gebhart/patrepeval huggingface dataset:
JSPChecker (2016)

JSPChecker is a static analysis tool that detects context-sensitive cross-site scripting vulnerabilities in legacy web applications. While cross-site scripting flaws can be mitigated through sanitisation, a process that removes dangerous characters from input values, proper sanitisation requires knowledge about the output context of input values. Indeed, web pages are built using a mix of different languages (e.g. HTML, CSS, JavaScript and others) that call for different sanitisation routines. Context-sensitive cross-site scripting vulnerabilities occur when there is a mismatch between sanitisation routines and output contexts.
Surfactant technology applied toward an active pharmaceutical ingredient: more than a simple green chemistry advance (2015)

Process Mass Intensity (PMI) for (a) process in organic solvents, (b) process in water with surfactants.
A functional analysis of protooncogene Vav's role in adult human hematopoiesis (1996)

The Vav protooncogene is expressed almost exclusively in hematopoietic cells, but its role in regulating adult human hematopoietic cell development remains uncertain. To analyze Vav function in adult blood cell formation, we used antisense (AS) oligodeoxynucleotides (ODN) to disrupt its expression in normal and malignant human hematopoietic cells. Bone marrow or peripheral blood mononuclear cells (MNC) were obtained from consenting normal donors and patients with acute or chronic myelogenous leukemia (AML and CML, respectively) and polycythemia vera (PV). Adherent and T-cell-depleted (A-T-) MNC or CD34+ MNC were exposed to unmodified sense, antisense, or scrambled sequence ODN corresponding to codons 2-7 of Vav's mRNA sequence. Cells were then assayed for Vav mRNA expression by reverse transcription-polymerase chain reaction and Vav protein expression by Western binding. After showing that Vav-targeted AS ODN could specifically diminish Vav mRNA and protein expression, we assessed the ability of Vav-deficient cells to form myeloid and erythroid colonies in methyl-cellulose cultures. When normal CD34+ MNC were exposed to Vav AS ODN, no effect on colony-forming unit-granulocyte-macrophage (CFU-GM) or CFU-megakaryocyte colony formation was observed. In contrast erythroid colony growth was inhibited by a mean +/- SD of 62% +/- 16%. In patients with hematopoietic malignancies. Vav-targeted AS ODN inhibited CFU-GM colony formation in a sequence-specific and dose-dependent manner in 1 of 3 AML, 13 of 17 CML, and 2 of 2 PV patients. At the highest concentration used, the Vav AS ODN inhibited CFU-GM colony formation from 66% to 81% when compared with control cell colony growth. Burst-forming unit-erythroid (BFU-E) colony-formation was also assessed in 7 PV patients. The Vav-targeted AS ODN inhibited BFU-E colony formation in all by a mean +/- SD of 81% +/- 4%. These findings suggest that Vav function may not be easily complemented in a significant subset of normal adult erythroid progenitor cells and may also be necessary for myeloid progenitor cell growth in a variety of hematopoietic malignancies.
LER detection using dark field spectroscopic reflectometry (2010)

Line edge roughness (LER) is an increasingly important issue as lithography scales down. Currently LER is usually measured using scanning electron microscopy (SEM) tools; however, using optical techniques to measure LER may have potential benefit due to less resist damage and higher throughput. In this paper, we explore the detection and potential measurement of LER using dark field spectroscopic reflectometry. We provide a proof of feasibility by showing LER spectra collected on several different applications, which behave consistently with scattering from small particles (Rayleigh) and decrease sharply with wavelength. Additionally, the dependence of the spectra on film thickness bears resemblance to thin film measurements. Finally, we also provide preliminary simulation results showing similar spectral characteristics to the measured spectra.
Actively Shaken In Situ Passive Sampler Platform for Methylmercury and Organics (2024)

