gebhart/patrepeval huggingface dataset:
Conditional Expression of the CTCF-Paralogous Transcriptional Factor BORIS in Normal Cells Results in Demethylation and Derepression of MAGE-A1 and Reactivation of Other Cancer-Testis Genes (2005)

Brother of the Regulator of Imprinted Sites (BORIS) is a mammalian CTCF paralog with the same central 11Zn fingers (11ZF) that mediate specific interactions with varying approximately 50-bp target sites. Regulated in vivo occupancy of such sites may yield structurally and functionally distinct CTCF/DNA complexes involved in various aspects of gene regulation, including epigenetic control of gene imprinting and X chromosome inactivation. The latter functions are mediated by meCpG-sensitive 11ZF binding. Because CTCF is normally present in all somatic cells, whereas BORIS is active only in CTCF- and 5-methylcytosine-deficient adult male germ cells, switching DNA occupancy from CTCF to BORIS was suggested to regulate site specificity and timing of epigenetic reprogramming. In addition to 11ZF-binding paternal imprinting control regions, cancer-testis gene promoters also undergo remethylation during CTCF/BORIS switching in germ cells. Only promoters of cancer testis genes are normally silenced in all somatic cells but activated during spermatogenesis when demethylated in BORIS-positive germ cells and are found aberrantly derepressed in various tumors. We show here that BORIS is also expressed in multiple cancers and is thus itself a cancer-testis gene and that conditional expression of BORIS in normal fibroblasts activates cancer-testis genes selectively. We tested if replacement of CTCF by BORIS on regulatory DNA occurs in vivo on activation of a prototype cancer-testis gene, MAGE-A1. Transition from a hypermethylated/silenced to a hypomethylated/activated status induced in normal cells by 5-aza-2'-deoxycytidine (5-azadC) was mimicked by conditional input of BORIS and is associated with complete switching from CTCF to BORIS occupancy at a single 11ZF target. This site manifested a novel type of CTCF/BORIS 11ZF binding insensitive to CpG methylation. Whereas 5-azadC induction of BORIS takes only few hours, derepression of MAGE-A1 occurred 1 to 2 days later, suggesting that BORIS mediates cancer-testis gene activation by 5-azadC. Indeed, infection of normal fibroblasts with anti-BORIS short hairpin RNA retroviruses before treatment with 5-azadC blocked reactivation of MAGE-A1. We suggest that BORIS is likely tethering epigenetic machinery to a novel class of CTCF/BORIS 11ZF target sequences that mediate induction of cancer-testis genes.
Early Posttransplant Serum Osteoprotegerin Levels Predict Long-Term (8-Year) Patient Survival and Cardiovascular Death in Renal Transplant Patients (2006)

The primary objectives of this analysis were to examine the effects of early posttransplantation (10 wk) serum levels of osteoprotegerin (OPG), mannose-binding lectin (MBL), and MBL-associated serine proteases (MASP; MASP-2 and MASP-3) on long-term (8-yr) patient survival, graft survival, and cardiovascular (CV) death. During a period of 16 mo (1995 to 1996), a total of 173 consecutive renal transplant recipients without diabetes before transplantation were included in a prospective study that was designed to address the impact of metabolic CV risk factors on survival and CV end points. Baseline sera from 172 patients were available for analysis. Follow-up data until January 1, 2004, were obtained from a national renal registry. Patients with high (fourth quartile) serum levels of OPG had significantly higher all-cause mortality (hazard ratio [HR] 6.3; 95% confidence interval [CI] 3.3 to 11.8; P<0.001) and CV death (HR 10.8; 95% CI 3.8 to 30.4; P<0.001) than patients with lower OPG concentrations. After multiple Cox regression analysis, high serum levels of OPG remained an independent predictor of all-cause mortality (HR 6.0; 95% CI 3.1 to 11.6, P<0.001) and CV death (HR 8.2; 95% CI 2.5 to 26.4; P<0.001). Multiple linear regression analysis revealed that age, creatinine clearance, and high-sensitivity C-reactive protein all were independently associated with OPG (R2=0.42). No significant association between OPG and death-censored graft loss was revealed. Serum levels of MBL, MASP-2, and MASP-3 were not significantly associated with patient survival, CV death, or graft loss. Early measured posttransplantation serum OPG is a highly significant independent predictor of death from any cause or CV death in white renal transplant recipients.
Disulfide Core Cross‐Linked PEGylated Polypeptide Nanogel Prepared by a One‐Step Ring Opening Copolymerization of N‐Carboxyanhydrides for Drug Delivery (2011)

