gebhart/patrepeval huggingface dataset:
Coordinate Autophagy and mTOR Pathway Inhibition Enhances Cell Death in Melanoma (2013)

The phosphatidylinositol 3-kinase/AKT/mammalian target of rapamycin (PI3K/AKT/mTOR) pathway promotes melanoma tumor growth and survival while suppressing autophagy, a catabolic process through which cells collect and recycle cellular components to sustain energy homeostasis in starvation. Conversely, inhibitors of the PI3K/AKT/mTOR pathway, in particular the mTOR inhibitor temsirolimus (CCI-779), induce autophagy, which can promote tumor survival and thus, these agents potentially limit their own efficacy. We hypothesized that inhibition of autophagy in combination with mTOR inhibition would block this tumor survival mechanism and hence improve the cytotoxicity of mTOR inhibitors in melanoma. Here we found that melanoma cell lines of multiple genotypes exhibit high basal levels of autophagy. Knockdown of expression of the essential autophagy gene product ATG7 resulted in cell death, indicating that survival of melanoma cells is autophagy-dependent. We also found that the lysosomotropic agent and autophagy inhibitor hydroxychloroquine (HCQ) synergizes with CCI-779 and led to melanoma cell death via apoptosis. Combination treatment with CCI-779 and HCQ suppressed melanoma growth and induced cell death both in 3-dimensional (3D) spheroid cultures and in tumor xenografts. These data suggest that coordinate inhibition of the mTOR and autophagy pathways promotes apoptosis and could be a new therapeutic paradigm for the treatment of melanoma.
Exploring the Energy-Time Tradeoff in MPI Programs on a Power-Scalable Cluster (2005)

Recently, energy has become an important issue in high-performance computing. For example, supercomputers that have energy in mind, such as BlueGene/L, have been built; the idea is to improve the energy efficiency of nodes. Our approach, which uses off-the-shelf, high-performance cluster nodes that are frequency scalable, allows energy saving by scaling down the CPU. This paper investigates the energy consumption and execution time of applications from a standard benchmark suite (NAS) on a power-scalable cluster. We study via direct measurement and simulation both intra-node and inter-node effects of memory and communication bottlenecks, respectively. Additionally, we compare energy consumption and execution time across different numbers of nodes. Our results show that a power-scalable cluster has the potential to save energy by scaling the processor down to lower energy levels. Furthermore, we found that for some programs, it is possible to both consume less energy and execute in less time when using a larger number of nodes, each at reduced energy. Additionally, we developed and validated a model that enables us to predict the energy-time tradeoff of larger clusters.
Evidence linking oxidative stress, mitochondrial dysfunction, and inflammation in the brain of individuals with autism (2014)

Autism spectrum disorders (ASDs) are a heterogeneous group of neurodevelopmental disorders that are defined solely on the basis of behavioral observations. Therefore, ASD has traditionally been framed as a behavioral disorder. However, evidence is accumulating that ASD is characterized by certain physiological abnormalities, including oxidative stress, mitochondrial dysfunction and immune dysregulation/inflammation. While these abnormalities have been reported in studies that have examined peripheral biomarkers such as blood and urine, more recent studies have also reported these abnormalities in brain tissue derived from individuals diagnosed with ASD as compared to brain tissue derived from control individuals. A majority of these brain tissue studies have been published since 2010. The brain regions found to contain these physiological abnormalities in individuals with ASD are involved in speech and auditory processing, social behavior, memory, and sensory and motor coordination. This manuscript examines the evidence linking oxidative stress, mitochondrial dysfunction and immune dysregulation/inflammation in the brain of ASD individuals, suggesting that ASD has a clear biological basis with features of known medical disorders. This understanding may lead to new testing and treatment strategies in individuals with ASD.
A guide to Dr Foster analyses (2010)

The publication of the Dr Foster Hospital Guide at the end of November sparked a debate about safety in hospitals. The national regulator, the Care Quality Commission (CQC), announced they were looking into problems at Basildon-the hospital which scored worst in Dr Foster's survey of hospital safety. But it failed to adequately explain why its own rating of the hospital gave it a clean bill of health. The opposition called for reform of the regulator. Andy Burnham, the Secretary of State for Health, answered questions in the House.
Thioreductase-Containing Epitopes Inhibit the Development of Type 1 Diabetes in the NOD Mouse Model (2016)

