gebhart/patrepeval huggingface dataset:
CPU-GPU hybrid bidiagonal reduction with soft error resilience (2013)

Soft errors pose a real challenge to applications running on modern hardware as the feature size becomes smaller and the integration density increases for both the modern processors and the memory chips. Soft errors manifest themselves as bit-flips that alter the user value, and numerical software is a category of software that is sensitive to such data changes. In this paper, we present a design of a bidiagonal reduction algorithm that is resilient to soft errors, and we also describe its implementation on hybrid CPU-GPU architectures. Our fault-tolerant algorithm employs Algorithm Based Fault Tolerance, combined with reverse computation, to detect, locate, and correct soft errors. The tests were performed on a Sandy Bridge CPU coupled with an NVIDIA Kepler GPU. The included experiments show that our resilient bidiagonal reduction algorithm adds very little overhead compared to the error-prone code. At matrix size 10110 x 10110, our algorithm only has a performance overhead of 1.085% when one error occurs, and 0.354% when no errors occur.
The influence of age and gender on remifentanil EC50for preventing rocuronium induced withdrawal movements (2010)

The EC(50) of remifentanil for preventing rocuronium induced withdrawal movements was lowest in the elderly and higher in children than male adult patients. No difference in the EC(50) of remifentanil was seen between male and female adult patients.
Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside (2021)

Despite impressive efforts invested in epigenetic research in the last 50 years, clinical applications are still lacking. Only a few university hospital centers currently use epigenetic biomarkers at the bedside. Moreover, the overall concept of precision medicine is not widely recognized in routine medical practice and the reductionist approach remains predominant in treating patients affected by major diseases such as cancer and cardiovascular diseases. By its' very nature, epigenetics is integrative of genetic networks. The study of epigenetic biomarkers has led to the identification of numerous drugs with an increasingly significant role in clinical therapy especially of cancer patients. Here, we provide an overview of clinical epigenetics within the context of network analysis. We illustrate achievements to date and discuss how we can move from traditional medicine into the era of network medicine (NM), where pathway-informed molecular diagnostics will allow treatment selection following the paradigm of precision medicine.
Electron Microscopy of Microtubule Cytoskeleton Assembly In Vitro (2013)

Cell-free cytoplasm isolated from meiotic Xenopus egg extracts reconstitutes microtubule phenomena in vitro. These crude extracts assemble bipolar meiotic spindles and are readily fractionated for biochemical assays, providing a good tool to dissect molecular mechanism. We developed techniques for immunoelectron microscopy of microtubule structures assembled in perfusion chambers and in solution.
Tyrosine phosphatase activity is restricted by basic charge substituting mutation of substrates (2022)

Phosphorylation controls important cellular signals and its dysregulation leads to disease. While most phospho-regulation studies are focused on kinases, phosphatases are comparatively overlooked. Combining peptide arrays with SAMDI mass spectrometry, we show that tyrosine phosphatase activity is restricted by basic amino acids adjacent to phosphotyrosines. We validate this model using two β-catenin mutants associated with cancer (T653R/K) and a mouse model for intellectual disability (T653K). These mutants introduce a basic residue next to Y654, an established phosphorylation site where modification shifts β-catenin from cell-cell adhesions and towards its essential nuclear role as Wnt-signaling effector. We show that T653-basic mutant β-catenins are less efficiently dephosphorylated by phosphatases, leading to sustained Y654 phosphorylation and elevated Wnt signals, similar to those observed for Y654E phospho-mimic mutant mice. This model rationalizes how basic mutations proximal to phosphotyrosines can restrict counter-regulation by phosphatases, providing new mechanismistic and treatment insights for 6000+ potentially relevant cancer mutations.
Thermocatalytic Conversion of Landfill Gas and Biogas to Alternative Transportation Fuels (2008)

