gebhart/patrepeval huggingface dataset:
Monoclonal antibody analysis of common surface protein(s) of Renibacterium salmoninarum. (1989)

We are reporting the development of two monoclonal antibodies which recognize ten separate isolates of Renibacterium salmoninarum. Both monoclonal antibodies recognize a 57 kDa protein doublet and several lower molecular weight antigens present in bacterial lysates. The 57 kDa antigen appears to correlate with a 57 kDa surface protein named Antigen F by GETCHELL et al. (1985).Antibody capture ELISA analysis indicates that the antibodies recognize different epitopes of the same protein (s). Cross-reactions were not observed with control bacteria or with normal chinook salmon serum proteins.
A single‐point mutation enables lactate dehydrogenase from <i>Bacillus subtilis</i> to utilize NAD<sup>+</sup> and NADP<sup>+</sup> as cofactor (2011)

Abstract The NAD + ‐dependent lactate dehydrogenase from Bacillus subtilis (BsLDH) catalyzes the enantioselective reduction of pyruvate to lactate. BsLDH is highly specific to NAD + and exhibits only a low activity with NADP + as cofactor. Based on the high activity and good stability of LDHs, these enzymes have been frequently used for the regeneration of NAD + . While an application in the regeneration of NADP + is not sufficient due to the cofactor preference of the BsLDH. In addition, NADP + ‐dependent LDHs have not yet been found in nature. Therefore, a structure‐based approach was performed to predict amino acids involved in the cofactor specificity. Methods of site‐saturation mutagenesis were applied to vary these amino acids, with the aim to alter the cofactor specificity of the BsLDH. Five constructed libraries were screened for improved NADP + acceptance. The mutant V39R was identified to have increased activity with NADP + relative to the wild type. V39R was purified and biochemically characterized. V39R showed excellent kinetic properties with NADP(H) and NAD(H), for instance the maximal specific activity with NADPH was enhanced 100‐fold to 90.8 U/mg. Furthermore, a 249‐fold increased catalytic efficiency was observed. Surprisingly, the activity with NADH was also significantly improved. Overall, we were able to successfully apply V39R in the regeneration of NADP + in an enzyme‐coupled approach combined with the NADP + ‐dependent alcohol dehydrogenase from Lactobacillus kefir . We demonstrate for the first time an application of an LDH in the regeneration of NADP + .
Atomic force microscope chamber for <i>in situ</i> studies of ice (2001)

To investigate the surface morphologies of biological systems in a controlled gaseous environment (e.g., the temperature, humidity and composition), most commercial atomic force microscopes require modification. We have designed a double-jacketed environmental chamber specifically for a Nanoscope IIIa (Digital Instruments, Santa Barbara, CA) force microscope. We use cold nitrogen and thermoelectric devices to control the temperature in the chamber; the nitrogen simultaneously serves to create an inert environment. We have also designed a temperature controlled sample stage utilizing thermoelectric devices for fine temperature regulation. A variation of this sample stage allows us to image samples in fluids at cold temperatures with an O-ringless configuration. The relative humidity within the chamber is also measured with commercially available relative humidity sensors. We investigate the surface morphology of ice Ih in its pure phase and shall extend the study to ice in the presence of biological molecules, such as antifreeze proteins. We present a detailed description of our design and our first images of polycrystalline ice and single crystals of ice grown in situ from the vapor.
Electrode optimization for high-speed traveling-wave integrated optic modulators (1998)

Different electrode configurations for LiNbO/sub 3/-based Mach-Zehnder traveling-wave electrooptic modulators are analyzed. It is found that the Z-cut coplanar waveguide (CPW) configuration provides the best compromise between the characteristic impedance, the half-wave voltage, and the driving power. To increase the bandwidth and simultaneously reduce the half-wave voltage, an optimum design of multisection phase reversal electrode is proposed. To verify the theoretical predictions experimentally, two modulators, both using the Z-cut LiNbO/sub 3/ CPW configuration, were fabricated and characterized, one with an optimized five-section phase reversal electrode and the other with a conventional single-section electrode. By comparing the performances of these two devices, it is confirmed that significant improvements on the bandwidth to half-wave voltage ratio and the flatness of the frequency response can indeed be obtained from using an optimized multisection phase reversal electrode.
Device characterization of a complete set of passive bubble logic functional elements. [(YSm)/sub 3/ (GaFe)/sub 5/O/sub 12/ garnet] (1976)

