gebhart/patrepeval huggingface dataset:
Directed, intramolecular electron transfer in mixed-valence dimers (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirected, intramolecular electron transfer in mixed-valence dimersJeffrey C. Curtis, James S. Bernstein, and Thomas J. MeyerCite this: Inorg. Chem. 1985, 24, 3, 385–397Publication Date (Print):January 1, 1985Publication History Published online1 May 2002Published inissue 1 January 1985https://pubs.acs.org/doi/10.1021/ic00197a028https://doi.org/10.1021/ic00197a028research-articleACS PublicationsRequest reuse permissionsArticle Views175Altmetric-Citations60LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The bacteriophage phi 29 DNA polymerase, a proofreading enzyme. (1992)

The bacteriophage phi 29 DNA polymerase, involved both in the protein-primed initiation and elongation steps of the viral DNA replication, displays a very processive 3',5'-exonuclease activity acting preferentially on single-stranded DNA. This exonucleolytic activity showed a marked preference for excision of a mismatched versus a correctly paired 3' terminus. These characteristics enable the phi 29 DNA polymerase to act as a proofreading enzyme. A comparative analysis of the wild-type phi 29 DNA polymerase and a mutant lacking 3',5'-exonuclease activity indicated that a productive coupling between the exonuclease and polymerase activities is necessary to prevent fixation of polymerization errors. Based on these data, the phi 29 DNA polymerase, a model enzyme for protein-primed DNA replication, appears to share the same mechanism for the editing function as that first proposed for T4 DNA polymerase and Escherichia coli DNA polymerase I on the basis of functional and structural studies.
New Therapeutic Strategy for Amino Acid Medicine: Glycine Improves the Quality of Sleep (2012)

Glycine is a non-essential amino acid that has indispensable roles in both excitatory and inhibitory neurotransmission via N-methyl-D-aspartate type glutamate receptors and glycine receptors, respectively. We recently reported that glycine ingestion before bedtime significantly ameliorated subjective sleep quality in individuals with insomniac tendencies. Oral administration of glycine to rats was found to induce a significant increase in the plasma and cerebrospinal fluid glycine concentrations and a significant decrease in the core body temperature associated with an increase in cutaneous blood flow. The decline in the core body temperature might be a mechanism underlying glycine's effect on sleep, as the onset of sleep is known to involve a decrease in the core body temperature. Moreover, a low core body temperature is maintained during sleep in humans. Pharmacological studies investigating the mechanisms of glycine on sleep were also performed. In this review, we will describe both our recent findings regarding how and where orally administered glycine acts and findings from our rat study and human trials.
Rapid High‐Specificity microRNA Detection Using a Two‐stage Isotachophoresis Assay (2013)

Focusing in on the small: A two-stage microRNA detection assay uses electrokinetic focusing to speed up hybridization and a functionalized hydrogel for affinity purification. This method detects microRNAs in 15 minutes with single-nucleotide specificity, and processes only 5 ng of total RNA. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Oxidant-Induced S-Glutathiolation Inactivates Protein Kinase C-α (PKC-α):  A Potential Mechanism of PKC Isozyme Regulation (2000)

