gebhart/patrepeval huggingface dataset:
An <i>O</i>-Acetylserine(thiol)lyase Homolog with <scp>l</scp>-Cysteine Desulfhydrase Activity Regulates Cysteine Homeostasis in Arabidopsis (2009)

Cysteine (Cys) occupies a central position in plant metabolism due to its biochemical functions. Arabidopsis (Arabidopsis thaliana) cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of Cys. Because they are localized in the cytosol, plastids, and mitochondria, this results in multiple subcellular Cys pools. Much progress has been made on the most abundant OASTL enzymes; however, information on the less abundant OASTL-like proteins has been scarce. To unequivocally establish the enzymatic reaction catalyzed by the minor cytosolic OASTL isoform CS-LIKE (for Cys synthase-like; At5g28030), we expressed this enzyme in bacteria and characterized the purified recombinant protein. Our results demonstrate that CS-LIKE catalyzes the desulfuration of L-Cys to sulfide plus ammonia and pyruvate. Thus, CS-LIKE is a novel L-Cys desulfhydrase (EC 4.4.1.1), and we propose to designate it DES1. The impact and functionality of DES1 in Cys metabolism was revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. Mutation of the DES1 gene leads to premature leaf senescence, as demonstrated by the increased expression of senescence-associated genes and transcription factors. Also, the absence of DES1 significantly reduces the total Cys desulfuration activity in leaves, and there is a concomitant increase in the total Cys content. As a consequence, the expression levels of sulfur-responsive genes are deregulated, and the mutant plants show enhanced antioxidant defenses and tolerance to conditions that promote oxidative stress. Our results suggest that DES1 from Arabidopsis is an L-Cys desulfhydrase involved in maintaining Cys homeostasis, mainly at late developmental stages or under environmental perturbations.
Fabrication of linearly and nonlinearly chirped Bragg grating filters written on curved fibers (2002)

In this paper we investigate the characteristics of writing gratings on curved fibers. Experimental results have shown that such a method can be used to generate both linear and nonlinear chirped gratings and we show for the first time the functional relationship between curvature and the order of chirping.
An adaptive channel allocation strategy using multiple overlaid priority for cellular systems (1997)

Dynamic channel assignment (DCA) is an essential technique in mobile telecommunication systems because it uses the limited radio spectrum efficiently. In recent years, adaptive channel allocation (ACA) has been receiving a lot of attention as a better way of utilizing DCA. This paper proposes a new strategy for ACA—multiple overlaid priority adaptive channel allocation (MOP-ACA). It achieves reuse partitioning through learning processes at each base station without exchanging information on channel usage among neighboring base stations or control stations. The characteristics of MOP-ACA are evaluated by computer simulations. It is shown that MOP-ACA equals the high spectrum efficiency achieved by flexible reuse and that the number of channel tests is smaller than is possible with channel segregation. In other words, MOP-ACA is effective for control load reduction and simple cell design as well as for high spectrum efficiency. © 1997 Scripta Technica, Inc. Electron Comm Jpn Pt 1, 80 (2):90–99, 1997
MRI-Visible Micellar Nanomedicine for Targeted Drug Delivery to Lung Cancer Cells (2009)

