gebhart/patrepeval huggingface dataset:
The Superagonistic Activity of Bovine Thyroid-stimulating Hormone (TSH) and the Human TR1401 TSH Analog Is Determined by Specific Amino Acids in the Hinge Region of the Human TSH Receptor (2009)

Bovine TSH (bTSH) has a higher affinity to the human TSHR (hTSHR) and a higher signaling activity than human TSH (hTSH). The molecular reasons for these phenomena are unknown. Distinct negatively charged residues (Glu297, Glu303, and Asp382) in the hinge region of the hTSHR are known to be important for bTSH binding and signaling. To investigate the potential relevance of these positions for differences between bTSH and hTSH in the interaction to the hTSHR, we determined bTSH- and hTSH-mediated cAMP production of several substitutions at these three hinge residues. To examine specific variations of hTSH, we also investigated the superagonistic hTSH analog TR1401 (TR1401), whose sequence differs from hTSH by four additional positively charged amino acids that are also present in bTSH. To characterize possible interactions between the acidic hTSHR positions Glu297, Glu303, or Asp382 and the additional basic residues of TR1401, we investigated TR1401 binding and signaling properties. Our data reveal increased cAMP signaling of the hTSHR using TR1401 and bTSH compared with hTSH. Whereas Asp382 seems to be important for bTSH- and TR1401-mediated but not for hTSH-mediated signaling, the substitution E297K exhibits a decreased signaling for all three TSH variants. Interestingly, bTSH and TR1401 showed only a slightly different binding pattern. These observations imply that specific residues of the hinge region are mediators of the superagonistic activity of bTSH and TR1401 in contrast to hTSH. Moreover, the simultaneous localization of binding components in the glycoprotein hormone molecule and the receptor hinge region permits important reevaluation of interacting hormone receptor domains.
Adaptive Parameter Estimation for Multisite Hydrologic Forecasting (1992)

TWO stochastic modeling approaches for multisite hydrologic forecasting are presented in this work. The models are of ARMAX class expressed in state‐space formulations. The first approach, the adaptive partitioning, models a large catchment by shifting the locations in their time‐lags and modeling the flows of the different subsystems one at a time. The adaptive partitioning approach reintroduces the partitioning proposed by Wood in 1981 in an adaptive and more flexible form. The second approach, the cascading, divides the large catchment into groups of locations and models the groups as subsystems. In both approaches, the models' parameters and noise statistics are updated on‐line in an adaptive manner along with the states. For this purpose, the work proposes an evaluation/ forecasting algorithm based on the three parallel filter theory‐, a state‐space, parameter‐space, and a noise‐space filter. The algorithm is a synthesis and development of two preceding studies by Hebson and Wood, in 1985, and Bergman and Delleur, in 1985. The proposed evaluation/forecasting algorithm introduces a more flexible and comprehensive algorithm for the adaptive parameter‐noise statistics estimation of stochastic models. The two multisite hydrologic forecasting approaches use this tool in modeling large‐scale systems. In this work, the proposed algorithm and the two modeling approaches have been applied to daily stream‐flow forecasting of the Fraser River, Canada.
A reusable traceability framework using patterns (2005)

To accomplish reusable traceability practices a common framework must be established. In this paper we describe a traceability framework which consists of a TRAceability Metamodel (TRAM) and a TRAceability Process (TRAP). TRAM provides a language for describing the elements of a traceability process. The TRAceability Process (TRAP) is a process authoring tool for publishing product lifecycle process configurations as a web site for practitioners to access. A key component of the traceability process is the introduction of traceability patterns which provide a standardized mechanism for the visualization and communication of reusable traceability practices.A tool environment supporting the traceability framework is described. The TRAceability Pattern Environment (TRAPEd) is an environment for the structured and collaborative design of a traceability metamodel, process and patterns. Finally we represent the traceability metamodel, process and patterns using Topic Maps (ISO 13250)
A CD4+ T cell line-secreted factor, growth promoting for normal and leukemic B cells, identified as thioredoxin (1995)

