Miracle-dz/UniFAR-FTUs huggingface dataset:
Quality of the Reviews Submitted by Attendees of a Workshop on Peer Review

Objective: The objective of the study was to study the methodological quality and error detection of the review by the participants of a peer review workshop. Methods: All participants of the workshop were invited to peer review a randomized controlled trial. The manuscript was E-mailed to them after introducing eight deliberate errors to it. Specific instructions and a deadline were provided. All the reviews were analyzed using review quality instrument (RQI). Furthermore, the rate and the type of errors identified were recorded. Results: Of 25 participants, 16 (64%) returned the reviews. The mean total score on RQI was 4.12 (standard deviation 0.70, 95% confidence interval 3.74–4.50); the items which most reviewers did not discuss where the importance of research question and originality of the paper. The number of errors correctly identified varied from 0 to 6 (median 3), the most common being a wrong conclusion (87.5%), randomization procedure (50%), written informed consent (50%), ethics committee approval (42.8%), and masking (31.2%). Only 5 (31.2%) gave an overall recommendation on whether the manuscript should be accepted or not. Conclusions: Major errors were readily identified by the reviewers; however, the need for training was felt in some areas in which the review quality was modest.
Under Consideration for Publication in Theory and Practice of Logic Programming Tabled Abduction in Logic Programs

Abduction has been on the back burner in logic programming, as abduction can be too difficult to implement, and costly to perform, in particular if abductive solutions are not tabled for reuse. On the other hand, current Prolog systems, with their tabling mechanisms, are mature enough to facilitate the specific introduction of tabling abductive solutions (tabled abduction) into them. Our contributions are as follows: (1) We conceptualize tabled abduction for abductive normal logic programs, permitting abductive solutions to be reused, from one abductive context to another. The approach relies on a transformation into tabled logic programs that makes use of the dual transformation, and enables efficiently handling the problem of abduction under negative goals, by introducing dual positive counterparts for them. (2) We realize tabled abduction in Tabdual, a system implemented in XSB Prolog, allowing dualization by-need only. (3) We refine the dual transformation in the context of Tabdual to permit executing programs with variables and non-ground queries. (4) We foster pragmatic approaches in Tabdual to cater to all varieties of loops in normal logic programs, now complicated by abduction. (5) We evaluate Tabdual in practice by examining five variants, according to various evaluation objectives. (6) We detail how Tabdual can be applied to declarative debugging and decision making. (7) Finally, we refer to related work, and discuss Tabdual's correctness, complexity, and features that could migrate to the engine level, in Logic Programming systems wanting to encompass tabled abduction. Eight appendices complement and detail the main text.
Association of the Endogenous Nitric Oxide Synthase Inhibitor ADMA With Carotid Artery Intimal Media Thickness in the Framingham Heart Study Offspring Cohort

Background and Purpose— Higher plasma concentrations of the endogenous nitric oxides synthase inhibitor asymmetrical dimethylarginine (ADMA) are associated with increased risk of cardiovascular and cerebrovascular events and death, presumably by promoting endothelial dysfunction and subclinical atherosclerosis. We hypothesized that plasma ADMA concentrations are positively related to common carotid artery intimal-media thickness (CCA-IMT) and to internal carotid (ICA)/bulb IMT. Methods— We investigated the cross-sectional relations of plasma ADMA with CCA-IMT and ICA/bulb IMT in 2958 Framingham Heart Study participants (mean age, 58 years; 55% women). Results— In unadjusted analyses, ADMA was positively related to both CCA-IMT (β per SD increment, 0.012; P<0.001) and ICA/bulb IMT (β per SD increment, 0.059; P<0.001). In multivariable analyses (adjusting for age, sex, systolic blood pressure, antihypertensive treatment, smoking status, diabetes, BMI, total-to-HDL cholesterol ratio, log C-reactive protein, and serum creatinine), plasma ADMA was not associated with CCA-IMT (P=0.991), but remained significantly and positively related to ICA/bulb IMT (β per SD increment, 0.0246; P=0.002). Conclusions— In our large community-based sample, we observed that higher plasma ADMA concentrations were associated with greater ICA/bulb IMT, but not with CCA-IMT. These data are consistent with the notion that ADMA promotes subclinical atherosclerosis in a site-specific manner, with a greater proatherogenic influence at known vulnerable sites in the arterial tree.
Evaluation of Hierarchical Vector Basis Functions for Quadrilateral Cells

New hierarchical vector basis functions for quadrilateral cells are introduced, and the matrix condition numbers associated with their use are compared to those of existing vector basis families to assess the relative linear independence of the functions. Scale factors are employed to improve the condition numbers. In addition, the proper use of subsets of these families to transition from one order to another (as needed for adaptive p-refinement) without exciting spurious modes is considered.
Convection-Allowing and Convection-Parameterizing Ensemble Forecasts of a Mesoscale Convective Vortex and Associated Severe Weather Environment