Polymeric micelles are emerging as a highly integrated nanoplatform for cancer targeting, drug delivery and tumor imaging applications. In this study, we describe a multifunctional micelle (MFM) system that is encoded with a lung cancer-targeting peptide (LCP), and encapsulated with superparamagnetic iron oxide (SPIO) and doxorubicin (Doxo) for MR imaging and therapeutic delivery, respectively. The LCP-encoded MFM showed significantly increased alpha(v)beta(6)-dependent cell targeting in H2009 lung cancer cells over a scrambled peptide (SP)-encoded MFM control as well as in an alpha(v)beta(6)-negative H460 cell control. (3)H-Labeled MFM nanoparticles were used to quantify the time- and dose-dependent cell uptake of MFM nanoparticles with different peptide encoding (LCP vs SP) and surface densities (20% and 40%) in H2009 cells. LCP functionalization of the micelle surface increased uptake of the MFM by more than 3-fold compared to the SP control. These results were confirmed by confocal laser scanning microscopy, which further demonstrated the successful Doxo release from MFM and accumulation in the nucleus. SPIO clustering inside the micelle core resulted in high T(2) relaxivity (>400 Fe mM(-1) s(-1)) of the resulting MFM nanoparticles. T(2)-weighted MRI images showed clear contrast differences between H2009 cells incubated with LCP-encoded MFM over the SP-encoded MFM control. An ATP activity assay showed increased cytotoxicity of LCP-encoded MFM over SP-encoded MFM in H2009 cells (IC(50) values were 28.3 +/- 6.4 nM and 73.6 +/- 6.3 nM, respectively; p < 0.005). The integrated diagnostic and therapeutic design of MFM nanomedicine potentially allows for image-guided, target-specific treatment of lung cancer.
Leukocyte Elastase Negatively Regulates Stromal Cell-derived Factor-1 (SDF-1)/CXCR4 Binding and Functions by Amino-terminal Processing of SDF-1 and CXCR4 (2002)

Activation of CXCR4 by the CXC chemokine stromal cell-derived factor-1 (SDF-1) requires interaction of the amino-terminal domains of both molecules. We report that proteinases released from either mononucleated blood cells or polymorphonuclear neutrophils degranulated by inflammatory stimuli generate an SDF-1 fragment that is deleted from amino-terminal residues Lys(1)-Pro(2)-Val(3), as characterized by mass spectrometry analysis. The proteolyzed chemokine fails to induce agonistic functions and is unable to prevent the fusogenic capacity of CXCR4-tropic human immunodeficiency viruses. Furthermore, we observed that exposure of CXCR4-expressing cells to leukocyte proteinases results in the proteolysis of the extracellular amino-terminal domain of the receptor, as assessed by flow cytometry analysis and electrophoretic separation of immunoprecipitated CXCR4. Blockade of SDF-1 and CXCR4 proteolysis by the specific leukocyte elastase inhibitor, N-methoxysuccinyl-alanine-alanine-proline-valine-chloromethyl ketone, identified elastase as the major enzyme among leukocyte-secreted proteinases that accounts for inactivation of both SDF-1 and CXCR4. Indeed, purified leukocyte elastase generated in either SDF-1 or CXCR4 a pattern of cleavage indistinguishable from that observed with leukocyte-secreted proteinases. Our findings suggest that elastase-mediated proteolysis of SDF-1/CXCR4 is part of a mechanism regulating their biological functions in both homeostatic and pathologic processes.
The Physiologic Effects of Pain on the Endocrine System (2013)

Severe pain has profound physiologic effects on the endocrine system. Serum hormone abnormalities may result and these serve as biomarkers for the presence of severe pain and the need to replace hormones to achieve pain control. Initially severe pain causes a hyperarousal of the hypothalamic-pituitary-adrenal system which results in elevated serum hormone levels such as adrenocorticotropin, cortisol, and pregnenolone. If the severe pain does not abate, however, the system cannot maintain its normal hormone production and serum levels of some hormones may drop below normal range. Some hormones are so critical to pain control that a deficiency may enhance pain and retard healing.
Removal of Arg<sup>141</sup>From the α Chain of Human Hemoglobin by Carboxypeptidases N and M (1996)

Abstract Both human plasma carboxypeptidase N (CPN) and membrane-bound carboxypeptidase M (CPM) released the C-terminal arginine (α-Arg 141 ) of the α chain of human adult hemoglobin. An arginase contamination present in the hemoglobin preparation, which converted the released arginine to ornithine, was removed by gel filtration. CPM was about 20 times more efficient than CPN or its active subunit in hydrolyzing oxyhemoglobin and cleaved oxyhemoglobin twice as fast as deoxyhemoglobin. The hydrolysis of the peptide bond of α-Arg 141 accelerated the dissociation rate of the tetramer deoxy-des-α-Arg 141 hemoglobin to dimers 2500-fold over that of deoxyhemoglobin, as measured by haptoglobin binding. Moreover, the dissociation of the deoxy-des-α-Arg 141 hemoglobin tetramer to dimers was not affected by 2,3-diphosphoglyceric acid. Des-α-Arg 141 hemoglobin had a higher oxygen affinity (P 50 , 5.51 mm Hg; control, 19.94 mm Hg [P 50 is the partial pressure of oxygen that gives 50% of the saturation of hemoglobin]) and a lower apparent cooperativity (Hill coefficient: n, 1.02; control, 2.24) than unhydrolyzed hemoglobin. After hemoglobin was incubated in human plasma, its oxygen-binding parameters, the P 50 , and the Hill coefficient decreased drastically due to cleavage by CPN. In the perfused rat heart, des-α-Arg 141 hemoglobin was a more effective coronary vasoconstrictor than hemoglobin, possibly because it dissociated to dimers in the coronary vascular bed. A covalently cross-linked hemoglobin was less active than native hemoglobin. The coronary vasoconstriction was caused by multiple factors, including interference with vasodilation by nitric oxide and eicosanoids. Thus, the hydrolysis of hemoglobin by CPM and CPN demonstrated the contribution of the α-Arg 141 residue to sustaining the tetrameric structure of hemoglobin and its normal oxygen affinity and vasoactivity.
In search of a new therapeutic target for the treatment of genetically triggered thoracic aortic aneurysms and cardiovascular conditions: insights from human and animal lathyrism (2010)

Lathyrism, or the effect of certain plants on connective tissue disruption, particularly involving the vascular and skeletal systems, especially aortic dissection/rupture, has been well documented in animals. Its impact on the pathogenesis of connective tissue diseases in humans is still unclear. An extensive review of the scientific literature from the 1800s until the present time was performed to examine the common pathways between animal and human lathyrism and genetically triggered thoracic aortic aneurysms and cardiovascular conditions in humans, with special focus on the identification of potential therapeutic targets. Search areas covered the following subjects: lathyrism/spontaneous aortic dissection/rupture in animals; beta-aminopropionitrile, semicarbazide and their effects; collagen and elastin synthesis and cross-linking; genetic and molecular biology characteristics of the genetically triggered thoracic aortic conditions. Search results demonstrate Marfan syndrome as a model for the genetically triggered thoracic aortic aneurysms, has been linked to mutations of the fibrillin-1 gene, via transforming growth factor beta-1. Several other conditions do not share this mutation. Inhibition of semicarbazide-sensitive amine oxidase [vascular adhesion protein-1 (VAP-1)] in animals has been shown to result in aortic dilatation due to disruption of elastin cross-linking. Significantly low activity of this enzyme was identified in annulo-aortic ectasia; a condition similar to Marfan syndrome. In conclusion, the precise molecular and genetic pathways responsible for the clinical findings in Marfan syndrome and related conditions remain unclear. Observational and experimental findings relating to the vascular and systemic effects of molecular pathways implicated in the phenomenon of animal and human lathyrism suggest that VAP-1 seems to be involved in the molecular and developmental pathways of the genetically triggered thoracic aortic diseases and thus could be a potential therapeutic target for these conditions.
A Survey of Actor-Critic Reinforcement Learning: Standard and Natural Policy Gradients (2012)

Policy-gradient-based actor-critic algorithms are amongst the most popular algorithms in the reinforcement learning framework. Their advantage of being able to search for optimal policies using low-variance gradient estimates has made them useful in several real-life applications, such as robotics, power control, and finance. Although general surveys on reinforcement learning techniques already exist, no survey is specifically dedicated to actor-critic algorithms in particular. This paper, therefore, describes the state of the art of actor-critic algorithms, with a focus on methods that can work in an online setting and use function approximation in order to deal with continuous state and action spaces. After starting with a discussion on the concepts of reinforcement learning and the origins of actor-critic algorithms, this paper describes the workings of the natural gradient, which has made its way into many actor-critic algorithms over the past few years. A review of several standard and natural actor-critic algorithms is given, and the paper concludes with an overview of application areas and a discussion on open issues.
Advanced methods in PCR product detection. (1994)

