gebhart/patrepeval huggingface dataset:
Facet‐Independent Electric‐Field‐Induced Volume Metallization of Tungsten Trioxide Films (2016)

Reversible metallization of band and Mott insulators by ionic-liquid gating is accompanied by significant structural changes. A change in conductivity of seven orders of magnitude at room temperature is found in epitaxial films of WO3 with an associated monoclinic-to-cubic structural reorganization. The migration of oxygen ions along open volume channels is the underlying mechanism.
Bioelectrical Impedance Analysis Measures of Body Composition and Condition, and Its Sensitivity to the Freezing Process (2013)

Measuring body composition and condition are integral parameters within seafood quality assurance methods. Bioelectrical impedance analysis (BIA) has been successful in measuring body composition and condition on a variety of fish that have never been frozen, but its applicability on previously frozen fish is unknown. The objectives of this study were to measure albacore tuna (Thunnus alalunga) with BIA prior to and after freezing. Predictions of body composition and measures of condition (measured by phase angle) were compared in fish that were just caught and again after they were frozen and allowed to thaw. Results indicate that BIA works well on fresh fish but not after they were thawed. Correlation scores (r) between predicted and actual values of water, dry mass, fat-free mass, ash, and protein in the fresh fish were > 0.69 and < 0.17 after they were frozen. Phase angles of the fresh fish were similar to other studies (˜ 24 degrees) and approached zero after they were frozen. Reactance values decreased dramatically in the frozen fish, and its usage on frozen fish may be useful to the seafood industry in determining if fish have previously been frozen.
Stronger acceptors can diminish nonlinear optical response in simple donor-acceptor polyenes (1993)

There has been much recent effort in the design of optimal chromophores for second-order nonlinear optical (NLO) applications. Most studies of organic molecules have focused on donor-acceptor π-conjugated molecules containing aromatic groups. We will show that the NLO response of aromatic donor-acceptor chromophores is dramatically different than their simple polyene analogs. Although there have been several computational studies of the first hyperpolarizability (β) of the simple organic donor-acceptor chromophores, the polyenes, few molecules in this class have been studied experimentally. These molecules are the prototypical conjugated donor-acceptor chromophores and as such can serve as a base line reference for both experimental and theoretical NLO structure/property relationships. Accordingly, we report the results of electric-field-induced second-harmonic generation (EFISH) studies of simple donor-acceptor polyenes as a function of donor and acceptor strengths and of molecular length.
Precision cryogenic magnetostrictive actuator using a persistent high TC magnet (2000)

Cryogenic magnetostrictive materials, such as rare earth zinc crystals, offer high strains and high forces with minimally applied magnetic fields, making the material ideally suited for deformable optics applications. For cryogenic temperature applications, such as Next Generation Space Telescope, the use of superconducting magnets offer the possibility of a persistent mode of operation, i.e., the magnetostrictive material will maintain a strain field without power. High temperature superconductors (HTS) are attractive options if the temperature of operation is higher than 10° Kelvin (K) and below 77 K. However, HTS wires have constraints that limit the minimum radius of winding, and even if good wires can be produced, the technology for joining superconducting wires does not exist. In this article, the design and capabilities of a rare earth zinc magnetostrictive actuator using bulk HTS is described. Bulk superconductors can be fabricated in the sizes required with excellent superconducting properties. Equivalent permanent magnets, made with this inexpensive material, are persistent, do not require a persistent switch as in HTS wires, and can be made very small. These devices are charged using a technique which is similar to the one used for charging permanent magnets, e.g., by driving them into saturation. A small normal conducting coil can be used for charging or discharging. Very fast charging and discharging of HTS tubes, as short as 100 μs, has been demonstrated. Because of the magnetic field capability of the superconductor material, a very small amount of superconducting magnet material is needed to actuate the rare earth zinc. In this article, several designs of actuators using YBCO and BSCCO 2212 superconducting materials are presented. Designs that include magnetic shielding to prevent interaction between adjacent actuators will also be described. Preliminary experimental results and comparison with theory for BSSCO 2212 with a magnetostrictive element will be discussed.
Understanding drug‐likeness (2011)

