gebhart/patrepeval huggingface dataset:
Mutagenic Studies on Histidine 98 of Methylglyoxal Synthase:  Effects on Mechanism and Conformational Change<sup>,</sup> (2004)

Two detailed mechanisms [Marks et al. (2001) Biochemistry 40, 6805] have been proposed to explain the activity of methylglyoxal synthase (MGS), a homohexameric allosterically regulated enzyme that catalyzes the elimination of phosphate from DHAP to form enol pyruvaldehyde. This enol then tautomerizes to methylglyoxal in solution. In one of these mechanisms His 98 plays an obligate role in the transfer of a proton from the O(3) oxygen of DHAP to the O2 oxygen. To test this hypothesized mechanism, the variants H98N and H98Q were expressed and purified. Relative to the wild-type enzyme, the H98N variant shows a 50-fold decrease in k(cat) with all other kinetic parameters (i.e., K(m), K(PGA), etc.) being nearly the same. By contrast, the apparent catalytic rate for the H98Q variant is 250-fold lower than that of the wild-type enzyme. Inorganic phosphate acts as a competitive inhibitor (with a K(i) of 15 microM) rather than as an allosteric-type inhibitor as it does in the wild-type enzyme, and the competitive inhibitor phosphoglyolate (PGA) acts as an activator of this variant. These facts are explained by a shift in the conformational equilibrium toward an "inactive" state. When activation by PGA is accounted for, the catalytic rate for the "active" state of H98Q is estimated to be only 6-fold less than that of the wild-type enzyme, and thus His 98 is not essential for catalysis. Primary deuterium isotope effect data were measured for the wild-type enzyme and the two variants. At pH 7.0, the (D)V isotope effect (1.5) and the absence of a (D)(V/K) isotope effect for the wild-type enzyme suggest that the rate for the isotopically sensitive step is partially rate limiting but greater than the rate of substrate dissociation. Both the (D)V (2.0) and (D)(V/K) (3.4) isotope effects were more pronounced in the H98N variant, while the H98Q variant displayed an unusual inverse (D)V (0.8) isotope effect and a normal (D)(V/K) (1.5) isotope effect. The X-ray crystal structures of PGA bound to the H98Q and H98N variants were both determined to a resolution of 2.2 A. These mutations had little effect on the overall structure. However, the pattern of hydrogen bonding in the active site suggests an explanation as to how in the wild-type and H98N mutated enzymes the "inactive to active" equilibrium lies toward the active state, while with the H98Q mutated enzyme the equilibrium lies toward the inactive state. Thus, the role of His 98 appears to be more as a regulator of the enzyme's conformation rather than as a critical contributor to the catalytic mechanism.
The Looping Algorithm Extended to Base 2&lt;sup&gt;t&lt;/sup&gt;Rearrangeable Switching Networks (1977)

Clos Rearrangeable Switching Networks (RSN's) are examined with regard to properties of imprimitivity. It is shown that a certain version of RSN's built by 2 × 2 matrices in all stages except in the center stage have properties that imply a routing procedure for base 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sup> RSN's ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</tex> is any positive integer) based on the looping procedure. The routing procedure gives, in turn, control data applicable to base 2, base 4, ..., base 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sup> RSN's. Necessary computing time increases only linearly with the number of inputs if the maximum degree of parallelism is utilized. The obtained results can be applied to networks with an arbitrary base <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> by omitting unnecessary parts of a suitable base 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sup> network.
<title>Near-infrared spectroscopy (NIRS) as a diagnostic tool in patients with suspected stroke or traumatic brain injury</title> (2001)

