gebhart/patrepeval huggingface dataset:
Purification and Characterization of a Novel Selenocysteine Lyase from Enterococcus faecalis (2014)

A previous study identified Enterococcus faecalis as one of two bacteria known to have the selD gene and other selenium related genes without having the genes necessary to make selenocysteine or selenouridine. EF2570, a gene in the cluster, was later shown to be upregulated during biofilm formation and also responsible for a selenite- and molybdate-dependent increase in biofilm formation in vitro. The protein encoded was identified as a selenium dependent molybdenum hydroxylase (SDMH), enzymes that contain a labile selenium atom required for activity. While the process of inserting selenocysteine into a protein is well known, the process by which a SDMH acquires a labile selenium atom has not yet been described. To begin unraveling this pathway, the nifS-like EF2568 from the gene cluster will be characterized. Some NifS-like proteins have been shown to have selenocysteine lyase activity, providing a source of selenium for selenophosphate synthetase, the selD gene product. Study of EF2568 has shown that it specifically reacts with L-selenocysteine to form selenide and alanine with L-cysteine inhibiting the reaction. Guided by homology to the well-characterized human and E. coli NifS-like proteins, mutants of the active site and substrate discerning residues were also characterized for activity with L-selenocysteine and L-cysteine. While mutation of the residue at position 112 thought to be responsible for substrate specificity did not affect reactivity of the enzyme with L-cysteine, it did affect reactivity with L-selenocysteine. Studying the characteristics of this novel group II selenocysteine lyase will provide a foundation for studying the remaining pathway.
Lymphocyte-induced angiogenesis: a quantitative and sensitive assay of the graft-vs.-host reaction. (1975)

A new and sensitive assay for the effect of intracutanous administration of immunocompentent lymphocytes into the skin of irradiated unimmunized mice is described. The assay, which we have termed lymphocyte-induced angiogenesis (LIA) involves enumeration of new vascular branches induced by the action of these competent cells. As is the case for the previously described normal lymphocyte transfer reaction, LIA is a manifestation of the graft-vs.-host reaction, as shown by experiments utilizing appropaiate genetic combinations. The reaction is dose-dependent, and within the dose range of 2 times 10 minus 5 -4 times 10-6 cells the mumber of vessels induced correlates with the mumber of immunocompetent cells injected. At these dose levels spleen, lumph node, and hydrocortisone-resistant thymocytes are effective; bone marrow and thymus cells are not. Spleen cells from nude mice are incapable of inducing LIA, while mitomycin-C and irradiated lymphocytes can initiate but not maintain the reaction. The relationship between lymphocyte-induced angiogenesis has been discussed as have the implications of these findings to delayed hypersensitivity, inflammation, and vascular pathology.
Mixture of beamformers for speech separation and extraction (2010)

In many audio applications, the signal of interest is corrupted by acoustic background noise, interference, and reverberation. The presence of these contaminations can significantly degrade the quality and intelligibility of the audio signal. This makes it important to develop signal processing methods that can separate the competing sources and extract a source of interest. The estimated signals may then be either directly listened to, transmitted, or further processed, giving rise to a wide range of applications such as hearing aids, noise-cancelling headphones, human-computer interaction, surveillance, and hands-free telephony. Many of the existing approaches to speech separation/extraction relied on beamforming techniques. These techniques approach the problem from a spatial point of view; a microphone array is used to form a spatial filter which can extract a signal from a specific direction and reduce the contamination of signals from other directions. However, when there are fewer microphones than sources (the underdetermined case), perfect attenuation of all interferers becomes impossible and only partial interference attenuation is possible. In this thesis, we present a framework which extends the use of beamforming techniques to underdetermined speech mixtures. We describe frequency domain non-linear mixture of beamformers that can extract a speech source from a known direction. Our approach models the data in each frequency bin via Gaussian mixture distributions, which can be learned using the expectation maximization algorithm. The model learning is performed using the observed mixture signals only, and no prior training is required. The signal estimator comprises of a set of minimum mean square error (MMSE), minimum variance distortionless response (MVDR), or minimum power distortionless response (MPDR) beamformers. In order to estimate the signal, all beamformers are concurrently applied to the observed signal, and the weighted sum of the beamformers’ outputs is used as the signal estimator, where the weights are the estimated posterior probabilities of the Gaussian mixture states. These weights are specific to each timefrequency point. The resulting non-linear beamformers do not need to know or estimate the number of sources, and can be applied to microphone arrays with two or more microphones with arbitrary array configuration. We test and evaluate the described methods on underdetermined speech mixtures. Experimental results for the non-linear beamformers in underdetermined mixtures with room reverberation confirm their capability to successfully extract speech sources.
Bioavailability of the Polyphenols: Status and Controversies (2010)