Landfill gas (LFG) and biogas are important renewable resources for production of alternative transportation fuels. The resources of LFG and biogas are vast and widely available but remain mostly unused. In this paper, the authors assess the technical feasibility of direct catalytic reforming (i.e., without preliminary methane recovery from these gases) of LFG and biogas to synthesis gas that could further be processed to synthetic liquid hydrocarbon fuels via Fischer–Tropsch (FT) synthesis. The catalytic activity and selectivity of a number of noble metal (Ru, Ir, Pt, Rh, Pd) and Ni-based catalysts for reforming of a model CH4−CO2 mixture mimicking a typical LFG into a synthesis gas were evaluated. The issues related to the catalysts stability and process sustainability under the conditions that are favorable for carbon deposition were explored. The experimental data are in a good agreement with AspenPlus simulation results. It was shown that the syngas produced by Ni-catalyzed steam-assisted reforming of a model LFG is suitable for production of liquid hydrocarbons via FT synthesis.
A file assignment problem model for extended local area network environments (2002)

A file assignment problem (FAP) designed specifically for file servers and work stations on an extended local area network (ELAN) is formulated and solved. Key properties of such an environment are modeled onto the FAP formulation. The FAP problem is NP-hard, and the approximate solution technique adopted uses Lagrangian (dual) relaxation. The dual FAP is solved by use of an accelerated subgradient method. The approach is efficient and also provides an estimate, called the approximate relative duality gap, of the quality of the solution. In all instances in which the method has been employed, the approximate relative duality gap is less than 1%. The algorithm is illustrated by several examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression of theMf1 gene in developing mouse hearts: Implication in the development of human congenital heart defects (1999)

The transcription factor FKHL7 gene has recently been associated with the anterior segment dysgenesis disorder of the eye known as Axenfeld-Rieger anomaly (ARA). A growing body of evidence indicates that mutations in FKHL7 cause not only defects in the anterior segment of the eye but defects in the heart valves and septa as well. In order to evaluate its contribution to normal heart septation and valve formation, expression of the mouse homologue Mf1 in embryonic hearts was analyzed by in situ hybridization. A weak but significant level of Mf1 expression could be detected in the endocardium of mouse embryos as early as day 8.5 post-conception (p.c.). Mf1 expression was undetectable in the hearts of day 9.5 p.c. embryos, but by day 10.5-11 p.c., Mf1 transcripts could be found again in the endocardium of both the atrium and ventricle and a relatively strong signal was observed in the dorsal portion of the septum primum, in what appeared to be the spinal vestibule. At day 13 p.c. when aortic and pulmonary trunks are separated, relatively more Mf1 transcripts were detected in the leaflets of aortic, pulmonary, and venous valves, the ventral portion of the septum primum, as well as in the single layer of cells on the edges of the atrioventricular cushion tissues. Surprisingly, there was no signal detected in the developing interventricular septum. At day 15 p.c., overall Mf1 signals were greatly decreased. However, significant levels of expression could still be observed in the atrial septum, the tricuspid valve, the mitral valve, and in the venous valve but not in the interventricular septum. The temporal and spatial expression patterns of the Mf1 gene in developing mouse hearts suggest that Mf1 may play a critical role in the formation of valves and septa with the exception of the interventricular septum. This is further supported by our studies showing that mutations in the FKHL7 gene were associated with defects in the anterior segment of the eye as well as atrial septal defects or mitral valve defects. Dev Dyn 1999;216:16-27.
Bounded-uncertainty estimation for correlated signal and noise (2006)

