gebhart/patrepeval huggingface dataset:
Scoring a diverse set of high‐quality docked conformations: A metascore based on electrostatic and desolvation interactions (2006)

Predicting protein-protein interactions involves sampling and scoring docked conformations. Barring some large structural rearrangement, rapidly sampling the space of docked conformations is now a real possibility, and the limiting step for the successful prediction of protein interactions is the scoring function used to reduce the space of conformations from billions to a few, and eventually one high affinity complex. An atomic level free-energy scoring function that estimates in units of kcal/mol both electrostatic and desolvation interactions (plus van der Waals if appropriate) of protein-protein docked conformations is used to rerank the blind predictions (860 in total) submitted for six targets to the community-wide Critical Assessment of PRediction of Interactions (CAPRI; http://capri.ebi.ac.uk). We found that native-like models often have varying intermolecular contacts and atom clashes, making unlikely that one can construct a universal function that would rank all these models as native-like. Nevertheless, our scoring function is able to consistently identify the native-like complexes as those with the lowest free energy for the individual models of 16 (out of 17) human predictors for five of the targets, while at the same time the modelers failed to do so in more than half of the cases. The scoring of high-quality models developed by a wide variety of methods and force fields confirms that electrostatic and desolvation forces are the dominant interactions determining the bound structure. The CAPRI experiment has shown that modelers can predict valuable models of protein-protein complexes, and improvements in scoring functions should soon solve the docking problem for complexes whose backbones do not change much upon binding. A scoring server and programs are available at http://structure.pitt.edu.
Monoclonal antibody that specifically inhibits a human <i>M</i> <sub>r</sub> 52,000 plasminogen-activating enzyme (1982)

Monoclonal antibodies against a human plasminogen activator of M(r) approximately 52,000 (HPA52) were derived by immunization of mice with an impure preparation of the enzyme (urokinase), subsequent hybridization of spleen cells with NSI-Ag4/1 myeloma cells, and cloning of the hybridomas. Selection of mice for hybridization and screening of hybridomas were based solely on direct inhibition of an enzymatic assay of the plasminogen activator with the impure enzyme preparation. A cloned hybridoma produced IgG1 antibodies that bound to and inhibited the enzymatic activity of HPA52 irrespective of whether the HPA52 was derived from urokinase or from human glioblastoma cells, whereas there was no inhibition of or binding to a plasminogen activator of M(r) approximately 70,000 from human melanoma cells or a plasminogen activator of M(r) approximately 36,000 that is a degradation product of HPA52 and present in urokinase. Nor did the anti-HPA52 IgG1 inhibit a murine plasminogen activator of M(r) approximately 48,000 derived from sarcoma virus-transformed cells. By using affinity chromatography with columns of anti-HPA52 IgG1 bound to Sepharose, HPA52 was purified from urokinase to homogeneity as evaluated by NaDodSO(4)/polyacrylamide gel electrophoresis. This study demonstrates that inhibitory monoclonal antibodies against enzymes can be derived with the sole use of impure enzyme preparations and shows how such antibodies subsequently can be used for enzyme purification.
A Composite Right/Left-Handed Rectangular Waveguide with Tilted Corrugations for Millimeter-wave Frequency Scanning Antenna (2008)

A novel structure for a composite right/left-handed (CRLH) corrugated waveguide that operates in the millimeter-wave band is proposed. The CRLH waveguide is comprised of a rectangular waveguide which has tilted corrugations on its bottom broad wall. By operating both above and below the cutoff frequency of the dominant mode, the rectangular waveguide provides, respectively, an inherent series inductance and shunt capacitance, and an inherent shunt inductance, and the tilted corrugations provide a series inductance and capacitance, which can support CRLH propagation. A frequency scanning antenna using this CRLH waveguide was also studied numerically and experimentally. The results demonstrate that the antenna can provide backward-to-forward beam scanning, including the broadside direction. A scanning angle from -9.9 to + 2.2deg was achieved within a 1.8-GHz frequency range in the 60 GHz band.
Compact microwave cavity for hydrogen atomic clock (1992)

Abstract : This paper gives a summary introduction to the compact microwave cavity used in the hydrogen atomic clock. Special emphasis is put on derivation of theoretical calculating equations of main parameters of the microwave cavity. A brief description is given of several methods for discriminating the oscillating modes. Experimental data and respective calculated values are also presented.
Recent evolution of the NF-κB and inflammasome regulating protein POP2 in primates (2011)

Our findings support the hypothesis that the NLR loci of mammals, encoding proteins involved in innate and adaptive immunity as well as mammalian development, have been subject to recent and strong selective pressures. Since POP2 is capable of regulating signaling events and processes linked to innate immunity and inflammation, its presence in the genomes of hominids and Old World primates further suggests that additional regulation of these signals is important in these species.
Longitudinal Volumetric Changes following Traumatic Brain Injury: A Tensor-Based Morphometry Study (2012)

After traumatic injury, the brain undergoes a prolonged period of degenerative change that is paradoxically accompanied by cognitive recovery. The spatiotemporal pattern of atrophy and the specific relationships of atrophy to cognitive changes are ill understood. The present study used tensor-based morphometry and neuropsychological testing to examine brain volume loss in 17 traumatic brain injury (TBI) patients and 13 controls over a 4-year period. Patients were scanned at 2 months, 1 year, and 4 years post-injury. High-dimensional warping procedures were used to create change maps of each subject's brain for each of the two intervals. TBI patients experienced volume loss in both cortical areas and white matter regions during the first interval. We also observed continuing volume loss in extensive regions of white matter during the second interval. Neuropsychological correlations indicated that cognitive tasks were associated with subsequent volume loss in task-relevant regions. The extensive volume loss in brain white matter observed well beyond the first year post-injury suggests that the injured brain remains malleable for an extended period, and the neuropsychological relationships suggest that this volume loss may be associated with subtle cognitive improvements.
A 45ns fully-static 16K MOS ROM (1981)

This report will discuss the design of a ROM that makes extensive use of small signal amplification and 0V threshold devices to reduce active power to 350mW and standby power to 75mW. The device is contact mask programmable and has a die size of 20,300 mil <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Production of Polyhydroxyalkanoates (PHAs) in Transgenic Plants (2002)

Abstract Introduction Historical Perspective Synthesis of PHA in Plants Synthesis of Poly(3HB) in Arabidopsis thaliana Synthesis of Poly(3HB) in Other Plants Synthesis of Poly(3HB‐ co ‐3HV) Copolymer in Plants Synthesis of MCL‐PHA in Plants Novel Uses for PHA in Plants PHA to Modify Fiber Properties PHA as a Feed Supplement PHA as a Tool to Study Plant Metabolic Pathways Patents on PHA in plants Perspective on PHA Production in Agricultural Crops
Lubricants and related products: Synthesis, properties, applications, international standards (1984)

General Introduction Tribology and Tribotechnology Viscosity Classification Production of Lubricating Oils from Petroleum Reconditioning and Regeneration of Used Lubricating Oils Synthetic Lubricants Solid Lubrication Gas Lubrication Additives Analysis and Testing Products Lubricating Greases Finishing of Lube Oils Storage and Transport Environmental Protection Toxicology References Index.
High-performance routing trees with identified critical sinks (1993)

We present two critical-sink routing tree (CSRT) constructions which exp!oit criticai-path information that becomes availab[e during timing-driven layout. Our CS-Steiner heuristics with "Giobai Slack Removal" modify traditional Stetner constructions and produce routing trees wtth szgntjicanthj lower criticalsink delays compared with existing performance-driven methods. We also propose a new class of Elrnore routing tree (ERT) constructions, which deratively add tree edges to minimize Elmore delay. This direct optimization of Elmore delay yields trees that improve delays to identified crztical sinks by up to 69% over minimum Steiner routtngs. ERTs also improve performance over such recent methods as [1] [6] when no critical stnks are specified. 1
The Fate of Limbal Epithelial Progenitor Cells during Explant Culture on Intact Amniotic Membrane (2007)

During ex vivo expansion on iAM, some limbal epithelial progenitor cells indeed migrate onto iAM from the explant surface, whereas some also invade the limbal stroma, very likely undergoing epithelial-mesenchymal transition. This new information should be taken into account in formulating new strategies to improve the expansion protocol.
Network Intrusion Detection using Selected Data Mining Approaches: A Review (2015)

Due to the rapid progress in network technologies, easy availability of the internet and lower cost of mobile devices with wireless network connection facility, the number of internet users is increasing at an exponential rate now-a-days, so does the number of intrusion. Despite the implausible advancement in Information Technology, Intrusion Detection has remained as one of the biggest challenges encountered by network security specialists. Data mining can play a vital role in addressing this issue. In this paper, some selected data mining algorithms available for Network Intrusion Detection have been reviewed, such as-Support Vector Machine, K-Nearest Neighbor, Nave Bayesian Classifier, Decision tree Algorithm (C4.
Characterization of Three Glycosyltransferases Involved in the Biosynthesis of the Phenolic Glycolipid Antigens from the Mycobacterium tuberculosis Complex (2004)

Mycobacterium tuberculosis and Mycobacterium leprae, the two main mycobacterial pathogens in humans, produce highly specific long chain beta-diols, the dimycocerosates of phthiocerol, and structurally related phenolic glycolipid (PGL) antigens, which are important virulence factors. In addition, M. tuberculosis also secretes glycosylated p-hydroxybenzoic acid methyl esters (p-HBAD) that contain the same carbohydrate moiety as the species-specific PGL of M. tuberculosis (PGL-tb). The genes involved in the biosynthesis of these compounds in M. tuberculosis are grouped on a 70-kilobase chromosomal fragment containing three genes encoding putative glycosyltransferases: Rv2957, Rv2958c, and Rv2962c. To determine the functions of these genes, three recombinant M. tuberculosis strains, in which these genes were individually inactivated, were constructed and biochemically characterized. Our results demonstrated that (i) the biosynthesis of PGL-tb and p-HBAD involves common enzymatic steps, (ii) the Rv2957, Rv2958c, and Rv2962c genes are involved in the formation of the glycosyl moiety of the two classes of molecules, and (iii) the product of Rv2962c catalyzes the transfer of a rhamnosyl residue onto p-hydroxybenzoic acid ethyl ester or phenolphthiocerol dimycocerosates, whereas the products of Rv2958c and Rv2957 add a second rhamnosyl unit and a fucosyl residue to form the species-specific triglycosyl appendage of PGL-tb and p-HBAD. The recombinant strains produced provide the tools to study the role of the carbohydrate domain of PGL-tb and p-HBAD in M. tuberculosis pathogenesis.
Virtual control panels (1988)

A virtual control panel is a collection of controls which are graphically represented on a screen and can be operated according to the direct manipulation paradigm. A control management system makes it possible to interactively create various control panels and interface them with arbitrary applications. In this paper we describe functions which should be supported by an interactive control management system, and present a case study of a system which we have designed and implemented on the Macintosh microcomputer.
Impact of Environmental and Genetic Factors on Biofilm Formation by the Probiotic Strain <i>Lactobacillus rhamnosus</i> GG (2007)

Lactobacillus rhamnosus GG (ATCC 53103) is one of the clinically best-studied probiotic organisms. Moreover, L. rhamnosus GG displays very good in vitro adherence to epithelial cells and mucus. Here, we report that L. rhamnosus GG is able to form biofilms on abiotic surfaces, in contrast to other strains of the Lactobacillus casei group tested under the same conditions. Microtiter plate biofilm assays indicated that in vitro biofilm formation by L. rhamnosus GG is strongly modulated by culture medium factors and conditions related to the gastrointestinal environment, including low pH; high osmolarity; and the presence of bile, mucins, and nondigestible polysaccharides. Additionally, phenotypic analysis of mutants affected in exopolysaccharides (wzb), lipoteichoic acid (dltD), and central metabolism (luxS) showed their relative importance in biofilm formation by L. rhamnosus GG.
Editor's Introduction (1982)

Research on higher education in the Soviet Union is an emerging field. For decades, educational research has largely been defined as studies applied to the development of the country's primary and secondary school system. Research in pedagogy and educational psychology has furnished the theoretical basis for the curricula, syllabi, and recommended teaching methods that are used in the national school system. Higher education, it had been traditionally reasoned, did not need a general theory of practice, and each field of specialization in the over eight hundred Soviet universities and professional institutes had been left primarily to its own devices in generating instructional techniques and materials.
Nonlinear Adaptive Flight Control Using Backstepping and Neural Networks Controller (2001)

Anonlinearadaptivee ightcontrol system isproposed using a backstepping and neural networks controller. The backstepping controlleris used to stabilize allstatevariablessimultaneously withoutthetwo-timescaleassumption that separatesthefastdynamics,involving theangularratesoftheaircraft,from theslowdynamics,whichincludes angle of attack, sideslip angle, and bank angle. It is assumed that the aerodynamic coefe cientsinclude uncertainty, and an adaptive controller based on neural networks is used to compensate for the effect of the aerodynamic modeling error. Under mild assumptions on the aerodynamic uncertainties and nonlinearities, it is shown by the Lyapunov stability theorem that the tracking errors and the weights of neural networks exponentially converge to a compactset. Finally, nonlinearsix-degree-of-freedom simulation resultsfor an F-16 aircraft model are presented to demonstrate the effectiveness of the proposed control law. Nomenclature F = aerodynamic force about the body-e xed frame I = moment of inertia L; M; N = aerodynamic rolling, pitching, yawing moment p;q;r = roll, pitch, yaw rate about the body-e xed frame N q = dynamic pressure T = thrust V = velocity ®;¯ = angle of attack, sideslip angle ±e;±a;±r = elevator, aileron, rudder angle A;µ;A = roll, pitch, yaw angle
[The effect of arginine vasopressin receptor antagonist on the rat cold-injured brain]. (1993)

Centrally released arginine vasopressin (AVP) has been reported to increase the water permeability of brain capillaries under both normal and pathological conditions. It is not known, however, whether AVP regulates the permeability of brain capillaries via a V1 receptor or a V2 receptor. In the present experiments, we attempted to suppress cold-induced brain edema with V1 or V2 receptor antagonists. Adult rats were intraventricularly administered with 5 ng, 50 ng, or 500 ng of V1 receptor antagonist, or 50 ng or 500 ng of V2 receptor antagonist. Ten minutes after administration, a cold injury was induced in the left hemisphere of the brain by applying a freezing probe, which had been cooled by liquid nitrogen, to the left parietal skull for 20 seconds. Brain water and tissue sodium content were then measured 24 hours after the cold-injury. In experiment 1, the brain water content had significantly increased in both the injured and non-injured hemispheres. The administration of 50 ng of V1 receptor antagonist resulted in a significant reduction in the brain water content of the bilateral hemispheres. Administration of 50 ng of V2 receptor antagonist produced a significant reduction in the brain water content of the non-injured hemisphere only. A 500 ng administration of both antagonists did not change the brain water content of the bilateral hemispheres. In experiment 2, we divided the cold injured brain into cortical and deep structures and observed the effect of the V1 receptor antagonist. Cold-injury induced significant increases in brain water and the tissue sodium content of the bilateral cortical structures, but no changes in bilateral deep structures.(ABSTRACT TRUNCATED AT 250 WORDS)
Mitochondrial Localization of AtOXA1, an Arabidopsis Homologue of Yeast Oxa1p Involved in the Insertion and Assembly of Protein Complexes in Mitochondrial Inner Membrane (2000)

Components of some protein complexes present in the inner membrane of mitochondria are encoded in both nuclear and mitochondrial genomes, and correct sorting and assembly of these proteins is necessary for proper respiratory function. Recent studies in yeast suggest that Oxa1p, a protein conserved between prokaryotes and eukaryotes, is an essential factor for protein sorting and assembly into membranes. We previously identified AtOXA1, an Arabidopsis homologue of OXA1 by functional complementation of a yeast oxa1- mutant. In this study, we investigated the genomic organization of AtOXA1 and localization of the AtOXA1 protein. Characterization of the AtOXA1 genomic region indicated that the gene consists of 10 exons and is located on chromosome V. A database search also revealed another gene coding for a putative protein homologous to AtOXA1 on chromosome II. Transient expression of a green fluorescent protein (GFP) fusion in suspension-cultured tobacco cells showed that AtOXA1 is targeted into mitochondria by its N-terminal presequence. Antibodies raised against AtOXA1 recognized a 38-kDa intrinsic protein of the inner mitochondrial membrane. Thus, localization of AtOXA1 in the mitochondrial inner membrane, together with our previous complementation experiment in yeast, suggested that it is a functional homologue of Oxa1p.
Assimilation of Endogenous Nicotinamide Riboside Is Essential for Calorie Restriction-mediated Life Span Extension in Saccharomyces cerevisiae (2009)

NAD(+) (nicotinamide adenine dinucleotide) is an essential cofactor involved in various biological processes including calorie restriction-mediated life span extension. Administration of nicotinamide riboside (NmR) has been shown to ameliorate deficiencies related to aberrant NAD(+) metabolism in both yeast and mammalian cells. However, the biological role of endogenous NmR remains unclear. Here we demonstrate that salvaging endogenous NmR is an integral part of NAD(+) metabolism. A balanced NmR salvage cycle is essential for calorie restriction-induced life span extension and stress resistance in yeast. Our results also suggest that partitioning of the pyridine nucleotide flux between the classical salvage cycle and the NmR salvage branch might be modulated by the NAD(+)-dependent Sir2 deacetylase. Furthermore, two novel deamidation steps leading to nicotinic acid mononucleotide and nicotinic acid riboside production are also uncovered that further underscore the complexity and flexibility of NAD(+) metabolism. In addition, utilization of extracellular nicotinamide mononucleotide requires prior conversion to NmR mediated by a periplasmic phosphatase Pho5. Conversion to NmR may thus represent a strategy for the transport and assimilation of large nonpermeable NAD(+) precursors. Together, our studies provide a molecular basis for how NAD(+) homeostasis factors confer metabolic flexibility.
Novel High Speed Telemetry System with Measurements Along the String Mitigate Drilling Risk and Improve Drilling Efficiency (2011)

Abstract Novel systems such as the wired-pipe or networked drillstring telemetry system have allowed broadband communication with downhole tools in various operating areas around the world, including in deepwater. Two capabilities are vital to offer operators and service companies with cost effective drilling and completion in challenging scenarios: High speed: real-time, bi-directional data transfer at a rate of 57,600 bits per second (bps) enables downhole and subsurface conditions to be measured and controlled, Measurements all along the string: annular pressure and temperature measurements distributed at network nodes beyond just at the drill bit enable early warning of developing trouble events. This paper describes cases where the broadband network provided downhole information for identifying poor hole cleaning, determining sweep efficiency, revealing cutting accumulation and recognizing pack offs early on. Further, examples are described that improved drilling risk mitigation by the capability to measure as many as 45 different drilling dynamics parameters that are updated every few seconds revealing bit whirl, stick slip, lateral and axial movement while drilling trouble zones. The successful mitigation of downhole vibration resulted in a 68% increase in time on bottom and a 58% increase in rate of penetration (ROP). Annular pressure evaluation all along the drillstring ensured adequate hole cleaning in challenging wellbores.
The effects of surface wettability on the fog and dew moisture harvesting performance on tubular surfaces (2016)

The efficient water harvesting from air-laden moisture has been a subject of great interest to address world-wide water shortage issues. Recently, it has been shown that tailoring surface wettability can enhance the moisture harvesting performance. However, depending on the harvesting condition, a different conclusion has often been reported and it remains unclear what type of surface wettability would be desirable for the efficient water harvesting under the given condition. Here we compare the water harvesting performance of the surfaces with various wettability under two different harvesting conditions-dewing and fogging, and show that the different harvesting efficiency of each surface under these two conditions can be understood by considering the relative importance of the water capturing and removal efficiency of the surface. At fogging, the moisture harvesting performance is determined by the water removal efficiency of the surface with the oil-infused surfaces exhibiting the best performance. Meanwhile, at dewing, both the water capturing and removal efficiency are crucial to the harvesting performance. And well-wetting surfaces with a lower barrier to nucleation of condensates exhibit a better harvesting performance due to the increasing importance of the water capture efficiency over the water removal efficiency at dewing.