Abstract ‘Drug‐likeness’, a qualitative property of chemicals assigned by experts committee vote, is widely integrated into the early stages of lead and drug discovery. Its conceptual evolution paralleled work related to Pfizer's ‘rule of five’ and lead‐likeness, and is placed within this framework. The discrimination between ‘drugs’ (represented by a collection of pharmaceutically relevant small molecules, some of which are marketed drugs) and ‘nondrugs’ (typically, chemical reagents) is possible using a wide variety of statistical tools and chemical descriptor systems. Here we summarize 18 papers focused on drug‐likeness, and provide a comprehensive overview of progress in the field. Tools that estimate drug‐likeness are valuable in the early stages of lead discovery, and can be used to filter out compounds with undesirable properties from screening libraries and to prioritize hits from primary screens. As the goal is, most often, to develop orally available drugs, it is also useful to optimize drug‐like pharmacokinetic properties. We examine tools that evaluate drug‐likeness and some of their shortcomings, challenges facing these tools, and address the following issues: What is the definition of drug‐likeness and how can it be utilized to reduce attrition rate in drug discovery? How difficult is it to distinguish drugs from nondrugs? Are nondrug datasets reliable? Can we estimate oral drug‐likeness? We discuss a drug‐like filter and recent advances in the prediction of oral drug‐likeness. The heuristic aspect of drug‐likeness is also addressed. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 760–781 DOI: 10.1002/wcms.52 This article is categorized under: Computer and Information Science > Chemoinformatics
Differential Reactivities of Recombinant Glycosylated Ectodomains of Mouse and Human Thyrotropin Receptors with Patient Autoantibodies<sup>1</sup> (1997)

We expressed the extracellular domain of the mouse TSH receptor (mET-gp) using the baculovirus expression system. The recombinant protein was identified as mET-gp by immunoblotting and N-terminal amino acid sequencing. Carbohydrate analysis of the recombinant protein showed that the protein is glycosylated. Experimental antibodies raised against the extracellular domain of the human TSHr (ETSHr) were assayed for reactivity against mET-gp and glycosylated human ETSHr (ETSHr-gp) in an ELISA and found to be comparable. Similarly, both mET-gp and ETSHr-gp proteins neutralized the TSH binding inhibitory immunoglobulin (TBII) activity of rabbit anti-ETSHr antibodies in a RRA. However, when these proteins were compared for their ability to neutralize TBII and blocking activities (TSBAb) of IgG from patients with thyroid autoimmune disorders, only ETSHr-gp was able to neutralize these activities. In contrast, mET-gp partially neutralized, whereas ETSHr-gp completely neutralized the stimulatory (TSAb) activities of IgG from patients. Analyses of reactivities of these two proteins against a panel of antipeptide and monoclonal antibodies and their protein sequences showed differences in some specific epitopes. These data showed that in spite of significant homology between the two proteins, they exhibit specific epitope differences that are sufficient to cause divergence in their ability to react with patient autoantibodies to TSHr. This suggests that the two proteins might differ in their three-dimensional structure.
Electrooptic Fabry-Perot filter: development for the study of solar oscillations (1987)

Observations of nonradial solar oscillations require Doppler velocity measurement at many points over the photosphere with a velocity resolution better than 1 m/s. An attractive form of imaging spectrophotometer for such a task utilizes a thin, solid, electrically tunable Fabry-Perot interference filter or etalon made of an electrooptic material such as lithium niobate (LiNbO(3)). The problems to be overcome in producing such an etalon for an imaging spectrophotometer are discussed and practical solutions demonstrated on the basis of measurements made on prototype devices.
Direct Silicon Bonded (DSB) Substrate Solid Phase Epitaxy (SPE) Integration Scheme Study for High Performance Bulk CMOS (2006)

