gebhart/patrepeval huggingface dataset:
First-principles study of native point defects in crystalline indium gallium zinc oxide (2009)

Materials in In–Ga–Zn–O system are promising candidates for channel layers of high-performance thin-film transistors (TFTs). We investigated the atomic arrangements and the electronic structures of crystalline InGaZnO4 containing point defects such as oxygen vacancy (VO), interstitial hydrogen (Hi), and interstitial oxygen (Oi) by density functional theory (DFT) using a plane-wave pseudopotential method. The calculations for the atomic structure relaxation suggest that Hi bonds to a lattice oxygen (OO), and Oi occupies a split interstitial site [Oi(split)] forming a chemical bond with OO which is similar to O2 molecule, or Oi occupies an octahedral interstitial site [Oi(oct)]. The electronic structure calculations reveal that VO forms fully occupied states around the middle of the DFT band gap, while Hi does not form a defect level in the band gap but raises the Fermi level above the conduction band minimum. Oi(split) forms fully occupied states above the valence band maximum of the defect-free model (VBM0), while Oi(oct) forms both occupied and unoccupied states above the VBM0. It is thus suggested that VO and Oi(split) are electrically inactive for electrons but work as hole traps, Hi acts as a donor, and Oi(oct) is electrically active, trapping both electrons and holes. These observations imply that VO and Oi(split) do not but Hi and Oi(oct) influence electrical properties of the n-channel TFTs based on the In–Ga–Zn–O semiconductor materials.
Adenovirus-mediated gene transfer into dissociated and explant cultures of rat hippocampal neurons (1996)

Genetic manipulation offers great potential for studying the molecular and cellular processes which control or regulate the complex developmental properties of neurons. Gene transfer into neurons, however, is notoriously difficult. In this study we have used a replication-defective adenovirus (Adv/RSV beta gal), expressing beta-galactosidase (beta-gal) as a reporter gene, to infect dissociated cultures of rat hippocampal neurons and hippocampal slice cultures. Because future studies will require either long-term (e.g., developmental) or short-term (e.g., electrophysiological) expression of recombinant genes in neuronal cultures, we have optimized infection conditions for each situation. The Adv/RSV beta gal construct infects neurons and glial cells equally well, with no apparent alterations in cellular morphology. In slice cultures, the same efficiency and temporal control of beta-gal expression following Adv/RSV beta gal infection was achieved. Focal application of the adenoviruses, by microinjection, permitted infection of discrete subregions within the hippocampal explants. Whole cell recordings of dissociated hippocampal neurons and field recordings from the explant cultures, infected with Adv/RSV beta gal at low multiplicities of infection, indicated no significant alteration in the electrophysiological profiles of neurons in these cultures. The results demonstrate the utility of adenoviruses as gene transfer vectors for primary cultures of neurons. Adenovirus-mediated gene transfer into slice cultures also provides an opportunity to study development or plasticity in an environment where the circuitry and cytoarchitecture of the tissue are preserved and the areas of genetic manipulation can be spatially isolated.
High performance liquid chromatography‐mass spectrometry analysis of protoberberine alkaloids in medicine herbs (2007)

RP-HPLC is the main method for the analysis of alkaloids. However, peak tailing is a problem that commonly occurs in the separation of alkaloids. In order to overcome this, three kinds of RP columns were compared for the analysis of protoberberine alkaloids in Coptidis Rhizoma and Phellodendri Cortex in this work. XTerra MS C18 column was the best one which gave the best symmetry factor under the same conditions. With this column, a good separation of the crude extracts of C. Rhizoma and P. Cortex was achieved using 0.1% v/v formic acid buffer and methanol as mobile phase. At the same time, the crude extracts of C. Rhizoma and P. Cortex were analyzed by the LC-ESI-MSn and LC-atmospheric pressure chemical ionization (APCI)-MSn methods. In the analysis of HPLC-ESI/MSn, structures of five protoberberine alkaloids were elucidated, compared to authentic standards, and data from the literature. At the same time, the structure of a novel compound was elucidated. In the HPLC-APCI/ MSn analysis, there was an interesting phenomenon that the relative abundance of the ions M+ and [M + 2]+ was different for different alkaloids. The possible fragmentation pathways of protoberberine alkaloids in APCI/MS analysis were studied for the first time in the present work.
Dissociation of NKT Stimulation, Cytokine Induction, and NK Activation In Vivo by the Use of Distinct TCR-Binding Ceramides (2004)

