gebhart/patrepeval huggingface dataset:
Overexpression of ribosomal RNA in prostate cancer is common but not linked to rDNA promoter hypomethylation (2011)

Alterations in nucleoli, including increased numbers, increased size, altered architecture and increased function are hallmarks of prostate cancer cells. The mechanisms that result in increased nucleolar size, number and function in prostate cancer have not been fully elucidated. The nucleolus is formed around repeats of a transcriptional unit encoding a 45S ribosomal RNA (rRNA) precursor that is then processed to yield the mature 18S, 5.8S and 28S RNA species. Although it has been generally accepted that tumor cells overexpress rRNA species, this has not been examined in clinical prostate cancer. We find that indeed levels of the 45S rRNA, 28S, 18S and 5.8S are overexpressed in the majority of human primary prostate cancer specimens as compared with matched benign tissues. One mechanism that can alter nucleolar function and structure in cancer cells is hypomethylation of CpG dinucleotides of the upstream rDNA promoter region. However, this mechanism has not been examined in prostate cancer. To determine whether rRNA overexpression could be explained by hypomethylation of these CpG sites, we also evaluated the DNA methylation status of the rDNA promoter in prostate cancer cell lines and the clinical specimens. Bisulfite sequencing of genomic DNA revealed two roughly equal populations of loci in cell lines consisting of those that contained densely methylated deoxycytidine residues within CpGs and those that were largely unmethylated. All clinical specimens also contained two populations with no marked changes in methylation of this region in cancer as compared with normal. We recently reported that MYC can regulate rRNA levels in human prostate cancer; here we show that MYC mRNA levels are correlated with 45S, 18S and 5.8S rRNA levels. Further, as a surrogate for nucleolar size and number, we examined the expression of fibrillarin, which did not correlate with rRNA levels. We conclude that rRNA levels are increased in human prostate cancer, but that hypomethylation of the rDNA promoter does not explain this increase, nor does hypomethylation explain alterations in nucleolar number and structure in prostate cancer cells. Rather, rRNA levels and nucleolar size and number relate more closely to MYC overexpression.
Glycoprotein VI is the collagen receptor in platelets which underlies tyrosine phosphorylation of the Fc receptor γ‐chain (1997)

We have recently shown that collagen activates platelets through a pathway dependent on the Fc receptor gamma-chain and the tyrosine kinase Syk. We report here that the Fc receptor gamma-chain and the candidate collagen receptor glycoprotein VI (GPVI) co-associate. Furthermore, cross-linking GPVI stimulates a similar pattern of tyrosine phosphorylation to that stimulated by collagen, including tyrosine phosphorylation of Fc receptor gamma-chain. These results support a model where GPVI couples collagen-stimulation of platelets to phosphorylation of the Fc receptor gamma-chain leading to activation of Syk and phospholipase Cgamma2.
Combination of Sleeping Beauty transposition and chemically induced dimerization selection for robust production of engineered cells (2012)

The main methods for producing genetically engineered cells use viral vectors for which safety issues and manufacturing costs remain a concern. In addition, selection of desired cells typically relies on the use of cytotoxic drugs with long culture times. Here, we introduce an efficient non-viral approach combining the Sleeping Beauty (SB) Transposon System with selective proliferation of engineered cells by chemically induced dimerization (CID) of growth factor receptors. Minicircles carrying a SB transposon cassette containing a reporter transgene and a gene for the F36VFGFR1 fusion protein were delivered to the hematopoietic cell line Ba/F3. Stably-transduced Ba/F3 cell populations with >98% purity were obtained within 1 week using this positive selection strategy. Copy number analysis by quantitative PCR (qPCR) revealed that CID-selected cells contain on average higher copy numbers of transgenes than flow cytometry-selected cells, demonstrating selective advantage for cells with multiple transposon insertions. A diverse population of cells is present both before and after culture in CID media, although site-specific qPCR of transposon junctions show that population diversity is significantly reduced after selection due to preferential expansion of clones with multiple integration events. This non-viral, positive selection approach is an attractive alternative for producing engineered cells.
Stability analysis of an intracavity pumped OPO (2013)