Two integration schemes for hybrid crystal orientation technology using direct silicon bonded (DSB) substrates and solid phase epitaxy (SPE) processes have been implemented. The shallow-trench-isolation (STI) before SPE approach suffers from trench-edge defects formed at STI edges, which causes high leakage current. The SPE-before-STI approach allows removal of edge defects of SPE by STI. SRAM in 65nm node and eDRAM in 90nm node have been demonstrated on DSB using the SPE-before-STI scheme
Spatially and temporally resolved calcium concentration changes in oscillating neurons of crab stomatogastric ganglion. (1989)

Calcium concentration changes during oscillations of the membrane potential of crab (Cancer irroratus or Cancer borealis) stomatogastric neurons were monitored at many positions by using the calcium indicator dye arsenazo III and a photodiode array. Data analysis algorithms using signal averaging techniques were developed to improve the time resolution of the measured calcium changes. As previously reported, calcium oscillations were detected from all regions of the neuropil but not from the soma or axon. In some cells step increases in intracellular neuropil calcium were correlated with each of the action potentials in the burst (on the peak of the voltage oscillation). In other cells we observed calcium oscillations phase-locked to the membrane potential with no spike-related component. A few cells had both spike-evoked and graded potential components to the calcium oscillations. In those cells, the spatial distribution of the spike-correlated calcium influx differed from that of the voltage-oscillation-correlated calcium influx, suggesting that different neurites might interact with their postsynaptic targets with different mixtures of graded and spike-correlated transmitter release.
Regulation of glucose metabolism via hepatic forkhead transcription factor 1 (FoxO1) by <i>Morinda citrifolia</i> (noni) in high-fat diet-induced obese mice (2011)

Renewed interest in alternative medicine among diabetic individuals prompted us to investigate anti-diabetic effects of Morinda citrifolia (noni) in high-fat diet (HFD)-fed mice. Type 2 diabetes is associated with increased glucose production due to the inability of insulin to suppress hepatic gluconeogenesis and promote glycolysis. Insulin inhibits gluconeogenesis by modulating transcription factors such as forkhead box O (FoxO1). Based on microarray analysis data, we tested the hypothesis that fermented noni fruit juice (fNJ) improves glucose metabolism via FoxO1 phosphorylation. C57BL/6 male mice were fed a HFD and fNJ for 12 weeks. Body weights and food intake were monitored daily. FoxO1 expression was analysed by real-time PCR and Western blotting. Specificity of fNJ-associated FoxO1 regulation of gluconeogenesis was confirmed by small interfering RNA (siRNA) studies using human hepatoma cells, HepG2. Supplementation with fNJ inhibited weight gain and improved glucose and insulin tolerance and fasting glucose in HFD-fed mice. Hypoglycaemic properties of fNJ were associated with the inhibition of hepatic FoxO1 mRNA expression, with a concomitant increase in FoxO1 phosphorylation and nuclear expulsion of the proteins. Gluconeogenic genes, phosphoenolpyruvate C kinase (PEPCK) and glucose-6-phosphatase (G6P), were significantly inhibited in mice fed a HFD+fNJ. HepG2 cells demonstrated more than 80 % inhibition of PEPCK and G6P mRNA expression in cells treated with FoxO1 siRNA and fNJ. These data suggest that fNJ improves glucose metabolism via FoxO1 regulation in HFD-fed mice.
Review of Pharmacological Effects of <i>Glycyrrhiza</i> sp. and its Bioactive Compounds (2008)

The roots and rhizomes of licorice (Glycyrrhiza) species have long been used worldwide as a herbal medicine and natural sweetener. Licorice root is a traditional medicine used mainly for the treatment of peptic ulcer, hepatitis C, and pulmonary and skin diseases, although clinical and experimental studies suggest that it has several other useful pharmacological properties such as antiinflammatory, antiviral, antimicrobial, antioxidative, anticancer activities, immunomodulatory, hepatoprotective and cardioprotective effects. A large number of components have been isolated from licorice, including triterpene saponins, flavonoids, isoflavonoids and chalcones, with glycyrrhizic acid normally being considered to be the main biologically active component. This review summarizes the phytochemical, pharmacological and pharmacokinetics data, together with the clinical and adverse effects of licorice and its bioactive components.
Scriptor: using deictics, dialog, and supervised learning to convey instructions (2002)