NKT and NK cells are important immune regulatory cells. The only efficient means to selectively stimulate NKT cells in vivo is alpha-galactosylceramide (alphaGalCer). However, alphaGalCer effectively stimulates and then diminishes the number of detectable NKT cells. It also exhibits a potent, indirect ability to activate NK cells. We have now discovered another ceramide compound, beta-galactosylceramide (betaGalCer) (C12), that efficiently diminishes the number of detectable mouse NKT cells in vivo without inducing significant cytokine expression or activation of NK cells. Binding studies using CD1d tetramers loaded with betaGalCer (C12) demonstrated significant but lower intensity binding to NKT cells when compared with alphaGalCer, but both ceramides were equally efficient in reducing the number of NKT cells. However, betaGalCer (C12), in contrast to alphaGalCer, failed to increase NK cell size, number, and cytolytic activity. Also in contrast to alphaGalCer, betaGalCer (C12) is a poor inducer of IFN-gamma, TNF-alpha, GM-CSF, and IL-4 gene expression. These qualitative differences in NKT perturbation/NK activation have important implications for delineating the unique in vivo roles of NKT vs NK cells. Thus, alphaGalCer (which triggers NKT cells and activates NK cells) efficiently increases the resistance to allogeneic bone marrow transplantation while betaGalCer (C12) (which triggers NKT cells but does not activate NK cells) fails to enhance bone marrow graft rejection. Our results show betaGalCer (C12) can effectively discriminate between NKT- and NK-mediated responses in vivo. These results indicate the use of different TCR-binding ceramides can provide a unique approach for understanding the intricate immunoregulatory contributions of these two cell types.
Magnetic properties of Ni nanowires in self-assembled arrays (2000)

Magnetic properties of Ni nanowires electrodeposited into self-assembled porous alumina arrays have been investigated. By anodizing aluminum in sulfuric acid and immersing the as-anodized template into phosphoric acid for different lengths of time, we are able to vary the diameters of the subsequently deposited nanowires between 8 and 25 nm. The coercivity measured along wire axis first increases with the wire diameter, reaches a maximum of 950 Oe near a diameter of 18 nm, and then decreases with further increase of wire diameter. The dependence of the magnetization of Ni nanowires is found to follow Bloch's law at low temperature but with the Bloch exponent decreasing from the bulk value and the Bloch constant increasing from the bulk value by an order of magnitude.
Monkeys immunized with intertypic chimeric dengue viruses are protected against wild-type virus challenge (1996)

Dengue epidemics caused by the four dengue virus serotypes continue to pose a major public health problem in most tropical and subtropical regions. A safe and effective vaccine against dengue is still not available. The current strategy for dengue immunization favors the use of a vaccine containing each of the four serotypes. We previously employed full-length dengue type 4 virus (DEN4) cDNA to construct a viable intertypic dengue virus of type 1 or type 2 antigenic specificity that contained the genes for the capsid-premembrane-envelope (C-pre-M-E) structural proteins of DEN1 or pre-M and E structural proteins of DEN2 substituting for the corresponding DEN4 genes. Chimeras DEN1/DEN4 and DEN2/DEN4, which express the nonstructural proteins of DEN4 and the C-pre-M-E structural proteins of DEN1 or the pre-M-E structural proteins of DEN2, and therefore the antigenicity of type 1 or type 2, were used to immunize rhesus monkeys. Other monkeys were inoculated with parental DEN1, DEN2, or cDNA-derived DEN4. Three of four monkeys immunized with DEN1/DEN4 developed neutralizing antibodies against DEN1 and were protected against subsequent DEN1 challenge. All four monkeys immunized with DEN2/DEN4 developed antibodies against DEN2 and were protected against subsequent DEN2 challenge. DEN1- and DEN2-immunized monkeys were protected against homologous virus challenge, but DEN4-immunized animals became viremic on cross-challenge with DEN1 or DEN2. In a second experiment, eight monkeys were immunized with equal mixtures of DEN1/DEN4 and DEN2/DEN4. Each of these monkeys developed neutralizing antibodies against both DEN1 and DEN2 and were protected against subsequent challenge with DEN1 or DEN2. Chimeric dengue viruses similar to those described here could be used to express serotype-specific antigens in a live attenuated tetravalent human vaccine.
Development of Air Drilling Motor Holds Promise for Specialized Directional Drilling Applications (1991)

