gebhart/patrepeval huggingface dataset:
Real-world design and evaluation of compiler-managed GPU redundant multithreading (2014)

Reliability for general purpose processing on the GPU (GPGPU) is becoming a weak link in the construction of reliable supercomputer systems. Because hardware protection is expensive to develop, requires dedicated on-chip resources, and is not portable across different architectures, the efficiency of software solutions such as redundant multithreading (RMT) must be explored. This paper presents a real-world design and evaluation of automatic software RMT on GPU hardware. We first describe a compiler pass that automatically converts GPGPU kernels into redundantly threaded versions. We then perform detailed power and performance evaluations of three RMT algorithms, each of which provides fault coverage to a set of structures in the GPU. Using real hardware, we show that compilermanaged software RMT has highly variable costs. We further analyze the individual costs of redundant work scheduling, redundant computation, and inter-thread communication, showing that no single component in general is responsible for high overheads across all applications; instead, certain workload properties tend to cause RMT to perform well or poorly. Finally, we demonstrate the benefit of architectural support for RMT with a specific example of fast, register-level thread communication
Secure Design and Development Cybersecurity Capability Maturity Model (SD2-C2M2) (2019)

The Secure Design and Development Cybersecurity Capability Maturity Model (SD2-C2M2) provides a browser-based tool that allows hardware and software developers to assess the maturity level of their design and development processes, allows management to determine desired maturity levels in seven domains, and allows developers to monitor process maturity improvements against management goals. The tool can be used by commercial developers as well as internal development organizations. This paper provides an overview of the tool and domains and presents a hypothetical case study of the tool to reduce software buffer overflow attack vulnerabilities by improving the software development process.
Reliability enhancement by a joint optimization of elastic optical path allocation methods (2017)

Increasing the number of lightpaths for protection accommodated onto an optical fibre network improves reliability of communication services. For this purpose, more optical paths can be accommodated by a spectrally efficient path assignment algorithm, while keeping spectral efficiency of the optical path higher. In this paper, we propose a joint optimization of elastic optical path allocation methods. The simulation results show that the joint optimization algorithm achieves reliability enhancement.
Introduction of an Automatic QT Interval Driven Rate Responsive Pacemaker (1988)

QT driven rate responsive pacemakers have been implanted since 1981. The more than 6 years experience and additional knowledge gained during several clinical studies have culminated in the design of an automatic rate responsive pacemaker. The adjustment of the rate responsive function to each individual patient is carried out automatically by the pacemaker, which therefore performs several measurements both at rest and during exercise. The results of these measurements are used to adapt the rate responsive parameters in order to optimize the rate response, even under changing circumstances.
Execution Time Analysis for Industrial Control Applications (2014)

Estimating the execution time of software components is often mandatory when evaluating the non-functional properties of software-intensive systems. This particularly holds for real-time embedded systems, e.g., in the context of industrial automation. In practice it is however very hard to obtain reliable execution time estimates which are accurate, but not overly pessimistic with respect to the typical behavior of the software. This article proposes two new concepts to ease the use of execution time analysis for industrial control applications: (1) a method based on recurring occurrences of code sequences for automatically creating a timing model of a given processor and (2) an interactive way to integrate execution time analysis into the development environment, thus making timing analysis results easily accessible for software developers. The proposed methods are validated by an industrial case study, which shows that a significant amount of code reuse is present in a set of representative industrial control applications.
Multifunctionalized Glycolurils (1999)

Synthetic approaches to a variety of substituted glycoluril compounds are presented herein. We have applied several of these compounds in the solution-phase synthesis of combinatorial libraries, and we have developed methods to differentiate individual reaction sites for the stepwise synthesis of individual polyfunctionalized compounds.
Conjugated Polymeric Zwitterions as Efficient Interlayers in Organic Solar Cells (2013)

Conjugated polymeric zwitterions, when utilized as interlayer materials in bulk heterojunction organic solar cells, lead to significantly enhanced power conversion efficiencies. The electrostatic model of self-aligning dipolar side groups in the vicinity of the metal surface rationalizes the effects of reduced cathode work function, a key factor behind the observed enhanced efficiency.
Asymmetric synthesis of batrachotoxin: Enantiomeric toxins show functional divergence against Na <sub>V</sub> (2016)

