Miracle-dz/UniFAR-FTUs huggingface dataset:
TITLE Integrated molecular phenotyping identifies genes and pathways disrupted in osteoarthritis

CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh, EH16 4UX, UK 15 MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK 20
Publication Bias in Meta-Analysis

Publication bias is the term for what occurs whenever the research that appears in the published literature is systematically unrepresentative of the population of completed studies. Simply put, when the research that is readily available differs in its results from the results of all the research that has been done in an area, readers and reviewers of that research are in danger of drawing the wrong conclusion about what that body of research shows. In some cases this can have dramatic consequences, as when an ineffective or dangerous treatment is falsely viewed as safe and effective. This can be illustrated by two events that received much media attention as this book was going to press in late 2004. These are the debate surrounding Merck’s recall of Vioxx, a popular arthritis drug (Merck maintained that it recalled Vioxx as soon as the data indicated the high prevalence of cardiovascular events among those who took Vioxx for more than 18 months, while media reports said that Merck hid adverse event evidence for years), and the use of selective serotonin reuptake inhibitor (SSRI) anti-depressants among adolescents (Elliott Spitzer, attorney general of New York State, filed a 2004 lawsuit against GlaxoSmithKline,
Extracellular Matrix Proteins Expression Profiling in Chemoresistant Variants of the A2780 Ovarian Cancer Cell Line

Ovarian cancer is the leading cause of death among gynaecological malignancies. Extracellular matrix (ECM) can affect drug resistance by preventing the penetration of the drug into cancer cells and increased resistance to apoptosis. This study demonstrates alterations in the expression levels of ECM components and related genes in cisplatin-, doxorubicin-, topotecan-, and paclitaxel-resistant variants of the A2780 ovarian cancer cell line. Affymetrix Gene Chip Human Genome Array Strips were used for hybridisations. The genes that had altered expression levels in drug-resistant sublines were selected and filtered by scatter plots. The genes that were up- or downregulated more than fivefold were selected and listed. Among the investigated genes, 28 genes were upregulated, 10 genes were downregulated, and two genes were down- or upregulated depending on the cell line. Between upregulated genes 12 were upregulated very significantly—over 20-fold. These genes included COL1A2, COL12A1, COL21A1, LOX, TGFBI, LAMB1, EFEMP1, GPC3, SDC2, MGP, MMP3, and TIMP3. Four genes were very significantly downregulated: COL11A1, LAMA2, GPC6, and LUM. The expression profiles of investigated genes provide a preliminary insight into the relationship between drug resistance and the expression of ECM components. Identifying correlations between investigated genes and drug resistance will require further analysis.
Enforcing trace properties by program transformation

We propose an automatic method to enforce trace properties on programs. The programmer specifies the property separately from the program; a program transformer takes the program and the property and automatically produces another “equivalent” pogram satisfying the property. This separation of concerns makes the program easier to develop and maintain. Our approach is both static and dynamic. It integrates static analyses in order to avoid useless transformations. On the other hand, it never rejects programs but adds dynamic checks when necessary. An important challenge is to make this dynamic enforcement as inexpensive as possible. The most obvious application domain is the enforcement of security policies. In particular, a potential use of the method is the securization of mobile code upon receipt.
Framing Climate Change: Exploring the Role of Emotion in Generating Advocacy Behavior

Substantial research examines the cognitive factors underlying proenviron-mental message effectiveness. In contrast, this study investigates the role of emotion, fear and hope specifically, in the gain/loss framing of environmental policy initiatives. The 2 (threat vs. no threat) × 2 (gain- vs. loss-framed efficacy) experiment revealed emotion, especially hope, as a key mediator between gain-framed messages and desired climate change policy attitudes and advocacy. Results further supported the value of sequencing emotional experiences to enhance persuasive effect. This research offers an inaugural test of emotional flow theorizing and highlights the need for additional research on emotional processes in environmental communication.
A Comparison of Sexual Aggression Risk Factors Between the United States and the Philippines

