nils-herrmann/clean_scirepeval huggingface dataset:
Associations and interactions between SNPs in the alcohol metabolizing genes and alcoholism phenotypes in European Americans.

Alcohol dependence is a major cause of morbidity and mortality worldwide and has a strong familial component. Several linkage and association studies have identified chromosomal regions and/or genes that affect alcohol consumption, notably in genes involved in the 2-stage pathway of alcohol metabolism.



Here, we use multiple regression models to test for associations and interactions between 2 alcohol-related phenotypes and SNPs in 17 genes involved in alcohol metabolism in a sample of 1,588 European American subjects.



The strongest evidence for association after correcting for multiple testing was between rs1229984, a nonsynonymous coding SNP in ADH1B, and DSM-IV symptom count (p = 0.0003). This SNP was also associated with maximum number of drinks in 24 hours (p = 0.0004). Each minor allele at this SNP predicts 45% fewer DSM-IV symptoms and 18% fewer max drinks. Another SNP in a splice site in ALDH1A1 (rs8187974) showed evidence for association with both phenotypes as well (p = 0.02 and 0.004, respectively), but neither association was significant after accounting for multiple testing. Minor alleles at this SNP predict greater alcohol consumption. In addition, pairwise interactions were observed between SNPs in several genes (p = 0.00002).



We replicated the large effect of rs1229984 on alcohol behavior, and although not common (MAF = 4%), this polymorphism may be highly relevant from a public health perspective in European Americans. Another SNP, rs8187974, may also affect alcohol behavior but requires replication. Also, interactions between polymorphisms in genes involved in alcohol metabolism are likely determinants of the parameters that ultimately affect alcohol consumption.

Field of study: Medicine
Kynurenic acid protects against the neurochemical and behavioral effects of unilateral quinolinic acid injections into the nucleus basalis of rats.

It has recently been demonstrated that kynurenic acid (KYN), an endogenous tryptophan metabolite, provides almost complete protection against the neurotoxic and mnemonic effects of another tryptophan metabolite quinolinic acid (QUIN) on the cell bodies of the nucleus basalis magnocellularis (nbm). The present study further investigated whether unilateral coinjections of KYN and QUIN into the rat nbm antagonized the effects of QUIN alone. Food-deprived rats were pretrained on an eight-arm radial maze, with four arms baited, until choice accuracy stabilized to greater than or equal to 87% correct. Postoperatively, rats were tested on the radial maze for 32 consecutive days. Feeding behavior and locomotor activity were also measured to determine if nonassociative factors accounted for any observed behavioral deficits. QUIN lesions resulted in significantly more working and reference memory errors compared with sham-operated and coinjected animals, which did not differ significantly from each other. There were no reliable group differences in amount of food eaten or locomotor activity. The QUIN group had a reliable decrease in cortical choline acetyltransferase, with no significant changes for the sham and coinjected groups. Results confirm that KYN antagonizes the neurotoxic and mnemonic effects of QUIN alone and suggest that the memory deficits induced by nbm lesions cannot be solely attributed to changes in feeding or locomotor activity.

Field of study: Biology, Psychology
Crystallization and preliminary X-ray diffraction analysis of naphthalene dioxygenase from Rhodococcus sp. strain NCIMB 12038.

The three-component naphthalene dioxygenase (NDO) enzyme system carries out the first step in the aerobic degradation of naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene by Rhodococcus sp. strain NCIMB 12038. The terminal oxygenase component (naphthalene 1,2-dioxygenase) that catalyzes this reaction belongs to the aromatic ring hydroxylating dioxygenase family and has been crystallized. These enzymes utilize a mononuclear non-heme iron centre to catalyze the addition of dioxygen to their respective substrates. In this reaction, two electrons, two protons and a dioxygen molecule are consumed. The Rhodococcus enzyme has only 33 and 29% sequence identity to the corresponding alpha- and beta-subunits of the NDO system of Pseudomonas putida NCIMB 9816-4, for which the tertiary structure has been reported. In order to determine the three-dimensional structure of the Rhodococcus NDO, diffraction-quality crystals have been prepared by the hanging-drop method. The crystals belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 87.5, b = 144, c = 185.6 A, alpha = beta = gamma = 90 degrees, and diffract to 2.3 A resolution.

Field of study: Chemistry
Tensor products of modular representations of $\operatorname{SL}_2(\mathbb{F}_p)$ and a random walk on their indecomposable summands

In this paper we give a novel, concise and elementary proof of the decomposition of tensor products of simple modular $\operatorname{SL}_2(\mathbb{F}_p)$-representations. This result is used to decompose tensor products involving their projective covers and to decompose symmetric squares. We define a Markov chain on the simple modular $\operatorname{SL}_2(\mathbb{F}_p)$-representations via tensoring with a fixed simple module and choosing an indecomposable summand according to a specified weighting; we show this chain is reversible and find its stationary distributions.

Field of study: Mathematics
The effect of pressure on the thermal conductivity of ordered and disordered alloys

A comparison is made between the results from experimental studies into the effect of hydrostatic pressures of up to 400 MPa in the temperature range 273–523 K on the phonon thermal conductivity of CdSnAs2 alloy and the effective thermal conductivity of granite. Pressure was demonstrated to lead to a change in the degree of structural ordering of the studied specimens.

Field of study: Physics
Detection of Algebraic Manipulation with Applications to Robust Secret Sharing and Fuzzy Extractors

Consider an abstract storage device Σ(G) that can hold a single element x from a fixed, publicly known finite group G. Storage is private in the sense that an adversary does not have read access to Σ(G) at all. However, Σ(G) is non-robust in the sense that the adversary can modify its contents by adding some offset Δ ∈ G. Due to the privacy of the storage device, the value Δ can only depend on an adversary's a priori knowledge of x. We introduce a new primitive called an algebraic manipulation detection (AMD) code, which encodes a source s into a value x stored on Σ(G) so that any tampering by an adversary will be detected. We give a nearly optimal construction of AMD codes, which can flexibly accommodate arbitrary choices for the length of the source s and security level. We use this construction in two applications: - We show how to efficiently convert any linear secret sharing scheme into a robust secret sharing scheme, which ensures that no unqualified subset of players can modify their shares and cause the reconstruction of some value s′ ≠ s. - We show how to build nearly optimal robust fuzzy extractors for several natural metrics. Robust fuzzy extractors enable one to reliably extract and later recover random keys from noisy and non-uniform secrets, such as biometrics, by relying only on non-robust public storage. In the past, such constructions were known only in the random oracle model, or required the entropy rate of the secret to be greater than half. Our construction relies on a randomly chosen common reference string (CRS) available to all parties.

Field of study: Computer science, Mathematics
Allogeneic Compact Bone-Derived Mesenchymal Stem Cell Transplantation Attenuates the Severity of Idiopathic Pneumonia Syndrome in a Murine Bone Marrow Transplantation Model

Idiopathic pneumonia syndrome (IPS) is a serious and life-threatening lung complication following allogeneic hematopoietic stem cell transplantation (allo-HSCT) and currently no effective therapies exist. This study was designed to determine whether transplantation of allogeneic murine compact bone derived- mesenchymal stem cells (CB-MSCs) could prevent the development of IPS.  We tested the effects of CB-MSCs transplantation on IPS using an established murine model of C57BL/6 (H-2b)→BALB/c (H-2d). Survival rates, body weight change, clinical GVHD scores, lung histological changes were assessed after IPS induction. Mechanistically, concentrations of cytokines (TNF-α, IFN-γ and IL-4) and chemokines (CCL5, CXCL9 and CXCL10) in bronchoalveolar lavage fluid (BALF) from the recipient mice were measured at different time point post-transplantation. CD4+CD25+Foxp3+ regulatory T cell (Treg) percentage, CCR5, CXCR3 and CCR7 expression on CD3+ T cells, and lung CXCR3, CCR5, CCR7, T-bet and GATA-3 mRNA levels were also evaluated at different time point post-transplantation.  Co-transplantation of CB-MSCs significantly attenuated the severity of lung injuries and increased survival rate of mice compared to non-cotransplanted mice. A higher Treg percentage, reduction of TNF-α, IFN-γ, CCL5, CXCL9 and CXCL10 levels, down-regulation of CXCR3 and CCR5, as well as up-regulation of CCR7, were observed in MSCs co-transplantation mice. Also, the prophylactic effect of CB-MSCs was associated with a shift of Th1/Th2 balance toward anti-inflammatory Th2 polarization.  Allogeneic CB-MSCs effectively controlled the occurrence of IPS due to its profound immunomodulatory capacity. This may offer a novel prophylactic approach for IPS after allo-HSCT.

Field of study: Biology, Chemistry
Time-driven activity-based costing in health care: A systematic review of the literature.

Health care organizations around the world are investing heavily in value-based health care (VBHC), and time-driven activity-based costing (TDABC) has been suggested as the cost-component of VBHC capable of addressing costing challenges. The aim of this study is to explore why TDABC has been applied in health care, how its application reflects a seven-step method developed specifically for VBHC, and implications for the future use of TDABC. This is a systematic review following the PRISMA statement. Qualitative methods were employed to analyze data through content analyses. TDABC is applicable in health care and can help to efficiently cost processes, and thereby overcome a key challenge associated with current cost-accounting methods The method's ability to inform bundled payment reimbursement systems and to coordinate delivery across the care continuum remains to be demonstrated in the published literature, and the role of TDABC in this cost-accounting landscape is still developing. TDABC should be gradually incorporated into functional systems, while following and building upon the recommendations outlined in this review. In this way, TDABC will be better positioned to accurately capture the cost of care delivery for conditions and to control cost in the effort to create value in health care.

Field of study: Medicine, Political science
Analysis of How Masters’ Curriculum Meets the Needs of Masters’ Students’ Use of Statistics in Research

Knowledge is valued as a vital asset for progress and prosperity in every sphere of human understanding.  Knowledge is attributed with successful innovation in firms. Research has been identified as the main source of knowledge. In Kenya, University students have been accused of doing low quality research. Statistics is important in research, it starts at the planning stage to establish the design and sample size. Studies have pointed to wrong use of statistics as a contributing factor towards low quality research. The purpose of this study was; to determine masters’ curriculum meets the needs of masters’ students’ use of statistics in research, a case of curriculums of universities of western Kenya. Three curriculums from 3 different universities were analyzed. The study established that; general objectives and specific objectives in courses related to statistics adequately covered the requirements for statistics training; the scheduled content for the core courses covered descriptive and inferential statistics; ICT concepts are catered for in the sampled masters’ curriculums, however, the courses are too wide to be effectively learned in one semester of 4 months; The study established that lectures, class discussion and students presentations are common methods of instruction across the sampled curriculums. The study established that continuous assessment tests and end of semester sit in exam were the common form of exams administered. In addition in one case there were also term papers and practical in some courses. However the end of semester exam carried more weight of 60%. The study recommended for proper integration of ICT and statistics, increase of statistical courses and use of open book examination.  Curriculum, Statistics, Research DOI : 10.7176/JEP/10-21-17 Publication date :July 31 st 2019

Field of study: Education
UniSpaCh: A text-based data hiding method using Unicode space characters

This paper proposes a text-based data hiding method to insert external information into Microsoft Word document. First, the drawback of low embedding efficiency in the existing text-based data hiding methods is addressed, and a simple attack, DASH, is proposed to reveal the information inserted by the existing text-based data hiding methods. Then, a new data hiding method, UniSpaCh, is proposed to counter DASH. The characteristics of Unicode space characters with respect to embedding efficiency and DASH are analyzed, and the selected Unicode space characters are inserted into inter-sentence, inter-word, end-of-line and inter-paragraph spacings to encode external information while improving embedding efficiency and imperceptivity of the embedded information. UniSpaCh is also reversible where the embedded information can be removed to completely reconstruct the original Microsoft Word document. Experiments were carried out to verify the performance of UniSpaCh as well as comparing it to the existing space-manipulating data hiding methods. Results suggest that UniSpaCh offers higher embedding efficiency while exhibiting higher imperceptivity of white space manipulation when compared to the existing methods considered. In the best case scenario, UniSpaCh produces output document of size almost 9 times smaller than that of the existing method.

Field of study: Computer science, Engineering
Microstructure and Mechanical Properties of Welded Joint of AZ61 Magnesium Alloy Plates by TIG Welding

AZ61 plates with 3 mm thickness were welded by TIG welding with AZ31 and AZ61 welding wires,respectively.The influences of welding wires on the strength of the welded joints of AZ61 magnesium alloy plates were investigated.By OM,SEM,X-ray diffraction and etc.,the morphology,microstructure,deposited phase and mechanical properties were analyzed.The results show that the good appearance of the welded joint can be obtained with both AZ31 and AZ61 welding wires,the morphology of the welded joint with AZ61 welding wire is better than with AZ31 welding wire.The microstructure of the welded zone is fine equiaxed grain,which consists of α-Mg and β-Mg17Al12,and the microstructure of the heat affected zone is coarser.The microhardness of the weld zone and heat affected zone is lower than the base metal with AZ31 welding wire.With AZ61 welding wire,the microhardness of the weld zone is higher than base metal,while that of the heat affected zone is lower.The tensile fracture always occurs in the coarse grain of heat affected zone.

Field of study: Materials science
Robust Mobile Terminal Tracking in NLOS Environments Based on Data Association

An algorithm for mobile terminal (MT) tracking based on time-of-arrival measurements in non-line-of-sight (NLOS) environments is proposed. It is based on NLOS detection together with a modified probabilistic data association approach where different subgroups of range measurements are constructed. Each of the subgroups provide a position estimate of the MT with it's corresponding covariance matrix that are both used in a hypothesis test for NLOS detection. The accepted position estimates are weighted with different probabilities in a Kalman filter framework. Simulation results show a significant increase in positioning accuracy in NLOS environments with respect to both, the extended Kalman filter (EKF) and a NLOS mitigation algorithm from the literature. In LOS environments similar performance to the EKF is achieved. The proposed method does not assume any statistical knowledge of the NLOS errors and only assumes the sensor noise variance to be known.

