gebhart/patrepeval huggingface dataset:
The Major CD9 and CD81 Molecular Partner (2001)

By associating with specific partner molecules and with each other, the tetraspanins are thought to assemble multimolecular complexes that may be especially relevant with respect to metastasis. We have previously identified a 135-kDa molecule (CD9P-1) as a major molecular partner of CD9 in cancer cell lines. This molecule was identified, after immunoaffinity purification and mass spectrometry analysis, as the protein encoded by the KIAA1436 gene and the human ortholog of a rat protein known as FPRP. Cross-linking experiments detected a complex of the size of CD9 plus CD9P-1, showing that these glycoproteins directly associate with each other, probably in the absence of any other molecule. The use of chimeric CD9/CD82 molecules revealed the role of the second half of CD9, comprising the large extracellular loop and the fourth transmembrane domain. CD9P-1 was also shown to form separate complexes with CD81 and with an unidentified 175-kDa molecule. It also associated with other tetraspanins under conditions maintaining tetraspanin/tetraspanin interactions. The identification of a protein strongly linked to the tetraspanin web and the production of a specific monoclonal antibody will help to further characterize the role of this "web" under physiological and pathological conditions.
Catalysis of aryl-halogen exchange by nickel(II) complexes using sodium hypochlorite (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalysis of aryl-halogen exchange by nickel(II) complexes using sodium hypochloriteKenneth J. O'Connor and Cynthia J. BurrowsCite this: J. Org. Chem. 1991, 56, 3, 1344–1346Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/jo00003a088https://doi.org/10.1021/jo00003a088research-articleACS PublicationsRequest reuse permissionsArticle Views426Altmetric-Citations33LEARN 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
Nucleotide sequence and genetic analysis of a 13.1-kilobase-pair Pseudomonas denitrificans DNA fragment containing five cob genes and identification of structural genes encoding Cob(I)alamin adenosyltransferase, cobyric acid synthase, and bifunctional cobinamide kinase-cobinamide phosphate guanylyltransferase (1991)

A 13.1-kb DNA fragment carrying Pseudomonas denitrificans cob genes has been sequenced. The nucleotide sequence and genetic analysis revealed that this fragment contained five different cob genes named cobN to cobQ and cobW. Based on the similarity of NH2-terminal sequences and molecular weights of the purified Cob proteins, CobQ was identified as cobyric acid synthase, CobP was identified as a bifunctional enzyme exhibiting both cobinamide kinase and cobinamide phosphate guanylyltransferase activities, and CobO was identified as cob(I)alamin adenosyltransferase. CobN is proposed to play a role in cobalt insertion reactions. Four other open reading frames were identified on the 13.1-kb fragment, but their chromosomal inactivation did not lead to a cobalamin-minus phenotype.
SWAP-70 Identifies a Transitional Subset of Actin Filaments in Motile Cells (2003)

Functionally different subsets of actin filament arrays contribute to cellular organization and motility. We report the identification of a novel subset of loose actin filament arrays through regulated association with the widely expressed protein SWAP-70. These loose actin filament arrays were commonly located behind protruding lamellipodia and membrane ruffles. Visualization of these loose actin filament arrays was dependent on lamellipodial protrusion and the binding of the SWAP-70 PH-domain to a 3'-phosphoinositide. SWAP-70 with a functional pleckstrin homology-domain lacking the C-terminal 60 residues was targeted to the area of the loose actin filament arrays, but it did not associate with actin filaments. The C-terminal 60 residues were sufficient for actin filament association, but they provided no specificity for the subset of loose actin filament arrays. These results identify SWAP-70 as a phosphoinositide 3-kinase signaling-dependent marker for a distinct, hitherto unrecognized, array of actin filaments. Overexpression of SWAP-70 altered the actin organization and lamellipodial morphology. These alterations were dependent on a proper subcellular targeting of SWAP-70. We propose that SWAP-70 regulates the actin cytoskeleton as an effector or adaptor protein in response to agonist stimulated phosphatidylinositol (3,4)-bisphosphate production and cell protrusion.
Amyloid-beta immunization effectively reduces amyloid deposition in FcRgamma-/- knock-out mice. (2003)

Direct immunization with amyloid beta protein (Abeta) and passive transfer of anti-Abeta antibodies reduce Abeta accumulation and attenuate cognitive deficits in transgenic models of Alzheimer's disease (AD). The reduction in Abeta deposition has been proposed to involve microglial phagocytosis of Abeta immune complexes via Fc receptors (FcRs). We have examined the efficacy of Abeta immunization in amyloid precursor protein (APP) transgenic mice crossed into FcR-gamma chain knock-out mice (FcRgamma-/-). As might be expected from previous studies on macrophages, phagocytosis of Abeta immune complexes via FcR was completely impaired in microglia cells isolated from FcRgamma-/- mice. Thus, we immunized APP Tg2576 transgenic mice that were crossed in the FcRgamma-/- background with Abeta1-42 and then analyzed the effect on Abeta accumulation. In APP Tg2576 transgenic mice crossed to FcRgamma-/-, Abeta1-42 immunization significantly attenuated Abeta deposition, as assessed by both biochemical and immunohistological methods. The reduction in Abeta accumulation was equivalent to the reduction in deposition seen in Abeta1-42 immunized, age-matched, FcR-sufficient Tg2576 mice. We conclude that after Abeta immunization, the effects of anti-Abeta antibodies on Abeta deposition in APP Tg2576 transgenic mice are not dependent on FcR-mediated phagocytic events.
Results of a Phase I Clinical Study Using Dendritic Cell Vaccinations for Thyroid Cancer (2007)

DC immunotherapy could be administered to patients with thyroid papillary or follicular cancer without substantial side effects.
The Natural History of the Systemic Inflammatory Response Syndrome (SIRS) (1995)

This prospective epidemiologic study of SIRS and related conditions provides, to our knowledge, the first evidence of a clinical progression from SIRS to sepsis to severe sepsis and septic shock.
Reflective-mode conversion with UV-induced phase gratings in two-mode fiber (2002)

In future fiber communications systems, efficient mode conversion has the potential to enable improved devices for dispersion compensation and wavelength routing. Previous reports of symmetric-asymmetric mode conversion in circular, multimode optical fibers have shown nonideal spectral characteristics due to polarization dependence and/or mode splitting of nearly degenerate components of the higher order LP/sub 11/ mode. This work avoids these problems through use of nominally polarization-independent UV-induced phase gratings while exploiting a reflective phase-matching condition that is much less sensitive to the mode splitting of the LP/sub 11/ mode than prior work.
On-the-fly intrusion detection for Web portals (2004)

Remote access to distributed hyperlinked information proves to be one of the killer applications for computer networks. More and more content in current inter and intranets is available as hyperdata, a form easing its distribution and semantic organization. In the framework of the Internet's Web-portals and pay-sites, mechanisms for login based on username and password enable the dynamic customization as well as partial protection of the content. In other applications (e.g. commercial intranets) various similar schemes of authentication are deployed. Nevertheless, stolen passwords are an easy avenue to identity theft, in both public and commercial data networks. Once a perpetrator enters a system, assuming an authorized user's identity, the task of actually detecting this intrusion becomes non-trivial and is often ignored completely. Thus, in addition to the initial authentication step we propose a runtime intrusion detection mechanism, required to maintain a virtually continuous user authentication process and detect identity theft and password misuses. The current paper focuses on designing a pervasive intrusion detection method for hyperdata systems, based on training on and analyzing of access patterns to hyperlinked data, aiming at detecting intruders and raising a red flag at the content provider's side. Our solution is based on a new technique, on-the-fly adaptive training for normality on streams of data access patterns. This enables runtime intrusion detection through analysis of correlations between current patterns and the adaptive past-knowledge. Such a method is to be used in conjunction with current username-password protection schemes. We introduce the motivation behind our solution, discuss the novel detection and training metrics and propose a real-life deployment design. We implement the main algorithm and perform experiments for assessing its intrusion detection ability, with very encouraging results. We also discuss the deployment of our method for detecting automatic spam-bot accesses.
5-hydroxytryptamine and atrial fibrillation: how significant is this piece in the puzzle? (2003)

5-Hydroxytryptamine, a recent addition to the list of hormonal triggers for atrial fibrillation (AF), may play a pivotal role in the induction of AF related not only to cardiac surgery but also to acute coronary syndromes, valvular heart disease, cardiomyopathies, alcoholism, aging, and conducting tissue disease. This review examines the supporting laboratory and clinical evidence and provides a comprehensive insight into the basic underlying mechanisms involved. It also delves into the potential benefits and limitations of 5-HT4 antagonists in the prevention and management of this arrhythmia.
Derivation versus validation (2000)

Assessing the probable clinical course of children presenting to their care is one of the day to day dilemmas facing the practising paediatrician. With accurate prognostication, invasive or expensive treatment may be targeted towards those most likely to benefit. There is little point in expending vital resources on, or administering invasive treatments to, children who are likely to recover without such intervention. Children with certain characteristics may tend to do better or worse than others. For example, younger children or those with specific clinical signs might be expected to deteriorate more rapidly. Past experience often acts as a guide for the experienced paediatrician. Algorithms (or prognostic models) can be developed to provide a means of transferring expert knowledge to the novice. For example, Apgar scores are routinely used to assess the health of newborn babies, and APACHE scores can be used as a measure of prognostication among admissions to paediatric intensive care. 1 In this issue, Brogan and RaZes 2 present an algorithm for identifying children presenting to A&E with fever and petechiae who are at increased risk of significant bacterial sepsis. It is interesting to note that of the many prognostic models that are published each year, 3 4 relatively few are suYciently validated and fewer still find their way into clinical practice. etermining which patients will benefit from treatment is only one use of prognostic algorithms. They also provide a means of informing parents of the likely outcome and can be used in research to give baseline measures of severity in diVerent groups.
Depth-First Search and Linear Graph Algorithms (1972)

The value of depth-first search or “backtracking” as a technique for solving problems is illustrated by two examples. An improved version of an algorithm for finding the strongly connected components of a directed graph and at algorithm for finding the biconnected components of an undirect graph are presented. The space and time requirements of both algorithms are bounded by $k_1 V + k_2 E + k_3 $ for some constants $k_1 ,k_2 $, and $k_3 $, where V is the number of vertices and E is the number of edges of the graph being examined.
Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing (2008)

During the clonal expansion of cancer from an ancestral cell with an initiating oncogenic mutation to symptomatic neoplasm, the occurrence of somatic mutations (both driver and passenger) can be used to track the on-going evolution of the neoplasm. All subclones within a cancer are phylogenetically related, with the prevalence of each subclone determined by its evolutionary fitness and the timing of its origin relative to other subclones. Recently developed massively parallel sequencing platforms promise the ability to detect rare subclones of genetic variants without a priori knowledge of the mutations involved. We used ultra-deep pyrosequencing to investigate intraclonal diversification at the Ig heavy chain locus in 22 patients with B-cell chronic lymphocytic leukemia. Analysis of a non-polymorphic control locus revealed artifactual insertions and deletions resulting from sequencing errors and base substitutions caused by polymerase misincorporation during PCR amplification. We developed an algorithm to differentiate genuine haplotypes of somatic hypermutations from such artifacts. This proved capable of detecting multiple rare subclones with frequencies as low as 1 in 5000 copies and allowed the characterization of phylogenetic interrelationships among subclones within each patient. This study demonstrates the potential for ultra-deep resequencing to recapitulate the dynamics of clonal evolution in cancer cell populations.
Uses of NHANES Biomarker Data for Chemical Risk Assessment: Trends, Challenges, and Opportunities (2015)

This article demonstrates growing use of NHANES chemical biomarker data in studies that can impact risk assessments. Best practices for analysis and interpretation must be defined and adopted to allow the full potential of NHANES to be realized.
The Fanconi anemia pathway and ubiquitin (2007)

Fanconi anemia (FA) is a rare genetic disorder characterized by aplastic anemia, cancer/leukemia susceptibility and cellular hypersensitivity to DNA crosslinking agents, such as cisplatin. To date, 12 FA gene products have been identified, which cooperate in a common DNA damage-activated signaling pathway regulating DNA repair (the FA pathway). Eight FA proteins form a nuclear complex harboring E3 ubiquitin ligase activity (the FA core complex) that, in response to DNA damage, mediates the monoubiquitylation of the FA protein FANCD2. Monoubiquitylated FANCD2 colocalizes in nuclear foci with proteins involved in DNA repair, including BRCA1, FANCD1/BRCA2, FANCN/PALB2 and RAD51. All these factors are required for cellular resistance to DNA crosslinking agents. The inactivation of the FA pathway has also been observed in a wide variety of human cancers and is implicated in the sensitivity of cancer cells to DNA crosslinking agents. Drugs that inhibit the FA pathway may be useful chemosensitizers in the treatment of cancer. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).
Carbohydrate structure of erythropoietin expressed in Chinese hamster ovary cells by a human erythropoietin cDNA. (1987)

The proper glycosylation of erythropoietin is essential for its function in vivo. Human erythropoietins were isolated from Chinese hamster ovary cells transfected with a human erythropoietin cDNA and from human urine. Carbohydrate chains attached to these proteins were isolated and fractionated by anion-exchange high performance liquid chromatography (HPLC) and HPLC employing a Lichrosorb-NH2 column. The structures of fractionated saccharides were analyzed by fast atom bombardment-mass spectrometry and methylation analysis before and after treatment with specific exoglycosidases. Both erythropoietins were found to contain one O-linked oligosaccharide/mol of the proteins, and its major component was elucidated to be NeuNAc alpha 2----3Gal beta 1----3(NeuNAc alpha 2----6)GalNAcOH (where NeuNAc represents N-acetylneuraminic acid) in both proteins. The N-linked saccharides of recombinant erythropoietin were found to consist of biantennary (1.4% of the total saccharides), triantennary (10%), triantennary with one N-acetyllactosaminyl repeat (3.5%), tetraantennary (31.8%), and tetraantennary with one (32.1%), two (16.5%), or three (4.7%) N-acetyllactosaminyl repeats. All of these saccharides are sialylated by 2----3-linkages. Tetraantennary with or without polylactosaminyl units are mainly present as disialosyl or trisialosyl forms, and these structures exhibit the following unique features. alpha 2----3-Linked sialic acid and N-acetyllactosaminyl repeats are selectively present in the side chains attached to C-6 and C-2 of 2,6-substituted alpha-mannose and C-4 of 2,4-substituted alpha-mannose. We have also shown that the carbohydrate moiety of urinary erythropoietin is indistinguishable from recombinant erythropoietin except for a slight difference in sialylation, providing the evidence that recombinant erythropoietin is valuable for biological as well as clinical use.
Glioblastoma multiforme: a review of where we have been and where we are going (2009)

Malignant gliomas such as glioblastoma multiforme (GBM) present some of the greatest challenges in the management of cancer patients worldwide, despite notable recent achievements in oncology. Even with aggressive surgical resections using state-of-the-art preoperative and intraoperative neuroimaging, along with recent advances in radiotherapy and chemotherapy, the prognosis for GBM patients remains dismal: median survival after diagnosis is about 14 months. Established good prognostic factors are limited, but include young age, high Karnofsky Performance Status (KPS), high mini-mental status examination score, O6-methylguanine methyltransferase promoter methylation, and resection of > 98% of the tumor. Standard treatment includes resection, followed by concurrent chemotherapy and radiotherapy. GBM research is being conducted worldwide at a remarkable pace, with some of the more recent promising studies focused on identification of aberrant genetic events and signaling pathways, tumor stem cell identification and characterization, modulation of tumor immunological responses, combination therapies, and understanding of the rare long-term survivors. Past treatment strategies have failed for various reasons; however, newer strategies in trials today and on the horizon encourage optimism. To help illustrate 'where we have been' with this fatal disease and 'where we are going' with contemporary studies, we include in this review a detailed history of Phase III clinical trials for GBM, with a final emphasis on exciting new treatment strategies that offer hope for future GBM therapy.
The chloroacetate esterase reaction (1979)

A method which utilizes the enzyme chloroacetate esterase as a marker for cells of the neutrophil series, monocytes, and mast cells in tissue that has been fixed in formalin and embedded in paraffin is described in detail.
Immunoglobulin switch transcript production in vivo related to the site and time of antigen-specific B cell activation. (1996)

Immunoglobulin (Ig) class switch recombination is associated with the production and splicing of germline IgCH messenger RNA transcripts. Levels of gamma 1 transcripts in mouse spleen sections were assessed by semiquantitative analysis of reverse transcriptase polymerase chain reaction (PCR) products during primary and secondary antibody responses to chicken gamma globulin (CGG). This was correlated with the appearance of CGG-specific B cells and their growth and differentiation to plasma cells. After primary immunization with CGG, gamma 1 switch transcripts appeared after 4 d, peaked at a median of six times starting levels between 10 and 18 d after immunization, and returned to background levels before secondary immunization at 5 wk. By contrast, after secondary challenge with CGG, a sevenfold increase in transcripts occurs during the first d. The level again doubles by day 3, when it is six times that which is seen at the peak of the primary response. After day 4, there was a gradual decline over the next 2-3 wk. Within 12 h of secondary immunization, antigen-specific memory B cells appeared in the outer I zone and by 24 h entered S phase, presumably as a result of cognate interaction with primed T cells. Over the next few hours, they migrated to the edge of the red pulp, where they grew exponentially until the fourth day, when they synchronously differentiated to become plasma cells. The same pattern was seen for the migration, growth, and differentiation of virgin hapten-specific B cells when CGG-primed mice were challenged with hapten protein. The continued production of transcripts after day 3 indicates that switching also occurs in germinal centers, but in a relatively small proportion of their B cells. The impressive early production of switch transcripts during T cell-dependent antibody responses occurs in cells that are about to undergo massive clonal expansion. It is argued that Ig class switching at this time, which is associated with cognate T cell-B cell interaction in the T zone, has a major impact on the class and subclasses of Ig produced during the response.
A New Family of Murine Retroviral Vectors with Extended Multiple Cloning Sites for Gene Insertion (1994)

Murine retroviral vectors with multiple unique cloning sites in the body and 3' long terminal repeat (LTR) are described. The various alterations to the vectors include changing the gag+ start codon (AUG) to a stop codon (UAA), a deletion of 468 bp from the envelope region, and an additional 387-bp deletion of the promoter and enhancer sequences from the 3' LTR. Multiple cloning sites in the body and 3' LTR facilitate double-copy vector construction. The hygromycin resistance and luciferase genes were subcloned into the body and 3' LTR to evaluate effects of vector modifications and effects of insert location (body vs. LTR and same orientation vs. reverse orientation with respect to the vector LTRs) on virus titer. The results indicate the modifications or insert position do not negatively influence potential vector titer and expression capacity. The described vectors have potentially useful characteristics for gene therapy studies.