Miracle-dz/UniFAR-FTUs huggingface dataset:
Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight novel adipocyte biology

To characterize latent components of genetic associations, we applied truncated singular value decomposition (DeGAs) to matrices of summary statistics derived from genome-wide association analyses across 2,138 phenotypes measured in 337,199 White British individuals in the UK Biobank study. We systematically identified key components of genetic associations and the contributions of variants, genes, and phenotypes to each component. As an illustration of the utility of the approach to inform downstream experiments, we report putative loss of function variants, rs114285050 (GPR151) and rs150090666 (PDE3B), that substantially contribute to obesity-related traits, and experimentally demonstrate the role of these genes in adipocyte biology. Our approach to dissect components of genetic associations across human phenotypes will accelerate biomedical hypothesis generation by providing insights on previously unexplored latent structures.
ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; peer review: 1 approved, 2 approved with reservations]

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.
Time-frequency analysis of heart rate variability during stress testing using “a priori” information of respiratory frequency

A parametric decomposition of the smoothed Wigner-Ville distribution is applied to estimate the instantaneous frequency and amplitude of the LF and HF components of HRV during stress testing. It is assumed that the instantaneous frequencies of the LF and HF components may vary linearly with time during stress testing, and that the frequency of the HF component can be approximated by the respiratory frequency. The effect of the inclusion of "a priori" information of respiratory frequency on the estimation of HRV parameters is studied. Results on a simulation study show that the inclusion of "a priori" information does not affect significantly the estimation of the LF parameters. However, the SD of the estimation error of the HF amplitude is reduced at the expense of introducing a bias for high SNRs while both the mean and SD of the HF amplitude error are decreased for lower SNRs (2.6%plusmn1.9% against 3.1%plusmn2.6%for a SNR of 20 dB and 7.6%plusmn5.8% against 12.0%plusmn9.7%for a SNR of 10 dB).
Assessing Water Quality Modeling in Subtropical Regions Based on a Case Study of the Aguamilpa Reservoir

ASSESSING WATER QUALITY MODELING IN SUBTROPICAL REGIONS BASED ON A CASE STUDY OF THE AGUAMILPA RESERVOIR Oliver Obregon Department of Civil and Environmental Engineering Master of Science The shortage of water in Mexico has made public and private institutions look at reservoirs as an alternative solution for present and future water supply. However, eighty percent of the existing reservoirs in Mexico are contaminated at some level, many severely. Water quality models are water-management tools used to diagnose water quality problems and the impact of various environmental conditions. They can be effective in assessing various measures of remediation leading to improved water quality. In most of the cases such water quality models have been successfully applied in reservoirs located in temperate climates. However, the use of water quality models in subtropical reservoirs, especially those in developing countries, have relatively little application because either basic data are not available or because they are not sufficient. In this study, a preliminary water quality model was developed for a subtropical reservoir to assess both the ability to collect adequate data and the model’s underlying applicability in a subtropical region. The Aguamilpa reservoir is located in the western part of Mexico (Nayarit). It was built for power generation, irrigation and as a fishery. CE-QUAL-W2 is a two-dimensional hydrodynamic and water quality model suitable for long and narrow water bodies. Geometrically the Aguamilpa reservoir is long and deep, making it an ideal candidate to be modeled by CE-QUAL-W2. The model was developed for 1995 and 1996 because of a wider availability of historical data during this period. In addition to a preliminary model and assessment of applicability in this subtropical region, a monitoring and data acquisition plan was designed to identify the minimum required data which must be used to update, calibrate and simulate the water quality parameters. Once the model is calibrated, it may be used to simulate the water quality changes occurring with respect to environmental, climatological and anthropogenic effects. Further, the model may be used to prescribe operating procedures upstream as well as at the dam which can serve to improve the overall water quality. The development of the model at Aguamilpa can serve as a guideline for developing similar water quality models in this and other similar subtropical locations.
Multi-Objective Optimization for Floating Point Mix-Precision Tuning

This paper proposes a multi-objective optimization method for mixed-precision computation. Unlike previous studies that often take mantissa length reduction as the only optimization target, our work models the actual performance and power consumption of mixed precision programs on the corresponding hardware platforms, and based on this model searches for the pareto optimal set of all precision configurations. Experiments show that this tool can obtain performance improvements of 15% - 71 % on floating-point benchmarks while satisfying accuracy requirements. Compared to some typical counterpart-work, an average 21 % improvement can be obtained in SIMD scenarios.
A new approach to characterize postural deficits in chemotherapy-induced peripheral 2 neuropathy and to analyze postural adaptions after an exercise intervention