HTML pages are designed to convey semantic information to human users through visual emphases, demarcations, spatial cues and repeating patterns which act as "perceptual markup". This human-centric syntax is not easy for machines to identify. Naturally-occurring HTML, especially the machine-generated variety, rarely follows strict markup rules and provides no semantic cues. The visual cues humans use to extract information from a Web page, however, must be reflected in the page's markup. If a human could convey the relationship between visual cues, available to the program as markup patterns, and semantic categories, passed to the program as user-supplied labels, the program would have been instructed in "how to extract information from that page". Scriptor is a program which, run in tandem with a Web browser, allows a user to interactively design a data extraction script for the Web site. It is intended for highly structured repetitive information such as is found in classified listings, online stores, tables for weather, stock or airline schedules, course listings, and other similar sources. Scriptor interleaves a variety of learning methods to allow the specification of extraction rules using extremely simple methods. These consist of repeating pattern recognition, supervised learning, deictics through highlighting, and dialogs in which the user selects the desired result for a set of possible extraction rules. Learning is augmented by direct instructions such as: "label text following '/spl sim/' as 'Author' ". Performance data for the authors and naive subjects are presented for a collection of Web pages showing the potential of this form of highly interactive instruction. Our results demonstrate that very simple programming by example techniques can generate effective parse rules in highly repetitive domains.
High frequency of activated natural killer and natural killer T-cells in patients with new onset of type 2 diabetes mellitus (2012)

Chronic low-grade inflammation is crucial for the development of insulin resistance and type 2 diabetes mellitus (T2DM), and immunocompetent cells, such as T-cells, B-cells, mast cells and macrophages, regulate the pathogenesis of T2DM. However, little is known about the role of natural killer (NK) and natural killer T (NKT) cells in the pathogenic process of T2DM. A total of 16 patients with new onset T2DM and nine healthy subjects were recruited, and the frequency of peripheral blood activated and inhibitory NK and NKT cells in individual subjects was determined by flow cytometry. The frequency of spontaneous and inducible interferon gamma (IFN-γ) and CD107a(+) NK cells was further examined, and the potential association of the frequency of NK cells with clinical measures was analyzed. While there was no significant difference in the frequency of peripheral blood NK and NKT cells between patients and controls, the frequency of NKG2D(+) NK and NKT cells in patients was significantly higher than those in the controls (P = 0.011). In contrast, the frequency of NKG2A(+) and KIR2DL3(+) inhibitory NK and NKT cells in patients was significantly lower than those in the controls (P = 0.002, P < 0.0001, respectively). Furthermore, the frequencies of NKG2D(+) NK cells were correlated significantly with the values of body mass index in patients. Moreover, the frequencies of spontaneous and inducible CD107a(+), but not IFN-γ-secreting, NK cells in patients were significantly higher than those in the controls (P < 0.004, P < 0.0001). Our data indicated that a higher frequency of activated NK cells may participate in the obesity-related chronic inflammation involved in the pathogenesis of T2DM.
Universal Kriging and Cokriging as a Regression Procedure (1991)