In this study, a B cell growth stimulatory factor, constitutively secreted by a human CD4+ T cell hybridoma clone, MP6, has been purified and characterized. Serum-free 24 h culture media from MP6 cells were collected, concentrated by ultrafiltration and separated by gel chromatography. Fractions were analyzed for stimulatory activity using [3H]thymidine incorporation in normal and leukemic (B-CLL) B cells as target cells. Activity was present in a 12 kDa protein peak. Upon storage this lost activity indicating that the factor was sensitive to air oxidation, a well-known property of mammalian thioredoxins (Trxs). Treatment of the inactive fraction with dithiothreitol restored full activity. When culture medium was analyzed with a radioimmunoassay for human placenta Trx, the MP6 clone was shown to release 30-50 ng/ml per million cells during 24 h. The B cell stimulatory activity of the MP6 medium was removed by Sepharose-bound anti-human placenta Trx IgG and activity was recovered by elution from the antibodies. Furthermore, MP6 medium showed Trx activity with NADPH and Trx reductase using an insulin disulfide reduction assay. Starting from 5 l of serum-free MP6 conditioned medium, the Trx was purified approximately 100,000-fold. After gel electrophoresis banding, the material was analyzed by peptide sequencing and a full length sequence of an 104 amino acid long protein was obtained. This Trx sequence was identical to the previously published sequence of human Trx from HTLV-1 transformed T cells, adult T cell leukemia-derived factor/Trx.(ABSTRACT TRUNCATED AT 250 WORDS)
UV‐induced cross‐linking of proteins to plasmid pBR322 containing 8‐azidoadenine 2′‐deoxyribonucleotides (1988)

An efficient method of cross-linking DNA to protein is described. The method is based on the incorporation of photoactive 8-azidoadenine 2'-deoxyribonucleotides into DNA. We have found that 8-N3dATP is a substrate for E. coli DNA polymerase I and that 8-N3dATP can be incorporated into plasmid pBR322 by nick-translation. Subsequently we were able to cross-link a set of different proteins to 8-azido-2'-deoxyadenosine-containing pBR322 by UV irradiation (366nm). No DNA-protein photocross-linking was observed under the same conditions when the non-photoactive plasmid pBR322 was used.
Mapping of antigenic sites in human neuron-specific enolase by expression subcloning (1994)

Human serum neuron-specific enolase (NSE) is a marker of neurons and of small-cell carcinoma of the lung; improved immunoassays of NSE remain an important goal. Here, we used overlapping complementary DNA (cDNA) clones for reconstruction to express full-length recombinant NSE, and also to express a set of cloned subfragments through the prokaryotic expression vectors pUEX and pUBEX. Subfragments expressed as fusion proteins were used to characterize immunogenic and antigenic regions and epitopes and, expressed as affinity matrices, to derive purified, fractionated polyclonal antibodies. NSE epitope data can be visualized with yeast enolase-1 crystal structure coordinates: The two protein sequences align almost perfectly and are 61% identical. This approach demonstrates the complementarity of cDNA expression with techniques of polyclonal antiserum and monoclonal antibody production and with chemical peptide synthesis in the refinement of immunodiagnostic reagents.
Polymerization of protecting-group-free peptides via ROMP (2013)

A study was conducted to survey the tolerance of ring-opening metathesis polymerization (ROMP) with respect to amino acid (a.a) identity of pentapeptide-modified norbornene-based monomers. A library of norbornyl-pentapeptides were prepared with the general structure, norbornyl-GX<sub>2</sub>PLX<sub>5</sub>, where residue 'X' was changed at each of the two positions (2 or 5) alternately to consist of the natural amino acids F, A, V, R, S, K, N, T, M, Q, H, W, C, Y, E, Q, and D. Each peptide monomer, free of protecting groups, was mixed in turn under a standard set of polymerization conditions with the ROMP initiator (IMesH<sub>2</sub>)C<sub>5</sub>H<sub>5</sub>N)<sub>2</sub>(Cl)<sub>2</sub>Ru=CHPh. Two sets of polymerization reactions were performed, one with Monomer:Initiator (M:I) ratio of 20:1, and another with M:I of 200:1. For the nucleophilic amino acids cysteine and lysine, polymerization reactions were quantitatively compared to those of their protected analogues. Furthermore, we describe polymerization of macromonomers containing up to 30 a.a. to test for tolerance of ROMP to peptide molecular weight. These reactions were studied via SEC-MALS and NMR. Finally, with knowledge of sequence scope in hand, we prepared a set of enzyme-substrate containing brush polymers and studied them with respect to their bioactivity.
On‐line coupled liquid chromatography and capillary supercritical fluid chromatography: Large‐volume injection system for capillary SFC (1992)

Abstract A sample introduction system for capillary SFC was developed to allow introduction of relatively large sample volumes without significant decrease in chromatographic efficiency and resolution. The system includes a sample inlet capillary which receives the liquid aliquot from the LC, whereupon the solvent is eliminated by passage of nitrogen gas. The inlet capillary is then pressurized with CO 2 and the analytes are transferred to an impactor interface where they are deposited. The analytes are then eluted through the impactor interface and the capillary SFC column by pressure programming of the CO 2 mobile phase. The system was demonstrated in a multidimensional mode using microcolumn liquid chromatography in the first dimension. Narrow bands were obtained in the final SFC step for C‐36 hydrocarbon and pentaerythritol tetrastearate.
UGT1A1 polymorphisms and colorectal cancer susceptibility (2002)

UDP-glucuronosyltransferase (UGT) 1A7 polymorphisms may be involved in the aetiology of colorectal cancer

The contribution of the xenobiotic metabolising enzymes (XMEs) to disease susceptibility, particularly cancer, has been a focus for a great deal of research over the last two decades.1 Many of these genes are polymorphic and exhibit significant interindividual variation in their activity. Although these enzymes all have endogenous substrates, they are also involved in the metabolism of exogenous, often mutagenic, substances to which humans are exposed.2

The central hypothesis of these studies has been that genetic changes functionally alter the enzymes and consequently modify an individual's response to a given exposure, putatively associated with the disease. The increased risk for the individual is likely to be small. However, the higher frequency of these alterations, compared with the risks associated with genetic defects implicated in familial syndromes, raises the possibility that the attributable risk, at the population level, may be substantial and therefore of considerable public health importance.3

The involvement of UDP-glucuronosyltransferase (UGT) 1A7 polymorphisms in the aetiology of colorectal cancer (CRC) is presented by Strassburg et al in this issue of Gut 4 [see page 851] is biologically plausible. The authors have shown that …
Dynamically Cross-linked Elastomer Hybrids with Light-Induced Rapid and Efficient Self-Healing Ability and Reprogrammable Shape Memory Behavior (2017)

Pristine carbon nanotubes (CNTs) were activated to exhibit Diels-Alder (DA) reactivity in a polymer matrix, which was modified with monomers containing furan groups. The DA-active polymer matrix was transferred into a dynamic reversible cross-linked inorganic-organic network via a Diels-Alder reaction with CNTs, where pristine CNTs were used as dienophile chemicals and furan-modified SBS acted as the macromolecular diene. In this system, the mechanical properties as well as resilience and solvent resistance were greatly improved even with the presence of only 1 wt % CNTs. Meanwhile, the hybrids retained recyclability and exhibited some smart behaviors, including self-healing and reprogrammable shape memory properties. Furthermore, due to the photothermal effect of CNTs, a retro-Diels-Alder (rDA) reaction was activated under laser irradiation, and healing of a crack on the hybrid surface was demonstrated in approximately 10 s with almost complete recovery of the mechanical properties. Such fast and efficient self-healing performance provides a new concept in designing self-healing nanocomposites with tunable structures and mechanical properties. Furthermore, the DA and rDA reactions could be combined to reprogram the shape memory behavior under laser irradiation or thermal treatment, wherein the temporary shape of the sample could be transferred to a permanent shape via the rDA reaction at high temperature.
Acceleration of Methaemoglobin Reduction by Riboflavin in Human Erythrocytes (1978)

The effect of riboflavin on nitrite treated erythrocytes from normal subjects and patients with hereditary methaemoglobinaemia due to the deficiency of NADH-cytochrome b5 reductase was studied in the presence of glucose, 2-deoxy-D-glucose or lactate. When glucose or 2-deoxy-D-glucose was used as a substrate for these erythrocytes, the rate of methaemoglobin reduction in these cells was accelerated more than two-fold in the presence of riboflavin. The acceleration was dependent on the concentration of riboflavin and was suppressed by the addition of atebrin. The stimulative effect of riboflavin was, however, not observed when lactate was used in place of glucose or 2-deoxy-D-glucose. On the basis of these results, the acceleration of methaemoglobin reduction by riboflavin was considered to be due to the activation of NADPH-flavin reductase (Yubisui et al, 1977) in erythrocytes by the reagent. The availability of riboflavin for patients with methaemoglobinaemia due to the deficiency of NADH-cytochrome b5 reductase and for those with toxic methaemoglobinaemia is discussed in relation to methaemoglobin reducing systems in erythrocytes.
Mass-produced parts traceability system based on automated scanning of “Fingerprint of Things” (2017)

This paper presents a prototype of parts traceability system which employs the “Fingerprint of Things”-based individual identification technique. Traceability of mass-produced tiny parts such as bolts and nuts are required to ensure quality and safety of big machines. However conventional systems using ID tags or serial marking are not applicable because of quantity and tiny size. To overcome this problem, we propose a tag-less traceability system which uses their appearance images as “fingerprints” to identify each of them. Our traceability system consists of three components; (i) automated fingerprints scanning machine for enrollment, (ii) mobile device for query and (iii) cloud server for identification from database. The key to success of our traceability system is enabling us to capture repeatable image features from the same parts in both of (i) enrollment and (ii) query. To this end, we designed the two lighting mechanisms; one for fast scanning of numerous bolts by automatic feeding, and another for a mobile device to capture one parts by hand. In our experiments, we achieve that 1,000 metal bolts produced with the same mold are perfectly identified by matching their surface images captured with our automatic scanning machine and a smart phone.
A Versatile Prodrug Approach for Liposomal Core-Loading of Water-Insoluble Camptothecin Anticancer Drugs (2002)

We describe a versatile prodrug strategy for loading the liposomal lumen with water-insoluble camptothecins. The procedure involves conversion of an active camptothecin analogue to a 20-OR omega-aminoalkanoanic ester prodrug in which R = CO[CH(2)](n)()NH(2) and n = 1-3. The basic amino group of the prodrug serves three roles. First, at pH ranges of 3-5, the amine enhances aqueous solubility. Second, it enhances responsiveness to a transmembrane ammonium sulfate gradient across the liposomal bilayer, thereby facilitating active loading of the agent into the liposomal aqueous core. Third, at a physiological pH of 7 or above (the pH to be encountered following drug release at the tumor site), the nucleophilicity of the amine manifests itself and cyclization to the C-21 carbonyl carbon occurs. This cyclization triggers a rapid and convenient nonenzymatic decomposition process that releases active camptothecin. Accordingly, this novel liposomal approach offers a potential system for tumor-targeting prodrugs of many water-insoluble camptothecins, including the highly lipophilic and clinically attractive analogues SN-38, 9-nitrocamptothecin and DB-67. The rate of formation of the active agent at the tumor site can be controlled through the selection of n (the length of the alkyl spacer group).
The world through the computer (1995)

Article Free Access Share on The world through the computer: computer augmented interaction with real world environments Authors: Jun Rekimoto Sony Computer Science Laboratory Inc., Takanawa Muse Building, 3-14-13, Higashi-gotanda, Shinagawa-ku, Tokyo 141 Japan Sony Computer Science Laboratory Inc., Takanawa Muse Building, 3-14-13, Higashi-gotanda, Shinagawa-ku, Tokyo 141 JapanView Profile , Katashi Nagao Sony Computer Science Laboratory Inc., Takanawa Muse Building, 3-14-13, Higashi-gotanda, Shinagawa-ku, Tokyo 141 Japan Sony Computer Science Laboratory Inc., Takanawa Muse Building, 3-14-13, Higashi-gotanda, Shinagawa-ku, Tokyo 141 JapanView Profile Authors Info & Claims UIST '95: Proceedings of the 8th annual ACM symposium on User interface and software technologyDecember 1995 Pages 29–36https://doi.org/10.1145/215585.215639Published:01 December 1995Publication History 258citation3,948DownloadsMetricsTotal Citations258Total Downloads3,948Last 12 Months334Last 6 weeks44 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
RnaViz 2: an improved representation of RNA secondary structure (2003)

Source code, binaries for Linux and MS Windows, and additional documentation are available athttp://rrna.uia.ac.be/rnaviz/
Inhibition of Dipeptidyl Peptidase-4 Augments Insulin Secretion in Response to Exogenously Administered Glucagon-Like Peptide-1, Glucose-Dependent Insulinotropic Polypeptide, Pituitary Adenylate Cyclase-Activating Polypeptide, and Gastrin-Releasing Peptide in Mice (2004)

Inhibition of dipeptidyl peptidase-4 (DPP-4) is currently being explored as a new approach to the treatment of type 2 diabetes. This concept has emerged from the powerful and rapid action of the enzyme to inactivate glucagon-like peptide-1 (GLP-1). However, other bioactive peptides with potential influence of islet function are also substrates of DPP-4. Whether this inactivation may add to the beneficial effects of DPP-4 inhibition is not known. In this study, we explored whether DPP-4 inhibition by valine-pyrrolidide (val-pyr; 100 micromol/kg administered through gastric gavage at t = -30 min) affects the insulin and glucose responses to iv glucose (1 g/kg) together with GLP-1 (10 nmol/kg), glucose-dependent insulinotropic polypeptide (GIP; 10 nmol/kg), pituitary adenylate cyclase-activating polypeptide 38 (PACAP38; 1.3 nmol/kg), or gastrin-releasing peptide (GRP; 20 nmol/kg) given at t = 0 in anesthetized C57BL/6J mice. It was found that the acute (1-5 min) insulin response to GLP-1 was augmented by val-pyr by 80% (4.2 +/- 0.4 vs. 7.6 +/- 0.8 nmol/liter), that to GIP by 40% (2.7 +/- 0.3 vs. 3.8 +/- 0.4 nmol/liter), that to PACAP38 by 75% (4.6 +/- 0.5 vs. 8.1 +/- 0.6 nmol/liter), and that to GRP by 25% (1.8 +/- 0.2 vs. 2.3 +/- 0.3 nmol/liter; all P < 0.05 or less). This was associated with enhanced glucose elimination rate after GLP-1 [glucose elimination constant (K(G)) 2.1 +/- 0.2 vs. 3.1 +/- 0.3%/min] and PACAP38 (2.1 +/- 0.3 vs. 3.2 +/- 0.3%/min; both P < 0.01), but not after GIP or GRP. The augmented insulin response to GRP by val-pyr was prevented by the GLP-1 receptor antagonist, exendin(3) (9-39), raising the possibility that GRP effects may occur secondary to stimulation of GLP-1 secretion. We conclude that DPP-4 inhibition augments the insulin response not only to GLP-1 but also to GIP, PACAP38, and GRP.
The Genome of the Obligately Intracellular Bacterium Ehrlichia canis Reveals Themes of Complex Membrane Structure and Immune Evasion Strategies (2006)

Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, alpha-proteobacterium, is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, 17 putative pseudogenes, and a substantial proportion of noncoding sequence (27%). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences and a unique serine-threonine bias associated with the potential for O glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associated with immune evasion were identified, one of which contains poly(G-C) tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Genes associated with pathogen-host interactions were identified, including a small group encoding proteins (n = 12) with tandem repeats and another group encoding proteins with eukaryote-like ankyrin domains (n = 7).
EXPRESSION OF MESSENGER RNAS FOR MEMBRANE-TYPE 1, 2, AND 3 MATRIX METALLOPROTEINASES IN HUMAN RENAL CELL CARCINOMAS (1999)

These three MT-MMPs may play an important role in the pathogenesis of human renal cell carcinoma, and MT1-MMP in particular is important in invasion by carcinoma cells. It is interesting that the expression of MT3-MMP was higher in carcinomas, especially clear cell carcinoma, than in normal parenchyma, so that MT3-MMP may provide a clue an understanding of the molecular mechanism of carcinogenesis in human kidney.
Current Methods in Medical Image Segmentation (2000)

Image segmentation plays a crucial role in many medical-imaging applications, by automating or facilitating the delineation of anatomical structures and other regions of interest. We present a critical appraisal of the current status of semi-automated and automated methods for the segmentation of anatomical medical images. Terminology and important issues in image segmentation are first presented. Current segmentation approaches are then reviewed with an emphasis on the advantages and disadvantages of these methods for medical imaging applications. We conclude with a discussion on the future of image segmentation methods in biomedical research.