gebhart/patrepeval huggingface dataset:
Computational enzymology: modelling the mechanisms of biological catalysts (2008)

Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and reliable predictions of mechanisms, revolutionizing enzymology.
Oxygen reduction reaction on a highly-alloyed Pt-Ni supported carbon electrocatalyst in acid solution (2010)

CSIR 3rd Beinnual Conference 2010, Science Real and Relevant, CSIR International Convention Center, Pretoria, South Africa
Clinical Review of Antidiabetic Drugs: Implications for Type 2 Diabetes Mellitus Management (2017)

Type 2 diabetes mellitus (T2DM) is a global pandemic, as evident from the global cartographic picture of diabetes by the International Diabetes Federation (http://www.diabetesatlas.org/). Diabetes mellitus is a chronic, progressive, incompletely understood metabolic condition chiefly characterized by hyperglycemia. Impaired insulin secretion, resistance to tissue actions of insulin, or a combination of both are thought to be the commonest reasons contributing to the pathophysiology of T2DM, a spectrum of disease originally arising from tissue insulin resistance and gradually progressing to a state characterized by complete loss of secretory activity of the beta cells of the pancreas. T2DM is a major contributor to the very large rise in the rate of non-communicable diseases affecting developed as well as developing nations. In this mini review, we endeavor to outline the current management principles, including the spectrum of medications that are currently used for pharmacologic management, for lowering the elevated blood glucose in T2DM.
Solvent Exchange Module for LC-NMR Hyphenation Using Machine Vision-Controlled Droplet Evaporation (2013)

We report the use of pendant droplet evaporation for exchange of eluents for (1)H nuclear magnetic resonance ((1)H NMR) purposes. Analytes are fed and retained in 500 nL droplets, which are concentrated by evaporation and subsequently redissolved in deuterated solvent. Droplet size is monitored by machine vision (MV), and heating rates are adjusted concordingly to maintain a stable droplet volume. Evaporation control is independent of solvent properties, and the setup handles feed rates up to 7 μL min(-1). The interface is capable of exchanging up to 90% of solvent for deuterated solvent, with a good recovery and repeatability for tomato extracts (Solanum lycopersicum). The system was capable of handling both polar and nonpolar analytes in one run. Volatiles such as formate, acetate, and lactate and the thermosensitive compound epigallocatechin gallate were recovered without significant losses. Ethanol and propionate were recovered with significant losses due to the formation of a minimum boiling azeotrope. The current setup is ideally suited for on- and off-line hyphenation of liquid chromatography and NMR, as it is comprehensive, fully automated, and easy to operate.
Applications of Magnetic Scanning to High Current Implantation (1981)

High current ion implantation systems employing beams of 75As+ at 10 mA or more at energies of the order of 100 keV depend upon electron space charge neutralization to preserve the ion optical quality of the beam during transport from the source to the wafer implant location. Time varying magnetic fields have been used to deflect these beams over lateral dimensions up to 300 mm at frequencies of the order of 0.1 Hz, without affecting low energy electrons trapped in the potential well of the beam, and without significant modification of the ion beam shape. Hybrid magnetic-mechanical scanning of high current ion beams has been shown to be capable of averaging the implanted dose with uniformities as good as 2σ < 1% across 100 mm diameter silicon wafers mounted on an 0.8 meter disc rotating in vacuum at 1000 r.p.m. The physical basis of angle corrected hybrid magnetic-mechanical scanning is analyzed leading to a calculated relationship for the deflection (X) dependent on the scanner magnetic field (Bs). This functional dependence X = f(Bs) has also been measured using the disc as a rotating beam profile monitor. From the measured dependence, implant dose uniformity across a long scan can be obtained as shown by sheet resistance maps of ion implanted wafers. The dependence of dose uniformity on the number of scans has also been evaluated, and data is presented illustrating uniformity 2σ < 2% can be achieved using a single scan across the wafer.
Dietary Phylloquinone Intakes and Metabolic Syndrome in US Young Adults (2009)

