gebhart/patrepeval huggingface dataset:
Characterization of T cell epitopes in measles virus nucleoprotein. (1999)

T cell epitopes of the measles virus (MV) nucleoprotein were studied by synthesizing overlapping 20 aa peptides over the known sequence of the protein and analysing the proliferation responses of a panel of MV-specific T cell lines and clones against these peptides. T cell lines were established from eleven healthy controls and seven multiple sclerosis patients, all with a history of past MV infection. The epitopes recognized by these lines were concentrated in a few regions of the polypeptide chain. Overlapping peptides containing aa 321-340 and 331-350 were most often recognized. Other epitopes were detected close to the amino-terminal end of the polypeptide chain as each of the peptides 1-20, 21-40, 31-50 and 51-70 contained stimulating moieties. Some responses were also detected towards peptides 151-200 and 221-250, but the carboxy-terminal end of the polypeptide was not recognized by any of the tested T cell lines. The amino acid sequences of the peptides that stimulated the T cell clones and lines, as a rule, contained binding motifs described for HLA-DR alleles found in T cell donors. The regions of protein sequence which did not reveal any T cell epitopes were, instead, relatively free of binding motifs. The results suggest that only a few epitopes of the MV nucleoprotein are important in establishing T cell immunity.
National Ignition Facility, High-Energy-Density and Inertial Confinement Fusion, Peer-Review Panel (PRP) Final Report (2014)

The National Ignition Facility (NIF) at Lawrence Livermore National Laboratory (LLNL) is operated as a National Nuclear Security Administration (NNSA) user facility in accordance with Department of Energy (DOE) best practices, including peer-reviewed experiments, regular external reviews of performance, and the use of a management structure that facilitates user and stakeholder feedback. NIF facility time is managed using processes similar to those in other DOE science facilities and is tailored to meet the mix of missions and customers that NIF supports. The NIF Governance Plan describes the process for allocating facility time on NIF and for creating the shot schedule. It also includes the flow of responsibility from entity to entity. The plan works to ensure that NIF meets its mission goals using the principles of scientific peer review, including transparency and cooperation among the sponsor, the NIF staff, and the various user communities. The NIF Governance Plan, dated September 28, 2012, was accepted and signed by LLNL Director Parney Albright, NIF Director Ed Moses, and Don Cook and Thomas D’Agostino of NNSA. Figure 1 shows the organizational structure for NIF Governance.
Interdigestive and Postprandial Motility in Small-Intestinal Bacterial Overgrowth (1996)

A significant proportion of patients with SIBO, compared with healthy subjects, lack interdigestive phase-III activity, not only in the small intestine but also in the gastric antrum. They also have fewer propagated contractions in the proximal duodenum during interdigestive phase II. On the other hand, the motility index in the distal part of the duodenum was higher in patients with SIBO during phase III, late phase II, and postprandially. The results are compatible with a reduced clearing function in the stomach and proximal duodenum and/or a compensatory increase of motility in the region of the duodenojejunal flexure.
The Stereochemistry of α-Haloketones. I. The Molecular Configurations of Some Monocyclic α-Halocyclanones (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Stereochemistry of α-Haloketones. I. The Molecular Configurations of Some Monocyclic α-HalocyclanonesElias J. CoreyCite this: J. Am. Chem. Soc. 1953, 75, 10, 2301–2304Publication Date (Print):May 1, 1953Publication History Published online1 May 2002Published inissue 1 May 1953https://pubs.acs.org/doi/10.1021/ja01106a004https://doi.org/10.1021/ja01106a004research-articleACS PublicationsRequest reuse permissionsArticle Views505Altmetric-Citations104LEARN 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
NephroCheck data compared to serum creatinine in various clinical settings (2015)

This bedside test detects biomarkers of renal injury. A rapid decline in AKIRisk was associated with the restoration of kidney function, whereas a prolonged high AKIRisk score was associated with end-stage renal disease. However, the dynamics seem to differ, depending on the cause and the extent of injury. Further studies will be needed to clarify the issue.
Coronary Plaque Classification With Intravascular Ultrasound Radiofrequency Data Analysis (2002)

