Miracle-dz/UniFAR-FTUs huggingface dataset:
Supporting Exploratory Hypothesis Testing and Analysis

Conventional hypothesis testing is carried out in a hypothesis-driven manner. A scientist must first formulate a hypothesis based on what he or she sees and then devise a variety of experiments to test it. Given the rapid growth of data, it has become virtually impossible for a person to manually inspect all data to find all of the interesting hypotheses for testing. In this article, we propose and develop a data-driven framework for automatic hypothesis testing and analysis. We define a hypothesis as a comparison between two or more subpopulations. We find subpopulations for comparison using frequent pattern mining techniques and then pair them up for statistical hypothesis testing. We also generate additional information for further analysis of the hypotheses that are deemed significant. The number of hypotheses generated can be very large, and many of them are very similar. We develop algorithms to remove redundant hypotheses and present a succinct set of significant hypotheses to users. We conducted a set of experiments to show the efficiency and effectiveness of the proposed algorithms. The results show that our system can help users (1) identify significant hypotheses efficiently, (2) isolate the reasons behind significant hypotheses efficiently, and (3) find confounding factors that form Simpson’s paradoxes with discovered significant hypotheses.
The impact of subcellular location on the near infrared-mediated thermal ablation of cells by targeted carbon nanotubes

Single-walled carbon nanotubes (SWNTs) are used in the near infrared (NIR)-mediated thermal ablation of tumor cells because they efficiently convert absorbed NIR light into heat. Despite the therapeutic potential of SWNTs, there have been no published studies that directly quantify how many SWNTs need be associated with a cell to achieve a desired efficiency of killing, or what is the most efficient subcellular location of SWNTs for killing cells. Herein we measured dose response curves for the efficiency of killing correlated to the measured amounts of folate-targeted SWNTs that were either on the surface or within the vacuolar compartment of normal rat kidney cells. Folate-targeted SWNTs on the cell surface were measured after different concentrations of SWNTs in medium were incubated with cells for 30 min at 4 °C. Folate-targeted SWNTs within the vacuolar compartments were measured after cells were incubated with different concentrations of SWNTs in medium for 6 h at 37 °C. It was observed that a SWNT load of ∼13 pg/cell when internalized was sufficient to kill 90% of the cells under standardized conditions of NIR light irradiation. When ∼3.5 pg/cell of SWNTs were internalized within the endosomal/lysosomal compartments, ∼50% of the cells were killed, but when ∼3.5 pg/cell of SWNTs were confined to the cell surface only ∼5% of the cells were killed under the same NIR irradiation conditions. The SWNT subcellular locations were verified using Raman imaging of SWNTs merged with fluorescence images of known subcellular markers. To our knowledge, this is the first time that SWNT amounts at known subcellular locations have been correlated with a dose-normalized efficacy of thermal ablation and the results support the idea that SWNTs confined to the plasma membrane are not as effective in NIR-mediated cell killing as an equivalent amount of SWNTs when internalized within the endosomal/lysosomal vesicles.
Modeling and Control of  $N$ -Paralleled Grid-Connected Inverters With LCL Filter Coupled Due to Grid Impedance in PV Plants

Designing adequate control laws for grid-connected inverters with LCL filters is complicated. The power quality standards and the system resonances burden the task. In order to deal with resonances, system damping has to be implemented. Active damping is preferred to passive damping so as to improve the efficiency of the conversion. In addition, paralleled grid-connected inverters in photovoltaic (PV) plants are coupled due to grid impedance. Generally, this coupling is not taken into account when designing the control laws. In consequence, depending on the number of paralleled grid-connected inverters and the grid impedance, the inverters installed in PV plants do not behave as expected. In this paper, the inverters of a PV plant are modeled as a multivariable system. The analysis carried out enables to obtain an equivalent inverter that describes the totality of inverters of a PV plant. The study is validated through simulation and field experiments. The coupling effect is described and the control law design of paralleled grid-connected inverters with LCL filters in PV plants is clarified.
Deletion of the high‐affinity cAMP phosphodiesterase encoded by PDE2 affects stress responses and virulence in Candida albicans

Previously, we have shown that PDE2 is required for hyphal development and cell wall integrity in Candida albicans. In the present study, we have investigated the effects of its deletion by genome‐wide transcriptome profiling. Changes in expression levels of genes involved in metabolism, transcription, protein and nucleic acids synthesis, as well as stress responses, cell wall and membrane biogenesis, adherence and virulence have been observed. By comparing these changes with previously reported transcriptome profiles of pde2Δ mutants of Saccharomyces cerevisiae, as well as cdc35Δ, ras1Δ and efg1Δ mutants of C. albicans, conserved and species‐specific cAMP‐regulated genes have been identified. The genes whose transcription is altered upon deletion of PDE2 in C. albicans has also allowed us to predict that the pde2Δ mutant would have a defective ability to adhere to, and invade host cells, and an impaired virulence as well as response to different stresses. Using appropriate assays, we have tested these predictions and compared the roles of the high‐ and low‐affinity cAMP phosphodiesterases, Pde2p and Pde1p in stress, adhesion and virulence. We suggest that phosphodiesterases, and in particular the high‐affinity cAMP phosphodiesterase encoded by PDE2, have real potential as targets for antifungal chemotherapy.
Cumulative Space in Black-White Pebbling and Resolution

We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko 2015] as a tool for obtaining results in cryptography. We consider instead the nondeterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10-15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordstrom 2008, 2011], we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure.
A Novel Flexible Virtual Fixtures for Teleoperation

This paper proposed a novel spatial-motion-constraints virtual fixtures (VFs) method for the human-machine interface collaborative technique. In our method, two 3D flexible VFs have been presented: warning pipe and safe pipe. And a potential-collision-detection method based on two flexible VFs has been proposed. The safe pipe constructs the safe workspace dynamically for the robot, which makes it possible to detect the potential collision between the robot and the obstacles. By calculating the speed and the acceleration of the robot end-effecter (EE), the warning pipe can adjust its radius to detect the deviation from the EE to the reference path. These spatial constraints serve as constraint conditions for constrained robot control. The approach enables multiobstacle manipulation task of telerobot in precise interactive teleoperation environment. We illustrate our approach on a teleoperative manipulation task and analyze the performance results. The performance-comparison experimental results demonstrate that the control mode employing our method can assist the operator more precisely in teleoperative tasks. Due to the properties such as collision avoidance and safety, operators can complete the tasks more efficiently along with reduction in operating tension.
Neurological soft signs in schizophrenic patients: Influence of age, age at onset, sex, and family history of schizophrenia

Neurological soft signs (NSS) are indicators of subtle neurodysfunction which are overrepresented in schizophrenics. The issue of the significance of NSS is still unclear in spite of a considerable amount of literature on the subject. The objective of this study was to investigate the impact on NSS of genetic and environmental factors presumed to be relevant to the etiology and prognosis of schizophrenia. Data on NSS (using a slightly modified version of the Neurological Evaluation Scale) and the age, age at onset, sex and family history of schizophrenia of 50 schizophrenic patients were collected. Extrapyramidal signs were measured with the Extrapyramidal Symptoms Rating Scale. Backward regression analyses with two-factor interactions regression were used to evaluate the influence of the variables on the NSS total score, subscores, and single items. Age at onset and the age-age at onset interaction influenced co-ordination tasks. Sex and the interaction between age and sex influenced sequencing tasks, with males having higher and females lower scores with increasing age. None of the other variables influenced the NSS total score or subscores. Schizophrenics with early onset of disease may perform worse than late-onset patients in motor co-ordination tasks at the onset, but the age-dependent deterioration of motor co-ordination may be more rapid in late-onset patients. Performance in sequencing tasks may be influenced by sex-bound variables.
Cervicovaginal human papillomavirus infection in human immunodeficiency virus-1 (HIV)-positive and high-risk HIV-negative women.

BACKGROUND Human papillomavirus (HPV) infection is associated with precancerous cervical squamous intraepithelial lesions commonly seen among women infected with human immunodeficiency virus-1 (HIV). We characterized HPV infection in a large cohort of HIV-positive and HIV-negative women participating in the Women's Interagency HIV Study to determine the prevalence of and risk factors for cervicovaginal HPV infection in HIV-positive women. METHODS HIV-positive (n = 1778) and HIV-negative (n = 500) women were tested at enrollment for the presence of HPV DNA in a cervicovaginal lavage specimen. Blood samples were tested for HIV antibody status, level of CD4-positive T cells, and HIV RNA load (copies/mL). An interview detailing risk factors was conducted. Univariate and multivariate analyses were performed. RESULTS Compared with HIV-negative women, HIV-positive women with a CD4+ cell count of less than 200/mm3 were at the highest risk of HPV infection, regardless of HIV RNA load (odds ratio [OR] = 10.13; 95% confidence interval [CI] = 7.32-14.04), followed by women with a CD4+ count greater than 200/mm3 and an HIV RNA load greater than 20,000 copies/mL (OR = 5.78; 95% CI = 4.17-8.08) and women with a CD4+ count greater than 200/mm3 and an HIV RNA load less than 20,000 copies/mL (OR = 3.12; 95% CI = 2.36-4.12), after adjustment for other factors. Other risk factors among HIV-positive women included racial/ethnic background (African-American versus Caucasian, OR = 1.64; 95% CI = 1.19-2.28), current smoking (yes versus no; OR = 1.55; 95% CI = 1.20-1.99), and younger age (age < 30 years versus > or = 40 years; OR = 1.75; 95% CI = 1.23-2.49). CONCLUSIONS Although the strongest risk factors of HPV infection among HIV-positive women were indicators of more advanced HIV-related disease, other factors commonly found in studies of HIV-negative women, including racial/ethnic background, current smoking, and age, were important in HIV-positive women as well.
Principles behind the multifarious control of signal transduction