Near-Infrared Spectroscopy (NIRS) as a diagnostic tool in patients with suspected stroke or brain injury S. Goldberg, C. Lott, M. Ostermeyer, H.-J. Hennes Absorption of Near-Infrared (NIR) light in the brain is mainly caused by hemoglobin. Superficial intracranial hematoma with a higher concentration of hemoglobin causes a higher absorption in NIRS. The existence of hemorrhage can be demonstrated by the difference of optical density, comparing identical measuring points at both hemispheres of the brain: absorption of NIR light is greater at the side of the hemorrhage, causing less reflection in NIRS. In a prospective, blinded study, 100 patients who were scheduled for CCT-scan for brain injury or symptoms of stroke have been measured by NIRS. The measurement results were proved by the CCT-diagnosis. A sensitivity of the NIR measurement of 65% and a specificity of 87% was achieved including all patients with any pathology, whereas the subgroup of 58 patients with suspected superficial hematoma and without other pathology showed pathologic findings by NIRS in all of 16 patients indicating superficial bleeding by CCT, pathology could be excluded by NIRS and CCT in 41 patients, one false positive and no false negative result. The results (sensitivity 98%, specificity 100%) support the hypothesis that NIRS is a reliable device for the detection of superficial intracranial hematoma.
A new DCT-based just-noticeable distortion estimator for images (2004)

Just-noticeable distortion (JND) based on human visual characteristics provides a good means to reflect the tolerance of image distortion with respect to human observers, for both data compression and quality measurement. In this paper, various existing JND models are surveyed and the typical models are benchmarked based on a uniform criterion. A new model is then developed and tested for different types of images. Experiments and the associated subjective tests show the improved performance of the proposed scheme over the existing models for luminance adaptation (especially in dark regions) and masking effect in edge regions.
Discontinuities in the level density of small quantum dots under strong magnetic fields (2002)

Exact diagonalization studies of the level density in a six-electron quantum dot under magnetic fields around 7 T (``filling factor'' around $\frac{1}{2})$ are reported. In any spin-polarization channel, two regimes are visible in the dot excitation spectrum: one corresponding to interacting quasiparticles (i.e., composite fermions) for excitation energies below 0.4 meV, and a second one for energies above 0.4 meV, in which the level density (exponentially) increases at the same rate as in the noninteracting composite-fermion model.
Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors Vandetanib (ZD6474) and AZD2171 in Lung Cancer (2007)

Vascular endothelial growth factor (VEGF) is a rational target for advanced non-small cell lung cancer (NSCLC), a hypothesis validated by the recent Eastern Cooperative Oncology Group E4599 trial showing that the addition of the VEGF monoclonal antibody bevacizumab to chemotherapy prolongs overall survival. Several new tyrosine kinase inhibitors targeting the VEGF pathway are currently in advanced clinical development for NSCLC and offer several possible advantages compared with monoclonal antibodies, including oral administration, more flexible dosing, a broader spectrum of target inhibition, and different toxicity profiles. Among these agents, vandetanib (ZD6474), an inhibitor of the VEGF receptor (VEGFR)-2 and epidermal growth factor receptor tyrosine kinase, has been the most extensively studied. In a randomized phase II study of patients with platinum-refractory NSCLC, including squamous histology, vandetanib prolonged progression-free survival compared with gefitinib. In another phase II trial, an improvement in progression-free survival was observed for vandetanib in combination with docetaxel compared with docetaxel alone. AZD2171 is an inhibitor of VEGFR-1, VEGFR-2, and VEGFR-3 and other tyrosine kinases that has shown clinical activity in NSCLC in combination with carboplatin and paclitaxel. Several phase III trials are under way testing these agents either as monotherapy or in combination with chemotherapy in patients with lung cancer. Early results with these agents, and others being tested, raise the possibility that there will eventually be multiple VEGF-targeted therapies available in the clinic that can potentially benefit a broader range of patients with advanced-stage NSCLC.
Analysis of the Expressed Genome of the Lone Star Tick, <i>Amblyomma americanum</i> (Acari: Ixodidae) Using an Expressed Sequence Tag Approach (2000)

