODS</title> In Study 1a, qualitative interviews will be conducted to determine which needs frequently occur for patients with idiopathic Parkinson disease. In Study 1b, the identified needs will then be rated for personal relevance by an independent group of patients in an online survey. In Study 2, a randomized controlled trial will be used to pretest different decision aids in a sample group of people who do not have a medical background and who do not have Parkinson disease. In Study 3, a randomized controlled trial will be used to investigate the effect of the decision aids that had been evaluated as positive in Study 2 with patients who have idiopathic Parkinson disease. </sec> <sec> <title>RESULTS</title> This series of studies received ethical approval in January 2020. As of June 2020, data collection for Study 1a has started, and it is estimated that Studies 1a, 1b, 2, and 3 will take approximately 4, 4, 6, and 6 months to complete, respectively. It is planned to present the results and analyses at international conferences and to submit the results to peer-reviewed journals for publication, once the studies have been completed. The findings will also be shared with clinicians and patients through presentations at information events. </sec> <sec> <title>CONCLUSIONS</title> This series of studies is intended to result in an evidence-based decision aid for patients with idiopathic Parkinson disease in order to support the informed and reflected shared decision-making process. We further intend to contribute to a deeper understanding of the individual preferences of patients with idiopathic Parkinson disease and the impact of those preferences on treatment decisions. </sec> <sec> <title>INTERNATIONAL REGISTERED REPORT</title> PRR1-10.2196/17482 </sec>
The Challenge and Opportunity to Diagnose Parkinson's Disease in Midlife
2019-12-17

Parkinson's disease (PD) is the most common neurodegenerative movement disorder that affects extensive regions of the nervous system. Its current clinical diagnosis is based on motor symptoms that appear late during disease progression when substantial proportions of the nigrostriatal dopaminergic neuron population are lost already. Although disturbances in sleep and other biofunctions often surface years prior to motor impairments and point to a long prodromal phase, these phenotypic signs in a person's midlife lack predictive power. They do, however, signal the unfolding of the disease and suggest molecular correlates that begin deviating early on. Revealing such trajectories, hence, promises not only a better understanding of prodromal PD but may also enable a much-needed earlier diagnosis. A nexus that may harbor such molecular trajectories is the epigenome as key etiological factors of PD-genetics, age, and environment-influence this substrate. An earlier diagnosis would also allow earlier interventions and lifestyle adjustments to improve brain function and reduce symptoms. In this review, we describe the challenges of diagnosing PD early on and highlight the opportunities that may arise from steering research efforts towards comprehensive interrogations of molecular layers during the long-time neglected midlife phase. In particular, we emphasize how existing cohorts of at-risk individuals, available animal models, and suitable markers may come together and aid in revealing molecular trajectories that offer diagnostic utility for PD in its prodromal stage.
Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast
2019-12-17

The coordination of metabolism and growth with cell division is crucial for proliferation. While it has long been known that cell metabolism regulates the cell division cycle, it is becoming increasingly clear that the cell division cycle also regulates metabolism. In budding yeast, we previously showed that over half of all measured metabolites change concentration through the cell cycle indicating that metabolic fluxes are extensively regulated during cell cycle progression. However, how this regulation is achieved still remains poorly understood. Since both the cell cycle and metabolism are regulated to a large extent by protein phosphorylation, we here decided to measure the phosphoproteome through the budding yeast cell cycle. Specifically, we chose a cell cycle synchronization strategy that avoids stress and nutrient-related perturbations of metabolism, and we grew the yeast on ethanol minimal medium to force cells to utilize their full biosynthetic repertoire. Using a tandem-mass-tagging approach, we found over 200 sites on metabolic enzymes and transporters to be phospho-regulated. These sites were distributed among many pathways including carbohydrate catabolism, lipid metabolism, and amino acid synthesis and therefore likely contribute to changing metabolic fluxes through the cell cycle. Among all one thousand sites whose phosphorylation increases through the cell cycle, the CDK consensus motif and an arginine-directed motif were highly enriched. This arginine-directed R-R-x-S motif is associated with protein-kinase A, which regulates metabolism and promotes growth. Finally, we also found over one thousand sites that are dephosphorylated through the G1/S transition. We speculate that the phosphatase Glc7/PP1, known to regulate both the cell cycle and carbon metabolism, may play an important role because its regulatory subunits are phospho-regulated in our data. In summary, our results identify extensive cell cycle dependent phosphorylation and dephosphorylation of metabolic enzymes and suggest multiple mechanisms through which the cell division cycle regulates metabolic signaling pathways to temporally coordinate biosynthesis with distinct phases of the cell division cycle.
Motor skill acquisition during a balance task as a process of optimization of motor primitives
2019-12-17

