gebhart/patrepeval huggingface dataset:
Immunogenicity and Contraceptive Potential of a Human Zona Pellucida 3 Peptide Vaccine1 (1997)

Immunization with zona pellucida 3 (ZP3) glycoprotein induces infertility in primates and is a target antigen for a contraceptive vaccine. However, loss of ovarian function is a long-term side effect. A possible mechanism is autoimmune ovarian disease induced by ZP3-specific autoreactive T cells, demonstrated in mice immunized with a murine ZP3 peptide in complete Freund's adjuvant. Indeed, a murine contraceptive vaccine that elicits antibodies to zona pellucida (ZP) without concomitant pathogenic T-cell activation has been achieved by a chimeric peptide (CP) consisting of a native ZP3 B-cell epitope and a foreign helper T-cell peptide. Herein, we evaluate the CP strategy in primate for human ZP3 (hZP3) vaccine development. A CP was constructed that consisted of a known helper T-cell epitope from the malarial circumsporozoite protein and a native B-cell epitope of hZP3. The human CP elicited antibodies to ZP3 in macaques without a measurable T-cell response to the hZP3 peptide. The serum antibodies reacted with macaque and human ZP and significantly inhibited human sperm binding to oocytes in vitro. Moreover, the CP elicited antibodies to human ZP in mice that lack murine major histocompatibility complex (MHC) class II molecules but express transgenic human HLA-DR3, -DQ6, or DQ8 molecules. Therefore, this study 1) provides evidence to support the feasibility of the CP strategy in hZP3 vaccine development and 2) describes a novel approach for evaluating the influence of polymorphic human MHC on vaccine immunogenicity without human immunization.
Suppression of hepatitis B virus expression and replication by hepatitis C virus core protein in HuH-7 cells (1993)

Hepatitis B and C viruses (HBV and HCV, respectively) are associated with acute and chronic liver diseases and hepatocellular carcinoma. To elucidate the molecular status of superinfection with these two hepatitis viruses, we cotransfected the full-length or truncated version of HCV structural genes (core and envelope 1) together with the cloned HBV DNA into a human hepatoma cell line (HuH-7). Expression of HBV-specific major transcripts (3.5 and 2.1 kb), as well as HBV antigens (hepatitis B surface antigen and hepatitis B e and core antigens), was reduced about two- to fourfold by the presence of the HCV structural genes. In addition, the secretion of HBV viral particles, including the viral nucleocapsid and mature virion, was drastically suppressed about 20-fold. Analysis of the intracellular HBV core protein-associated nucleic acid indicated that the encapsidated HBV pregenomic RNA was similarly reduced about 14-fold. Deletion analysis of the HCV structural genes demonstrated that the core gene alone or the fragment containing the core protein's N-terminal 122 amino acid residues conferred the same level of suppressive activity as the full-length structural genes. By indirect immunofluorescence, we found that the core protein of HCV was located in the cytoplasm of transfected HuH-7 cells at day 3 posttransfection and was targeted to the nucleus at day 6. Thus, the kinetics of the suppressive effect exerted by HCV constructs matched the timing of core protein entrance into the nucleus. Our results substantiate the clinical finding that HBV markers are suppressed by superinfection with HCV and further imply that this inhibitory effect may occur in the processes of transcription and encapsidation of HBV pregenomic RNA and may be mediated by the core protein of HCV. The deduced amino acid sequence of the HCV core protein has revealed that it is a basic protein which contains a putative DNA-binding motif (SPRG), as well as triplicate nuclear localization signals and several putative protein kinase A and C recognition sites. These characteristics imply that the HCV core protein can also function as a gene-regulatory protein.
The complementary deoxyribonucleic acid sequence, tissue distribution, and cellular localization of the rat granulin precursor (1993)

Granulins (grns; also called epithelins) are cysteine-rich polypeptides with pleiotropic effects on epithelial cell growth in vitro. The grn/epi gene is widely expressed in epithelial cell lines, many of which respond to the gene product, raising the possibility of autocrine or paracrine regulation. In vitro the grn gene is expressed in cell types of diverse lineages, including epithelial cells, lymphoid and myeloid cells, and fibroblasts, but it is not known which cells express the gene in vivo. To understand the physiological role of the grn gene products it is necessary to know the context of grn gene expression in vivo. We have isolated the rat grn precursor complementary DNA and determined, by Northern blot analysis and in situ hybridization, the tissue distribution and cellular localization of grn gene expression. The complementary DNA predicts a 589-amino acid protein of M(r) 63,500 with seven and one-half grn repeats arranged in tandem and shows an overall identity of 75% with human progrn. The grn gene is expressed in a variety of tissues derived from all three embryonic germ layers but is most abundant in the spleen and several tissues of endocrine significance including the adrenal glands, epididymis, placenta, and ovary. Although widely expressed in tissues, gene expression is restricted to specific cell types. For example in the kidney, grn messenger RNA was detected in epithelial cells of the proximal and distal convoluted tubules and Bowman's capsule but not in medullary epithelia. In the spleen, grn messenger RNA expression was localized in lymphocytes, whereas hybridization signals were detected over scattered hepatocytes in the liver. Thus, although the grn gene is widely expressed in tissues and cell lines of many lineages in vitro, its expression in situ is restricted to hematopoietic and some epithelial cells. The restricted cell distribution suggests that the expression of the grn gene is more closely regulated in vivo than in cell cultures. Its localization to epithelial cells in situ supports an autocrine or paracrine role for these factors.
Three dimensional polarization sensitive OCT of human skin in vivo (2004)

We present three dimensional images of backscattered intensity, and to the best of our knowledge, the first 3D-images of retardation and fast axis orientation of human skin in vivo. The images were recorded with a phase resolved, polarization sensitive optical coherence tomography (OCT) system which is based on a fast transversal scanning of the sample. The three dimensional data sets were obtained by recording several en face images at different depths within the sample. Intensity and retardation images are combined to a 4 dimensional animation to enhance the visualization of the three dimensional data set. The three dimensional information enables a more accurate interpretation of the structural and birefringence information as compared to 2 dimensional B-scans. Birefringence properties of different skin regions are presented and discussed.
The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic (2014)

An expert panel was convened in October 2013 by the International Scientific Association for Probiotics and Prebiotics (ISAPP) to discuss the field of probiotics. It is now 13 years since the definition of probiotics and 12 years after guidelines were published for regulators, scientists and industry by the Food and Agriculture Organization of the United Nations and the WHO (FAO/WHO). The FAO/WHO definition of a probiotic--"live microorganisms which when administered in adequate amounts confer a health benefit on the host"--was reinforced as relevant and sufficiently accommodating for current and anticipated applications. However, inconsistencies between the FAO/WHO Expert Consultation Report and the FAO/WHO Guidelines were clarified to take into account advances in science and applications. A more precise use of the term 'probiotic' will be useful to guide clinicians and consumers in differentiating the diverse products on the market. This document represents the conclusions of the ISAPP consensus meeting on the appropriate use and scope of the term probiotic.
A sensory neuron-specific, proton-gated ion channel (1998)

Proton-gated channels expressed by sensory neurons are of particular interest because low pH causes pain. Two proton-gated channels, acid-sensing ionic channel (ASIC) and dorsal root ASIC (DRASIC), that are members of the amiloride-sensitive ENaC/Degenerin family are known to be expressed by sensory neurons. Here, we describe the cloning and characterization of an ASIC splice variant, ASIC-beta, which contains a unique N-terminal 172 aa, as well as unique 5' and 3' untranslated sequences. ASIC-beta, unlike ASIC and DRASIC, is found only in a subset of small and large diameter sensory neurons and is absent from sympathetic neurons or the central nervous system. The patterns of expression of ASIC and ASIC-beta transcripts in rat dorsal root ganglion neurons are distinct. When expressed in COS-7 cells, ASIC-beta forms a functional channel with electrophysiological properties distinct from ASIC and DRASIC. The pH dependency and sensitivity to amiloride of ASIC-beta is similar to that described for ASIC, but unlike ASIC, the channel is not permeable to calcium, nor are ASIC-beta-mediated currents inhibited by extracellular calcium. The unique distribution of ASIC-beta suggests that it may play a specialized role in sensory neuron function.
Bolaamphiphiles (2004)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBolaamphiphilesJürgen-Hinrich Fuhrhop and Tianyu WangView Author Information Institut für Organische Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany Cite this: Chem. Rev. 2004, 104, 6, 2901–2938Publication Date (Web):March 12, 2004Publication History Received22 October 2003Published online12 March 2004Published inissue 1 June 2004https://pubs.acs.org/doi/10.1021/cr030602bhttps://doi.org/10.1021/cr030602bresearch-articleACS PublicationsCopyright © 2004 American Chemical SocietyRequest reuse permissionsArticle Views7273Altmetric-Citations552LEARN 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 SUBJECTS:Gold,Hydrophobicity,Membranes,Monolayers,Vesicles Get e-Alerts
Experiences Building an Object-Based Storage System based on the OSD T-10 Standard (2005)

With ever increasing storage demands and management costs, object based storage is on the verge of becoming the next standard storage interface. The American National Standards Institute (ANSI) ratified the object based storage interface standard (also referred to as OSD T-10) in January 2005. In this paper we present our experiences building a reference implementation of the T10 standard based on an initial implementation done at Intel Corporation. Our implementation consists of a file system, object based target and a security manager. To the best of our knowledge, there is no reference implementation suite that is as complete as ours. Efforts are underway to open source our implementation very soon. We also present performance analysis of our implementation and compare it with an iSCSI based SAN and NFS storage configurations. In future, we intend to use this implementation as a platform to explore different forms of storage intelligence.
WNT5A expression in human breast cancer. (2005)

The Wnt family encodes secreted signaling molecules involved in cell adhesion and, by implication, cell growth. Wnt5a has been shown to behave as a putative oncogene and also as a tumour suppressor gene. This is a reflection of its role within a multi-step pathway and in the variety of ways in which its production can be stimulated or switched off. Wnt genes can be functionally separated into two classes; those that activate the canonical Wnt/beta-catenin pathway and those that activate the Wnt/Ca++ pathway. Wnt5a signals through frizzled receptors and, depending upon which frizzled receptor is present, may activate either pathway. Therefore the observed function of Wnt5a is entirely dependent upon its context, hence the confusion over its role in tumorigenesis. This study examines Wnt5a mRNA expression using RT-PCR in human breast cancer.One hundred and twenty malignant breast tumours and 33 normal breast tissues were analysed. The levels of transcription of Wnt5a were determined using real-time quantitative PCR. Levels of expression were analysed against staging, nodal involvement, grade, distant metastasis and survival over a 6-year follow-up period.Levels of Wnt5a mRNA were lower in tumours than in normal tissue (mean values: 107 vs. 62.7). They fell further with increasing stage using the Nottingham Prognostic Index. This became statistically significant when NPI3 was compared to normal tissue (p=0.043, t-test). There was a trend towards lower levels of Wnt5a in those with progressive disease, however, this did not reach statistical significance. In patients with ER-negative disease, lower levels of Wnt5a were significantly associated with a worse clinical outcome (p=0.016).There is a trend for mRNA levels to be lower in cancerous tissue and lower still in those showing more aggressive behaviour. This is consistent with the hypothesis that Wnt5a is a tumour suppressor gene with potential clinical applications.
Peptides with sequences similar to glycine, arginine-rich motifs in proteins interacting with RNA are efficiently recognized by methyltransferase(s) modifying arginine in numerous proteins (1993)

Several proteins that interact with RNA, e.g. the heterogenous ribonucleoprotein particle A and B proteins, fibrillarin and nucleolin, contain the modified amino acid NG,NG-dimethylarginine. Here, we report that two synthetic peptides, Ac-GGRGGFGGRGGFGGRGGFG-NH2 (R3) and GGFGGRGGFG-NH2 (R1), which are based on methylated sequences in fibrillarin and nucleolin, inhibit the methylation of a large majority of the methyl-accepting proteins observed in extracts of adenosine dialdehyde-treated PC12 cells. Concomitantly, the peptides themselves become methylated, suggesting that they compete for the same enzyme that carries out the bulk of N-methylation in PC12 cells. R3 potently inhibits formation of NG,NG-dimethylarginine in PC12 substrates, with a lesser effect on NG-monomethylarginine and NG,N'G-dimethylarginine. Bovine brain contains an activity that methylates PC12 methyl acceptors. After partial purification, the bovine methyltransferase efficiently modifies R3 and R1, yielding half-maximal rates of methylation at approximately 0.2 and approximately 2 microM peptide, respectively. A search of the GenPept database for the FGGRGGF motif revealed 13 candidate methyl acceptors containing arginine and at most two similar substitutions or one mismatch. Of these, 10 are known or presumed to interact with RNA. These findings are consistent with the hypothesis that a majority of proteins containing NG,NG-dimethylarginine interact with RNA.
A Learning Algorithm for Continually Running Fully Recurrent Neural Networks (1989)

The exact form of a gradient-following learning algorithm for completely recurrent networks running in continually sampled time is derived and used as the basis for practical algorithms for temporal supervised learning tasks. These algorithms have (1) the advantage that they do not require a precisely defined training interval, operating while the network runs; and (2) the disadvantage that they require nonlocal communication in the network being trained and are computationally expensive. These algorithms allow networks having recurrent connections to learn complex tasks that require the retention of information over time periods having either fixed or indefinite length.
Gene Expression Signature of Cigarette Smoking and Its Role in Lung Adenocarcinoma Development and Survival (2008)

Our work provides insight into the smoking-related mechanisms of lung neoplasia, and shows that the very mitotic genes known to be involved in cancer development are induced by smoking and affect survival. These genes are candidate targets for chemoprevention and treatment of lung cancer in smokers.
Genetic variability: The key problem in the prevention and therapy of RNA‐based virus infections (2003)