Autoreactive CD4(+) T cells recognizing islet-derived antigens play a primary role in type 1 diabetes. Specific suppression of such cells therefore represents a strategic target for the cure of the disease. We have developed a methodology by which CD4(+) T cells acquire apoptosis-inducing properties on antigen-presenting cells after cognate recognition of natural sequence epitopes. We describe here that inclusion of a thiol-disulfide oxidoreductase (thioreductase) motif within the flanking residues of a single MHC class II-restricted GAD65 epitope induces GAD65-specific cytolytic CD4(+) T cells (cCD4(+) T). The latter, obtained either in vitro or by active immunization, acquire an effector memory phenotype and lyse APCs by a Fas-FasL interaction. Furthermore, cCD4(+) T cells eliminate by apoptosis activated bystander CD4(+) T cells recognizing alternative epitopes processed by the same APC. Active immunization with a GAD65 class II-restricted thioreductase-containing T cell epitope protects mice from diabetes and abrogates insulitis. Passive transfer of in vitro-elicited cCD4(+) T cells establishes that such cells are efficient in suppressing autoimmunity. These findings provide strong evidence for a new vaccination strategy to prevent type 1 diabetes.
Comparison of three PCR-based methods to detect a Piedmontese cattle point mutation in the Myostatin gene (2009)

Despite many recent advances in single nucleotide polymorphism (SNP) genotyping technologies, there is still the need for methodologies with a reasonable throughput. In this study, we compared three PCR-based methods for SNP detection: (1) a conventional PCR-based allele detection system with fluorescent genotyping technology, (2) a SNaPshot methodology by single nucleotide primer extension and, (3) a real-time PCR-based method by allele-specific minor groove-binder probes. These three methodologies were used to analyze 104 meat samples of a particular Italian cattle breed known for producing excellent quality meat and for a characteristic increased development of muscle mass, caused by a point mutation (C313Y) in the Myostatin gene. The analysis revealed 98 samples to be homozygous (mh/mh) and five to be heterozygous (mh/+) for the mutation whereas one sample resulted to be homozygous for the wild type (+/+). The results obtained with the three different assays were consistent. Overall, all three methodologies proved to be efficient for allelic discrimination studies; however, real-time PCR was faster and allowed to genotype up to 96 samples in a single step, minimizing the number of steps required for samples manipulation.
Bi<sub>2</sub>ZnTiO<sub>6</sub>:  A Lead-Free Closed-Shell Polar Perovskite with a Calculated Ionic Polarization of 150 μC cm<sup>-2</sup> (2006)

Bi2ZnTiO6, a lead-free analogue of PbTiO3, has been prepared by high-pressure solid-state synthesis methods. Structural analysis reveals that the tetragonal distortion (c/a ratio = 1.21) of Bi2ZnTiO6 is the largest reported for any d0 B site Pb or Bi based perovskite. Significant cation displacements result in a point-charge calculated polarization of 150 μC cm-2.
A new algorithm for measuring atrial fibrillation organization (2002)

Subjective and quantitative measures of atrial fibrillation (AF) organization exist. The authors' introduce a new quantitative method and compare it to 2 previous algorithms. In the authors' method, 2 atrial electrograms are processed with 2 linear adaptive filters to predict 1 electrogram from the other. The mean-squared error (MSE) of the prediction quantifies the non-linearity or disorganization between the electrograms. From atrial epicardial recordings, MSE during sinus rhythm and atrial tachycardias were similar, but showed more organization than AF with different levels of vagal stimulation (VS). All 3 algorithms for quantifying AF organization showed low VS AF to be more organized than high VS AF, with MSE showing the most significant difference compared to the other 2 methods. MSE discriminates between AF and organized rhythms and is sensitive to different degrees of AF organization.
Fast algorithms for recovering a corrupted low-rank matrix (2009)

This paper studies algorithms for solving the problem of recovering a low-rank matrix with a fraction of its entries arbitrarily corrupted. This problem can be viewed as a robust version of classical PCA, and arises in a number of application domains, including image processing, web data ranking, and bioinformatic data analysis. It was recently shown that under surprisingly broad conditions, it can be exactly solved via a convex programming surrogate that combines nuclear norm minimization and ¿ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> -norm minimization. This paper develops and compares two complementary approaches for solving this convex program. The first is an accelerated proximal gradient algorithm directly applied to the primal; while the second is a gradient algorithm applied to the dual problem. Both are several orders of magnitude faster than the previous state-of-the-art algorithm for this problem, which was based on iterative thresholding. Simulations demonstrate the performance improvement that can be obtained via these two algorithms, and clarify their relative merits.
Macrophage colony-stimulating factor mediates astrocyte-induced microglial ramification in human fetal central nervous system culture. (1994)

Colony-stimulating factors are important mediators of microglial growth and function. Microglia, derived from ameboid precursor cells, undergo a series of morphological changes in the central nervous system to become ramified, a morphological hallmark of differentiated microglia. The cellular mechanisms and environmental factors involved in microglial ramification in the developing brain are not known. In the present study, we examined the role of macrophage colony-stimulating factor (M-CSF) in the induction of ramification of microglia in human fetal glial cultures. Human fetal microglia underwent spontaneous conversion from ameboid to ramified shape when co-cultured with human fetal astrocytes. Concurrently, high levels of M-CSF also accumulated in cultures of unstimulated human fetal astrocytes. That the M-CSF was essential in inducing microglial ramification was demonstrated by almost complete inhibition of ramification by an antibody to human M-CSF receptor, c-fms. Furthermore, profound inhibition of microglial ramification was exerted by herbimycin A, a specific inhibitor of tyrosine kinase (a component of the signal cascade of c-fms), supporting the role of M-CSF/c-fms in the induction of microglial ramification. Our results suggest a pivotal role played by astrocytes and astrocyte-produced M-CSF in the induction of microglial maturation and differentiation in the developing human brain.
Sensor Technology for Integrated Vehicle Health Management of Aerospace Vehicles (2003)

NASA is focusing considerable efforts on technology development for Integrated Vehicle Health Management systems. The research in this area is targeted toward increasing aerospace vehicle safety and reliability, while reducing vehicle operating and maintenance costs. On‐board, real‐time sensing technologies that can provide detailed information on structural integrity are central to such a health management system. This paper describes a number of sensor technologies currently under development for integrated vehicle health management. The capabilities, current limitations, and future research needs of these technologies are addressed.
Rational Design of Cesium‐Selective Ionophores: Dihydrocalix[4]arene Crown‐6 Ethers (2003)

Abstract Molecular mechanics calculations performed on calix[4]arene crown‐6 ethers predict that the 1,3‐dihydro derivatives will exhibit greater complementarity for potassium and cesium ions than the parent 1,3‐bis(alkyloxy) calixcrowns. The X‐ray crystal structures of 1,3‐ alt ‐bis(octyloxy)calix[4]arene benzocrown‐6 ether, dihydrocalix[4]arene benzocrown‐6 ether, and the cesium nitrate complex of dihydrocalix[4]arene benzocrown‐6 ether were determined. The structure of the cesium complex corresponds closely to the structure predicted by molecular mechanics. The dihydrocalix[4]arene crown‐6 ethers exhibit enhanced cesium selectivity in the extraction of alkali‐metal salts. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
A Pharmacokinetic Model of a Tissue Implantable Insulin Sensor (2014)

While implantable sensors such as the continuous glucose monitoring system have been widely studied, both experimentally and mathematically, relatively little attention has been applied to the potential of insulin sensors. Such sensors can provide feedback control for insulin infusion systems and pumps and provide platforms for the monitoring of other biomarkers in vivo. In this work, the first pharmacokinetic model of an affinity sensor is developed for insulin operating subcutaneously in the limit of where mass transfer across biological membranes reaches a steady state. Using a physiological, compartmental model for glucose, insulin, and glucagon metabolism, the maximum sensor response and its delay time relative to plasma insulin concentration, are calculated based on sensor geometry, placement, and insulin binding parameters for a sensor localized within adipose tissue. A design relation is derived linking sensor dynamics to insulin time lag and placement within human tissue. The model should find utility in understanding dynamic insulin responses and forms the basis of model predictive control algorithms that incorporate sensor dynamics.
Impact of <i>in situ</i> oxygen plasma cleaning on the resistance of Ru and Au-Ru based rf microelectromechanical system contacts in vacuum (2010)