Protein kinase C (PKC) isozymes are subject to inactivation by reactive oxygen species (ROS) through as yet undefined oxidative modifications of the isozyme structure. We previously reported that Cys-containing, Arg-rich peptide-substrate analogues spontaneously form disulfide-linked complexes with PKC isozymes, resulting in isozyme inactivation. This suggested that PKC might be inactivated by oxidant-induced S-glutathiolation, i.e., disulfide linkage of the endogenous molecule glutathione (GSH) to PKC. Protein S-glutathiolation is a reversible oxidative modification that has profound effects on the activity of certain enzymes and binding proteins. To directly examine whether PKC could be inactivated by S-glutathiolation, we used the thiol-specific oxidant diamide because its oxidant activity is restricted to induction of disulfide bridge formation. Diamide weakly inactivated purified recombinant cPKC-alpha, and this was markedly potentiated to nearly full inactivation by 100 microM GSH, which by itself was without effect on cPKC-alpha activity. Diamide inactivation of cPKC-alpha and its potentiation by GSH were both fully reversed by DTT. Likewise, GSH markedly potentiated diamide inactivation of a PKC isozyme mixture purified from rat brain (alpha, beta, gamma, epsilon, zeta) in a DTT-reversible manner. GSH potentiation of diamide-induced cPKC-alpha inactivation was associated with S-glutathiolation of the isozyme. cPKC-alpha S-glutathiolation was demonstrated by the DTT-reversible incorporation of [(35)S]GSH into the isozyme structure and by an associated change in the migration position of cPKC-alpha in nonreducing SDS-PAGE. Diamide treatment of NIH3T3 cells likewise induced potent, DTT-reversible inactivation of cPKC-alpha in association with [(35)S] S-thiolation of the isozyme. Taken together, the results indicate that PKC isozymes can be oxidatively inactivated by S-thiolation reactions involving endogenous thiols such as GSH.
A literature survey on planning and control of warehousing systems (1999)

We present a literature survey on methods and techniques for the planning and control of warehousing systems. Planning refers to management decisions that affect the intermediate term (one or multiple months), such as inventory management and storage location assignment. Control refers to the operational decisions that affect the short term (hours, day), such as routing, sequencing, scheduling and order-batching. Prior to the literature survey, we give an introduction into warehousing systems and a classification of warehouse management problems
The Activation of Type 1 and Type 2 Plasminogen by Type I and Type II Tissue Plasminogen Activator (1995)

Tissue plasminogen activator (tPA) was fractionated using lysine-Sepharose affinity chromatography. Type I, type II, and a minor peak with high affinity for lysine (designated type D) tPA were recovered. In an indirect amidolytic assay involving native human Glu-plasminogen and fibrin, type II tPA showed a 2-fold higher activity than type I. To explore the combinatorial effect of the variable glycosylation status of both tPA and plasminogen, kinetic constants for fibrin-dependent plasminogen activation were determined for combinations of type I, II, and D tPA with type 1 and 2 plasminogen. Within a 4-fold range, the fastest rate was achieved from the combination of type D (type II + D) tPA and type 2 plasminogen. N-Glycosylation of plasminogen increased the Km value for activation by all tPA variants; N-glycosylation of type I tPA at Asn184 decreased the kcat (turnover) values for the fibrin-dependent activation of plasminogen over type II tPA, while type D tPA showed the highest turnover rate. In the presence of fibrinogen fragments, N-glycosylation of plasminogen at site 289 modulates the kinetics of association of enzyme and substrate, while N-glycosylation at site 184 on tPA modulates the turnover rate of the enzyme.
Preanesthetic medication in children: A comparison of intranasal dexmedetomidine versus oral midazolam (2011)

Intranasal dexmedetomidine appears to be a better choice for preanesthetic medication than oral midazolam in our study. Dexmedetomidine was associated with lower sedation levels, lower anxiety levels, and easier child-parent separation at the time of transferring patients to the operating room than children who received oral midazolam. Moreover, intranasal dexmedetomidine has better analgesic property than oral midazolam with discharge time from postanesthetic care unit similar to oral midazolam.
AmtR, a global repressor in the nitrogen regulation system of Corynebacterium glutamicum (2000)

