Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray Meta-Analysis Identifies Acute Lung Injury Biomarkers in Donor Lungs That Predict Development of Primary Graft Failure in Recipients

Objectives To perform a meta-analysis of gene expression microarray data from animal studies of lung injury, and to identify an injury-specific gene expression signature capable of predicting the development of lung injury in humans. Methods We performed a microarray meta-analysis using 77 microarray chips across six platforms, two species and different animal lung injury models exposed to lung injury with or/and without mechanical ventilation. Individual gene chips were classified and grouped based on the strategy used to induce lung injury. Effect size (change in gene expression) was calculated between non-injurious and injurious conditions comparing two main strategies to pool chips: (1) one-hit and (2) two-hit lung injury models. A random effects model was used to integrate individual effect sizes calculated from each experiment. Classification models were built using the gene expression signatures generated by the meta-analysis to predict the development of lung injury in human lung transplant recipients. Results Two injury-specific lists of differentially expressed genes generated from our meta-analysis of lung injury models were validated using external data sets and prospective data from animal models of ventilator-induced lung injury (VILI). Pathway analysis of gene sets revealed that both new and previously implicated VILI-related pathways are enriched with differentially regulated genes. Classification model based on gene expression signatures identified in animal models of lung injury predicted development of primary graft failure (PGF) in lung transplant recipients with larger than 80% accuracy based upon injury profiles from transplant donors. We also found that better classifier performance can be achieved by using meta-analysis to identify differentially-expressed genes than using single study-based differential analysis. Conclusion Taken together, our data suggests that microarray analysis of gene expression data allows for the detection of “injury" gene predictors that can classify lung injury samples and identify patients at risk for clinically relevant lung injury complications.
Supervised learning of a regression model based on latent process. Application to the estimation of fuel cell life time

This paper describes a pattern recognition approach aiming to estimate fuel cell duration time from electrochemical impedance spectroscopy measurements. It consists in first extracting features from both real and imaginary parts of the impedance spectrum. A parametric model is considered in the case of the real part, whereas regression model with latent variables is used in the latter case. Then, a linear regression model using different subsets of extracted features is used fo r the estimation of fuel cell time duration. The performances of the proposed approach are evaluated on experimental data set to show its feasibility. This could lead to interesting perspectives for predictive maintenance policy of fuel cell.
Preliminary results of autotuning GEMM kernels for the NVIDIA Kepler architecture-GeForce GTX 680

Preliminary Results of Autotuning GEMM Kernels for the NVIDIA Kepler Architecture – GeForce GTX 680 – LAPACK Working Note 267 Jakub Kurzak 1 Piotr Luszczek 1 Stanimire Tomov 1 Jack Dongarra 1,2,3 1 Electrical Engineering and Computer Science, University of Tennessee Science and Mathematics Division, Oak Ridge National Laboratory 3 School of Mathematics & School of Computer Science, University of Manchester 2 Computer Abstract Kepler is the newest GPU architecture from NVIDIA, and the GTX 680 is the first commercially available graphics card based on that architecture. Matrix multi- plication is a canonical computational kernel, and often the main target of initial optimization efforts for a new chip. This article presents preliminary results of au- tomatically tuning matrix multiplication kernels for the Kepler architecture using the GTX 680 card. Introduction Accelerators are gradually making their way into the world of High Performance Computing (HPC). Before graphics cards entered the arena, the IBM Cell processor made a brief appearance in HPC (from 2006 to 2009), culminating in the deploy- ment of the Roadrunner supercomputer at the Los Alamos National Laboratory, which secured the first place on the TOP500 list in June 2008, as the first machine to cross the performance of one PetaFLOPS. However, development of the Cell ar- chitecture was canceled by IBM in November 2009 and, in the meantime, graphics cards have been gradually turning towards general programmability and steadily gaining ground in HPC. The introduction of the Compute Unified Device Architec- ture (CUDA) by NVIDIA in November 2006 was a significant milestone towards adoption of GPUs for general purpose computing. Another one was the introduc- tion of the GF100 (Fermi) architecture in April 2010, with an array of essential numerical computing features. These developments culminated in the deployment of the Tianhe-1A supercomputer at the National Supercomputer Center in Tianjin,
Numerical Simulations of Mountain Waves in the Middle Atmosphere Over The Southern Andes

We use a two-dimensional nonlinear compressible mesoscale model to study mountain waves in the middle atmosphere over the southern Andes. Using realistic temperatures, winds and topography, the model generates large-amplitude long-wavelength breaking mountain waves in the middle atmosphere that compare favorably with satellite measurements. Modeled waves have preferred horizontal wavelengths. Spectral analysis reveals correspondences between these wavelengths S and peaks in the spectrum of Andean topographic elevations. The shorter waves reach the stratosphere well before the longer ones, consistent with group velocity arguments, with longer wavelengths ultimately dominating. At later times we find evidence of downward propagating secondary waves produced by upper-level breaking of the primary waves.
The efficacy of a scaffold-free Bio 3D conduit developed from human fibroblasts on peripheral nerve regeneration in a rat sciatic nerve model