This paper reports the operating characteristics of a set of passive logic elements. The elements were fabricated on (YSm)/sub 3/ (GaFe)/sub 5/O/sub 12/ garnet using identical chip fabrication parameters. The set consists of generator, annihilator, bubble splitter, AND/OR gate, and bubble crossover. Results show that all elements except the crossover operate with an overlapping bias range of 8 to 10 Oe in a 40 Oe drive field at 100 kHz.
Context-aware Sequential Recommendation (2016)

Since sequential information plays an important role in modeling user behaviors, various sequential recommendation methods have been proposed. Methods based on Markov assumption are widely-used, but independently combine several most recent components. Recently, Recurrent Neural Networks (RNN) based methods have been successfully applied in several sequential modeling tasks. However, for real-world applications, these methods have difficulty in modeling the contextual information, which has been proved to be very important for behavior modeling. In this paper, we propose a novel model, named Context-Aware Recurrent Neural Networks (CA-RNN). Instead of using the constant input matrix and transition matrix in conventional RNN models, CA-RNN employs adaptive context-specific input matrices and adaptive context-specific transition matrices. The adaptive context-specific input matrices capture external situations where user behaviors happen, such as time, location, weather and so on. And the adaptive context-specific transition matrices capture how lengths of time intervals between adjacent behaviors in historical sequences affect the transition of global sequential features. Experimental results show that the proposed CA-RNN model yields significant improvements over state-of-the-art sequential recommendation methods and context-aware recommendation methods on two public datasets, i.e., the Taobao dataset and the Movielens-1M dataset.
Molecular Genetics of Chronic Granulomatous Disease (1989)

Chronic granulomatous disease is an inherited disorder characterized by the failure of phagocytic cells to produce superoxide upon the ingestion of microorganisms due to a lesion in a membrane-associated NADPH-oxidase. The components of the oxidase have been incompletely characterized by standard biochemical approaches. A genetic strategy has recently led to the identification of the gene affected in the common X-linked form of CGD without reference to its protein product. The X-CGD gene, assigned to chromosome position Xp21.1, encodes a phagocyte-specific RNA transcript that is mutated in patients with X-CGD. Antisera directed toward the predicted protein product of the X-CGD gene recognize a 90 kD membrane glycoprotein, which corresponds to the larger subunit of the phagocyte b-cytochrome heterodimer. The recent genetic and biochemical findings provide an explanation for the consistent absence of the b-cytochrome spectrum in X-CGD, and establish this cytochrome as an essential component of the phagocyte oxidase. The primary amino acid sequence of both the 90 kD b-cytochrome subunit and the 22 kD subunit (cloned as the cDNA using a specific antisera) have no significant similarity to other proteins, including previously studied cytochromes. As both subunits of the b-cytochrome heterodimer are absent in X-CGD, despite a genetic deficiency of only the larger polypeptide, a close interaction between the two subunits may be important for b-cytochrome stability and function. Expression of the b-cytochrome large subunit mRNA is increased by interferon-gamma, an important macrophage activator. Partial or complete restoration of oxidase activity in some X-CGD patients treated with interferon-gamma suggests new therapeutic approaches in the management of this disorder. Molecular reagents prepared from the cloned X-CGD cDNA or gene may prove to be clinically useful in prenatal diagnosis and may provide a basis for somatic gene therapy in future.
The demonstration of an interleukin-2 like activity in the synovial fluids of rheumatoid arthritis patients. (1983)

It has been shown that synovial tissues and fluids contain activated T lymphocytes. We examined the synovial fluids of rheumatoid arthritis patients and control (noninflammatory) fluids for the presence of interleukin 2 (IL-2) activity, a lymphokine essential to maintaining cells in an activated state. Using an IL-2 dependent T cell line it was found that 10/14 (71%) of rheumatoid synovial fluids contained IL-2 like activity while 0/8 control fluids demonstrated activity. The active material was resistant to heat (56 degrees C for 1h), was less than 50,000 molecular weight by gel filtration fractionation and was not precipitated by 50% saturated ammonium sulphate. It is therefore not immune complex in nature.
Simultaneous analysis of DNA replication and apoptosis during treatment of HL-60 cells with camptothecin and hyperthermia and mitogen stimulation of human lymphocytes. (1994)

A new method is described which combines the identification of DNA replicating and apoptotic cells in a single measurement by flow cytometry. The detection of DNA replicating cells is based on incorporation of 5-bromo-2'-deoxyuridine or 5-iodo-2'-deoxyuridine, followed by selective photolysis at the site of incorporation of the halogenated DNA precursors. Single-strand breaks in DNA resulting from the photolysis are subsequently labeled with digoxygenin or biotin-conjugated dUTP in a reaction catalyzed by exogenous terminal deoxynucleotidyl transferase. The double-stranded DNA breaks in apoptotic cells resulting from activation of the endonuclease can be labeled in this reaction as well. However, in contrast to the photolysed DNA, the low molecular weight fraction of DNA of apoptotic cells is extractable from the cells, and the degree of DNA elution can be modulated by cross-linking with formaldehyde. Thus, apoptotic cells can be distinguished and quantified by virtue of their fractional DNA content. Replication of less than 1% of a genome of a cell in the presence of 5-bromo-2'-deoxyuridine (equivalent of a 5-min 10 microM 5-bromo-2'-deoxyuridine pulse) can be detected by the selective photolysis method. The method was applied to study apoptosis and proliferation of human leukemic HL-60 cells and normal, mitogen-stimulated lymphocytes. Whereas apoptosis of HL-60 cells induced by the DNA topoisomerase I inhibitor camptothecin was selective to DNA replicating cells, apoptosis induced by hyperthermia showed no such selectivity. Lymphocytes that preferentially underwent apoptosis in cultures stimulated by phytohemagglutinin did not initiate DNA replication. By offering the possibility for identification of both DNA replicating and apoptotic cells in a single measurement, the method may find an application in studies of the prognostic value of both cell proliferation and death in human tumors and the apoptotic response of DNA replicating vs. nonreplicating cells to different treatments.
Intracellular translocation and differential accumulation of cell-penetrating peptides in bovine spermatozoa: evaluation of efficient delivery vectors that do not compromise human sperm motility (2013)

CPP technologies have significant potential to deliver selected bioactive moieties and so could modulate the biology and physiology of human sperm biology both prior- and post-fertilization.
Inhibition of phorbol ester tumor promoter 12-O-tetradecanoylphorbol-13- acetate-caused inflammatory responses in SENCAR mouse skin by black tea polyphenols (1997)

Over the past 10 years many studies from several laboratories defined anticarcinogenic and anti-inflammatory effects of tea, a widely consumed beverage by the human population. Much of such work has been conducted with green tea or its polyphenolic constituents. Regarding black tea, studies have shown that its water extract affords protection against tumor promotion caused by chemical carcinogens or ultraviolet B radiation in murine skin carcinogenesis models. Several studies have shown that topical application of chemical tumor promoters to murine skin results in the induction of epidermal edema, hyperplasia and ornithine decarboxylase (ODC) and cyclo-oxygenase activities, and interleukin-1 alpha (IL-1alpha) and ODC mRNA expression. In this study, we assessed whether topical application of polyphenols isolated from black tea leaves (hereafter referred to as BTP) mainly consisting of theaflavine gallates and (-)-epigallocatechin-3-gallate, inhibits phorbol ester tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA)-caused induction of these markers of inflammatory responses in murine skin. Topical application of BTP (6 mg in 0.2 ml acetone/animal) 30 min prior to TPA application on to the mouse skin resulted in significant inhibition against TPA-caused induction of epidermal edema (40%, P < 0.01), hyperplasia (57%, P < 0.005), leukocytes infiltration (50%), and induction of epidermal ODC (57%) and pro-inflammatory cytokine IL-1alpha mRNA expression (69%). Pre-application of BTP to that of TPA also resulted in significant inhibition of TPA-caused induction of epidermal ODC (23-73%, P < 0.005-0.0001), and cyclo-oxygenase, in terms of prostaglandins metabolites formation (38-65%, P < 0.01-0.0005), enzyme activities. Our data indicate that the inhibition of TPA-caused changes in these markers of inflammatory responses in murine skin by BTP may be one of the possible mechanisms of chemopreventive effects associated with black tea against tumorigenesis. The results of this study suggest that black tea, specifically polyphenols present therein, may be useful against cutaneous inflammatory responses in human population.
AN INVESTIGATION OF TRANSVERSE MODE COMBUSTION INSTABILITY IN LIQUID PROPELLANT ROCKET MOTORS (1961)