The uptake and assimilation of nitrogen sources is effectively regulated in bacteria. In the Gram-negative enterobacterium Escherichia coli, the NtrB/C two-component system is responsible for the activation of transcription of different enzymes and transporters, depending on the nitrogen status of the cell. In this study, we investigated regulation of ammonium uptake in Corynebacterium glutamicum, a Gram-positive soil bacterium closely related to Mycobacterium tuberculosis. As shown by Northern blot hybridizations, regulation occurs on the level of transcription upon nitrogen starvation. In contrast to enterobacteria, a repressor protein is involved in regulation, as revealed by measurements of methylammonium uptake and beta-galactosidase activity in reporter strains. The repressor-encoding gene, designated amtR, was isolated and sequenced. Deletion of amtR led to deregulation of transcription of amt coding for the C. glutamicum (methyl)ammonium uptake system. E. coli extracts from amtR-expressing cells were applied in gel retardation experiments, and binding of AmtR to the amt upstream region was observed. By deletion analyses, a target motif for AmtR binding was identified, and binding of purified AmtR protein to this motif, ATCTATAGN1-4ATAG, was shown. Furthermore, the binding of AmtR to this sequence was proven in vivo using a yeast one-hybrid system. Subsequent studies showed that AmtR not only regulates transcription of the amt gene but also of the amtB-glnK-glnD operon encoding an amt paralogue, the signal transduction protein PII and the uridylyltransferase/uridylyl-removing enzyme, key components of the nitrogen regulatory cascade. In summary, regulation of ammonium uptake and assimilation in the high G+C content Gram-positive bacterium C. glutamicum differs significantly from the mechanism found in the low G+C content Gram-positive model organism Bacillus subtilis and from the paradigm of nitrogen control in the Gram-negative enterobacteria.
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data (2020)

Major histocompatibility complex (MHC) molecules are expressed on the cell surface, where they present peptides to T cells, which gives them a key role in the development of T-cell immune responses. MHC molecules come in two main variants: MHC Class I (MHC-I) and MHC Class II (MHC-II). MHC-I predominantly present peptides derived from intracellular proteins, whereas MHC-II predominantly presents peptides from extracellular proteins. In both cases, the binding between MHC and antigenic peptides is the most selective step in the antigen presentation pathway. Therefore, the prediction of peptide binding to MHC is a powerful utility to predict the possible specificity of a T-cell immune response. Commonly MHC binding prediction tools are trained on binding affinity or mass spectrometry-eluted ligands. Recent studies have however demonstrated how the integration of both data types can boost predictive performances. Inspired by this, we here present NetMHCpan-4.1 and NetMHCIIpan-4.0, two web servers created to predict binding between peptides and MHC-I and MHC-II, respectively. Both methods exploit tailored machine learning strategies to integrate different training data types, resulting in state-of-the-art performance and outperforming their competitors. The servers are available at http://www.cbs.dtu.dk/services/NetMHCpan-4.1/ and http://www.cbs.dtu.dk/services/NetMHCIIpan-4.0/.
Coagulation Factor XIIIa Undergoes a Conformational Change Evoked by Glutamine Substrate (1998)

Coagulation factor XIIIa, plasma transglutaminase (endo-gamma-glutamine:epsilon-lysine transferase EC 2.3.2.13) catalyzes isopeptide bond formation between glutamine and lysine residues and rapidly cross-links fibrin clots. A monoclonal antibody (5A2) directed to a fibrinogen Aalpha-chain segment 529-539 was previously observed from analysis of end-stage plasma clots to block fibrin alpha-chain cross-linking. This prompted the study of its effect on nonfibrinogen substrates, with the prospect that 5A2 was inhibiting XIIIa directly. It inhibited XIIIa-catalyzed incorporation of the amine donor substrate dansylcadaverine into the glutamine acceptor dimethylcasein in an uncompetitive manner with respect to dimethylcasein utilization and competitively with respect to dansylcadaverine. Uncompetitive inhibition was also observed with the synthetic glutamine substrate, LGPGQSKVIG. Theoretically, uncompetitive inhibition arises from preferential interaction of the inhibitor with the enzyme-substrate complex but is also found to inhibit gamma-chain cross-linking. The conjunction of the uncompetitive and competitive modes of inhibition indicates in theory that this bireactant system involves an ordered reaction in which docking of the glutamine substrate precedes the amine exchange. The presence of substrate enhanced binding of 5A2 to XIIIa, an interaction deemed to occur through a C-terminal segment of the XIIIa A-chain (643-658, GSDMTVTVQFTNPLKE), 55% of which comprises sequences occurring in the fibrinogen epitope Aalpha-(529-540) (GSESGIFTNTKE). Removal of the C-terminal domain from XIIIa abolishes the inhibitory effect of 5A2 on activity. Crystallographic studies on recombinant XIIIa place the segment 643-658 in the region of the groove through which glutamine substrates access the active site and have predicted that for catalysis, a conformational change may accompany glutamine-substrate binding. The uncompetitive inhibition and the substrate-dependent binding of 5A2 provide evidence for the conformational change.
MODELING AND SIMULATION OF A NONISOTHERMAL CATALYTIC MEMBRANE REACTOR (1995)