A novel disulfide core cross-linked PEGylated polypeptide nanogel has been synthesized by a one-step ring opening copolymerization of γ-benzyl L-glutamate N-carboxyanhydride and L-cystine N-carboxyanhydride using an amino group-terminated poly(ethylene glycol) methyl ether as initiator. Characterization of products confirms the formation of a core cross-linked PEGylated nanogel with disulfide linkages with a size of about 250 nm, and these studies also confirm that this nanogel can easily be broken by glutathione. Cell viability experiments show the good biocompatibility of the as-prepared polymer. Studies relating to loading and controlled release of indomethacin under reduction-sensitive conditions reveal that the nanogel is a good candidate for drug delivery systems.
Uveoscleral aqueous outflow in the rhesus monkey: importance of uveal reabsorption. (1977)

The uveal absorption of aqueous humor at two different intraocular pressures was measured in rhesus monkeys by sampling vortex vein blood during anterior chamber perfusion of Ringer's solution containing both fluorescein and 125I albumin. At 20 mm. Hg, an excess of fluorescein equivalent in amount to 0.45 microliter/min. of anterior chamber perfusate and an excess of 125I albumin equivalent to 0.18 microliter/min. of perfusate was found in the vortex vein blood compared to systemic blood. At 32 mm. Hg, an excess of 0.86 microliter/min. of fluorescein and 0.26 microliter/min. of 125I albumin was measured. The increase in fluorescein absorption at the higher intraocular pressure was significant (0.025 less than p less than 0.05), with a uveal outflow facility of 0.034 microliter/min./mm. Hg. At an intraocular pressure of 20 mm. Hg, uveal aqueous outflow is less than 10% of total aqueous outflow. The pressure dependence of the uveal uptake of fluorescein implies an aqueous reabsorption into the uveal vessels by ultrafiltration. Uveoscleral aqueous "outflow" appears to consist of intraocular uveal reabsorption of water and small molecules from the aqueous, with only larger molecules like albumin actually leaving the eye through posterior scleral vessel perforations. This reabsorption plays a minor role in intraocular pressure regulation under normal conditions.
The Reticulin Content of Bone Marrow in Acute Leukaemia in Adults (1979)

Marrow reticulin was studied by trephine biopsy in 44 patients with adult acute leukaemia at presentation and subsequently during the course of their illness. The findings indicate that: (1) an increase in marrow reticulin is common at presentation in patients with both acute lymphoblastic and acute non-lymphoblastic leukaemia; (2) effective anti-leukaemic therapy results in resolution of some or all of the increased marrow reticulin and is not contraindicated, even in patients with a marked increase in marrow reticulin; and (3) reappearance of an increase in marrow reticulin may be a sign of relapse of the leukaemia.
Nuclear polyhedrosis virus detection: relative capabilities of clones developed from Trichoplusia ni ovarian cell line TN-368 to serve as indicator cells in a plaque assay (1975)

Cloned cell lines from the established Trichoplusia ni line TN-368 appear to differ from one another in their relative capabilities to serve as plaque assay indicator cell lines for Autographa californica nuclear polyhedrosis virus. Although there seems to be little correlation between their relative generation times and their efficiency in supporting plaque formation as indicator cell lines, there does seem to be a relationship within a given line between its capability to serve as an indicator and its phase of growth as a population; i.e., lag, logarithmic, or stationary. Both the parent line and clone 10 were more efficient indicators when they were in the logarithmic phase of growth than when in either the lag or stationary phases. Also, there appears to be a rough correlation between the capability of a given clone to serve as an indicator and the rate at which polyhedra first appear in the nuclei of the infected cells, with the best indicators producing polyhedra first. Increased incubation time has no effect on equalizing the plaque assay results for the less efficient clones. It was observed, also, that those clones that are the least efficient as plaque assay indicators produce the most external PFU per cell.
Proteasome activity is altered in skeletal muscle tissue of tumour-bearing rats a leucine-rich diet (2004)

