gebhart/patrepeval huggingface dataset:
InspectJS: Leveraging Code Similarity and User-Feedback for Effective Taint Specification Inference for JavaScript (2021)

Static analysis has established itself as a weapon of choice for detecting security vulnerabilities. Taint analysis in particular is a very general and powerful technique, where security policies are expressed in terms of forbidden flows, either from untrusted input sources to sensitive sinks (in integrity policies) or from sensitive sources to untrusted sinks (in confidentiality policies). The appeal of this approach is that the taint-tracking mechanism has to be implemented only once, and can then be parameterized with different taint specifications (that is, sets of sources and sinks, as well as any sanitizers that render otherwise problematic flows innocuous) to detect many different kinds of vulnerabilities. But while techniques for implementing scalable inter-procedural static taint tracking are fairly well established, crafting taint specifications is still more of an art than a science, and in practice tends to involve a lot of manual effort. Past work has focussed on automated techniques for inferring taint specifications for libraries either from their implementation or from the way they tend to be used in client code. Among the latter, machine learning-based approaches have shown great promise. In this work we present our experience combining an existing machine-learning approach to mining sink specifications for JavaScript libraries with manual taint modelling in the context of GitHub's CodeQL analysis framework. We show that the machine-learning component can successfully infer many new taint sinks that either are not part of the manual modelling or are not detected due to analysis incompleteness. Moreover, we present techniques for organizing sink predictions using automated ranking and code-similarity metrics that allow an analysis engineer to efficiently sift through large numbers of predictions to identify true positives.
Diene Cyclization toward Chiral Acyliminium Ions. (1996)

The Grignard reaction of 10-bromo-7-methyldeca-2, 6-diene (5) with a C2-symmetric chiral imide 1gave a corresponding hydroxy lactam 6 in 67% yield. Acid cyclization of 6 gave chiral carbocycles 7 and 8 in 53 and 15% yields, respectively. The stereochemistry of 8 was deduced by the NOE and CD spectra of the derived ketone 10. In a similar manner, the acid cyclization of the hydroxy lactam 12, prepared from the bromide 5 and a chiral imide 11, afforded a chiral carbocycle, which was purified as an acetate 13 in 27% yield. The stereochemistry of 13 was confirmed by correlating to that of 8.
Stabilization of DNA methyltransferase levels and CpG island hypermethylation precede SV40-induced immortalization of human fibroblasts. (1994)

De novo methylation of normally unmethylated CpG islands and increased expression of DNA (cytosine-5)-methyltransferase (DNA MTase) are common characteristics of immortalized cell lines and human tumors. To examine the acquisition of these properties with respect to cellular immortalization, we studied CpG island methylation and DNA MTase expression in aging normal human fibroblasts and their SV40-infected preimmortal (precrisis) and immortal (postcrisis) derivatives. The levels of DNA MTase enzyme activity decreased by 50% as normal fibroblasts were cultured to senescence. By contrast, DNA MTase activity did not decrease in SV40-infected pre- or postcrisis cells but remained similar to that of young fibroblasts and 2-4-fold higher than that of senescent fibroblasts. DNA MTase mRNA levels paralleled those of enzyme activity. Several loci were examined to determine the relationship between the dynamics of DNA MTase expression and the appearance of de novo CpG island methylation. Ten CpG island loci examined were unmethylated in normal young fibroblasts. By contrast, four of these loci (the CALC1, MyoD, and IGF-2 genes on chromosome 11p and the estrogen receptor gene on chromosome 6q) were de novo methylated in fully immortalized, postcrisis cells. Two of these four were actually methylated in extended life span precrisis cells, and one, the estrogen receptor locus, exhibited de novo methylation with aging in normal fibroblasts. The data indicate that an ability to maintain DNA MTase levels is acquired with SV40-induced escape from senescence. Furthermore, aberrant CpG island methylation can be established prior to immortalization, either as a function of normal aging or in response to SV40-induced escape from senescence.
Characterization and Analysis of Early Enzymes for Petrobactin Biosynthesis in Bacillus anthracis (2007)

