gebhart/patrepeval huggingface dataset:
Structure of an Fab Fragment against a C-terminal Peptide of hCG at 2.0 Å Resolution (1998)

3A2 is an antibody raised against human chorionic gonadotropin and recognizes a linear epitope on the C-terminal peptide of the human chorionic gonadotropin beta-subunit. Its three-dimensional structure has been determined to 2-A resolution using molecular replacement and refined to a conventional R-factor of 18.2%. The protein exhibits the typical immunoglobulin fold, and the model contains 944 ordered water molecules and one sulfate ion. A comparison of the complementarity-determining regions of the Fab3A2 with those from the Protein Data Bank following the canonical structure method reveals a canonical main chain conformation. This antibody belongs to the canonical structure class (combination of canonical conformations of the complementarity determining loops) that shows a preference for haptens and not for peptides. However, the shape of the surface of the antigen binding loops resembles that of an anti-peptide antibody.
A Readily Available Non-preorganized Neutral Acyclic Halide Receptor with an Unusual Nonplanar Binding Conformation (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Readily Available Non-preorganized Neutral Acyclic Halide Receptor with an Unusual Nonplanar Binding ConformationKonstantinos Kavallieratos, Susan R. de Gala, David J. Austin, and Robert H. CrabtreeView Author Information Sterling Chemistry Laboratory Department of Chemistry, Yale University New Haven, Connecticut 06520-8107 Cite this: J. Am. Chem. Soc. 1997, 119, 9, 2325–2326Publication Date (Web):March 5, 1997Publication History Received20 November 1996Published online5 March 1997Published inissue 1 March 1997https://pubs.acs.org/doi/10.1021/ja964018ehttps://doi.org/10.1021/ja964018erapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1776Altmetric-Citations198LEARN 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 SUBJECTS:Anions,Halogens,Inorganic compounds,Noncovalent interactions,Receptors Get e-Alerts
Tumor necrosis factor induces enhanced responses to platelet‐activating factor and differentiation in human monocytic Mono Mac 6 cells (1993)

Human Mono Mac 6 cells exhibit characteristics of mature blood monocytes. Treatment of these cells with human recombinant human tumor necrosis factor (TNF) resulted in an increase in phagocytosis and phorbol myristate acetate-stimulated superoxide anion production at 12 h and growth retardation occurring at 24 h. Moreover, TNF induced a moderate increase of CD14 surface antigen expression, used as a phenotypic marker of monocyte/macrophage differentiation. Platelet-activating factor (PAF) stimulated a rapid rise in cytosolic free Ca++ ([Ca++]i) of 308 +/- 93 nM in TNF-treated cells compared to untreated cells (33 +/- 8 nM, n = 4). The effect of TNF was dose and time dependent, evident after 12 h and maximal at 48 h. The enhanced PAF-induced [Ca++]i rise was inhibited by the PAF receptor antagonist L-659,989 and EGTA, indicating receptor-dependent Ca++ influx. Furthermore, L-659,989 and PAF inhibited specific 3H-labeled PAF binding in TNF-treated, but not in untreated cells. Consistently, PAF stimulated arachidonic acid release only in TNF-treated cells. Preincubation of cells with anti-TNF monoclonal antibodies abolished TNF-induced effects, but failed to block lipopolysaccharide (LPS) effects. Distinct mechanisms of action by LPS were reflected by the different ability to induce surface antigen expression. In conclusion, the enhancement of PAF responses by TNF, associated with functional characteristics of differentiation in Mono Mac 6 cells, may represent a specific mechanism of cooperative interaction between PAF and TNF in inflammation, sepsis, immunoregulation and atherogenesis.
Intelligent network routing using CCS7 and ISDN (2002)

With the advent of integrated services digital network (ISDN) and common channel signaling system 7 (CCS7) protocols, call-related information is now transported in the network. By using this information, the networks have taken on increased intelligence in their methods of routing and offering telecommunication services. The authors discuss how ISDN and CCS7 protocols in call- and non-call-associated modes support the intelligent networking of services. The benefits, i.e., resource savings, of intelligent networking are discussed with specific examples of services such as intelligent networked automatic call distribution.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Epigenetic Modulation of Collagen 1A1: Therapeutic Implications in Fibrosis and Endometriosis1 (2016)

Progressive fibrosis is recalcitrant to conventional therapy and commonly complicates chronic diseases and surgical healing. We evaluate here a novel mechanism that regulates scar-tissue collagen (COL1A1/Col1a1) expression and characterizes its translational relevance as a targeted therapy for fibrosis in an endometriosis disease model. Endometriosis is caused by displacement and implantation of uterine endometrium onto abdominal organs and spreads with progressive scarring. Transcription factor KLF11 is specifically diminished in endometriosis lesions. Loss of KLF11-mediated repression of COL1A1/Col1a1 expression resulted in increased fibrosis. To determine the biological significance of COL1A1/Col1a1 expression on fibrosis, we modulated its expression. In human endometrial-stromal fibroblasts, KLF11 recruited SIN3A/HDAC (histone deacetylase), resulting in COL1A1-promoter deacetylation and repression. This role of KLF11 was pharmacologically replicated by a histone acetyl transferase inhibitor (garcinol). In contrast, opposite effects were obtained with a HDAC inhibitor (suberoyl anilide hydroxamic acid), confirming regulatory specificity for these reciprocally active epigenetic mechanisms. Fibrosis was concordantly reversed in Klf11(-/-)animals by histone acetyl transferase inhibitor and in wild-type animals by HDAC inhibitor treatments. Aberrant lesional COL1A1 regulation is significant because fibrosis depended on lesion rather than host genotype. This is the first report demonstrating feasibility for targeted pharmacological reversal of fibrosis, an intractable phenotype of diverse chronic diseases.
A design for implementation of a distributed host architecture for distributed interactive simulations (1999)

This document contains a design for the implementation of a Distributed Host Architecture, or\nDHA, for running Distributed Interactive Simulations (DIS). The proposal is standards-based, built upon and extending the DIS 1278.1 standard.\nDifferent models of distributing simulations over networks are discussed, including the centralized server, peer-to-peer and distributed server model. The pros and cons of each model are reviewed with examples from existing software. The distributed server model is chosen for the DHA proposal for its inherent scale ability and suitability to the emerging broadband infrastructures available today and which will become commonplace in the near future.
Clinical Study with Recombinant Interferon Gamma versus Interferon Alpha-2C in Patients with Condylomata Acuminata (1992)

A multi-centre, randomized, open-label trial was conducted to evaluate the safety and efficacy of recombinant interferon (rIFN) alpha-2c versus rIFN gamma in patients with recurrent or persistent condylomata acuminata (CA). Thirty-three such patients were treated either with 6 micrograms rIFN alpha-2c or with 0.1 mg rIFN gamma (both equivalent to 2 x 10E6 IU), single dose, subcutaneously 3 times a week for 6 weeks. In case of no complete clearance at week 10, a second course of treatment with the other type of rIFN was given. There was no significant difference in the complete clearance proportions at week 10 between the two treatment groups (3/16 vs 6/17). No relapses occurred in these patients during the 16 weeks' follow-up. Further clearances during the follow-up resulted in a total complete clearance proportion of 14/33 at the end of study. The treatment was well tolerated. Repeated interferon therapy has its place in treating persistent or recurrent condylomas.
An Overlapping Protein-Coding Region in Influenza A Virus Segment 3 Modulates the Host Response (2012)

Influenza A virus (IAV) infection leads to variable and imperfectly understood pathogenicity. We report that segment 3 of the virus contains a second open reading frame ("X-ORF"), accessed via ribosomal frameshifting. The frameshift product, termed PA-X, comprises the endonuclease domain of the viral PA protein with a C-terminal domain encoded by the X-ORF and functions to repress cellular gene expression. PA-X also modulates IAV virulence in a mouse infection model, acting to decrease pathogenicity. Loss of PA-X expression leads to changes in the kinetics of the global host response, which notably includes increases in inflammatory, apoptotic, and T lymphocyte-signaling pathways. Thus, we have identified a previously unknown IAV protein that modulates the host response to infection, a finding with important implications for understanding IAV pathogenesis.
Three-dimensional sunspot classification system (1989)

This paper describes the McIntosh (1984) Sunspot Classification System, which uses three parameters: the modified Zurich Class, the type of largest spot, and sunspot distribution. The system, described and diagramed here, has proven very successful in making 24-hour predictions of flare occurrences.
Exploiting skeletal structure in computer vision annotation with Benders decomposition (2017)

Many annotation problems in computer vision can be phrased as integer linear programs (ILPs). The use of standard industrial solvers does not to exploit the underlying structure of such problems eg, the skeleton in pose estimation. The leveraging of the underlying structure in conjunction with industrial solvers promises increases in both speed and accuracy. Such structure can be exploited using Bender's decomposition, a technique from operations research, that solves complex ILPs or mixed integer linear programs by decomposing them into sub-problems that communicate via a master problem. The intuition is that conditioned on a small subset of the variables the solution to the remaining variables can be computed easily by taking advantage of properties of the ILP constraint matrix such as block structure. In this paper we apply Benders decomposition to a typical problem in computer vision where we have many sub-ILPs (eg, partitioning of detections, body-parts) coupled to a master ILP (eg, constructing skeletons). Dividing inference problems into a master problem and sub-problems motivates the development of a plethora of novel models, and inference approaches for the field of computer vision.
Control of Myoblast Proliferation with a Synthetic Ligand (2001)

Skeletal myoblast grafts can form contractile tissue to replace scar and repair injured myocardium. Although potentially therapeutic, generating reproducible and sufficiently large grafts remains a challenge. To control myoblast proliferation in situ, we created a chimeric receptor composed of a modified FK506-binding protein (F36V) fused with the fibroblast growth factor receptor-1 cytoplasmic domain. Mouse MM14 myoblasts were transfected with this construct and treated with AP20187, a dimeric F36V ligand, to induce receptor dimerization. Transfected myoblasts proliferated in response to dimerizer (comparable with basic fibroblast growth factor (bFGF) treatment), whereas the dimerizer had no effect on non-transfected cells. Similar to bFGF treatment, dimerizer treatment blocked myotube formation and myosin heavy chain expression and stimulated mitogen-activated protein (MAP) kinase phosphorylation in transfected cells. Non-transfected cells differentiated normally and showed no MAP kinase phosphorylation with dimerizer treatment. Furthermore, myoblasts treated with dimerizer for 30 days in culture reduced MAP kinase phosphorylation, withdrew from the cell cycle, and differentiated normally upon drug withdrawal, demonstrating reversibility of the effect. Thus, forced dimerization of the fibroblast growth factor receptor-1 cytoplasmic domain reproduces critical aspects of bFGF signaling in myoblasts. We hypothesize that in vivo administration of AP20187 following myoblast grafting may allow control over graft size and ultimately improve cardiac function.
Cox-2 inactivates Smad signaling and enhances EMT stimulated by TGF-  through a PGE2-dependent mechanisms (2008)

Although it is well established that mammary tumorigenesis converts transforming growth factor-beta (TGF-beta) from a tumor suppressor to a tumor promoter, the molecular, cellular and microenvironmental mechanisms underlying the dichotomous nature of TGF-beta in mammary epithelial cells (MECs) remains to be determined definitively. Aberrant upregulation of the inducible cyclooxygenase, Cox-2, occurs frequently in breast cancers and is associated with increasing disease severity and the acquisition of metastasis; however, the impact of Cox-2 expression on normal and malignant MEC response to TGF-beta remains unknown. We show here that TGF-beta induced Cox-2 expression in normal MECs during their acquisition of an epithelial-mesenchymal transition (EMT) phenotype. Moreover, stable Cox-2 expression in normal MECs stimulated their invasion, EMT and anchorage-independent growth and inhibited their activation of Smad2/3 by TGF-beta. Conversely, antagonizing TGF-beta signaling in malignant, metastatic MECs significantly reduced their expression of Cox-2 as well as enhanced their activation of Smad2/3 by TGF-beta. Along these lines, elevated Cox-2 expression elicited prostaglandin E(2) (PGE(2)) production and the autocrine activation of EP receptors, which antagonized Smad2/3 signaling in normal and malignant MECs. Importantly, rendering normal and malignant MECs Cox-2 deficient inhibited their production of PGE(2) and acquisition of an EMT morphology as well as potentiated their nuclear accumulation of Smad2/3 and transcription of plasminogen activator inhibitor-1 and p15 messenger RNA. Collectively, our findings establish Cox-2 as a novel antagonist of Smad2/3 signaling in normal and malignant MECs; they also suggest that chemotherapeutic targeting of Cox-2 may offer new inroads in restoring the tumor-suppressing activities of TGF-beta in malignant, metastatic breast cancers.
Pathogenicity of <i>Leptographium longiclavatum </i>associated with <i>Dendroctonus ponderosae</i> to <i>Pinus contorta</i> (2006)

We assessed the pathogenicity of Leptographium longiclavatum sp. nov., a recently reported fungal associate of the mountain pine beetle, Dendroctonus ponderosae (Hopkins, 1902). In September 2003, 30 lodgepole pines (Pinus contorta Dougl. ex Loud. var latifolia Engelm. ex S. Wats) between 98 and 130 years old were inoculated with L. longiclavatum, the known pathogen Ophiostoma clavigerum, or an agar control. Inoculation densities consisted of 200 and 800 points/m 2 in a 60 cm wide band at breast height. The inoculated trees were examined in July 2004, 9 months after inoculation. Five of six trees inoculated with L. longiclavatum at high density (800 points/m 2 ) developed yellow crowns, while the foliage of all trees inoculated at low density (200 points/m 2 ) remained green. Both O. clavigerum and L. longiclavatum generated significantly longer necrotic lesions in the phloem and more occlusions in the sapwood than in the agar controls. In addition, the sapwood colonized by both fungi had a reduced moisture content compared with controls. These results suggest that L. longiclavatum is pathogenic and may contribute to the mortality of mountain pine beetle infested pines.
Randomized double‐blind comparison of chimeric monoclonal antibody to tumor necrosis factor α (infliximab) versus placebo in active spondylarthropathy (2002)

Tumor necrosis factor alpha blockade with infliximab in patients with active SpA was well tolerated and resulted in significant clinical and laboratory improvements in this short-term, placebo-controlled study. However, the occurrence of tuberculosis in one patient necessitates strict inclusion criteria and long-term followup.
Preconditioning protects ischemic rabbit heart by protein kinase C activation (1994)

Myocardial protection in the rabbit induced by ischemic preconditioning is thought to be adenosine receptor linked, but the signaling pathway responsible for the protection has yet to be identified. This study tests whether protein kinase C could be involved. Either of two inhibitors of protein kinase C, staurosporine (50 micrograms/kg) or polymyxin B (24 mg/kg), were administered to rabbits subjected to 30 min regional myocardial ischemia followed by 180 min reperfusion. Half of the rabbits were preconditioned while the other half served as nonpreconditioned controls. Nonpreconditioned hearts without drug or treated with staurosporine or polymyxin B resulted in 37.8 +/- 3.1, 40.5 +/- 2.8, and 42.0 +/- 7.0% infarction of the risk zone, respectively. Preconditioning limited infarct size to 7.3 +/- 2.7%. Both inhibitors blocked protection in preconditioned hearts with 36.2 +/- 2.7 and 40.9 +/- 2.5% of the risk zone infarcted, respectively. Activation of protein kinase C with 4 beta-phorbol 12-myristate 13-acetate (PMA) or with 1-oleyl-2-acetyl glycerol (OAG) mimicked preconditioning in buffer-perfused hearts. PMA (0.01 nmol/min) or OAG (10 nmol/min) for 5 min was followed by 10 min of washout. Infarct size after 30 min regional ischemia was limited in the PMA and OAG groups (6.4 +/- 1.4 and 11.7 +/- 3.3 vs. 28.0 +/- 4.5% in untreated controls) and was equipotent with ischemic preconditioning (11.8 +/- 2.2%). Polymyxin B also blocked protection from ischemic preconditioning in the isolated heart (33.0 +/- 5.0%).(ABSTRACT TRUNCATED AT 250 WORDS)
Interactive water monitoring system accessible by cordless telephone (1985)

A battery-operated, microcomputer-controlled monitoring device linked with a cordless telephone has been developed for remote measurements. This environmental sensor is self-contained and collects and processes data according to the information sent to its on-board computer system. An RCA model 1805 microprocessor forms the basic controller with a program encoded in memory for data acquisition and analysis. Signals from analog sensing devices used to monitor the environment are converted into digital signals and stored in random access memory of the microcomputer. This remote sensing system is linked to the laboratory by means of a cordless telephone whose base unit is connected to regular telephone lines. This offshore sensing system is simply accessed by a phone call originating from a computer terminal in the laboratory. Data acquisition is initiated upon request: Information continues to be processed and stored until the computer is reprogrammed by another phone call request. Information obtained may be recalled by a phone call after the desired environmental measurements are finished or while they are in progress. Data sampling parameters may be reset at any time, including in the middle of a measurement cycle. The range of the system is limited only by existing telephone grid systems and by the transmission characteristics of the cordless phone used as a communications link. This use of a cordless telephone, coupled with the on-board computer system, may be applied to other field studies requiring data transfer between an on-site analytical system and the laboratory.
Addition of a 29 Residue Carboxyl-terminal Tail Converts a Simple HMG Box-containing Protein into a Transcriptional Activator (1995)

Human mitochondrial transcription factor A (h-mtTFA) is essential for initiation of transcription from the two promoters located in the displacement-loop region of human mitochondrial DNA. This 25 kDa protein contains two tandem, HMG box DNA-binding domains separated by a 27 amino acid residue linker region and followed by a 25 residue carboxyl-terminal tail; both the linker and tail are rich in basic amino acid residues. Mutational analysis of h-mtTFA revealed that the tail region is important for specific DNA recognition and essential for transcriptional activation. The critical role of the human tail in transcription was confirmed by constructing chimeric proteins that exchanged similar regions between h-mtTFA and its Saccharomyces cerevisiae homolog, sc-mtTFA. Wild-type sc-mtTFA is unable to activate transcription from the human mitochondrial light-strand promoter (LSP). Addition of the human tail region to sc-mtTFA conferred LSP-specific promoter activation. In all of the different h-mtTFA mutations tested, transcriptional activation was correlated with specific DNA-binding activity, suggesting that these two functions may be inseparable, a situation entirely consistent with previous mutational analyses of human mitochondrial promoters.
Proteomics of gluten: mapping of subunit 1 Ax2* in Cheyenne cultivar by matrix‐assisted laser desorption/ionization (2001)

This paper reports results on the verification of the 1Ax2* high molecular weight glutenin subunit sequence in Cheyenne cultivar. The gene sequence of the protein is known but recently some text changes have been made, and furthermore until now no characterization of post-translational modifications has been reported. The two published sequences, named I and II, differ in four residues at positions 23, 208, 475, and 611. The first sequence contains 20 Arg and 6 Lys residues, producing 26 tryptic fragments, since the Arg(109)-Pro(110) bond is generally not cleaved by trypsin. The second sequence contains 19 Arg and 6 Lys residues, producing 25 tryptic peptides, again because of the Arg(109)-Pro(110) bond. Both sequences generate two cyanogen bromide fragments. Matrix-assisted laser desorption/ionization analysis of the tryptic digest of the high-MW glutenin subunit 1Ax2* resulted in the identification of 24 out of the 26 expected peptides for sequence I, a sequence coverage of 99.5%. These results were sufficient to rule out sequence II and any protein glycosylation and any other post-translational modifications to within the detection limits of the method. It was found that the choice of matrix considerably influenced the sequence coverage in peptide mapping.