Contact resistance measurements are reported for radio frequency microelectromechanical system switches operating in an ultrahigh vacuum system equipped with in situ oxygen plasma cleaning capabilities. Ru-based contacts were prepared by means of standard sputtering techniques, sputtering followed by postdeposition oxidation, (surface RuO2) or reactive sputtering in the presence of oxygen (bulk RuO2). In situ oxygen plasma cleaning lowered the resistance of Ru contacts by two or more orders of magnitude but not lower than Au contacts, irrespective of whether the Au contacts were cleaned. The time dependence of the resistance was fit to power law extrapolations to infer contact creep properties and resistance values at t=∞. Time-dependent creep properties of mixed Au-Ru contacts were observed to be similar to those of Au-Au contacts, while the absolute value of the resistance of such contacts was more comparable to Ru-Ru contacts. Prior to, and for short oxygen plasma exposure times, bulk RuO2 resistance values exhibited much larger variations than values measured for surface RuO2. For O2 plasma exposure times exceeding about 5 min, the bulk and surface RuO2 resistance values converged, at both t=0 and t=∞, with the t=∞ values falling within experimental error of theoretical values predicted for ideal surfaces. The data strongly support prior reports in the surface science literature of oxygen plasma induced thickening of oxide layers present on Ru surfaces. In addition, they demonstrate that vacuum alone is insufficient to remove contaminants from the contact surfaces and/or prevent such contaminants from reforming after oxygen plasma exposure.
Increased proportion of CD16<sup>+</sup> NK cells in the colonic lamina propria of inflammatory bowel disease patients, but not after azathioprine treatment (2010)

Natural killer cells with cytolytic potential are enriched in the colonic lamina propria of individuals with IBD. Azathioprine is associated with a reduction in these cells and a normalization of natural killer cell populations.
Cathodoluminescence and annealing study of plasma-deposited polycrystalline diamond films (1991)

We have measured the cathodoluminescence spectra of microwave plasma-assisted chemical-vapor deposited (CVD) polycrystalline diamond films at 77 K over the spectral range of 2300–8000 Å. Annealing studies of these spectra have been carried out at 500, 800, 1000, 1200, and 1350 °C. Rich spectra are observed. Many of them are stable up to the highest annealing temperature. Two peaks at 3.188 and 2.638 eV and the 5RL lines are destroyed, while other lines at 3.57 and 3.462 eV appear, after a 1200 °C anneal. The two neighboring peaks at 2.330 and 2.320 eV are probably responsible for the broadness of the often observed peak at 2.328 eV in CVD diamond films. We also compare some of the annealing behavior of the CVD diamond films with those of natural single-crystal diamond, and conclude that while most of the annealing characteristics of plasma-deposited diamond films are similar with those which have been reported for single-crystal natural diamonds, some of the annealing behaviors are different for these two types of materials.
Simple questions to improve pseudo-relevance feedback results (2006)

We explore interactive methods to further improve the performance of pseudo-relevance feedback. Studies \citeria suggest that new methods for tackling difficult queries are required. Our approach is to gather more information about the query from the user by asking her simple questions. The equally simple responses are used to modify the original query. Our experiments using the TREC Robust Track queries show that we can obtain a significant improvement in mean average precision averaging around 5% over pseudo-relevance feedback. This improvement is also spread across more queries compared to ordinary pseudo-relevance feedback, as suggested by geometric mean average precision.
Dealing with Commodity Price Uncertainty (1999)

