gebhart/patrepeval huggingface dataset:
Scheduling Issues in Optimistic Parallelization (2007)

Irregular applications, which rely on pointer-based data structures, are often difficult to parallelize. The input-dependent nature of their execution means that traditional parallelization techniques are unable to exploit any latent parallelism in these algorithms. Instead, we turn to optimistic parallelism, where regions of code are speculatively run in parallel while runtime mechanisms ensure proper execution. The performance of such optimistically parallelized algorithms is often dependent on the schedule for parallel execution; improper choices can prevent successful parallel execution. We demonstrate this through the motivating example of Delaunay mesh refinement, an irregular algorithm, which we have parallelized optimistically using the Galois system. We apply several scheduling policies to this algorithm and investigate their performance, showing that careful consideration of scheduling is necessary to maximize parallel performance.
ChemInform Abstract: SYNTHESIS, ANTIINFLAMMATORY AND ANALGESIC ACTIVITY OF 5‐AROYL‐1,2‐DIHYDRO‐3H‐PYRROLO(1,2‐A)PYRROLE‐1‐CARBOXYLIC ACIDS AND RELATED COMPOUNDS (1985)

Abstract Die Carbon‐ Säuren (I) erhält man aus bicyclischen Nitrilen oder Estern durch Acylierung und anschließende Hydrolyse.
A tunable capacitor using an immiscible bifluidic dielectric (2004)

A tunable capacitor using two immiscible fluids of different dielectric constants as a dielectric material are investigated and the feasibility of its RF application is demonstrated. Large capacitance change is obtained when the two fluids have large differences of dielectric constant. When deionized water and air are used as the two fluids, the tunability (T[%]=100/spl times/(C/sub water/-C/sub air/)/C/sub air/) shows a maximum of 6700% at low frequency. Silicone oil (dielectric constant of 2.5) and air is used for the high frequency application to ensure low dielectric loss in the RF frequency range. Nominal tunability and Q-factor at 2.5 GHz is 15.7% and 17.4, respectively. Barium strontium titanate (BST) nano powder mixture with silicone oil (43 wt% of BST) shows 12% more tunability than that of a pure silicone oil capacitor (due to the high permittivity contribution of BST) without concomitant Q-factor degradation. A tunable resonator consisting of the fluidic tunable capacitor combined with a line inductor is fabricated and a tuning bandwidth of 15% (0.27 GHz) is obtained at 1.8 GHz.
Terabus: a chip-to-chip parallel optical interconnect (2005)

Terabus is based on a chip-like optoelectronic packaging structure (Optochip) assembled directly onto an organic card with integrated waveguides (Optocard). To-date, Terabus has demonstrated 4times12-array optical transmitters and receivers operating up to 20 Gb/s and 14 Gb/s per channel
Statistical methodology for modeling non-IID memory fails events (2014)

We propose a comprehensive and computationally efficient methodology for the estimation of correlated memory fail probabilities. The methodology allows, for the first time, to accurately predict the number of failing memory parts in the presence of correlation between the memory fails due to shared peripheral logic. It relies on importance sampling to model the fail region and emulate different memory architectures. Unlike traditional yield analysis methodologies that assume independent and identically distributed fail events, we record a high overdispersion rate, variance to mean ratio, due to the correlations. This in turn leads to an increase in the number of memory bit fails compared to IID events and is itself a strong function of the memory/peripheral logic grouping. Under extreme operating conditions, our experiments demonstrate overdispersion ratios larger than 10, and more than 23% increase in the number of fails at the 90 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> percentile level of the array samples/population. However, from a redundancy perspective, the correlations result in reduced column redundancy quota requirements with demonstrated cases with more than 20% reduction in the required quota compared to the IID assumption.
Salivary biomarkers for pancreatic cancer detection (2009)