Despite extraordinary progress that has recently been made in biomedical sciences, viral infectious diseases still remain one of the most serious world health problems. Among the different types of viruses, those using RNA as their genetic material (RNA viruses and retroviruses) are especially dangerous. At present there is no medicine allowing an effective treatment of RNA-based virus infections. Many RNA viruses and retroviruses need only a few weeks to escape immune response or to produce drug-resistant mutants. This seems to be the obvious consequence of the unusual genetic variability of RNA-based viruses. An individual virus does not form a homogenous population but rather a set of similar but not identical variants. In consequence, RNA-based viruses can easily adapt to environmental changes, also those resulting from immune system response or therapy. The modifications identified within viral genes can be divided into two groups: point mutations and complex genome rearrangements. The former arises mainly during error-prone replication, whereas RNA recombination and generic reassortment are responsible for the latter. This article shortly describes major strategies used to control virus infections. Then, it presents the various mechanisms generating the genetic diversity of RNA-based viruses, which are most probably the main cause of clinical problems.
Ranking-Dominance and Many-Objective Optimization (2007)

An alternative relation to Pareto-dominance is studied. The relation is based on ranking a set of solutions according to each separate objective and an aggregation function to calculate a scalar fitness value for each solution. The relation is called as ranking-dominance and it tries to tackle the curse of dimensionality commonly observed in multi-objective optimization. Ranking-dominance can be used to sort a set of solutions even for a large number of objectives when the Pareto-dominance relation cannot distinguish solutions from one another anymore. This permits the search to advance even with a large number of objectives. Experimental results indicate that in some cases the selection based on ranking-dominance is able to advance the search towards the Pareto-front better than the selection based on Pareto-dominance. However, in some cases it is also possible that the search does not proceed into direction of the Pareto-front because the ranking-dominance relation permits deterioration of individual objectives. The results also show that when the number of objectives increases, the selection based on just Pareto-dominance without diversity maintenance is able to advance the search better than with diversity maintenance. Therefore, diversity maintenance connives at difficulties solving problems with a high number of objectives.
Templated wide band-gap nanostructures (2004)

In this two-pronged work we report (a) a study of defect nucleation in three-dimensional confined nanoislands and (b) a surface-elasticity induced size effect in the optoelectronic properties of embedded and templated semiconducting nanostructures. Several key features in the design of nanostructure templates are analyzed and dislocation free contour maps are presented for combination of various lattice mismatches, substrates, and geometrical dimensions. Unlike the case for thin epitaxial films, it is found that for nanostructures, below a certain critical lateral dimension, dislocation free structures of any thickness can be grown. With regards to the optoelectronic properties of nanostructures, while size dependency due to quantum confinement and electrostatic interactions are well known, we show that an additional size-dependent strain is caused by the distinct elastic behavior of surfaces and interfaces at the nanoscopic scale compared to the macroscopic scale. This is in contrast to the usual way strain is linked to optoelectronic properties, i.e., via classical elasticity, which ignores surface energies and is intrinsically size independent. Surface strains appear to be only influential in the nanometer regime due to appreciable surface-to-volume ratios. Among our major conclusions are that errors as large as 100 meV in band-gap prediction can incur if this size-dependent surface effect is ignored.
A patatin-like protein with galactolipase activity is induced by drought stress in Vigna unguiculata leaves (2000)

This paper reports the cloning of a cDNA (Vupat 1) expressed in Vigna unguiculata leaves coding for a protein with 48% sequence homology to patatin, the major protein from potato tuber which has lipolytic acylhydrolase activity. Two cultivars differing in drought tolerance were ex-amined in Northern-blot analyses. Expression of Vupat 1 is stimulated by drought stress, especially in the drought-sensitive cultivar. Vupat 1 was expressed in the baculovirus system as a fusion protein secreted in the culture medium. The recombinant protein displays lipolytic activity towards monogalactosyldiacylglycerol, digalactosyldiacylglycerol and sulphoquinovosyldiacylglycerols.
ATM based multimedia servers (1995)

Next-generation multiprocessors will be deployed as servers in a multimedia environment. Current servers cannot handle multimedia traffic internally and effectively deliver the network's high bandwidth to the processing and storage subsystems. Three proposed scalable, subsystem-based, multimedia server architectures use ATM to tackle this problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Advances in immunotherapy of hematologic malignancies (1998)

The chimeric anti-CD20 antibody rituxamab, as well as radiolabeled anti-CD20 monoclonal antibodies, have demonstrated significant activity against B-cell non-Hodgkin's lymphoma. Idiotype vaccination in remission may prevent relapse in follicular non-Hodgkin's lymphoma. The campath-1H antibody has activity in chronic lymphocytic leukemia, and additional unconjugated, radiolabeled, and drug-conjugated monoclonal antibodies (anti-CD45 and anti-CD33) have shown activity in acute myeloid leukemia. Adoptive cellular therapy is active against posttransplantation relapse and lymphoproliferative disorders in most patients, and complications of graft-versus-host disease may be controlled by suicide gene transfection of the donor lymphocytes.