Mean reported dietary phylloquinone intakes suggested that most US young adults consume an insufficient amount of vitamin K from their diet. A high intake of phylloquinone may favorably affect MetS or its components, probably through an overall more heart-healthy dietary pattern. The pathogenesis of MetS is profoundly complex and may involve other factors and/or mechanisms, in addition to vitamin K nutriture. Although our data suggest a potential role of vitamin K in MetS, the biological mechanisms underlying the observed associations must be elucidated.
Design and performance of a permanent-magnet rotary refrigerator. (2005)

In order to demonstrate the potential of magnetic refrigeration to provide useful cooling near room temperature, Astronautics Corporation of America constructed a rotary magnetic refrigerator (RMR) in 2001. The RMR uses the active magnetic regeneration cycle with an aqueous heat transfer fluid. The required change in magnetic field is produced by the rotation of a wheel packed with porous beds of magnetocaloric material through a permanent magnet with steel flux concentration poles. A pump, and valves mounted to the wheel, control heat transfer fluid flow through the magnetocaloric beds and heat exchangers. This rotary design allows quiet, reliable operation over a range of frequencies (0.5 to 4 Hz), heat transfer fluid flow rates and cooling power. The performance of the device using Gd and Gd alloy spherical particles is reported and analyzed. The authors also describe the performance effects of introducing layered beds and a La(Fe-Six)H alloy with a first order magnetic transition.
Experiments on insulation of relativistic electron flows in oblique and tapered magnetic fields (1988)

Several experiments on magnetically insulated electron flows will be reported. These include experiments in combined axial and azimuthal magnetic fields like those seen in powerful ion diodes, and flows in which the degree of insulation is changed along the flow path. Conservation of transverse electron canonical momentum implies that the flows cannot be exactly in the ExB direction. Measurements of the field pitch (the ratio of the axial to the azimuthal magnetic field) show a tendency to flow in the ExB direction with very little current along the magnetic field. However, it was also found that the flow tended to find an equilibrium where electrons in ExB flow have only small transverse canonical momentum. Other data show a surprising degree of electron recapture at the cathode under some conditions. This has important implications for multi-terrawatt devices. 4 refs., 7 figs.
Happiness: a revolution in economics (2008)

A leading economist discusses the potential of happiness research (the quantification of well-being) to answer important questions that standard economics methods are unable to analyze.Revolutionary developments in economics are rare. The conservative bias of the field and its enshrined knowledge make it difficult to introduce new ideas not in line with received theory. Happiness research, however, has the potential to change economics substantially in the future. Its findings, which are gradually being taken into account in standard economics, can be considered revolutionary in three respects: the measurement of experienced utility using psychologists' tools for measuring subjective well-being; new insights into how human beings value goods and services and social conditions that include consideration of such non-material values as autonomy and social relations; and policy consequences of these new insights that suggest different ways for government to affect individual well-being. In Happiness, emphasizing empirical evidence rather than theoretical conjectures, Bruno Frey substantiates these three revolutionary claims for happiness research. After tracing the major developments of happiness research in economics and demonstrating that we have gained important new insights into how income, unemployment, inflation, and income demonstration affect well-being, Frey examines such wide-ranging topics as democracy and federalism, self-employment and volunteer work, marriage, terrorism, and watching television from the new perspective of happiness research. Turning to policy implications, Frey describes how government can provide the conditions for people to achieve well-being, arguing that a crucial role is played by adequate political institutions and decentralized decision making. Happiness demonstrates the achievements of the economic happiness revolution and points the way to future research.
Synthesis and Absolute Configuration of Axially Chiral Binaphthoquinones (1998)

