gebhart/patrepeval huggingface dataset:
Positional Cloning of “Lisch-like”, a Candidate Modifier of Susceptibility to Type 2 Diabetes in Mice (2008)

In 404 Lep(ob/ob) F2 progeny of a C57BL/6J (B6) x DBA/2J (DBA) intercross, we mapped a DBA-related quantitative trait locus (QTL) to distal Chr1 at 169.6 Mb, centered about D1Mit110, for diabetes-related phenotypes that included blood glucose, HbA1c, and pancreatic islet histology. The interval was refined to 1.8 Mb in a series of B6.DBA congenic/subcongenic lines also segregating for Lep(ob). The phenotypes of B6.DBA congenic mice include reduced beta-cell replication rates accompanied by reduced beta-cell mass, reduced insulin/glucose ratio in blood, reduced glucose tolerance, and persistent mild hypoinsulinemic hyperglycemia. Nucleotide sequence and expression analysis of 14 genes in this interval identified a predicted gene that we have designated "Lisch-like" (Ll) as the most likely candidate. The gene spans 62.7 kb on Chr1qH2.3, encoding a 10-exon, 646-amino acid polypeptide, homologous to Lsr on Chr7qB1 and to Ildr1 on Chr16qB3. The largest isoform of Ll is predicted to be a transmembrane molecule with an immunoglobulin-like extracellular domain and a serine/threonine-rich intracellular domain that contains a 14-3-3 binding domain. Morpholino knockdown of the zebrafish paralog of Ll resulted in a generalized delay in endodermal development in the gut region and dispersion of insulin-positive cells. Mice segregating for an ENU-induced null allele of Ll have phenotypes comparable to the B.D congenic lines. The human ortholog, C1orf32, is in the middle of a 30-Mb region of Chr1q23-25 that has been repeatedly associated with type 2 diabetes.
Theoretical x-ray absorption fine structure standards (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheoretical x-ray absorption fine structure standardsJ. J. Rehr, J. Mustre de Leon, S. I. Zabinsky, and R. C. AlbersCite this: J. Am. Chem. Soc. 1991, 113, 14, 5135–5140Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/ja00014a001https://doi.org/10.1021/ja00014a001research-articleACS PublicationsRequest reuse permissionsArticle Views2510Altmetric-Citations1544LEARN 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
Multiple angiopoietin recombinant proteins activate the Tie1 receptor tyrosine kinase and promote its interaction with Tie2 (2005)

The Tie1 receptor tyrosine kinase was isolated over a decade ago, but so far no ligand has been found to activate this receptor. Here, we have examined the potential of angiopoietins, ligands for the related Tie2 receptor, to mediate Tie1 activation. We show that a soluble Ang1 chimeric protein, COMP-Ang1, stimulates Tie1 phosphorylation in endothelial cells with similar kinetics and angiopoietin dose dependence when compared with Tie2. The phosphorylation of overexpressed Tie1 was weakly induced by COMP-Ang1 also in transfected cells that do not express Tie2. When cotransfected, Tie2 formed heteromeric complexes with Tie1, enhanced Tie1 activation, and induced phosphorylation of a kinase-inactive Tie1 in a ligand-dependent manner. Tie1 phosphorylation was also induced by native Ang1 and Ang4, although less efficiently than with COMP-Ang1. In conclusion, we show that Tie1 phosphorylation is induced by multiple angiopoietin proteins and that the activation is amplified via Tie2. These results should be important in dissecting the signal transduction pathways and biological functions of Tie1.
PDZ domains and their binding partners: structure, specificity, and modification (2010)

PDZ domains are abundant protein interaction modules that often recognize short amino acid motifs at the C-termini of target proteins. They regulate multiple biological processes such as transport, ion channel signaling, and other signal transduction systems. This review discusses the structural characterization of PDZ domains and the use of recently emerging technologies such as proteomic arrays and peptide libraries to study the binding properties of PDZ-mediated interactions. Regulatory mechanisms responsible for PDZ-mediated interactions, such as phosphorylation in the PDZ ligands or PDZ domains, are also discussed. A better understanding of PDZ protein-protein interaction networks and regulatory mechanisms will improve our knowledge of many cellular and biological processes.
Evidence on the Incremental Information Content of Additional Firm Disclosures Made Concurrently with Earnings (1986)

Robert E. Hoskin, John S. Hughes, William E. Ricks, Evidence on the Incremental Information Content of Additional Firm Disclosures Made Concurrently with Earnings, Journal of Accounting Research, Vol. 24, Studies on Alternative Measures of Accounting Income (1986), pp. 1-32
Extensive Domain Motion and Electron Transfer in the Human Electron Transferring Flavoprotein·Medium Chain Acyl-CoA Dehydrogenase Complex (2004)

