gebhart/patrepeval huggingface dataset:
AutoCog (2014)

The booming popularity of smartphones is partly a result of application markets where users can easily download wide range of third-party applications. However, due to the open nature of markets, especially on Android, there have been several privacy and security concerns with these applications. On Google Play, as with most other markets, users have direct access to natural-language descriptions of those applications, which give an intuitive idea of the functionality including the security-related information of those applications. Google Play also provides the permissions requested by applications to access security and privacy-sensitive APIs on the devices. Users may use such a list to evaluate the risks of using these applications. To best assist the end users, the descriptions should reflect the need for permissions, which we term description-to-permission fidelity. In this paper, we present a system AutoCog to automatically assess description-to-permission fidelity of applications. AutoCog employs state-of-the-art techniques in natural language processing and our own learning-based algorithm to relate description with permissions. In our evaluation, AutoCog outperforms other related work on both performance of detection and ability of generalization over various permissions by a large extent. On an evaluation of eleven permissions, we achieve an average precision of 92.6% and an average recall of 92.0%. Our large-scale measurements over 45,811 applications demonstrate the severity of the problem of low description-to-permission fidelity. AutoCog helps bridge the long-lasting usability gap between security techniques and average users.
P1‐088: NOVEL NUCLEAR FACTOR‐KAPPAB TARGETING PEPTIDE SUPPRESSES PATHOLOGY IN PRE‐CLINICAL MODELS OF ALZHEIMER'S DISEASE (2019)

Emerging treatments for Alzheimer's disease (AD) focus on developing disease-modifying therapies that attempt to slow and/or prevent disease progression. Considerable evidence suggests that the amyloid beta (Aβ) plaques and other noxious stimuli promote a disproportionate increase in activated nuclear factor-kappa B (NF-κB) p65 dimers and mediate neuroinflammation leading to neurodegeneration. Hence, selective targeting of activated p65 is an excellent therapeutic strategy for AD. Adopting information from the NF-κB interactome, we designed, structural analogs of a p65 interacting protein, the glucocorticoid induced leucine zipper (GILZ). By virtue of binding the transactivation domain of p65 exposed after release from the inhibitory IκB proteins in activated cells, the Provaidya GILZ analogs (PGA) analogs can act as highly selective inhibitors of activated p65 with minimal potential for off-target effects. Here, we investigate the efficacy of PGA in models of AD. PGA and control peptides were synthesized covalently as peptide amides with the cell penetrating agent. The half minimal lethal dose of GA was determined by in-vitro toxicity assays in human neuroblastoma cells. Groups of 5xFAD mice were administered intraperitoneally PGA-1 or PGA-2 or control peptide (CP) at LD50 dosage on alternate days for six weeks. The brain tissues of PGA-1 and PGA-2 treated mice exhibited significantly fewer activated Iba+ microglial cells, glial fibrillary acidic protein (GFAP)+ astrocytes, reduced Aβ deposition, suppressed inflammatory cytokines and elevated anti-apoptotic factors. The inhibitory effects of PGA could be attributed to the observed reduction in activated p65 in brain tissues.
Globally Normalized Reader (2017)

Rapid progress has been made towards question answering (QA) systems that can extract answers from text.Existing neural approaches make use of expensive bidirectional attention mechanisms or score all possible answer spans, limiting scalability.We propose instead to cast extractive QA as an iterative search problem: select the answer's sentence, start word, and end word.This representation reduces the space of each search step and allows computation to be conditionally allocated to promising search paths.We show that globally normalizing the decision process and back-propagating through beam search makes this representation viable and learning efficient.We empirically demonstrate the benefits of this approach using our model, Globally Normalized Reader (GNR), which achieves the second highest single model performance on the Stanford Question Answering Dataset (68.4 EM, 76.21 F1 dev) and is 24.7x faster than bi-attention-flow.We also introduce a data-augmentation method to produce semantically valid examples by aligning named entities to a knowledge base and swapping them with new entities of the same type.This method improves the performance of all models considered in this work and is of independent interest for a variety of NLP tasks.
Adaptive Iterative Learning Control for High Precision Motion Systems (2008)

Iterative learning control (ILC) is a very effective technique to reduce systematic errors that occur in systems that repetitively perform the same motion or operation. However, several characteristics have prevented standard ILC from being widely used for high precision motion systems. Most importantly, the learned feedforward signal depends on the motion profile (setpoint trajectory) and if this is altered, the learning process has to be repeated. Secondly, ILC amplifies non-repetitive disturbances and noise. Finally, its performance may be limited due to position-dependent dynamics. This paper presents the design and implementation of a time-frequency adaptive ILC that is applicable for motion systems which executes the same motion or operation. It employs the same control system block diagram as standard ILC, but instead of a fixed robustness filter it uses a time-varying filter. By using the results of the time-frequency adaptive ILC, i.e., the shape of the learned feedforward signal, a ldquopiecewise ILCrdquo is proposed that leads to the design of a single learned feedforward signal suitable for different setpoints. The results are experimentally shown to work for a high precision motion system.
Influence of sheet thickness ratio on fracture mechanisms of Al-steel resistance spot welds produced using multi-ring domed electrode (2019)

Resistance spot welds with three aluminium to steel sheet thickness ratios were welded using electrodes featuring a plurality of rings and multiple solidification weld schedules. The average shear strength of the intermetallic layer was measured directly using a mini-shear test while the shear stress at the interface was calculated using finite element analysis. The results demonstrated that the fracture modes changed from interfacial fracture to fracture in aluminium when the steel thickness increased or the aluminium thickness was thinner than the steel. Therefore, interfacial fracture can be minimised by decreasing aluminium to steel thickness ratio. This was due to a reduced shear to tensile stress ratio and a lower shear stress than the shear strength at the weld faying interface.
Realization of an ultrathin acoustic lens for subwavelength focusing in the megasonic range (2018)

In this study, we report the first experimental realization of an ultrathin (0.14λ, λ = 1.482 mm means wavelength at 1 MHz in the water medium) subwavelength focusing acoustic lens that can surpass the Rayleigh diffraction limit (0.61λ/NA, NA means numerical aperture). It is termed a Super-Oscillatory Acoustic Lens (SOAL), and it operates in the megasonic range. The SOAL represents an interesting feature allowing the achievement of subwavelength focusing without the need to operate in close proximity to the object to be imaged. The optimal layout of the SOAL is obtained by utilizing a systematic design approach, referred to here as topology optimization. To this end, the optimization formulation is newly defined. The optimized SOAL is fabricated using a photo-etching process and its subwavelength focusing performance is verified experimentally via an acoustic intensity measurement system. From these measurements, we found that the proposed optimized SOAL can achieve superior focusing features with a Full Width at Half Maximum (FWHM) of ~0.40λ/NA ≃ 0.84 mm (for our SOAL, NA = 0.707) with the transmission efficiency of 26.5%.
Newborn screening and diagnosis of mucopolysaccharidoses: application of tandem mass spectrometry. (2014)

Mucopolysaccharidoses (MPS) are a group of lysosomal storage disorders caused by the deficiency of lysosomal enzymes. The enzymes are required to break down glycosaminoglycans (GAGs) that help build bone, cartilage, tendons, corneas, skin and connective tissue. In patients with MPS, a missing enzyme leads to the accumulation of GAGs in the cells, blood, connective tissues, and multiple organs. The consequence is permanent, with progressive cellular damage affecting patients' appearance, physical abilities, organ and system function, and skeletal and mental development. The measurement of each specific GAG in a variety of specimens is required to establish the correlation between GAGs and physiological status of patients and/or prognosis and pathogenesis of the disease and to separate the patients with MPS from the healthy controls. We have developed a highly accurate, sensitive, and cost-effective liquid chromatography tandem mass spectrometry (LC-MS/MS) method for measurements of disaccharides derived from four specific GAGs [chondroitin sulfate (CS), dermatan sulfate (DS), heparan sulfate (HS), and keratan sulfate (KS)]. Disaccharides were produced by specific enzyme digestion of each GAG, and subsequently, quantified by negative ion mode of multiple reaction monitoring. Subclasses of GAGs with the same molecular weights can be separated by liquid chromatography. We have also developed another GAG assay by high-throughput mass spectrometry (HT-MS/MS). The HT-MS/MS consists of an integrated solid phase extraction robot that binds and de-salts samples from assay plates and directly injects them into a MS/MS detector, reducing sample processing time to within ten seconds. HT-MS/MS consequently yields much faster throughput than conventional LC-MS/MS-based methods; however, the HT-MS/MS system does not use a chromatographic step, and therefore, cannot separate GAGs that have the same molecular weights. Both techniques can be applied to the analysis of dried blood spots, blood, and urine specimens. In this review, we describe the assay methods for GAGs and the application to newborn screening and diagnosis of MPS.
Improved Colorimetric Methods and Field Test Kits for Analyzing Anionic Surfactants in Water and Wastewater. (1973)

This report is about various methods for the analysis of surfactants in aqueous solution that were reviewed, evaluated, and/or assessed. Emphasis was placed on the development of field test kits based on two improved colorimetric methods involving the use of methylene blue and Azure A. The simplified and improved Methylene Blue Method and Azure A Method require only 5 or 6 ml of aqueous reagent and 25 ml of chloroform for analyzing one sample. The principles, analytical procedures and limitations of the two methods are described in detail. A field test kit based on the use of a portable spectrophotometer (or photometer), and a field test kit based on the use of color comparison device(s) are proposed for use by military personnel with limited training in chemistry.
Label-free, high-throughput holographic screening and enumeration of tumor cells in blood (2017)

We introduce inline digital holographic microscopy (in-line DHM) as a label-free technique for detecting tumor cells in blood. The optimized DHM platform fingerprints every cell flowing through a microchannel at 10 000 cells per second, based on three features - size, maximum intensity and mean intensity. To identify tumor cells in a background of blood cells, we developed robust gating criteria using machine-learning approaches. We established classifiers from the features extracted from 100 000-cell training sets consisting of red blood cells, peripheral blood mononuclear cells and tumor cell lines. The optimized classifier was then applied to targeted features of a single cell in a mixed cell population to make quantitative cell-type predictions. We tested our classification system with tumor cells spiked at different levels into a background of lysed blood that contained predominantly peripheral blood mononuclear cells. Results show that our holographic screening method can readily detect as few as 10 tumor cells per mL, and can identify tumor cells at a false positive rate of at most 0.001%. This purely optical approach obviates the need for antibody labeling and allows large volumes of sample to be quickly processed. Moreover, our in-line DHM approach can be combined with existing circulation tumor cell enrichment strategies, making it a promising tool for label-free analysis of liquid-biopsy samples.
Potential Health Impact of Nanoparticles (2009)

Although mankind stands to obtain great benefit from nanotechnology, it is important to consider the potential health impacts of nanomaterials (NMs). This consideration has launched the field of nanotoxicology, which is charged with assessing toxicological potential as well as promoting safe design and use of NMs. Although no human ailments have been ascribed to NMs thus far, early experimental studies indicate that NMs could initiate adverse biological responses that can lead to toxicological outcomes. One of the principal mechanisms is the generation of reactive oxygen species and oxidant injury. Because oxidant injury is also a major mechanism by which ambient ultrafine particles can induce adverse health effects, it is useful to consider the lessons learned from studying ambient particles. This review discusses the toxicological potential of NMs by comparing the possible injury mechanisms and adverse health effects of engineered and ambient ultrafine particles.
Formation of zirconia films by aerosol gas deposition method using zirconia powder produced by break-down method (2010)

The purpose of this study is to form a film of dry-milled zirconia powders by aerosol gas deposition (AGD). Recently, we reported that we could form a high-density zirconia film using wet-type zirconia powders prepared wet-chemically. From the stand point of industrial use, the dry-milled zirconia powder seems to be much more advantageous than the wet type. In this study, we examined the possibility to fabricate zirconia film using commercially available dry-milled zirconia powders with a mean diameter range that is nearly the same as those of wet-type ones, for example, 0.73 to 10.2 µm in mean diameter. As a result, we were able to make a zirconia film from all powders, although the film formation conditions for the wet-type powder was very much limited in the diameter and the specific surface area. In conclusion, dry-milled zirconia powders are considered to have high potential for industrial use.
Zooming In on a Quantitative Trait for Tomato Yield Using Interspecific Introgressions (2004)

To explore natural biodiversity we developed and examined introgression lines (ILs) containing chromosome segments of wild species (Solanum pennellii) in the background of the cultivated tomato (S. lycopersicum). We identified Brix9-2-5, which is a S. pennellii quantitative trait locus (QTL) that increases sugar yield of tomatoes and was mapped within a flower- and fruit-specific invertase (LIN5). QTL analysis representing five different tomato species delimited the functional polymorphism of Brix9-2-5 to an amino acid near the catalytic site of the invertase crystal, affecting enzyme kinetics and fruit sink strength. These results underline the power of diverse ILs for high-resolution perspectives on complex phenotypes.
New 2‐phenyl‐4,5,6,7‐tetrahydro‐2<i>H</i>‐indazole derivatives as paddy field herbicides (2004)

A series of 3-chloro-2-(4-chloro-2-fluorophenyl)-4,5,6,7-tetrahydro-2H-indazole derivatives containing various substituted isoxazolinylmethoxy groups at the 5-position of the benzene ring were synthesized and their herbicidal activities assessed under greenhouse and flooded paddy conditions. Among them, compounds having a phenyl or cyano substituent at the 3-position of the 5-methyl-isoxazolin-5-yl structure demonstrated good rice selectivity and potent herbicidal activity against annual weeds at 16-63 g AI ha(-1) under greenhouse conditions. Field trials indicated that these two compounds controlled a wide range of annual weeds rapidly with a good tolerance on transplanted rice seedlings by pre-emergence application. They showed a low mammalian and environmental toxicity in various toxicological tests.
ChemInform Abstract: Thromboxane A2 Synthase Inhibitors. 5‐(3‐Pyridylmethyl)benzofuran‐2‐ carboxylic Acids. (1987)

Abstract The preparation of the pyridyl derivatives (I) ‐ (IV) is described.
Occurrence of Arsenic-Based Defects and Techniques for Their Elimination (2005)

Arsenic based defects were found on the surfaces of advanced CMOS patterned wafers after the pre-silicidation HF clean. Investigations into the mechanism of formation were done using representative As-implanted bare silicon, polysilicon and HDP silicon oxide films. The nature and composition of these As-based defects are believed to be arsenic and arsenic oxide. Methods of defect removal include the application of hydrogen peroxide containing solutions and hydrogen plasma dry cleaning.
Synchronic Biotransformation of 1,4-Dioxane and 1,1-Dichloroethylene by a Gram-Negative Propanotroph<i>Azoarcus</i>sp. DD4 (2018)

Bioremediation of 1,4-dioxane is strongly challenged by the concurrent contamination of chlorinated solvents, particularly 1,1-dichloroethylene (1,1-DCE), a potent inhibitor of archetypic 1,4-dioxane degraders (e.g., Pseudonocardia and Mycobacterium). Vegetative growth and aggregation behavior of these Gram-positive Actinomycetes also hinder their field application. A new Gram-negative bacterium Azoarcus sp. DD4 was isolated from an activated sludge sample. Notably, DD4 can sustain the concurrent co-oxidation of 1,4-dioxane and 1,1-DCE using propane as the primary substrate without observable formation of clumps. Microcosm assays prepared with source zone groundwater samples from a contaminated site indicated DD4 can efficiently remove dioxane, with the concentration decreasing from an initial value of 10.4 mg/L to <0.4 μg/L within 14 days of incubation. Removal of 1,4-dioxane was partially inhibited when an excessive amount of 1,1-DCE (3.28 ± 0.19 mg/L) was artificially spiked into the microcosms but significantly accelerated immediately after the complete depletion of 1,1-DCE. Furthermore, a gene encoding a putative propane monooxygenase was discovered, which may contribute to the oxidation of propane, 1,4-dioxane, and/or 1,1-DCE. Detection of 2-S-glutathionyl acetate and synchronic dechlorination suggest that DD4 detoxifies its primary metabolite, 1,1-DCE epoxide, via conjugation with glutathione. All these findings indicate the suitability of DD4 as a robust inoculum candidate for in situ bioaugmentation to remediate co-contamination by dioxane and 1,1-DCE.
Physics-based full-chip TDDB assessment for BEOL interconnects (2016)