General and simple principles are identified that govern signal transduction. The effects of kinase and phosphatase inhibition on a MAP kinase pathway are first examined in silico. Quantitative measures for the control of signal amplitude, duration and integral strength are introduced. We then identify and prove new principles, such that total control on signal amplitude and on final signal strength must amount to zero, and total control on signal duration and on integral signal intensity must equal −1. Collectively, kinases control amplitudes more than duration, whereas phosphatases tend to control both. We illustrate and validate these principles experimentally: (a) a kinase inhibitor affects the amplitude of EGF‐induced ERK phosphorylation much more than its duration and (b) a phosphatase inhibitor influences both signal duration and signal amplitude, in particular long after EGF administration. Implications for the cellular decision between growth and differentiation are discussed.
Histone deacetylase inhibitors decrease reelin promoter methylation in vitro

We investigated the effects of agents that induce reelin mRNA expression in vitro on the methylation status of the human reelin promoter in neural progenitor cells (NT2). NT2 cells were treated with the histone deacetylase inhibitors, trichostatin A (TSA) and valproic acid (VPA), and the methylation inhibitor aza‐2′‐deoxycytidine (AZA) for various times. All three drugs reduced the methylation profile of the reelin promoter relative to untreated cells. The acetylation status of histones H3 and H4 increased following treatment with VPA and TSA at times as short as 15 min following treatment; a result consistent with the reported mode of action of these drugs. Chromatin immunoprecipitation experiments showed that these changes were accompanied by changes occurring at the level of the reelin promoter as well. Interestingly, AZA decreased reelin promoter methylation without concomittantly increasing histone acetylation. In fact, after prolonged treatments with AZA, the acetylation status of histones H3 and H4 decreased relative to untreated cells. We also observed a trend towards reduced methylated H3 after 18 h treatment with TSA and VPA. Our data indicate that while TSA and VPA act to increase histone acetylation and reduce promoter methylation, AZA acts only to decrease the amount of reelin promoter methylation.
LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser

UNLABELLED LASAGNA-Search 2.0 is an integrated webtool for transcription factor (TF) binding site search and visualization. The tool is based on the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm. It eliminates manual TF model collection and promoter sequence retrieval. Search results can be visualized locally or in the University of California Santa Cruz Genome Browser. Gene regulatory network inference based on the search results offers another way of visualization. A list of TFs and target genes is all a user needs to start using the tool. LASAGNA-Search 2.0 currently offers 1792 TF models and supports 15 species for automatic promoter retrieval and visualization in the University of California Santa Cruz Genome Browser. It is a user-friendly tool designed for non-bioinformaticians and is suitable for research and teaching. We describe important changes made since the initial release. AVAILABILITY AND IMPLEMENTATION LASAGNA-Search 2.0 is freely available without registration at http://biogrid.engr. uconn.edu/lasagna_search/.
Functional equivalence checking for verification of algebraic transformations on array-intensive source code

The development of energy and performance-efficient embedded software increasingly relies on the application of complex transformations on critical parts of the source code. Designers applying such nontrivial source code transformations are often faced with the problem of ensuring functional equivalence of the original and transformed programs. Currently, they have to rely on incomplete and time-consuming simulation. Formal automatic verification of the transformed program against the original is desirable instead. This calls for equivalence checking tools similar to the ones available for comparing digital circuits. We present such a tool to compare array-intensive programs related through a combination of important global transformations like expression propagations, loop and algebraic transformations. When the transformed program fails to pass the equivalence check, the tool provides specific feedback on the possible locations of errors.
Multiphase flow of immiscible fluids on unstructured moving meshes

In this paper, we present a method for animating multiphase flow of immiscible fluids using unstructured moving meshes. Our underlying discretization is an unstructured tetrahedral mesh, the deformable simplicial complex (DSC), that moves with the flow in a Lagrangian manner. Mesh optimization operations improve element quality and avoid element inversion. In the context of multiphase flow, we guarantee that every element is occupied by a single fluid and, consequently, the interface between fluids is represented by a set of faces in the simplicial complex. This approach ensures that the underlying discretization matches the physics and avoids the additional book-keeping required in grid-based methods where multiple fluids may occupy the same cell. Our Lagrangian approach naturally leads us to adopt a finite element approach to simulation, in contrast to the finite volume approaches adopted by a majority of fluid simulation techniques that use tetrahedral meshes. We characterize fluid simulation as an optimization problem allowing for full coupling of the pressure and velocity fields and the incorporation of a second-order surface energy. We introduce a preconditioner based on the diagonal Schur complement and solve our optimization on the GPU. We provide the results of parameter studies as well as a performance analysis of our method.
Rate of utilization of a given fraction of W′ (the curvature constant of the power–duration relationship) does not affect fatigue during severe‐intensity exercise

