gebhart/patrepeval huggingface dataset:
Selective Screening of a Large Phage Display Library of Plasminogen Activator Inhibitor 1 Mutants to Localize Interaction Sites with Either Thrombin or the Variable Region 1 of Tissue-type Plasminogen Activator (1996)

Phage display technology has been exploited to study in detail the interaction between plasminogen activator inhibitor 1 (PAI-1) and either thrombin or an essential positively charged "loop" of tissue-type plasminogen activator (t-PA), denoted variable region 1 (VR1). For this purpose, a PAI-1 mutant phage library was used that served as a reservoir of PAI-1 proteins potentially deficient in the interaction with either VR1 or thrombin. A stringent two-step selection procedure was developed. (i) A negative selection was performed by incubating the pComb3/PAI-1 mutant library with an excess of a thrombin mutant with its VR1 domain substituted with that of t-PA (thrombin-VR1). (ii) The remaining phages were complexed with t-PA (positive selection) and selected by panning with an immobilized anti-t-PA monoclonal antibody. Four consecutive panning rounds yielded an enrichment of pComb3/PAI-1 mutant phages of approximately 50-fold. Sequence analysis of 16 different cDNAs, encoding PAI-1 mutants that are hampered in the binding to thrombin-VR1, revealed the following mutations. Four independent variants share a mutation of the P4' residue (Glu350 --> Lys). Nine independent PAI-1 variants share a substitution of P1' (Met347 --> Lys), whereas three others share a P2 substitution (Ala345 --> Asp). Kinetic analysis of representative PAI-1 mutants provides evidence that the P4' residue is essential for the interaction with the VR1 domain, consistent with the data of Madison et al. (Madison, E.L., Goldsmith, E.J., Gething, M.J., Sambrook, J.F., and Gerard, R.D. (1990) J. Biol. Chem. 265, 21423-21426), whereas the P1' and P2 residues confer thrombin specificity. Concordant with the design of the selection procedure, mutants were obtained that inhibit thrombin-VR1 at least 100-fold slower than wild-type PAI-1, identifying residues that are central to the interaction with either thrombin or VR1. This study demonstrates that phage technology can be used to analyze large numbers of mutants defective in their interaction with other (domains of) proteins, provided an adequate selection scheme is devised.
Molecular Determinants of Intrinsic Multidrug Resistance in Cancer Cells and Tumors (2007)

Intrinsic drug or multidrug resistance in previously untreated tumors is often the major obstacle to the success of cancer chemotherapy. Understanding the molecular mechanisms underlying these conditions is a prerequisite to the design of novel strategies aimed at improving current clinical protocols. This chapter focuses on recent experimental evidence concerning two of the features most commonly encountered in multidrug resistant cancer cells: (over)expression of multidrug transporters and disabling of apoptotic pathways.
Short term wind speed prediction by finite and infinite impulse response filters: A state space model representation using discrete markov process (2009)

The importance of Integrating wind power generation into electric power grids has rapidly progressed over the past decade. But the intermittency of wind power presents a special challenge for utility system operations as well as the market structure mechanisms. The problem arises from the uncertainty and variability in wind resources that causes fluctuations in the output of wind power generators. This paper presents a short-term wind speed prediction using linrealized time series model. Wind data are first collected from a weather station in ten minute resolution for a period of one year followed by a fitted two Weibull distribution parameters model being estimated from regression analysis on the logarithms of wind speed data. Transformation from Weibull into normal distribution is then held and linear predictive coefficients calculated using finite impulse response filter (FIR) and infinite impulse response filter (IRR) are evaluated for the normalized wind speed random process. Results of 10 minute ahead, one hour ahead, 12 hours ahead and 24 hours ahead wind speed predictions are presented and model accuracy in each of these time-ahead prediction scale are discussed. Also a remarkable observation of the independencies between future and historical wind speed data allows a state space representation model using discrete Markov Process to best represent the stochastic behavior of wind speed signal. In doing so, optimum quantization parameters are first done for both Weibull and normal wind speed distributions and a transition probability matrices are evaluated in each case showing smooth state transition levels in wind data.
Al0.17Ga0.83N Film Using Middle-Temperature Intermediate Layer Grown on (0001) Sapphire Substrate by Metal-Organic Chemical Vapor Deposition (2007)