The steroidal neurotoxin (-)-batrachotoxin functions as a potent agonist of voltage-gated sodium ion channels (Na<sub>V</sub>s). Here we report concise asymmetric syntheses of the natural (-) and non-natural (+) antipodes of batrachotoxin, as well both enantiomers of a C-20 benzoate-modified derivative. Electrophysiological characterization of these molecules against Na<sub>V</sub> subtypes establishes the non-natural toxin enantiomer as a reversible antagonist of channel function, markedly different in activity from (-)-batrachotoxin. Protein mutagenesis experiments implicate a shared binding side for the enantiomers in the inner pore cavity of Na<sub>V</sub> These findings motivate and enable subsequent studies aimed at revealing how small molecules that target the channel inner pore modulate Na<sub>V</sub> dynamics.
Online SERS detection and characterization of eight biologically-active peptides separated by capillary zone electrophoresis (2015)

There is a need for low cost, sensitive and chemical specific detectors for routine characterization of biomolecules. In this study, we utilize sheath-flow surface-enhanced Raman scattering (SERS) to analyze a mixture of eight biologically-active peptides separated by capillary zone electrophoresis (CZE). Analysis of the SERS electropherogram resulting from online detection resolves the characteristic Raman bands attributed to the amino acid constituents of each peptide, which enables identification. The detection limit by SERS was found to be 10(-8) M. Our results suggest that the structural information obtained from the detected vibrational modes provides complementary characterization to other chemically specific detectors like mass spectrometry and improved chemical identification over other commonly used optical-based post-chromatographic detection methods. In addition, the sheath-flow SERS detection results in band narrowing in the observed electropherogram that enables distinction of closely migrating species. The results presented here indicate that this platform can provide fast, robust, reproducible, and chemical specific detection to facilitate the characterization of peptides.
A high-performance silicon tactile imager based on a capacitive cell (1985)

An 8 × 8-element silicon-based tactile imager fabricated using integrated-circuit process technology is described. The imager consists of an X-Y organized array of capacitive force sensors on 2-mm centers. Each transducer has a zero-pressure capacitance of 1.6 pF, an average sensitivity of 60 mV/g, and a maximum operating force of about 10 g/element. The operating force can be scaled over a wide range without changing the process or lateral array dimensions. The array is read out using a switched-capacitor charge integrator which has been shown capable of a resoiutionof about 1 fF(5 fC), giving a resolution for the imager itself (pad excluded) of more than 8 bit. The readout scheme permits off-chip electronics to be used so that the fabrication sequence requires only five noncritical masks. The array is addressed as a memory, with an access time of less than 20 µsec for 8 pixels. Scaling of the array size to other dimensions is examined and performance limitations are discussed.
Dispersing and Separating Carbon Nanotubes with Novel Surfactant Formulations (2010)

Abstract : As-synthesized single-walled carbon nanotubes (SWNTs) typically possess a range of diameters and electronic properties. This polydispersity has hindered the development of many SWNT-based technologies and encouraged the development of post-synthetic methods for sorting SWNTs by their physical and electronic structure. Herein, we demonstrate that nonionic, biocompatible block copolymers can be used to isolate semiconducting and metallic SWNTs using density gradient ultracentrifugation. Separations conducted with different Pluronic block copolymers reveal that Pluronics with shorter hydrophobic chain lengths lead to higher purity semiconducting SWNTs, resulting in semiconducting purity levels in excess of 99% obtained for Pluronic F68. In contrast, X-shaped Tetronic block copolymers display an affinity for metallic SWNTs, yielding metallic purity levels of 74% for Tetronic 1107. These results suggest that high fidelity and high yield density gradient separations can be achieved using nonionic block copolymers with rationally designed homopolymer segments, thus generating biocompatible monodisperse SWNTs for a range of applications.
Abstract ED04-02: The role of genes in protecting against age-related disease in cancer (2008)