The crystal structure of the human electron transferring flavoprotein (ETF).medium chain acyl-CoA dehydrogenase (MCAD) complex reveals a dual mode of protein-protein interaction, imparting both specificity and promiscuity in the interaction of ETF with a range of structurally distinct primary dehydrogenases. ETF partitions the functions of partner binding and electron transfer between (i) the recognition loop, which acts as a static anchor at the ETF.MCAD interface, and (ii) the highly mobile redox active FAD domain. Together, these enable the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. Disorders in amino acid or fatty acid catabolism can be attributed to mutations at the protein-protein interface. Crucially, complex formation triggers mobility of the FAD domain, an induced disorder that contrasts with general models of protein-protein interaction by induced fit mechanisms. The subsequent interfacial motion in the MCAD.ETF complex is the basis for the interaction of ETF with structurally diverse protein partners. Solution studies using ETF and MCAD with mutations at the protein-protein interface support this dynamic model and indicate ionic interactions between MCAD Glu(212) and ETF Arg alpha(249) are likely to transiently stabilize productive conformations of the FAD domain leading to enhanced electron transfer rates between both partners.
Making good features track better (2002)

This paper addresses robust feature tracking. We extend the well-known Shi-Tomasi-Kanade tracker by introducing an automatic scheme for rejecting spurious features. We employ a simple and efficient outlier rejection rule, called X84, and prove that its theoretical assumptions are satisfied in the feature tracking scenario. Experiments with real and synthetic images confirm that our algorithm makes good features track better; we show a quantitative example of the benefits introduced by the algorithm for the case of fundamental matrix estimation. The complete code of the robust tracker is available via ftp.
Autocrine transformation by fibroblast growth factor 9 (FGF-9) and its possible participation in human oncogenesis (1997)

Transfection of human fibroblast growth factor 9 (FGF-9) cDNA into mouse BALB/c 3T3 clone A31 cells led to morphological transformation of the cells and foci formation 4 weeks later. Isolated transformants had a higher saturation density than parental A31 cells, could grow in soft agar, and secreted FGF-9 into the culture supernatant. The introduction of FGF-9 N33 cDNA, which encodes a truncated protein that has 33 N-terminal amino acids deleted and has the same mitogenic potency as FGF-9, failed to lead to foci formation. Although FGF-9 is a secretory protein, it does not have a typical secretory signal sequence, and the secreted protein retains the full sequence coded in the cDNA except for the initiating methionine. The produced FGF-9 N33 was not secreted and remained within the cell. It is possible that FGF-9 has an uncleavable signal sequence within the first 33 N-terminal amino acids. All of the phenotypes acquired by transformation could be arrested by treatment with a neutralizing anti-human FGF-9 monoclonal antibody (MAb) 150-59. Additionally, transformants formed tumors in nude mice. Injection of MAb 150-59 suppressed tumor formation in nude mice and caused existing tumors to regress. Our results suggest that the cellular transformation mediated by FG F-9 is produced by autocrine stimulation. We have detected FGF-9 production in the human tumor cell lines glioma NMC-G1, from which FGF-9 was originally purified, and stomach carcinoma AZ-521. The growth of NMC-G1 was not affected by MAb 150-59, but that of AZ-521 was arrested by MAb 150-59 in the presence of heparin. Moreover, the growth of the AZ-521 cell tumor in nude mice could be partially arrested by antibody treatment. The possibility of a participation of FGF-9 in the formation of human tumors is suggested.
Patterns of expression of the six alternatively spliced exons affecting the structures of the COL1 and NC2 domains of the alpha 1(XIII) collagen chain in human tissues and cell lines. (1992)

Reverse transcription-polymerase chain reactions and RNA protection experiments were used to examine alternative splicing of the six exons 3B-5, 12, and 13 affecting the COL1 and NC2 domains of type XIII collagen in seven human tissues and four cell lines. Distinct differences in the proportions of the variant mRNAs were found. With respect to the COL1 domain, all studied samples contained mRNAs corresponding to the shortest COL1 variants of 57 and 66 residues, with the former variant being prominent in most samples. Most of the samples also contained notable amounts of mRNAs that corresponded to the longest COL1 variants, mainly those of 104 and 95 residues. Particularly the extent of inclusion of exon 12 and 13 sequences, encoding most of the NC2 domain, varied according to the type of tissue or cell analyzed. Bone, cartilage, and colon adenocarcinoma samples contained little or none of the mRNAs corresponding to the long NC2 variants, whereas in fibroblast, lung, muscle, and osteosarcoma cells, those mRNAs were the major variants. The relative proportions of the various combinations of exons 3B-5, 12, and 13 were evaluated in four of the RNA samples. Interestingly, each of these samples appeared to contain only one to three major combinations of the six exons, representing about 40% to nearly 100% of all variants.
Subunit S1 of pertussis toxin: mapping of the regions essential for ADP-ribosyltransferase activity. (1988)