Abstract It has been argued that the central nervous system relies on combining simple movement elements (i.e. motor primitives) to generate complex motor outputs. However, how movement elements are generated and combined during the acquisition of new motor skills is still a source of debate. Herein, we present results providing new insights into the role of movement elements in the acquisition of motor skills that we obtained by analysing kinematic data collected while healthy subjects learned a new motor task. The task consisted of playing an interactive game using a platform with embedded sensors whose aggregate output was used to control a virtual object in the game. Subjects learned the task over multiple blocks. The analysis of the kinematic data was carried out using a recently developed technique referred to as “movement element decomposition.” The technique entails the decomposition of complex multi‐dimensional movements in one‐dimensional elements marked by a bell‐shaped velocity profile. We computed the number of movement elements during each block and measured how closely they matched a theoretical velocity profile derived by minimizing a cost function accounting for the smoothness of movement and the cost of time. The results showed that, in the early stage of motor skill acquisition, two mechanisms underlie the improvement in motor performance: 1) a decrease in the number of movement elements composing the motor output and 2) a gradual change in the movement elements that resulted in a shape matching the velocity profile derived by using the above‐mentioned theoretical model.
International knowledge transfer in religious education: universal validity or regional practices? Backgrounds, considerations and open questions concerning a new debate
2019-12-17

This article refers to the new European discussion on international knowledge transfer in religious education. Readers are introduced to the background of the recent manifesto ‘International Knowledge Transfer in Religious Education: A Manifesto for Discussion’ which was the outcome of a first international consultation of researchers in the field of religious education in October 2018. In a first step, the demand for international knowledge transfer in religious education is described. Furthermore, the question of the validity of knowledge in religious education is taken up and discussed in the sense of the presuppositions of international transfer and cooperation. Special attention is given to the relationship between universal and contextual elements or dimensions of knowledge in religious education and their epistemological implications which the authors consider a general and fruitful challenge for the discipline, in international as well as in national contexts. In conclusion, the authors set forth a number of perspectives for future research concerning international knowledge transfer in religious education.
Borehole-image-log characterization of deltaic deposits from a behind-outcrop well: Opportunities and limitations
2019-12-17

ABSTRACT Borehole imaging (BHI) is a fast and precise method for collecting subsurface data. Rock calibration may reduce uncertainties inherent in interpretations of BHI logs. However, only few data sets are published that link borehole image facies to core and outcrop facies of deltaic successions. The objective of this paper is to compare and contrast sedimentologic features as seen in BHI, core, and outcrop, using a structured and hierarchical workflow. The research will provide a global framework for the interpretation of borehole images in similar environments. A shallow, behind outcrop, research well (“Mondot-1”) drilled in NW Spain, penetrated a 185.50 m (TVD) thick section of the deltaic Sobrarbe Formation. A Formation MicroImager (FMI) borehole image log and a comprehensive well log suite was acquired in the fully cored well. The Eocene Sobrarbe Formation consists mostly of siliciclastic and some carbonate facies. Rapid vertical and lateral facies changes over a few tens of meters are observed in outcrops of the Sobrarbe Formation. The cored part of the formation is composed of argillaceous sandstone and carbonate with few diagnostic sedimentary features that can be used to constrain a conceptual depositional model. To provide a sedimentologically sound interpretation of this FMI log, we focused on layers showing diagnostic sedimentary features. Subsequently, facies associations and stratigraphic sequences were interpreted. Each facies association contained sedimentologic tie points that anchored the interpretation with diagnostic features such as slumps. This paper suggests interpreting BHI false-color images of deltaic successions using conceptual geologic constraints such as 1) depositional tie points, 2) genetically related facies associations, and 3) a hierarchical stratigraphic framework, to establish meaningful conceptual depositional models.
Semantic Parameters and Universals
2019-12-17

This chapter investigates what kinds of semantic variation current theories of compositional variation lead us to expect. Examples of recent analyses of crosslinguistic variation in semantics are presented against this background. The result is a set of candidate parameters and candidate universals provided for further empirical testing.
Attentive or Not? Toward a Machine Learning Approach to Assessing Students’ Visible Engagement in Classroom Instruction
2019-12-18

Abstract Teachers must be able to monitor students’ behavior and identify valid cues in order to draw conclusions about students’ actual engagement in learning activities. Teacher training can support (inexperienced) teachers in developing these skills by using videotaped teaching to highlight which indicators should be considered. However, this supposes that (a) valid indicators of students’ engagement in learning are known and (b) work with videos is designed as effectively as possible to reduce the effort involved in manual coding procedures and in examining videos. One avenue for addressing these issues is to utilize the technological advances made in recent years in fields such as machine learning to improve the analysis of classroom videos. Assessing students’ attention-related processes through visible indicators of (dis)engagement in learning might become more effective if automated analyses can be employed. Thus, in the present study, we validated a new manual rating approach and provided a proof of concept for a machine vision-based approach evaluated on pilot classroom recordings of three lessons with university students. The manual rating system was significantly correlated with self-reported cognitive engagement, involvement, and situational interest and predicted performance on a subsequent knowledge test. The machine vision-based approach, which was based on gaze, head pose, and facial expressions, provided good estimations of the manual ratings. Adding a synchrony feature to the automated analysis improved correlations with the manual ratings as well as the prediction of posttest variables. The discussion focuses on challenges and important next steps in bringing the automated analysis of engagement to the classroom.
Prevalence of autoimmune disease in women with premature ovarian failure
2019-12-18

<b>Objective:</b> The aim of the study was to investigate the relationship between premature ovarian failure and autoimmune disease.<b>Methods:</b> This interdisciplinary prospective study included 52 consecutively recruited women with premature ovarian failure, aged 18-40 years. Diagnosis of premature ovarian failure was defined as amenorrhoea lasting more than 4 months and anti-Müllerian hormone levels below the age-appropriate range. Women with an abnormal karyotype or Fragile X syndrome were excluded from the study. All participants were screened by a rheumatologist for the presence of underlying autoimmune disease.<b>Results:</b> The average age at first diagnosis of premature ovarian failure was 29.5 years; 92.3% of participants (<i>n</i> = 48) presented with a secondary amenorrhoea, while only 7.7% (<i>n</i> = 4) had primary amenorrhoea. Of all 52 participants, 40.4% (<i>n</i> = 21) had at least one confirmed autoimmune disease, including Hashimoto's disease, systemic lupus erythematosus, rheumatoid arthritis, psoriasis, Crohn's disease, polyglandular autoimmune syndrome and coeliac disease. Response rates for hormonal stimulation therapy were low and the presence of autoimmune disease was associated with poor infertility treatment outcome.<b>Conclusions:</b> We found a high prevalence of autoimmune disease in women with premature ovarian failure. Screening for autoimmune diseases should be offered to all women with premature ovarian failure.
Maximal Quantum Fisher Information for Mixed States
2019-12-18

We study quantum metrology for unitary dynamics. Analytic solutions are given for both the optimal unitary state preparation starting from an arbitrary mixed state and the corresponding optimal measurement precision. This represents a rigorous generalization of known results for optimal initial states and upper bounds on measurement precision which can only be saturated if pure states are available. In particular, we provide a generalization to mixed states of an upper bound on measurement precision for time-dependent Hamiltonians that can be saturated with optimal Hamiltonian control. These results make precise and reveal the full potential of mixed states for quantum metrology.
Single Molecule Molecular Inversion Probes for High Throughput Germline Screenings in Dystonia
2019-12-18

<b>Background:</b> This study's aim was to investigate a large cohort of dystonia patients for pathogenic and rare variants in the <i>ATM</i> gene, making use of a new, cost-efficient enrichment technology for NGS-based screening. <b>Methods:</b> Single molecule Molecular Inversion Probes (smMIPs) were used for targeted enrichment and sequencing of all protein coding exons and exon-intron boundaries of the <i>ATM</i> gene in 373 dystonia patients and six positive controls with known <i>ATM</i> variants. Additionally, a rare-variant association study was performed. <b>Results:</b> One patient (0.3%) was compound heterozygous and 21 others were carriers of variants of unknown significance (VUS) in the <i>ATM</i> gene. Although mutations in sporadic dystonia patients are not common, exclusion of pathogenic variants is crucial to recognize a potential tumor predisposition syndrome. SmMIPs produced similar results as routinely used NGS-based approaches. <b>Conclusion:</b> Our results underline the importance of implementing <i>ATM</i> in the routine genetic testing of dystonia patients and confirm the reliability of smMIPs and their usability for germline screenings in rare neurodegenerative conditions.
Hypertonicity-Affected Genes Are Differentially Expressed in Clear Cell Renal Cell Carcinoma and Correlate with Cancer-Specific Survival
2019-12-18

The heterogeneity of renal cell carcinoma (RCC) subtypes reflects the cell type of origin in the nephron, with consequences for therapy and prognosis. The transcriptional cues that determine segment-specific gene expression patterns are poorly understood. We recently showed that hypertonicity in the renal medulla regulates nephron-specific gene expression. Here, we analyzed a set of 223 genes, which were identified in the present study by RNA-Seq to be differentially expressed by hypertonicity, for the prediction of cancer-specific survival (CSS). Cluster analyses of these genes showed discrimination between tumor and non-tumor samples of clear cell RCC (ccRCC). Refinement of this gene signature to a four-gene score (OSM score) through statistical analyses enabled prediction of CSS in ccRCC patients of The Cancer Genome Atlas (TCGA) (n = 436) in univariate (HR = 4.1; 95% CI: 2.78−6.07; p = 4.39 × 10−13), and multivariate analyses including primary tumor (T); regional lymph node (N); distant metastasis (M); grading (G)(p = 2.3 × 10−5). The OSM score could be validated in an independent ccRCC study (n = 52) in univariate (HR = 1.29; 95% CI = 1.05–1.59; p = 0.011) and multivariate analyses (p = 0.016). Cell culture experiments using RCC cell lines demonstrated that the expression of the tumor suppressor ELF5 could be restored by hypertonicity. The innovation of our novel gene signature is that these genes are physiologically regulated only by hypertonicity, thereby providing the possibility to be targeted for therapy.