Abstract ED04-02 Despite evidence for a substantial genetic component, the inherited biological factors that promote extended life span (longevity) in humans remain unknown. We have comprehensively characterized over 450 Ashkenazi Jewish families with exceptional longevity (survival in good health to at least age 95) and have identified several biological markers that may be causative in their longevity. These subjects and their offspring have 2-3 fold increases in rates of polymorphism in 3 genes all validated by other in other studies. Two genes are regulating lipoprotein--cholesterol ester transfer protein (CETP) and apolipoprotein C-3 (APOC-3)--and decrease in plasma levels CETP and APOC-3. Another gene is Adiponectin (ADIPOQ) regulating insulin action and inflammation. We have also demonstrated that these genotypes and phenotypes are associated with less hypertension (HTN), cardiovascular disease (CVD) and metabolic syndrome (MS), and improved cognitive function. However, these genes have not been shown yet to protect against cancer. Modulation of GH/IGF-1 axis is conferring longevity in mamalians and low IGF-1 levels is associated with decreased rates of cancers in humans. We demonstrated a gender-specific increase in serum IGFI associated with a smaller stature in female offspring of centenarians. Sequence analysis of the IGF1 and IGF1 receptor (IGF1R) genes of female centenarians showed overrepresentation of heterozygous mutations in the IGF1R gene among centenarians relative to controls that are associated with high serum IGFI levels and reduced activity of the IGFIR as measured in transformed lymphocytes. Thus, genetic alterations in the human IGF1R that result in altered IGF signaling pathway confer an increase in susceptibility to human longevity, suggesting a role of this pathway in modulation of human lifespan, possibly by protecting against cancer. Citation Information: Cancer Prev Res 2008;1(7 Suppl):ED04-02.
Digital staining for histopathology multispectral images by the combined application of spectral enhancement and spectral transformation (2011)

In this paper we introduced a digital staining method for histopathology images captured with an n-band multispectral camera. The method consisted of two major processes: enhancement of the original spectral transmittance and the transformation of the enhanced transmittance to its target spectral configuration. Enhancement is accomplished by shifting the original transmittance with the scaled difference between the original transmittance and the transmittance estimated with m dominant principal component (PC) vectors;the m-PC vectors were determined from the transmittance samples of the background image. Transformation of the enhanced transmittance to the target spectral configuration was done using an nxn transformation matrix, which was derived by applying a least square method to the enhanced and target spectral training data samples of the different tissue components. Experimental results on the digital conversion of a hematoxylin and eosin (H&E) stained multispectral image to its Masson's trichrome stained (MT) equivalent shows the viability of the method.
Development of Small Molecule MEIS Inhibitors that modulate HSC activity (2020)

Meis1, which belongs to TALE-type class of homeobox gene family, appeared as one of the key regulators of hematopoietic stem cell (HSC) self-renewal and a potential therapeutical target. However, small molecule inhibitors of MEIS1 remained unknown. This led us to develop inhibitors of MEIS1 that could modulate HSC activity. To this end, we have established a library of relevant homeobox family inhibitors and developed a high-throughput in silico screening strategy against homeodomain of MEIS proteins using the AutoDock Vina and PaDEL-ADV platform. We have screened over a million druggable small molecules in silico and selected putative MEIS inhibitors (MEISi) with no predicted cytotoxicity or cardiotoxicity. This was followed by in vitro validation of putative MEIS inhibitors using MEIS dependent luciferase reporter assays and analysis in the ex vivo HSC assays. We have shown that small molecules named MEISi-1 and MEISi-2 significantly inhibit MEIS-luciferase reporters in vitro and induce murine (LSKCD34<sup>l</sup>°<sup>w</sup> cells) and human (CD34<sup>+</sup>, CD133<sup>+</sup>, and ALDH<sup>hi</sup> cells) HSC self-renewal ex vivo. In addition, inhibition of MEIS proteins results in downregulation of Meis1 and MEIS1 target gene expression including Hif-1α, Hif-2α and HSC quiescence modulators. MEIS inhibitors are effective in vivo as evident by induced HSC content in the murine bone marrow and downregulation of expression of MEIS target genes. These studies warrant identification of first-in-class MEIS inhibitors as potential pharmaceuticals to be utilized in modulation of HSC activity and bone marrow transplantation studies.
Molecular Identification of the Catabolic Vinyl Chloride Reductase from <i>Dehalococcoides</i> sp. Strain VS and Its Environmental Distribution (2004)

