gebhart/patrepeval huggingface dataset:
Plasmid DNA Expressing a Secreted or a Nonsecreted Form of Hepatitis C Virus Nucleocapsid: Comparative Studies of Antibody and T-Helper Responses Following Genetic Immunization (1997)

In a murine model, we have compared humoral and T-helper (Th) responses induced following genetic immunization with two hepatitis C virus (HCV) plasmid-derived immunogens: a plasmid expressing the full-length nucleocapsid (CAP) as a nonsecreted antigen (pCMVC2) and a plasmid expressing the amino-terminal part of CAP as a secreted antigen (pS2S.C2N). In BALB/c mice, intramuscular injection of either plasmid induced IgG2a antibodies associated with a Th1-like profile characterized by the in vitro splenic production of interleukin-2 (IL-2) and interferon-gamma (IFN-gamma). The pS2S.C2N plasmid induced antibody titers three- to five-fold higher than those obtained with the pCMVC2 plasmid (maximal titers 1:1,500 versus 1:500). In control experiments, immunization using purified CAP antigen induced a predominant, but not exclusive, Th2-like profile as determined by the splenic production of IL-4 and IL-10. Six putative Th determinants were identified using a panoply of overlapping synthetic peptides in in vitro stimulation assays: amino acids 20-44, 39-63, 79-113, 89-113, 118-142, and 138-152. For all CAP immunogens, MHC haplotype of immunized mice was found to influence seroconversion rates but not the type of cytokines produced in vitro. H-2d mice were faster responders and displayed recall T-cell activation by a larger number of peptides than H-2b mice, whereas H-2s mice were overall very poor responders. Splenic stimulation by at least one determinant, amino acids 79-103, appeared to be highly specific of the H-2b background and of DNA immunization only. These data indicate that DNA immunogens expressing different forms of HCV-CAP are not associated with different Th profiles but rather different seroconversion rates and antibody titers and that collaboration of distinct T-help epitopes can be restricted by the MHC background.
Studies on ColE1-plasmid DNA and its interactions with histones: sedimentation velocity studies of monodisperse complexes reconstituted with calf-thymus histones (1977)

Complexes between the four calf-thymus histones (H2A, H2B, H3 and H4) and colE1-plasmid DNA have been reconstituted using the procedure of Oudet et al. ((1975), Cell 4, 281-300). The sedimentation rates of the complexes formed were studied under a variety of conditions. In 0.4 MNaCL, 0.1 M Tris pH 7.50, 0.01 M EDTA and 0.02 M NaHSO3, the final dialy-sis-solvent in the reconstitution procedure, the sedimentation coefficients s23 were found to increase when the complexes were reconstituted at increasing histone to DNA ratios. True plateau regions were reached in the case of the relaxed circular and linear forms of the plasmid DNA. The sedimenting boundaries observed for the complexes at saturation are sharp, reflecting a narrow distribution of sedimentation coefficients and a homogeneity of the complex comparable to that of the uncomplexed DNA. Studies of the dependence of s 23 on the concentration of the complex at constant DNA to histones ratio have been undertaken at salt concentrations between 0.4 and 1.5 M NaCL in the above solvent. The formation of the complexes is reversible, at least at the higher ionic strengths. At salt concentrations below 0.36 M the complex precipitates from solution. Omission of histone H4 from the reconstitution mixture abolishes complex formation.
Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples (2004)

Analysis of genomic DNA derived from cells and fresh or fixed tissues often requires whole genome amplification prior to microarray screening. Technical hurdles to this process are the introduction of amplification bias and/or the inhibitory effects of formalin fixation on DNA amplification. Here we demonstrate a balanced-PCR procedure that allows unbiased amplification of genomic DNA from fresh or modestly degraded paraffin-embedded DNA samples. Following digestion and ligation of a target and a control genome with distinct linkers, the two are mixed and amplified in a single PCR, thereby avoiding biases associated with PCR saturation and impurities. We demonstrate genome-wide retention of allelic differences following balanced-PCR amplification of DNA from breast cancer and normal human cells and genomic profiling by array-CGH (cDNA arrays, 100 kb resolution) and by real-time PCR (single gene resolution). Comparison of balanced-PCR with multiple displacement amplification (MDA) demonstrates equivalent performance between the two when intact genomic DNA is used. When DNA from paraffin-embedded samples is used, balanced PCR overcomes problems associated with modest DNA degradation and produces unbiased amplification whereas MDA does not. Balanced-PCR allows amplification and recovery of modestly degraded genomic DNA for subsequent retrospective analysis of human tumors with known outcomes.
Biocompatible CdSe−ZnS Core−Shell Quantum Dots Coated with Hydrophilic Polythiols (2009)

