Miracle-dz/UniFAR-FTUs huggingface dataset:
Subgroup analyses in randomised controlled trials: cohort study on trial protocols and journal publications

Objective To investigate the planning of subgroup analyses in protocols of randomised controlled trials and the agreement with corresponding full journal publications. Design Cohort of protocols of randomised controlled trial and subsequent full journal publications. Setting Six research ethics committees in Switzerland, Germany, and Canada. Data sources 894 protocols of randomised controlled trial involving patients approved by participating research ethics committees between 2000 and 2003 and 515 subsequent full journal publications. Results Of 894 protocols of randomised controlled trials, 252 (28.2%) included one or more planned subgroup analyses. Of those, 17 (6.7%) provided a clear hypothesis for at least one subgroup analysis, 10 (4.0%) anticipated the direction of a subgroup effect, and 87 (34.5%) planned a statistical test for interaction. Industry sponsored trials more often planned subgroup analyses compared with investigator sponsored trials (195/551 (35.4%) v 57/343 (16.6%), P<0.001). Of 515 identified journal publications, 246 (47.8%) reported at least one subgroup analysis. In 81 (32.9%) of the 246 publications reporting subgroup analyses, authors stated that subgroup analyses were prespecified, but this was not supported by 28 (34.6%) corresponding protocols. In 86 publications, authors claimed a subgroup effect, but only 36 (41.9%) corresponding protocols reported a planned subgroup analysis. Conclusions Subgroup analyses are insufficiently described in the protocols of randomised controlled trials submitted to research ethics committees, and investigators rarely specify the anticipated direction of subgroup effects. More than one third of statements in publications of randomised controlled trials about subgroup prespecification had no documentation in the corresponding protocols. Definitive judgments regarding credibility of claimed subgroup effects are not possible without access to protocols and analysis plans of randomised controlled trials.
A Space-Time Fractional Optimal Control Problem: Analysis and Discretization

We study a linear-quadratic optimal control problem involving a parabolic equation with fractional diffusion and Caputo fractional time derivative of orders $s \in (0,1)$ and $\gamma \in (0,1]$, respectively. The spatial fractional diffusion is realized as the Dirichlet-to-Neumann map for a nonuniformly elliptic operator. Thus, we consider an equivalent formulation with a quasi-stationary elliptic problem with a dynamic boundary condition as state equation. The rapid decay of the solution to this problem suggests a truncation that is suitable for numerical approximation. We consider a fully discrete scheme: piecewise constant functions for the control and, for the state, first-degree tensor product finite elements in space and a finite difference discretization in time. We show convergence of this scheme and, under additional data regularity, derive a priori error estimates for the case $s \in (0,1)$ and $\gamma = 1$.
Identification of the zebrafish maternal and paternal transcriptomes

Transcription is an essential component of basic cellular and developmental processes. However, early embryonic development occurs in the absence of transcription and instead relies upon maternal mRNAs and proteins deposited in the egg during oocyte maturation. Although the early zebrafish embryo is competent to transcribe exogenous DNA, factors present in the embryo maintain genomic DNA in a state that is incompatible with transcription. The cell cycles of the early embryo titrate out these factors, leading to zygotic transcription initiation, presumably in response to a change in genomic DNA chromatin structure to a state that supports transcription. To understand the molecular mechanisms controlling this maternal to zygotic transition, it is important to distinguish between the maternal and zygotic transcriptomes during this period. Here we use exome sequencing and RNA-seq to achieve such discrimination and in doing so have identified the first zygotic genes to be expressed in the embryo. Our work revealed different profiles of maternal mRNA post-transcriptional regulation prior to zygotic transcription initiation. Finally, we demonstrate that maternal mRNAs are required for different modes of zygotic transcription initiation, which is not simply dependent on the titration of factors that maintain genomic DNA in a transcriptionally incompetent state.
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BACKGROUND & AIMS Data on the association between erosive esophagitis and obesity are inconsistent because of variations in study populations and methods used to determine obesity. METHODS Participants in a prospective health-screening cohort underwent esophagogastroduodenoscopy and computed tomography. The association between erosive esophagitis and obesity (measured by body mass index [BMI], waist circumference, and abdominal visceral adipose tissue volume) was estimated with odds ratios (ORs) and 95% confidence intervals (CIs), adjusting for confounding factors. We also analyzed the association between obesity and erosive esophagitis by sex. RESULTS The prevalence of erosive esophagitis was 9.3% (495/5329). The OR for erosive esophagitis correlated with obesity measured by BMI, waist circumference, and abdominal visceral adipose tissue volume (P < .001 for each factor). The multivariate OR for erosive esophagitis was 1.97 (95% CI: 1.34-2.90) for a visceral adipose tissue volume of 500-999 cm(3), 2.27 (95% CI: 1.51-3.39) for 1000-1499 cm(3), and 2.94 (95% CI: 1.87-4.62) for ≥1500 cm(3), compared with participants who had visceral adipose tissue volumes less than 500 cm(3). When measures of obesity were analyzed simultaneously, abdominal visceral adipose tissue volume, but not BMI or waist circumference, was associated with erosive esophagitis. The 3 measures of obesity were significantly associated with erosive esophagitis in males, but only visceral adipose tissue volume was associated with erosive esophagitis in females (P = .002). CONCLUSIONS In contrast to BMI or waist circumference, abdominal visceral adipose tissue volume is associated with an increased risk of erosive esophagitis in males and females.
The effects of acute cocaine administration in paradoxical sleep‐deprived rats