What is the central question of this study? Does the rate of utilization of W′ (the curvature constant of the power–duration relationship) affect fatigue during severe‐intensity exercise? What is the main finding and its importance? The magnitude of fatigue after two severe‐intensity exercises designed to deplete the same fraction of W′ (70%) at two different rates of utilization (fast versus slow) was similar after both exercises. Moreover, the magnitude of fatigue was related to critical power (CP), supporting the contention that CP is a key determinant in fatigue development during high‐intensity exercise. Thus, the CP model is a suitable approach to investigate fatigue mechanisms during high‐intensity exercise.
Musical Instrument Modeling and Classification

Independent Components Analysis is commonly used to separate different sources of sounds in a set of recordings. ICA produces the original unmixed input signals as output, but not in a known order. It is up to the listener to identify or interpret the sounds separately. This task is easy for a human who is familiar with the nature of the sounds being mixed (e.g., human voices), but may be more difficult if the sounds are not already known to the speaker. We propose and implement a technique to label the unmixed sounds produced by ICA. Specifically, we were able to use a set of Support Vector Machines trained to identify each of four different musical instruments. To find a feature mapping the SVMs can use to label arbitrary sounds beyond those similar to its training set, we used "Yet Another Audio Feature Extractor" or Yaafe, an open-source audio feature toolkit [1]. We tested our instrument SVMs on randomly generated sounds from known instruments and found that, using the appropriate set of features from Yaafe, we obtained a 95% prediction accuracy. We also tested the instrument SVMs on the outputs of ICA, which have some lingering components of other instruments mixed in due to an imperfect unmixing matrix, and found a prediction accuracy of 75%.
[Validation of the Spanish version of the social adaptation scale in depressive patients].

INTRODUCTION The Social Adaptation Self-evaluation Scale (SASS) allows a very easy evaluation of the individual's perspective about himself and his environment, together with his behaviour and social motivation. Taking into account that social maladjustment is high prevalent and well documented for depressed subjects and it is one of the most limiting aspects of their global performance, the aim of the present work is to validate the Spanish version of SASS for its application in subjects diagnosed as suffering major depression (DSM-IV). METHODOLOGY A cross sectional multicentre study was carried out by collecting information on 464 patients (34.7% men and 65.3% women range 18 to 65 years), which included their answers to the scale and relevant sociodemographic and clinical variables. RESULTS The principal component analysis corroborated the identification of 4 main factors: the first one being extrafamily relationships (31.4% of inertia); the second, work and leisure (7.6% of inertia); the third, social and cultural interests (5.6% of inertia); and the fourth factor, family relationships and behavioral strategies (5.5% of intertia). The scale has provided adequate reliability and validity indexes as well as sensitivity to the severity of the depressive episode. CONCLUSIONS The Spanish version of the SASS has proven to be an adequate instrument for evaluating social adjustment in depressive subjects. However, future studies must corroborate its sensitivity to the effects of antidepressant treatment and potential differences between the antidepressant agents employed.
Impact of on-chip interconnects on vertical signal propagation in 3D ICs

Three-dimensional integrated circuits (3D ICs) provide a promising solution for overcoming delay/power problems of 2D ICs by stacking chips vertically. Signal propagation speed among the stacked chips is very important for 3D IC systems. We propose a simple model for analyzing the vertical signal propagation in through-silicon-via-based 3D ICs and discuss the impact of physical parameter variations on propagation delay. Experimental results show that on-chip interconnects greatly affect vertical signal propagation when there are dense general interconnects near the vertical signal interconnect, large amount of fanout, and interconnect length of a driver and receivers is long.
On the epipolar geometry of the Crossed-Slits projection

The Crossed-Slits (X-Slits) camera is defined by two nonintersecting slits, which replace the pinhole in the common perspective camera. Each point in space is projected to the image plane by a ray which passes through the point and the two slits. The X-Slits projection model includes the pushbroom camera as a special case. In addition, it describes a certain class of panoramic images, which are generated from sequences obtained by translating pinhole cameras. In this paper we develop the epipolar geometry of the X-Slits projection model. We show an object which is similar to the fundamental matrix; our matrix, however, describes a quadratic relation between corresponding image points (using the Veronese mapping). Similarly the equivalent of epipolar lines are conics in the image plane. Unlike the pin-hole case, epipolar surfaces do not usually exist in the sense that matching epipolar lines lie on a single surface; we analyze the cases when epipolar surfaces exist, and characterize their properties. Finally, we demonstrate the matching of points in pairs of X-Slits panoramic images.