To utilize PCR to its fullest potential, the identification and measurement of PCR products, or amplicons, must be improved compared with traditional methods. Amplicons must be identified by their specific nucleotide sequence to prevent false or ambiguous results caused by primer-dimer formation, nonspecific amplification, or target sequence variation. Quantitation of amplicon levels is an important first step for the estimation of the relative number of initial target molecules.
Diagnosis of Dengue Infection Using Conventional and Biosensor Based Techniques (2015)

Dengue is an arthropod-borne viral disease caused by four antigenically different serotypes of dengue virus. This disease is considered as a major public health concern around the world. Currently, there is no licensed vaccine or antiviral drug available for the prevention and treatment of dengue disease. Moreover, clinical features of dengue are indistinguishable from other infectious diseases such as malaria, chikungunya, rickettsia and leptospira. Therefore, prompt and accurate laboratory diagnostic test is urgently required for disease confirmation and patient triage. The traditional diagnostic techniques for the dengue virus are viral detection in cell culture, serological testing, and RNA amplification using reverse transcriptase PCR. This paper discusses the conventional laboratory methods used for the diagnosis of dengue during the acute and convalescent phase and highlights the advantages and limitations of these routine laboratory tests. Subsequently, the biosensor based assays developed using various transducers for the detection of dengue are also reviewed.
Design and Synthesis of a New Class of Selective Integrin α5β1 Antagonists (2007)

Starting from the structure of integrin alphavbeta3 in a complex with a peptidic ligand plus SAR data on nonpeptidic ligands, we derived a new class of integrin alpha5beta1 antagonists (1). Several synthesis strategies were applied to evaluate the chemical space around the essential pharmacophore groups R1 to R3 to obtain highly active and selective pyrrolidine derivatives as integrin alpha5beta1 antagonists. Integrin selectivity was controlled by switching from a sulfonamide moiety to a mesitylene amide moiety for R3. This finding represents a general feature for modulating selectivity toward other related integrin receptors. On the basis of the encouraging results from various in vitro studies, the most active compounds were selected for further in vivo studies in animal models and preclinical development.
Monoclonal antibody binding affinity determined by microchip‐based capillary electrophoresis (1998)

The affinity constant of a monoclonal antibody to fluorescently labeled bovine serum albumin (BSA) was measured in diluted mouse ascites fluid using a microfluidic chip to perform affinity capillary electrophoresis. Borofloat glass-based devices could be used repeatedly with samples for many months. On-chip separations were performed in less than 60 s, and 30-60 s was required for manual sample exchange. The change in peak height for BSA with increasing BSA/anti-BSA concentration ratio was used to determine concentration changes in bound and free BSA. A Scatchard plot analysis gave an affinity constant (more exactly the intrinsic association constant) of 3.5+/-0.6 x 10(7) M(-1) for a 1:1 stoichiometric ratio. Two affinity complexes were separated. One complex was identified by the Scatchard method as having a 1:1 stoichiometric ratio. The other complex is proposed to have a stoichiometry with an excess of anti-BSA to BSA, most likely (anti-BSA)2-BSA, on the basis of a faster migration time than the 1:1 complex, a decrease in the amount of this complex with increasing [BSA], and predictions of theoretical models for multi-valent antigens. Potential applications of microchip-based devices in affinity measurements are discussed.
Bacterial surface display of GFP(uv) on bacillus subtilis spores. (2007)

To analyze a cotG-based Bacillus subtilis spore display system directly, GFP(uv) was expressed on the surface of Bacillus subtilis spores. When GFP(uv) was fused to the C-terminal of the cotG structural gene and expressed, the existence of a CotG-GFP(uv) fusion protein on the B. subtilis spore was confirmed by flow cytometry confocal microscopic analysis. When the cotG anchoring motif was deleted, no fluorescence emission was observed under flow cytometry and confocal microscopic analysis from the purified spore, confirming the essential role of CotG as an anchoring motif. This GFP(uv) displaying spore might be used for another signaling application triggered by intracellular or extracellular stimuli.
WSCE: a flexible Web Service Composition Environment (2004)

In this paper, we propose the concepts of virtual partner and inspector into the Web services composition. Virtual partner, as an IT level concept, is a Web service (pseudo Web service) using the same interface with the actual partner but different binding message. A virtual partner can be invoked directly by a business process described by BPEL, so that the BPEL programmer can test both application's functionality and non functionality performance early in the development cycle to avoid any problems in the final runtime, or test the selection of their partners in business level design. The IT virtual partners provide developers with a range of the techniques which let them explore every aspect of their program. Inspector is proposed when using the third-party process engine. An inspector itself is also a Web service. The programmer can register any required output information in it. The IT virtual partner and the inspector concepts have been integrated in our WSCE, a flexible Web Services Composition Environment for a business process. WSCE is a prototype of autonomic modeling and simulation environment. With the help of a third-party BPEL engine, it provides programmer with concepts and tools to facilitate business process programming.
Back surface fields for GaInP/sub 2/ solar cells (2002)

Back surface passivation of the GaInP top cell in GaInP/sub 2//GaAs two-terminal tandem cells is discussed. Because of the requirement of current matching of the top and bottom cell, the top cell must be made very thin (on the order of 1 mu m), and thus proper passivation of the top cell back surface is important in achieving high open-circuit voltages. A comparison is made of two candidate top-cell back surface fields: (1) an AlGaInP quarternary, and (2) GaInP/sub 2/ grown to give a bandgap higher than that of the base of the cell.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A new mode of rotating gel electrophoresis for fractionating linear and circular duplex DNA: the effects of electrophoresis during the gel's rotation. (1989)

Linear and circular DNA have been fractionated by use of rotating gel electrophoresis (RGE; RGE is a form of pulsed-field gel [PFG] electrophoresis) in a mode not previously described. This new mode consists of electrophoresis while repeating the following two-step process: rotating the gel by 2 pi radians, followed by holding the gel motionless. With this new mode of RGE: (1) The fractionation by length of linear DNA is greater than that achieved without changing the direction of the field. (2) The simultaneous separation of open circular DNA (48.5-97 Kb) from linear DNA (1-180 Kb) and fractionation by length of open circular DNA is achieved. These latter separations have not previously been achieved by a one-dimensional electrophoresis. The mechanism of linear DNA's sieving in the new mode appears different from that of all previously described procedures of PGF electrophoresis.
Embedded menus: selecting items in context (1986)

In many situations, embedded menus represent an attractive alternative to the more traditional explicit menus, particularly in touchtext, spelling checkers, language-based program editors, and graphics-based systems.
Quantifying Electrochemical Nucleation and Growth of Nanoscale Clusters Using Real-Time Kinetic Data (2006)

Electrochemical techniques are used widely for the fabrication of nanostructured materials, yet a quantitative understanding of nucleation and growth remains elusive. Here we probe electrochemical nucleation and growth of individual nanoclusters in real time by combining current-time measurements with simultaneous video imaging. We show discrepancies between the growth kinetics measured for individual nanoclusters and the predictions of models, and we describe a significant revision to conventional models that can explain the results. This improved understanding of nucleation and growth allows a more quantitative approach to the electrochemical fabrication of nanoscale structures.
Asymmetric Transformation of Enones with <i>Synechococcus</i> sp. PCC 7942 (2004)

Abstract Asymmetric transformation of enones was investigated with cultured cells of Synechococcus sp. PCC 7942 (a cyanobacterium). The cells reduced both the endocyclic C–C double bond of s-trans enones and the exocyclic C–C double bond of s-cis enones with high enantioselectivity to afford optically active α-substituted (S)-ketones under illumination. In addition, the reduction of the double bond of these enones was accompanied by the formation of saturated alcohols. The cells preferentially reduced simple aliphatic ketones rather than cyclic ones to the corresponding (S)-alcohols with excellent enantioselectivity.