Simulation of quasi-phase-matching processes for ultrafast pulses in an intracavity pumped OPO is presented. Results reveal an effective cross phase modulation which introduces the coupling between OPO and pump cavities.
Astrocytes protect neurons from hydrogen peroxide toxicity (1996)

Recent reports indicate that neurons are particularly sensitive to hydrogen peroxide (H2O2). The present study was undertaken to investigate the putative role of astrocytes in the modulation of the neurotoxic effect of H2O2. The exposure to H2O2 of cultured striatal neurons from mouse embryos induced a concentration-dependent (10-1000 microM) cell death as estimated 24 hr later. Two methods were used to estimate neuronal survival: the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assay or an enzyme-linked immunosorbent assay with antibodies directed against an antigen located in neurons (microtubule-associated protein-2). The neurotoxic effect of H2O2 on neurons cocultured with astrocytes was strongly attenuated compared with that observed on a pure population of neurons seeded at the same density. Moreover, the protective effect of astrocytes depended on the astrocytes/neurons ratio, a significant neuroprotection being detectable for 1 astrocyte to 20 neurons. Catalase seems to be the main hydrogen peroxidase activity involved in the neuroprotective effect of astrocytes. Indeed, in the culture conditions used, this enzymatic activity was enriched in this cell type compared with neurons; its inhibition, and not that of glutathione peroxidase, reduced the disappearance rate of the oxidant. On the contrary, glutathione peroxidase appeared to be the main enzymatic activity involved in the neuronal defense against H2O2 toxicity. Therefore, astrocytes could delay neuronal death in pathological situations in which H2O2 has been, at least partially, demonstrated to be involved.
Optical antennas for nano-photonic applications (2005)

Antenna-coupled optical detectors, also named optical antennas, are being developed and proposed as alternative detection devices for the millimetre, infrared, and visible spectra. Optical and infrared antennas represent a class of optical components that couple electromagnetic radiation in the visible and infrared wavelengths in the same way as radioelectric antennas do at the corresponding wavelengths. The size of optical antennas is in the range of the detected wavelength and they involve fabrication techniques with nanoscale spatial resolution. Optical antennas have already proved and potential advantages in the detection of light showing polarization dependence, tuneability, and rapid time response. They also can be considered as point detectors and directionally sensitive elements. So far, these detectors have been thoroughly tested in the mid-infrared with some positive results in the visible. The measurement and characterization of optical antennas requires the use of an experimental set-up with nanometric resolution. On the other hand, a computation simulation of the interaction between the material structures and the incoming electromagnetic radiation is needed to explore alternative designs of practical devices. © 2005 IOP Publishing Ltd.
In search of candidate genes critically expressed in the human endometrium during the window of implantation (2005)

Using a strict bioinformatics approach of microarray data, we demonstrated significant changes in candidate genes during the transition of the early to the mid-luteal phase of the human endometrium that may have functional significance for the opening and maintenance of the window of implantation.
Synthesis and biological activity of some 8-substituted selenoguanosine cyclic 3',5'-phosphates and related compounds (1975)

8-Bromoguanosine cyclic 3',5'-monophosphate, 8-bromoguanosine 5'-monophosphate, and 8-bromoguanosine served as intermediates for the chemical synthesis of a series of 8-substituted seleno cyclic nucleotides, nucleotides, and their nucleosides. Selenourea was found to be a useful reagent in synthesizing these seleno-substituted nucleoside, nucleotide, and cyclic nucleotide. A nucleic acid analyzer was used to study the hydrolysis of these cyclic nucleotides by phosphodiesterase. It was found that all of the 8-substituted selenoguanosine cyclic 3',5'-phosphates synthesized, except 8-MeSe-cGMP, were resistant to hydrolyze by phosphodiesterase. These 8-substituted seleno cyclic GMP derivatives showed some antitumor activities against murine leukemic cells (L5178Y) in vitro and in vivo.
Chemical Vapor Deposition of HfO[sub 2] Thin Films Using a Novel Carbon-Free Precursor: Characterization of the Interface with the Silicon Substrate (2002)