4630 Pancreatic cancer is the 4th leading cause of cancer death. Lack of early detection technology for pancreatic cancer invariably leads to a typical clinical presentation of incurable disease at initial diagnosis. We evaluated the performance and translational utilities of the salivary transcriptomic and microbial biomarkers for pancreatic cancer detection. Biomarker discovery strategies were used to profile transcriptome in saliva supernatant and microflora in saliva pellet. The Affymetrix Human Genome U133+2.0 array was used to discover altered gene expression in saliva supernatant. The Human Oral Microbe Identification Microarray (HOMIM) was used to investigate microflora shift in saliva pellet. Biomarkers selected from both studies were subjected to an independent clinical validation using a cohort of 30 pancreatic cancer, 30 chronic pancreatitis and 30 healthy matched-control saliva samples. Two panels of salivary biomarkers, including eleven mRNA biomarkers and two microbial biomarkers were discovered and validated for pancreatic cancer detection. The logistic regression model with the combination of three mRNA biomarkers (ACRV1, DMXL2 and DPM1) yielded a ROC-plot AUC value of 0.974 (95% CI, 0.896 to 0.997; P < 0.0001) with 93.3% sensitivity and 90% specificity in distinguishing pancreatic cancer patients from healthy subjects. The logistic regression model with the combination of two bacterial biomarkers (Neisseria elongata and Streptococcus mitis) yielded a ROC-plot AUC value of 0.895 (95% CI, 0.784 to 0.961; P < 0.0001) with 96.4% sensitivity and 82.1% specificity in distinguishing pancreatic cancer patients from healthy subjects. More importantly, the logistic regression model with the combination of four biomarkers (mRNA biomarkers, ACRV1, DMXL2 and DPM1; bacterial biomarker, S. mitis) could differentiate pancreatic cancer patients from all non-cancer subjects (chronic pancreatitis and healthy control), yielding a ROC-plot AUC value of 0.949 (95% CI, 0.877 to 0.985; P < 0.0001) with 92.9% sensitivity and 85.5% specificity. This is the first report demonstrating the value of multiplex salivary biomarkers for the non-invasive detection of a high impact systemic cancer. No significant financial relationships to disclose.
Understanding Silicon Nitride’s Biological Properties: From Inert to Bioactive Ceramic (2018)

Due to the favourable combination of mechanical strength and fracture toughness, silicon nitride has been applied as a load-bearing bioceramic, in particular for implants used in spinal fusion surgery. Only recently it has been observed that the supposedly inert surface of silicon nitride is actually bioactive: a slow, but not negligible, pH controlled, ionic exchange between nitrogen and oxygen leads to the formation and elution of silicic acid and ammonia groups, also resulting in an effective protection against bacteria colonization. These properties could be further modulated by chemical and mechanical treatments.
Molecular Cloning of Endo-β- <scp>d</scp> -1,4-Glucanase Genes, <i>rce1</i> , <i>rce2</i> , and <i>rce3</i> , from <i>Rhizopus oryzae</i> (2003)

Three endoglucanase genes, designated the rce1, rce2, and rce3 genes, were isolated from Rhizopus oryzae as the first cellulase genes from the subdivision ZYGOMYCOTA: All the amino acid sequences deduced from the rce1, rce2, and rce3 genes consisted of three distinct domains: cellulose binding domains, linker domains, and catalytic domains belonging to glycosyl hydrolase family 45. The rce3 gene had two tandem repeated sequences of cellulose binding domains, while rce1 and rce2 had only one. rce1, rce2, and rce3 had various lengths of linker sequences.
The regulatory element READ1 epistatically influences reading and language, with both deleterious and protective alleles (2015)

READ1 and KIAHap show interdependence--READ1 risk alleles synergise with KIAHap, whereas READ1 protective alleles act epistatically to negate the effects of KIAHap. The family data suggest that these variants interact in trans genetically, while the 3C results show that a region of DCDC2 containing READ1 interacts physically with the region upstream of KIAA0319. These data support a model in which READ1 regulates KIAA0319 expression through KIAHap and in which the additive effects of READ1 and KIAHap alleles are responsible for the trans genetic interaction.
<title>Video summarization using motion descriptors</title> (2001)

We describe a technique for video summarization that uses motion descriptors computed in the compressed domain to speed up conventional color based video summarization technique. The basic hypothesis of the work is that the intensity of motion activity of a video segment is a direct indication of its 'summarizability.' We present experimental verification of this hypothesis. We are thus able to quickly identify easy to summarize segments of a video sequence since they have a low intensity of motion activity. Moreover, the compressed domain extraction of motion activity intensity is much simpler than the color-based calculations. We are able to easily summarize these segments by simply choosing a key-frame at random from each low- activity segment. We can then apply conventional color-based summarization techniques to the remaining segments. We are thus able to speed up color-based summarization techniques by reducing the number of segments on which computationally more expensive color-based computation is needed.
A 158 pJ/bit 1.0 Mbps Bluetooth Low Energy (BLE) Compatible Backscatter Communication System for Wireless Sensing (2019)

Wireless links using backscatter communication offer the advantages of reduced complexity and orders of magnitude lower power consumption than active radios. However, the need for specialized receiver systems has limited the use of backscatter in wireless sensing applications. To address this need, we introduce the first backscatter-based wireless sensor tag that can stream sensor data to any of the billions of existing Bluetooth 4.0 Low Energy (BLE) devices, including smartphones, tablets, and PCs. The FPGA-based “BLE Backscatter Sensor Node” (BBSN) uses an external carrier source and requires no modifications to smartphone, tablet, or PC hardware or software whatsoever. The device transmits a 1.0 Mbps data stream with BLE-compatible frequency-shift keying modulation. The backscatter modulator consumes only 158 pJ/bit, making it over 60X more energy efficient than a conventional BLE active radio (>10 nJ/bit).
Robust Adaptive Heart-Rate Monitoring Using Face Videos (2018)

Heart rate (HR) monitoring is indispensable for several real-world scenarios, especially when acquired in a non-contact manner. It can be accomplished using face videos acquired from ubiquitous cameras in an inexpensive, non-invasive and unobtrusive manner. But the HR monitoring can be erroneous when the video contains facial expressions, out-of-plane movements, change in camera parameters (like focus) and variations in environmental factors (like illumination). The proposed system mitigates these problems for improving the HR monitoring. For this, it defines an adaptive temporal signal selection mechanism which identifies and removes the facial areas affected by facial expressions. Moreover, it introduces a novel post-processing mechanism which perform HR monitoring by utilizing face reconstruction and quality. The post-processing is used when the face video contains facial movements. Experimental results reveal that incorporation of adaptive temporal signal selection and post-processing mechanisms can significantly improve the HR monitoring. It depicts that the Pearson correlation between actual and estimated HR is 0.95 while the average absolute error is 1.63 beats per minute, which indicates that the proposed system provides good HR monitoring.
Structural Definition of the Active Site and Catalytic Mechanism of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase (2002)

X-ray crystal structures of L-3,4-dihydroxy-2-butanone-4-phosphate synthase from Magnaporthe grisea are reported for the E-SO(4)(2-), E-SO(4)(2-)-Mg(2+), E-SO(4)(2)(-)-Mn(2+), E-SO(4)(2)(-)-Mn(2+)-glycerol, and E-SO(4)(2)(-)-Zn(2+) complexes with resolutions that extend to 1.55, 0.98, 1.60, 1.16, and 1.00 A, respectively. Active-site residues of the homodimer are fully defined. The structures were used to model the substrate ribulose 5-phosphate in the active site with the phosphate group anchored at the sulfate site and the placement of the ribulose group guided by the glycerol site. The model includes two Mg(2+) cations that bind to the oxygen substituents of the C2, C3, C4, and phosphate groups of the substrate, the side chains of Glu37 and His153, and water molecules. The position of the metal cofactors and the substrate's phosphate group are further stabilized by an extensive hydrogen-bond and salt-bridge network. On the basis of their proximity to the substrate's reaction participants, the imidazole of an Asp99-His136 dyad from one subunit, the side chains of the Asp41, Cys66, and Glu174 residues from the other subunit, and Mg(2+)-activated water molecules are proposed to serve specific roles in the catalytic cycle as general acid-base functionalities. The model suggests that during the 1,2-shift step of the reaction, the substrate's C3 and C4 hydroxyl groups are cis to each other. A cis transition state is calculated to have an activation barrier that is 2 kcal/mol greater than that of the trans transition state in the absence of the enzyme.
An HSV-2 nucleoside-modified mRNA genital herpes vaccine containing glycoproteins gC, gD, and gE protects mice against HSV-1 genital lesions and latent infection (2020)

HSV-1 causes 50% of first-time genital herpes infections in resource-rich countries and affects 190 million people worldwide. A prophylactic herpes vaccine is needed to protect against genital infections by both HSV-1 and HSV-2. Previously our laboratory developed a trivalent vaccine that targets glycoproteins C, D, and E present on the HSV-2 virion. We reported that this vaccine protects animals from genital disease and recurrent virus shedding following lethal HSV-2 challenge. Importantly the vaccine also generates cross-reactive antibodies that neutralize HSV-1, suggesting it may provide protection against HSV-1 infection. Here we compared the efficacy of this vaccine delivered as protein or nucleoside-modified mRNA immunogens against vaginal HSV-1 infection in mice. Both the protein and mRNA vaccines protected mice from HSV-1 disease; however, the mRNA vaccine provided better protection as measured by lower vaginal virus titers post-infection. In a second experiment, we compared protection provided by the mRNA vaccine against intravaginal challenge with HSV-1 or HSV-2. Vaccinated mice were totally protected against death, genital disease and infection of dorsal root ganglia caused by both viruses, but somewhat better protected against vaginal titers after HSV-2 infection. Overall, in the two experiments, the mRNA vaccine prevented death and genital disease in 54/54 (100%) mice infected with HSV-1 and 20/20 (100%) with HSV-2, and prevented HSV DNA from reaching the dorsal root ganglia, the site of virus latency, in 29/30 (97%) mice infected with HSV-1 and 10/10 (100%) with HSV-2. We consider the HSV-2 trivalent mRNA vaccine to be a promising candidate for clinical trials for prevention of both HSV-1 and HSV-2 genital herpes.
Synthesis, Antitumor Activity, and Tolerability of Phospholipids Containing Nitrogen Homologues (1995)

Replacing the N atom with an As or P atom in antineoplastically active phospholipids 1 and 2 (Z  N) leads to homologous compounds (Z  As, P) that are equally effective against tumors and have fewer side effects than the N-containing phospholipids. This marks definite progress in cancer treatment with chemotherapeutically active phospholipids.
ChemInform Abstract: 4′‐Methylangelicins: New Potential Agents for the Photochemotherapy of Psoriasis. (1984)

Abstract Wie im Formelschema beschrieben, werden die Angelicin‐Derivate (VII) dargestellt, von denen (VIIc) ein wirksames Psoriasis‐Mittel darstellt.
In Situ Localized Growth of Ordered Metal Oxide Hollow Sphere Array on Microheater Platform for Sensitive, Ultra-Fast Gas Sensing (2017)

A simple and versatile strategy is presented for the localized on-chip synthesis of an ordered metal oxide hollow sphere array directly on a low power microheater platform to form a closely integrated miniaturized gas sensor. Selective microheater surface modification through fluorinated monolayer self-assembly and its subsequent microheater-induced thermal decomposition enables the position-controlled deposition of an ordered two-dimensional colloidal sphere array, which serves as a sacrificial template for metal oxide growth via homogeneous chemical precipitation; this strategy ensures control in both the morphology and placement of the sensing material on only the active heated area of the microheater platform, providing a major advantage over other methods of presynthesized nanomaterial integration via suspension coating or printing. A fabricated tin oxide hollow sphere-based sensor shows high sensitivity (6.5 ppb detection limit) and selectivity toward formaldehyde, and extremely fast response (1.8 s) and recovery (5.4 s) times. This flexible and scalable method can be used to fabricate high performance miniaturized gas sensors with a variety of hollow nanostructured metal oxides for a range of applications, including combining multiple metal oxides for superior sensitivity and tunable selectivity.
Liquid‐Phase Reaction‐Bonding of Silicon Carbide Using Alloyed Silicon‐Molybdenum Melts (1990)

We have investigated reaction‐forming of silicon carbide by the infiltration of carbonaceous preforms using alloyed silicon melts, in order to synthesize composite materials free of the residual silicon phase that has previously limited mechanical properties and upper use temperatures. In this approach, rejection of the alloying component(s) from the primary silicon carbide phase into the remaining melt results in the formation of a secondary refractory phase, such as a silicide, in place of residual free silicon. Experiments conducted in the Si‐Mo melt system show that relatively dense (>90%) silicon carbide‐molybdenum silicide materials free of residual silicon and residual carbon can be obtained. A model for reactive infiltration based on time‐dependent permeabilities is proposed. Processing variables important for control of the reaction rate relative to the infiltration rate, and associated processing flaws, are discussed.
Evaluation of Barrier Creams against Sulphur Mustard (2002)

The purpose of this study was to assess the effectiveness of a range of passive and reactive barrier cream formulations against the chemical warfare agent sulphur mustard (SM) using an in vitro diffusion cell system containing human skin. In general, proprietary formulations were relatively effective under occluded conditions, but ineffective under unoccluded conditions. For example, SM skin absorption rates through occluded control and Stokoderm pre-treated skin were 538 +/- 193 and 200 +/- 51 microg x cm(-2) x h(-1), respectively (p < 0.05). Under unoccluded conditions, control and Stokoderm pre-treated skin absorption rates were 4.41 +/- 1.90 and 36.84 +/- 15.19 microg x cm(-2) x h(-1) (p < 0.05). Novel (perfluorinated) barrier creams were generally more effective under unoccluded conditions; pre-treatment with one formulation led to an 18-fold reduction in skin absorption rate and reduced the total amount of SM penetrated by 95% of the applied dose. Several proprietary formulations also had adverse effects on the effectiveness of the skin decontaminant fuller's earth. The rate (Jss) and total amount (percentage of dose) of SM absorbed through the skin were deemed to be independent parameters of barrier cream performance. These data indicate that (1) perceived conditions of use, (2) compatibility with existing protective equipment and (3) the rate and extent of SM skin absorption must all be taken into account when evaluating barrier creams in vitro.
Generating AMF Configurations from Software Vendor Constraints and User Requirements (2009)

The service availability forum (SAF) has defined a set of service API specifications addressing the growing need of commercial-off-the-shelf high availability solutions. Among these services, the availability management framework (AMF) is the service responsible for managing the high availability of the application services by coordinating redundant application components. To achieve this task, an AMF implementation requires a specific logical view of the organization of the application's services and components known as an AMF configuration. Developing manually such a configuration is a complex, error prone, and time consuming task. In this paper, we present an approach for automatic generation of AMF configurations from a set of requirements given by the configuration designer and the description of the software as provided by the vendor. Our approach alleviates the need of configuration designers dealing with a large number of AMF entities and their relations.
Near‐Field Optical Microscopy in Jerusalem (1996)

Abstract During the past decade the area of near‐field optics has seen an exponential growth. This is a result of the resolution of the technical problems that had prevented the potential of this powerful optical methodology from being generally applied. As a result of committed and steady progress in resolving these technical problems the fundamental principles of near‐field optics are now generally accepted and the technology is widely used. The potential of these advances has important implications in a variety of areas, from chemistry to information storage to the characterization of structures with potential in fundamental mesoscopic physics, and in the characterization of practical devices in electronics and photonics which are rapidly reaching nanometer dimensionalities. In this paper, the progress that has been made in Jerusalem in developing a near‐field microscope fully integrated with conventional far‐field, confocal far‐field, and all forms of force and other scanned probe microscopies will be described. The potential of this unique imaging system in chemical applications is also discussed.
Lipoxin A<sub>4</sub> and aspirin‐triggered 15‐epi‐LXA<sub>4</sub> inhibit tumor necrosis factor‐α‐initiated neutrophil responses and trafficking: novel regulators of a cytokine—chemokine axis relevant to periodontal diseases (1999)

The impact of lipoxin A4 (LXA4) and aspirin-triggered-lipoxins (ATL) was investigated in tumor necrosis factor (TNF alpha)-initiated neutrophil (PMN) responses in vitro and in vivo using LX analogs that are metabolically more stable. At nanomolar levels, the LXA4 and ATL analog 15 R/S-methyl-LXA4 each blocked TNF alpha-stimulated IL-1 beta release by isolated human PMN in vitro. These LXA4-ATL actions were time- and concentration-dependent. The TNF alpha-induced IL-1 beta gene expression was also regulated by 15 R/S-methyl-LXA4. In addition, 15 R/S-methyl-LXA4 added to murine air pouches dramatically inhibited TNF alpha-stimulated leukocyte trafficking in vivo, as well as altered the appearance of both macrophage inflammatory peptide-2 and IL-1 beta and concomitantly stimulated IL-4 in pouch exudates. These findings from in vitro and in vivo experiments indicate that both LXA4 and ATL are regulators of TNF alpha-directed neutrophil actions and stimulate IL-4 in exudates and thus regulate mediators that are held to play an important role in the pathogenesis of periodontal disease.