ABSTRACT Sexual violence against women is a global problem, prompting the need to investigate the risk factors among males in non-Western, non-industrialized countries. Using the expanded Confluence Model, this study examined and compared risk factors of sexual aggression between male college students in the Philippines and the United States. Using path analysis and multiple group analysis, results indicated that the expanded Confluence Model was generally invariant between countries. Direct paths from hostile attitudes toward women and impersonal sex to sexual aggression were non-significant, but indirect effects from hostile attitudes toward women, alcohol consumption, and impersonal sex to sexual aggression via the frequency of misperceiving a woman’s sexual intent were observed. Additional risk analysis indicated that the number of elevated risk factors were associated with higher self-reports of sexual aggression.
Utilization of cassava brown streak diseased roots as replacement for maize on growth performance of broiler chickens

Cassava roots afflicted with Cassava Brown Streak Disease (CBSD) were used in a study involving 600 Hubbard broiler chicks to evaluate their utility as a substitute for maize meal in broiler rations. The chicks were allocated to three dietary treatments with varying damages and cassava inclusion levels (CL1 – CL3) each with 60 birds in a complete randomized design. Three diets were formulated to keep ME content at between 12-12.55MJ/kgDM and the CP around 18-20%. The CBSD cassava replaced maize at 25%, 50% and 75%. Average voluntary feed intake per bird for CL1 at 25,50 and 75% inclusions were respectively 130.31±8.46, 110.86±3.32 and 108.76±5.01; the corresponding intakes for CL2 were 104.33±2.20, 105.10±7.02 and 105.31±4.42 ; and for CL3 were 90.06±14.71, 90.06±14.71 and 103.10±4.90. At 50% and 75 % levels of inclusions intakes were significantly lower (P<0.05) than that of the Control diet (128.23±6.53) regardless of class of root damage. The Average Daily Gain (ADG) per bird for CL1 at 25, 50 and 75% inclusion were respectively 30.48± 1.84, 27.57±0.62 and 27.35±0.94; for CL2 were 25.75±1.57, 26.15±2.58 and 24.98±0.84; and for CL3 were 22.17±2.11, 23.11±2.87 and 24.29±1.84. While for control diet was 30.62±1.59. It is concluded that CBSD afflicted cassava can replace Maize meal for up to 25% inclusion level. Keywords: Cassava, intake, diets, broiler, carcass
DeepDriving: Learning Affordance for Direct Perception in Autonomous Driving

Today, there are two major paradigms for vision-based autonomous driving systems: mediated perception approaches that parse an entire scene to make a driving decision, and behavior reflex approaches that directly map an input image to a driving action by a regressor. In this paper, we propose a third paradigm: a direct perception approach to estimate the affordance for driving. We propose to map an input image to a small number of key perception indicators that directly relate to the affordance of a road/traffic state for driving. Our representation provides a set of compact yet complete descriptions of the scene to enable a simple controller to drive autonomously. Falling in between the two extremes of mediated perception and behavior reflex, we argue that our direct perception representation provides the right level of abstraction. To demonstrate this, we train a deep Convolutional Neural Network using recording from 12 hours of human driving in a video game and show that our model can work well to drive a car in a very diverse set of virtual environments. We also train a model for car distance estimation on the KITTI dataset. Results show that our direct perception approach can generalize well to real driving images. Source code and data are available on our project website.
A tutorial on decomposition methods for network utility maximization