thin films were deposited on Si wafers by a chemical vapor deposition (CVD) technique at temperatures ranging from 200 to 400°C using a new carbon-free precursor The growth behavior was under a steady state when the interfacial oxide layer was excluded in film thickness estimation by ellipsometry. The as-grown interfacial layer formed at 200°C was apparently composed of Hf, Si, and O. Postannealing under a atmosphere at temperatures >500°C resulted in a decrease in interfacial layer thickness by decomposition of the Hf-Si-O layer to and The film showed a crystalline microstructure even in the as-deposited state when the film thickness was 170 Å. However, the films were amorphous when the film thickness was <70 Å. The dielectric constant of the as-deposited and postannealed thin films were approximately 18 and 22, respectively. © 2001 The Electrochemical Society. All rights reserved.
Mixed-Disulfide Folding Intermediates between Thyroglobulin and Endoplasmic Reticulum Resident Oxidoreductases ERp57 and Protein Disulfide Isomerase (2005)

We present the first identification of transient folding intermediates of endogenous thyroglobulin (Tg; a large homodimeric secretory glycoprotein of thyrocytes), which include mixed disulfides with endogenous oxidoreductases servicing Tg folding needs. Formation of disulfide-linked Tg adducts with endoplasmic reticulum (ER) oxidoreductases begins cotranslationally. Inhibition of ER glucosidase activity blocked formation of a subgroup of Tg adducts containing ERp57 while causing increased Tg adduct formation with protein disulfide isomerase (PDI), delayed adduct resolution, perturbed oxidative folding of Tg monomers, impaired Tg dimerization, increased Tg association with BiP/GRP78 and GRP94, activation of the unfolded protein response, increased ER-associated degradation of a subpopulation of Tg, partial Tg escape from ER quality control with increased secretion of free monomers, and decreased overall Tg secretion. These data point towards mixed disulfides with the ERp57 oxidoreductase in conjunction with calreticulin/calnexin chaperones acting as normal early Tg folding intermediates that can be "substituted" by PDI adducts only at the expense of lower folding efficiency with resultant ER stress.
Molecular Characterization of a Novel, Widespread Nuclear Protein That Colocalizes with Spliceosome Components (1998)

We report the identification and molecular characterization of a novel type of constitutive nuclear protein that is present in diverse vertebrate species, from Xenopus laevis to human. The cDNA-deduced amino acid sequence of the Xenopus protein defines a polypeptide of a calculated mass of 146.2 kDa and a isoelectric point of 6.8, with a conspicuous domain enriched in the dipeptide TP (threonine-proline) near its amino terminus. Immunolocalization studies in cultured cells and tissues sections of different origin revealed an exclusive nuclear localization of the protein. The protein is diffusely distributed in the nucleoplasm but concentrated in nuclear speckles, which represent a subnuclear compartment enriched in small nuclear ribonucleoprotein particles and other splicing factors, as confirmed by colocalization with certain splicing factors and Sm proteins. During mitosis, when transcription and splicing are downregulated, the protein is released from the nuclear speckles and transiently dispersed throughout the cytoplasm. Biochemical experiments have shown that the protein is recovered in a approximately 12S complex, and gel filtration studies confirm that the protein is part of a large particle. Immunoprecipitation and Western blot analysis of chromatographic fractions enriched in human U2 small nuclear ribonucleoprotein particles of distinct sizes (12S, 15S, and 17S), reflecting their variable association with splicing factors SF3a and SF3b, strongly suggests that the 146-kDa protein reported here is a constituent of the SF3b complex.
Limitations of the Odds Ratio in Gauging the Performance of a Diagnostic, Prognostic, or Screening Marker (2004)