Prototype of a periodically vibrated device used to deploy passive samplers in sediments.Accurate bioavailability measurements are needed for improved site risk assessments, proper selection of remedy, and post-remediation monitoring. While freely dissolved porewater concentrations of organic chemicals of concern and aqueous concentrations of bioavailable forms of trace metals in sediments have been demonstrated to be the ideal metrics for assessing bioavailability, accurate measurements of the low environmentally relevant concentrations have been a challenge. Passive sampling for sediment porewater has emerged as a very promising approach, but in situ measurements are complicated by slow mass transfer of strongly hydrophobic compounds. For methylmercury (MeHg), development of passive samplers has been hindered by the lack of an approach that adequately predicts porewater concentrations in complex milieu. This project was conducted in two phases. Phase I efforts successfully demonstrated the feasibility of using periodic vibration to enhance mass transfer and accuracy of measurement of strongly hydrophobic compounds and also demonstrated the feasibility of an equilibrium passive sampling approach for MeHg. The results of Phase I studies can be found in the Final Report. During Phase II, this research focused on advancing passive sampling on two major fronts: 1) use of mathematical modeling and device development to enable short-term passive sampling for hydrophobic pollutants, and 2) development of an equilibrium passive sampler for methylmercury in water and sediment porewater. The proof-of-concept developments in the Phase I project were successfully advanced with further testing and field deployments, paving the way for the extension of passive sampling to these heretofore difficult to measure analytes/conditions.
Production of ethanol from biopolymers by anaerobic, thermophilic, and extreme thermophilic bacteria. I. Regulation of carbohydrate utilization in mutants of Thermoanaerobacter ethanolicus (1983)

One mutant of T. ethanolicus JW200 Fe(4) was characterized by studying fermentations of xylose, glucose, cellobiose, and soluble corn starch and mixtures of two or three of these substrates. JW200 Fe(4) does not show diauxic growth characteristics if xylose and hexose are supplied together. However, in mixtures, glucose is used prior to the breakdown of cellobiose or starch. 13 references, 5 figures.
Membranes: Chlorine Resistant Glutaraldehyde Crosslinked Polyelectrolyte Multilayer Membranes for Desalination (Adv. Mater. 17/2015) (2015)

Novel membranes are fabricated for use in desalination and water purification applications by F. Caruso, S. E. Kentish, and co-workers, described on page 2791. The crosslinked polyelectrolyte multilayer membranes are synthesized on a porous polysulfone support within aqueous media and are crosslinked with glutaraldehyde. This leads to NaCl rejections of up to 97%. The incorporation of a highly sulfonated polysulfone polyanion results in outstanding chlorine resistance.
A beat-pattern based error concealment scheme for music delivery with burst packet loss (2001)

Error concealment is an important method to mitigate the degradation of the audio quality when compressed audio packets are lost in error prone channels, such as mobile Internet and digital audio broadcasting. This paper presents a novel error concealment scheme, which exploits the beat and rhythmic pattern of music signals. Preliminary simulations show significantly improved subjective sound quality in comparison with conventional methods in the case of burst packet losses. The new scheme is proposed as a complement to prior arts. It can be adopted to essentially all existing perceptual audio decoders such as an MP3 decoder for streaming music.
Acellular Cardiac Extracellular Matrix as a Scaffold for Tissue Engineering: <i>In Vitro</i> Cell Support, Remodeling, and Biocompatibility (2009)

We have developed an efficient decellularization process for the isolation of extracellular matrix (ECM) from native cardiac tissue. The isolated ECM exhibited desirable mechanical properties in terms of elasticity, strength and durability-properties required from scaffolds used for cardiac tissue repair. This study further investigates the potential use of this scaffold for cardiac tissue engineering in terms of interactions with seeded cells and biocompatibility. We used the commonly studied fibroblasts, cardiomyocytes, and mesenchymal stem cells, which were isolated and seeded onto the scaffold. Cell density and distribution were followed by 3,3'-dioctadecyloxacarbocyanine perchlorate staining, and their proliferation and viability were assessed by AlamarBlue assay and fluorecein-diacetate/propidium iodide staining. Fibroblast-seeded scaffolds shrank to 1-2 mm(3) spheroids, and their glycosaminoglycans significantly increased by 23%. The expression of ECM remodeling-related mRNAs of collagens I and III, matrix metalloproteinase 2, and type 1 tissue inhibitor of metalloproteinases was quantified by real-time polymerase chain reaction, and was found significantly elevated in fibroblast-seeded scaffold, compared with the control cells on plates. Fibroblast-seeded scaffolds lost some flexibility, yet gained strength compared with the acellular scaffolds, as shown by mechanical testing. Scaffold seeded with cardiomyocyte began to beat in concert few days after seeding, and the myocytes expressed typical functional cardiac markers such as alpha-actinin, troponin I, and connexin43. The cells revealed aligned elongated morphology, as presented by immunofluorescent staining and scanning electron microscopy. Mesenchymal stem cell-seeded scaffolds maintained viability over 24 days in culture. These findings further strengthen the potential use of acellular cardiac ECM as a biomaterial for heart regeneration.
Growth of a delta-doped silicon layer by molecular beam epitaxy on a charge-coupled device for reflection-limited ultraviolet quantum efficiency (1992)

We have used low-temperature silicon molecular beam epitaxy to grow a δ-doped silicon layer on a fully processed charge-coupled device (CCD). The measured quantum efficiency of the δ-doped backside-thinned EG&G Reticon CCD is in agreement with the reflection limit for light incident on the back surface in the spectral range of 260–600 nm. The 2.5 nm silicon layer, grown at 450 °C, contained a boron δ-layer with surface density ∼2×1014 cm−2. Passivation of the surface was done by steam oxidation of a nominally undoped 1.5 nm Si cap layer. The UV quantum efficiency was found to be uniform and stable with respect to thermal cycling and illumination conditions.
Micro-Pressure Sensors Based on Photonic Crystal Waveguide Couplers (2014)

Micro-pressure sensors using laterally coupled waveguides in Silicon photonic crystal (PC) membranes is presented. A new mechanism using coupled waveguide modes is devised to detect pressure changes on a membrane structure which produces change in the optical transmission of coupled modes of the photonic crystal waveguide. Coupled mode theory, plane wave expansion and finite difference time domain techniques have been used to analyze and design a highly sensitive micro-pressure sensor. The performance of this device is compared to coupled modes of a ridge waveguide. It is seen that photonic crystal pressure sensor can be up to 4 times smaller than standard coupled waveguides for similar performance.
Targeting hepatic pyruvate dehydrogenase kinases restores insulin signaling and mitigates ChREBP-mediated lipogenesis in diet-induced obese mice (2018)

Our findings establish that specific targeting of hepatic PDKs with the PDK inhibitor PS10 is an effective therapeutic approach to maintaining glucose and lipid homeostasis in obesity and T2D, without the harmful ketoacidosis associated with systemic inhibition of PDKs.
A novel method for sputter-deposition of high T/sub c/ superconductor films via a computer-controlled mass analyzed ion beam. [Y-Ba-Cu-O] (1987)

A novel concept is demonstrated for ion beam sputter-induced deposition of high T/sub c/ superconductor films. The concept involves the use of a well-focused ion beam which can be sequentially directed via a set of x-y electrostatic deflection plates onto three or more different elemental or compound target which are constituents of the desired composite film. The deflection plates are driven by two +-1000 volt bipolar programmable power supplies which are controlled by a DEC LSI 11/73 computer. A custom program drives two D/A converters to provide the +-10 volt analog signal which is used to drive the power supplies in such a way that the ion beam is positioned on selected spots on the different targets. By programming the dwell time for each target according to the known sputtering yield and desired layer thickness for each material, it is possible to deposit composite films from a well-controlled sub-monolayer up to thicknesses determined only by the available deposition time. Initial results on the deposition of Y-Ba-CuO films are presented to demonstrate the concept, which in principle can also be applied to the deposition of high T/sub c/ superconducting films by electron- and laser-induced evaporation of elemental or oxide targets. 26more » refs., 5 figs.« less
Improvement of x-ray intensifying screen efficiency by special design of the screen. (1982)

An investigation of light diffusion in x-ray intensifying screens and the prospects for improvement by confining light spread with a special structure are reported. Light diffusion in CaWO4 screens was studied theoretically using computer simulation. The proportion and spatial distribution of light emerging from different depths in the screen were calculated. The introduction of narrow gaps in the screens made it possible to improve these proportions and distributions. The gaps improved the line spread functions, the screen efficiencies, and the average contribution of the absorbed quanta to the light output.
Current State of Regenerative Medicine: Moving Stem Cell Research from Animals into Humans for Clinical Trials (2013)

