gebhart/patrepeval huggingface dataset:
Bardoxolone methyl (BARD) ameliorates ischemic AKI and increases expression of protective genes Nrf2, PPARγ, and HO-1 (2011)

Ischemic acute kidney injury (AKI) triggers expression of adaptive (protective) and maladaptive genes. Agents that increase expression of protective genes should provide a therapeutic benefit. We now report that bardoxolone methyl (BARD) ameliorates ischemic murine AKI as assessed by both renal function and pathology. BARD may exert its beneficial effect by increasing expression of genes previously shown to protect against ischemic AKI, NF-E2-related factor 2 (Nrf2), peroxisome proliferator-activated receptor-γ (PPARγ), and heme oxygenase 1 (HO-1). Although we found that BARD alone or ischemia-reperfusion alone increased expression of these genes, the greatest increase occurred after the combination of both ischemia-reperfusion and BARD. BARD had a different mode of action than other agents that regulate PPARγ and Nrf2. Thus we report that BARD regulates PPARγ, not by acting as a ligand but by increasing the amount of PPARγ mRNA and protein. This should increase ligand-independent effects of PPARγ. Similarly, BARD increased Nrf2 mRNA; this increased Nrf2 protein by mechanisms in addition to the prolongation of Nrf2 protein half-life previously reported. Finally, we localized expression of these protective genes after ischemia and BARD treatment. Using double-immunofluorescence staining for CD31 and Nrf2 or PPARγ, we found increased Nrf2 and PPARγ on glomerular endothelia in the cortex; Nrf2 was also present on cortical peritubular capillaries. In contrast, HO-1 was localized to different cells, i.e., tubules and interstitial leukocytes. Although Nrf2-dependent increases in HO-1 have been described, our data suggest that BARD's effects on tubular and leukocyte HO-1 during ischemic AKI may be Nrf2 independent. We also found that BARD ameliorated cisplatin nephrotoxicity.
Do Mobile Phone Applications Improve Glycemic Control (HbA1c) in the Self-management of Diabetes? A Systematic Review, Meta-analysis, and GRADE of 14 Randomized Trials (2016)

Apps may be an effective component to help control HbA<sub>1c</sub> and could be considered as an adjuvant intervention to the standard self-management for patients with type 2 diabetes. Given the reported clinical effect, access, and nominal cost of this technology, it is likely to be effective at the population level. The functionality and use of this technology need to be standardized, but policy and guidance are anticipated to improve diabetes self-management care.
White LED light coupling into light guides with diffraction gratings (2006)

Radial diffractive gratings are used to couple light of a white LED into a light guide. Theoretical coupling efficiencies are evaluated with rigorous diffraction theory in a pure conical mounting. It is shown that when the refractive index of the grating increases from 1.46 to 2.05 the incoupling efficiency increases from 42% to 63%. Also, with the increasing refractive index the incoupling efficiency is shown to become more nearly uniform over the visible spectrum. Experimental results for the incoupled efficiencies and the color coordinates of the incoupled spectra are introduced for refractive indices n=1.46 and n=1.56.
Cancer Proteomics: In Pursuit of “True” Biomarker Discovery (2005)

For the past several years, we have seen an increasing number of reports on the clinical application of proteomics research for risk assessment, diagnosis, prognosis, and management of cancer. These reports have generated a high level of excitement. At the same time, they have attracted critical
Monolayer chemical lithography and characterization of fluoropolymer films (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMonolayer chemical lithography and characterization of fluoropolymer filmsTerrence G. Vargo, Patrick M. Thompson, Louis J. Gerenser, Robert F. Valentini, Patrick Aebischer, Daniel J. Hook, and Joseph A. Gardella Jr.Cite this: Langmuir 1992, 8, 1, 130–134Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/la00037a025https://doi.org/10.1021/la00037a025research-articleACS PublicationsRequest reuse permissionsArticle Views300Altmetric-Citations62LEARN 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
Production of multiple cytokines and induction of cachexia in athymic nude mice by a new anaplastic thyroid carcinoma cell line (2003)

An anaplastic thyroid cancer cell line, Thena, was recently established in our laboratory following radical thyroidectomy of a patient with anaplastic thyroid cancer. Microscopically, Thena cells were spindle-shaped or small round cells. Thena cells were reactive with cytokeratin AE1/AE3 antibodies, epithelial membrane antigen, interleukin (IL)-6, epithelial growth factor receptor, transforming growth factor (TGF)-alpha, vascular endothelial growth factor, and vimentin. Thena cells secreted high levels of IL-6, leukemia inhibitor factor (LIF), tumor necrosis factor (TNF)-alpha, and TGF-beta1 in the culture supernatants, as determined by enzyme-linked immunosorbent assay. When subcutaneously injected with Thena cells, athymic nude mice developed tumor masses in the skin within 2 weeks. Furthermore, Thena cells induced cachexia in these tumor-bearing mice. High levels of human IL-6, LIF and TGF-beta1 were detected in the mouse sera. To our knowledge, the Thena cell line is the first thyroid cancer cell line reported to induce cachexia in nude mice. This cachectic animal model is worthy of further study to explore the treatment of thyroid cancer-induced cachexia.
Insertion Reactions into Pd−O and Pd−N Bonds:  Preparation of Alkoxycarbonyl, Carbonato, Carbamato, Thiocarbamate, and Thioureide Complexes of Palladium(II) (2003)