The current interest in polyphenols has been driven primarily by epidemiological studies. However, to establish conclusive evidence for the effectiveness of dietary polyphenols in disease prevention, it is useful to better define the bioavailability of the polyphenols, so that their biological activity can be evaluated. The bioavailability appears to differ greatly among the various phenolic compounds, and the most abundant ones in our diet are not necessarily those that have the best bioavailability profile. In the present review, we focus on the factors influencing the bioavailability of the polyphenols. Moreover, a critical overview on the difficulties and the controversies of the studies on the bioavailability is discussed.
Inhibitor Selectivity for Cyclin‐Dependent Kinase 7: A Structural, Thermodynamic, and Modelling Study (2017)

Deregulation of the cell cycle by mechanisms that lead to elevated activities of cyclin-dependent kinases (CDK) is a feature of many human diseases, cancer in particular. We identified small-molecule inhibitors that selectively inhibit CDK7, the kinase that phosphorylates cell-cycle CDKs to promote their activities. To investigate the selectivity of these inhibitors we used a combination of structural, biophysical, and modelling approaches. We determined the crystal structures of the CDK7-selective compounds ICEC0942 and ICEC0943 bound to CDK2, and used these to build models of inhibitor binding to CDK7. Molecular dynamics (MD) simulations of inhibitors bound to CDK2 and CDK7 generated possible models of inhibitor binding. To experimentally validate these models, we gathered isothermal titration calorimetry (ITC) binding data for recombinant wild-type and binding site mutants of CDK7 and CDK2. We identified specific residues of CDK7, notably Asp155, that are involved in determining inhibitor selectivity. Our MD simulations also show that the flexibility of the G-rich and activation loops of CDK7 is likely an important determinant of inhibitor specificity similar to CDK2.
ACC/AHA 2002 Guideline Update for Exercise Testing: Summary Article (2002)

Heart Association (AHA) Task Force on Practice Guidelines regularly reviews existing guidelines to determine when an update or full revision is needed.This process gives priority to areas where major changes in text, and particularly recommendations, are mentioned on the basis of new understanding or evidence.Minor
Design of a personal digital video recorder/player (2002)

We present the hardware and software system architecture for a personal digital video player and recorder using a media processor and an MPEG-2 video codec.
The Ergogenic Potential of Arginine (2004)

Arginine is a conditionally essential amino acid that is involved in protein synthesis, the detoxification of ammonia, and its conversion to glucose as well as being catabolized to produce energy. In addition to these physiological functions, arginine has been purported to have ergogenic potential. Athletes have taken arginine for three main reasons: 1) its role in the secretion of endogenous growth hormone; 2) its involvement in the synthesis of creatine; 3) its role in augmenting nitric oxide. These aspects of arginine supplementation will be discussed as well as a review of clinical investigations involving exercise performance and arginine ingestion.
Quantification of serum hepatitis C virus core protein level in patients chronically infected with different hepatitis C virus genotypes. (1996)

This study showed that FEIA (1) is a good assay for the detection and quantification of serum HCV core protein level, (2) is also very sensitive in detecting HCV core protein in patients with HCV type 2 infection, and (3) may have a role as a predictor of subsequent response to interferon therapy.
Analysis of neocortex in three males with the fragile X syndrome (1991)

Fragile X [fraX] syndrome is a common hereditary disorder associated with a fragile site marker at Xq27.3 which clinically presents as a form of mental retardation (MR). Postmortem investigation of 3 fraX positive males with mild to moderate MR did not document any gross neuropathological changes. Golgi analysis of neocortical dendritic spine morphology extended our previous observations of immature, long, tortuous spines in one adult case of fraX (Rudelli, et al., Acta Neuropathologica 67:289-295, 1985) to 2 new cases. Evidence for similar dendritic spine abnormalities was found, although Golgi analysis was less than optimal because of incomplete dendritic stain impregnation. Neocortical intra-layer cell density was also investigated in all 3 cases. Cresyl violet stained neurons were counted in 10 randomly selected fields in neocortical layers II-VI of cingulate and temporal association areas (Brodmann's areas 23 and 38). Neuron counts in fraX and control neocortex showed no significant differences. Thus, abnormal dendritic spine morphology with preservation of neuronal density appears to characterize the neocortex in individuals with this common form of mental retardation.
Indirect pushing based automated micromanipulation of biological cells using optical tweezers (2014)

In this paper, we introduce an indirect pushing based technique for automated micromanipulation of biological cells. In indirect pushing, an optically trapped glass bead pushes a freely diffusing intermediate bead that in turn pushes a freely diffusing target cell towards a desired goal. Some cells can undergo significant changes in their behaviors as a result of direct exposure to a laser beam. Indirect pushing eliminates this problem by minimizing the exposure of the cell to the laser beam. We report an automated feedback planning algorithm that combines three motion maneuvers, namely, push, align, and backup for micromanipulation of cells. We have developed a dynamics based simulation model of indirect pushing dynamics and also identified parameters of measurement noise using physical experiments. We present an optimization-based approach for automated tuning of planner parameters to enhance its robustness. Finally, we have tested the developed planner using our optical tweezers physical setup and carried out a detailed analysis of the experimental results. The developed approach can be utilized in biological experiments for studying collective cell migration by accurately arranging the cells in arrays without exposing them to a laser beam.
Band Formation in Mixtures of Oppositely Charged Colloids Driven by an ac Electric Field (2011)

We present experiments on pattern formation in a Brownian system of oppositely charged colloids driven by an ac electric field. Using confocal laser scanning microscopy we observe complete segregation of the two particle species into bands perpendicular to a field of sufficient strength when the frequency is in a well-defined range. Because of its Brownian nature the system spontaneously returns to the equilibrium mixture after the field is turned off. We show that band formation is linked to the time scale associated with collisions between particles moving in opposite directions.
The utility of alizarin red s staining in calcium pyrophosphate dihydrate crystal deposition disease. (2003)

Standard H&E staining reduces the number of visible CPPD crystals, probably due to the strong acidity of both hematoxylin and eosin solutions, whereas the ARS stain seems to preserve a large number of CPPD crystals. The utility of ARS staining may improve the identification of CPPD crystals and contribute to a correct diagnosis of CPPD crystal deposition.
Transport of glutathione prostaglandin A conjugates by the multidrug resistance protein 1 (1997)

The human multidrug resistance protein MRP1 mediates transport of organic substrates conjugated to glutathione, glucuronide, or sulfate. The naturally occurring prostaglandins A1 and A2 can form two diastereomeric glutathione S-conjugates, and it has been speculated that these might be substrates for MRP1. Here we present evidence that polarized MDCKII cells expressing MRP1 cDNA transport PGA1-GS to the basolateral side of a cell monolayer, in accordance with the lateral localization of human MRP1 in these cells. Furthermore, we show that vesicles made from yeast cells expressing MRP1 cDNA and from mouse erythrocytes (known to contain mrpl) actively accumulate both diastereomers of PGA2-GS with a similar efficiency. Recently, we generated mice with a homozygous mutant mrp1 allele. Uptake of PGA2-GS in vesicles made from erythrocytes of these mice was 3.2 times lower than in wild-type vesicles, but was still significantly above background. This residual transport activity was partly inhibited by methotrexate and cAMP, whereas mrp1-mediated activity was unaffected by these compounds. We conclude that mouse erythrocytes contain at least two transport systems for PGA2-GS. One of these is mrp1; the other one has not been identified yet, but can be inhibited by methotrexate and cAMP.
Structure of primary anti‐(4‐hydroxy‐3‐nitro‐phenyl)acetyl (NP) antibodies in normal and idiotypically suppressed C57BL/6 mice (1985)

Eight monoclonal antibodies from the primary response of C57BL/6 mice against the hapten (4-hydroxy-3-nitrophenyl)acetyl (NP) were isolated. The antibodies carry lambda 1 light chains and have similar affinities for the immunizing hapten. Sequence analysis at the level of mRNA reveals that all antibodies express the VH gene 186.2 and all but one the DFl 16.1 gene segment. The J segment of the heavy chain is JH2 in six cases and JH4 in two. Somatic point mutations are scarcely detectable in the antibodies, but there is extensive sequence variability at the boundaries of the D gene segment, mainly at its 5' end. However, seven of eight antibodies express tyrosine in position 99 of the heavy chain, encoded either by the 5' codon of DFl 16.1 or by presumed N sequences. In the former case, the tyrosine is the first of a stretch of three (positions 99-101). In the latter, a similar stretch (positions 99, 101, 102) is interrupted by aspartic acid, asparagine or cysteine in position 100. These variations profoundly affect idiotypic specificity. Six of the eight monoclonal antibodies came from mice neonatally suppressed by an anti-idiotope antibody whose target idiotope is regularly expressed in primary anti-NP responses and depends upon a non-germ-line-encoded aspartic acid in position 100 of the heavy chain. The sequence data show that the mice circumvent suppression by expressing antibodies which lack this aspartic acid but are otherwise structurally very similar to anti-NP antibodies from normal animals. Since suppression in the animals is partly controlled by regulatory T cells, we conclude that these T cells are highly restricted in their specificity in that they preferentially see a determinant which also depends upon the aspartic acid in position 100. The data suggest that the VH to D boundary serves as a target of idiotypic selection.
Research on the Route of New Urbanization in Jiangsu Province (2019)