We designed four polymeric ligands for semiconductor quantum dots and synthesized these macromolecular constructs in four steps, starting from commercial precursors. These ligands have a poly(methacrylate) backbone with pendant thiol groups and poly(ethylene glycol) chains. The thiol groups anchor these ligands on the surface of preformed CdSe-ZnS core-shell quantum dots, and the poly(ethylene glycol) chains impose hydrophilic character on the resulting assemblies. Indeed, three of the four sets of quantum dots are soluble in aqueous environments and are stable under these conditions for days over a wide pH range (5.0-9.0). Furthermore, the polymeric coatings wrapped around the inorganic nanoparticles preserve the photophysical properties of the CdSe core and ensure relatively compact dimensions. Specifically, the luminescence quantum yield is ca. 0.4 and the hydrodynamic diameter ranges from 15 to 29 nm with the nature of the polymeric ligand. Model studies with human umbilical vein endothelial cells demonstrated that these hydrophilic quantum dots cross the cell membrane and localize either in the cytosol or in the nucleus. The length of the poly(ethylene glycol) chains appears to guide the intracellular localization of these luminescent probes. In addition, these studies indicated that these particular nanoparticles are not cytotoxic. In fact, their cellular internalization has essentially no influence on cell growth. In summary, we developed novel polymeric ligands able to impose hydrophilic character and biocompatibility on CdSe-ZnS core-shell nanoparticles. Thus, our results can lead to a new family of valuable luminescent probes for cellular imaging, based on the unique photophysical properties of semiconductor quantum dots.
Methodology employed for the structure determination of tumour necrosis factor, a case of high non-crystallographic symmetry (1991)

The structure of the protein tumour necrosis factor (TNF) was determined from crystals of space group P3(1)21 which contain six copies of the TNF monomer per crystallographic asymmetric unit [Jones, Stuart & Walker (1989). Nature (London), 338, 225-228]. The nature of these crystals (relatively high crystallographic symmetry coupled with multiple copies of the protein in the asymmetric unit) led to some peculiarly challenging problems at several points in the structure determination. In particular, (1) self-rotation function calculations failed to yield clearly interpretable solutions, (2) the analysis of difference Patterson maps for heavy-atom derivatives required the development of a Patterson search program suite GROPAT. The redundancy in the asymmetric unit allowed refinement of poor-quality isomorphous phases at 4 A resolution and phase extension from 4 to 2.9 A resolution using real-space symmetry averaging and solvent flattening in the absence of any isomorphous phase information. Despite further difficulties caused by structural differences between the six independent copies of the monomer the resultant electron density map was of high quality and proved to be easily interpretable.
The chemistry of indoles. XXXIX. A facile synthetic method for 7-substituted indoles. (1987)

A simple four-step synthetic method for 7-iodo-, 7-bromo-and 7-chloroindole was established with high overall yield starting from 2, 3-dihydroindole. Several 7-substituted indoles carrying a carbon side chain and 7-methoxyindole were also synthesized.
Cell shape modulation alters glycosylation of a metastatic melanoma cell‐surface antigen (1987)

B16-F1 melanoma cells cultivated in vitro as spheroids on a non-adhesive substrate acquire in a reversible fashion an increase in lung colonization in vivo as compared to cells cultured as a monolayer. After neuraminidase treatment of protein blots, the spheroidal cells expressed an increased binding of 125I-labelled peanut lectin (PNA) to a unique glycoprotein of Mr 78,000 (gp78) which after desialylation migrated in SDS-polyacrylamide gels as an Mr 86,000 protein. Antibodies were generated against this glycoprotein purified on PNA-Sepharose and its expression on the surface of viable B16-F1 cells was demonstrated. Growth of B16-F1 melanoma cells in suspension is associated with the altered glycosylation of gp78 which may be related to the increased metastatic ability of these cells. In vitro treatment of B16-F1 cells with anti-gp78 Fab fragments prior to their injection into the tail veins of syngeneic mice resulted in a 2-fold increase in the appearance of tumor lung colonies.
Light emission by magnetic and electric dipoles close to a plane dielectric interface II Radiation patterns of perpendicular oriented dipoles (1977)

We have derived analytical expressions for the angular distribution P(α) of the power radiated by magnetic or electric dipoles located at distance z0 from a dielectric interface and oriented perpendicular to it. For dipoles in the rarer medium very close to the interface, evanescent waves in the dipoles’ near field give rise to strong radiation into the denser medium. The resulting large maximum of P(α) shows characteristic differences for magnetic and electric dipoles when the relative refractive index of the two dielectrics is greater than √2. For dipoles lying on the interface a symmetry relation is established connecting the power distributions P(α) for the values n and 1/n of the relative refractive index.
Continuous blood pressure monitoring using pulse wave delay (2005)