In this paper we present a class of bounded- uncertainty estimators as the solution of an estimation problem involving unknown statistics. The estimators are derived under the assumption of correlated signal and noise. The bounded- uncertainty framework gives an additional degree of freedom for estimator design that can benefit its performance. It also provides an indirect way of verifying hypotheses regarding unknown statistics for an application domain by examining the behavior of the estimator as a function of bound(s) placed on unknown statistics. If the unknown statistics are within a lower bound than the worst-case limit assumed by a minimax estimator, the quality of the estimation is increased. The derived estimators are applied to the filtering of quantization noise in coded and reconstructed video frames. improve the performance of estimators for the application of interest. Therefore, in this paper we propose an approach for de- signing a more general class of estimators that achieve a better balance between performance and robustness conditions. The estimation problem is formulated and solved under the assumption of correlation between signal and noise (quan- tization noise in our application). Rather than follow the minimax formulation in this context, we describe a more general approach to the determination of an optimal linear estimator. This approach is based on the placement of a bound in the acceptable interval of the unknown statistic (e.g., signal- noise correlation), and the derivation of the estimator as a function of the bound and of estimates of the signal and noise power. Various formulations can be used for deriving these types of estimators. For example, an estimator formulation is also considered where the estimation criterion is designed to express a degree of confidence in a particular assumption about the unknowns, counter-balanced by a term that handles violations of that assertion.
Quantification of left-ventricular regional dyssynergy by radionuclide angiography. (1987)

To determine whether variables obtained from Fourier analysis of gated equilibrium radionuclide angiographic (RNA) images can detect and quantify changes in left-ventricular (LV) regional wall motion induced by transient ischemia, 11 chronically instrumented dogs were simultaneously studied with hemodynamic measurements and RNA during control, left circumflex (LCx) coronary artery occlusion, and postocclusion conditions. The dogs were preinstrumented with aortic and LV catheters, electromagnetic aortic and LCx coronary artery flow probes, high-fidelity LV micromanometers, LCx coronary artery occluders, and 4-mm ultrasonic transverse LV diameter and 2-mm regional LV segment crystal pairs. Radionuclide LV regional phase and amplitude variables were calculated for each condition. The absolute changes in LCx region RNA mean, median, and standard deviation of mean phase correlated with the percent changes in LCx segment crystal fractional shortening (r = -0.71, -0.64, and -0.51, respectively; all p less than or equal to 0.01). Similarly, the absolute changes and percent changes in LCx region RNA mean amplitude per pixel correlated with the percent changes in LCx segment crystal fractional shortening (r = 0.89 and 0.94, respectively; both p less than 0.001). When these LCx region RNA phase variables were subgrouped according to mild or severe depression or augmentation in LCx segment crystal fractional shortening, progressive differences were observed between the average values for these subgroups (p less than 0.05 to p less than 0.001). These data, therefore, suggest that these regional RNA phase variables may be able to detect and quantify alterations in LV contraction patterns due to transient ischemia.
Concomitant use of adalimumab and immunomodulators or corticosteroids compared with adalimumab alone (2011)

more rapid response was needed), the protocol was amended to prespecify enrollment of 390 additional patients who were randomized 1:1:1 to the original adalimumab 160-/80-mg regimen; adalimumab 80 mg at Week 0 and 40 mg at Weeks 2, 4, and 6; or placebo. HRQOL was measured by the Inflammatory Bowel Disease Questionnaire (IBDQ) and Mental and Physical Component Summary (MCS and PCS) scores of the Short Form 36 Health Survey (SF-36). The intentionto-treat population enrolled after the protocol amendment was analyzed. Changes from baseline were compared using 1-way analysis of covariance with treatment as a factor and baseline value as a covariate. RESULTS: Patients treated with the 160-/80-mg induction regimen had significant improvements in IBDQ and SF-36 PCS scores vs. placebo at Week 4 that were maintained at Week 8 (table ). With the 80-/40-mg induction regimen, only SF-36 scores at Week 4 were significantly better than placebo. SF-36 MCS scores were not significantly improved in either adalimumab group. CONCLUSION: Anti-TNF-naive patients with moderate to severe ulcerative colitis who failed conventional therapy experienced significant improvements in IBDQ and SF-36 PCS scores through Week 8 with adalimumab 160-/80-mg induction therapy vs. placebo. HRQOL improvements with the 80-/40-mg induction were inconsistent.
Synthesis of a mutagenic principle isolated from tryptophan pyrolysate. (1977)

A potent mutagen, 3-amino-1-methyl-5H-pyrido [4, 3-b] indole isolated from tryptophan pyrolysate was synthesized.
<title>Design and fabrication of passive optical polymer waveguide components for multimode parallel optical links</title> (1997)

The development of multimode passive polymer optical waveguide components for board and backplane interconnect applications, such as in the DARPA-sponsored, polymer optical interconnect technology (POINT) program, require several optics design issues to be addressed including efficiency and modal noise. For example, the mating of arrays of sources, detectors, and fibers requires appropriate fanout structures to match the component pitch. Here we consider designs for such structures employing multimode polymer waveguides, including both abrupt and smooth bending elements. We investigate these structures using a new multimode BPM simulation CAD tool, and consider the bend losses as a function of geometry, angle, and source condition. The results are compared with experimental observations on devices fabricated for use in the POINT demonstration module. The simulation closely matches the experiment, demonstrating the utility of such efforts in practical component development.
Athermal operation of Silicon waveguides: spectral, second order and footprint dependencies (2010)

We report the design criteria and performance of Si ring resonators for passive athermal applications in wavelength division multiplexing (WDM). The waveguide design rules address i) positive-negative thermo-optic (TO) composite structures, ii) resonant wavelength dependent geometry to achieve constant confinement factor (Gamma), and iii) observation of small residual second order effects. We develop exact design requirements for a temperature dependent resonant wavelength shift (TDWS) of 0 pm/K and present prototype TDWS performance of 0.5 pm/K. We evaluate the materials selection tradeoffs between high-index contrast (HIC) and low-index contrast (LIC) systems and show, remarkably, that FSR and footprint become comparable under the constraint of athermal design.
Video Compression and Noise Reduction using Transform/Subband Coding and Adaptive Amplitude Modulation (1991)

This paper presents in a unifying and tutorial manner, the basic ideas behind transform and sub-band representations of a signal. Although transform and subband representations appear to be different, we discuss how, in fact, they are equivalent. This theoretical relationship gives useful insights into the design of video processing and compression systems. An application of this result to the design of an adaptive amplitude modulation/demodulation (AM/DM) system for noise reduction of images is then described. We discuss the AM noise reduction technique for additive noise, and then present a method to reduce the AM side information by exploiting the transform representation of an image.
In vivo integrated photoacoustic and confocal microscopy of hemoglobin oxygen saturation and oxygen partial pressure (2011)

We developed dual-modality microscope integrating photoacoustic microscopy (PAM) and fluorescence confocal microscopy (FCM) to noninvasively image hemoglobin oxygen saturation (sO₂) and oxygen partial pressure (pO₂) in vivo in single blood vessels with high spatial resolution. While PAM measures sO₂ by imaging hemoglobin optical absorption at two wavelengths, FCM quantifies pO₂ using phosphorescence quenching. The variations of sO₂ and pO₂ values in multiple orders of vessel branches under hyperoxic (100% oxygen) and normoxic (21% oxygen) conditions correlate well with the oxygen-hemoglobin dissociation curve. In addition, the total concentration of hemoglobin is imaged by PAM at an isosbestic wavelength.
Learning to Look around Objects for Top-View Representations of Outdoor\n Scenes (2018)

Given a single RGB image of a complex outdoor road scene in the perspective\nview, we address the novel problem of estimating an occlusion-reasoned semantic\nscene layout in the top-view. This challenging problem not only requires an\naccurate understanding of both the 3D geometry and the semantics of the visible\nscene, but also of occluded areas. We propose a convolutional neural network\nthat learns to predict occluded portions of the scene layout by looking around\nforeground objects like cars or pedestrians. But instead of hallucinating RGB\nvalues, we show that directly predicting the semantics and depths in the\noccluded areas enables a better transformation into the top-view. We further\nshow that this initial top-view representation can be significantly enhanced by\nlearning priors and rules about typical road layouts from simulated or, if\navailable, map data. Crucially, training our model does not require costly or\nsubjective human annotations for occluded areas or the top-view, but rather\nuses readily available annotations for standard semantic segmentation. We\nextensively evaluate and analyze our approach on the KITTI and Cityscapes data\nsets.\n
Trihalides (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Mechanisms of hepatocyte growth factor-induced retinal endothelial cell migration and growth. (2000)

HGF and its receptor are expressed in BREC, and HGF stimulates both BREC growth and migration at concentrations observed in the human eye with diabetic retinopathy. HGF signaling appears to involve activation of both PKC and PI3 kinase, inducing MAPK phosphorylation that is critical for migration and growth. However, VEGF does not appear to mediate these initial HGF effects. These results indicate that HGF could have a significant role in mediating retinal endothelial cell proliferation and migration in diabetic retinopathy, and they begin to elucidate the signal transduction pathway by which this action may occur.
Kinetic Energy Release (KER) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Electrical Resistivity of A-15 Compound V3Sn (1980)

Normal-state electrical resistivity of an A-15 compound V 3 Sn with a resistivity ratio of 5.78 and a T c of 4.10 K is reported as a function of temperature. The low temperature results are fit well with the T 3 law of the Wilson theory. The high temperature results, on the other hand, show a deviation from the linear T law. This deviation cannot be explained by taking into account the actual electronic density of states and the anharmonicity of phonon mode, which are introduced to improve the Wilson theory. The phenomenological expression based on the saturation model is well fitted to the high temperature results.
Leeside Separation of Hypersonic Weapons (1996)

Abstract : A cooperative effort between Hughes Missile Systems Company, NASA Langley Research Center and AF Wright Laboratory was performed to evaluate the adequacy of simplified aerodynamic predictive methods for estimating the leeside separation of weapons from a hypersonic air vehicle. Aerodynamic test results were obtained at the NASA Mach 6 wind tunnel facility (Reference 1), where typical store-shaped test models were traversed in the 'shielding' influence of an inclined flat plate. These data largely verify that aerodynamic predictive methods, based on Newtonian impact 'line-of-sight' approximation methods, yield representative force and moment characteristics acting on stores during their leeside carriage and upward eject launch. Based on these predicted data, simulated leeside launch trajectories of advanced submunition weapons show that they can be safely separated from a carriage vehicle at hypersonic speeds.
The Use of Magnetic Resonance Imaging and Plain Radiographs Among Adolescents With Back Pain and Adolescent Idiopathic Scoliosis (2018)

There is substantial use of both MRI and radiographs for adolescents with LBP and/or AIS. Clinicians should be aware of the impact these diagnostic tests have on the patient and the overall health care system.
A bioinspired molybdenum–copper molecular catalyst for CO 2 electroreduction (2020)

Non-noble metal molecular catalysts mediating the electrocatalytic reduction of carbon dioxide are still scarce. This work reports the electrochemical reduction of CO<sub>2</sub> to formate catalyzed by the bimetallic complex [(bdt)Mo<sup>VI</sup>(O)S<sub>2</sub>Cu<sup>I</sup>CN]<sup>2-</sup> (bdt = benzenedithiolate), a mimic of the active site of the Mo-Cu carbon monoxide dehydrogenase enzyme (CODH2). Infrared spectroelectrochemical (IR-SEC) studies coupled with density functional theory (DFT) computations revealed that the complex is only a pre-catalyst, the active catalyst being generated upon reduction in the presence of CO<sub>2</sub>. We found that the two-electron reduction of [(bdt)Mo<sup>VI</sup>(O)S<sub>2</sub>Cu<sup>I</sup>CN]<sup>2-</sup> triggers the transfer of the oxo moiety to CO<sub>2</sub> forming CO<sub>3</sub> <sup>2-</sup> and the complex [(bdt)Mo<sup>IV</sup>S<sub>2</sub>Cu<sup>I</sup>CN]<sup>2-</sup> and that a further one-electron reduction is needed to generate the active catalyst. Its protonation yields a reactive Mo<sup>V</sup>H hydride intermediate which reacts with CO<sub>2</sub> to produce formate. These findings are particularly relevant to the design of catalysts from metal oxo precursors.