A marker strongly associated with outcome (or disease) is often assumed to be effective for classifying persons according to their current or future outcome. However, for this assumption to be true, the associated odds ratio must be of a magnitude rarely seen in epidemiologic studies. In this paper, an illustration of the relation between odds ratios and receiver operating characteristic curves shows, for example, that a marker with an odds ratio of as high as 3 is in fact a very poor classification tool. If a marker identifies 10% of controls as positive (false positives) and has an odds ratio of 3, then it will correctly identify only 25% of cases as positive (true positives). The authors illustrate that a single measure of association such as an odds ratio does not meaningfully describe a marker's ability to classify subjects. Appropriate statistical methods for assessing and reporting the classification power of a marker are described. In addition, the serious pitfalls of using more traditional methods based on parameters in logistic regression models are illustrated.
Ligation of CD69 induces apoptosis and cell death in human eosinophils cultured with granulocyte-macrophage colony-stimulating factor (1996)

Peripheral blood (PB) eosinophils rapidly undergo apoptosis and cell death in vitro unless cultured in the presence of cytokines such as granulocyte-macrophage colony-stimulating factor (GM-CSF) in which their survival is prolonged for up to 10 days. CD69 is a type II membrane antigen expressed by cytokine-activated, but not freshly isolated, PB human eosinophils. We have examined the effect of ligation of CD69 by specific monoclonal antibody (MoAb) on the viability of human eosinophils cultured with recombinant human (rh)GM-CSF. Eosinophils were purified by immunomagnetic selection and cultured with GM-CSF (10(-10) mol/L). Eighteen hours after the start of culture, a panel of CD69 MoAb or controls (anti-CR3 or isotype-matched control MoAb) were added. Viability was assessed by trypan blue exclusion and apoptosis by morphologic assessment, DNA laddering, and flow cytometric analysis of eosinophil red autofluorescence. Up to 50% of the eosinophils had undergone apoptosis 48 hours after addition of anti-CD69 MoAb compared with less than 10% apoptosis for CR3 or the isotype matched control. The majority of apoptotic eosinophils excluded trypan blue at 48 hours post CD69 ligation. More apoptotic eosinophils were observed at later time-points and this was associated with loss of viability. At 120 hours post-addition of the anti-CD69 MoAb MLR3, 24% +/- 10.6% eosinophils were viable compared with 84% +/- 3.4% for the CR3 control (P < .001). A F(ab)2 fragment of CD69 MoAb P8, also induced apoptosis in GM-CSF cultured eosinophils. A more rapid induction of eosinophil apoptosis was obtained with CD69 MoAb immobilized via their Fc portions on protein-A coated plastic 96 well plates. Ligation of CD69 or CR3 resulted in the release of comparable quantities of eosinophil peroxidase at 48 hours post-ligation. These levels of EPO were consistent with the viability of these cells at 48 hours as assessed by exclusion of trypan blue. Finally, a neutralizing MoAb to TGF beta 1 had no effect on CD69-dependent apoptosis induction nor were there detectable quantities of TGF beta 1 in supernatants from GM-CSF--cultured eosinophils ligated with CD69 or control MoAb. These results suggest that eosinophils cultured with GM-CSF can be induced to undergo apoptosis as a result of cell signalling mediated by perturbation of CD69. This may represent an important physiologic mechanism for eosinophil removal in vivo.
Pharmacotherapy of gastroparesis (2009)

Gastroparesis is a relatively common and often disabling condition that is characterized by a broad range of clinical presentation ranging from dyspeptic symptoms to nausea, vomiting, abdominal pain, malnutrition, frequent hospitalizations and incapacitation. The treatment of gastroparetic symptoms can be challenging to the gastroenterologist and the intensity of therapy varies with the physician's knowledge. Hence the determination that a patient is refractory to 'standard medical therapy' is an assessment that is subspeciality-based and could differ around the world depending on medications available. In this article, we review the use of available prokinetics, antiemetic agents, the approach for analgesia in the context of gastroparesis, and also discuss potential and evolving pharmacotherapies. The progress has been relatively limited as far as availability of new medications for gastroparesis is concerned; however, active research in developing newer prokinetics holds great promise for the future of management of this challenging entity.
Towards a user environment integrating hypermedia browsers, scientific visualization programs and numerical simulation programs (1994)