Reductive dehalogenation of vinyl chloride (VC) to ethene is the key step in complete anaerobic degradation of chlorinated ethenes. VC-reductive dehalogenase was partially purified from a highly enriched culture of the VC-respiring Dehalococcoides sp. strain VS. The enzyme reduced VC and all dichloroethene (DCE) isomers, but not tetrachloroethene (PCE) or trichloroethene (TCE), at high rates. By using reversed genetics, the corresponding gene (vcrA) was isolated and characterized. Based on the predicted amino acid sequence, VC reductase is a novel member of the family of corrinoid/iron-sulfur cluster containing reductive dehalogenases. The vcrA gene was found to be cotranscribed with vcrB, encoding a small hydrophobic protein presumably acting as membrane anchor for VC reductase, and vcrC, encoding a protein with similarity to transcriptional regulators of the NosR/NirI family. The vcrAB genes were subsequently found to be present and expressed in other cultures containing VC-respiring Dehalococcoides organisms and could be detected in water samples from a field site contaminated with chlorinated ethenes. Therefore, the vcrA gene identified here may be a useful molecular target for evaluating, predicting, and monitoring in situ reductive VC dehalogenation.
Self-Registered Self-Assembly of Block Copolymers (2017)

Directed self-assembly (DSA) of block copolymer (BCP) thin films, especially with density multiplication, is one of the most promising options for further improving resolution and throughput in nanolithography. However, controlling defect density has been one of the major hurdles for many DSA applications. Both thermodynamically and kinetically, defect-free patterns favor the use of low density multiplication factors and thinner films, which undermine the promise of enhanced resolution and the formation of robust masks for pattern transfer. Here, we demonstrate a self-registered self-assembly method to enable nearly perfect DSA on loosely defined chemical patterns with high density multiplication factor. Self-registered self-assembly involves two DSA steps. In the first step, an ultrathin BCP blend film is used to obtain vanishingly low defect densities. Concurrently as the film is annealed, preloaded chemical markers separate into the different polymer blocks and graft to the substrate locking in a new chemical contrast pattern with 1:1 feature registration. After thorough removal of the blend film, the remaining self-registered chemical pattern can establish defect-free DSA of thick BCP films.
Uses of vaccinia virus as a vector for the production of live recombinant vaccines (1984)

Abstract Vaccinia virus, the world's oldest vaccine, was used originally for the eradication of smallpox. It is now being genetically engineered to create new live vaccines for use against other infectious agents of medical and veterinary importance. Genes coding for antigens of several pathogens have been linked to vaccinia virus transcriptional regulatory signals and inserted into the vaccinia virus genome. The resultant recombinant viruses are infectious, express the foreign gene, stimulate specific immune responses in vaccinated animals and can protect against disease caused by the corresponding pathogen.
H<sup>+</sup>‐Gated Cation Channels<sup>a</sup> (1999)

H(+)-gated cation channels are members of a new family of ionic channels, which includes the epithelial Na+ channel and the FMRFamide-activated Na+ channel. ASIC, the first member of the H(+)-gated Na+ channel subfamily, is expressed in brain and dorsal root ganglion cells (DRGs). It is activated by pHe variations below pH 7. The presence of this channel throughout the brain suggests that the H+ might play an essential role as a neurotransmitter or neuromodulator. The ASIC channel is also present in dorsal root ganglion cells, as is its homolog DRASIC, which is specifically present in DRGs and absent in the brain. Since external acidification is a major factor in pain associated with inflammation, hematomas, cardiac or muscle ischemia, or cancer, these two channel proteins are potentially central players in pain perception. ASIC activates and inactivates rapidly, while DRASIC has both a fast and sustained component. Other members of this family such as MDEG1 and MDEG2 are either H(+)-gated Na+ channels by themselves (MDEG1) or modulators of H(+)-gated channels formed by ASIC and DRASIC. MDEG1 is of particular interest because the same mutations that produce selective neurodegeneration in C. elegans mechanosensitive neurons, when introduced in MDEG1, also produce neurodegeneration. MDEG2 is selectively expressed in DRGs, where it assembles with DRASIC to radically change its biophysical properties, making it similar to the native H(+)-gated channel, which is presently the best candidate for pain perception.
ChemInform Abstract: PYRIMIDO(4,5‐C)PYRIDAZINES. 1. CYCLIZATIONS WITH α‐KETO ESTERS (1979)

Abstract Aus den 2‐Amino‐6‐hydrazino‐4‐pyrimidinonen (I) erhält man mit den 2‐Ketoestern (II) die Cyclisierungsprodukte (III).
Prophylactic Effect of Black Tea Extract as Gargle against Influenza (1997)

We examined whether gargling with black tea prevents influenza infection. Tests were carried out during a five month period (October 1992 to March 1993). The control group that followed their normal daily routine, whereas the test group that gargled with 0.5 w/v% black tea extract twice daily (at 8 a.m. and 5 p.m.). Influenza viruses were isolated from influenza patients and an antigen analysis was carried out. As a result, two strains of influenza A viruses (H3N2) and ten strains of B virus were detected. An HI test was done using paired sera of the control group and the test group. The HI titers raised a four fold or greater in 48.8% (61/125) in the control group and 35.1% (35/134) in the test group. There was a significant difference (p < 0.05) between the control and test groups. These results indicate that black tea extract is effective as a prophylactic agent against influenza infection.
A Method for Calculating Nominal Structural Stress of Spot-Welded Structure : Application to the Spot Welded Cylindrical Shell Structure(<Special Issue>Solid Mechanics Indispensable for Automobile Engineering) (2009)

In order to improve a fatigue life prediction technology of a spot welded structure, the method to evaluate the fatigue life by a nominal structural stress (NSS) was proposed. The authors have proposed the method to obtain the NSS accurately for spot welded structure composed of flat sheets. The proposed method uses the general loads of the nugget and the displacements on the circumference of the diameter D with the center of the nugget, which are obtained from finite element analysis. In this study, the proposed method was applied to a spot welded cylindrical shell structure. As the result, it was found that the proposed method was able to accurately obtain the NSS by using the displacements on the circumference of the small diameter D.
Modeling Polychlorinated Biphenyl Mass Transfer after Amendment of Contaminated Sediment with Activated Carbon (2006)

The sorption kinetics and concentration of polychlorinated biphenyls (PCBs) in historically polluted sediment is modeled to assess a remediation strategy based on in situ PCB sequestration by mixing with activated carbon (AC). We extend our evaluation of a model based on intraparticle diffusion by including a biomimetic semipermeable membrane device (SPMD) and a first-order degradation rate for the aqueous phase. The model predictions are compared with the previously reported experimental PCB concentrations in the bulk water phase and in SPMDs. The simulated scenarios comprise a marine and a freshwater sediment, four PCB congeners, two AC grain sizes, four doses of AC, and comparison with laboratory experiments for up to 540 days of AC amendment slowly mixed with sediment. The model qualitatively reproduces the observed shifts in the PCB distribution during repartitioning after AC amendment but systematically overestimates the overall effect of the treatment in reducing aqueous and SPMD concentrations of PCBs by a factor of 2-6. For our AC application in sediment, competitive sorption of the various solutes apparently requires a reduction by a factor of 16 of the literature values for the AC-water partitioning coefficient measured in pure aqueous systems. With this correction, model results and measurements agree within a factor of 3. We also discuss the impact of the nonlinearity of the AC sorption isotherm and first-order degradation in the aqueous phase. Regular mixing of the sediment accelerates the benefit of the proposed amendment substantially. But according to our scenario, after AC amendment is homogeneously mixed into the sediment and then left undisturbed, aqueous PCB concentrations tend toward the same reduction after approximately 5 or more years.