Background Although autologous nerve grafting is the gold standard treatment of peripheral nerve injuries, several alternative methods have been developed, including nerve conduits that use supportive cells. However, the seeding efficacy and viability of supportive cells injected in nerve grafts remain unclear. Here, we focused on a novel completely biological, tissue-engineered, scaffold-free conduit. Methods We developed six scaffold-free conduits from human normal dermal fibroblasts using a Bio 3D Printer. Twelve adult male rats with immune deficiency underwent mid-thigh-level transection of the right sciatic nerve. The resulting 5-mm nerve gap was bridged using 8-mm Bio 3D conduits (Bio 3D group, n = 6) and silicone tube (silicone group, n = 6). Several assessments were conducted to examine nerve regeneration eight weeks post-surgery. Results Kinematic analysis revealed that the toe angle to the metatarsal bone at the final segment of the swing phase was significantly higher in the Bio 3D group than the silicone group (-35.78 ± 10.68 versus -62.48 ± 6.15, respectively; p < 0.01). Electrophysiological studies revealed significantly higher compound muscle action potential in the Bio 3D group than the silicone group (53.60 ± 26.36% versus 2.93 ± 1.84%; p < 0.01). Histological and morphological studies revealed neural cell expression in all regions of the regenerated nerves and the presence of many well-myelinated axons in the Bio 3D group. The wet muscle weight of the tibialis anterior muscle was significantly higher in the Bio 3D group than the silicone group (0.544 ± 0.063 versus 0.396 ± 0.031, respectively; p < 0.01). Conclusions We confirmed that scaffold-free Bio 3D conduits composed entirely of fibroblast cells promote nerve regeneration in a rat sciatic nerve model.
Occupation or Home: Comparison Housewives and Working Women in the Variables of Stress, Depression and Perception of Quantitative, Mental and Emotional Home Demands

In recent years, the employment rate of women, particularly in the service sector has been increasing and at the same time, researchers interested on the psycho-social consequences of women’s employment especially on health. This study compared housewives and working women in terms of stress, depression and perception quantitative, mental and emotional home demands. For this purpose, a sample consists of 94 working women and 94 housewives among Isfahan women selected via convenience sampling and completed warttig et al. perceived stress questionnaire, Beck Depression II and peters et al. home demands questionnaire. Results revealed that working women perceived more depression and quantitative and mental home demands, but no differences between working women and housewives in terms of stress and emotional home demands. According to effort-recovery model, it seems that the pressures of work and family role, especially time pressure means that despite the positive role of work in working women, they were psychologically vulnerable because of the multiplicity of tasks. The results highlight the importance of culture in terms of the role of men in the house, especially in the case of families who identify working women.
HLA-B∗44 Is Associated with Dengue Severity Caused by DENV-3 in a Brazilian Population

Human leukocyte antigen (HLA) alleles have been correlated with susceptibility or resistance to severe dengue; however, few immunogenetic studies have been performed in Latin American (LA) populations. We have conducted immunogenetic studies of HLA class I and II alleles in a cohort of 187 patients with DENV-3 infection and confirmed clinical diagnosis of either severe dengue, known as dengue hemorrhagic fever (DHF), or the less severe form, dengue fever (DF), in Recife, Pernambuco, Brazil. An association analysis was performed using Fisher's association test, with odds ratios (ORs) calculated using conditional maximum likelihood estimates. HLA-B∗44 (P = 0.047, OR = 2.025, 95% CI = 0.97–4.24) was found to be associated with increased susceptibility to DHF in response to DENV-3 infection. In addition, HLA-B∗07 (P = 0.048, OR = 0.501, one-sided 95% CI = 0–0.99) and HLA-DR∗13 (P = 0.028, OR = 0.511, one-sided 95% CI = 0–0.91) were found to be associated with resistance to secondary dengue infection by DENV-3. These results suggest that HLA-B∗44 supertype alleles and their respective T-cell responses might be involved in susceptibility to severe dengue infections, whereas the HLA-B∗07 supertype alleles and DR∗13 might be involved in cross-dengue serotype immunity.
Muscle dysmorphia: Could it be classified as an addiction to body image?