Background Postural instability presents a common and disabling consequence of chemotherapy-induced 45 peripheral neuropathy (CIPN). However, knowledge about postural behavior of CIPN patients is 46 sparse. With this pilot study, we used a new approach to i) characterize postural impairments as 47 compared to healthy subjects, ii) allocate possible abnormalities to a set of parameters describing 48 sensorimotor function, and iii) evaluate the effects of a balance-based exercise intervention. We analyzed spontaneous and externally perturbed postural control in eight CIPN patients before and 51 after a balance-based exercise intervention by using a modification of an established postural control 52 model. These findings were compared to 15 matched healthy subjects. Spontaneous sway amplitude and velocity were larger in CIPN patients compared to healthy subjects. 55 CIPN patients’ reactions to external perturbations were smaller compared to healthy subjects, 56 indicating that patients favor vestibular over proprioceptive sensory information. The balance-based 57 exercise intervention up-weighted proprioceptive information in patients. CIPN patients’ major postural deficit may relate to underuse of proprioceptive information that results 60 in a less accurate posture control as spontaneous sway results indicate. The balance-based exercise 61 intervention is able to partially correct for this abnormality. Our study contributes to a better 62 understanding of postural impairments in CIPN patients and suggests an effective treatment strategy. 63
Visualization of Chemical Grout Permeation in Transparent Soil

This paper presents an experiment that visualizes the permeation of chemical grout in transparent soil. The low initial viscosity (5 mPa · s) urea-formaldehyde resin (UFR) was chosen as grouting material in this experiment. The transparent soil used in this study is made of fused silica and a calcium bromide solution with the same refractive index. Triaxial and permeability tests are carried out to demonstrate that the geotechnical properties and hydraulic permeability of this transparent soil are typical of granular soils and suitable for modeling natural sand in permeation problem. A combined grouting and optical measurement system is developed for this study, which consists of an air pressure driven grout injection station to inject grout into a transparent soil model, laser to illuminate the cross-section of interest inside the model, and a charge-coupled device (CCD) camera to capture a series of images during the whole grout injection and permeation process. Image processing techniques including digital image correlation (DIC) are applied to sequence of images to detect the edges of the grout bulb and displacement distribution. The relationship of the grouting radius and grouting time corresponds to Maag's formula on permeation grouting. As a result, the validity of this innovative experiment has been verified.
Modularity of some potentially Barsotti–Tate Galois representations

We prove a portion of a conjecture of Conrad, Diamond, and Taylor, yielding some new cases of the Fontaine–Mazur conjectures, specifically, the modularity of certain potentially Barsotti–Tate Galois representations. The proof follows the template of Wiles, Taylor–Wiles, and Breuil–Conrad–Diamond–Taylor, and relies on a detailed study of the descent, across tamely ramified extensions, of finite flat group schemes over the ring of integers of a local field. This makes crucial use of the filtered $\phi_1$-modules of Breuil.
Development of a 'universal-reporter' outcome measure (UROM) for patient and healthcare a mixed methods study demonstrating a novel concept for optimal

Objectives To describe the novel concept of, and methods for developing, a ‘universal-reporter’ outcome measure (UROM); a single questionnaire for completion by patients and/or healthcare professionals (HCPs) when views on the same subject are required. Design A mixed methods study with three phases— phase I: identification of relevant content domains from existing clinical tools, patient questionnaires and in-depth interviews with multistakeholders; phase II: item development using a novel approach that considered plain language in conjunction with medical terminology; and phase III: pretesting with multistakeholders using cognitive interviews. setting A case study in surgical wound assessment undertaken in two
Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production

Although respiratory syncytial virus (RSV) is responsible for more human deaths each year than influenza, its pathogenic mechanisms are poorly understood. Here high-resolution quantitative imaging, bioenergetics measurements and mitochondrial membrane potential- and redox-sensitive dyes are used to define RSV’s impact on host mitochondria for the first time, delineating RSV-induced microtubule/dynein-dependent mitochondrial perinuclear clustering, and translocation towards the microtubule-organizing centre. These changes are concomitant with impaired mitochondrial respiration, loss of mitochondrial membrane potential and increased production of mitochondrial reactive oxygen species (ROS). Strikingly, agents that target microtubule integrity the dynein motor protein, or inhibit mitochondrial ROS production strongly suppresses RSV virus production, including in a mouse model with concomitantly reduced virus-induced lung inflammation. The results establish RSV’s unique ability to co-opt host cell mitochondria to facilitate viral infection, revealing the RSV-mitochondrial interface for the first time as a viable target for therapeutic intervention.
ORES-2010 Ontology Repositories and Editors for the Semantic Web

Based on the IEEE 1074-1995 standard for software development process we define a set of complement criteria for the evaluation of existing ontology development and management methodologies. We use this evaluation framework in order to benchmark the most well known approaches for developing ontologies from scratch, as well as reusing ontologies that are stored in ontology repositories. The result of the evaluation process is to identify the shortcomings of existing ontology development and management methodologies and validate the use of the aforementioned criteria for the establishment of a generic evaluation framework. Moreover, the conducted evaluation procedure reveals the degree of conformance of the benchmarked methodologies to a set of standardized criteria. In order to include the newly introduced evaluation criteria whose purpose is to support more ontology-specific evaluation aspects, we extend the evaluation framework introduced in the Ontoweb project by also adding nine additional methodologies.
Journal of Experimental Botany Advance Access published June 24, 2009 Journal of Experimental Botany, Page 1 of 10

Dormancy-associated MADS genes from the EVG locus of peach [Prunus persica (L.) Batsch] have distinct seasonal and photoperiodic expression patterns Abstract Mapping and sequencing of the non-dormant evg mutant in peach [Prunus persica (L.) Batsch] identified six tandem-arrayed DAM (dormancy-associated MADS-box) genes as candidates for regulating growth cessation and terminal bud formation. To narrow the list of candidate genes, an attempt was made to associate bud phenology with the seasonal and environmental patterns of expression of the candidates in wild-type trees. The expression of the six peach DAM genes at the EVG locus of peach was characterized throughout an annual growing cycle in the field, and under controlled conditions in response to a long day–short day photoperiod transition. DAM1, 2, 4, 5, and 6 were responsive to a reduction in photoperiod in controlled conditions and the direction of response correlated with the seasonal timing of expression in field-grown trees. DAM3 did not respond to photoperiod and may be regulated by chilling temperatures. The DAM genes in peach appear to have at least four distinct patterns of expression. DAM1, 2, and 4 are temporally associated with seasonal elongation cessation and bud formation and are the most likely candidates for control of the evg phenotype.
Journal of Experimental Botany Advance Access published November 18, 2009 Journal of Experimental Botany, Page 1 of 14

Sulphur flux through the sulphate assimilation pathway is differently controlled by adenosine 5#-phosphosulphate reductase under stress and in transgenic poplar plants overexpressing g-ECS, SO, or APR Abstract Sulphate assimilation provides reduced sulphur for the synthesis of cysteine, methionine, and numerous other essential metabolites and secondary compounds. The key step in the pathway is the reduction of activated sulphate, adenosine 5#-phosphosulphate (APS), to sulphite catalysed by APS reductase (APR). In the present study, [ 35 S]sulphur flux from external sulphate into glutathione (GSH) and proteins was analysed to check whether APR controls the flux through the sulphate assimilation pathway in poplar roots under some stress conditions and in transgenic poplars. (i) O-Acetylserine (OAS) induced APR activity and the sulphur flux into GSH. (ii) The herbicide Acetochlor induced APR activity and results in a decline of GSH. Thereby the sulphur flux into GSH or protein remained unaffected. (iii) Cd treatment increased APR activity without any changes in sulphur flux but lowered sulphate uptake. Several transgenic poplar plants that were manipulated in sulphur metabolism were also analysed. (i) Transgenic poplar plants that overexpressed the g-glutamylcysteine synthetase (g-ECS) gene, the enzyme catalysing the key step in GSH formation, showed an increase in sulphur flux into GSH and sulphate uptake when g-ECS was targeted to the cytosol, while no changes in sulphur flux were observed when g-ECS was targeted to plastids. (ii) No effect on sulphur flux was observed when the sulphite oxidase (SO) gene from Arabidopsis thaliana, which catalyses the back reaction of APR, that is the reaction from sulphite to sulphate, was overexpressed. (iii) When Lemna minor APR was overexpressed in poplar, APR activity increased as expected, but no changes in sulphur flux were observed. For all of these experiments the flux control coefficient for APR was calculated. APR as a controlling step in sulphate assimilation seems obvious under OAS treatment, in g-ECS and SO overexpressing poplars. A possible loss of control under certain conditions, that is Cd treatment, Acetochlor treatment, and in APR overexpressing poplar, is discussed.
Automated Generation of Assessment Tests from Domain Ontologies