Recent studies demonstrate the action of cocaine on reward pathways, which are activated by pleasant stimuli. Cocaine's mechanism of action involves the blockade of dopamine and norepinephrine reuptake by the presynaptic terminal. Paradoxical sleep (PS) deprivation is known to induce several behavioural alterations most of which suggest the occurrence of supersensitivity of D 2 and a subsensitivity of b 1 and b 2 receptors.The present study sought to examine the effects of PS deprivation on the actions of cocaine on the erection and ejaculation behaviours in rats. Four different doses of cocaine (3.5, 7.0, 15.0 and 30.0 mg/kg) were acutely administered to Wistar male rats, at the end of a 4‐day period of PS deprivation or at the equivalent time‐point to control animals. Moreover, 15 mg/kg of cocaine were administered in animals submitted to immobilization, footshock and forced swimming. The data were analysed by the Chi‐square test, and revealed that only PS‐deprived animals exhibited penile erections and ejaculation behaviours, which were absent in control animals. PS deprivation increases the sexual behaviour of male rats, probably due to its action on dopaminergic systems. However, further studies need to be carried out in order to clarify the mechanisms involved between PS deprivation and cocaine.
Unclassified variants identified in BRCA1 exon 11: Consequences on splicing

Numerous mutations identified in breast/ovarian cancer families occur in splice sites of the BRCA1 gene. Splicing can also be disrupted by mutations occurring in exonic splicing enhancer (ESE) sequences. It is important to identify those mutations among the large number of nontruncating sequence variants that are identified during molecular diagnosis, as this could help to classify some of them as cancer predisposing. Several software programs have been designed to identify ESEs and can therefore be used to predict the outcome of genetic variation. However, it is not known whether these predictions are relevant in the case of BRCA1 exon 11 (3.4 kb). In this study, we assessed the consequences on splicing of 108 exon 11 variants identified in French breast/ovarian cancer families, most of them predicted to alter putative ESEs, and of nine variants located in the exon 11 alternative donor splice site. We employed a BRCA1 minigene consisting of exon 10 to 12, into which we introduced separately each of the variants to be tested. RNA was analyzed by RT‐PCR after transient transfection of the resulting minigenes. None of the tested variants was found to dramatically alter splicing through disruption of an ESE. However, we identified several variants in the alternative donor splice site that are likely to be of biological significance as they appear to favor the expression of BRCA1‐Δ11b over that of the full‐length transcript. The results of this study will be of value to classify BRCA1 exon 11 variants of unknown significance. This article contains Supplementary Material available at http://www.interscience. wiley.com/jpages/1045‐2257/suppmat. © 2008 Wiley‐Liss, Inc.
Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

ABSTRACT Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)—CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)—was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.
Sexual Health Communication Within Religious African-American Families

While research suggests youth prefer parents and family members to serve as the primary sources of sexual health information, fear and discomfort around discussing sex with their parents may leave youth misinformed and underinformed. This study explored sexual heath communication within religious African-American families. Thirty adolescents participated in four focus groups, and 19 adults and 30 adolescents participated in six focus groups, at two predominantly African-American Christian churches in Flint, MI. All data were analyzed inductively using a constant comparison approach. Nearly all participants reported attending church weekly. Three themes emerged and are described: initiating sex talks, using mistakes as teaching tools, and clarifying prevention messages. Participants highlighted the need for religious parents to offer both religious and practical guidance to adolescents about sexual health. Findings from this study may be used to inform future sexual health promotion interventions for religious African-American families.
Effect of Waste Expanded Polypropylene-Based Aggregate on Mechanical and Thermal Properties of Lightweight Concrete