Abstract A two-dimensional nonisothermal mathematical model has been developed to simulate a tube-and-shell configuration, catalytic membrane reactor. The three-layer membrane consists of an inert large-pore support, an o2 semipermeable dense perovskite layer and a porous catalytic layer. The model is applied to the simulation of the partial oxidation or methane to syngas (oxyreforming). The membrane reactor simultaneously supplies oxygen to the catalytic reaction along the reactor length, and separates oxygen from the air feed, using a dense perovskite layer which is a mixed conductor, thus allowing rapid oxygen permeation without the use of an external circuit. Two configurations of catalytic membrane reactors are simulated, for both bench-scale and industrial-scale conditions. Comparisons are made to the conventional fixed-bed reactor, and to membrane reactors which are isothermal, adiabatic or wall-cooled. The simulation results imply that the temperature rise in exothermic partial oxidation reactions may be mitigated substantially by the use of a dense membrane reactor,
Hedge Funds as Investors of Last Resort? (2009)

Frequency: Yearly ISSN: 0015-198X eISSN: 1938-3312 https://www.tandfonline.com/doi/abs/10.1080/0015198X.2021.1965861 Abstract Assets whose carry is trending up, namely, assets with high carry momentum, tend to have higher returns than those with low carry momentum. Using data from different asset classes, we show that portfolios with high-carry-momentum assets delivered higher returns than portfolios with low-carry-momentum assets. The return differentials cannot be explained by exposure to traditional market risks or by such seemingly related factors as time-series momentum and carry. The results can be motivated by a model in which investors’ demand for an asset depends on the market’s view on the expected returns. An increase in carry raises investors’ belief in the attractiveness of an asset, leading to the possibility for higher demand in the market and in turn to the potential for higher prices and positive returns.
pH-Specific Synthetic Chemistry and Solution Studies in the Binary System of Iron(III) with the α-Hydroxycarboxylate Substrate Quinic Acid: Potential Relevance to Iron Chemistry in Plant Fluids (2009)

Iron is an essential metal ion in plant growth and development. Mobilization and further use of that metal by cellular structures in metabolic pathways entails the existence of soluble forms complexed with indigenous organic substrates, such as the low molecular mass d-(-)-quinic acid. In an effort to understand the relevant aqueous chemistry involving well-defined forms of iron, research efforts were carried out on the binary Fe(III)-quinic acid system. pH-specific reactions of FeCl(3).6H(2)O with quinic acid in a molar ratio 1:3 led to the isolation of the mononuclear Fe(III)-quinate complexes, K[Fe(C(7)H(11)O(6))(3)].(OH).3H(2)O (1), (NH(4))[Fe(C(7)H(11)O(6))(3)].(OH) (2), and Na[Fe(C(7)H(11)O(6))(3)].(OH).8H(2)O (3). Compounds 1-3 were characterized by analytical, spectroscopic techniques (UV/vis, FT-IR, Electron Paramagnetic Resonance (EPR), and Mossbauer spectroscopy), cyclic voltammetry, and magnetic susceptibility measurements. Compound 1 crystallizes in P2(1)3, with a = 15.1693(9) A, V = 3490.6(4) A(3), and Z = 4. Compound 2 crystallizes in P2(1)3, with a = 15.2831(9) A, V = 3569.7(4) A(3), and Z = 4. Compound 3 crystallizes in P2(1)3, with a = 15.6019(14) A, V = 3797.8(6) A(3), and Z = 4. The X-ray crystal structures of 1-3 reveal a mononuclear Fe(III) ion bound by three quinates in an octahedral fashion. Each quinate ligand binds Fe(III) through the alpha-hydroxycarboxylate group as a singly deprotonated moiety, retaining the alcoholic hydrogen. EPR measurements in solution suggest that 1 dissociates, releasing free quinate. Solution speciation studies of the binary system (a) unravel the aqueous species distribution as a function of pH and reagent molar ratio, and (b) corroborate the EPR results proposing the existence of a neutral Fe(III)-quinate complex form. The collective physicochemical properties of 1-3 formulate a well-defined profile for the Fe(III) assembly in aqueous media and project structural features consistent with solubilized Fe(III)-hydroxycarboxylate binary forms potentially mobilized into plant (bio)chemical processes.
Selection of a forward error correcting code for the data communication radio link of the Advanced Train Control System (1989)

A method for selecting a forward error correcting (FEC) code for the Advanced Train Control System (ATCS) radio data link is described. The application of the ATCS and the performance issues involved in selecting a code are detailed. On the basis of the data, the ATCS Communications Component Specification Drafting Committee chose the Reed-Solomon 2 code as the FEC code for ATCS. This choice was based on best overall performance in providing throughput and good performance relative to other codes on other metrics.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The effect of head-induced interaural time and level differences on speech intelligibility in noise (1988)

A study was made of the effect of interaural time delay (ITD) and acoustic headshadow on binaural speech intelligibility in noise. A free-field condition was simulated by presenting recordings, made with a KEMAR manikin in an anechoic room, through earphones. Recordings were made of speech, reproduced in front of the manikin, and of noise, emanating from seven angles in the azimuthal plane, ranging from 0 degree (frontal) to 180 degrees in steps of 30 degrees. From this noise, two signals were derived, one containing only ITD, the other containing only interaural level differences (ILD) due to headshadow. Using this material, speech reception thresholds (SRT) for sentences in noise were determined for a group of normal-hearing subjects. Results show that (1) for noise azimuths between 30 degrees and 150 degrees, the gain due to ITD lies between 3.9 and 5.1 dB, while the gain due to ILD ranges from 3.5 to 7.8 dB, and (2) ILD decreases the effectiveness of binaural unmasking due to ITD (on the average, the threshold shift drops from 4.6 to 2.6 dB). In a second experiment, also conducted with normal-hearing subjects, similar stimuli were used, but now presented monaurally or with an overall 20-dB attenuation in one channel, in order to simulate hearing loss. In addition, SRTs were determined for noise with fixed ITDs, for comparison with the results obtained with head-induced (frequency dependent) ITDs.(ABSTRACT TRUNCATED AT 250 WORDS)
In vivo dynamic human retinal blood flow imaging using ultra-high-speed spectral domain optical Doppler tomography (2003)

An ultra-high-speed spectral domain optical Doppler tomography (SD-ODT) system is used to acquire images of blood flow in a human retina in vivo, at 29,000 depth profiles (A-lines) per second and with data acquisition over 99% of the measurement time. The phase stability of the system is examined and image processing algorithms are presented that allow accurate determination of bi-directional Doppler shifts. Movies are presented of human retinal flow acquired at 29 frames per second with 1000 A-lines per frame over a time period of 3.28 seconds, showing accurate determination of vessel boundaries and time-dependent bi-directional flow dynamics in artery-vein pairs. The ultra-high-speed SD-ODT system allows visualization of the pulsatile nature of retinal blood flow, detects blood flow within the choroid and retinal capillaries, and provides information on the cardiac cycle. In summary, accurate video rate imaging of retinal blood flow dynamics is demonstrated at ocular exposure levels below 600 microW.
The Structure of Haplotype Blocks in the Human Genome (2002)

Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia. We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are highly correlated across populations. We demonstrate that such haplotype frameworks provide substantial statistical power in association studies of common genetic variation across each region. Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease.