gebhart/patrepeval huggingface dataset:
O-Linked N-Acetylglucosamine Proteomics of Postsynaptic Density Preparations Using Lectin Weak Affinity Chromatography and Mass Spectrometry (2006)

O-GlcNAc is a widespread dynamic carbohydrate modification of cytosolic and nuclear proteins with features analogous to phosphorylation. O-GlcNAc acts critically in many cellular processes, including signal transduction, protein degradation, and regulation of gene expression. However, the study of its specific regulatory functions has been limited by difficulties in mapping sites of O-GlcNAc modification. We report methods for direct enrichment and identification of in vivo O-GlcNAc-modified peptides through lectin weak affinity chromatography (LWAC) and mass spectrometry. The effectiveness of this strategy on complex peptide mixtures was demonstrated through enrichment of 145 unique O-GlcNAc-modified peptides from a postsynaptic density preparation. 65 of these O-GlcNAc-modified peptides were sequenced and belonged to proteins with diverse functions in synaptic transmission. Beta-elimination/Michael addition, MS(3) on O-GlcNAc neutral loss ions, and electron capture dissociation were shown to facilitate analysis of O-GlcNAc-modified peptides/sites from lectin weak affinity chromatography enriched postsynaptic density samples. Bassoon and Piccolo, proteins critical to synapse assembly and vesicle docking, were extensively modified by O-GlcNAc. In some cases, O-GlcNAc was mapped to peptides previously identified as phosphorylated, indicating potential interplay between these modifications. Shared substrate amino acid context was apparent in subsets of O-GlcNAc-modified peptides, including "PVST" and a novel "TTA" motif (two hydroxyl-containing amino acids adjacent to an alanine). The results suggest specific roles for O-GlcNAc modification in synaptic transmission, establish a basis for site-specific regulatory studies, and provide methods that will facilitate O-GlcNAc proteome analysis across a wide variety of cells and tissues.
Cluster Analysis in Diagnosis (1992)

The purpose of this paper is to survey the usefulness of cluster analysis in the special case of diagnoses. This complex topic is restricted, however, to the application on laboratory characteristics, separately or in connection with clinical data. The article is subdivided into three parts: (a) the fields of a possible use of cluster analysis, detection of diseases or subgroups of diseases, and data reduction by detection of structures; (b) a brief mathematical description of hierarchical and partitioning classification techniques (as a crucial point, the problems associated with these methods are discussed); (c) a critical review of 24 publications of the past 10 years concerning cluster analysis and diagnoses.
A receptor for vascular endothelial growth factor that stimulates endothelial apoptosis. (2001)

Vascular endothelial growth factor (VEGF) is a dimeric angiogenic factor that is overexpressed by many tumors and stimulates tumor angiogenesis. VEGF initiates signaling by dimerizing the receptors VEGFR-1 and VEGFR-2. The Fas receptor stimulates apoptosis, and artificial dimerization of the Fas cytoplasmic domain has been shown to induce apoptosis. We constructed a chimeric receptor (VEGFR2Fas) combining the extracellular and transmembrane domains of VEGFR-2 with the cytoplasmic domain of Fas receptor. When VEGFR2Fas was stably expressed in endothelial cells in vitro, treatment with VEGF rapidly induced cell death with features characteristic of Fas-mediated apoptosis. These findings demonstrate that VEGFR2Fas functions as a VEGF-triggered death receptor and raise the possibility that introduction of VEGFR2Fas into tumor endothelium or tumor cells in vivo may convert tumor-derived VEGF from an angiogenic factor into an antiangiogenesis agent.
Thematic Review Series: Lipid Posttranslational Modifications. Prelamin A, Zmpste24, misshapen cell nuclei, and progeria—new evidence suggesting that protein farnesylation could be important for disease pathogenesis (2005)

Prelamin A undergoes multistep processing to yield lamin A, a structural protein of the nuclear lamina. Prelamin A terminates with a CAAX motif, which triggers farnesylation of a C-terminal cysteine (the C of the CAAX motif), endoproteolytic release of the last three amino acids (the AAX), and methylation of the newly exposed farnesylcysteine residue. In addition, prelamin A is cleaved a second time, releasing 15 more residues from the C terminus (including the farnesylcysteine methyl ester), generating mature lamin A. This second cleavage step is carried out by an endoplasmic reticulum membrane protease, ZMPSTE24. Interest in the posttranslational processing of prelamin A has increased with the recognition that certain progeroid syndromes can be caused by mutations that lead to an accumulation of farnesyl-prelamin A. Recently, we showed that a key cellular phenotype of these progeroid disorders, misshapen cell nuclei, can be ameliorated by inhibitors of protein farnesylation, suggesting a potential strategy for treating these diseases. In this article, we review the posttranslational processing of prelamin A, describe several mouse models for progeroid syndromes, explain the mutations underlying several human progeroid syndromes, and summarize recent data showing that misshapen nuclei can be ameliorated by treating cells with protein farnesyltransferase inhibitors.
Establishment and Large-scale Expansion of Minimally cultured “Young” Tumor Infiltrating Lymphocytes for Adoptive Transfer Therapy (2011)

Treatment of metastatic melanoma patients with adoptively transferred tumor infiltrating lymphocytes (TIL) has developed into an effective therapy. Various studies reported objective responses of 50% and more. The use of unselected, minimally cultured, bulk TIL (Young-TIL) has simplified the TIL production process and may therefore, allow the accessibility of this approach to cancer centers worldwide. This article describes the precise process leading to the large-scale production of Young-TIL for therapy. We have enrolled 55 melanoma patients and optimized their Young-TIL generation process. Young-TIL cultures were successfully established for 51 of 55 (93%) patients in 16.7 ± 5.5 days. In a large-scale expansion procedure Young-TIL of 32 patients were further expanded to treatment levels, resulting in a final number of 4.5 x 10¹⁰ ± 2.0 x 10¹⁰ TIL. Fifteen of 31 (48%) patients, who were evaluated, achieved a clinical response, including 4 complete and 11 partial responses. We confirmed the significant correlation between short culture duration, high number of infused cells, and tumor regression. A high percentage of CD8 T cells in the infusion product was beneficial to achieve an objective response. All responding patients were treated with Young-TIL cultures established in < 20 days. In summary, we describe here an efficient and reliable method to generate Young-TIL for adoptive transfer therapy, which may easily be adopted by other cancer centers and can lead to objective responses in 50% of refractory melanoma patients. In the future this approach may be used also in other types of malignancies.
Itch-Associated Responses of Afferent Nerve Innervating the Murine Skin: Different Effects of Histamine and Serotonin in ICR and ddY Mice (2000)

To assess the itch-associated response of primary afferents innervating the murine skin in vivo, dose-response curves and time-courses for itch-scratching and cutaneous nerve firing responses to intradermal injections of pruritogens (histamine and serotonin) were compared in ICR and ddY mice. Serotonin increased the itch-scratch response and cutaneous nerve firing in either ICR or ddY mice. Histamine increased these two responses in ICR, but not ddY, mice. The dose-response curves and time-courses for serotonin- and histamine-induced nerve firing were similar to those for the itch-scratch response. The results suggest that cutaneous nerve firing evoked by peripherally given pruritogens includes the itch-associated response.
Molecular dynamics simulations of plasma - surface chemistry (1996)

Molecular dynamics (MD) simulations were conducted of impact (normal incidence; 10, 25 and 50 eV) onto an initially pure Si surface until approximately steady state Cl coverages had been obtained. A variety of quantities were obtained from these simulations, including steady state Cl coverages, the yields associated with various etching mechanisms and the degree of surface roughness that evolves during surface chlorination. The most direct comparison to experimental measures of etching yield are from vacuum beam experiments utilizing mass- and energy-selected ion beams. In order to compare to these measurements, we took chlorinated Si layers and impacted upon them at a variety of energies. Quantitative agreement between the simulations and measurements was obtained for ion energies in the range 20 - 75 eV and qualitative agreement was obtained for 75 - 300 eV.
The interaction of nitriles with a potassium-promoted gold(100) surface (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe interaction of nitriles with a potassium-promoted gold(100) surfaceT. Solomun, H. Baumgaertel, and K. ChristmannCite this: J. Phys. Chem. 1991, 95, 24, 10041–10049Publication Date (Print):November 1, 1991Publication History Published online1 May 2002Published inissue 1 November 1991https://pubs.acs.org/doi/10.1021/j100177a079https://doi.org/10.1021/j100177a079research-articleACS PublicationsRequest reuse permissionsArticle Views105Altmetric-Citations11LEARN 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 options Get e-Alerts
Action Tubelet Detector for Spatio-Temporal Action Localization (2017)

Current state-of-the-art approaches for spatio-temporal action localization rely on detections at the frame level that are then linked or tracked across time. In this paper, we leverage the temporal continuity of videos instead of operating at the frame level. We propose the ACtion Tubelet detector (ACT-detector) that takes as input a sequence of frames and outputs tubelets, i.e., sequences of bounding boxes with associated scores. The same way state-of-the-art object detectors rely on anchor boxes, our ACT-detector is based on anchor cuboids. We build upon the SSD framework [19]. Convolutional features are extracted for each frame, while scores and regressions are based on the temporal stacking of these features, thus exploiting information from a sequence. Our experimental results show that leveraging sequences offrantes significantly improves detection performance over using individual frames. The gain of our tubelet detector can be explained by both more accurate scores and more precise localization. Our ACT-detector outperforms the state-of-the-art methods for frame-mAP and video-mAP on the J-HMDB [12] and UCF-101 [31] datasets, in particular at high overlap thresholds.
Analytical applications of ion-molecule reactions (1997)

This review covers applications of ion-molecule reactions for solving increasingly complex analytical problems. Because gas-phase reactions are frequently fast and efficient, the use of ion-molecule reactions provides a diverse frontier for extending the boundaries of mass spectrometry. Product distributions from ion-molecule reactions may provide key diagnostic information for structure identification, and particular product ions may afford more structurally informative fragmentation patterns than those patterns of ions that are generated by conventional methods. Applications range from those areas involving the development of novel chemical ionization reagents that show structural specificity upon reactions with analytes, to those areas in which ion-molecule reactions are combined with collisionally activated dissociation in unusual sequences, to those areas involving ion-molecule reactions of species formed by laser desorption or electrospray ionization. In electrospray ionization applications, the use of ion-molecule reactions allows the concentration of ion current into fewer multicharged ions, permits the counting of acidic or basic sites, and provides indirect information about protein structures and thermochemical data about individual sites in large molecules. © 1997 John Wiley & Sons, Inc., Mass Spectrom Rev 16 (2), 91–110, 1997
Polymers, Dimers and Radical Cations from Electrochemical Oxidation of Interring-Bridged Thiophene and Thiophene-Phenylene Tetramers (2001)

The electrochemical oxidation of 2,5-thienylene- (T) and 1,4-phenylene- (P) based arylene tetramers T4, TP2T and PT2P, in which the torsion angles between couples of adjacent rings are blocked by a chemical bridge, has been performed in acetonitrile. The products have been characterised by cyclic voltammetry, MALDI mass spectrometry, FT-IR, UV-vis and ESR spectroscopies, and in-situ conductivity and identified as radical cations, dimers or polymers depending on the T–P sequence in the monomer.
Identification of a 52 kb deletion downstream of the SOST gene in patients with van Buchem disease (2002)

Van Buchem disease is an autosomal recessive skeletal dysplasia characterised by generalised bone overgrowth, predominantly in the skull and mandible. Clinical complications including facial nerve palsy, optic atrophy, and impaired hearing occur in most patients. These features are very similar to those of sclerosteosis and the two conditions are only differentiated by the hand malformations and the tall stature appearing in sclerosteosis. Using an extended Dutch inbred van Buchem family and two inbred sclerosteosis families, we mapped both disease genes to the same region on chromosome 17q12-q21, supporting the hypothesis that van Buchem disease and sclerosteosis are caused by mutations in the same gene. In a previous study, we positionally cloned a novel gene, called SOST, from the linkage interval and identified three different, homozygous mutations in the SOST gene in sclerosteosis patients leading to loss of function of the underlying protein. The present study focuses on the identification of a 52 kb deletion in all patients from the van Buchem family. The deletion, which results from a homologous recombination between Alu sequences, starts approximately 35 kb downstream of the SOST gene. Since no evidence was found for the presence of a gene within the deleted region, we hypothesise that the presence of the deletion leads to a down regulation of the transcription of the SOST gene by a cis regulatory action or a position effect.
Cloning the Heavy Chain of Human HLA-DR Antigen Using Synthetic Oligodeoxyribonucleotides As Hybridization Probes (1983)

The recent development of the amino acid microsequence technique allows us to obtain partial sequence information using an extremely small amount of protein. Two sets of mixed oligonucleotide probes were chemically synthesized using the amino acid sequence information for the heavy chain of human HLA-DR antigen obtained by the microsequence technique. These two hybridization probes were used to screen cDNA clones constructed from cytoplasmic poly(A)+ mRNA from a human B lymphoblastoid homozygous cell line (LG-2). Of the 10,000 clones screened, two clones hybridized with the probes. DNA sequence analysis showed that the longer one of the two cDNA clones was 1183 nucleotides long, including the entire coding region, the signal peptide region, and the complete 3'-noncoding region. The deduced amino acid sequence of the HLA-DR alpha chain is identical to that of other cell lines with a different HLA-DR typing. However, several nucleotide differences are found in the 3'-untranslated region compared with that of other DR haplotypes.
Current status of cardiac resynchronization therapy device optimization in Japan (2013)

Abstract Background Cardiac resynchronization therapy (CRT) is known to be effective for patients with heart failure. However, despite data suggesting that routine atrioventricular (AV) and interventricular (VV) delay optimization may play significant roles in CRT, there is no standard on how and when the CRT device should be optimized. The aim of this study was to characterize the current practice of CRT optimization in Japan. Methods A survey was conducted to collect information on the procedural aspects of AV and VV delay optimization. The key survey items concerned what method is used for optimization, when optimization is performed, and what factors limit repetitive optimization. Results Fifty‐two physicians participated in the survey. Echocardiography was the chosen method for assessing AV and VV delays by 79.6% and 65.3% of physicians, respectively, and routine optimization was performed by 28.3%. The majority optimized the settings only once at pre‐hospital discharge or on an “as‐needed” basis. The factors limiting repeated optimization were the lack of available time (71.2%), qualified staff (53.8%), and reliable methods (55.8%). Conclusions Repetitive CRT optimization is infrequently performed in Japan. Lack of time, human resource, and reliable methods were the major factors affecting the number of routine CRT optimization.
Mechanisms of platelet production. (1989)

The precise mechanism by which platelets are formed from megakaryocytes (MK) remains unclear, despite numerous studies which have been performed during this century. Models have been proposed that attempt to account for platelet formation from disruption of elongated processes of MK cytoplasm, designated proplatelets, or by fragmentation of MK cytoplasm. MK demarcation membranes are hypothesized by some investigators to delineate platelet territories in the MK cytoplasm, and by others to act as a membrane reservoir for MK process formation. Platelet production has been variously speculated to occur primarily in the bone marrow or lung. Each theory or model has attempted to elucidate the phenomenon of size heterogeneity of circulating platelets and the changes that occur under conditions of altered thrombopoiesis. In this article, we have analyzed and compared the characteristics of previously proposed models for platelet production and suggested additional techniques for future studies of thrombopoiesis.
Pathways of angiotensin‐(1–7) metabolism in the kidney (2001)

Angiotensin-(1-7) [Ang-(1-7)], which can be formed directly from angiotensin I (Ang I) bypassing the requisite production of Ang II, is a bioactive component of the renin-angiotensin system that may oppose the actions of Ang II. In contrast to the generation of Ang II, angiotensin-converting enzyme (ACE) hydrolyses Ang-(1-7) to inactive fragments. ACE inhibitors substantially augment circulating levels of Ang-(1-7) and increase the peptide's half-life. Thus, this enzymatic pathway constitutes a key regulatory point in the vasculature to balance the actions of Ang II, Ang-(1-7) and bradykinin. In contrast, the renal pathways for the metabolism of Ang-(1-7) appear quite distinct. Characterization of this pathway may shed new light on the potential actions of the peptide in the kidney, as well as the mechanisms of novel vasoactive peptidase therapies. We summarize recent experimental and clinical studies that begin to reveal novel pathways in the formation and degradation of Ang-(1-7) in the kidney.
Soybean (<i>Glycine max</i>) Transformation Using Immature Cotyledon Explants (2006)

Agrobacterium tumefaciens-mediated transformation of soybeans can be accomplished using immature zygotic cotyledons as target tissues providing an alternate explant to embryogenic tissue cultures, proliferating meristems, and cotyledonary nodes. The immature cotyledon method includes direct induction of transgenic somatic embryos from the explant plated on selective media after cocultivation, followed by maturation and regeneration of individual somatic embryos into whole plants. Although this method has been improved to be simple, rapid, reproducible, and applicable to a range of cultivars in different maturity groups, the transformation efficiency (Southern-positive, independent plants produced per 100 immature cotyledon explants) is 1.7% and needs to be further increased to make this a robust soybean transformation system. Further refinements of cocultivation conditions, tissue culture, and selection of regenerated transgenic plants will probably result in increases in transformation efficiency.
Signaling Pathways for Early Brain Injury after Subarachnoid Hemorrhage (2004)

Few studies have examined the signaling pathways that contribute to early brain injury after subarachnoid hemorrhage (SAH). Using a rat SAH model, the authors explored the role of vascular endothelial growth factor (VEGF) and mitogen-activation protein kinase (MAPK) in early brain injury. Male Sprague-Dawley rats (n = 172) weighing 300 to 350 g were used for the experimental SAH model, which was induced by puncturing the bifurcation of the left anterior cerebral and middle cerebral arteries. The blood-brain barrier (BBB), brain edema, intracranial pressure, and mortality were evaluated at 24 hours after SAH. The phosphorylation of VEGF and different MAPK subgroups (ERK1/2, p38, and JNK) were examined in both the cortex and the major cerebral arteries. Experimental SAH increased intracranial pressure, BBB permeability, and brain edema and produced high mortality. SAH induced phosphorylation of VEGF and MAPKs in the cerebral arteries and, to a lesser degree, in the cortex. PP1, an Src-family kinase inhibitor, reduced BBB permeability, brain edema, and mortality and decreased the phosphorylation of VEGF and MAPKs. The authors conclude that VEGF contributes to early brain injury after SAH by enhancing the activation of the MAPK pathways, and that the inhibition of these pathways might offer new treatment strategies for SAH.
The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant (2001)

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).