This paper -- a product of the Commodity Policy and Analysis Unit, International Economics Department -- is part of a larger effort in the department to investigate alternative price risk management and finance systems under market liberalization. Copies of the paper are available free from the World Bank, 1818 H Street NW, Washington, DC 20433. Please contact Jean Jacobson, room N5-032, telephone 202-47.t-3710, fax 202-522-3564, lnternet address jjacobson(worldbank.org. October 1996. (44 pages) The Policy Research Working Paper Series dissemtnates the findings of work in progress to encourage the exchange o[ ideas about development tssues. An objective of the series is to get the findings out quickly, even if the presentations are less than fully polished. The papers car O, the names of the authors and should be used and cited accordingly. The findings, interpretations. and conclusions are the authors&apos; own and should not be attributed to the World Bank, its Executive Board o[ Directors, or any o[ its member countries
O‐GlcNAc Transferase Promotes Compensated Cardiac Function and Protein Kinase A O‐GlcNAcylation During Early and Established Pathological Hypertrophy From Pressure Overload (2019)

Background Protein posttranslational modifications by O-linked β-N-acetylglucosamine (O-GlcNAc) increase with cardiac hypertrophy, yet the functional effects of these changes are incompletely understood. In other organs, O-GlcNAc promotes adaptation to acute physiological stressors; however, prolonged O-GlcNAc elevations are believed to be detrimental. We hypothesize that early O-GlcNAcylation improves cardiac function during initial response to pressure overload hypertrophy, but that sustained elevations during established pathological hypertrophy negatively impact cardiac function by adversely affecting calcium handling proteins. Methods and Results Transverse aortic constriction or sham surgeries were performed on littermate controls or cardiac-specific, inducible O-GlcNAc transferase knockout (OGTKO) mice to reduce O-GlcNAc levels. O-GlcNAc transferase deficiency was induced at different times. To evaluate the initial response to pressure overload, OGTKO was completed preoperatively and mice were followed for 2 weeks post-surgery. To assess prolonged O-GlcNAcylation during established hypertrophy, OGTKO was performed starting 18 days after surgery and mice were followed until 6 weeks post-surgery. In both groups, OGTKO with transverse aortic constriction caused significant left ventricular dysfunction. OGTKO did not affect levels of the calcium handling protein SERCA2a. OGTKO reduced phosphorylation of phospholamban and cardiac troponin I, which would negatively impact cardiac function. O-GlcNAcylation of protein kinase A catalytic subunit, a kinase for phospholamban, decreased with OGTKO. Conclusions O-GlcNAcylation promotes compensated cardiac function in both early and established pathological hypertrophy. We identified a novel O-GlcNAcylation of protein kinase A catalytic subunit, which may regulate calcium handling and cardiac function.
Understanding Scalability and Fine-Grain Parallelism of Synchronous Data Parallel Training (2019)

In the age of big data, deep learning has emerged as a powerful tool to extract insight and exploit its value, both in industry and scientific applications. With increasing complexity of learning models and amounts of training data, data-parallel approaches based on frequent all-reduce synchronization steps are increasingly popular. Despite the fact that high-performance computing (HPC) technologies have been designed to address such patterns efficiently, the behavior of data-parallel approaches on HPC platforms is not well understood. To address this issue, in this paper we study the behavior of Horovod, a popular data-parallel approach that relies on MPI, on Theta, a pre-Exascale machine at Argonne National Laboratory. Using two representative applications, we explore two aspects: (1) how performance and scalability is affected by important parameters such as number of nodes, number of workers, threads per node, batch size; (2) how computational phases are interleaved withall-reduce communication phases at fine granularity and what consequences this interleaving has in terms of potential bottlenecks. Our findings show that pipelining of back-propagation, gradient reduction and weight updates mitigate the effects of stragglers during all-reduce only partially. Furthermore, there can be significant delays between weights update, which can be leveraged to mask the overhead of additional background operations that are coupled with the training.
Investigation of the Temperature Dependence of the Pitch of a Cholesteric Liquid Crystal (1976)

Abstract The pitch and the refractive index of a cholesteryl chloride-cholesteryl nonanoate mixture as a function of temperature have been measured separately by using selective reflections and total reflections. The magnitude of the influence on the pitch due to the temperature dependence of the refreactive index and the density has been determined.