Proposed paper is a part of a research to develop a convenient method for continuous monitoring of blood pressure by non-invasive and non-oscillometric way. The method is based on a presumption that there is a singular relationship between the velocity of pulse wave and blood pressure for a person. The detection of the velocity of pulse wave is based on the registration of the mechanical movements of blood vessel's walls and computing the time delay in different regions of the human body using an ECG as a reference signal. Additional information about the blood pressure evaluation is gotten from the photoplethysmographic (PPG) channel. Used optical method, which is able to detect pulsation profiles of the blood vessels, is based on the self-mixing that occurs in the diode laser cavity when the radiation, scattered back by the skin into the laser, interferes with the field inside it and causes the changes of the laser pump current. National Instruments software LabView for Windows is used for output signal digitalization and processing purposes.
Adsorption and surface structural chemistry of thiophenol, benzyl mercaptan, and alkyl mercaptans. Comparative studies at silver(111) and platinum(111) electrodes by means of Auger spectroscopy, electron energy loss spectroscopy, low energy electron diffraction and electrochemistry (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdsorption and surface structural chemistry of thiophenol, benzyl mercaptan, and alkyl mercaptans. Comparative studies at silver(111) and platinum(111) electrodes by means of Auger spectroscopy, electron energy loss spectroscopy, low energy electron diffraction and electrochemistryJohn Y. Gui, Donald A. Stern, Douglas G. Frank, Frank. Lu, Donald C. Zapien, and Arthur T. HubbardCite this: Langmuir 1991, 7, 5, 955–963Publication Date (Print):May 22, 1991Publication History Published online1 May 2002Published inissue 22 May 1991https://pubs.acs.org/doi/10.1021/la00053a024https://doi.org/10.1021/la00053a024research-articleACS PublicationsRequest reuse permissionsArticle Views1181Altmetric-Citations110LEARN 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
Inclusion-body myositis (2006)

Sporadic inclusion-body myositis (s-IBM), the most common muscle disease of older persons, is of unknown cause and there is no successful treatment. We summarize our most recent findings, which provide a better understanding of the steps in the pathogenetic cascade. We suggest that s-IBM is primarily a myodegenerative disease. Intriguing are the phenotypic similarities between s-IBM muscle fibers and the brains of Alzheimer disease, the most common neurodegenerative disease of older persons. In s-IBM, abnormal accumulation of the amyloid-beta (Abeta) precursor protein and its proteolytic fragment, Abeta, associated with the aging intracellular milieu of the muscle fiber, appear to be key upstream pathogenic events. We propose that the identified abnormal accumulation, misfolding, and aggregation of proteins, perhaps provoked by the aging milieu and aggravated by the oxidative stress, lead to the s-IBM-specific vacuolar degeneration and atrophy of muscle fibers.
Exon/intron organization of the gene encoding the mouse epithelin/granulin precursor (acrogranin) (1993)

Mouse genomic clones encoding the epithelin/granulin gene and its 5'- and 3'-flanking regions have been isolated and sequenced. This gene was found to be a single-copy gene, and contained 13 exons interrupted by 12 introns. Eight out of the 12 introns are classified as phase 0, and are located within the central part of each of the tandem repeats in the amino acid sequence of the epithelin/granulin precursor. The first intron is unique because of the interruption of the 5'-untranslated region and its fairly large size (approximately 2.4 kbp). Consensus sequences for several of the potential regulatory elements are present in the 5'-flanking sequence, including a common CCAAT sequence.
Importance of Estrogen Receptors in Hepatic LDL Receptor Regulation (1997)

Treatment with pharmacological doses of estrogen is the most potent way to stimulate hepatic LDL receptor expression in vivo. The mechanism for this effect is unclear, in part because of difficulties in inducing this stimulation in vitro. A fundamental question, whether estrogen receptors (ERs) mediate this stimulation, has not been addressed. The aim of the current study was to determine the involvement of ERs in the estrogen-induced stimulation of LDL receptors. Treatment of rats with high doses of ethynylestradiol for 7 days increased the hepatic LDL receptor protein and mRNA levels four- and threefold, respectively. LDL receptor stimulation in estrogen-treated rats was not due to their reduced food intake because hepatic LDL receptor expression did not increase in rats fasted for 72 hours. Treatment with antiestrogen (tamoxifen or clomiphene) abolished the LDL receptor stimulatory effect of ethynylestradiol at both the protein and mRNA levels. Antiestrogen alone had no effect on hepatic LDL receptor expression and did not influence the strong resistance to dietary cholesterol normally present in rats. It is concluded that ERs are critically involved in the induction of hepatic LDL receptor expression by ethynylestradiol. The known role of growth hormone for the expression of hepatic ERs may therefore play a role in the modulation of the effects of estrogen on cholesterol metabolism and hepatic LDL receptors in the rat.
JAK inhibition alleviates the cellular senescence-associated secretory phenotype and frailty in old age (2015)

Chronic, low grade, sterile inflammation frequently accompanies aging and age-related diseases. Cellular senescence is associated with the production of proinflammatory chemokines, cytokines, and extracellular matrix (ECM) remodeling proteases, which comprise the senescence-associated secretory phenotype (SASP). We found a higher burden of senescent cells in adipose tissue with aging. Senescent human primary preadipocytes as well as human umbilical vein endothelial cells (HUVECs) developed a SASP that could be suppressed by targeting the JAK pathway using RNAi or JAK inhibitors. Conditioned medium (CM) from senescent human preadipocytes induced macrophage migration in vitro and inflammation in healthy adipose tissue and preadipocytes. When the senescent cells from which CM was derived had been treated with JAK inhibitors, the resulting CM was much less proinflammatory. The administration of JAK inhibitor to aged mice for 10 wk alleviated both adipose tissue and systemic inflammation and enhanced physical function. Our findings are consistent with a possible contribution of senescent cells and the SASP to age-related inflammation and frailty. We speculate that SASP inhibition by JAK inhibitors may contribute to alleviating frailty. Targeting the JAK pathway holds promise for treating age-related dysfunction.
Adenine nucleotide changes in the remnant liver: An early signal for regeneration after partial hepatectomy (2008)

The rapid loss of adenine nucleotides after PHx generates early stress signals that contribute to the onset of liver regeneration.
Bcl-2 antisense oligonucleotides are effective against systemic but not central nervous system disease in severe combined immunodeficient mice bearing human t(14;18) follicular lymphoma. (2002)

The t(14;18) is present in 85-90% of follicular lymphomas. It results in overexpression of the Bcl-2 protein, which inhibits apoptosis and plays a role in lymphomagenesis. Bcl-2 antisense oligonucleotides (ODNs) down-regulate Bcl-2 expression and inhibit growth of the follicular lymphoma cell line WSU-FSCCL. In this study, we have established a human lymphoma xenograft model in severe combined immunodeficient (SCID) mice using the WSU-FSCCL cell line. s.c., i.v., or i.p. injection of WSU-FSCCL cells into SCID mice results in the development of disseminated tumors, with the liver, spleen, bone marrow, and lymph nodes as major sites of disease. Tumors were fatal in 7-14 weeks, depending on cell inoculum and route of administration. Immunohistochemistry, flow cytometry, and cytogenetic analysis confirmed the human B-cell origin of tumor cells in the xenograft. Phosphorothioate ODNs against the translation initiation site of bcl-2 mRNA in the antisense and mismatched antisense sequences were administered i.v. or i.p. to the xenograft models three times a week for 2 weeks, starting on day 7 after tumor injections. Antisense-treated animals had significantly longer survival (mean, 11.6 weeks) compared with 7.6 weeks for the control group and 7.5 weeks for the mismatched antisense-treated animals (P = 0.002 and 0.004, respectively). More significantly, a pathological examination showed no tumor in the liver, spleen, or bone marrow of the antisense group. However, subsequent experiments showed that the central nervous system was involved, causing mice to die although other sites were disease free. We conclude that bcl-2 antisense ODN therapy is effective against systemic FSCCL disease in SCID mice xenografts; however, it does not prevent disease dissemination into the central nervous system causing animal death.
INHIBITION OF MAMMALIAN GLUCOSE-6-PHOSPHATE DEHYDROGENASE BY STEROIDS (1960)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
MUC1 Expression Is Correlated With Nuclear Grade and Tumor Progression in pT1 Renal Clear Cell Carcinoma (2002)

We studied, by immunohistochemical analysis, the expression of MUC1 and epithelial membrane antigen in 44 stage pT1 renal cell carcinomas (RCCs). Six patients had a metastatic evolution. The percentage of stained cells was determined for each tumor. All tumors and normal adjacent renal parenchyma were stained. In normal kidney, distal convoluted tubules and collecting ducts stained strongly with an apical distribution. In tumors, there was a significant statistical correlation of the MUC1 expression level with the nuclear grade and with tumor progression. High-grade tumors had more stained cells than did low-grade tumors. Metastatic tumors also were more stained than nonmetastatic lesions. By using the Kaplan-Meier method and the log-rank test, we observed that patients with fewer than 10% of stained cells had no metastatic evolution. In contrast, patients with 70% or more stained cells had significantly lower metastasis-free survival rates. We conclude that MUC1 is expressed in RCC and is associated with tumor progression in pT1 RCC.
A shortest path dependency kernel for relation extraction (2005)

We present a novel approach to relation extraction, based on the observation that the information required to assert a relationship between two named entities in the same sentence is typically captured by the shortest path between the two entities in the dependency graph. Experiments on extracting top-level relations from the ACE (Automated Content Extraction) newspaper corpus show that the new shortest path dependency kernel outperforms a recent approach based on dependency tree kernels.