The toxicity of pertussis toxin is mediated by the ADP-ribosyltransferase activity of subunit S1. To understand the structure-function relationship of subunit S1 and guide the construction of nontoxic molecules suitable for vaccines, we constructed and expressed in Escherichia coli a series of amino-terminal and carboxyl-terminal deletion mutants as well as a number of molecules containing amino acid substitutions. The shortest peptide still retaining enzymatic activity contains amino acids 2-179. Within this region we identified three mutants in which amino acid substitutions abolish the enzymatic activity. Mutation of amino acids 8 and 9 or 50 and 53, located within the region of the S1 subunit of pertussis toxin homologous to cholera toxin, causes loss of enzymatic activity. Outside this homology region, substitution of Glu-129 with glycine or aspartic acid also eliminates the enzymatic activity of the S1 subunit. In this respect, Glu-129 resembles the glutamic acid that is crucial for the catalytic activity of diphtheria and Pseudomonas toxins. Once introduced into the Bordetella pertussis chromosome, the above mutations should lead to the synthesis of nontoxic pertussis toxin molecules suitable for vaccine production.
Chiral Peptide Nucleic Acids with a Substituent in the N-(2-Aminoethy)glycine Backbone (2012)

A peptide nucleic acid (PNA) is a synthetic nucleic acid mimic in which the sugar-phosphate backbone is replaced by a peptide backbone. PNAs hybridize to complementary DNA and RNA with higher affinity and superior sequence selectivity compared to DNA. PNAs are resistant to nucleases and proteases and have a low affinity for proteins. These properties make PNAs an attractive agent for biological and medical applications. To improve the antisense and antigene properties of PNAs, many backbone modifications of PNAs have been explored under the concept of preorganization. This review focuses on chiral PNAs bearing a substituent in the N-(2-aminoethyl)glycine backbone. Syntheses, properties, and applications of chiral PNAs are described.
Effects of Growth Factors on Doxorubicin-Induced Skin Necrosis: Documentation of Histomorphological Alterations and Early Treatment by GM-CSF and G-CSF (2002)

In Brief Extravasation of vesicant antineoplastic agents such as doxorubicin into the skin or subcutaneous tissues may result in loss of the full thickness of the skin or underlying structures. Several treatment methods have been advocated but none has demonstrated any superiority to the others. The authors designed a controlled animal study in 88 rats to test three methods of early treatment of extravasation of the vesicant antineoplastic agent doxorubicin. The first step of the study included 48 Sprague–Dawley rats. All animals received intradermal injections of 1 mg doxorubicin superficially to the panniculus carnosus in the dorsum. The rats were then divided into four groups of 12 rats each, as follows: group 1, no treatment; group 2, immediate intradermal injection of 0.1 ml saline to the same site; group 3, immediate intradermal injection of 10 μg granulocyte macrophage–colony stimulating factor (GM-CSF) in 0.1 ml saline to the same site; group 4, immediate intradermal injection of 10 μg granulocyte–colony stimulating factor (G-CSF) in 0.1 ml saline to the same site. During the next 6 weeks the rats were observed for the development of necrosis. Ulcers developed and reached maximum size two weeks after the injections. The largest ulcers according to area were observed in group 1 and the mean value was 21.25 mm2 (p < 0.05). Although wound areas were significantly smaller in the saline group than in the control group and the mean value was 7.58 mm2 (p < 0.05), the smallest lesions were observed in groups 3 and 4, and the mean values were 1.08 mm2 and 0.83 mm2 respectively (p < 0.05). There was statistically no difference with regard to mean ulcer area between groups 3 and 4. During the second step of the experiment, the remaining 40 Sprague–Dawley rats were used. Groups containing 10 rats each were designed similarly after all animals received intradermal injections of 1 mg doxorubicin into the back. On the 10th day after the injection, the entire area of the ulcer together with the underlying panniculus carnosus was excised for pathological examination and for determination of glucose 6-phosphate dehydrogenase (G6PD) activity. On microscopic examination, the extravasated ulcer consisted of a large area of ischemic necrosis. There was marked damage to small blood vessels in the form of fibrinoid necrosis and vasculitis. Injured vessel counts were higher in the control group (group 1;p < 0.05). No difference was observed in G6PD activity between the groups. The authors conclude that both saline and tissue growth factors (GM-CSF and G-CSF) are useful for the early treatment of doxorubicin extravasation; however, GM-CSF and G-CSF are more beneficial. In a rat doxorubicin-extravasation model, the immediate injection of GM-CSF or G-CSF resulted in substantial reduction of the area of necrosis. However, the G6PD levels were no different whether the cytokines were or were not used.
The Glycoprotein Allergen Ag-54 (C1a h II) from <i>Cladosporium herbarum</i> (1988)

The carbohydrate moiety of an important allergen, Ag-54 in Cladosporium herbarum was studied by alkaline-borohydride treatment, gel filtration, high-performance liquid chromatography, methylation analysis, gas liquid chromatography and mass spectometry. The Ag-54 protein core possessed a very limited number of sugar chains. The carbohydrate moiety consisted mainly of one large highly branched polysaccharide chain which accounted for nearly 75% of the total molecular weight of the glycoprotein. The carbohydrate moiety is made up of D-mannose and D-glucose units in pyranose form having D-galactofuranose side chains attached. Mannose is both 1,2- and 1,6-linked, while glucose is 1,4- and 1,6-linked. Some of the 1,6-linked galactofuranose side chains are bound through C-2 of the 1,6-linked mannose units, and the rest to C-3 of 1,6-linked mannose and 1,2-linked mannose units. A few oligoglucosidic chains of approximately 4 glucose units are also attached to the protein.
Wide‐angle wave field propagation using paraxial extrapolators (1988)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1988Wide‐angle wave field propagation using paraxial extrapolatorsAuthors: Robert W. GravesRobert W. ClaytonRobert W. GravesCalifornia Institute of Technology and Robert W. ClaytonCalifornia Institute of Technologyhttps://doi.org/10.1190/1.1892516 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1892516FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1988ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1988 Pages: 1359 publication data© 1988 Copyright © 1988 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 10 Feb 2005 CITATION INFORMATION Robert W. Graves and Robert W. Clayton, (1988), "Wide‐angle wave field propagation using paraxial extrapolators," SEG Technical Program Expanded Abstracts : 1297-1300. https://doi.org/10.1190/1.1892516 Plain-Language Summary PDF DownloadLoading ...
Origin of periodic void formation during fiber fuse (2005)

An optical discharge running through a single-mode silica glass fiber during fiber fuse was observed and the front part of the generated damage was examined. Their pump power dependences were investigated using a 1.48 mum laser light at powers ranging from 1.1 to 9.0 W. Periodic voids were left by an optical discharge that was in a cavity with a tail. The tail appears because the optical discharge is strongly enclosed in core region. Another mode of periodic void formation was found at near the threshold pump power for fiber fuse propagation. The optical discharge in this case also forms a transient tail during the void formation cycle.
Discriminability Tests for Visualization Effectiveness and Scalability (2019)

The scalability of a particular visualization approach is limited by the ability for people to discern differences between plots made with different datasets. Ideally, when the data changes, the visualization changes in perceptible ways. This relation breaks down when there is a mismatch between the encoding and the character of the dataset being viewed. Unfortunately, visualizations are often designed and evaluated without fully exploring how they will respond to a wide variety of datasets. We explore the use of an image similarity measure, the Multi-Scale Structural Similarity Index (MS-SSIM), for testing the discriminability of a data visualization across a variety of datasets. MS-SSIM is able to capture the similarity of two visualizations across multiple scales, including low level granular changes and high level patterns. Significant data changes that are not captured by the MS-SSIM indicate visualizations of low discriminability and effectiveness. The measure's utility is demonstrated with two empirical studies. In the first, we compare human similarity judgments and MS-SSIM scores for a collection of scatterplots. In the second, we compute the discriminability values for a set of basic visualizations and compare them with empirical measurements of effectiveness. In both cases, the analyses show that the computational measure is able to approximate empirical results. Our approach can be used to rank competing encodings on their discriminability and to aid in selecting visualizations for a particular type of data distribution.
Design and performance analysis of thermally actuated MEMS circuit breakers (2005)

The use of MEMS electrical switches as miniature electrically resettable circuit breakers is described. A prototype based on nickel thermal actuators on silicon has been fabricated and tested, and thermo-mechanical analysis is presented showing the relation between design parameters and performance. Temperature dependence of trip current is shown to be below 0.2% K−1, and analysis is presented indicating that variation of resistivity is the main cause. Trip time, and its dependence on over-current level, is analysed and the results compared with measurements.
Structural comparison of self-assembled monolayers of n-alkanoic acids on the surfaces of silver, copper, and aluminum (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural comparison of self-assembled monolayers of n-alkanoic acids on the surfaces of silver, copper, and aluminumYu Tai TaoCite this: J. Am. Chem. Soc. 1993, 115, 10, 4350–4358Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://doi.org/10.1021/ja00063a062RIGHTS & PERMISSIONSArticle Views3211Altmetric-Citations441LEARN 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 InReddit PDF (3 MB) Get e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts