nils-herrmann/clean_scirepeval huggingface dataset:
Impute.me: An Open-Source, Non-profit Tool for Using Data From Direct-to-Consumer Genetic Testing to Calculate and Interpret Polygenic Risk Scores

To date, interpretation of genomic information has focused on single variants conferring disease risk, but most disorders of major public concern have a polygenic architecture. Polygenic risk scores (PRSs) give a single measure of disease liability by summarizing disease risk across hundreds of thousands of genetic variants. They can be calculated in any genome-wide genotype data-source, using a prediction model based on genome-wide summary statistics from external studies. As genome-wide association studies increase in power, the predictive ability for disease risk will also increase. Although PRSs are unlikely ever to be fully diagnostic, they may give valuable medical information for risk stratification, prognosis, or treatment response prediction. Public engagement is therefore becoming important on the potential use and acceptability of PRSs. However, the current public perception of genetics is that it provides “yes/no” answers about the presence/absence of a condition, or the potential for developing a condition, which in not the case for common, complex disorders with polygenic architecture. Meanwhile, unregulated third-party applications are being developed to satisfy consumer demand for information on the impact of lower-risk variants on common diseases that are highly polygenic. Often, applications report results from single-nucleotide polymorphisms (SNPs) and disregard effect size, which is highly inappropriate for common, complex disorders where everybody carries risk variants. Tools are therefore needed to communicate our understanding of genetic vulnerability as a continuous trait, where a genetic liability confers risk for disease. Impute.me is one such tool, whose focus is on education and information on common, complex disorders with polygenetic architecture. Its research-focused open-source website allows users to upload consumer genetics data to obtain PRSs, with results reported on a population-level normal distribution. Diseases can only be browsed by International Classification of Diseases, 10th Revision (ICD-10) chapter–location or alphabetically, thus prompting the user to consider genetic risk scores in a medical context of relevance to the individual. Here, we present an overview of the implementation of the impute.me site, along with analysis of typical usage patterns, which may advance public perception of genomic risk and precision medicine.

Field of study: Biology
BIG FISH, LITTLE FISH: TWO NEW ULTRA-FAINT SATELLITES OF THE MILKY WAY

We report the discovery of two new Milky Way satellites in the neighboring constellations of Pisces and Pegasus identified in data from the Sloan Digital Sky Survey. Pisces II, an ultra-faint dwarf galaxy lies at the distance of ~180 kpc, some 15? away from the recently detected Pisces I. Segue 3, an ultra-faint star cluster lies at the distance of 16 kpc. We use deep follow-up imaging obtained with the 4-m Mayall Telescope at Kitt Peak National Observatory to derive their structural parameters. Pisces II has a half-light radius of ~60 pc, while Segue 3 is 20 times smaller at only 3 pc.

Field of study: Physics
Classroom Behavior of Retarded Children before and after Integration into Regular Classes

Childhood; *Educable Mentally Handicapped; *Exceptional Child Research; Mentally Handicapped; *Regular Class Placement; *Social Adjustment The classroom behavior of 11 segregated and 11 integrated educable mentally retarded (EMR) children, 8 to 13 years of age, was compared on a 12-category observation schedule when all EMR children were in special classes, four months after some children had been reintegrated, and at the conclusion of an academic year. The results indicated that integrated children differed from segregated children on a factor that included prosocial behavior, with the integrated group exhibiting more prosocial behaviors. No significant differences between the two study groups appeared on two other factors which included verbal and physical aggressive behavior.

Field of study: Education
A Study of Farmers' Participation into the Supervision of New Rural Co-operative Medical System

The paper aims at researching into the contents, forms and influencing factors of farmers'participation into the supervision of New Rural Cooperative Medical System (hereinafter NRCMS). Through correspondence inquiries of the NRCMS work staff in some 263 pilot counties throughout China, the paper conducts quantitative and qualitative spot investigations among the NRCMS beneficiaries from Yuexi County, Jixi County, Nanling County and Ningguo City in Anhui Province. We believe that the influencing factors of farmers' participation into the supervision of NRCMS mainly include farmers'education background, time, and policy supporting. The contents of farmers'participation into the supervision of NRCMS mainly include compensation methods, circumstances of compensation reimbursement, medical charge and the fund spending. The forms of the supervision are informants'hot-line telephone, suggestion box, and village committee. The organizational form ofthe supervision is the NRCMS's supervisor system.

Field of study: Agricultural and Food sciences
Ipsilateral ureteroureterostomy: does function of the obstructed moiety matter?

Upper pole nephrectomy has been the traditional surgical management of children with poorly functioning upper pole moieties in duplex renal collecting systems having ureteral ectopia and ureterocele. However, ablative surgery confers a risk of functional loss to the remnant moiety due to vasospasm or vascular injury. It was hypothesized that ipsilateral ureteroureterostomy (IUU) is a safe and feasible approach for the management of these patients and that residual function in the obstructed upper pole does not affect surgical outcomes.



All patients with duplex systems who underwent IUU between 2010 and 2016 were retrospectively reviewed. Patients were sorted into two groups based on pre-operative imaging: those having <10% upper pole moiety function (UPMF) and those having ≥ 10% UPMF. Outcomes assessed were postoperative complications (Clavien-Dindo classification), need for secondary surgery, and radiological outcomes.



The study cohort comprised 53 children with ectopia or ureterocele affecting the upper pole in a duplex system, 21 with UPMF <10% (median function 0% and median age 1.49 years) and 32 with UPMF ≥ 10% (median function 15% and median age 0.91 years). Median follow-up was 27.4 months and 27.6 months. In both the groups, prenatal hydronephrosis was the most common presentation (57% and 56%, respectively; p = 0.18) followed by urinary tract infection. Mann-Whitney U test comparing the two groups revealed no significant differences in any of the outcomes assessed. No patient required secondary surgery.



Ipsilateral ureteroureterostomy is a safe, definitive surgical intervention that preserves the renal architecture in children with duplex collecting systems regardless of upper pole function.

Field of study: Medicine
Crystallization and preliminary X-ray studies of rhamnogalacturonase A from Aspergillus aculeatus.

Recombinant rhamnogalacturonase A from Aspergillus aculeatus has been crystallized and X-ray diffraction data has been collected. Crystals were grown by the hanging-drop vapour-diffusion technique, under the conditions 10% PEG 8000, 0.05 M KH(2)PO(4) and 0.1 M sodium acetate buffered at pH 3.5. The crystals diffract beyond 2.0 A resolution and belong to one of the orthorhombic space groups I2(1)2(1)2(1) or I222, with the unit-cell parameters a = 62.9, b = 125.4 and c = 137.0 A. There is one molecule in the asymmetric unit and a solvent content of approximately 54%. The enzyme is highly glycosylated corresponding to 5.9 kDa.

Field of study: Chemistry
The 1,1'-trimethylenebis(pyridinyl) diradical and its photosensitive cyclomers.

Reduction of 1,1′-trimethylenebis(pyridinium) dibromide with sodium amalgam produces the cyclomers of 1,1′-trimethylene-bis(pyridinyl) diradical. Meso and dl forms of the cyclomers are convertible to each other. Two conformations of the diradical are observed in the triplet ESR spectrum at 77 K.

Field of study: Chemistry
What can we learn from the directed flow in heavy-ion collisions at BES RHIC energies?

Analysis of directed flow ($ v_{1}$) of protons, antiprotons and pions in heavy-ion collisions is performed in the range of collision energies $ \sqrt{s_{NN}} = 2.7--39$ GeV. Simulations have been done within a three-fluid model employing a purely hadronic equation of state (EoS) and two versions of the EoS with deconfinement transitions: a first-order phase transition and a smooth crossover transition. The crossover EoS is unambiguously preferable for the description of the most part of experimental data in this energy range. The directed flow indicates that the crossover deconfinement transition takes place in semicentral Au+Au collisions in a wide range of collision energies $ 4 \lesssim \sqrt{s_{NN}} \lesssim 30$ GeV. The obtained results suggest that the deconfinement EoS’s in the quark-gluon sector should be stiffer at high baryon densities than those used in the calculation. The latter finding is in agreement with that discussed in astrophysics.

Field of study: Physics
Citizen science regarding invasive lionfish in Dutch Caribbean MPAs : Drivers and barriers to participation

Understanding the drivers and barriers to participation in citizen science initiatives for conservation is important if long-term involvement from volunteers is expected. This study investigates the motivations of individuals from five marine protected areas (MPAs) in the Dutch Caribbean to (not) participate in different initiatives around lionfish. Following an interpretive approach, semi-structured interviews with seventy-eight informants were conducted and analyzed using thematic network analysis. Approximately 60% (n = 48) of informants indicated that they had participated in citizen science initiatives at the outset of the invasion. From this group, almost half said that they still participated in some type of data collection, but only a few did so within a citizen science context. Many informants were initially motivated to participate in lionfish detection and response initiatives due to concern for the environment. Personal meanings attached to both the data collection experiences and to the data influenced informants’ motivations to sustain or cease data collection and/or sharing. In time, the view of lionfish as a threat changed for many informants as this species’ recreational and/or commercial value increased. Enabling and constraining factors for data collection and sharing were identified at the personal, interpersonal, organizational and technical levels. Our findings have implications for the design of future citizen science initiatives focused on invasive species.

Field of study: Environmental science
Stability of methane oxidation capacity to variations in methane and nutrient concentrations

Uptake rate constants for atmospheric methane consumption by the 4–6 cm depth interval of a forest soil did not change during 4 months incubation in vitro, even though atmospheric methane concentrations were significantly higher than in situ concentrations. Uptake rate constants were also unaffected by continous incubation at a constant methane concentration of 17 ppm for 2 weeks and 170 ppm for 3 weeks. Uptake rates during incubation with 1000 ppm methane increased 176-fold when assayed with 1000 ppm methane and 5.5-fold when assayed with 1.7 ppm methane. These enhancements were lost after subsequent incubation with atmospheric methane. The ratio of methane oxidized to carbon dioxide produced varied from 49–53% at methane concentrations up to 170 ppm. Incorporation of 14C-methane into phospholipids was 0.35% and 0.22% at atmospheric and 170 ppm methane concentrations, respectively, suggesting that patterns of assimilation were independent of methane concentrations. Addition of several carbon substrates (glucose, starch, yeast extract, methanol, ethanol, formate, acetate, malate, or lactate) to soils incubated at 1.7 or 100 ppm methane did not stimulate methane oxidation. Addition of copper, nitrate or a mineral medium also did not affect methane oxidation. However, incubations with 0.2 or 2% oxygen resulted in lower activity than with ambient air. The methane-consuming capacity of soil decreased exponentially with time when starved for methane by continuous incubation with air containing < 0.03 ppm methane. After 6.3 days of starvation, the soil lost 50% of its original activity; activity was not recoverable after further incubation with atmospheric methane. Methane uptake by soil was rapidly inhibited by the addition of antibacterial antibiotics (streptomycin, chloro-tetracycline, chloramphenicol, ampicillin) as well as by the eukaryotic antibiotic, cycloheximide. Culture suspensions of Methylosinus trichosporium OB3b showed a similar sensitivity to both types of antibiotics. Cell suspensions of Methylosinus trichosporium OB3b and Methylobacter albus consumed atmospheric methane, but consumption rates decreased continuously over a period of 15 days. In contrast, methane consuuption by soil incubated under the same conditions was temporally stable. However, cell suspensions of both cultures showed higher consumption rates for atmospheric methane when sprayed on sand relative to incubations in liquid media.

Field of study: Biology, Environmental science
Design and Implementation of Indoor Map Based on SVG Technology

The needs of indoor environment navigation in today's increasingly cause for concern. Currently existing indoors environment map use a common technology that calls it tile map technology, but it limits the display of the indoor environment. Indoor and outdoor map feature has many differences, in particular the storage space is far less than the outdoor map. Besides,with the performance of mobile terminal rising, it can handle more complex tasks. Based on this, indoor maps in the mobile terminal independently map the task of parsing and display becomes possible, without affecting the user experience. Experiments show that uses SVG as indoor map data source parsing and display of the mobile terminal is feasible and has a better user experience.

Field of study: Computer science
FUNCTIONAL EQUATIONS AND MAXIMUM RANGE

The current interest in rockets and space travel has aroused a corresponding interest in the determination of maximum range, minimum time, and so on, for various types of trajectories. A variety of questions of this type have been treated by means of the theory of dynamic programming. Here it is shown how to use functional equations to determine the range, the maximum elevation, and similar quantities, as functions of initial position and velocities.

Field of study: Mathematics
DEMO Central Solenoid Design Based on the Use of HTS Sections at Highest Magnetic Field

Previous studies indicated that the use of high-temperature superconductors (HTS) in the highest field allows us achieving the required magnetic flux in the central solenoid (CS) of the European DEMO at a reduced outer diameter, which would enable a reduced overall size and cost of DEMO. The proposed winding pack design of the CS1 module is based on ten layer-wound subcoils using an HTS, react and wind Nb3Sn, and NbTi conductors in the high, medium, and low field sections, respectively. The design utilizes a stainless steel and a superconductor grading leading to different overall current densities in each of the ten subcoils. Both, the hoop stress and the vertical loads are taken into consideration for determination of the required stainless steel cross-section in the winding pack. The stainless steel grading has been found to have an even more pronounced effect on the overall subcoil current densities than the superconductor grading. A preliminary estimation of the space required for the precompression structure is also reported.

Field of study: Physics
Clear Choices and Guesswork in Peremptory Challenges in Federal Criminal Trials

The traditional practice of permitting lawyers to strike jurors by peremptory challenge is being subjected to new questioning in the USA. Previous studies of strikes have used simulations or questionnaires, raising doubt about their relevance in actual trials. In this paper we report on a study that uses actual trial data and a mathematical model to estimate the extent to which the lawyers' selections are clear choices on which all lawyers would agree or are guesswork involving essentially random choices. The results are that only a small proportion of the challenges are clear choices, a conclusion that is consistent with the findings of simulation studies.

Field of study: Mathematics
Machine learning-based preoperative predictive analytics for lumbar spinal stenosis.

OBJECTIVEPatient-reported outcome measures (PROMs) following decompression surgery for lumbar spinal stenosis (LSS) demonstrate considerable heterogeneity. Individualized prediction tools can provide valuable insights for shared decision-making. The authors aim to evaluate the feasibility of predicting short- and long-term PROMs, reoperations, and perioperative parameters by machine learning (ML) methods.METHODSData were derived from a prospective registry. All patients had undergone single- or multilevel mini-open facet-sparing decompression for LSS. The prediction models were trained using various ML-based algorithms to predict the endpoints of interest. Models were selected by area under the receiver operating characteristic curve (AUC). The endpoints were dichotomized by minimum clinically important difference (MCID) and included 6-week and 12-month numeric rating scales for back pain (NRS-BP) and leg pain (NRS-LP) severity and the Oswestry Disability Index (ODI), as well as prolonged surgery (> 45 minutes), extended length of hospital stay (> 28 hours), and reoperations.RESULTSA total of 635 patients were included. The average age was 62 ± 10 years, and 333 patients (52%) were male. At 6 weeks, MCID was seen in 63%, 76%, and 61% of patients for ODI, NRS-LP, and NRS-BP, respectively. At internal validation, the models predicted MCID in these variables with accuracies of 69%, 76%, and 85%, and with AUCs of 0.75, 0.79, and 0.92. At 12 months, 66%, 63%, and 51% of patients reported MCID; the observed accuracies were 62%, 74%, and 66%, with AUCs of 0.68, 0.72, and 0.79. Reoperations occurred in 60 patients (9.5%), of which 27 (4.3%) occurred at the index level. Overall and index-level reoperations were predicted with 69% and 63% accuracy, respectively, and with AUCs of 0.66 and 0.61. In 15%, a length of surgery greater than 45 minutes was observed and predicted with 78% accuracy and AUC of 0.54. Only 15% of patients were admitted to the hospital for longer than 28 hours. The developed ML-based model enabled prediction of extended hospital stay with an accuracy of 77% and AUC of 0.58.CONCLUSIONSPreoperative prediction of a range of clinically relevant endpoints in decompression surgery for LSS using ML is feasible, and may enable enhanced informed patient consent and personalized shared decision-making. Access to individualized preoperative predictive analytics for outcome and treatment risks may represent a further step in the evolution of surgical care for patients with LSS.