Background Muscle dysmorphia (MD) describes a condition characterised by a misconstrued body image in which individuals who interpret their body size as both small or weak even though they may look normal or highly muscular. MD has been conceptualized as a type of body dysmorphic disorder, an eating disorder, and obsessive–compulsive disorder symptomatology. Method and aim Through a review of the most salient literature on MD, this paper proposes an alternative classification of MD – the ‘Addiction to Body Image’ (ABI) model – using Griffiths (2005) addiction components model as the framework in which to define MD as an addiction. Results It is argued the addictive activity in MD is the maintaining of body image via a number of different activities such as bodybuilding, exercise, eating certain foods, taking specific drugs (e.g., anabolic steroids), shopping for certain foods, food supplements, and the use or purchase of physical exercise accessories). In the ABI model, the perception of the positive effects on the self-body image is accounted for as a critical aspect of the MD condition (rather than addiction to exercise or certain types of eating disorder). Conclusions Based on empirical evidence to date, it is proposed that MD could be re-classified as an addiction due to the individual continuing to engage in maintenance behaviours that may cause long-term harm.
Power Efficient Systems in Wireless Communication

It is commonly known that mobile communication networks will have an increasing ecological and economic impact worldwide, and recently, initiatives to reduce the energy consumption of network operation and reduce the carbon footprint of these networks have gained momentum. Thus, climate and cost issues now shift the research focus of wireless communications to energy consumption and energy efficiency. Two approaches can be followed: Incremental improvements of existing systems or a clean slate re-design with a fundamental change of paradigms. We describe two such initiatives and discuss their differences. The paper aiming for a reduction of the overall energy consumption of 4G mobile broadband networks by 50%, regarding network aspects and individual radio components from a holistic point of view. The literature often states that small cells will reduce transmit power. We have shown that with realistic macro base stations (BS) power models smaller cell sizes increase the total power consumption. Heterogeneous deployments with macro cells and small cells are beneficial for indoor or can be alternatives to a densified macro only deployment. Relaying is a well-known technique to improve data transmission in cell-edge or to provide coverage in new areas. Installation of new relays nodes instead densifying the macro only network can be 30% more energy efficient. The main goal of our apporach is to reduce the power consumption of cellular networks by 50%. These technologies include deployment strategies, network management concepts, radio resource management techniques and some proposals for future architectures that are inherently designed to be energy efficient.
DYNAMICAL TIDES IN ROTATING PLANETS AND STARS

Tidal dissipation may be important for the internal evolution as well as the orbits of short-period massive planets—hot Jupiters. We revisit a mechanism proposed by Ogilvie and Lin for tidal forcing of inertial waves, which are short-wavelength, low-frequency disturbances restored primarily by Coriolis rather than buoyancy forces. This mechanism is of particular interest for hot Jupiters, because it relies upon a rocky core, and because these bodies are otherwise largely convective. Compared to waves excited at the base of the stratified, externally heated atmosphere, waves excited at the core are more likely to deposit heat in the convective region and thereby affect the planetary radius. However, Ogilvie and Lin's results were numerical, and the manner of the wave excitation was not clear. Using WKB methods, we demonstrate the production of short waves by scattering of the equilibrium tide off the core at critical latitudes. The tidal dissipation rate associated with these waves scales as the fifth power of the core radius, and the implied tidal Q is of order ten million for nominal values of the planet's mass, radius, orbital period, and core size. We comment upon an alternative proposal by Wu for exciting inertial waves in an unstratified fluid body by means of compressibility rather than a core. We also find that even a core of rock is unlikely to be rigid. But Ogilvie and Lin's mechanism should still operate if the core is substantially denser than its immediate surroundings.
Annexin A1 and the Resolution of Inflammation: Modulation of Neutrophil Recruitment, Apoptosis, and Clearance

Neutrophils (also named polymorphonuclear leukocytes or PMN) are essential components of the immune system, rapidly recruited to sites of inflammation, providing the first line of defense against invading pathogens. Since neutrophils can also cause tissue damage, their fine-tuned regulation at the inflammatory site is required for proper resolution of inflammation. Annexin A1 (AnxA1), also known as lipocortin-1, is an endogenous glucocorticoid-regulated protein, which is able to counterregulate the inflammatory events restoring homeostasis. AnxA1 and its mimetic peptides inhibit neutrophil tissue accumulation by reducing leukocyte infiltration and activating neutrophil apoptosis. AnxA1 also promotes monocyte recruitment and clearance of apoptotic leukocytes by macrophages. More recently, some evidence has suggested the ability of AnxA1 to induce macrophage reprogramming toward a resolving phenotype, resulting in reduced production of proinflammatory cytokines and increased release of immunosuppressive and proresolving molecules. The combination of these mechanisms results in an effective resolution of inflammation, pointing to AnxA1 as a promising tool for the development of new therapeutic strategies to treat inflammatory diseases.
Design and Validation of a Mental and Social Stress Induction Protocol - Towards Load-invariant Physiology-based Stress Detection