ABSTRACT The development of a new motor designed specifically for use in holes drilled with air and mist is chronicled, from initial use of modified mud motors in air drilling applications, through development to date of an air drilling motor currently in use. Until recently, air drilling was accomplished using either an air hammer or, for a more directionally controlled well, a Moineau type positive displacement mud motor (PDM) adapted to an air drilling environment. In such cases, bottom hole assembly performance proved heavily dependent on motor life and lithology type.1 Greatly reduced stator life and accelerated damage to bearings designed for mud lubrication meant that conventional motor runs on air usually were shorter than with mud systems. Ultimately, conventional PDMs exhibit many economic limitations when used on air for directional drilling. The new air drilling motor, which features a Moineau motor with a novel geometrical design of the power section, an adjustable kick off sub and a modified bearing assembly, represents the latest step in the continuing development of a downhole motor suitable for directional and horizontal drilling using air or mist. This design has been successful in US air drilling applications, which are detailed in case histories.
Online multistep-ahead inundation depth forecasts by recurrent NARX networks (2013)

Abstract. Various types of artificial neural networks (ANNs) have been successfully applied in hydrological fields, but relatively scant on multistep-ahead flood inundation forecasting, which is very difficult to achieve, especially when dealing with forecasts without regular observed data. This study proposes a recurrent configuration of nonlinear autoregressive with exogenous inputs (NARX) network, called R-NARX, to forecast multistep-ahead inundation depths in an inundation area. The proposed R-NARX is constructed based on the recurrent neural network (RNN), which is commonly used for modeling nonlinear dynamical systems. The models were trained and tested based on a large number of inundation data generated by a well validated two-dimensional simulation model at thirteen inundation-prone sites in Yilan County, Taiwan. We demonstrate that the R-NARX model can effectively inhibit error growth and accumulation when being applied to online multistep-ahead inundation forecasts over a long lasting forecast period. For comparison, a feedforward time-delay and an online feedback configuration of NARX networks (T-NARX and O-NARX) were performed. The results show that (1) T-NARX networks cannot make online forecasts due to unavailable inputs in the constructed networks even though they provide the best performances for reference only; and (2) R-NARX networks consistently outperform O-NARX networks and can be adequately applied to online multistep-ahead forecasts of inundation depths in the study area during typhoon events.
Voltage-Induced Tunneling Conduction in Granular Metals at Low Temperatures (1972)

We have observed a new conduction mechanism in granular metals at low temperatures and high electric fields $\mathcal{E}$ characterized by a field-dependent conductivity ${\ensuremath{\sigma}}_{0}\mathrm{exp}(\frac{\ensuremath{-}{\mathcal{E}}_{0}}{\mathcal{E}})$. A theory based on a simple model of field-induced electron-hole generation in the bulk of the granular metal predicts the observed field dependence and gives expressions for ${\ensuremath{\sigma}}_{0}$ and ${\mathcal{E}}_{0}$ which are functions of the granular-metal parameters: metal grain size, and thickness and height of the tunneling barriers separating the metal grains. Agreement between theory and experiment is satisfactory.
Detection of nitroxyl (HNO) by a prefluorescent probe (2011)

Recent research has shown that nitroxyl (HNO) has important and unique biological activity, especially as a potential alternative to current treatments of cardiac failure. HNO is a reactive molecule that spontaneously dimerizes and subsequently dehydrates to form nitrous oxide (N 2 O), making its detection in solution or biologically relevant preparations difficult. The prefluorescent probe 4‐((9‐acridinecarbonyl)amino)‐2,2,6,6‐tetramethylpiperidin‐1‐oxyl (TEMPO‐9‐AC) has been used to detect HNO in aqueous solution and to differentiate it from nitric oxide (NO). TEMPO‐9‐AC reacts with HNO via a net hydrogen abstraction to produce the highly fluorescent TEMPO‐9‐AC‐H and NO. The utility of TEMPO‐9‐AC as a probe for HNO has been shown using the common HNO donors Angeli's salt and Piloty's acid (PA) along with a recently reported HNO donor, 2‐bromo‐PA. The use of TEMPO‐9‐AC is complicated by intermolecular fluorescence quenching and competitive HNO trapping by the NO produced, but nonetheless, it can be used to study HNO reactivity in aqueous solution. Copyright © 2011 John Wiley &amp; Sons, Ltd.
The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP‐d‐rhamnose biosynthesis pathway (2009)

The rare 6-deoxysugar D-rhamnose is a component of bacterial cell surface glycans, including the D-rhamnose homopolymer produced by Pseudomonas aeruginosa, called A-band O polysaccharide. GDP-D-rhamnose synthesis from GDP-D-mannose is catalyzed by two enzymes. The first is a GDP-D-mannose-4,6-dehydratase (GMD). The second enzyme, RMD, reduces the GMD product (GDP-6-deoxy-D-lyxo-hexos-4-ulose) to GDP-d-rhamnose. Genes encoding GMD and RMD are present in P. aeruginosa, and genetic evidence indicates they act in A-band O-polysaccharide biosynthesis. Details of their enzyme functions have not, however, been previously elucidated. We aimed to characterize these enzymes biochemically, and to determine the structure of RMD to better understand what determines substrate specificity and catalytic activity in these enzymes. We used capillary electrophoresis and NMR analysis of reaction products to precisely define P. aeruginosa GMD and RMD functions. P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. RMD catalyzes the stereospecific reduction of GDP-6-deoxy-D-lyxo-hexos-4-ulose, as predicted. Reconstitution of GDP-D-rhamnose biosynthesis in vitro revealed that the P. aeruginosa pathway may be regulated by feedback inhibition in the cell. We determined the structure of RMD from Aneurinibacillus thermoaerophilus at 1.8 A resolution. The structure of A. thermoaerophilus RMD is remarkably similar to that of P. aeruginosa GMD, which explains why P. aeruginosa GMD is also able to catalyze the RMD reaction. Comparison of the active sites and amino acid sequences suggests that a conserved amino acid side chain (Arg185 in P. aeruginosa GMD) may be crucial for orienting substrate and cofactor in GMD enzymes.
Anterior cervical discectomy without bone graft (1977)

Anterior cervical discectomy without bone grafting may become the procedure of choice for acute cervical disc protrusions. This operation was performed on 71 patients, all of whom were followed from 1 to 6 years. Complications were minor in nature. The results were excellent and sustained.
A Phase 1c Trial Comparing the Efficacy and Safety of a New Aqueous Formulation of Alphaxalone with Propofol (2015)

PHAX causes fast-onset, short-duration anesthesia with fast cognitive recovery similar to propofol, but with less cardiovascular depression, or airway obstruction and no pain on injection.
Cell biology of paget's disease (1999)

Paget's disease is characterized by markedly increased osteoclast formation and bone resorption followed by excessive new bone formation. Osteoclasts in Paget's disease are increased both in number and size, contain paramyxoviral-like nuclear inclusions, and can have up to 100 nuclei per cell. Marrow culture studies have identified several abnormalities in osteoclast formation in Paget's disease. Osteoclast-like multinucleated cells formed more rapidly in marrow cultures from patients with Paget's disease, produced increased levels of interleukin-6 (IL-6), and expressed high levels of IL-6 receptors compared to normals. IL-6 levels were also increased in bone marrow and peripheral blood of patients with Paget's disease. In addition, osteoclast precursors from patients with Paget's disease are hyperresponsive to 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) and calcitonin. The increased sensitivity of osteoclast precursors to 1,25(OH)2D3 is mediated through the vitamin D receptor (VDR), since 24-hydroxylase activity is also up-regulated at concentrations of 1,25(OH)2D3 that are one log less than that needed to induce 24-hydroxylase activity in osteoclast precursors from normals. However, VDR numbers and affinity for 1,25(OH)2D3 do not differ in osteoclast precursors from Paget's patients compared to those from normals. Synergistic interactions between cytokines such as IL-6 and 1,25(OH)2D3 also cannot explain the enhanced sensitivity of osteoclast precursors from patients with Paget's disease to 1,25(OH)2D3. Interestingly, coculture studies of osteoclast precursors and cells from the marrow microenvironment of patients with Paget's disease and normals have demonstrated that the marrow microenvironment is more osteoclastogenic than normal. Thus, studies of the cell biology of osteoclasts in Paget's disease have demonstrated an increased rate of osteoclast formation and abnormalities in both osteoclast precursors and the marrow microenvironment. Enhanced IL-6 production by osteoclasts in Paget's disease may further amplify the increased osteoclast formation already ongoing in the pagetic lesion, and may explain the increased bone turnover at uninvolved sites distant from the pagetic lesion.
Growth of Crystalline SrTiO3 Films on Si Substrates Using Thin Fluoride Buffer Layers and Their Electrical Properties (1994)

Strontium titanate ( SrTiO 3 : STO) films were grown epitaxially on Si (111) and (100) substrates using thin SrF 2 buffer layers. The SrF 2 buffer layer was used for preventing the formation of an amorphous SiO 2 layer on the Si substrate during deposition of an STO film. It was found from X-ray diffraction (XRD) analysis that well (110)-oriented STO films were grown on Si(111) substrates by a two-step growth method, in which a thin (8 nm thick) STO film was predeposited on the SrF 2 buffer layer at 450°C and a thick (80 nm thick) STO film was successively deposited at 750°C. It was also found from XRD and Auger electron spectroscopy (AES) measurements that the SrF 2 buffer layer was completely dissolved during STO film deposition at 750°C, and no fluorine (F) atoms existed in the buffer layer. The epitaxial relationship on Si(111) substrates revealed by X-ray pole figure measurements was (110) S T O //(111) S i and &lt;110&gt; S T O //&lt;112&gt; S i , while that on Si(100) substrates was (100) S T O //(100) S i and &lt;110&gt; S T O //&lt;110&gt; S i or &lt;110&gt; S T O //&lt;100&gt; S i . Concerning the electrical properties of STO films, the best values of breakdown field (at 1 µ A/cm 2 ), resistivity (at 1 MV/cm), and relative dielectric constant were 2.3 MV/cm, 8.2×10 12 Ω· cm and 72, respectively.
A low-noise demultiplexing system for active multichannel microelectrode arrays (1991)

This paper reports a low-noise demultiplexing system capable of reconstructing multichannel single-unit neural signals derived from multiplexed microelectrode arrays. The overall multiplexing-demultiplexing system realizes ten channels, a per-channel gain of 68 dB, a bandwidth from 100 Hz to 6 kHz, and an equivalent noise level (referred to the probe input) of 13 microV rms. It provides for signaling over the power supply to allow control of on-chip probe functions such as self-testing. The interchannel crosstalk is less than 3%, and switching noise is suppressed by blanking the transition intervals. The 200 kHz probe sample clock is tracked automatically over a range from 150 to 250 kHz. Neural signals as low as 20 microV (typically 640 microV at the demultiplexing system input) can be reconstructed. The overall system organization is compatible with the demultiplexing of as many as 40 time-multiplexed electrode channels from a single probe data line.
Disturbed CD4+ T Cell Homeostasis and In Vitro HIV-1 Susceptibility in Transgenic Mice Expressing T Cell Line–tropic HIV-1 Receptors (1998)

T cell line-tropic (T-tropic) HIV type 1 strains enter cells by interacting with the cell-surface molecules CD4 and CXCR4. We have generated transgenic mice predominantly expressing human CD4 and CXCR4 on their CD4-positive T lymphocytes (CD4+ T cells). Their primary thymocytes are susceptible to T-tropic but not to macrophage-tropic HIV-1 infection in vitro, albeit with a viral antigen production less efficient than human peripheral blood mononuclear cells. Interestingly, even without HIV infection, transgenic mice display a CD4+ T cell depletion profile of peripheral blood reminiscent of that seen in AIDS patients. We demonstrate that CD4+ T cell trafficking in transgenic mice is biased toward bone marrow essentially due to CXCR4 overexpression, resulting in the severe loss of CD4+ T cells from circulating blood. Our data suggest that CXCR4 plays an important role in lymphocyte trafficking through tissues, especially between peripheral blood and bone marrow, participating in the regulation of lymphocyte homeostasis in these compartments. Based on these findings, we propose a hypothetical model in which the dual function of CXCR4 in HIV-1 infection and in lymphocyte trafficking may cooperatively induce progressive HIV-1 infection and CD4+ T cell decline in patients.