The transverse modes of high frequency combustion instability in liquid propellant rocket motors are studied theoretically and experimentally. Preliminary experiment demonstrates the need for ADDITIONAL THEORETICAL ANALYSIS TO EXPLAIN: (1) the influence on stability of the orientation of the elements of the injection pattern with respect to the radial direction; (2) the greater tendency to instability of the spinning forms of tangential modes as compared to the standing forms; and (3) the effect of the distribution of injection across the injector face. The basic theory is derived for the case of a circularly cylindrical combustion chamber with uniformly distributed injection. Extensions of the basic theory are made to cover the cases of nonuniformly distributed injection, a variable angle sector motor, and more general time lag formulations. A series of experiments using both sector and full cylindrical motors is described.
Non-radioactive chemical sequencing of biotin labelled DNA (1989)

Methods for the nonradioactive chemical sequencing of DNA are described. A biotin marker molecule, attached chemically to an oligonucleotide primer or enzymatically in an endfilling reaction of restriction enzyme sites, is stable during the base-specific chemical modification and strand scission reactions. Following fragment separation by direct blotting electrophoresis, the membrane bound sequence pattern can be visualized by a streptavidin-bridged enzymatic color reaction. The biotin labeling is also applicable for DNA sequencing by random degradation of phosphothioates, thus showing to be a universal label for nonradioactive DNA sequencing.
STANDING-WAVE SATURATION RESONANCES IN THE CO2 10.6-μ TRANSITIONS OBSERVED IN A LOW-PRESSURE ROOM-TEMPERATURE ABSORBER GAS (1970)

The standing-wave saturation resonances are observed by subjecting the CO2 absorber gas to the standing-wave 10.6-μ laser field and detecting the change induced in the entire 4.3-μ (001) → (000) spontaneous emission band as the laser frequency is tuned within the Doppler profile of a specific 10.6-μ transition. Long-term stabilization on any oscillating transition is achieved.
Passivation of the GaAs surface by an amorphous phosphorus overlayer (1984)

We have investigated the effects of an amorphous phosphorus (P) overlayer on the intrinsic properties of the surface of n-GaAs by means of Raman and photoluminescence spectroscopy. We report a lowering of the surface barrier from 0.7 to 0.18 eV and a reduction of one order of magnitude in surface recombination velocity. These results indicate that the Fermi level is no longer pinned at midgap, but is moved closer to the conduction band. A model is proposed in which the P atoms at the interface reduce the number of As-missing lattice defects that pin the Fermi level at midgap in n-GaAs.
Coexpression of NRASQ61R and BRAFV600E in Human Melanoma Cells Activates Senescence and Increases Susceptibility to Cell-Mediated Cytotoxicity (2006)

Activating mutations in BRAF and NRAS oncogenes in human melanomas are mutually exclusive. This finding has suggested an epistatic relationship but is consistent even with synthetic lethality. To evaluate the latter possibility, a mutated NRAS(Q61R) oncogene was expressed, under a constitutive or a doxycycline-regulated promoter, in a metastatic melanoma clone (clone 21) harboring an activated BRAF(V600E) oncogene. After the first 10 to 12 in vitro passages, the constitutive NRAS(Q61R) transfectant displayed progressive accumulation in G(0)-G(1) phase of the cell cycle and stained for the senescence-associated beta-galactosidase activity (SA-beta-Gal). Inducible expression of NRAS(Q61R), by the Tet-Off system, in clone 21 cells (21NRAS(61ON)) led to overactivation of the RAS/RAF/mitogen-activated protein kinase signaling pathway and, after the 10th in vitro passage, led to promotion of senescence. This was documented by reduced proliferation, flattened cell morphology, reduced growth in Matrigel, positive staining for SA-beta-Gal, and expression of AMP-activated protein kinase and of the cell cycle inhibitor p21(waf1/Cip1). These effects were detected neither in 21 cells with silenced NRAS(Q61R) (21NRAS(61OFF)) nor in cells transfected with an inducible wild-type NRAS gene (21NRAS(WTON)). In addition, when compared with parental 21 cells, or with 21NRAS(61OFF), 21NRAS(61ON) and constitutive NRAS(Q61R) transfectants cells showed increased susceptibility to cytotoxicity by both HLA class I antigen-restricted and nonspecific T cells and up-regulation of several MHC class I antigen processing machinery components. These results suggest a relationship of synthetic lethality between NRAS and BRAF oncogenes, leading to selection against "double-mutant" cells.
Proteomic expression profiling of Haemophilus influenzae grown in pooled human sputum from adults with chronic obstructive pulmonary disease reveal antioxidant and stress responses (2010)

Proteomic expression profiling of H. influenzae grown in pooled human sputum revealed increased expression of antioxidant, stress-response proteins and cofactor and nutrient uptake systems compared to media grown cells.These observations suggest that H. influenzae adapts to the oxidative and nutritionally limited conditions of the airways in adults with chronic obstructive pulmonary disease by increasing expression of molecules necessary for survival in these conditions.
Ultra-wideband millimetre-wave self-oscillating mixer (1983)

The performance of an ultra-wideband millimetre-wave GaAs self-oscillating harmonic mixer (SOHM) is presented. Conversion gain, minimum detectable signal (MDS) and `self-pumping? power level have been measured for the 30 GHz frequency coverage centred at ~ 85 GHz. Sensitivity better than ?71 dBm (without automatic frequency control) using 33 MHz bandwidth, and conversion gain as high as 12 dB have been achieved. For input mm-wave dynamic range of 55 dB (from ?20 dBm to ?75 dBm), a useful down-conversion gain-compression has led to a corresponding variation of only 0.5 mV in the peak-to-peak 70 MHz IF signal (from 0.94 mV to 0.44 mV).
Therapeutic potential of tyrosine kinase 2 in autoimmunity (2014)

Until recently, no patent filings had claimed selective inhibitors of Tyk2. Both CP-690,500 and CMP6 failed to be used in clinical treatment due to the difficulties of finding suitable selective leads or due to detrimental toxicities. Although the result of Cmpd1 is promising, it remains to be seen how specific the Tyk2 inhibitor is and how they are working. Currently, structure-based drug design (SBDD) technology has provided us with a quite useful window for SBDD of Tyk2 inhibitors.
Emulating AC OPF solvers for Obtaining Sub-second Feasible, Near-Optimal Solutions (2020)

Using machine learning to obtain solutions to AC optimal power flow has recently been a very active area of research due to the astounding speedups that result from bypassing traditional optimization techniques. However, generally ensuring feasibility of the resulting predictions while maintaining these speedups is a challenging, unsolved problem. In this paper, we train a neural network to emulate an iterative solver in order to cheaply and approximately iterate towards the optimum. Once we are close to convergence, we then solve a power flow to obtain an overall AC-feasible solution. Results shown for networks up to 1,354 buses indicate the proposed method is capable of finding feasible, near-optimal solutions to AC OPF in milliseconds on a laptop computer. In addition, it is shown that the proposed method can find "difficult" AC OPF solutions that cause flat-start or DC-warm started algorithms to diverge.
Metallurgical analysis and hot storage testing of lead-free solder interconnects: SAC versus SACC (2008)

Lead free solder alloys have been developed which contain small concentrations of rare earth additives such as cerium and lanthanum. It is believed that rare earth element additives refine the microstructure of the solder and improve the mechanical durability and thermomechanical integrity of lead free solder joints. This paper presents the results of a comparative analysis of solder joints with the commonly used SAC 305 alloy (Sn 3.0% Ag 0.5% Cu) and a SACC alloy (Sn 3.0% Ag 0.5% Cu 0.019% Ce), which contains a small concentration of a Cerium additive. The influence of cerium on the microstructural refinement of the bulk solder; the metallurgy of the intermetallic compounds; and the damage evolution of the solder during thermal aging tests are investigated. Mechanical die shear tests and lead pull strength tests have been conducted to compare the mechanical strength and the morphology of the fracture surfaces of SAC and SACC solder joints. Lead pull testing of samples with the cerium doped, SACC alloy exhibit more ductile fracture surfaces and PCB pad lifts, rather than in SAC alloy samples, which exhibit brittle interfacial failures. This change in the fracture surface morphology suggests that cerium additives improve the mechanical integrity of the bulk solder, and correlates with previous materials testing on bulk solder samples of SACC and SAC, which show that SACC solder has a higher Young’s modulus (higher stiffness), higher yield stress, and higher strength over a wide range of strain rates and temperature conditions. On the other hand, in the hot storage tests, the SACC samples exhibit thicker intermetallic formations at the bulk solder to component interface than in SAC samples, which suggests that SACC alloy solder joints could be less mechanically robust than SAC solder joints under dynamic loading conditions such as drop testing.