Leucine can modulate skeletal muscle metabolism by enhancing protein synthesis and decreasing proteolysis. In this study, we investigated the effects of leucine on the ubiquitin-proteasome system in skeletal muscle of pregnant tumour-bearing rats fed a leucine-rich diet. Pregnant Wistar rats were distributed into three groups that were fed a semi-purified control diet (C, control; W, Walker tumour-bearing; P, pair-fed) and three other groups of pregnant rats fed a semi-purified leucine-rich diet (L, leucine; WL, Walker tumour-bearing; PL, pair-fed). The tumour-bearing rats were injected subcutaneously with a suspension of Walker 256 tumour cells. Protein synthesis and degradation were measured in gastrocnemius muscle; the total protein content and tissue chymotrypsin-like and alkaline phosphatase enzyme activities were also determined. Muscle protein extracts were run on SDS-PAGE to assess the expression of the myosin heavy chain (MHC), 20S alpha proteasome subunit, 19S MSSI ATPase regulator subunit and 11S alpha subunit. Although tumour growth decreased the incorporation of [3H]-Phe, the concomitant feeding of a leucine-rich diet increased the rate of protein synthesis. Muscle proteolysis in both tumour-bearing groups was increased more than in the respective control groups. Conversely, the leucine-rich diet caused less protein breakdown in the WL group than in the W group. Only the W group showed a significant reduction (71%) in the myosin content. In WL rats, the 20S proteasome content (32 kDa band) was reduced, while the expression of the 19S subunit was 3-fold less than in the W group and the 11S proteasome subunit reduced, to around 32% less than in the W group. These findings clearly indicate that leucine can stimulate protein synthesis and inhibit protein breakdown in pregnant rats, probably by modulating the activation of the ubiquitin-proteasome system during tumour growth.
Establishment of 2-docosanol as a cellular marker compound in the identification of Mycobacterium xenopi (1989)

Sixteen strains of Mycobacterium xenopi were studied by gas chromatography and thin-layer chromatography. Data on the cellular fatty acids, fatty alcohols, mycolic acids, and glycolipids indicated that this bacterium possesses a specific lipid composition. 2-Docosanol, detected in all studied strains, was found to constitute a useful chemical marker in the identification of M. xenopi.
Cellular translocation of proteins by transportan (2001)

ABSTRACT Proteins with molecular masses ranging from 30 kDa (green fluorescent protein, GFP) to 150 kDa (monoclonal and polyclonal antibodies) were coupled to the cellular translocating peptide transportan. We studied the ability of the resulting protein–peptide constructs to penetrate into Bowes melanoma, BRL, and COS‐7 cells. After 0.5–3 h incubation with recombinant GFP coupled to transportan, most of the GFP fluorescence was found in intracellular membranes of BRL and COS‐7 cells, which suggests that transportan could internalize covalently linked proteins of about 30 kDa in a folded state. Transportan could internalize covalently coupled molecules of even larger size; that is, avidin and antibodies, (up to 150 kDa). The covalent bond between the transport peptide and its cargo is not obligatory because streptavidin was translocated into the cells within 15 min as a noncovalent complex with biotinylated transportan. Inside the cells, the delivered streptavidin was first located mainly in close proximity to the plasma membrane and was later distributed to the perinuclear region. Most of the internalized streptavidin was confined to vesicular structures, but a significant fraction of the protein was distributed in the cytoplasm. Our data suggest that transportan can deliver proteins and other hydrophilic macromolecules into intact mammalian cells, and this finding demonstrates good potential as powerful cellular delivery vector for scientific and therapeutic purposes.
Rlbp1Promoter Drives Robust Muller Glial GFP Expression in Transgenic Mice (2009)

Regulatory elements in a restricted region of the Rlbp1 gene are sufficient to drive GFP expression in vivo. This transgenic line provides robust GFP expression that can be used to visualize retinal progenitor cells during postnatal development and Müller glia during their differentiation and in the healthy or degenerating adult retina.
The ATP4- receptor of rat mast cells (1980)

The concentration-dependence on exogenous ATP of activation and inhibition of mast-cell histamine secretion, phosphatidylinositol labelling and leakage of metabolites shows that all these functions are regulated by the free acid ATP4-. Maximal histamine secretion and phosphatidylinositol labelling occur with ATP4- at approx. 2 microM, but higher concentrations, which cause inhibition of secretion and phosphatidylinositol labelling, are required to maximize leakage of 32P-labelled metabolites. Both enhancement and inhibition of phosphatidylinositol labelling (due to low and high concentrations of ATP4- respectively) are rapid in onset; histamine secretion is characterized by a delay, especially at low concentrations of ATP4- (approx. 1 microM). Phosphatidylinositol labelling and histamine secretion are dependent on extracellular Ca2+. Metabolite leakage due to the presence of exogenous ATP4- is slow and does not require Ca2+. Of 18 analogues of ATP that were tested, only four were agonists for secretion, and only these four permitted leakage of 32P-labelled metabolites. It is argued that activation and inhibition of histamine secretion, phosphatidylinositol labelling and metabolite leakage are all initiated by ATP4- acting at the same receptor. For mast cells stimulated with ATP4- enhancement of phosphatidylinositol metabolism is not sufficient by itself to cause Ca2+-dependent secretion.
Reduced dynamin-related protein 1 protects against phosphorylated Tau-induced mitochondrial dysfunction and synaptic damage in Alzheimer’s disease (2016)

The purpose of our study was to understand the protective effects of a partial reduction of dynamin-related protein 1 (Drp1) in Alzheimer’s disease (AD) progression and pathogenesis. Increasing evidence suggests that phosphorylated Tau and mitochondrial abnormalities are involved in the loss of synapses, defective axonal transport and cognitive decline, in patients with AD. In the current study, we investigated whether a partial reduction of Drp1 protect neurons from phosphorylated Tau-induced mitochondrial and synaptic toxicities in AD progression. We crossed Drp1+/− mice with Tau transgenic mice (P301L line) and created double mutant (TauXDrp1+/−) mice. Using real-time RT-PCR, immunoblotting and immunostaining analyses, we measured mRNA expressions and protein levels of genes related to the mitochondrial dynamics—Drp1 and Fis1 (fission), Mfn1, Mfn2 and Opa1 (fusion), CypD (matrix), mitochondrial biogenesis—Nrf1, Nrf2, PGC1α and TFAM and synaptic—synaptophysin, PSD95, synapsin 1, synaptobrevin 1, neurogranin, GAP43 and synaptopodin in brain tissues from 6-month-old Drp1+/−, Tau, TauXDrp1+/− and wild-type mice. Using biochemical and immunoblotting methods, mitochondrial function and phosphorylated Tau were measured. Decreased mRNA and protein levels of fission and matrix and increased levels of fusion, mitochondrial biogenesis, and synaptic genes were found in 6-month-old TauXDrp1+/− mice relative to Tau mice. Mitochondrial dysfunction was reduced in TauXDrp1+/− mice relative to Tau mice. Phosphorylated Tau found to be reduced in TauXDrp1+/− mice relative to Tau mice. These findings suggest that a partial reduction of Drp1 decreases the production of phosphorylated Tau, reduces mitochondrial dysfunction, and maintains mitochondrial dynamics, enhances mitochondrial biogenesis and synaptic activity in Tau mice. Findings of this study may have implications for the development of Drp1 based therapeutics for patients with AD and other tauopathies.
Cerebrospinal Fluid Oligoclonal Bands in the Diagnosis of Multiple Sclerosis (2003)

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system. We compared the diagnostic performance of isoelectric focusing (IEF) combined with IgG immunoblotting to high-resolution agarose gel electrophoresis for the detection of intrathecal synthesis of IgG due to the MS disease process.

In 20 patients with definite MS, IEF and high-resolution agarose gel electrophoresis had sensitivities of 90% and 60%, respectively. In the 51 patients with no evidence of MS, the methods had specificities of 94% and 96%, respectively. With a prevalence of 15% in this test population, IEF and high-resolution agarose gel electrophoresis had positive predictive values of 73% and 73% and negative predictive values of 98% and 93%, respectively.

The IEF method improves the sensitivity and the negative predictive value of the oligoclonal-banding assay, the IEF gels are easier to interpret, and the IEF assay requires a smaller cerebrospinal fluid volume.
Estrogen Attenuates P2X7‐R — Mediated Apoptosis of Uterine Cervical Cells by Blocking Calcium Influx (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Wireless Sensor Networks and Chemo-/Biosensing (2008)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTWireless Sensor Networks and Chemo-/BiosensingDermot Diamond, Shirley Coyle, Silvia Scarmagnani, and Jer HayesView Author Information Adaptive Sensors Group, National Centre for Sensor Research, School of Chemical Sciences, Dublin City University, Dublin 9, Ireland Cite this: Chem. Rev. 2008, 108, 2, 652–679Publication Date (Web):January 24, 2008Publication History Received2 June 2007Published online24 January 2008Published inissue 1 February 2008https://pubs.acs.org/doi/10.1021/cr0681187https://doi.org/10.1021/cr0681187research-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views6669Altmetric-Citations215LEARN 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:Electrodes,Liquids,Polymers,Power,Sensors Get e-Alerts
A new algorithm for EEG source reconstruction based on LORETA by contracting the source region (2002)

A new method is presented for EEG source reconstruction based on multichannel surface EEG recordings. From the low-resolution tomography obtained by the low resolution electromagnetic tomography algorithm (LORETA), this method acquires the source tomography, which has high-resolution by contracting the source region. In contrast to focal underdetermined system solver (FOCUSS), this method can gain more accurate result under certain circumstances.
Functional aspects of three molecules associated with metastasis development in human malignant melanoma. (1989)

To identify molecules which may be functionally associated with the development of metastasis in human melanoma, monoclonal antibodies which discriminate between benign and malignant melanocytic lesions in situ were selected. Biochemical studies and cDNA cloning identified the antigens HLA-DR, ICAM-1 and MUC18 which showed an expression pattern on primary tumors correlating with vertical tumor thickness, the most predictive parameter for the development of metastasis in melanoma. ICAM-1 and MUC18 show sequence similarity to a family of cell adhesion molecules which include the neural cell adhesion molecule NCAM. Both HLA-DR and ICAM-1 can be induced on melanoma cells by lymphokines, suggesting a role of the mononuclear cell infiltrate in the control of tumor cell phenotype. Knowledge of the normal function of these molecules allows one to hypothesize how they may contribute to the successful development of metastases.
Quantification of Hydroxyl Radicals Produced in Aqueous Phase Pulsed Electrical Discharge Reactors (2006)

High voltage pulsed electrical discharges in water are of interest for a number of applications, for example, in chemistry, water treatment, electrical transmission, and bioengineering, because of the formation of highly reactive molecular and radical species (including the hydroxyl radical). While the existence of hydroxyl radicals in these systems has been demonstrated by emission spectroscopy, accurate quantification of the rates of formation of this species is needed to develop insight into the means by which electrical discharge can promote useful chemical reactions. This paper focuses on quantification of hydroxyl radicals using chemical probes (dimethyl sulfoxide (DMSO) and disodium salt of terephthalic acid (NaTA)).
In vitro activity of LY146032, a new lipopeptide antibiotic, against gram-positive cocci (1987)

The activity of LY146032, a new lipopeptide antibiotic, was compared in vitro with those of vancomycin, oxacillin, and ampicillin against 261 staphylococcal and 154 streptococcal isolates. The MICs of LY146032 and vancomycin were similar, but the bactericidal activity and killing kinetics of LY146032 were more pronounced.