Field of study: Engineering
The Smeagol method for spin- and molecular-electronics

{\it Ab initio} computational methods for electronic transport in nanoscaled systems are an invaluable tool for the design of quantum devices. We have developed a flexible and efficient algorithm for evaluating $I$-$V$ characteristics of atomic junctions, which integrates the non-equilibrium Green's function method with density functional theory. This is currently implemented in the package {\it Smeagol}. The heart of {\it Smeagol} is our novel scheme for constructing the surface Green's functions describing the current/voltage probes. It consists of a direct summation of both open and closed scattering channels together with a regularization procedure of the Hamiltonian, and provides great improvements over standard recursive methods. In particular it allows us to tackle material systems with complicated electronic structures, such as magnetic transition metals. Here we present a detailed description of {\it Smeagol} together with an extensive range of applications relevant for the two burgeoning fields of spin and molecular-electronics.

Field of study: Physics
The kinetics of T lymphocyte subpopulations in guinea-pigs sensitized with allogeneic transplantation antigens.

The kinetics of specifically sensitized T lymphocytes in the circulation and lymphoid tissues of guinea-pigs immunized with allogeneic transplantation antigens or with synthetic peptide sequence known to induce delayed-type hypersensitivity were documented by the antigen-stimulated active rosette-forming T cell (AgARFC) assay. The results show that immunologically functional cells sensitized to a particular antigen do not remain in the circulation when the antigenic source has been withdrawn. These cells become sequestered in lymphoid tissue and may be recalled into the circulation shortly after the de novo administration of sensitizing antigen. The detection of antigen-sensitive T cells in the circulation was indicative of the presence of and failure to detect these cells and their eventual appearance in lymphoid tissues was related to depletion of the antigenic source.

Field of study: Biology, Medicine
BRIEF COMMUNICATIONS: Investigation of nonlinear absorption in H2O vapors subjected to strong optical fields with linear and circular polarizations

The optoacoustic method was used to investigate the change in the collisional profile of the 694.38 nm absorption line of H2O subjected to strong fields of laser radiations with linear and circular polarizations. The measurements were carried out with a resolution of 0.015 cm−1 using laser radiations of intensities up to 50 MW/cm2. The study of nonlinear absorption was made for H2O–air, H2O–N2, H2O–Ar, and H2O–Xe mixtures at total pressures in excess of 180 Torr using radiations of several intensities.

Field of study: Engineering, Physics
Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements

The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.

Field of study: Biology, Environmental science
Longitudinal survey of anxiety and depression in drug users and addicts.

As a follow-up to our 1990 study of anxiety and depression among drug users, after two years 44 men differed in their experience with drugs and from the first phase of the study five of the 20 controls became drug users, two of the 20 drug users became addicts, and one of the 20 drug abusers died from AIDS. These findings do not confirm the 1989 thesis of Newcomb and Bentler on the etiology of addiction, that depression and anxiety imply greater drug use. Positive correlations were found for drug use with anxiety and depression. Such data confirm those found by De Moja in 1990.

Field of study: Psychology
Regulation of ApoE receptor proteolysis by ligand binding.

Two brain receptors for apolipoprotein E (apoE), the apoE receptor 2 (apoEr2) and the very low density lipoprotein receptor (VLDLr), are important in neuronal migration during development. Using a series of tagged constructs, we found that these two receptors undergo extracellular cleavages to release secreted forms of the receptors and intramembranous cleavages to degrade the C-terminal fragments. Release of the extracellular domains was blocked by an inhibitor of metalloproteinases and increased by PMA. Accumulation of the intracellular domain was increased by the presence of an inhibitor of gamma-secretase. ApoE binding to these receptors caused increased release of the extracellular domain and accumulation of the intracellular domains; similar increases in receptor proteolytic domains were observed from endogenous apoEr2 after treatment of primary neurons or rat hippocampus with an apoE-derived peptide. The human apoE isoforms promoted proteolysis to different degrees, with apoE2 resulting in a greater accumulation of the C-terminal fragments of apoEr2 compared with apoE4. These effects of apoE on receptor proteolysis were mediated by the ligand binding domain of the receptor. Similar promotion of receptor cleavage was seen with two other ligands, reelin and activated alpha2-macroglobulin. We suggest that signaling promoted by these receptors depends in part on these regulated proteolytic events.

Field of study: Biology