As technology advances, Time-Dependent Dielectric Breakdown (TDDB) has become one of the major reliability threats for Copper/low-k interconnects. This article presents a novel approach, techniques, and flow for the physics-based chip-scale assessment of backend low-k TDDB. In our work, the breakdown development is considered as the complementary combination of electric current path generation by means of diffusing metal ions and field-based hoping conductivity of the current carriers. It replaces the widely accepted across-layout electrostatic field based TDDB assessment. As a result, the model generated time-to-failure (TTF) is governed by kinetics of the electric current path generation, which is controlled by a time-dependent minimum metal ion concentration in the inter-metal dielectrics (IMD) gap-fill. Finite element analysis (FEA)-based simulations are used for populating the set of lookup tables, which provide a time to breakdown for any interconnect pattern with given geometries and voltages. A pattern-matching technique is used for extracting from the layout all patterns belonging to different classes of pattern shapes with different geometries, locations and electric loads. Experimental results obtained on a test chip show that upon the calibration the proposed flow provides a capability to evaluate chip-scale low-k TDDB reliability based on the calculated TTF and detect most leaking shapes in the layout.
A Potent, Nonpeptidyl 1<i>H</i>-Quinolone Antagonist for the Gonadotropin-Releasing Hormone Receptor (2001)

Extensive development of the structure-activity relationships of a screening lead determined three important pharmacophores for gonadotropin-releasing hormone (GnRH) receptor antagonist activity. Incorporation of the 3,4,5-trimethylphenyl group at the 3-position, 2-(2(S)-azetidinyl)ethoxy group at the 4-position, and N-4-pyrimidinylcarboxamide at the 6-position of the quinolone core resulted in the identification of 4-(2-(azetidin-2(S)-yl)ethoxy)-7-chloro-2-oxo-3-(3,4,5-trimethylphenyl)-1,2-dihydroquinoline-6-carboxylic acid pyrimidin-4-ylamide (1) as a potent antagonist of the GnRH receptor. A 10(4)-fold increase in in vitro binding affinity is observed for the GnRH receptor as compared to the initial screening lead. Compound 1 exhibits nanomolar binding activity and functional antagonism at the human receptor and is 7-fold less active at the rhesus receptor. Intravenous administration of compound 1 to rhesus monkeys results in a significant decrease of the serum levels of downstream hormones, luteinizing hormone (79% decrease in area under the curve) and testosterone (92% decrease in area under the curve), at a dose of 3 mg/kg. Quinolone 1 is a potent nonpeptidyl antagonist for the human GnRH receptor that is efficacious for the suppression of luteinizing hormone and testosterone in primates.
Clinical Results of the Clarion® Magnetless Cochlear Implant (1999)

This paper reports initial results for the CLARION Multi-Strategy Cochlear Implant, presently under investigational study in Europe. A magnetless implantable cochlear stimulator (ICS) with an ear-mold-supported headpiece was designed in response to an increasing demand for a magnetic resonance imaging (MRI)-compatible cochlear implant. Surgical technique, accompanying magnetless headpiece, and MRI compatibility were evaluated in 11 deaf patients (ages 6 to 62 years) who were implanted with a magnetless Clarion implant. Because of the headset mechanics, the ICS was implanted closer behind the ear than a magnet-containing ICS. The ICS-MRI compatibility was investigated with 1.5- and 0.3-T MRI. Results showed that the surgery was relatively safe and easy to learn. The headset was stable and reliable. The MRI compatibility tests indicate that the ICS poses no contraindication for patients needing MRI. Overall, the results suggest that the Clarion magnetless cochlear implant is relatively safe and easy to implant, is MRI-compatible, and functions well with the ear-mold-supported headpiece.