gebhart/patrepeval huggingface dataset:
A purple acidophilic di-ferric DNA ligase from <i>Ferroplasma</i> (2008)

We describe here an extraordinary purple-colored DNA ligase, LigFa, from the acidophilic ferrous iron-oxidizing archaeon Ferroplasma acidiphilum, a di-ferric enzyme with an extremely low pH activity optimum. Unlike any other DNA ligase studied to date, LigFa contains two Fe(3+)-tyrosinate centers and lacks any requirement for either Mg(2+) or K(+) for activity. DNA ligases from closest phylogenetic and ecophysiological relatives have normal pH optima (6.0-7.5), lack iron, and require Mg(2+)/K(+) for activity. Ferric iron retention is pH-dependent, with release resulting in partial protein unfolding and loss of activity. Reduction of the Fe(3+) to Fe(2+) results in an 80% decrease in DNA substrate binding and an increase in the pH activity optimum to 5.0. DNA binding induces significant conformational change around the iron site(s), suggesting that the ferric irons of LigFa act both as structure organizing and stabilizing elements and as Lewis acids facilitating DNA binding at low pH.
Semi-insulating In0.49Ga0.51P grown at reduced substrate temperature by low-pressure metalorganic chemical vapor deposition (1997)

High-resistivity unintentionally-doped In0.49Ga0.51P lattice matched to GaAs has been grown via low-pressure metalorganic chemical vapor deposition at a reduced growth temperature. These layers have excellent surface quality and are single crystal. The resistivity increases exponentially as the growth temperature is decreased from 550 to 490 °C, resulting in a resistivity of ∼109 Ω cm for samples grown at 490 °C. In addition, the photoluminescence intensity decreases exponentially for growth temperatures below 550 °C, indicating an increase in nonradiative recombination related to an increasing trap concentration. For samples grown at 550 °C, constant capacitance deep level transient spectroscopy measurements show a strong broad peak at ∼200 °K with an ionization energy of 0.40±0.04 eV, verifying the presence of an electron trap. The gummel plot and I–V characteristics of an InGaP/GaAs heterojunction bipolar transistor (HBT) with a 2000-Å-thick InGaP buffer layer grown at 500 °C are identical to that of an HBT grown without the InGaP buffer layer, indicating that the semi-insulating InGaP layer is compatible with GaAs-based device epitaxy.
Power-limiting breakdown effects in GaAs MESFET's (1981)

State-of-the-art GaAs MESFET'S exhibit an output power saturation as the input power is increased. Experiments indicated that this power saturation is due to the combined effects of forward gate conduction and reverse gate-to-drain breakdown. This reverse breakdown was studied in detail by performing two-dimensional numerical simulations of planar and recessed-gate FET's. These simulations demonstrated that the breakdown occurs at the drain-side edge of the gate. The results of the numerical simulations suggested a model of the depletion layer configuration which could be solved analytically. This model demonstrated that the breakdown voltage was inversely proportional to the product of the doping level and the active layer thickness.
Dissolution and formation of nuclear materials in molten media (2001)

Abstract As innovative means to recover actinides from irradiated fuels, pyrochemical processes are proposed. In the Japan Atomic Energy Research Institute (JAERI), the feasibility of applying molten-salts processes to nitride fuels containing transuranium elements for transmutation is investigated. In the course of study, experiments and analyses have been made on the high-temperature chemistry of M­N­Cl systems, the effects of oxygen impurities, and the implications of the divalent state along with the normal trivalent state of lanthanides and actinides. Thermodynamic calculation and the electrochemical measurements are compared in a few aspects of dissolution and precipitation of nuclear materials in molten halides.
Open ACC Programs Examined: A Performance Analysis Approach (2015)

The Open ACC standard has been developed to simplify parallel programming of heterogeneous systems. Based on a set of high-level compiler directives it allows application developers to offload code regions from a host CPU to an accelerator without the need for low-level programming with CUDA or Open CL. Details are implicit in the programming model and managed by Open ACC API-enabled compilers and runtimes. However, it is still possible for the application developer to explicitly specify several performance-related details for the execution. To tune an Open ACC program and efficiently utilize available hardware resources, sophisticated performance analysis tools are required. In this paper we present a framework for detailed analysis of Open ACC applications. We describe new analysis capabilities introduced with an Open ACC tools interface and depict the integration of performance analysis for low-level programming models. As proof of concept we implemented the concept into the measurement infrastructure Score-P and the trace browser Vampir. This provides the program developer with a clearer understanding of the dynamic runtime behavior of the application and for systematic identification of potential bottlenecks.
Interferon-gamma is a potent inducer of catagen-like changes in cultured human anagen hair follicles (2005)

These data suggest that IFN-gamma is a potent catagen inducer in normal human scalp hair follicles, which express cognate receptors, and show that IFN-gamma administration offers an excellent tool for experimental catagen induction in organ-cultured human hair follicles. This catagen induction probably occurs at least in part via upregulation of the recognized catagen-stimulatory growth factor TGF-beta2.
Long term stability and quality factors of degenerately n-type doped silicon resonators (2014)

Effect of degenerate doping on the long term stability and quality factors of silicon resonators was studied. The long term stability of electrostatically coupled tuning fork and width extensional mode resonators was found to be better than 1 ppm during a measurement spanning 220 days. Resonators were phosphorus doped to a carrier concentration of 4.1×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−3</sup> . Quality factors of ∼10-MHz Lamé mode resonators on wafers doped up to a concentration of 7.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−3</sup> were found to range from 900,000 to 1,500,000, which is comparable to that reported for similar resonators with moderate doping. The results indicate that the effect from heavy phosphorus doping on resonator stability or on silicon intrinsic losses is low at the studied doping levels.
EFFECT OF CONTRACTION ON TENDERNESS OF POULTRY MUSCLE COOKED IN THE PRERIGOR STATE (1970)

SUMMARY Effects on tenderness caused by contraction of excised chicken muscles, induced by immediate post‐mortem treatments consisting of electrical stimulation, beating, freeze‐thawing, end heating, and followed by cooking in the prerigor state were measured. One member of each pair of muscles was held in restraint while exposed to the same conditions. In terms of percentage of original rest length, electrical stimulation reduced muscle length to 59%, and when followed by cooking to 44%; freeze‐thawing reduced the length to 42%, and when followed by cooking to 40%; beating to 95%, and when followed by cooking to 52%; cooking alone to 48–53%. With the exception of the beating‐heating combination, all contraction‐inducing treatments resulted in a reduction of the shear values (force per cross‐sectional area) of cooked muscle to about one‐half those of uncontracted controls. These results with chicken muscles on intense contraction followed by cooking in the prerigor state agree with recent similar observations on red meat muscles.
Therapeutic implications of nitric oxide generation by tumor-targeting Salmonella typhimurium strains (2007)

C103 Nitric oxide (NO) can inhibit cancer cells proliferation and promote apoptosis. Many bacterial species can tolerate high concentrations of nitric oxide. Certain species of the genus Salmonella areespeciallynoteworthy for their nitric oxide resistance, allowing them to overcome macrophage attack. We hypothesized that a tumor targeting attenuated Salmonella (SL 7838-ChrR6), overproducing NO, will kill tumor cells and will work in an additive manner when employed with reductive prodrug chemotherapy. NO was found to be produced inside the cells either when nitrate (NO3) or nitrite (NO2) were provided as indicated by DAF-FM di-acetate (NO specific fluorescent dye). We examined the tumor microenvironment within a living organism, using a newly developed NO micro-sensor. NO Concentration, in all three regions measured of the control mouse were very low but in the infected with SL 7838-ChrR6mouse, significant niches of NO production were found within the tumor. NO production coincided with the presence of SL7838-ChrR6, as revealed by in vivo bioluminescence imaging. The tumor cell killing mediated by SL7838-ChrR6 was measured in vitro using 4T1 murine adenocarcinoma breast cancer cells supplemented with nitrate, 6-chloro-9-nitro-5-oxo-5H-benzo[a]phenoxazine (CNOB; a reductive prodrug) or both. Addition of nitrate at 100 μM (concentration found in the serum) led to increased cell killing by approximately 50% compared to control with no nitrate added. Combination of nitrate and CNOB in a concentration as little as 3μM elevated the cell killing efficiency to ~97% compared to controls.
Bio‐based production of organic acids with <i> <scp>C</scp> orynebacterium glutamicum </i> (2012)

The shortage of oil resources, the steadily rising oil prices and the impact of its use on the environment evokes an increasing political, industrial and technical interest for development of safe and efficient processes for the production of chemicals from renewable biomass. Thus, microbial fermentation of renewable feedstocks found its way in white biotechnology, complementing more and more traditional crude oil-based chemical processes. Rational strain design of appropriate microorganisms has become possible due to steadily increasing knowledge on metabolism and pathway regulation of industrially relevant organisms and, aside from process engineering and optimization, has an outstanding impact on improving the performance of such hosts. Corynebacterium glutamicum is well known as workhorse for the industrial production of numerous amino acids. However, recent studies also explored the usefulness of this organism for the production of several organic acids and great efforts have been made for improvement of the performance. This review summarizes the current knowledge and recent achievements on metabolic engineering approaches to tailor C. glutamicum for the bio-based production of organic acids. We focus here on the fermentative production of pyruvate, L- and D-lactate, 2-ketoisovalerate, 2-ketoglutarate, and succinate. These organic acids represent a class of compounds with manifold application ranges, e.g. in pharmaceutical and cosmetics industry, as food additives, and economically very interesting, as precursors for a variety of bulk chemicals and commercially important polymers.
Derivatives of tetraphenylmethane and tetraphenylsilane: Synthesis of new tetrahedral building blocks for molecular construction (2003)

Useful derivatives of tetraphenylmethane and tetraphenylsilane have been synthesized by efficient methods that give crystalline products without chromatographic purification. New compounds include tetrakis(4-hydroxyphenyl)methane (21), tetrakis(4-formylphenyl)methane (22), tetrakis[(4-hydroxymethyl)phenyl]methane (23), tetrakis(4-bromophenyl)silane (24), tetrakis(4-iodophenyl)silane (25), tetrakis(4-hydroxyphenyl)silane (26), tetrakis[(4-hydroxymethyl)phenyl]silane (27), and tetrakis[(4-chloromethyl)phenyl]silane (28). These compounds are valuable precursors for the construction of complex molecules with tetrahedral geometries.Key words: organic synthesis, molecular and supramolecular design and construction, tetraphenylmethane, tetraphenyl silane, tetrahedral building blocks.
A directional adaptive least-mean-square acoustic array for hearing aid enhancement (1995)

This paper introduces directional microphones to adaptive array processing for hearing aid applications. Acoustic fixed arrays are designed to match a focused array gain pattern, while acoustic adaptive arrays are designed to attenuate interference noises with changing characteristics. However, as currently constructed, acoustic adaptive arrays cannot stay focused with a limited number of microphones available in a cosmetically acceptable hearing aid. In this paper, a technique is discussed that combines fixed and adaptive arrays in a system which enhances the desired signal while effectively attenuating interference speech and background noise. In particular, the design and performance of a directional adaptive least-mean-square (LMS) acoustic four-element array with a restricted geometry, where the array microphones are directional microphones, are examined. Simulations show that the directivity index of the directional adaptive array using four hypercardioid microphones is improved to between 8.6 and 11 dB. The array reduces the interference noises by 29.7 to 42.3 dB and provides a signal-to-noise ratio improvement of 11.5 to 12.2 dB over a single omnidirectional microphone. The sensitivity analysis is also discussed. It is concluded that the small size (four-element) microphone array can spatially filter interference noise effectively and so improve SNR performance significantly.
Bone Marrow Multipotent Mesenchymal Stroma Cells Act as Pericyte-like Migratory Vehicles in Experimental Gliomas (2008)

Bone marrow-derived multipotent mesenchymal stroma cells (MSCs) have emerged as cellular vectors for gene therapy of solid cancers. We implanted enhanced green fluorescent protein-expressing rat MSCs directly into rat malignant gliomas to address their migratory capacity, phenotype, and effects on tumor neovascularization and animal survival. A single intratumoral injection of MSCs infiltrated the majority of invasive glioma extensions (72 +/- 14%) and a substantial fraction of distant tumor microsatellites (32 +/- 6%). MSC migration was highly specific for tumor tissue. Grafted MSCs integrated into tumor vessel walls and expressed pericyte markers alpha-smooth muscle actin, neuron-glia 2, and platelet-derived growth factor receptor-beta but not endothelial cell markers. The pericyte marker expression profile and perivascular location of grafted MSCs indicate that these cells act as pericytes within tumors. MSC grafting did not influence tumor microvessel density or survival of tumor-bearing animals. The antiangiogenic drug Sunitinib markedly reduced the numbers of grafted MSCs migrating within tumors. We found no MSCs within gliomas following intravenous (i.v.) injections. Thus, MSCs should be administered by intratumoral implantations rather than by i.v. injections. Intratumorally grafted pericyte-like MSCs might represent a particularly well-suited vector system for delivering molecules to affect tumor angiogenesis and for targeting cancer stem cells within the perivascular niche.
Evaluation and validation of candidate endogenous control genes for real-time quantitative PCR studies of breast cancer (2007)

We have validated two endogenous control genes, MRPL19 and PPIA, for RQ-PCR analysis of gene expression in primary breast tissue. Of the genes in current use in this field, the above combination offers increased accuracy and resolution in the quantitation of gene expression data, facilitating the detection of smaller changes in gene expression than otherwise possible. The combination identified here is a good candidate for use as a two-gene endogenous control in a broad spectrum of future research and diagnostic applications in breast cancer.
A Phase-Channel Combiner, Mod. I, for the NRL Space Surveillance System (1963)

The Space Surveillance System developed at Naval Research Laboratory (NRL) for the detection of earth satellites forms a fence across the southern part of the United States. Four receiving sites are altered with three transmitting sites which iluminate satellites with radio energy as they traverse the fence. The angle of arrival of the reflected signals is measured at each receiving station by a compound radio interferometer. These signals yield a multiplicity of channels which are normally recorded on paper and analyzed manually by visual aids and special slide rules. With the increasing satellite population and the repetitive nature of their orbits, the number of fence crossings has increased considerably. Automation in the detection process is needed to facilite identification and sorting of satellites from each other (and from refuse) if a large backlog of data is to be avoided. An electronic system has been developed which automatically combines the phase channels into one unambiguous channel and depicts the angles of arrival of the radio energy from the satellites. The basic technique used in the phase-channel combiner is as follows. Since complete a priori information on the incoming signals is known, simulated signal waveforms, locally generated, are correlated channel by channel with each signal channel from the radio interferometer. At the moment of coincidence between each simulated and live signal channel, a "marker" pulse is generated. This process is applied simultaneously to all of the output channels of the multichannel radio interferometer.
Type III effectors orchestrate a complex interplay between transcriptional networks to modify basal defence responses during pathogenesis and resistance (2006)

To successfully infect a plant, bacterial pathogens inject a collection of Type III effector proteins (TTEs) directly into the plant cell that function to overcome basal defences and redirect host metabolism for nutrition and growth. We examined (i) the transcriptional dynamics of basal defence responses between Arabidopsis thaliana and Pseudomonas syringae and (ii) how basal defence is subsequently modulated by virulence factors during compatible interactions. A set of 96 genes displaying an early, sustained induction during basal defence was identified. These were also universally co-regulated following other bacterial basal resistance and non-host responses or following elicitor challenges. Eight hundred and eighty genes were conservatively identified as being modulated by TTEs within 12 h post-inoculation (hpi), 20% of which represented transcripts previously induced by the bacteria at 2 hpi. Significant over-representation of co-regulated transcripts encoding leucine rich repeat receptor proteins and protein phosphatases were, respectively, suppressed and induced 12 hpi. These data support a model in which the pathogen avoids detection through diminution of extracellular receptors and attenuation of kinase signalling pathways. Transcripts associated with several metabolic pathways, particularly plastid based primary carbon metabolism, pigment biosynthesis and aromatic amino acid metabolism, were significantly modified by the bacterial challenge at 12 hpi. Superimposed upon this basal response, virulence factors (most likely TTEs) targeted genes involved in phenylpropanoid biosynthesis, consistent with the abrogation of lignin deposition and other wall modifications likely to restrict the passage of nutrients and water to the invading bacteria. In contrast, some pathways associated with stress tolerance are transcriptionally induced at 12 hpi by TTEs.
Analysis of genes causing hypertension and stroke in spontaneously hypertensive rats: Gene expression profiles in the brain (2014)

Spontaneously hypertensive rats (SHR) and stroke-prone SHR (SHRSP) are frequently used as rat models not only of essential hypertension and stroke, but also of attention-deficit hyperactivity disorder (ADHD). Normotensive Wistar-Kyoto rats (WKY) are used as the control rats in these cases. An increasing number of studies has demonstrated the critical role of the central nervous system in the development and maintenance of hypertension. In a previous study, we analyzed the gene expression profiles in the adrenal glands of SHR. Thus, in this study, we analyzed gene expression profiles in the brains of SHR in order to identify the genes responsible for causing hypertension and stroke, as well as those involved in ADHD. Using genome-wide microarray technology, we examined the gene expression profiles in the brains of 3 rat strains (SHR, SHRSP and WKY) when the rats were 3 and 6 weeks of age, a period in which the rats are considered to be in a pre-hypertensive state. Gene expression profiles in the brain were compared between SHR and WKY, and between SHRSP and SHR. A total of 179 genes showing a >4- or <-4-fold change in expression were isolated, and candidate genes were selected using two different web tools: the first tool was the Database for Annotation, Visualization and Integrated Discovery (DAVID), which was used to search for significantly enriched genes, and categorized them using Gene Ontology (GO) terms, and the second was the network explorer of Ingenuity Pathway Analysis (IPA), which was used to search for interaction networks among SHR- and SHRSP-specific genes. The IPA of SHR-specific genes revealed that prostaglandin E receptor 4 (Ptger4) is one of the candidate genes responsible for causing hypertension in SHR, and that albumin (Alb) and chymase 1 (Cma1) are also responsible for causing hypertension in SHR in the presence of angiotensinogen (Agt). Similar analyses of SHRSP-specific genes revealed that the angiotensin II receptor-associated gene (Agtrap) interacts with the FBJ osteosarcoma oncogene (Fos), and with the angiotensin II receptor type-1b (Agtr1b). As Agtrap and Agtr1b not only participate in the 'uptake of norepinephrine' and 'blood pressure', but also in the 'behavior' of SHRSP at 6 weeks of age, our data demonstrate a close association between hypertension and ADHD.