Stress is a major societal issue with negative impacts on health and economy. Physiological computing offers a continuous, direct, and unobtrusive method for stress level assessment and computer-assisted stress management. However, stress is a complex construct and its physiology can vary depending on its source: cognitive workload or social evaluation. To study the feasibility of physiology-based load-invariant psychosocial stress-detection, we designed a stress-induction protocol able to independently vary the relevant types of psychophysiological activity: mental and psychosocial stress. Here, we validate the efficacy of our protocol to induce psychosocial and mental stress. Our participants (N=24) had to perform a cognitive task associated with two workload conditions (low/high mental stress), in two contexts (low/high psychosocial stress), during which we recorded subjects’ self-reports, behaviour, physiology and neurophysiology. Questionnaires showed that the subjectively perceived level of stress varied with the psychosocial stress induction, while perceived arousal and mental effort levels vary with mental stress induction. Behaviour and physiology further corroborated the validity of our protocol. Heart rate and skin conductance globally increased after psychosocial stress induction relative to the non-stressful condition. Moreover, we demonstrated that higher workload tasks (mental stress) led to decrease in performance and a marked increase of heart rate.
The Molecular Diversity of Freshwater Picoeukaryotes Reveals High Occurrence of Putative Parasitoids in the Plankton

Eukaryotic microorganisms have been undersampled in biodiversity studies in freshwater environments. We present an original 18S rDNA survey of freshwater picoeukaryotes sampled during spring/summer 2005, complementing an earlier study conducted in autumn 2004 in Lake Pavin (France). These studies were designed to detect the small unidentified heterotrophic flagellates (HF, 0.6–5 µm) which are considered the main bacterivores in aquatic systems. Alveolates, Fungi and Stramenopiles represented 65% of the total diversity and differed from the dominant groups known from microscopic studies. Fungi and Telonemia taxa were restricted to the oxic zone which displayed two fold more operational taxonomic units (OTUs) than the oxycline. Temporal forcing also appeared as a driving force in the diversification within targeted organisms. Several sequences were not similar to those in databases and were considered as new or unsampled taxa, some of which may be typical of freshwater environments. Two taxa known from marine systems, the genera Telonema and Amoebophrya, were retrieved for the first time in our freshwater study. The analysis of potential trophic strategies displayed among the targeted HF highlighted the dominance of parasites and saprotrophs, and provided indications that these organisms have probably been wrongfully regarded as bacterivores in previous studies. A theoretical exercise based on a new ‘parasite/saprotroph-dominated HF hypothesis’ demonstrates that the inclusion of parasites and saprotrophs may increase the functional role of the microbial loop as a link for carbon flows in pelagic ecosystems. New interesting perspectives in aquatic microbial ecology are thus opened.
Process-Tracing Methods in Decision Making: On Growing Up in the 70s

Decision research has experienced a shift from simple algebraic theories of choice to an appreciation of mental processes underlying choice. A variety of process-tracing methods has helped researchers test these process explanations. Here, we provide a survey of these methods, including specific examples for subject reports, movement-based measures, peripheral psychophysiology, and neural techniques. We show how these methods can inform phenomena as varied as attention, emotion, strategy use, and understanding neural correlates. Two important future developments are identified: broadening the number of explicit tests of proposed processes through formal modeling and determining standards and best practices for data collection.
Uncertainty estimation for random sample consensus

The RANdom SAmple Consensus (RANSAC) algorithm, as a robust parameter estimator, has been widely used to remove gross errors. However, there is less work on analyzing the uncertainty produced by the RANSAC. This paper fills this gap by presenting an uncertainty estimation algorithm for the RANSAC. Based on a thorough analysis on the uncertainty of the model parameters generated during the random hypothesis sampling process of the RANSAC, we derive the probability that each hypothesis is selected as the best hypothesis by the RANSAC. Using the probability of the best hypothesis, we characterize the error expectation and error covariance of the model parameter estimates and compute the probability of each data point being an inlier. Three models including line fitting, homography, and essential matrix are used to evaluate the performance of the uncertainty estimation algorithm. Results demonstrate that the uncertainty produced by the RANSAC is characterized successfully by the proposed algorithm.
Politician Effort and Voter Inference ∗

This paper explores a psychologically motivated model of belief formation in a political context. Using a retrospective voting framework, we specifically examine the implications of a common inference bias in which voters overweight the effect of an incumbent’s unobserved effort on realized outcomes. This bias is motivated by and consistent with the fundamental attribution error in social psychology, whereby people over-attribute the cause of observed outcomes to personal and dispositional causes and underweigh ∗Patty gratefully acknowledges the financial support of the Alfred P. Sloan Foundation and the Division of Humanities and Social Sciences at the California Institute of Technology.