The synthesis of (+)-(S)-1',4-dihydroxy-2,3'-dimethyl-1,2'-binaphthalene-5,5',8,8'-tetrone (62) and (+)-(S)-4,5',8'-trihydroxy-2,3'-dimethyl-1,2'-binaphthalene-1',4',5,8-tetrone (55), compounds which are atrop-isomeric with the naturally occurring binaphthoquinones (–)-isodiospyrin and (–)-8'-hydroxyisodiospyrin, respectively, is described. The binaphthyl linkages in these compounds were stereoselectively constructed by using oxazoline chemistry. The stereochemical assignments were based on X-ray crystal structure determination and circular dichroic spectroscopy.
Structure determination of adeno-associated virus 2: three complete virus particles per asymmetric unit (2003)

The atomic structure of adeno-associated virus 2 (AAV-2) has been determined to 3.0 A resolution. AAV-2 crystallized in space group P1, with unit-cell parameters a = 249.7, b = 249.7, c = 644.8 A, alpha = 90.0, beta = 101.2, gamma = 120.0 degrees. The crystals contained three full virus particles in the asymmetric unit, allowing 180-fold non-crystallographic symmetry averaging. The particle orientations were determined using the self-rotation function and found to have similar but resolvably different orientations. Approximate alignment of icosahedral and interparticle threefold screw symmetry led to a native Patterson that was interpretable in terms of approximate particle positions. Accurate positions required a Patterson correlation search that was constrained to be consistent with non-crystallographic threefold projection symmetry evident in the diffraction intensities. Initial phases to 15.0 A resolution were calculated by molecular replacement using the known structure of a distantly related homolog (23% sequence identity). Real-space averaging was performed and phases were extended from 15.0 to 3.0 A. An atomic model was fitted and refined using a simulated-annealing real-space procedure.
Plasma Protein Profiling for Diagnosis of Pancreatic Cancer Reveals the Presence of Host Response Proteins (2005)

Plasma protein profiling using separations coupled to matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) has great potential in translational research; it can be used for biomarker discovery and contribute to disease diagnosis and therapy. Previously reported biomarker searches have been done solely by MS protein profiling followed by bioinformatics analysis of the data. To add to current methods, we tested an alternative strategy for plasma protein profiling using pancreatic cancer as the model. First, offline solid-phase extraction is done with 96-well plates to fractionate and partially purify the proteins. Then, multiple profiling and identification experiments can be conducted on the same protein fractions because only 5% of the fractions are used for MALDI MS profiling. After MALDI MS analysis, the mass spectra are normalized and subjected to a peak detection algorithm. Over three sets of mass spectra acquired using different instrument variables, approximately 400 unique ion signals were detected. Classification schemes employing as many as eight individual peaks were developed using a training set with 123 members (82 cancer patients) and a blinded validation set with 125 members (57 cancer patients). The sensitivity of the study was 88%, but the specificity was significantly lower, 75%. The reason for the low specificity becomes apparent upon protein identification of the ion signals used for the classification. The identifications reveal only common serum proteins and components of the acute phase response, including serum amyloid A, alpha-1-antitrypsin, alpha-1-antichymotrypsin, and inter-alpha-trypsin inhibitor.
Transport Systems for Alanine, Serine, and Glycine in <i>Escherichia coli</i> K-12 (1973)

At least two transport systems serve for the entry of alanine, glycine, and serine into Escherichia coli. One of these systems serves mainly for glycine, d-alanine, and d-serine and to some extent for l-alanine, whereas the second serves for l-alanine and perhaps l-serine. These two transport systems have been characterized by kinetic studies and by inhibition analysis. Reciprocal plots for l-alanine entry are distinctly biphasic, giving rise to K(m) values of about 2 and 27 muM. The major route of glycine entry can be described by a single K(m) value of about 4 muM. A higher K(m) value for glycine of around 70 to 100 muM shows that other routes of entry may serve at high concentrations of amino acid. The glycine, d-serine and d-alanine transport system is defective in a d-serine-resistant mutant, strain EM1302. The mutation, dagA, is recessive in dagA/dagA(+) merodiploids and is 7 to 12% linked by phage P1 transduction to the pyrB locus of E. coli. E. coli with the dagA mutation are unable to utilize d-alanine as a carbon source, providing an additional basis for selecting such mutants. The remaining l-alanine uptake in dagA mutants is subject to inhibition by l-serine, l-threonine, and l-leucine. It is also sensitive to osmotic shock treatment and repressed by growth of the cells on l-leucine. It appears from a comparison of the properties of the second l-alanine system with those of the leucine, isoleucine, and valine system (LIV system) that the LIV system also serves for the transport of l-alanine and l-threonine and perhaps l-serine.
The lupus autoantigens and the pathogenesis of systemic lupus erythematosus (1986)

Thus, the nucleosome, the U1 snRNP, and the Ro scRNP appear to elicit hierarchies of antibodies in patients with SLE, just as any complex foreign protein might do when injected into an experimental animal. There must be a permissive factor in operation that allows these normally weak antigens (the great paradox of SLE!) to escape tolerance mechanisms. That factor could be an exogenous agent, such as a chemical that structurally alters selected macromolecules. Such a mechanism seems likely in patients with drug-induced lupus in whom autoimmune responses are focused against the same histone epitopes that are recognized by sera from patients with spontaneous SLE. Alternatively, foreign substances may elicit cross-reactive antibodies that recognize "self" determinants, or endogenous metabolic disturbances might enhance exposure of selected macromolecules to the immune system. In any case, it now seems clear that the result in SLE patients is autoimmunity with a repetitive focus. Future research should concentrate on the 3 particles described here in order to identify common denominators that set them apart from other cellular elements and which predispose them to a role as autoantigens, to determine the extent to which these particles make contact with the immune system, and to learn how structural, humoral, or metabolic alterations might predispose individuals to respond to them immunologically.
Optical and electronic properties of TiCxNy films (2001)

The optical and electronic properties of TiCxNy(x+y∼1,0&lt;y&lt;1) thin films have been investigated by spectroscopic ellipsometry in the 1.5–4.5 eV energy range and by valence band x-ray photoemission spectroscopy as a function of the composition. The dielectric functions measured in the energy range of intraband transitions are analyzed in terms of a Drude-like approximation. Both the free plasma energy and the damping constant are observed to depend on the nitrogen content of the samples, suggesting a certain tunability of the optical and electronic properties of these films. Analysis of the valence band reveals that the C 2p band shifts toward higher binding energies upon an increase of the nitrogen content, in good agreement with the shift observed in the minimum of the optical reflectivity associated with the threshold of the interband transitions. The enhancement of the metallic character of the films as the nitrogen content increases is also evidenced by x-ray photoemission spectroscopy as a continuous intensity growth of the conduction band at the Fermi level.
Spatial and Temporal Variations of Groundwater Arsenic in South and Southeast Asia (2010)

Over the past few decades, groundwater wells installed in rural areas throughout the major river basins draining the Himalayas have become the main source of drinking water for tens of millions of people. Groundwater in this region is much less likely to contain microbial pathogens than surface water but often contains hazardous amounts of arsenic--a known carcinogen. Arsenic enters groundwater naturally from rocks and sediment by coupled biogeochemical and hydrologic processes, some of which are presently affected by human activity. Mitigation of the resulting health crisis in South and Southeast Asia requires an understanding of the transport of arsenic and key reactants such as organic carbon that could trigger release in zones with presently low groundwater arsenic levels.
Information management in the product lifecycle - the role of networked RFID (2005)

Radio frequency identification (RFID) is receiving significant attention at present through its low cost deployment in the retail supply chain. This work introduces the concept of networked RFID developed by the Auto ID Center, and examines its role in supporting more effective product lifecycle management (PLM). In particular, the product tagging approach initiated by the Auto ID Center has centered on ability to access complete and accurate information about a product in a timely manner and is demonstrated to be important for decision making at different stages along its lifecycle.
Online Optical Coherence Tomography during Subthreshold Laser Irradiation (2011)

Online OCT is able to identify non-ophthalmoscopically visible lesions during subthreshold laser irradiation either in artificial samples or in pig iris.
ChemInform Abstract: Styryls of the α‐Pyrylium Series and Nature of Their Absorption Bands. (1987)

Abstract The pyrylium salts (I) are coupled with the benzaldehydes (II) to give the styrylpyrylium salts (III).
General Road Detection From a Single Image (2010)

Given a single image of an arbitrary road, that may not be well-paved, or have clearly delineated edges, or some a priori known color or texture distribution, is it possible for a computer to find this road? This paper addresses this question by decomposing the road detection process into two steps: the estimation of the vanishing point associated with the main (straight) part of the road, followed by the segmentation of the corresponding road area based upon the detected vanishing point. The main technical contributions of the proposed approach are a novel adaptive soft voting scheme based upon a local voting region using high-confidence voters, whose texture orientations are computed using Gabor filters, and a new vanishing-point-constrained edge detection technique for detecting road boundaries. The proposed method has been implemented, and experiments with 1003 general road images demonstrate that it is effective at detecting road regions in challenging conditions.
Consequences of reduced intracellular coenzyme A content in Escherichia coli (1986)

Escherichia coli beta-alanine auxotrophs (panD2) were used to manipulate the specific cellular content of coenzyme A (CoA) and assess the associated physiological effects. Growth-limiting concentrations of CoA resulted in an increase in phospholipid/protein ratio in relA1 mutants, but not in their rel+ counterparts, indicating that protein biosynthesis was more severely affected by CoA deprivation than phospholipid biosynthesis. Acetyl-CoA was the dominant component (79.8%) of the CoA pool in cells exponentially growing in glucose-minimal medium, with significant concentrations of CoA (13.8%) and succinyl-CoA (5.9%) also detected. Malonyl-CoA was a minor species (0.5%), and the mixed disulfide of CoA and glutathione was not present. Acetyl-CoA was also the major constituent in cells depleted of CoA. On the other hand, succinyl-CoA was absent, suggesting that the protein synthesis defect may be due to the inability to generate sufficient quantities of precursors via the tricarboxylic acid cycle to support amino acid biosynthesis. Production of acyl carrier protein was controlled in part by the availability of CoA, and the lower concentration of acyl carrier protein in CoA-depleted cells was associated with a concomitant decrease in the saturated/unsaturated fatty acid ratio.
Cognitive and communicative function: The effects of chronological age and “handicap age” (1990)

Abstract Three classes of cognitive tests (short-term memory, long-term memory access/recall, and verbal ability) and one class of communicative tests (visual speech-reading) were administered to 49 hearing-impaired and 69 normal hearing subjects, varying in age between 23 and 75 years. It was found that when dB-loss and “handicap age” were partialled out, the negative effects of cognitive ageing remained: Speed in accessing alphanumeric symbols from long-term memory and as rehearsal speed correlated substantially with chronological age. Discriminant analyses revealed a communality between the discrimination of old from young subjects, and skilled from less skilled speech-readers: Visual decoding skill and rehearsal speed constituted the common discriminators. Departing from this result, an age-dependent componential model of visual speech-reading is delineated. with particular reference to the assumption that a temporally early lexical access system is crucial to the decoding of lip movements.
Multi-Channel Viterbi Decoder LSI Development (1986)

A multi-channel Viterbi decoder LSI chip has been developed at Harris Corporation, GCSD. This chip, targeted for implementation in SAJI-4 technology, can service up to 50 channels of encoded data at an aggregate channel symbol rate up to 120 KHz. The LSI design includes all decoder functions on-chip except those functions requiring large amounts of memory such as path metric and trellis bit storage. It also provides the capability for external or internal symbol synchronization and includes provisions for handling block formatted data. This paper discusses the development of the CMOS LSI design. Topics include system considerations, design trade-offs and methodologies used for simulation, verification, and testing of the multi-channel Viterbi decoder LSI chip.