Abstract An analysis of a regional severe weather outbreak that was related to a mesoscale convective vortex (MCV) is performed. The MCV-spawning mesoscale convection system (MCS) formed in northwest Kansas along the southern periphery of a large cutoff 500-hPa low centered over western South Dakota. As the MCS propagated into eastern Kansas during the early morning of 1 June 2007, an MCV that became evident from multiple data sources [e.g., Weather Surveillance Radar-1988 Doppler (WSR-88D) network, visible satellite imagery, wind-profiler data, Rapid Update Cycle 1-hourly analyses] tracked through northwest Missouri and central Iowa and manifested itself as a well-defined midlevel short-wave trough. Downstream of the MCV in southeast Iowa and northwest Illinois, southwesterly 500-hPa winds increased to around 25 m s−1 over an area with southeasterly surface winds and 500–1500 J kg−1 of surface-based convective available potential energy (CAPE), creating a favorable environment for severe weather. In the .
Homologs of Mycobacterium leprae 18-kilodalton and Mycobacterium tuberculosis 19-kilodalton antigens in other mycobacteria

Most of the antigens of Mycobacterium leprae and M. tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18-kDa M. leprae antigen and the 19-kDa M. tuberculosis antigen are strongly cross-reaction between these two species and are coded within very similar genes. Studies of T cell reactivity against mycobacterial antigens have indicated that M. tuberculosis bears epitopes that are cross-reactive with the M. leprae 18-kDa antigen, but attempts to identify an 18-kDa antigen-like protein or protein coding sequence in M. tuberculosis have been unsuccessful. We have used a combination of low-stringency DNA hybridization and polymerase chain reaction techniques to identify, isolate, and sequence genes from M. avium and M. intracellulare that are very similar to the 18-kDa antigen gene of M. leprae and others that are homologs of the 19-kDa antigen gene of M. tuberculosis. Unlike M. leprae, which contains a single 18-kDa antigen gene, M. avium and M. intracellulare each have two 18-kDa antigen coding sequences. Although the M. leprae, M. avium, and M. intracellulare 18-kDa antigen genes are all very similar to one another, as are the M. tuberculosis, M. avium, and M. intracellulare 19-kDa antigen genes, we have been unable to detect any 18-kDa antigen-like coding sequences in DNA from M. tuberculosis.
Experimental Infection of Rhesus Macaques and Common Marmosets with a European Strain of West Nile Virus

West Nile virus (WNV) is a mosquito-borne flavivirus that infects humans and other mammals. In some cases WNV causes severe neurological disease. During recent years, outbreaks of WNV are increasing in worldwide distribution and novel genetic variants of the virus have been detected. Although a substantial amount of data exists on WNV infections in rodent models, little is known about early events during WNV infection in primates, including humans. To gain a deeper understanding of this process, we performed experimental infections of rhesus macaques and common marmosets with a virulent European WNV strain (WNV-Ita09) and monitored virological, hematological, and biochemical parameters. WNV-Ita09 productively infected both monkey species, with higher replication and wider tissue distribution in common marmosets compared to rhesus macaques. The animals in this study however, did not develop clinical signs of WNV disease, nor showed substantial deviations in clinical laboratory parameters. In both species, the virus induced a rapid CD56dimCD16bright natural killer response, followed by IgM and IgG antibody responses. The results of this study show that healthy rhesus macaques and common marmosets are promising animal models to study WNV-Ita09 infection. Both models may be particularly of use to evaluate potential vaccine candidates or to investigate WNV pathogenesis.
Sensitivity and selectivity in protein structure comparison

Seven protein structure comparison methods and two sequence comparison programs were evaluated on their ability to detect either protein homologs or domains with the same topology (fold) as defined by the CATH structure database. The structure alignment programs Dali, Structal, Combinatorial Extension (CE), VAST, and Matras were tested along with SGM and PRIDE, which calculate a structural distance between two domains without aligning them. We also tested two sequence alignment programs, SSEARCH and PSI‐BLAST. Depending upon the level of selectivity and error model, structure alignment programs can detect roughly twice as many homologous domains in CATH as sequence alignment programs. Dali finds the most homologs, 321–533 of 1120 possible true positives (28.7%–45.7%), at an error rate of 0.1 errors per query (EPQ), whereas PSI‐BLAST finds 365 true positives (32.6%), regardless of the error model. At an EPQ of 1.0, Dali finds 42%–70% of possible homologs, whereas Matras finds 49%–57%; PSI‐BLAST finds 36.9%. However, Dali achieves >84% coverage before the first error for half of the families tested. Dali and PSI‐BLAST find 9.2% and 5.2%, respectively, of the 7056 possible topology pairs at an EPQ of 0.1 and 19.5, and 5.9% at an EPQ of 1.0. Most statistical significance estimates reported by the structural alignment programs overestimate the significance of an alignment by orders of magnitude when compared with the actual distribution of errors. These results help quantify the statistical distinction between analogous and homologous structures, and provide a benchmark for structure comparison statistics.
A meta-analysis of soil microbial biomass responses to forest disturbances

Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm) and biotic (insect, pathogen) disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7, 19.1, and 41.7% reductions in microbial biomass, respectively). In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics.
Modeling and Simulation of Delaminations in FML Using Step Pulsed Active Thermography

— The study focuses to investigate the thermal response of delaminations and develop mathematical models using numerical results to obtain the optimum heat requirement and time to identify delaminations in GLARE type of Fibre Metal Laminates (FML) in both reflection mode and through-transmission (TT) mode of step pulsed active thermography (SPAT) method in the type of nondestructive testing and evaluation (NDTE) technique. The influence of applied heat flux and time on various sizes and depth of delaminations in FML is analyzed to investigate the thermal response through numerical simulations. A finite element method (FEM) is applied to simulate SPAT through ANSYS software based on 3D transient heat transfer principle with the assumption of reflection mode and TT mode of observation individually. The results conclude that the numerical approach based on SPAT in reflection mode is more suitable for analysing smaller size of near- surface delaminations located at the thermal stimulator side and TT mode is more suitable for analysing smaller size of deeper delaminations located far from thermal stimulator side or near thermal detector/Infrared camera side. The mathematical models provide the optimum q and T at the required MRTD to identify unidentified delamination 7 with 25015.0022W/m 2 at 2.531sec and delamination 8 with 16663.3356 W/m 2 at 1.37857sec in reflection mode. In TT mode, the delamination 1 with 34954W/m 2 at 13.0399sec, delamination 2 with 20002.67W/m 2 at 1.998sec and delamination 7 with 20010.87 W/m 2 at 0.6171sec could be identified.
Casein Kinase II Motif-Dependent Phosphorylation of Human Papillomavirus E7 Protein Promotes p130 Degradation and S-Phase Induction in Differentiated Human Keratinocytes

ABSTRACT The E7 proteins of human papillomaviruses (HPVs) promote S-phase reentry in differentiated keratinocytes of the squamous epithelia to support viral DNA amplification. In this study, we showed that nuclear p130 was present in the differentiated strata of several native squamous epithelia susceptible to HPV infection. In contrast, p130 was below the level of detection in HPV-infected patient specimens. In submerged and organotypic cultures of primary human keratinocytes, the E7 proteins of the high-risk mucosotrophic HPV-18, the benign cutaneous HPV-1, and, to a lesser extent, the low-risk mucosotropic HPV-11 destabilized p130. This E7 activity depends on an intact pocket protein binding domain and a casein kinase II (CKII) phosphorylation motif. Coimmunoprecipitation experiments showed that both E7 domains were important for binding to p130 in extracts of organotypic cultures. Metabolic labeling in vivo demonstrated that E7 proteins were indeed phosphorylated in a CKII motif-dependent manner. Moreover, the efficiencies of the E7 proteins of various HPV types or mutations to induce S-phase reentry in spinous cells correlated with their relative abilities to bind and to destabilize p130. Collectively, these data support the notion that p130 controls the homeostasis of the differentiated keratinocytes and is therefore targeted by E7 for degradation to establish conditions permissive for viral DNA amplification.
Feature extraction through local learning

RELIEF is considered one of the most successful algorithms for assessing the quality of features. It has been recently proved that RELIEF is an online learning algorithm that solves a convex optimization problem with a margin‐based objective function. Starting from this mathematical interpretation, we propose a novel feature extraction algorithm, referred to as local feature extraction (LFE), as a natural generalization of RELIEF. LFE collects discriminant information through local learning and can be solved as an eigenvalue decomposition problem with a closed‐form solution. A fast implementation of LFE is derived. Compared to principal component analysis, LFE also has a clear physical meaning and can be implemented easily with a comparable computational cost. Compared to other feature extraction algorithms, LFE has an explicit mechanism to remove irrelevant features. Experiments on synthetic and real‐world data are presented. The results demonstrate the effectiveness of the proposed algorithm. © 2009 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 2: 34‐47, 2009
Rorschach Personality Predictors of Weight Loss With Behavior Modification in Obesity Treatment

Weight loss outcome for 49 obese patients after 6 months treatment in a behavior modification program was related to Rorschach personality characteristics according to the Comprehensive System (Exner, 2003), also including the Rorschach Oral Dependency Scale (Bornstein, 1996; Masling & Rabie, 1967). Less weight loss was predicted by signs of perceptual and cognitive distortions indicated by the Schizophrenia Index. More weight loss was predicted by Food Contents, suggesting a food preoccupation and possibly a benign dependency orientation. Patients with a focus on food and dependent needs could benefit above all from the treatment program implying learning how to handle food and eating in a supportive setting, as evidenced by more weight loss. Distortions in perception and cognition could constitute more profound difficulties in weight reduction important to recognize in obesity treatment.
Arterial Stiffness and Autonomic Modulation After Free-Weight Resistance Exercises in Resistance Trained Individuals

Abstract Kingsley, JD, Mayo, X, Tai, YL, and Fennell, C. Arterial stiffness and autonomic modulation after free-weight resistance exercises in resistance trained individuals. J Strength Cond Res 30(12): 3373–3380, 2016—We investigated the effects of an acute bout of free-weight, whole-body resistance exercise consisting of the squat, bench press, and deadlift on arterial stiffness and cardiac autonomic modulation in 16 (aged 23 ± 3 years; mean ± SD) resistance-trained individuals. Arterial stiffness, autonomic modulation, and baroreflex sensitivity (BRS) were assessed at rest and after 3 sets of 10 repetitions at 75% 1-repetition maximum on each exercise with 2 minutes of rest between sets and exercises. Arterial stiffness was analyzed using carotid-femoral pulse wave velocity (cf-PWV). Linear heart rate variability (log transformed [ln] absolute and normalized units [nu] of low-frequency [LF] and high-frequency [HF] power) and nonlinear heart rate complexity (Sample Entropy [SampEn], Lempel-Ziv Entropy [LZEn]) were measured to determine autonomic modulation. BRS was measured by the sequence method. A 2 × 2 repeated measures analysis of variance (ANOVA) was used to analyze time (rest, recovery) across condition (acute resistance exercise, control). There were significant increases in cf-PWV (p = 0.05), heart rate (p = 0.0001), normalized LF (LFnu; p = 0.001), and the LF/HF ratio (p = 0.0001). Interactions were also noted for ln HF (p = 0.006), HFnu (p = 0.0001), SampEn (p = 0.001), LZEn (p = 0.005), and BRS (p = 0.0001) such that they significantly decreased during recovery from the resistance exercise compared with rest and the control. There was no effect on ln total power, or ln LF. These data suggest that a bout of resistance exercise using free-weights increases arterial stiffness and reduces vagal activity and BRS in comparison with a control session. Vagal tone may not be fully recovered up to 30 minutes after a resistance exercise bout.
Pairing Computation on Elliptic Curves of Jacobi Quartic Form

This paper proposes explicit formulae for the addition step and doubling step in Miller's algorithm to compute Tate pairing on Jacobi quartic curves. We present a geometric interpretation of the group law on Ja- cobi quartic curves, which leads to formulae for Miller's algorithm. The doubling step formula is competitive with that for Weierstrass curves and Edwards curves. More- over, by carefully choosing the coe-cients, there exist quartic twists of Jacobi quartic curves from which pairing computation can beneflt a lot. Finally, we provide some examples of supersingular and ordinary pairing friendly Jacobi quartic curves.
Early behavioral intervention, brain plasticity, and the prevention of autism spectrum disorder

Abstract Advances in the fields of cognitive and affective developmental neuroscience, developmental psychopathology, neurobiology, genetics, and applied behavior analysis have contributed to a more optimistic outcome for individuals with autism spectrum disorder (ASD). These advances have led to new methods for early detection and more effective treatments. For the first time, prevention of ASD is plausible. Prevention will entail detecting infants at risk before the full syndrome is present and implementing treatments designed to alter the course of early behavioral and brain development. This article describes a developmental model of risk, risk processes, symptom emergence, and adaptation in ASD that offers a framework for understanding early brain plasticity in ASD and its role in prevention of the disorder.
The Diffusion Tensor Imaging Toolbox

During the past few years, The Journal of Neuroscience has published more than 30 articles that describe investigations that used Diffusion Tensor Imaging (DTI) and related techniques as a primary observation method. This illustrates a growing interest in DTI within the basic and clinical neuroscience communities. This article summarizes DTI methodology in terms that can be immediately understood by the neuroscientist who has little previous exposure to DTI. It describes the fundamentals of water molecular diffusion coefficient measurement in brain tissue and illustrates how these fundamentals can be used to form vivid and useful depictions of white matter macroscopic and microscopic anatomy. It also describes current research applications and the technique's attributes and limitations. It is hoped that this article will help the readers of this Journal to more effectively evaluate neuroscience studies that use DTI.