Coronary plaque composition can be predicted through the use of IVUS radiofrequency data analysis. Autoregressive classification schemes performed better than classic Fourier methods. These techniques allow real-time analysis of IVUS data, enabling in vivo plaque characterization.
Crystal structures of leukotriene A 4 hydrolase in complex with captopril and two competitive tight‐binding inhibitors (2002)

Leukotriene (LT) A4 hydrolase/aminopeptidase is a bifunctional zinc enzyme that catalyzes the final step in the biosynthesis of LTB4, a potent chemoattractant and immune modulating lipid mediator. Here, we report a high-resolution crystal structure of LTA4 hydrolase in complex with captopril, a classical inhibitor of the zinc peptidase angiotensin-converting enzyme. Captopril makes few interactions with the protein, but its free thiol group is bound to the zinc, apparently accounting for most of its inhibitory action on LTA4 hydrolase. In addition, we have determined the structures of LTA4 hydrolase in complex with two selective tight-binding inhibitors, a thioamine and a hydroxamic acid. Their common benzyloxyphenyl tail, designed to mimic the carbon backbone of LTA4, binds into a narrow hydrophobic cavity in the protein. The free hydroxyl group of the hydroxamic acid makes a suboptimal, monodentate complex with the zinc, and strategies for improved inhibitor design can be deduced from the structure. Taken together, the three crystal structures provide the molecular basis for the divergent pharmacological profiles of LTA4 hydrolase inhibitors. Moreover, they help define the binding pocket for the fatty acid-derived epoxide LTA4 as well as the subsites for a tripeptide substrate, which in turn have important implications for the molecular mechanisms of enzyme catalyses.
Expression and identification of p90 as the murine mitochondrial glycerol-3-phosphate acyltransferase (1993)

Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the initial and committed step in glycerolipid biosynthesis. Mitochondrial GPAT, unlike the microsomal isozyme, prefers saturated fatty acids as a substrate. We have recently reported cloning of a cDNA to an unidentified 6.8-kb mRNA by a differential hybridization. The mRNA contains an open reading frame of 827 amino acids (p90) with 30% sequence homology in a 300 amino acid stretch to Escherichia coli GPAT. The 6.8-kb mRNA was induced dramatically when fasted mice were refed a high-carbohydrate diet. Here, we have expressed the open reading frame as trpE fusion proteins and used them to generate antibodies. The antibodies recognized a polypeptide of 90 kDa (p90) when the 6.8-kb cDNA sequence was used for in vitro transcription and translation. By Western blot analysis using these antibodies, we detected p90 in mitochondrial fractions of liver, and the p90 level was increased by refeeding. The increase in the p90 level correlated with the increase in mitochondrial GPAT activity. Moreover, p90 was not detectable in 3T3-L1 preadipocytes but markedly increased during adipose conversion. This increase was consistent with the 11-fold increase we observed in N-ethylmaleimide (NEM)-resistant mitochondrial GPAT activity during adipocyte differentiation. In addition, we have expressed p90 in CHO cells by stable transfection. The transfected genes in both correct and reverse orientations produced distinct 3.9-kb transcripts owing to the truncation of a part of the noncoding regions of the endogenous 6.8-kb mRNA before insertion into the pMSXND vector. The transfected CHO cells were treated with 2-aminopurine, an agent that increases expression of exogenous genes.(ABSTRACT TRUNCATED AT 250 WORDS)
Aberrant methylation in gastric cancer associated with the CpG island methylator phenotype. (1999)

Aberrant methylation of 5' CpG islands is thought to play an important role in the inactivation of tumor suppressor genes in cancer. In colorectal cancer, a group of tumors is characterized by a hypermethylator phenotype termed CpG island methylator phenotype (CIMP), which includes methylation of such genes as p16 and hMLH1. To study whether CIMP is present in gastric cancer, the methylation status of five newly cloned CpG islands was examined in 56 gastric cancers using bisulfite-PCR. Simultaneous methylation of three loci or more was observed in 23 (41%) of 56 cancers, which suggests that these tumors have the hypermethylator phenotype CIMP. There was a significant concordance between CIMP and the methylation of known genes including p16, and hMLH1; methylation of p16 was detected in 16 (70%) of 23 CIMP+ tumors, 1 (8%) of 12 CIMP intermediate tumors, and 1 (5%) of 21 CIMP- tumors (P<0.0001). Methylation of the hMLH1 gene was detected in three of five tumors that showed microsatellite instability, and all three of the cases were CIMP+. The CIMP phenotype is an early event in gastric cancer, being present in the normal tissue adjacent to cancer in 5 of 56 cases. These results suggest that CIMP may be one of the major pathways that contribute to tumorigenesis in gastric cancers.
Differentiation and heterogeneity in T‐antigen immortalized precursor cell lines from mouse cerebellum (1991)

Recently, various techniques have been developed to transfer oncogenes into brain cells in order to generate immortalized neural cell lines. It is of interest to establish how well such cell lines reflect their cellular origin. Here we report the characterization of sixteen cell lines from mouse cerebellum and, as a control, six cell lines from skin. Lines were established by immortalizing postnatal primary cell cultures with a retrovirus carrying a modified temperature-sensitive variant of SV40 large T antigen. The cell lines reflect many properties of the cell type from which they were derived. All of the sixteen cerebellar lines expressed one or more markers of the neural precursor cells, namely, nestin and epitopes for NG2 and A2B5. In contrast, none of the six skin lines expressed neural precursor markers. Both types of cell lines expressed vimentin and fibronectin. Differentiation occurred in some of the cerebellar lines and was enhanced in defined medium. A small percentage of cerebellar cells, usually less than 5%, was positive for a marker of differentiation, e.g., glial fibrillary acidic protein (GFAP), galactocerebroside (GalC), or L1. Expression of GFAP colocalized with that of nestin at varying levels of intensity, indicating a gradual replacement of nestin by GFAP in the cytoskeleton. Both the cells positive for precursor markers and those positive for differentiation markers tended to be located in clusters, suggesting that stochastic processes or cell-cell interactions are important for the determination of the fate of cells within a clonal cell line in vitro. The degree of differentiation seemed to correlate with a shift from serum-containing to defined medium, but not with a shift from the permissive to the nonpermissive temperature for T antigen expression. The immortalization approach described here thus allows the establishment of cell lines which are "captured" in the precursor state of the developing mouse neuroepithelium.
Resistance of the double random phase encryption against various attacks (2007)

Several attacks are proposed against the double random phase encryption scheme. These attacks are demonstrated on computer-generated ciphered images. The scheme is shown to be resistant against brute force attacks but susceptible to chosen and known plaintext attacks. In particular, we describe a technique to recover the exact keys with only two known plain images. We compare this technique to other attacks proposed in the literature.
The Role of Pericytes in Neurovascular Unit Remodeling in Brain Disorders (2014)

Neurons are extremely vulnerable cells that tightly rely on the brain's highly dynamic and complex vascular network that assures an accurate and adequate distribution of nutrients and oxygen. The neurovascular unit (NVU) couples neuronal activity to vascular function, controls brain homeostasis, and maintains an optimal brain microenvironment adequate for neuronal survival by adjusting blood-brain barrier (BBB) parameters based on brain needs. The NVU is a heterogeneous structure constituted by different cell types that includes pericytes. Pericytes are localized at the abluminal side of brain microvessels and contribute to NVU function. Pericytes play essential roles in the development and maturation of the neurovascular system during embryogenesis and stability during adulthood. Initially, pericytes were described as contractile cells involved in controlling neurovascular tone. However, recent reports have shown that pericytes dynamically respond to stress induced by injury upon brain diseases, by chemically and physically communicating with neighboring cells, by their immune properties and by their potential pluripotent nature within the neurovascular niche. As such, in this paper, we would like to review the role of pericytes in NVU remodeling, and their potential as targets for NVU repair strategies and consequently neuroprotection in two pathophysiologically distinct brain disorders: ischemic stroke and Alzheimer's disease (AD).
Enthalpy versus Entropy-Driven Binding of Bisphosphonates to Farnesyl Diphosphate Synthase (2006)