A systematic understanding of the decomposability structures in network utility maximization is key to both resource allocation and functionality allocation. It helps us obtain the most appropriate distributed algorithm for a given network resource allocation problem, and quantifies the comparison across architectural alternatives of modularized network design. Decomposition theory naturally provides the mathematical language to build an analytic foundation for the design of modularized and distributed control of networks. In this tutorial paper, we first review the basics of convexity, Lagrange duality, distributed subgradient method, Jacobi and Gauss-Seidel iterations, and implication of different time scales of variable updates. Then, we introduce primal, dual, indirect, partial, and hierarchical decompositions, focusing on network utility maximization problem formulations and the meanings of primal and dual decompositions in terms of network architectures. Finally, we present recent examples on: systematic search for alternative decompositions; decoupling techniques for coupled objective functions; and decoupling techniques for coupled constraint sets that are not readily decomposable
The yeast dynamin-related GTPase Vps1p functions in the organization of the actin cytoskeleton via interaction with Sla1p

Recent studies have suggested that the function of the large GTPase dynamin in endocytosis in mammalian cells may comprise a modulation of actin cytoskeleton. The role of dynamin in actin cytoskeleton organization in the yeast Saccharomyces cerevisiae has remained undefined. In this report, we found that one of the yeast dynamin-related proteins, Vps1p, is required for normal actin cytoskeleton organization. At both permissive and non-permissive temperatures, the vps1 mutants exhibited various degrees of phenotypes commonly associated with actin cytoskeleton defects: depolarized and aggregated actin structures, hypersensitivity to the actin cytoskeleton toxin latrunculin-A, randomized bud site selection and chitin deposition, and impaired efficiency in the internalization of membrane receptors. Over-expression of the GTPase mutants of vps1 also led to actin abnormalities. Consistent with these actin-related defects, Vps1p was found to interact physically, and partially co-localize, with the actin-regulatory protein Sla1p. The normal cellular localization of Sla1p required Vps1p and could be altered by over-expression of a region of Vps1p that was involved in the interaction with Sla1p. The same region also promoted mis-sorting of the vacuolar protein carboxypeptidase Y upon over-expression. These findings suggest that the functions of the dynamin-related protein Vps1p in actin cytoskeleton dynamics and vacuolar protein sorting are probably related to each other.
The Risk Premium for Equity: Implications for Resource Allocation, Welfare and Policy

Analysis of the equity premium puzzle has focused on private sector capital markets. The object of this paper is to consider the welfare and policy implications of each of the broad classes of explanations of the equity premium puzzle. As would be expected, the greater the deviation from the first-best outcome implied by a given explanation of the equity premium puzzle, the more interventionist are the implied policy conclusions. Nevertheless, even explanations of the equity premium puzzle consistent with a general consumption-based asset pricing model have important welfare and policy implications.
Evaluation of the bond strength of root-end placed mineral trioxide aggregate and Biodentine in the absence/presence of blood contamination

Objective: Mineral trioxide aggregate (MTA) has been accepted as an appropriate root-end filling material in endodontic microsurgery because of setting ability in the wet environment. The aim of this study was to assess the bond strength of root-end placed MTA and Biodentine (Septodont, Saint Maur des Fossés, France) in the absence/presence of blood contamination. Materials and Methods: Forty-eight single-rooted maxillary incisors were used. subsequent to root-end resection and apical preparation using ultrasonic retro-tips, the specimens were randomly separated into two groups according to the root-end filling materials: MTA (Cerkamed Medical Company, Stalowa, Poland) or Biodentine. The specimens were then separated into two subgroups according to storage condition (absence/presence of blood) (n = 12). After obtaining 2.0 ± 0.1 mm slices, push-out tests were performed. Each slice was examined under a stereomicroscope to evaluate the failure mode. The data were analyzed using two-way analysis of variance and Tukey's post hoc test for multiple comparisons. The failure modes were analyzed using the Chi-square test (P = 0.05). Results: The bond strength was significantly affected by the presence of blood contamination and root-end filling material type (P < 0.001). Biodentine had better bond strength than MTA (P < 0.001). The most common failure type was adhesive failure. According to the Chi-square test, there were no statistically significant differences among the groups (P = 0.394). Conclusions: Biodentine had better bond strength values compared to MTA, and the bond strength of both MTA and Biodentine as root-end filling materials was negatively affected by the presence of blood.
The use of naltrexone in the treatment of alcohol dependence : pharmacological aspects