Field of study: Medicine
Suprasubduction-zone ophiolite generation, emplacement, and initiation of subduction: A perspective from geochemistry, metamorphism, geochronology, and regional geology

Ophiolites are on-land remnants of oceanic lithosphere, and most of the more extensive ophiolites apparently formed above a subduction zone, a tectonic setting known as a suprasubduction-zone setting. Thin sheets of high-grade metamorphic rocks, known as metamorphic soles, crop out structurally beneath many suprasubduction-zone ophiolites. Such rocks may have formed during the inception of subduction beneath young and hot oceanic lithosphere. Disagreement exists as to whether suprasubduction-zone ophiolites are emplaced over the same subduction zone over which they once formed or over a later one. High-grade metamorphic rocks (blocks-in-melange and coherent sheets) from the Franciscan Complex may represent a metamorphic sole beneath the suprasubduction-zone Coast Range ophiolite. Trace-element and isotopic data indicate that the Franciscan high-grade metamorphic rocks formed in a suprasubduction-zone envi ronment, requiring the existence of a pre-Franciscan sub duction zone, whereas later-subducted, lower-grade oceanic rocks are of mid-ocean-ridge or oceanic-island basalt affi ni ties. The Coast Range ophiolite and Franciscan high-grade rock protoliths formed over a pre-Franciscan subduction zone that may have dipped westward. The high-grade Franciscan rocks were metamorphosed at the inception of east-dipping subduction beneath the Coast Range ophiolite, and the ophiolite was subsequently emplaced over this later subduction zone. Suprasubduction-zone protolith signatures have been obtained for other metamorphic soles beneath suprasubduction-zone ophiolites, suggesting that our proposed model of suprasubduction-zone ophiolite generation over one subduction zone and emplacement over a second one may be globally applicable. Regional geology suggests that this dual subduction-zone model may also apply to suprasubduction-zone ophiolites with midocean-ridge and/or oceanic-island basalt soles.

Field of study: Geology
New Trends in Energy and Environment Researches with System Engineering Methods

In this paper, the author describes the historical development of the energy related researches briefly and then introduces how this area has been affected by the social circumstances. Since the oil crisises in 1973 and 1978, energy conservation has been the key factor as well as the “deregulation” of the market. These two factors shifted the energy supply-demand structure from one-way flow to the birateral network involving multiple players. System methods such as gamie theory and multi agent systems are introduced to see how the energy market behaves. New transmission and distribution system is proposed to establish the flexible and reliable power system. When we look into the regional energy and environmental issues, the policy maker has to solve the interactions among energy technologies, waste management and utilization technologies and transportaion systems. The system engineering methods have to provide the solution in such an interdisplinary area.

Field of study: Computer science
Return Rates of “Lost” Letters as a Function of Whether the Letter is Stamped and Amount of Money Apparently in the Letter

150 stamped and 150 unstamped letters with 3 different amounts of “play” money in them were “lost.” The return rate for stamped letters was significantly higher than the return rate for unstamped letters. Amount of “play” money in the letter did not have a significant effect upon return rate.

Field of study: Psychology