OWL-ontologies are structures which are used for representing knowledge of a domain, in the form of logical axioms. Research on pedagogical usefulness of these knowledge structures has gained much attention these days. This is mainly due to the number of on-line ontology repositories and the ease in publishing knowledge in the form of ontologies. One another reason for this trend in research, is due to the changing education-style — more learners prefer to take-up on-line courses, than attending a course in a typical room setup. In this case, assessments — both prerequisite and post-course-requirement evaluations — will be a challenging task. In this paper, we explore an automated technique for generating question items like multiple choice questions (MCQs), from a given domain ontology. Furthermore, we investigate the aspects such as (1) how to find the difficulty-level of a generated MCQ; (2) what are the heuristics to follow to select a small set of MCQs which are relevant to the domain; (3) how to set a test which is having higher, medium or lower hardness level, in detail. We propose novel techniques to address these issues. We tested the applicability of the proposed techniques by generating MCQs from several on-line ontologies, and verified our results in a class-room setup — incorporating real-students and domain-experts.
Engagement by Looking: Behaviors for Robots When Collaborating with People

This paper reports on research on develop-ing the ability for robots to engage with humans in a collaborative conversation for hosting activities. It defines the engagement process in collaborative conversation, and reports on our progress in creating a robot to perform hosting activities. The paper then presents the analysis of a study that tracks the looks between collaborators and dis-cusses rules that will allow a robot to track humans so that engagement is maintained.
Investigating Intervention Components and Exploring States of Receptivity for a Smartphone App to Promote Physical Activity: Study Protocol of the ALLY Micro-Randomized Trial

Background: Smartphones enable the implementation of just-in-time adaptive interventions (JITAIs) that tailor the delivery of health interventions over time to user and time-varying context characteristics. Ideally, JITAIs include effective intervention components and delivery tailoring is based on effective moderators of intervention effects. Using machine learning techniques to infer each user’s context from smartphone sensor data is a promising approach to further enhance tailoring. Objective: The primary objective is to quantify main effects, interactions and moderators of three intervention components of a smartphone-based intervention for physical activity. The secondary objective is the exploration of participants’ states of receptivity, i.e. situations in which participants are more likely to react to intervention notifications, through collection of smartphone sensor data. Methods: In 2017, we developed the Assistant to Lift your Level of activitY (Ally), a chatbotbased mHealth intervention for increasing physical activity that utilizes incentives, planning and self-monitoring prompts to help participants meet personalized step goals. We used a microrandomized trial design to meet the study objectives. Insurees of large Swiss insurance company were invited to use the Ally app over a 12-day baseline and a six-week intervention period. Upon enrolment, participants were randomly allocated to either a financial incentive, a charity incentive or a no incentive condition. Over the course of the intervention period, participants were repeatedly randomized on a daily basis to either receive prompts that support selfmonitoring or not, and on a weekly basis to receive one of two planning interventions or no planning. Participants completed a web-based questionnaire at baseline and post-intervention follow-up. Results: Data collection finished in January 2018. In total, 274 insurees enrolled in the study and installed the Ally app on their smartphones. Main reasons for declining participation were having an incompatible smartphone (37/191; 19.4%) and collection of sensor data (35/191; 18.3%). Step data is available for 227/274 participants (82.8%) and smartphone sensor data is available for 247/274 participants (90.1%). Conclusions: This study describes the evidence-based development of a JITAI for increasing physical activity. If components prove to be efficacious, they will be included in a revised version of the app that offers scalable promotion of physical activity at low cost. Trial Registration: ClinicalTrials.gov NCT03384550
RANDOMIZATION-BASED CAUSAL INFERENCE FROM SPLIT-PLOT DESIGNS ∗ By

Under the potential outcomes framework, we propose a randomization based estimation procedure for causal inference from split-plot designs, with special emphasis on 2 designs that naturally arise in many social, behavioral and biomedical experiments. For the 2 splitplot design, point estimators of factorial effects are obtained and their sampling variances are derived in closed form as linear combinations of the betweenand within-group covariances of the potential outcomes. Results are compared to those under complete randomization as measures of design efficiency. Conservative estimators of these sampling variances are proposed. Connection of the randomization-based approach to inference based on the linear mixed effects model is explored. Results on sampling variances of point estimators and their estimators are extended to general split-plot designs. The superiority over existing model-based alternatives in frequency coverage properties is reported under a variety of simulation settings for both binary and continuous outcomes.