Clinical studies performed over the past decades have unambiguously indicated that combined therapy, involving pharmacoand psychotherapy, is an optimal approach to alcohol dependence. Both pharmacoand psychotherapy should be personalised with a careful balance between the patient’s needs and his/her clinical characteristics. The aim of the present article is to review the basic pharmacological features of naltrexone and its use in the treatment of alcohol dependence.
The resonance of moderate feminism and the gendered relations of austerity

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The sorting sequence of the peroxisomal integral membrane protein PMP47 is contained within a short hydrophilic loop

No targeting sequence for peroxisomal integral membrane proteins has yet been identified. We have previously shown that a region of 67 amino acids is necessary to target Pmp47, a protein that spans the membrane six times, to peroxisomes. This region comprises two membrane spans and the intervening loop. We now demonstrate that the 20 amino acid loop, which is predicted to face the matrix, is both necessary and sufficient for peroxisomal targeting. Sufficiency was demonstrated with both chloramphenicol acetyltransferase and green fluorescent protein as carriers. There is a cluster of basic amino acids in the middle of the loop that we predict protrudes from the membrane surface into the matrix by a flanking stem structure. We show that the targeting signal is composed of this basic cluster and a block of amino acids immediately down-stream from it.
Mitral Isthmus Ablation: Is the Conduction Block Completed? The Importance of the Marshall Bundle Epicardial Connections.

A 66-year-old man underwent electrophysiological study and catheter ablation for persistent atrial fibrillation. At the beginning of the procedure, sinus rhythm was restored by internal cardioversion. Circumferential pulmonary vein isolation was performed, and the electric isolation of all 4 pulmonary veins was confirmed. Subsequently, linear ablation of a left atrial roof and the mitral isthmus (MI) was performed. The MI ablation was applied from the 4 o’clock direction of the mitral annulus (MA) to the left-side pulmonary vein bottoms, and further radiofrequency applications were delivered within the coronary sinus (CS) opposite of the endocardial MI line. We confirmed the complete conduction block of the roof line, and the activation sequence of the CS during the left atrial appendage (LAA) pacing was changed from distal to proximal (Figure 1A) to proximal to distal (Figure 1B) while the MI ablation was being performed. Furthermore, the conduction time from the distal CS electrodes (CS 1–2) to the LAA during CS 1 to 2 pacing was longer than the conduction time from the proximal CS electrodes (CS 7–8) to the LAA during CS 7 to 8 pacing after the MI ablation (Figure 1C and 1D). Was the conduction block of the MI completed? Figure 1. Intracardiac electrograms before and after the mitral isthmus (MI) ablation. A , Before the MI ablation, the activation sequence of the coronary sinus (CS) was distal to proximal. B , After the MI ablation, the activation sequence of the CS was changed to proximal to distal. C , After the MI ablation, the conduction time from CS 1 to 2 to the left atrial appendage (LAA) was 106 ms during CS 1 to 2 pacing. D , After the MI ablation, the conduction time from CS 7 to 8 to the LAA was 87 ms during CS 7 to 8 pacing. …
Examining the influence of athletes’ punishment experiences on decisions to cease participation in competitive hockey

This study examined athletes’ experiences of punishment in competitive hockey and the potential influence of these experiences on their decisions to cease participation in the sport. Semi-structured interviews were conducted with 10 former female and male competitive hockey athletes, 18–19 years of age. Data were analysed using inductive thematic analysis. Participant accounts revealed that yelling, benching, and physical conditioning exercises were forms of punishment experienced regularly throughout their hockey involvement. These punishment experiences reportedly had negative effects on the participants’ perceived athletic worth, enjoyment and fun in hockey, and sport relationships, and enhanced their interests in other activities. Findings are interpreted to suggest that punishment experiences contributed to athletes’ decisions to cease participation in competitive hockey. Recommendations for future research and practice are suggested.
A State of the Art on Supply Planning and Inventory Control under Lead Time Uncertainty