An expressed sequence tag (EST) approach was used to study the genome of two developmental stages of the lone star tick, Amblyomma americanum. cDNA libraries were constructed from the larval and adult stages of A. americanum. In total, 1942 ESTs were sequenced (1462 adult ESTs and 480 larval ESTs) and analyzed using bioinformatic programs. Contig assembly using the CAPII program revealed 11% and 15% redundancy of sequences in the larval and adult ESTs, respectively. Of the 1942 ESTs, 1738 sequences were considered quality sequences and of these, 771 or approximately 44.4% of the sequences were putatively identified based on amino acid identity using the protein Basic Local Alignment Search Tool (BLAST) algorithm. Putatively identified sequences were classified according to their predicted gene function. In total, 967 sequences, or 55.6% of the quality sequences, had limited or no protein similarity to previously identified gene products. Sequences lacking protein homology were analyzed using an automated sequence annotation system for predicted protein characteristics such as open reading frames, signal peptides, protein motifs, and transmembrane regions. In this paper we describe the sequencing of the largest number of ESTs obtained from an arachnid species to date and the subsequent detailed analysis of these sequences.
New method to measure magnetic susceptibility (1993)

A convenient new force method for the measurement of volume magnetic susceptibility is described. It is based on a commercial balance that is used to measure the force between a magnet placed on the pan of the balance and the sample supported just above. Samples of almost arbitrary shape and size can be measured quickly. The sensitivity of the device is sufficient to measure the susceptibility of many common diamagnetic materials, such as water, to a few per cent. A complete theoretical analysis is given along with experimental results. The method is particularly useful for screening materials for use in the construction of precision scientific apparatus.
Murine JAK3 is preferentially expressed in hematopoietic tissues and lymphocyte precursor cells (1996)

To elucidate the role of cytokine receptor signal transduction in T-cell development, we have investigated the expression pattern and biochemical characteristics of the murine Janus family tyrosine kinase, JAK3. Previous studies have shown that JAK3 is expressed in lymphoid and myeloid tumor cell lines and in a small number of lymphoid tissues. To further characterize JAK3 expression, we used a quantitative polymerase chain reaction approach to compare JAK3 mRNA levels at multiple stages of T-cell differentiation and in a broad range of mouse tissues. These studies, in conjunction with analyses of JAK3 protein expression, show that the highest levels of JAK3 are in adult, 2-week-old, and fetal thymus, followed by somewhat lower levels in bone marrow, spleen, fetal liver, and adult CD4-CD8- thymocytes. We also show that different forms of JAK3 mRNA arise by alternative splicing. Finally, our biochemical studies show that the JAK3 kinase domain, but not the pseudo-kinase domain, has tyrosine kinase activity and, furthermore, that JAK3 kinase activity is abolished by an amino acid substitution of the conserved lysine in the kinase domain (K851R). These studies show that JAK3 expression is profoundly skewed to hematopoietic and lymphoid precursor cells, strongly suggesting a role for JAK3 in hematopoiesis and T- and B-cell development.
Interleukin-1 induces interleukin-6 production in peripheral blood monocytes (1990)

Interleukin-6 (IL-6), a multifunctional cytokine produced in monocytes, fibroblasts, endothelial cells, and keratinocytes, is induced by a variety of stimulating signals, including lipopolysaccharide (LPS), poly (I), poly (C), IL-1, tumor necrosis factor (TNF), and platelet-derived growth factor. Some of these signals induce IL-6 effectively only in one cell type, and this selectivity of induction may explain selectivity of biologic effects. In the present study, we show that IL-1 beta, previously known to be a potent inducer of IL-6 in fibroblasts, endothelial cells, and keratinocytes, but not in monocytes, is also a potent inducer of IL-6 in peripheral blood monocytes. High level IL-6 activity that could be neutralized by specific antibodies to IL-6 was detected in supernatants of IL-1-stimulated monocytes. Maximal induction required IL-1 concentrations of 10 ng/mL. As judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions, IL-6 species of relative molecular mass of 19 to 26 Kd could be specifically immunoprecipitated from supernatants of IL-1-induced monocytes. Size heterogeneity is a reported feature of IL-6 produced in a variety of cell types, and monocyte-derived IL-6 induced by either IL-1 or LPS displayed similar size heterogeneity. The highly purified recombinant IL-1 beta preparation used contained little, if any, LPS. In addition, monocyte production of IL-6, induced by IL-1 beta, was specifically neutralized by anti-IL-1 beta antibodies, demonstrating that IL-1, rather than a contaminant in the IL-1 preparation, was responsible for IL-6 induction. A number of biologic activities have been ascribed both to IL-1 and IL-6. The finding that IL-1 induced IL-6 in monocytes may help in defining the spectrum of biologic activities of each of these interactive cytokines.
Bringing Federated Identity to Grid Computing (2016)