The reduction of the dislocation density in a high-temperature (HT)-Al0.17Ga0.83N epitaxial layer was achieved by a middle-temperature (MT)-intermediate layer technique, in which the HT and the MT were 1050 and 950 °C, respectively. For one set of the MT-intermediate layer, the structure was 4.5-µm-thick HT-Al0.17Ga0.83N/1-µm-thick MT-intermediate layer/100-nm-thick HT-Al0.17Ga0.83N layer/low-temperature (LT)-GaNP buffer/trenched (0001) sapphire. The full-width at half maximum values of (0002) and (1012) diffraction peaks of the X-ray diffraction for the Al0.17Ga0.83N epitaxial layer using one set of the MT-intermediate layer were improved to 359 and 486 arcsec compared with 401 and 977 arcsec for the film without the MT-intermediate layer technique, respectively. Transmission electron microscopy result showed that the dislocation density in the Al0.17Ga0.83N film using one set of MT-intermediate layer was reduced from (1–4)×1010 to 1.7×109 cm-2. The Al0.17Ga0.83N epitaxial film including two sets of MT-intermediate layers improved the most, showing a dislocation density of 9.3×108 cm-2.
Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis[W] (2003)

The Arabidopsis genome contains approximately 200 genes that encode proteins with similarity to the nucleotide binding site and other domains characteristic of plant resistance proteins. Through a reiterative process of sequence analysis and reannotation, we identified 149 NBS-LRR-encoding genes in the Arabidopsis (ecotype Columbia) genomic sequence. Fifty-six of these genes were corrected from earlier annotations. At least 12 are predicted to be pseudogenes. As described previously, two distinct groups of sequences were identified: those that encoded an N-terminal domain with Toll/Interleukin-1 Receptor homology (TIR-NBS-LRR, or TNL), and those that encoded an N-terminal coiled-coil motif (CC-NBS-LRR, or CNL). The encoded proteins are distinct from the 58 predicted adapter proteins in the previously described TIR-X, TIR-NBS, and CC-NBS groups. Classification based on protein domains, intron positions, sequence conservation, and genome distribution defined four subgroups of CNL proteins, eight subgroups of TNL proteins, and a pair of divergent NL proteins that lack a defined N-terminal motif. CNL proteins generally were encoded in single exons, although two subclasses were identified that contained introns in unique positions. TNL proteins were encoded in modular exons, with conserved intron positions separating distinct protein domains. Conserved motifs were identified in the LRRs of both CNL and TNL proteins. In contrast to CNL proteins, TNL proteins contained large and variable C-terminal domains. The extant distribution and diversity of the NBS-LRR sequences has been generated by extensive duplication and ectopic rearrangements that involved segmental duplications as well as microscale events. The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges.
Dopamine D4 receptor gene polymorphism is associated with attention deficit hyperactivity disorder. (1996)

Dopamine is believed to play a major role in the manifestation of attention deficit hyperactivity disorder (ADHD), which affects 3-6% of school-age children and shows evidence of familiarity. The dopamine D4 receptor, which is preferentially distributed in cortical and limbic regions of the brain, is currently of major interest because of the high degree of functionally relevant variability in its gene (DRD4), and the association of this gene with Novelty Seeking behavior. We examined the variability in the length of a region of DRD4 that contains a 48-bp repeat sequence in children with ADHD and controls matched for ethnicity. ADHD children differed from controls in that the 7-fold repeat form of DRD4 occurred significantly more frequently than in the control sample. This form of the receptor has previously been shown to mediate a blunted intracellular response to dopamine. Although ADHD is likely to be multifactorial in its etiology and its heritability is likely to be polygenetic, the present findings suggest that polymorphic variation in the gene encoding the D4 dopamine receptor may be a contributing factor in the expression of symptoms associated with ADHD.
A wireless, passive carbon nanotube-based gas sensor (2002)

A gas sensor, comprised of a gas-responsive multiwall carbon nanotube (MWNT)-silicon dioxide (SiO/sub 2/) composite layer deposited on a planar inductor-capacitor resonant circuit is presented here for the monitoring of carbon dioxide (CO/sub 2/), oxygen (O/sub 2/), and ammonia (NH/sub 3/). The absorption of different gases in the MWNT-SiO/sub 2/ layer changes the permittivity and conductivity of the material and consequently alters the resonant frequency of the sensor. By tracking the frequency spectrum of the sensor with a loop antenna, humidity, temperature, as well as CO/sub 2/, O/sub 2/ and NH/sub 3/ concentrations can be determined, enabling applications such as remotely monitoring conditions inside opaque, sealed containers. Experimental results show the sensor response to CO/sub 2/ and O/sub 2/ is both linear and reversible. Both irreversible and reversible responses are observed in response to NH/sub 3/, indicating both physisorption and chemisorption of NH/sub 3/ by the carbon nanotubes. A sensor array, comprised of an uncoated, SiO/sub 2/ coated, and MWNT-SiO/sub 2/ coated sensor, enables CO/sub 2/ measurement to be automatically calibrated for operation in a variable humidity and temperature environment.
Strain sensing based on coherent Rayleigh scatteringin an optical fibre (2000)

A fibre optic strain sensor based on Rayleigh backscatter using a time division multiplexing scheme with an optical pulse is presented. The sensor has a gauge length of &lt; 0.5 m and a strain sensitivity of &lt; 1 nɛ/√Hz at 2 kHz.
Chondroitin sulfate proteoglycan with neurite‐inhibiting activity is up‐regulated following peripheral nerve injury (1998)

Numerous findings support the possibility that highly sulfated proteoglycans are inhibitory molecules which, at high concentration relative to growth-promoting signals, may regulate or guide axonal growth. Although most studies implicate sulfated proteoglycans in the poor regenerative capacity of the central nervous system, inhibitory proteoglycans also may play an important role in the successful regeneration of axons within peripheral nerve. Cultured rat schwannoma and Schwann cells produce chondroitin sulfate proteoglycan (CSPG) which binds to and inhibits the neurite-promoting activity of laminin [Muir et al. (1989) J. Cell Biol. 109:2353]. In the present study, we found a similar neurite-inhibiting activity associated with CSPG isolated from normal adult rat sciatic nerve. Following nerve crush injury, this inhibitory activity was increased sevenfold in regenerating nerve distal to the injury. This increase was largely attenuated by in vivo administration of the proteoglycan synthesis inhibitor β-D-xyloside. In normal adult nerve, immunolabeling for CSPG core protein was concentrated in slender bands surrounding axon-Schwann cell units and within nodes of Ranvier. Following nerve crush injury, immunolabeling of CSPG and laminin became more intense in distal nerve and CSPG increased within endoneurium and surrounding nerve sheaths. Embryonic dorsal root ganglionic neurons cultured on longitudinal nerve sections extended neurites along the exposed surfaces of Schwann cell basal lamina. The length of neurites was increased 58% on normal nerve sections pretreated with chondroitinase. Even though laminin levels were elevated in basal lamina of injured nerve, neuritic growth on sections of injured nerve was not significant increased unless sections were pretreated with chondroitinase. These results indicate that inhibitory CSPG is up-regulated in injured nerve and plays a role in regulating axonal regeneration. © 1998 John Wiley & Sons, Inc. J Neurobiol 34: 41–54, 1998
An automatic extraction of key paragraphs based on context dependency (1997)

In this paper, we propose a method for extracting key paragraphs in articles based on the degree of context dependency. Like Luhn's technique, our method assumes that the words related to theme in an article appear throughout paragraphs. Our extraction technique of keywords is based on the degree of context dependency that how strongly a word is related to a given context. The results of experiments demonstrate the applicability of our proposed method.
Wave function-dependent mobility and suppression of interface roughness scattering in a strained SiGe p-channel field-effect structure (2000)

The 4 K Hall mobility has been measured in a top-gated, inverted, modulation-doped Si/Si0.8Ge0.2 structure having a Si:B doping layer beneath the alloy. From comparisons with theoretical calculations, we argue that, unlike an ordinary enhancement-mode SiGe p-channel metal–oxide–semiconductor structure, this configuration leads to a decrease of interface roughness scattering with increasing sheet carrier density. We also speculate on the nature of the interface charge observed in these structures at low temperature.
A one-pot three-component synthesis of β-nitro-α-amino acids and their N-alkyl derivatives (1999)

P. A. Coghlan and C. J. Easton, J. Chem. Soc., Perkin Trans. 1, 1999, 2659 DOI: 10.1039/A906223H
Networked virtual environments (1992)

The Virtual Environment Realtime Network (VERN) is an object oriented testbed for the interconnection of environments over a network of graphical workstations. VERN is based on extensions to the networking technology of the DARPA sponsored SIMNET combined combat training system and the Distributed Interactive Simulation protocol being developed as a DOD standard. It allows for multiple participants to interact in an environment. sharing ideas and solving problems, regardless of their physical locations. Furthermore, dramatic reconstructions of historical events for education or entertainment will be possible. Indeed, much of the impact of VERN is likely to result from the ability of participants to learn from each other even if they and their machines are separated by long distances.
T Cell Activity After Dendritic Cell Vaccination Is Dependent on Both the Type of Antigen and the Mode of Delivery (2000)

Previous work in both human and animal models has shown that CTL responses can be generated against proteins derived from tumors using either peptide-pulsed dendritic cells (DCs) or nucleic acids from the tumor transfected into autologous DCs. Despite the efficacy of this approach for vaccine therapy, many questions remain regarding whether the route of administration, the frequency of administration, or the type of Ag is critical to generating T cell responses to these Ags. We have investigated methods to enhance CTL responses to a peptide derived from the human proto-oncogene HER-2/neu using mice containing a chimeric HLA A2 and H2Kb allele. Changes in amino acids in the anchor positions of the peptide enhanced the binding of the peptide to HLA-A2 in vitro, but did not enhance the immunogenicity of the peptide in vivo. In contrast, when autologous DCs presented peptides, significant CTL activity was induced with the altered, but not the wild-type, peptide. We found that the route of administration affected the anatomic site and the time to onset of CTL activity, but did not impact on the magnitude of the response. To our surprise, we observed that weekly administration of peptide-pulsed DCs led to diminishing CTL activity after 6 wk of treatment. This was not found in animals injected with DCs every 3 wk for six treatments or in animals initially given DCs weekly and then injected weekly with peptide-pulsed C1R-A2 transfectants.
Scaling effect on specific contact resistivity in nano-scale metal-semiconductor contacts (2013)

Progressive downscaling has allowed semiconductor industries to continuing improve the performance of integrated circuits (ICs) [1]. The downscaling adversely affects the performance of interconnects. Specifically, the resistivity of metal interconnects and metal-semiconductor contacts increases due to downscaling. The metal-semiconductor contact resistance is becoming a performance limiting factor as it takes larger fraction of the total on-state resistance [2]. Hence, the contact resistance must be reduced to meet ITRS performance requirements of future technology nodes. As metal-semiconductor interface shrinks simultaneously as device shrinks, it becomes questionable if the resistivity still can meet the ITRS requirements when it reaches to the certain scaling limit (sub-10nm). Specific contact resistivity (ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</sub> ) is one of important factors affecting total contact resistance, and it is determined by important factors such as metal-semiconductor Schottky barrier height and semiconductor doping. This work investigates the effects of contact geometry, Schottky barrier height, and doping concentration on the specific contact resistivity.
Serum allopregnanolone in women with postpartum “blues” (2001)

Serum allopregnanolone levels were detectable postpartum and were significantly decreased in women with maternity "blues."
Digital pictures: representation and compression (1988)

For thousands of years mankind has been creating pictures which attempt to portray real or imagined scenes as perceived by human vision.Cave drawings, paintings and photographs are able to stimulate the visual system and conjure up thoughts of faraway places, imagined situations or pleasant sensations.The art of motion picture creation has advanced to the point where viewers often undergo intense emotional experiences.On-thespot news coverage gives the impression of actually witnessing events as they unfold.Relatively recently, other forms of visual information have been invented which do not, in themselves, stimulate the eye.For example, voltage variations in an electrical signal, as in television, can represent in analogous fashion the brightness variations in a picture.In this form the visual information can be stored on magnetic tape or transmitted over long distances, and, at least for engineering purposes, it is often much more useful than other forms which do stimulate human vision.With the evolution of digital techniques for information processing, storage, and transmission, the need arises for digital representation of visual information, that is, the representation of images by a sequence of integer numbers (usually binary).In this form, computer processing and digital circuit techniques can be utilized which were undreamed of only a short time ago.Machine manipulation and interpretation of visual information becomes possible.Sophisticated techniques can be employed for efficient storage of images.And processing methods can be used to significantly reduce the costs of picture transmission.Many methods have evolved for representing (or coding) visual information into a stream of numbers suitable for digital processing.Some have the virtue of easy implementation, while others have special features which make them well suited for specific applications.Most of the coding
External anal sphincter responses after S3 spinal root surface electrical stimulation (2006)

Our data can serve as reference values for future study in patients with pelvic floor dysfunction. EAS responses following S3 percutaneous electrical stimulation can represent a useful aid in the selection of candidates to SNM.
Digital radiology using active matrix readout of amorphous selenium: Detectors with high voltage protection (1998)

A flat-panel x-ray imaging detector is being investigated for digital radiography and fluoroscopy. The detector uses a layer of amorphous selenium (a-Se) to convert x rays to a charge image, which is then electronically read out with a two-dimensional array of thin film transistors (TFTs). In order to sensitize the a-Se layer to x rays, a high voltage (of the order of several thousand volts) is applied to its top surface. The TFTs, which are at the bottom surface of the a-Se layer, are not subjected to any high voltage under normal radiological operational conditions since the pixel potential is < 10 V. However under a fault condition where these two events occur simultaneously: (1) suspended detector scan; and (2) an x-ray exposure more than ten times higher than normal, the voltage on the TFTs could rise to a damaging value. This paper describes a method for protecting the TFTs from high voltage damage under this fault condition. It employs a dual-gate TFT structure, one gate is for scanning control and the other is connected to the pixel electrode for high voltage protection. Before the pixel potential reaches a damaging value, the protection gate turns on the TFT automatically and drains excess charge away from the pixel thus providing a safe pixel saturation potential. In this paper, the characteristic curves of dual-gate TFTs are studied both theoretically and experimentally. The pixel x-ray response for imaging detectors with high voltage protection are predicted, and it is shown that with practical TFT designs the detector can provide a safe pixel saturation potential as well as satisfy the dynamic range required for diagnostic x-ray imaging applications.
Delivery of liposomes into cultured KB cells via folate receptor-mediated endocytosis. (1994)

Folic acid was covalently conjugated to 66-nm liposomes via spacers of various lengths in an attempt to target the liposomes to KB cells expressing folate receptors. Spacers of short and intermediate lengths were unable to mediate association of folate-conjugated liposomes with receptor-bearing cells, however, use of a 250 A polyethyleneglycol spacer (PEG, M(r) approximately 3350) permitted avid uptake of the liposomes at approximately 2.5 x 10(5) sites/cell. The binding of folate-PEG liposomes to KB cells could be competitively inhibited by excess free folate or by antiserum against the folate receptor, demonstrating the interaction is mediated by the cell surface folate-binding protein. Following binding, cell-associated folate-PEG liposomes were internalized by folate-receptor-mediated endocytosis at 37 degrees C but not at 4 degrees C. These folate-PEG liposomes show potential for delivering large quantities of low molecular weight compounds nondestructively into folate receptor-bearing cells.