Recently, iron acquisition and, more specifically, enzymes involved in siderophore biosynthesis have become attractive targets for discovery of new antibiotics. Accordingly, targeted inhibition of the biosynthesis of petrobactin, a virulence-associated siderophore encoded by the asb locus in Bacillus anthracis, may hold promise as a potential therapy against anthrax. This study describes the biochemical characterization of AsbC, the first reported 3,4-dihydroxybenzoic acid-AMP ligase, and a key component in the biosynthesis of DHB-spermidine (DHB-SP), the first isolable intermediate in petrobactin biosynthesis. AsbC catalyzes adenylation to the corresponding AMP ester of the unusual precursor 3,4-dihydroxybenzoate, in addition to benzoate substrates bearing hydrogen bond-donating substituents at the para and meta positions on the phenyl ring. In a second reaction, AsbC catalyzes transfer of the activated starter unit to AsbD, an aryl carrier protein similar to acyl and peptidyl carrier proteins that function in fatty acid, polyketide, and nonribosomal peptide biosynthesis. A third protein, AsbE, is shown to be responsible for condensation of 3,4-dihydroxybenzoyl-AsbD with spermidine, providing the DHB-spermidine arms that are linked to citrate for assembly of petrobactin. On the basis of the selective substrate profile of AsbC, a nonhydrolyzable analogue of 3,4-DHB-AMP was synthesized and shown to effectively inhibit AsbC function in vitro.
Serum LD1 isoenzyme and blood lymphocyte subsets as prognostic indicators for severe acute respiratory syndrome (2004)

Apart from age, serum LD1 activity was the best prognostic indicator for predicting death in patients with SARS compared with serum total LD activity, haemoglobin concentration, leucocyte and lymphocyte counts. Its release could possibly be from blood erythrocytes and body tissues other than the myocardium. Blood CD3+, CD4+, CD8+ and natural killer cell counts were found to be good prognostic indicators for predicting admission to ICU in patients with SARS compared with age, leucocyte count and LD isoenzymes. The suppressed CD3+, CD4+, CD8+, and natural killer cell counts were also implicated in the pathophysiology of SARS. Patients with increased serum LD1 should be closely monitored to ensure prompt management, and preparation for admission to ICU could be planned ahead for patients with suppressed lymphocyte subsets.
A 2 million pixel FIT-CCD image sensor for HDTV camera system (1990)

The image area of the frame FIT (frame-interline-transfer)-CCD (charge-coupled-device) image sensor is 14.0 mm (H)*7.9 mm (V), the effective number of pixels is 1920 (H)*1036 (V) and the unit cell size of a pixel is 7.3 mu m (H)*7.6 mu m (V). These specifications are for the high-definition-television (HDTV) format. The horizontal shift register consists of dual-channel, two-phase CCDs driven by a 37.125-MHz clock pulse. The readout phase of each channel is the same, which allows the reset gate of each channel to be connected together. To adapt to the 74.25-MHz readout frequency, one of the output signals is delayed by 13.47 ns through a sample-hold circuit. To reduce the voltage drop of the vertical shift register (V-CCD) drive pulse along the poly-Si transfer gate, an Al wire is put onto the transfer gate and interconnected to decrease the resistance. This Al wire works also as a photoshield. In addition, another poly-Si layer placed between the Al wire and the transfer gate prevents potential shift by separating the poly-Si contact of the transfer gate/poly-Si layer, from the Al contact of the poly-Si layer/Al wire.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fabrication of carbon nanotube lateral field emitters (2003)

We report on the fabrication and field emission of carbon nanotube lateral field emitters. Due to its high aspect ratio and mechanical strength, we use vertically aligned multi-wall carbon nanotubes prepared by plasma-enhanced chemical vapour deposition as cathodes, which makes the fabrication of cantilever type lateral field emitters possible. The emission characteristics show that the field emission initiates at 11–17 V. The device has high geometrical enhancement factors (9.3 × 106 cm−1) compared to standard Spindt tips, which may be due to increased field concentration at the nanotube tip and the close proximity of the anode (<1μm). The relative ease of fabrication compared to vertical field emitters and enhanced field emission characteristics observed makes the carbon nanotube lateral field emitter a good candidate for future integrated nano-electronic devices.
Bonding dense Si/sub 3/N/sub 4/ components to steel for elevated-temperature cycling applications (1985)

A ceramic-to-metal bond has been developed for dense Si/sub 3/N/sub 4/ and steel. The large thermal expansion mismatch was taken into account in the design of such bonds to prevent failure upon thermal cycling. Selection of bonding materials was restricted by the bonding temperature that would allow diffusion of such materials but would not overheat the steel. Previous bond developments had minimized such restrictions as expansion mismatch and bonding temperature by selecting a refractory metal (Mo) to be bonded directly to reaction-bonded Si/sub 3/N/sub 4/. Here, these temperature/expansion restrictions were minimized by going to a two-stage bonding technique.
Dendritic Cell Development: Multiple Pathways to Nature's Adjuvants (1997)

Dendritic cells are a system of bone marrow-derived antigen-presenting cells specialized for interaction with T lymphocytes and essential for initiating primary T cell immune responses. Recent investigation indicates that dendritic cells are of diverse origin, with at least two types of myeloid precursors and a lymphoid precursor implicated in their generation. Mature dendritic cell subtypes, while sharing the capacity to activate T cells, show additional functional specialization. Some dendritic cells are equipped with additional mechanisms to regulate the response of the T cells they activate, while others are able to interact with B cells and modify B cell responses.
RNA splicing programs define tissue compartments and cell types at single-cell resolution (2021)

The extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach, to detect cell-type-specific splicing in >110K cells from 12 human tissues. Using 10X Chromium data for discovery, 9.1% of genes with computable SpliZ scores are cell-type-specifically spliced, including ubiquitously expressed genes <i>MYL6</i> and <i>RPS24</i>. These results are validated with RNA FISH, single-cell PCR, and Smart-seq2. SpliZ analysis reveals 170 genes with regulated splicing during human spermatogenesis, including examples conserved in mouse and mouse lemur. The SpliZ allows model-based identification of subpopulations indistinguishable based on gene expression, illustrated by subpopulation-specific splicing of classical monocytes involving an ultraconserved exon in <i>SAT1</i>. Together, this analysis of differential splicing across multiple organs establishes that splicing is regulated cell-type-specifically.
Highly Linear Ku-Band SiGe PIN Diode Phase Shifter in Standard SiGe BiCMOS Process (2009)

This letter presents a fully integrated highly linear 4-bit SiGe PIN diode phase shifter MMIC for <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ku</i> -band phase-array application in the standard SiGe BiCMOS process. High-performance customized SiGe PIN diode switches are employed for high linearity and low insertion loss. The use of differential inductors in the hybrid switched filters makes this phase shifter compact in size. Measurements show 20 dB ±5 dB input/output return loss, less than ± 1.8° phase variation, and maximum 37 dBm input-referred IP3 over the 14.5-15.5 GHz frequency range, while this phase shifter draws an average current of 3.5 mA from a 3.3 V power supply. To the authors' best knowledge, this 4-bit phase shifter MMIC achieves the highest linearity at <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ku</i> -band in the standard SiGe BiCMOS process without utilizing any post-fabrication process for low loss transmission lines.
Transient Thermal Analysis of the 12.5 kW HERMeS Hall Thruster (2016)