Given the limited capacity of the central nervous system (CNS) and the heart for self-repair or renewal, cell-based therapy represents a promising therapeutic approach closest to provide a cure to restore normal tissue and function for neurological and cardiovascular disorders. Derivation of human embryonic stem cell (hESCs) from the in vitro fertilization (IVF) leftover embryos has brought a new era of cellular medicine for the damaged CNS and heart. Recent advances and technology breakthroughs in hESC research have overcome some major obstacles in moving stem cell research from animals towards humans trials, including resolving minimal essential human requirements for de novo derivation and long-term maintenance of clinically-suitable stable hESC lines and direct conversion of such pluripotent hESCs into a large supply of clinical-grade functional human neuronal or cardiomyocyte cell therapy products. Such breakthrough stem cell technologies have demonstrated the direct pharmacologic utility and capacity of hESC cell therapy derivatives for human CNS and myocardium regeneration, thus, presented the hESC cell therapy derivatives as a powerful pharmacologic agent of cellular entity for CNS and heart repair. The availability of human stem/progenitor/ precursor cells in high purity and large commercial scales with adequate cellular neurogenic or cardiogenic capacity will greatly facilitate developing safe and effective cell-based regeneration and replacement therapies against a wide range of CNS and heart disorders. Transforming non-functional pluripotent hESCs into faterestricted functional human cell therapy derivatives or products dramatically increases the clinical efficacy of graft-dependent repair and safety of hESC-derived cellular products, marking a turning point in cell-based regenerative medicine from current
Large Margin Training for Attention Based End-to-End Speech Recognition (2019)

A method of attention-based end-to-end (E2E) automatic speech recognition (ASR) training, includes performing cross-entropy training of a model, based on one or more input features of a speech signal, performing beam searching of the model of which the cross-entropy training is performed, to generate an n-best hypotheses list of output hypotheses, and determining a one-best hypothesis among the generated n-best hypotheses list. The method further includes determining a character-based gradient and a word-based gradient, based on the model of which the cross-entropy training is performed and a loss function in which a distance between a reference sequence and the determined one-best hypothesis is maximized, and performing backpropagation of the determined character-based gradient and the determined word-based gradient to the model, to update the model.
Feasibility of Higher-Order Differential Ion Mobility Separations Using New Asymmetric Waveforms (2006)

Technologies for separating and characterizing ions based on their transport properties in gases have been around for three decades. The early method of ion mobility spectrometry (IMS) distinguished ions by absolute mobility that depends on the collision cross section with buffer gas atoms. The more recent technique of field asymmetric waveform IMS (FAIMS) measures the difference between mobilities at high and low electric fields. Coupling IMS and FAIMS to soft ionization sources and mass spectrometry (MS) has greatly expanded their utility, enabling new applications in biomedical and nanomaterials research. Here, we show that time-dependent electric fields comprising more than two intensity levels could, in principle, effect an infinite number of distinct differential separations based on the higher-order terms of expression for ion mobility. These analyses could employ the hardware and operational procedures similar to those utilized in FAIMS. Methods up to the 4th or 5th order (where conventional IMS is 1st order and FAIMS is 2nd order) should be practical at field intensities accessible in ambient air, with still higher orders potentially achievable in insulating gases. Available experimental data suggest that higher-order separations should be largely orthogonal to each other and to FAIMS, IMS, and MS.
Synthesis and Antitumor Activity of Novel C-7 Paclitaxel Ethers:  Discovery of BMS-184476 (2001)

The preparation of C-7 paclitaxel ethers is described. Various substituted ethers were prepared via activation of the corresponding methylthiomethyl ether followed by alcohol addition. Variation of the C-7 ether group as well the 3' side chain position led to the discovery of a novel taxane, BMS-184476 (4), with preclinical antitumor activity superior to paclitaxel.
Monolithically integrated atomic vapor cell for quantum optics on a chip (2006)

We report the first monolithically integrated rubidium vapor cell on a chip. Hollow-core ARROW waveguides are used to create cell volumes of 500 picoliters and mode areas of 30µm2–ideal for low-level nonlinear optics.
A Novel Atomic Layer Deposition Process for Depositing Metal Fluoride Thin Films (2007)

This paper introduces a novel Atomic Layer Deposition (ALD) process for preparation of fluoride thin films at temperature range of 225-450 °C. The crystallinity, morphology, composition, thicknesses, refractive indices, and transmittance of the films were analyzed. Low impurity levels were obtained at 350-400 °C with good stoichiometry. Refractive indices were 1.34-1.42 for MgF2, 1.43 for CaF2 and 1.57-1.61 for LaF3 films.
Nitric oxide-generating hydrogels inhibit neointima formation (2005)

This study evaluated the effects of localized delivery of nitric oxide (NO) from hydrogels covalently modified with S-nitrosocysteine (Cys-NO) on neoinitma formation, a key component of restenosis, in a rat balloon-injury model. Soluble Cys-NO was used in preliminary studies to identify dosage ranges that were able to simultaneously inhibit smooth muscle cell proliferation, enhance endothelial cell proliferation, and reduce platelet adhesion. Photo-cross-linked PEG-based hydrogels were formed with covalently immobilized Cys-NO. These materials release NO for approximately 24 h and can be applied to tissues and photo-cross-linked in situ to form local drug-delivery systems. Localized delivery of NO from hydrogels containing Cys-NO inhibited neointima formation in a rat balloon-injury model by approximately 75% at 14 days.
The Efficacy of Traditional Chinese Herbal Therapy in Atopic Eczema (1994)

A traditional Chinese herbal therapy (Zemaphyte) for the treatment of atopic eczema (AE) is currently being assessed. This review attempts to highlight its success in patients who are recalcitrant to Western forms of treatment and the rationale behind its use. The herbal preparation is a mixture of 10 herbs with some known pharmacological agents and actions. The concept of such a complex mixture in clinical treatment is anathema to Western medicine but acceptable in traditional Chinese medicine. As this formation has been shown to be effective in two double-blind crossover trials, investigative work on components from the mixture must be established in order to find the active constituent(s) and describe their mode of action. This research will also lead to a greater understanding of the complex immunopathology of AE.
Stationary cycling induced by switched functional electrical stimulation control (2014)

Functional electrical stimulation (FES) is used to activate the dysfunctional lower limb muscles of individuals with neuromuscular disorders to produce cycling as a means of exercise and rehabilitation. In this paper, a stimulation pattern for quadriceps femoris-only FES-cycling is derived based on the effectiveness of knee joint torque in producing forward pedaling. In addition, a switched sliding-mode controller is designed for the uncertain, nonlinear cycle-rider system with autonomous state-dependent switching. The switched controller yields ultimately bounded tracking of a desired trajectory in the presence of an unknown, time-varying, bounded disturbance, provided a reverse dwell-time condition is satisfied by appropriate choice of the control gains and a sufficient desired cadence. Stability is derived through Lyapunov methods for switched systems, and experimental results demonstrate the performance of the switched control system under typical cycling conditions.
Global-Locally Self-Attentive Encoder for Dialogue State Tracking (2018)

Dialogue state tracking, which estimates user goals and requests given the dialogue context, is an essential part of taskoriented dialogue systems. In this paper, we propose the Global-Locally Self-Attentive Dialogue State Tracker (GLAD), which learns representations of the user utterance and previous system actions with global-local modules. Our model uses global modules to share parameters between estimators for different types (called slots) of dialogue states, and uses local modules to learn slot-specific features. We show that this significantly improves tracking of rare states and achieves stateof-the-art performance on the WoZ and DSTC2 state tracking tasks. GLAD obtains 88.1% joint goal accuracy and 97.1% request accuracy on WoZ, outperforming prior work by 3.7% and 5.5%. On DSTC2, our model obtains 74.5% joint goal accuracy and 97.5% request accuracy, outperforming prior work by 1.1% and 1.0%.