In literature, most papers examine several stochastic demand processes where order lead times are constant. In reality, manufacturing firms use inventory management software, especially MRP, which ignored lead time uncertainty. It is true that in certain special cases, lead time uncertainty has essentially no effect and can be ignored. Nevertheless more often, lead time fluctuations strongly degrade tools performance and cause high production costs, just as demand uncertainty does. Seemingly, uncertainty has been neglected for a long time in favour of studying demand uncertainties. Industry agrees that it is overdue and there is a need to rectify this oversight. Nowadays, this gap in research activity begins to be filled in order to respond to companies having non-deterministic lead-times constraints. This paper reviews some of existing literature of supply planning tools under uncertainty of lead times. The extensive literature review that we compiled consists of citations from 1970 to 2012. A classification scheme for supply planning under uncertainty is defined.
Associations between smoking and depression in adolescence: an integrative review.

BACKGROUND Although research has established the existence of an association between smoking and depression among adolescents, researchers have not reached consensus on the nature of the association. OBJECTIVES The purpose of this paper is to review the literature, to examine the nature of the relationship between smoking and depression in adolescence, and to suggest future research directions. METHOD A literature search was conducted from the following six databases: (a) Ovid MEDLINE, (b) CINAHL, (c) PubMed Unrestricted, (d) PsycINFO, (e) ERIC, and (f) Sociological Abstracts. The combinations of the words, "depression," "smoking," "tobacco," "adolescent," and "teen" were used for keyword searches to find relevant articles. RESULTS In 47 of 57 studies, significant associations between smoking and depression were found. However, these significant relationships may either be spurious or unrelated to depression because a substantial number of studies did not adjust for confounders or did not use validated instruments to measure depression. Additionally, if the relationship is causal, its direction remains controversial. Five relationships have been suggested: (a) Depression causes smoking, (b) smoking causes depression, (c) there is a bidirectional relationship between smoking and depression, (d) smoking and depression occur due to confounders, and (e) subgroups with different relationships between the two conditions exist. CONCLUSIONS It is necessary to further explore the relationship between smoking and depression. Future research should consider the need for: (a) longitudinal research designs, (b) more accurate measurement of depression, and (c) the control of confounders between smoking and depression.
L1-Penalized Quantile Regression in High Dimensional Sparse Models

We consider median regression and, more generally, quantile regression in high-dimensional sparse models. In these models the overall number of regressors p is very large, possibly larger than the sample size n, but only s of these regressors have non-zero impact on the conditional quantile of the response variable, where s grows slower than n. Since in this case the ordinary quantile regression is not consistent, we consider quantile regression penalized by the L1-norm of coefficients (L1-QR). First, we show that L1-QR is consistent at the rate of the square root of (s/n) log p, which is close to the oracle rate of the square root of (s/n), achievable when the minimal true model is known. The overall number of regressors p affects the rate only through the log p factor, thus allowing nearly exponential growth in the number of zero-impact regressors. The rate result holds under relatively weak conditions, requiring that s/n converges to zero at a super-logarithmic speed and that regularization parameter satisfies certain theoretical constraints. Second, we propose a pivotal, data-driven choice of the regularization parameter and show that it satisfies these theoretical constraints. Third, we show that L1-QR correctly selects the true minimal model as a valid submodel, when the non-zero coefficients of the true model are well separated from zero. We also show that the number of non-zero coefficients in L1-QR is of same stochastic order as s, the number of non-zero coefficients in the minimal true model. Fourth, we analyze the rate of convergence of a two-step estimator that applies ordinary quantile regression to the selected model. Fifth, we evaluate the performance of L1-QR in a Monte-Carlo experiment, and provide an application to the analysis of the international economic growth.