Resource efficiency and building energy consumption is in recent years an open question for construction industry. Recycled plastic aggregate can be used as an alternative aggregate to produce lightweight concrete with low environmental impact of both concrete and waste plastic and moreover, the obtained lightweight concrete is characterized by improved thermal insulation properties. In the present study, waste expanded polypropylene (EPP) aggregate is used for partial replacement of natural aggregate to produce lightweight cement-based composites containing synthetic coagulated amorphous SiO2 as supplementary cementitious material. For the applied EPP, basic physical properties were measured and specific attention was paid to thermal transport and storage properties that were studied in dependence on compacting time. The effect of EPP content on the mechanical characteristics and on the thermal properties of developed material was investigated for 28 and 90 days water cured samples. Composite with incorporated EPP aggregates exhibits enhanced thermal insulation properties with sufficient mechanical resistance and can be considered as promising material for building subsoil or floor structures.
Screening key genes and miRNAs in early-stage colon adenocarcinoma by RNA-sequencing

Colon adenocarcinoma is the third leading cause of cancer-related deaths across the world, developing novel and non-invasive diagnostic and prognostic biomarkers for the early-stage colon adenocarcinoma at molecular level is essential. In our study, RNA-sequencing was performed to identify the differentially expressed genes and miRNAs (DEmiRNAs) in early-stage colon adenocarcinoma compared to tissues of precancerous lesions, colonic intraepithelial neoplasia. The DEmiRNA-target interaction network was constructed and functional annotation of targets of DEmiRNAs was performed. The Cancer Genome Atlas was used to verify the expression of selected differentially expressed genes. The receiver operating characteristic analyses of selected differentially expressed genes was performed. In total, 865 differentially expressed genes, 26 DEmiRNAs, and 329 DEmiRNA-target pairs were obtained. Based on the early-stage colon adenocarcinoma network, miR-548c-5p, miR-548i, and miR-548am-5p were the top three DEmiRNAs that covered most differentially expressed genes. NTRK2, DTNA, and BTG2 were the top three differentially expressed genes regulated by most DEmiRNAs. Cancer and colorectal cancer pathways were two significantly enriched pathways in early-stage colon adenocarcinoma. The common differentially expressed genes in both the pathways were AXIN2, Smad2, Smad4, PIK3R1, and BCL2. The expression levels of eight differentially expressed genes (NTRK2, DTNA, BTG2, COL11A1, Smad2, Smad4, PIK3R1, and BCL2) in The Cancer Genome Atlas database were compatible with our RNA-sequencing. All these eight differentially expressed genes and AXIN2 had the potential diagnosis value for Colon adenocarcinoma. In conclusion, a total of ten differentially expressed genes (NTRK2, DTNA, BTG2, COLCA1, COL11A1, AXIN2, Smad2, Smad4, PIK3R1, and BCL2) and four DEmiRNAs (miR-548c-5p, miR-548i, mir-424-5p, and miR-548am-5p) may be involved in the pathogenesis of early-stage colon adenocarcinoma which may make a contribution for developing new diagnostic and therapeutic strategies for early-stage colon adenocarcinoma.
Angiotensin-converting enzyme activity and cognitive impairment during hypoglycaemia in healthy humans

Introduction: In type 1 diabetes increased risk of severe hypoglycaemia is associated with high angiotensin-converting enzyme (ACE) activity. We tested in healthy humans the hypothesis that this association is explained by the reduced ability of subjects with high ACE activity to maintain normal cognitive function during hypoglycaemia. Methods: Sixteen healthy volunteers selected by either particularly high or low serum ACE activity were subjected to hypoglycaemia (plasma glucose 2.7 mmol/L). Cognitive function was assessed by choice reaction tests. Results: Despite a similar hypoglycaemic stimulus in the two groups, only the group with high ACE activity showed significant deterioration in cognitive performance during hypoglycaemia. In the high ACE group mean reaction time (MRT) in the most complex choice reaction task was prolonged and error rate (ER) was increased in contrast to the low ACE group. The total hypoglycaemic symptom response was greater in the high ACE group than in the low ACE group (p=0.031). There were no differences in responses of counterregulatory hormones or in concentrations of substrates between the groups. Conclusion: Healthy humans with high ACE activity are more susceptible to cognitive dysfunction and report higher symptom scores during mild hypoglycaemia than subjects with low ACE activity.
Channel-Aware Medium Access Control in Multichannel Cognitive Radio Networks

Distributed medium access control (MAC) is important for efficient exploitation of spectrum opportunities in cognitive radio networks. This letter proposes a channel-aware distributed MAC protocol for multichannel cognitive radio networks. The transmitting nodes use channel state information to exploit the available multiuser and multichannel diversity, by contending only under relatively favorable channel conditions. Towards this end, each node utilizes a threshold that is dynamically updated according to certain rules. Simulation results corroborate the throughput gains achieved by the proposed protocol.
Fatigue life prediction for cables in cyclic tension

Cables are used in civil and mining engineering applications, such as in cable stays for suspension bridges, elevators, construction cranes, mining shovels and draglines. Such cables are mainly used for supporting or hoisting and can be considered to be either stationary or running cables. In supporting functions, cables are subjected to cyclic tension, with the primary mode of failure due to fretting fatigue of individual wires that make up the cables as they abrade against each other. Stationary cables subjected to cyclic tension (tension–tension) fatigue are the focus of this work, and although other researchers have investigated the fatigue life of such cables, there remains much of the cyclic tensile behavior that needs further investigation. The stress condition of several cables such as 19-, 91- and 92-wire strands; independent wire rope core; and the 6 × 19 Seale–independent wire rope core wire ropes was investigated using finite element modeling techniques. A stress-based approach was used with the results of finite element modeling to obtain the fatigue life for these cables. In practice, it would be challenging for a finite element analysis to be carried out each time the fatigue life of a cable is needed, so in a preventive maintenance stance, regression coefficients have been proposed for use with a fatigue life prediction model.
Nonlinear channel equalization for QAM signal constellation using artificial neural networks

Application of artificial neural networks (ANN's) to adaptive channel equalization in a digital communication system with 4-QAM signal constellation is reported in this paper. A novel computationally efficient single layer functional link ANN (FLANN) is proposed for this purpose. This network has a simple structure in which the nonlinearity is introduced by functional expansion of the input pattern by trigonometric polynomials. Because of input pattern enhancement, the FLANN is capable of forming arbitrarily nonlinear decision boundaries and can perform complex pattern classification tasks. Considering channel equalization as a nonlinear classification problem, the FLANN has been utilized for nonlinear channel equalization. The performance of the FLANN is compared with two other ANN structures [a multilayer perceptron (MLP) and a polynomial perceptron network (PPN)] along with a conventional linear LMS-based equalizer for different linear and nonlinear channel models. The effect of eigenvalue ratio (EVR) of input correlation matrix on the equalizer performance has been studied. The comparison of computational complexity involved for the three ANN structures is also provided.
Psychoacoustic Analysis of High Frequency Elasto-Acoustic Emissions from Hollow Driveshaft Tubes

Lightly damped non-linear systems such as vehicular drivelines undergo a plethora of Noise, Vibration and Harshness (NVH) problems. The clonk phenomenon is one concern which occurs as the result of impulsive torque input in the form of sudden clutch actuation or throttle tip-in and back-out. The resulting impact of meshing gear pairs propagate structural waves down the driveline. With lightly damped thin-walled tubes having high modal density, elasto-acoustic coupling occurs. High frequency noise emission is of metallic nature and quite disconcerting to vehicle occupants as well as passers-by. It is perceived as structural failure and/or poor-quality build. Therefore, the occurrence of the phenomenon is a concern to vehicle manufacturers and progressively constitutes a warranty concern. This paper investigates the clonk phenomenon through use of a long-wheel base rear drive light truck test rig. The investigation uses psychoacoustic metrics to establish the severity of clonk noise in different maneuvers. This is an attempt to quantify the effect of transient clonk event which is usually ascertained through subjective evaluation ratings in a customer/jury clinic in industry. Alternatively, detailed numerical analysis is carried out with parametric studies to quantify different clonk events, a very time consuming approach which is not usually correlated with occupants’ perception of the event. Therefore, the experimental NVH monitoring-psycho-acoustic approach is new for the case of clonk and not hitherto reported in literature. The study corroborates the results and conclusions of previous work, pointing to the loudness and sharpness of high frequency short-lived “metallic” response, which is attuned to human aural perception. The psychoacoustic analysis has shown this to be as the result of short duration hard impact (accelerative period). This hard impact duration accounts for the bulk loudness and sharpness of the overall event. Therefore, effective palliation should focus on the attenuation of particular frequency bands, which carry the main contribution to loudness and sharpness.