Mononuclear palladium hydroxo complexes of the type [Pd(N[bond]N)(C(6)F(5))(OH)] [(N[bond]N = 2,2'-bipyridine (bipy), 4,4'-dimethyl-2,2'-bipyridine (Me(2)bipy), 1,10-phenanthroline (phen), or N,N,N',N'-tetramethylethylenediamine (tmeda)] have been prepared by reaction of [Pd(N[bond]N)(C(6)F(5))(acetone)]ClO(4) with KOH in methanol. These hydroxo complexes react, in methanol, with CO (1 atm, room temperature) to yield the corresponding methoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)Me)]. Similar alkoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)R)] (N[bond]N = bis(3,5-dimethylpyrazol-1-yl)methane); R = Me, Et, or (i)Pr) are obtained when [Pd(N[bond]N)(C(6)F(5))Cl] is treated with KOH in the corresponding alcohol ROH and CO is bubbled through the solution. The reactions of [Pd(N[bond]N)(C(6)F(5))(OH)] (N[bond]N = bipy or Me(2)bipy) with CO(2), in tetrahydrofuran, lead to the formation of the binuclear carbonate complexes [(N[bond]N)(C(6)F(5))Pd(mu-eta(2)-CO(3))Pd(C(6)F(5))(N[bond]N)]. Complexes [Pd(N[bond]N)(C(6)F(5))(OH)] react in alcohol with PhNCS to yield the corresponding N-phenyl-O-alkylthiocarbamate complexes [Pd(N[bond]N)(C(6)F(5))[SC(OR)NPh]]. Similarly, the reaction of [Pd(bipy)(C(6)F(5))(OH)] with PhNCO in methanol gives the N-phenyl-O-methylcarbamate complex [Pd(bipy)(C(6)F(5))[NPhC(O)OR]]. The reactions of [(N[bond]N)Pd(C(6)F(5))(OH)] with PhNCS in the presence of Et(2)NH yield the corresponding thioureidometal complexes [Pd(N[bond]N)(C(6)F(5))[NPhCSNR(2)]]. The crystal structures of [Pd(tmeda)(C(6)F(5))(CO(2)Me)], [Pd(2)(Me(2)bipy)(2)(C(6)F(5))(2)(mu-eta(2)-CO(3))].2CH(2)Cl(2), and [Pd(tmeda)(C(6)F(5))[SC(OMe)NPh]] have been determined.
Glutathione S‐transferase mu genotype (GSTM1*0) in Alzheimer's patients with tacrine transaminitis. (1995)

1. Tacrine (1,2,3,4-tetrahydro-9-aminoacridine) which is used in Alzheimer's disease, causes elevation of liver transaminases ('tacrine transaminitis') in 40-50% of patients. This may be related to the formation of a chemically reactive metabolite from tacrine, which can be detoxified in vitro by glutathione. 2. Glutathione-S-transferase mu (GSTM1), a detoxication enzyme, is polymorphically expressed being absent in about 50% of patients. Its role in the detoxication of the reactive metabolite of tacrine is not known. 3. The frequency of the enzyme deficiency (GSTM1*0) has been investigated in patients with tacrine transaminitis using polymerase chain reaction (PCR) to determine whether the GSTM1 status can be used as an absolute predictive factor for susceptibility to tacrine transaminitis. 4. The frequency of the GSTM1*0 genotype in patients with tacrine transaminitis (n = 33; 45.5%) was not significantly different from that in patients treated with tacrine without liver dysfunction (n = 37; 43%), and when compared with all the controls used in the study (n = 167; 56%). 5. The frequency of the GSTM1*0 genotype in patients with Alzheimer's disease (n = 79; 46%) was not significantly different from that in healthy volunteers (n = 121; 59.5%). 6. Our results indicate that the GSTM1 status cannot be used clinically to predict individual susceptibility to tacrine transaminitis, and that patients with the GSTM1*0 genotype are unlikely to have an increased risk of tacrine-induced liver damage. Furthermore, the GSTM1 status was not associated with Alzheimer's disease.
[Cystomanometric study of bladder sensation during sacral neuromodulation test]. (2005)

A significant correlation was observed between the two methods of clinical and urodynamic assessment. Our results suggest the use of the cystomanometric increase of bladder volume at B1 and B3 as selection criterion for candidates for SNM with non-neurological hyperactive bladder.
Molecular Characterization of Infectious Clones of the Minute Virus of Canines Reveals Unique Features of Bocaviruses (2009)

Minute virus of canines (MVC) is a member of the genus Bocavirus in the family Parvoviridae. We have molecularly cloned and sequenced the 5'- and 3'-terminal palindromes of MVC. The MVC genome, 5,404 nucleotides (nt) in length, shared an identity of 52.6% and 52.1% with that of human bocavirus and bovine parvovirus, respectively. It had distinct palindromic hairpins of 183 nt and 198 nt at the left-end and right-end termini of the genome, respectively. The left-end terminus was also found in two alternative orientations (flip or flop). