gebhart/patrepeval huggingface dataset:
An empirical energy function for threading protein sequence through the folding motif (1993)

In this paper we present a new residue contact potential derived by statistical analysis of protein crystal structures. This gives mean hydrophobic and pairwise contact energies as a function of residue type and distance interval. To test the accuracy of this potential we generate model structures by "threading" different sequences through backbone folding motifs found in the structural data base. We find that conformational energies calculated by summing contact potentials show perfect specificity in matching the correct sequences with each globular folding motif in a 161-protein data set. They also identify correct models with the core folding motifs of hemerythrin and immunoglobulin McPC603 V1-domain, among millions of alternatives possible when we align subsequences with alpha-helices and beta-strands, and allow for variation in the lengths of intervening loops. We suggest that contact potentials reflect important constraints on nonbonded interaction in native proteins, and that "threading" may be useful for structure prediction by recognition of folding motif.
Increased biological activity of deglycosylated recombinant human granulocyte/macrophage colony-stimulating factor produced by yeast or animal cells. (1987)

Human granulocyte/macrophage colony-stimulating factor (hGM-CSF) produced by several recombinant sources including Escherichia coli, yeast, and animal cells was studied. Recombinant animal cells produced hGM-CSF in low quantities and in multiple forms of varying size. Mammalian hGM-CSF was purified 200,000-fold using immunoaffinity and lectin chromatography. Partially purified proteins produced in yeast and mammalian cells were assayed for the effects of deglycosylation. Following enzymatic deglycosylation, immunoreactivity was measured by radioimmunoassay and biological activity was measured in vitro on responsive human primary cells. Removal of N-linked oligosaccharides from both proteins increased their immunoreactivities by 4- to 8-fold. Removal of these oligosaccharides also increased their specific biological activities about 20-fold, to reach approximately the specific activity of recombinant hGM-CSF from E. coli. The E. coli produced-protein--lacking any carbohydrate--had by far the highest specific activity observed for the recombinant hGM-CSFs.
&lt;title&gt;Liquid-crystal-based tunable optical filtering devices for DWDM&lt;/title&gt; (2001)

We report a new configuration of tunable optical filter for DWDM applications. In this design, first-order diffracted signal light by a grating is directed to a lens and focused on to a transmission-type liquid crystal spatial light modulator (LC-SLM). Wavelength channels are selected by opening the appropriate pixels of the LC-SLM for transmission. The device is demonstrated by using a broad-band AR-coated laser diode as the signal light. For conceptual demonstration, we use optical fibers with a core diameter of 50 microns instead of the LC-SLM. A total of 37 channels, spanning 33.6 nm were successfully selected with channel spacing of 0.94 nm and bandwidth of 0.4 nm. With 100 micron-wide pixels separated by 5 microns in the LC-SLM and a 1800 lines/mm grating, we show selection of five channels with channel spacing of 0. 78 nm. The bandwidth is 0.43 nm. The channel isolation is better than 20 dB. At a wavelength of 1.5 micron, channel spacing as small as 12.4 GHz can be realized. This device is also expected to be useful for other DWDM applications, e.g., switching and routing.
Prominent Gelation and Chiral Aggregation of Alkylamides Derived from <i>trans</i>‐1,2‐Diaminocyclohexane (1996)

Between 2 and 44 gL−1 of the diamide 1 are necessary to obtain stable gels with a wide variety of organic solvents. The circular dichroism of the gels can be attributed to the formation of chiral aggregates from 1, which are held together by hydrogen bonds and van der Waals interactions.
Dielectric Properties of Zirconium Oxide Grown by Atomic Layer Deposition from Iodide Precursor (2001)

films were grown from and on p-Si(100) substrates using the atomic layer deposition technique. The influence of deposition conditions on the dielectric properties of films was investigated. The breakdown field exceeded 2 MV/cm in the films grown at 325-500°C. The relative permittivity measured at 10 kHz was 20-24 in the films deposited at 275-325°C. The dissipation factor of these films was as low as 0.02-0.03. The relative permittivity decreased to 7 and the dissipation factor increased to 0.6 when the growth temperature was raised to 450-500°C. Variation of the measurement frequency from 1 to 100 kHz had only a slight influence on the permittivity values. Hysteresis of the capacitance-voltage curves indicated that a considerable amount of deep levels at the oxide-semiconductor interface and/or in the oxide were recharged under dc bias. The density of rechargeable states increased with the deposition temperature, and the recharging mechanism also depended on the substrate temperature used for the growth. © 2001 The Electrochemical Society. All rights reserved.
Detection of atrial persistent rhythm based on P-wave recognition and RR interval variability (2002)

In order to improve a classification system for arrhythmia analysis, we developed an algorithm for automatic detection of ventricular response to atrial flutter and fibrillation episodes. As an intermediate step to differentiate these rhythms from the normal, the algorithm detects the presence of sinus P-waves, by analyzing single lead ECG. When P-waves are detected for six successive beats, the rhythm is labeled as normal. If this detection fails, the mean RR interval is computed and analyzed. The rhythm is labelled atrial fibrillation when the mean is between two thresholds. The algorithm identifies as atrial flutter, epochs with high cardiac frequency and low variability. All other rhythms are labeled as abnormal, requiring posterior QRS shape analysis for correct classification. The algorithm was tested with the MIT-BIH Arrhythmia Database.
Novel wireless power supply system for wireless communication devices in industrial automation systems (2003)

There have been considerable advances in low power, integration and micro-systems technologies, enabling wireless communication for very small, affordable, lightweight and high performance devices. These technologies are still mainly used for consumer and office applications, but significant advantages can be obtained by applying the technologies to new areas. One area of particular interest industrial is automation and control systems, such as robotics and factory automation. In this paper we discuss the main challenges involved with realizing a reliable, wireless, and energy autonomous communication system suited for industrial automation. Special emphasis is placed on providing an overview of suitable power supply possibilities and describing a novel magnetic medium frequency power supply concept enabling true wireless energy supply within cell-volumes of more than 100 m/sup 3/ with sufficiently small infrastructure. The novel resonant power supply concept uses medium frequencies (/spl sim/120 kHz) in a "coreless transformer", enabling the supply of devices within a certain volume, for example a production cell, surrounded by coils. By using omni-directional or rotating magnetic fields, together with three orthogonal receiver coils, it enables a shielding tolerant supply system with unique properties. Compared to primary battery technologies, the new approach offers approximately 50 times higher energy densities over the application lifetime.
Determinants of Enzymatic Specificity in the Cys-Met-Metabolism PLP-Dependent Enzyme Family: Crystal Structure of Cystathionine γ-Lyase from Yeast and Intrafamiliar Structure Comparison (2003)

The crystal structure of cystathionine gamma-lyase (CGL) from yeast has been solved by molecular replacement at a resolution of 2.6 A. The molecule consists of 393 amino acid residues and one PLP moiety and is arranged in the crystal as a tetramer with D2 symmetry as in other related enzymes of the Cys-Met-metabolism PLP-dependent family like cystathionine beta-lyase (CBL). A structure comparison with other family members revealed surprising insights into the tuning of enzymatic specificity between the different family members. CGLs from yeast or human are virtually identical at their active sites to cystathionine gamma-synthase (CGS) from E. coli. Both CGLs and bacterial CGSs exhibit gamma-synthase and gamma-lyase activities depending on their position in the metabolic pathway and the available substrates. This group of enzymes has a glutamate (E333 in yeast CGL) which binds to the distal group of cystathionine (CTT) or the amino group of cysteine. Plant CGSs use homoserine phosphate instead of O-succinyl-homoserine as one substrate. This is reflected by a partially different active site structure in plant CGSs. In CGL and CBL the pseudosymmetric substrate must dock at the active site in different orientations, with S in gamma-position (CBL) or in delta-position (CGL). The conserved glutamate steers the substrate as seen in other CGLs. In CBLs this position is occupied by either tyrosine or hydrophobic residues directing binding of CTT such that S is in the in gamma-position. In methionine gamma-lyase a hydrophic patch operates as recognition site for the methyl group of the methionine substrate.
Economic and Size-Tunable Synthesis of InP/ZnE (E = S, Se) Colloidal Quantum Dots. (2015)

We present synthesis protocols, based on indium halide and aminophosphine precusors, that allow for the economic, up-scaled production of InP quantum dots (QDs). The reactions attain a close to full yield conversion – with respect to the indium precursor – and we demonstrate that size tuning at full chemical yield is possible by changing the nature of the indium halide salt. In addition, we present ZnS and ZnSe shell growth procedures that lead to InP/ZnS and InP/ZnSe core/shell QDs that emit from 510 to 630 nm with an emission line width between 46 and 63 nm. This synthetic method is an important step toward performing Cd-free QDs, and it could help the transfer of colloidal QDs from the academic field to product applications.
Performance of Fractured Oil Reservoirs (1953)

Fractured reservoir rocks may be considered as made up of at least two porosity-permeability systems: one which accounts for the largest void space fraction of the reservoir and which makes up the pore space between the grains (intergranular porosity); the other which accounts for the smallest void space fraction and which makes up the pore space of the fractures and fissures. The former generally exhibits a low permeability, whereas the latter provides channels of high permeability which are the main reservoir fluid carriers to the wells, provided sufficient lateral continuity exists. In most cases, vertical continuity of the highly permeable system is also present and gravity segregation of the reservoir fluids may exist to a large degree. Under certain conditions of re ervoir rock wettability, the fluids will segregate into two zones of saturation, a lower zone of high oil saturation and an upper zone of high gas saturation. This results in a rapidly increasing gas-oil ratio in the early stage of depletion and in a low ultimate oil recovery. An alternative explanation of the behavior of fractured reservoir is also proposed whereby the low recovery by depletion drive is explained by capillary end effect which contributes to retaining a large fraction of the oil inside the blocks between fractures while permitting the evolution of solution gas. This end-effect capillary retention hypothesis would be particularly effective while low pressure gradients prevail within the reservoir. The hypothesis submitted herein for the explanation of the low oil recoveries from fractured reservoirs are intended to stimulate thinking so that experiments may perhaps be designed for their verification and for finding some solution to increasing recovery from such fields. Various approaches to this problem are suggested, but they have not received as yet the sanction of field use.
Curcumin improves sclerosing cholangitis in Mdr2 <sup>−/−</sup> mice by inhibition of cholangiocyte inflammatory response and portal myofibroblast proliferation (2010)

These results show that curcumin may have multiple targets in liver including activation of PPARgamma in cholangiocytes and inhibition of ERK1/2 signalling in MFBs, thereby modulating several central cellular events in a mouse model of cholangiopathy. Targeting these pathways may be a promising therapeutic approach to cholangiopathies.
Flavour formation by lactic acid bacteria and biochemical flavour profiling of cheese products (2005)

Flavour development in dairy fermentations, most notably cheeses, results from a series of (bio)chemical processes in which the starter cultures provide the enzymes. Particularly the enzymatic degradation of proteins (caseins) leads to the formation of key-flavour components, which contribute to the sensory perception of dairy products. More specifically, caseins are degraded into peptides and amino acids and the latter are major precursors for volatile aroma compounds. In particular, the conversion of methionine, the aromatic and the branched-chain amino acids are crucial. A lot of research has focused on the degradation of caseins into peptides and free amino acids, and more recently, enzymes involved in the conversion of amino acids were identified. Most data are generated on Lactococcus lactis, which is the predominant organism in starter cultures used for cheese-making, but also Lactobacillus, Streptococcus, Propionibacterium and species used for surface ripening of cheeses are characterised in their flavour-forming capacity. In this paper, various enzymes and pathways involved in flavour formation will be highlighted and the impact of these findings for the development of industrial starter cultures will be discussed.
Hyaluronate is synthesized at plasma membranes (1984)

The hybrid cell B6 line, which synthesizes large amounts of hyaluronate as the predominant glycosaminoglycan, was grown in the presence of [3H]glucosamine. The [3H]hyaluronate has a high molecular weight and was excluded by Sephacryl S-1000. After disruption of the cells the [3H]hyaluronate could further be elongated by incubation with UDP-GlcNAc and UDP-[14C]GlcA, yielding a hybrid molecule of hyaluronate labelled with [3H]GlcNAc and [14C]GlcA. Treatment of the cells with hyaluronidase before disruption eliminated the large [3H]hyaluronate and elongation of nascent chains in vitro commenced from low-molecular-weight chains. Thus nascent hyaluronate chains were degraded extracellularly by hyaluronidase and were therefore synthesized at the inner side of plasma membranes and extruded to the cell surface.
Masking fields: a massively parallel neural architecture for learning, recognizing, and predicting multiple groupings of patterned data (1987)

A massively parallel neural network architecture, called a masking field, is characterized through systematic computer simulations. A masking field is a multiple-scale self-similar automatically gain-controlled cooperative- competitive feedback network F(2). Network F(2) receives input patterns from an adaptive filter F(1) ? F(2) that is activated by a prior processing level F(1). Such a network F(2) behaves like a content-addressable memory. It activates compressed recognition codes that are predictive with respect to the activation patterns flickering across the feature detectors of F(1) and competitively inhibits, or masks, codes which are unpredictive with respect to the F(1) patterns. In particular, a masking field can simultaneously detect multiple groupings within its input patterns and assign activation weights to the codes for these groupings which are predictive with respect to the contextual information embedded within the patterns and the prior learning of the system. A masking field automatically rescales its sensitivity as the overall size of an input pattern changes, yet also remains sensitive to the microstructure within each input pattern. In this way, a masking field can more strongly activate a code for the whole F(1) pattern than for its salient parts, yet amplifies the code for a pattern part when it becomes a pattern whole in a new input context. A masking field can also be primed by inputs from F(1): it can activate codes which represent predictions of how the F(1) pattern may evolve in the subsequent time interval. Network F(2) can also exhibit an adaptive sharpening property: repetition of a familiar F(1) pattern can tune the adaptive filter to elicit a more focal spatial activation of its F(2) recognition code than does an unfamiliar input pattern. The F(2) recognition code also becomes less distributed when an input pattern contains more contextual information on which to base an unambiguous prediction of which the F(1) pattern is being processed. Thus a masking field suggests a solution of the credit assignment problem by embodying a real-time code for the predictive evidence contained within its input patterns. Such capabilities are useful in speech recognition, visual object recognition, and cognitive information processing. An absolutely stable design for a masking field is disclosed through an analysis of the computer simulations. This design suggests how associative mechanisms, cooperative-competitive interactions, and modulatory gating signals can be joined together to regulate the learning of compressed recognition codes. Data about the neural substrates of learning and memory are compared to these mechanisms.
Electronic odour sensing systems (1993)

An odour sensing instrument has been developed and used to classify many different materials, including beers, spirits and alcohols. The next stage in development is to begin to relate subjective odour descriptors (e.g. fruity, minty) to quantitative sensor array measurements. This task is being approached using both neural network and multivariate statistical techniques. The ultimate goal is to provide a measurement standard for odours. This exciting prospect requires the integration of sensor technology, signal conditioning, data acquisition and pattern recognition.
Effect of Mechanical Ventilation on Inflammatory Mediators in Patients With Acute Respiratory Distress Syndrome (1999)

Mechanical ventilation can induce a cytokine response that may be attenuated by a strategy to minimize overdistention and recruitment/derecruitment of the lung. Whether these physiological improvements are associated with improvements in clinical end points should be determined in future studies.
Automated Percutaneous Discectomy at the L5-S1 Level (1989)

Previously, a major limitation to percutaneous disc decompression to relieve symptoms of sciatica was the inability to approach the L5-S1 level. Obstruction by the iliac crest prevented the instrumentation from entering the L5-S1 disc space. In this paper, the authors describe a curved cannula which can be placed down to the L5-S1 disc space over a straight trocar that has been anchored at the annulus. The cannula bends the flexible aspiration probe back into the plane of the disc so that it is no longer obstructed by the sacral end plate. Using this system, the L5-S1 disc space was successfully removed in 90% of 30 cases.
Pulsed laser deposition of /MgO bilayered films on Si wafer in waveguide form (1996)

Strontium barium niobate (SBN) thin films were grown on Si (111) substrates coated with MgO buffer by the pulsed laser deposition (PLD) technique. The thickness of SBN and MgO films were of the order of 1200 nm and 840 nm respectively. X-ray energy dispersive spectrometry (XREDS) showed that SBN films have stoichiometric composition identical to the target material, and no Si diffusion into the SBN film was found. X-ray diffraction (XRD) scans indicated that MgO films were highly (111) textured, but the SBN films were polycrystalline without preferential orientation. The surface of the SBN film was smooth, dense and crack-free and no large droplets were observed when studied under a scanning electron microscope (SEM). A favourable optical waveguiding property of the bilayered films was demonstrated by a prism coupler method.
Aligned Mats from Electrospun Single Fibers (2008)

Highly aligned electrospun micro- and nanoscale fibers and pseudowoven mats were produced via electrospinning by incorporating an auxiliary counter electrode to create an electric field of controlled geometry and magnitude. Two polymers were examined using this technique: a polyimide (CP2) and a biodegradable polymer, poly(glycolic acid) (PGA). Highly aligned electrospun CP2 fibers were on the order of 10 μm in diameter, and fiber spacing in the spun mats ranged between 25 and 30 μm. Electrospun PGA aligned fibers were on the order of 500 nm in diameter with spacing between fibers ranging from 7 to 10 μm in the spun mats. High-speed videography illustrated the influence of the auxiliary electrode on the elimination of jet whipping and bending instability commonly associated with the electrospinning process. The data presented here demonstrate the direct influence of an opposing electric field on the degree of fiber alignment and control of fiber placement.
A 16×1 WDM Transmitter with Integrated DBR Lasers and Electroabsorption Modulators (1993)

Semiconductor laser arrays are being realized for wavelength-division-multiplexed (WDM) lightwave communication systems. Such arrays can increase the amount of transmitted information through a fiber link, or can be used for optical switching applications. By combining the signals on chip, the alignment of fibers to individual lasers is eliminated.
Ursodeoxycholic acid for primary biliary cirrhosis (2012)

This systematic review did not demonstrate any significant benefits of ursodeoxycholic acid on all-cause mortality, all-cause mortality or liver transplantation, pruritus, or fatigue in patients with primary biliary cirrhosis. Ursodeoxycholic acid seemed to have a beneficial effect on liver biochemistry measures and on histological progression compared with the control group. All but one of the included trials had high risk of bias, and there are risks of outcome reporting bias and risks of random errors as well. Randomised trials with low risk of bias and low risks of random errors examining the effects of ursodeoxycholic acid for primary biliary cirrhosis are needed.