NASA’s Dawn spacecraft entered orbit around the dwarf planet Ceres on March 6, 2015 thereby becoming the first mission to orbit two celestial bodies outside of the Earth-moon system. This feat was made possible due to the use of electric propulsion (EP) to provide the 11 km/s of delta-V that was necessary. This type of propulsion is also enabling for many of NASA’s future missions, such as the proposed Asteroid Redirect Robotic Mission (ARRM). Specifically, the Hall Effect Rocket with Magnetic Shielding (HERMeS) is the propulsive design baseline due to its long operational lifetime and high specific impulse. Extensive modeling is required to verify the thruster's predicted thermal performance and survival during the bounding mission phases. Since the thruster would constrain plasma on the order of tens of thousands of hours, components in the thruster must be able to accommodate much higher sustained temperatures than typical spacecraft hardware. Furthermore, the high temperatures necessitate care in analyzing thermal gradients within the thruster. In this paper, we describe a thermal model of the HERMeS thruster and focus upon the thruster's transient performance under different initial firing conditions. The thruster's transient thermal response is critical to verify margin in the thermal stresses inherent in the thruster and to determine safe start-up procedures to protect the thruster's critical components. This model is used to perform transient thermal analysis of the thruster during startup and shutdown, provide temperature maps for structural analysis, and plan for thermal cycle testing conducted at JPL. The thermal cycle testing includes thruster starts at the cold temperature limits and operation at maximum expected external heat flux. This work will support laboratory environmental testing of the HERMeS thruster, which is being conducted at JPL in 2016.
Lithium niobate processing and testing. End of year report for FY92 (1993)

Major accomplishments/projects during FY92 were: annealed proton exchange waveguide processing on 3-inch wafers, electroplating of 3- inch wafers, 50-ohm electrode development, resonant electrode phase modulator, transfer of processing from Building 131 to Building 153, and miscellaneous projects with outside industry.
In-situ regolith seismic velocity measurement at the InSight landing site on Mars (2022)

InSight’s seismometer package SEIS was placed on the surface of Mars at about 1.2 m distance from the thermal properties instrument HP3 that includes a self-hammering probe. Recording the hammering noise with SEIS provided a unique opportunity to estimate the seismic wave velocities of the shallow regolith at the landing site. However, the value of studying the seismic signals of the hammering was only realised after critical hardware decisions were already taken. Furthermore, the design and nominal operation of both SEIS and HP3 are non-ideal for such high-resolution seismic measurements. Therefore, a series of adaptations had to be implemented to operate the self-hammering probe as a controlled seismic source and SEIS as a high-frequency seismic receiver including the design of a high-precision timing and an innovative high-frequency sampling workflow. By interpreting the first-arriving seismic waves as a P-wave and identifying first-arriving S-waves by polarisation analysis, we determined effective P- and S-wave velocities of vP = 119+45-21 m/s and vS = 63+11-7 m/s, respectively, from around 2,000 hammer stroke recordings. These velocities likely represent bulk estimates for the uppermost several 10’s of cm of regolith. An analysis of the P-wave incidence angles provided an independent vP/vS ratio estimate of 1.84+0.89-0.35 that compares well with the traveltime based estimate of 1.86+0.42-0.25. The low seismic velocities are consistent with those observed for low-density unconsolidated sands and are in agreement with estimates obtained by other methods.
Separation of high-purity propylene through propane-selective CAU-3 isomorphs (2023)

The development of a suitable C3H8-selective adsorbent has been of interest to achieve high energy efficiency. Herein, we report an energy-efficient C3H8-selective CAU-3 BDC and CAU-3-NDC adsorbent. The separation performance was evaluated using a single-component adsorption isotherm, and preferential C3H8 uptake over C3H6 was observed, revealing their C3H8-selective features. To demonstrate the separation ability, a breakthrough experiment was performed on CAU-3-BDC with a 1/15 (v/v) C3H8/C3H6 gas mixture, and the high-purity C3H6 (>99.95%) can be produced during multi-cycle operation. Further, the binding affinity of the C3H8 molecule was determined using computational calculations.
Phase error assessment of MIRAS/SMOS by means of the redundant space calibration (2011)

SMOS is the acronym for the Soil Moisture and Ocean Salinity mission by the European Space Agency (ESA) [1]. Its single payload, the Mcrowave Imaging Radiometer using Aperture Synthesis (MΓRAS), was successfully launched in November 2009. A six months Commissioning Phase was devoted to bring the satellite into a fully operational condition and to characterize the payload using specific orbits to check all instrument modes [2]. An on- going activity is devoted to analyze the contribution of each single calibration procedure to the overall radiometric accuracy in order to assess the dominant sources of spatial errors. In this framework, this paper is devoted to assess the performance of the phase calibration procedures by means of the so called Redundant Space Calibration (RSC) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .
Elucidation and Evolution of the Active Component within Cu/Fe/ZSM-5 for Catalytic Methane Oxidation: From Synthesis to Catalysis (2013)

The development of a catalytic, one-step route for the oxidation of methane to methanol remains one of the greatest challenges within catalysis. Of particular importance is the need to develop an efficient route that proceeds under mild reaction conditions so as to avoid deeper oxidation and the economic limitations of the currently practiced syngas route. Recently, it was demonstrated that a copper- and iron-containing zeolite is an efficient catalyst for such a one-step process. The catalyst in question (Cu–Fe–ZSM-5) is capable of selectively transforming methane to methanol in an aqueous medium with hydrogen peroxide as the terminal oxidant. Nevertheless, despite its high activity and unparalleled methanol selectivity, the origin of its activity and the precise nature of its active species are not yet fully understood. Through a combination of catalytic and spectroscopic studies, we hereby demonstrate that extraframework Fe species are the active component of the catalyst for methane oxidation, although the speciation of these sites from synthesis to catalysis significantly alters the observed activity and selectivity. The analogies and differences between this system and other iron-containing zeolite-catalyzed processes, such as N2O-mediated benzene hydroxylation, are also considered.
Supplementary Figure 3K from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus (2023)

Supplementary Figure 3K from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus
SiC Epitaxial Layer Growth in a 6x150 mm Warm-Wall Planetary Reactor (2012)

Initial results are presented for SiC-epitaxial growths employing a novel 6x150-mm/10x100-mm Warm-Wall Planetary Vapor-Phase Epitaxial (VPE) Reactor. The increased areal throughput offered by this reactor and 150-mm diameter wafers, is intended to reduce the cost per unit area for SiC epitaxial layers, increasing the market penetration of already successful commercial SiC Schottky and MOSFET devices [1]. Growth rates of 20 micron/hr and short &lt;2 hr fixed-cycle times (including rapid heat-up and cool-down ramps), while maintaining desirable epitaxial layer quality were achieved. No significant change in 150 mm diameter wafer shape is observed upon epitaxial growth consistent with good-quality, low-stress substrates and low (&lt;5°C) cross-wafer epitaxial reactor temperature variation. Specular epitaxial layer morphology was obtained, with morphological defect densities consistent with projected 5x5 mm die yields as high as 80% and surface roughness, Ra, of 0.3 nm. Intrawafer thickness uniformity is good, averaging only 1.6% and within a run wafer-to-wafer thickness variation is 2.7%. N-type background doping densities less that 1E14 cm-3 have been measured by CV. Doping uniformity and wafer-to-wafer variation currently average ~12% requiring further improvement. The first 100 m thick 150-mm diameter epitaxial growths are reported.
HIV-1 vaccine design through minimizing envelope metastability (2018)

Overcoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For 10 strains across five clades, we demonstrate that the gp41 ectodomain (gp41<sub>ECTO</sub>) is the main source of envelope metastability by replacing wild-type gp41<sub>ECTO</sub> with BG505 gp41<sub>ECTO</sub> of the uncleaved prefusion-optimized (UFO) design. These gp41<sub>ECTO</sub>-swapped trimers can be produced in CHO cells with high yield and high purity. The crystal structure of a gp41<sub>ECTO</sub>-swapped trimer elucidates how a neutralization-resistant tier 3 virus evades antibody recognition of the V2 apex. UFO trimers of transmitted/founder viruses and UFO trimers containing a consensus-based ancestral gp41<sub>ECTO</sub> suggest an evolutionary root of metastability. The gp41<sub>ECTO</sub>-stabilized trimers can be readily displayed on 24- and 60-meric nanoparticles, with incorporation of additional T cell help illustrated for a hyperstable 60-mer, I3-01. In mice and rabbits, these gp140 nanoparticles induced tier 2 neutralizing antibody responses more effectively than soluble trimers.