Prediction of a property on the basis of a set of point measurements in a region is required if a map of this property for the region is to be made. Of the spatial interpolation and prediction techniques, kriging is optimal among all linear procedures, as it is unbiased and has minimal variance of the prediction error. In cokriging, which has this same attractive property, additional observations of one or more covariables are used, which may lead to increased precision of the predictions. Both techniques are often applicable in different fields such as soil science, meteorology, medicine, agriculture, biology, public health, and environmental sciences (e.g., atmospheric or soil pollution). In this study we try to remove the cloud of obscurity covering the notions of kriging and cokriging by embedding them into regression procedures. This leads to a straightforward formulation of the two techniques. It turns out that kriging and cokriging differ only slightly from each other. The procedures are illustrated by two numerical examples, one to demonstrate the methodology, and one practical problem encountered in a soil study. Cokriging is found to be most valuable when a highly correlated covariable is sampled intensely.
Structural Context of Disease-Associated Mutations and Putative Mechanism of Autoinhibition Revealed by X-Ray Crystallographic Analysis of the EZH2-SET Domain (2013)

The enhancer-of-zeste homolog 2 (EZH2) gene product is an 87 kDa polycomb group (PcG) protein containing a C-terminal methyltransferase SET domain. EZH2, along with binding partners, i.e., EED and SUZ12, upon which it is dependent for activity forms the core of the polycomb repressive complex 2 (PRC2). PRC2 regulates gene silencing by catalyzing the methylation of histone H3 at lysine 27. Both overexpression and mutation of EZH2 are associated with the incidence and aggressiveness of various cancers. The novel crystal structure of the SET domain was determined in order to understand disease-associated EZH2 mutations and derive an explanation for its inactivity independent of complex formation. The 2.00 Å crystal structure reveals that, in its uncomplexed form, the EZH2 C-terminus folds back into the active site blocking engagement with substrate. Furthermore, the S-adenosyl-L-methionine (SAM) binding pocket observed in the crystal structure of homologous SET domains is notably absent. This suggests that a conformational change in the EZH2 SET domain, dependent upon complex formation, must take place for cofactor and substrate binding activities to be recapitulated. In addition, the data provide a structural context for clinically significant mutations found in the EZH2 SET domain.
Kernel methods match Deep Neural Networks on TIMIT (2014)

Despite their theoretical appeal and grounding in tractable convex optimization techniques, kernel methods are often not the first choice for large-scale speech applications due to their significant memory requirements and computational expense. In recent years, randomized approximate feature maps have emerged as an elegant mechanism to scale-up kernel methods. Still, in practice, a large number of random features is required to obtain acceptable accuracy in predictive tasks. In this paper, we develop two algorithmic schemes to address this computational bottleneck in the context of kernel ridge regression. The first scheme is a specialized distributed block coordinate descent procedure that avoids the explicit materialization of the feature space data matrix, while the second scheme gains efficiency by combining multiple weak random feature models in an ensemble learning framework. We demonstrate that these schemes enable kernel methods to match the performance of state of the art Deep Neural Networks on TIMIT for speech recognition and classification tasks. In particular, we obtain the best classification error rates reported on TIMIT using kernel methods.
A Micromachined Capacitive Pressure Sensor Using a Cavity-Less Structure with Bulk-Metal/Elastomer Layers and Its Wireless Telemetry Application (2008)

This paper reports a micromachined capacitive pressure sensor intended for applications that require mechanical robustness. The device is constructed with two micromachined metal plates and an intermediate polymer layer that is soft enough to deform in a target pressure range. The plates are formed of micromachined stainless steel fabricated by batch-compatible micro-electro-discharge machining. A polyurethane roomtemperature- vulcanizing liquid rubber of 38-μm thickness is used as the deformable material. This structure eliminates both the vacuum cavity and the associated lead transfer challenges common to micromachined capacitive pressure sensors. For frequency-based interrogation of the capacitance, passive inductor-capacitor tanks are fabricated by combining the capacitive sensor with an inductive coil. The coil has 40 turns of a 127-μmdiameter copper wire. Wireless sensing is demonstrated in liquid by monitoring the variation in the resonant frequency of the tank via an external coil that is magnetically coupled with the tank. The sensitivity at room temperature is measured to be 23-33 ppm/KPa over a dynamic range of 340 KPa, which is shown to match a theoretical estimation. Temperature dependence of the tank is experimentally evaluated.