We report the results of an ITC (isothermal titration calorimetry) investigation of the binding of six bisphosphonates to the enzyme farnesyl diphosphate synthase (FPPS; EC 2.5.1.10) from Trypanosoma brucei. The bisphosphonates investigated were zoledronate, risedronate, ibandronate, pamidronate, 2-phenyl-1-hydroxyethane-1,1-bisphosphonate, and 1-(2,2-bisphosphonoethyl)-3-iodo pyridinium. At pH = 7.4, both risedronate and the phenylethane bisphosphonate bind in an enthalpy-driven manner (DeltaH approximately -9 to 10 kcal mol-1), but the other four bisphosphonates bind in an entropy-driven manner (DeltaS varying from 31.2 to 55.1 cal K-1 mol-1). However, at pH = 8.5, zoledronate binding switches from entropy to enthalpy-driven. The DeltaG results are highly correlated with FPPS inhibition results obtained using a radiochemical assay (R2 = 0.85, N = 11, P < 0.001). The DeltaH and DeltaS results are interpreted in terms of a model in which bisphosphonates with charged side chains have positive DeltaH values, due to the enthalpic cost of desolvation (due to strong ion-dipole interactions) and, likewise, a positive DeltaS, due to an increase in water entropy (both ligand and protein associated) on ligand binding to FPPS: the hydrophobic effect. For the neutral side chains (risedronate at pH 7.4, 8.5 and zoledronate at pH 8.5, as well as the phenylethane bisphosphonate), binding is overwhelmingly enthalpy-driven, with the enhanced activity of the basic side chain containing species being attributable to their becoming protonated in the active site. Given the large size of the bisphosphonate market and the potential importance of the development of these compounds for cancer immunotherapy and anti-parasitic chemotherapy, these results are of broad general interest in the context of the development of new, potent, and selective FPPS inhibitors.
The functional activity of Fc gamma RII and Fc gamma RIII on subsets of human lymphocytes. (1992)

Subsets of human lymphocytes were isolated from peripheral blood using magnetic beads coated with anti-CD4, -CD8, -CD19 or -CD56 antibodies to yield T4, T8, B and natural killer (NK) cell suspensions with greater than 95% purity. The functional activity of Fc gamma receptor II (Fc gamma RII) and Fc gamma receptor III (Fc gamma RIII) on these subsets was assessed by measuring rosette formation with red cells sensitized with known levels of either rabbit IgG or human (monoclonal or polyclonal) IgG1 anti-D, IgG3 anti-D or IgG3 anti-c (E-IgG). Lysis of red cells by K cells (mediated by Fc gamma RIII) in antibody-dependent cell-mediated cytotoxicity (ADCC) assays was promoted by polyclonal and some monoclonal antibodies. Using these 'ADCC+' antibodies, minimum red cell sensitization levels required to promote rosette formation with NK cells were 2000 IgG1 or IgG3 molecules/red cell compared to 15,000 IgG1 or 4000 IgG3 molecules/red cell with 'ADCC-' monoclonal antibodies. The greater efficiency of ADCC+ antibodies is consistent with their previously reported ability to bind Fc gamma RIII via CH2 and CH3 domains whereas ADCC- antibodies bind only via CH3 domains. B cells formed rosettes only at high levels of sensitization: approximately 60,000 IgG1 or 20,000 IgG3 anti-D molecules/cell. These data reflect the low affinity of Fc gamma RII for monomeric human IgG. Although over 90% of NK cells bound anti-CD16, and 70% formed rosettes with red cells sensitized with rabbit IgG (30,000 molecules/cell), only 25% of NK cells formed rosettes with E-IgG3 at 100,000 IgG molecules/cell. Approximately 35% of B cells, 10% of T8 cells but no T4 cells formed rosettes with E-IgG (100,000 IgG3 molecules/cell). With T8, B and NK cells, IgG3 anti-D promoted greater rosette formation than IgG1 anti-D at comparable levels of sensitization. Presumably the longer hinge region of IgG3 enabled it to bridge the gap between negatively charged lymphocytes and red cells more efficiently than IgG1.
A Randomized Controlled Trial of Etilevodopa in Patients With Parkinson Disease Who Have Motor Fluctuations (2006)

Despite the theoretical pharmacokinetic advantage of etilevodopa, there was no improvement in TTON, response failures, or off time compared with levodopa.
Robotic partial nephrectomy: the real benefit (2010)

Purpose of review Robot-assisted partial nephrectomy (RPN) is an option for patients desiring minimally invasive nephron-sparing surgery. RPN outcomes, including safety, functional results, and oncological control, continue to be reported as the technique emerges. In the current review, we chronicle the development, recent advances, and current status of RPN. Recent findings RPN appears to have a shorter learning curve when compared to alternative minimally invasive techniques. Outcomes from recent series have confirmed the safety and feasibility of RPN in the management of small renal masses, many of them in complex locations. Recent comparative studies have demonstrated favorable-to-equivalent outcomes for RPN when compared to laparoscopic partial nephrectomy (LPN), particularly in regards to decreased warm ischemia time. Novel technical developments include use of TilePro, the fourth robotic arm, sliding-clip renorrhaphy, and selective clamping techniques. Summary RPN appears to have favorable early-to-intermediate stage outcomes. RPN helps with the technical challenges of LPN, potentially extending the benefits of minimally invasive nephron-sparing surgery to a wider audience of patients and surgeons.
The WHO Classification of Tumors of the Nervous System (2002)

The new World Health Organization (WHO) classification of nervous system tumors, published in 2000, emerged from a 1999 international consensus conference of neuropathologists. New entities include chordoid glioma of the third ventricle, cerebellar liponeurocytoma, atypical teratoid/rhabdoid tumor, and perineurioma. Several histological variants were added, including tanycytic ependymoma, large cell medulloblastoma, and rhabdoid meningioma. The WHO grading scheme was updated and, for meningiomas, extensively revised. In recognition of the emerging role of molecular diagnostic approaches to tumor classification, genetic profiles have been emphasized, as in the distinct subtypes of glioblastoma and the already clinically useful 1p and 19q markers for oligodendroglioma and 22q/INI1 for atypical teratoid/rhabdoid tumors. In accord with the new WHO Blue Book series, the actual classification is accompanied by extensive descriptions and illustrations of clinicopathological characteristics of each tumor type, including molecular genetic features, predictive factors, and separate chapters on inherited tumor syndromes. The 2000 WHO classification of nervous system tumors aims at being used and implemented by the neuro-oncology and biomedical research communities worldwide.
Cytotoxic T-lymphocytes derived from patients with breast adenocarcinoma recognize an epitope present on the protein core of a mucin molecule preferentially expressed by malignant cells. (1991)

A population of tumor-reactive cytotoxic T-cells can be propagated from tumor-draining lymph nodes of patients with breast adenocarcinoma. These T-cells specifically recognize breast and pancreatic tumor cells in a major histocompatibility complex (MHC)-unrestricted fashion but not other tumors of epithelial origin or the natural killer target K562. The tumor-specific but MHC-unrestricted lytic activity of these cytotoxic T-lymphocytes (CTLs) is mediated through the alpha/beta T-cell receptor. The molecule recognized by these CTLs is ductal epithelial mucin produced by breast and pancreatic adenocarcinomas. The protein core of the mucin consists of multiple tandem repeats of a 20-amino acid sequence. Antibody SM3, directed against a determinant on the mucin protein core preferentially expressed on malignant cells is able to significantly inhibit lysis of tumor cells by the CTL, while other antibodies binding to different core epitopes are not. Normal breast epithelial lines, which also express mucin but not the SM3 epitope, are not lysed by these tumor-reactive CTLs or act as cold target inhibitors of lysis of tumor lines. The data suggest that the highly repetitive nature of the mucin allows cross-linking of the T-cell receptor on mucin-specific T-cells and therefore accounts for the lack of MHC restriction seen in this system. They further suggest that the mucin core epitope recognized on tumor cells is not expressed on normal epithelial cells in a manner that can be recognized by tumor-reactive CTLs. These findings support the role of mucins as important tumor-associated antigens mediating the cellular response to certain human cancers and suggest that epithelial mucin core sequences might form the basis for an effective vaccine to augment the antitumor immune response.