The Fermi National Accelerator Laboratory (FNAL) is facing the challenge of providing scientific data access and grid submission to scientific collaborations that span the globe but are hosted at FNAL. Researchers in these collaborations are currently required to register as FNAL users and obtain FNAL credentials to access grid resources to perform their scientific computations. These requirements burden researchers with managing additional authentication credentials, and put additional load on FNAL for managing user identities. Our design integrates the existing InCommon federated identity infrastructure, CILogon Basic CA, and MyProxy with the FNAL grid submission system to provide secure access for users from diverse experiments and collaborations without requiring each user to have authentication credentials from FNAL. The design automates the handling of certificates, so users do not need to manage them manually. Although the initial implementation is for FNAL's grid submission system, the design and the core of the implementation are general and could be applied to other distributed computing systems.
ChemInform Abstract: CHIRAL β‐DIMETHYLAMINOALKYLPHOSPHINES. HIGHLY EFFICIENT LIGANDS FOR A NICKEL COMPLEX CATALYZED ASYMMETRIC GRIGNARD CROSS‐COUPLING REACTION (1980)

Abstract Aminosäuren (I) werden in Form ihrer Antipoden über die an sich bekannten Zwischenstufen (II) und (III) in die basischen Phosphine (IV) umgewandelt.
Learning to Recognize Actions From Limited Training Examples Using a Recurrent Spiking Neural Model (2018)

A fundamental challenge in machine learning today is to build a model that can learn from few examples. Here, we describe a reservoir based spiking neural model for learning to recognize actions with a limited number of labeled videos. First, we propose a novel encoding, inspired by how microsaccades influence visual perception, to extract spike information from raw video data while preserving the temporal correlation across different frames. Using this encoding, we show that the reservoir generalizes its rich dynamical activity toward signature action/movements enabling it to learn from few training examples. We evaluate our approach on the UCF-101 dataset. Our experiments demonstrate that our proposed reservoir achieves 81.3/87% Top-1/Top-5 accuracy, respectively, on the 101-class data while requiring just 8 video examples per class for training. Our results establish a new benchmark for action recognition from limited video examples for spiking neural models while yielding competitive accuracy with respect to state-of-the-art non-spiking neural models.
A VQ/DCT coding scheme for colour images (2002)

A VQ/DCT (vector quantization/discrete cosine transform) coding scheme for color images is examined. In this coding scheme, VQ is first employed to code a 24-bits/pixel color image, which is composed of three components, R, G, B, into an 8-bits/pixel index image. Then the DCT is applied to the index image. One major problem in this coding scheme is that the codebook produced by the VQ process is randomly arranged. Using this codebook to VQ-code color images destroys the correlation present in the original images. Some techniques for producing a codebook which retains a reasonable degree of correlation are proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Recent advances: Neurosurgery (1999)

<b>Introduction:</b> Bronchiolitis is the most common cause of hospitalization in infants and recent evidences in literature suggest its heterogeneity. <b>Aims and Objectives:</b> Our aim was to investigate whether different clinical profiles exist among infants hospitalised with bronchiolitis. <b>Methods:</b> we consecutively enrolled children < 12 months of age hospitalised for acute bronchiolitis during the epidemic season 2017-2018. For each patient vital signs, physical examination, family history and laboratory results were collected. Bronchiolitis profiles were determined by latent class analysis (LCA) (R). <b>Results:</b> 176 infants participated in the study. LCA identified four profiles. Profile A (n=14) had the highest family history of atopy (asthma 94.5%, eczema 85%) and wheeze on chest auscultation (100%), with milder clinical presentation (need of oxygen therapy in 19.2% of cases). In contrast, profile B (n=58) identifies the most severely ill infants (need of oxygen in 100% of cases), with a lower family history of asthma (36.6%) and eczema (29.6%). Profile C (n=38) was similar to profile A, but with lower family history of atopy (asthma in 47.5% and eczema in 44.4%). Profile D patients (n=66) were similar to profile B, but with no need of oxygen therapy and the least family history of asthma (2.8%). Infants with respiratory syncytial virus belonged more frequently to Profile B and D (42.4% and 37.3% respectively). <b>Conclusions:</b> The identification of different clinical endotypes among infants with bronchiolitis might be the first step towards future research regarding the management of the disease and long-term consequences.
Total Synthesis of (−)-Huperzine A (2009)

The total synthesis of (-)-huperzine A was accomplished in 23 steps from a commercially available anhydride. Our synthetic route features a facile construction of the bicyclo[3.3.1] skeleton equipped with proper functionalities to introduce the remaining substructures.
Gas-Blending Apparatus (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGas-Blending ApparatusDonald N. Hanson and Arturo. MaimoniCite this: Anal. Chem. 1959, 31, 1, 158–159Publication Date (Print):January 1, 1959Publication History Published online14 June 2002Published inissue 1 January 1959https://pubs.acs.org/doi/10.1021/ac60145a605https://doi.org/10.1021/ac60145a605research-articleACS PublicationsRequest reuse permissionsArticle Views45Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Insolubilized enzymes. Kinetic behaviour of glucose oxidase bound to porous glass particles (1971)

1. The spectrophotometric and steady-state kinetic properties of glucose oxidase (EC 1.1.3.4, from Aspergillus niger) that is covalently linked to porous glass beads have been examined. These properties have been compared with those of soluble glucose oxidase, for which the kinetic mechanism at pH5.5 and 25 degrees C has been established previously by a combination of conventional and rapid-reaction techniques to be the following: [Formula: see text] where E(o) and E(r) represent oxidized and reduced forms of the enzyme, respectively. 2. The ratio k(+4)/k(+2) is unchanged after insolubilization, and evidence is presented which suggests that the absolute magnitudes of k(+4) and k(+2) are unchanged. 3. The kinetic efficiency of the insolubilized enzyme is greatly enhanced because of a 14-fold increase in the apparent affinity of glucose for E(o). This effect is attributed either to the binding of glucose to the glass surface or to a change in enzyme structure imposed by the insolubilization process. 4. Only 6% of the insolubilized enzyme which can be reduced by glucose is catalytically active. It is shown by calculation and direct experimental evidence that this fraction of catalytically active enzyme is bound to the exterior bead surface. The remaining 94% of the enzyme is bound within the pore network and may be subject to severe substrate diffusion control.
Effects of α<sub>2</sub>‐adrenoceptor agonists and of related compounds on aggregation of, and on adenylate cyclase activity in, human platelets (1984)

A range of 2-(,5-dihydroimidazolyl)-benzene, -quinoline, and -quinoxaline derivatives and 2-morpholino-4-catechol have been characterized as agonists or partial agonists for human platelet aggregation; and for inhibition of adenylate cyclase by measurement of their effect on platelet [cyclic-3',5'-AMP]. Antagonist activity for these compounds versus adrenaline as agonist has also been assessed for these two responses. The compounds can be divided into 4 groups. Group I contains compounds that are agonists for both responses; group II, compounds that are agonists for inhibition of adenylate cyclase but antagonists for the aggregatory response; group III, compounds that are agonists for the aggregatory response but are antagonists for inhibition of adenylate cyclase by adrenaline; and group IV, compounds that are antagonists for both responses. In group I the EC50 values for induction of aggregation are not significantly different from the EC50 values for inhibition of adenylate cyclase except for 2-morpholino-4-catechol which is significantly more potent as an inhibitor of adenylate cyclase. In group IV a linear correlation is observed between the K1 values for the two responses for 8 compounds but 2 other compounds do not conform to this correlation. The data are not consistent with a model in which a single chi 2-adrenoceptor mediates both the aggregatory response and inhibition of adenylate cyclase and hence support a model in which unique chi 2-adrenoceptors mediate these two responses.