The success of projects like CERN World Wide Web has spurred the development of many hypermedia browsers on Internet. One of them, NCSA Mosaic, has a rather sophisticated ability of supporting user defined layouts of widgets, comparable to what is available in simple interface builders, and can be easily interfaced to other programs. In this article we will describe an experimental set-up that tries to explore the possibility of integrating, under a single user interface: a) hypermedia document browsing b) data feeding to scientific visualization programs c) parameter feeding and running numerical simulation programs.
Signaling networks in joint development (2016)

Here we review studies identifying regulatory networks responsible for synovial, cartilaginous, and fibrous joint development. Synovial joints, characterized by the fluid-filled synovial space between the bones, are found in high-mobility regions and are the most common type of joint. Cartilaginous joints such as the intervertebral disc unite adjacent bones through either a hyaline cartilage or a fibrocartilage intermediate. Fibrous joints, which include the cranial sutures, form a direct union between bones through fibrous connective tissue. We describe how the distinct morphologic and histogenic characteristics of these joint classes are established during embryonic development. Collectively, these studies reveal that despite the heterogeneity of joint strength and mobility, joint development throughout the skeleton utilizes common signaling networks via long-range morphogen gradients and direct cell-cell contact. This suggests that different joint types represent specialized variants of homologous developmental modules. Identifying the unifying aspects of the signaling networks between joint classes allows a more complete understanding of the signaling code for joint formation, which is critical to improving strategies for joint regeneration and repair. Developmental Dynamics 246:262-274, 2017. © 2016 Wiley Periodicals, Inc.
Preparation and characterization of sulfanilazo and arsanilazo proteins (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and characterization of sulfanilazo and arsanilazo proteinsGary J. Pielak, Mickey S. Urdea, and J. Ivan LeggCite this: Biochemistry 1984, 23, 4, 596–603Publication Date (Print):February 14, 1984Publication History Published online1 May 2002Published inissue 14 February 1984https://pubs.acs.org/doi/10.1021/bi00299a003https://doi.org/10.1021/bi00299a003research-articleACS PublicationsRequest reuse permissionsArticle Views96Altmetric-Citations8LEARN 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
Ovarian Cancer Cell Detachment and Multicellular Aggregate Formation Are Regulated by Membrane Type 1 Matrix Metalloproteinase: A Potential Role in I.p. Metastatic Dissemination (2009)

An early event in the metastasis of epithelial ovarian carcinoma is shedding of cells from the primary tumor into the peritoneal cavity followed by diffuse i.p. seeding of secondary lesions. Anchorage-independent metastatic cells are present as both single cells and multicellular aggregates (MCA), the latter of which adhere to and disaggregate on human mesothelial cell monolayers, subsequently forming invasive foci. Although this unique metastatic mechanism presents a distinct set of therapeutic challenges, factors that regulate MCA formation and dissemination have not been extensively evaluated. Proteolytic activity is important at multiple stages in i.p. metastasis, catalyzing migration through the mesothelial monolayer and invasion of the collagen-rich submesothelial matrix to anchor secondary lesions, and acquisition of membrane type 1 matrix metalloproteinase (MT1-MMP; MMP-14) expression promotes a collagen-invasive phenotype in ovarian carcinoma. MT1-MMP is regulated posttranslationally through multiple mechanisms including phosphorylation of its cytoplasmic tail, and the current data using ovarian cancer cells expressing wild-type, phosphomimetic (T567E-MT1-MMP), and phosphodefective (T567A-MT1-MMP) MT1-MMP show that MT1-MMP promotes MCA formation. Confluent T567E-MT1-MMP-expressing cells exhibit rapid detachment kinetics, spontaneous release as cell-cell adherent sheets concomitant with MT1-MMP-catalyzed alpha(3) integrin ectodomain shedding, and robust MCA formation. Expansive growth within three-dimensional collagen gels is also MT1-MMP dependent, with T567E-MT1-MMP-expressing cells exhibiting multiple collagen invasive foci. Analysis of human ovarian tumors shows elevated MT1-MMP in metastases relative to paired primary tumors. These data suggest that MT1-MMP activity may be key to ovarian carcinoma metastatic success by promoting both formation and dissemination of MCAs.