In recent years, China proposed a series of emerging concepts based on the current development of urbanization. New urbanization is the one. For Jiangsu Province, new urbanization is an inevitable choice for modernization. There is a clear difference between this way and the traditional way. In order to promote the rapid development of the new urbanization process, Jiangsu Province needs to face up to the problems existing in the current urbanization development process and take effective way to solve it.
Breast Masses: Removal of All US Evidence during Biopsy by Using a Handheld Vacuum-assisted Device—Initial Experience (2003)

After removal of all US evidence of breast masses with a VAB device, there was a substantial probability that residual lesion that was not visualized during the procedure would later be found at surgery or follow-up imaging. A palpable mass (< or =1.2 cm in mean diameter) was eliminated in 88% of cases, and patient tolerance and perceptions of the procedure were favorable.
Characteristics of texts affecting relevance judgments (1993)

Abstract: We report on preliminary results from two studies, investigating the factors which underlie people&apos;s judgments of the relevance or usefulness of documents to particular information problems. The studies aimed to see whether factors other than topical relevance are significant in such decisions, to identify any such factors, and to relate such factors both to the users &apos; situations and goals, and to representation and retrieval strategies for IR systems, which would take account of such factors. Six facets of the judgment of document usefulness or relevance were identified, only two of which seem directly related to topical relevance. These facets are interpreted in the framework of user goals and situation, and some example strategies for their use in IR systems are presented. 1.
THE KINETICS OF REACTION BETWEEN <scp>L</scp>-CYSTEINE HYDROCHLORIDE AND SOME MALEIMIDES (1964)

not available
Monitoring optic nerve function during craniotomy (1976)

During surgical removal of a pituitary adenoma, conduction in the anterior visual pathways was monitored by continuous recording of visual evoked responses (VER). The method employed a scleral contact lens with an embedded flashing diode for delivery of visual stimuli. Evoked potentials of nearly normal latency, amplitude, and form were recorded from occipital scalp electrodes immediately after the optic nerves were decompressed. Restoration of the VER was correlated with restoration of normal vision.
Immunotherapy of Acute Myeloid Leukemia: Current Approaches (2009)

Following standard therapy that consists of chemotherapy with or without stem cell transplantation, both relapsed and refractory disease shorten the survival of acute myeloid leukemia (AML) patients. Therefore, additional treatment options are urgently needed, especially to fight residual AML cells. The identification of leukemia-associated antigens and the observation that administration of allogeneic T cells can mediate a graft-versus-leukemia effect paved the way to the development of active and passive immunotherapy strategies, respectively. The aim of these strategies is the eradication of AML cells by the immune system. In this review, an overview is provided of both active and passive immunotherapy strategies that are under investigation or in use for the treatment of AML. For each strategy, a critical view on the state of the art is given and future perspectives are discussed.
High-quality protein knowledge resource: SWISS-PROT and TrEMBL (2002)

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and a high level of integration with other databases. Together with its automatically annotated supplement TrEMBL, it provides a comprehensive and high-quality view of the current state of knowledge about proteins. Ongoing developments include the further improvement of functional and automatic annotation in the databases including evidence attribution with particular emphasis on the human, archaeal and bacterial proteomes and the provision of additional resources such as the International Protein Index (IPI) and XML format of SWISS-PROT and TrEMBL to the user community.
Query-focused Multi-Document Summarization: Combining a Topic Model with Graph-based Semi-supervised Learning (2014)

Graph-based learning algorithms have been shown to be an effective approach for query-focused multi-document summarization (MDS). In this paper, we extend the standard graph ranking algorithm by proposing a two-layer (i.e. sentence layer and topic layer) graph-based semi-supervised learning approach based on topic modeling techniques. Experimental results on TAC datasets show that by considering topic information, we can effectively improve the summary performance.
Analysis of integrated-optics near 3 dB coupler and Mach-Zehnder interferometric modulator using four-port scattering matrix (1982)

The scattering matrix formalism for a lossless four-port device is used to describe the interferometric performance of the integrated-optics near 3 dB coupler and, consequently, the Mach-Zehnder interferometric modulator as a function of coupler and/or power imbalance. For the case of a coupler consisting of three single-mode dielectric guides forming a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y</tex> junction, a fourth port is incorporated which takes all the power radiated out of the guided-wave system in the vicinity of the junction. The interferometric properties of the coupler are shown to be relatively insensitive to fabrication and/or design errors of a magnitude which would make the use of this junction in the reverse direction as a 3 dB divider very marginal. A coupler with an extinction ratio as an interferometer better than -26 dB corresponds to a power divider which couples 22 percent more power into one arm than the other. It is also shown that the near 3 dB coupler used as the output of an interferometric modulator is similarly insensitive to the inequality of the powers in the two arms.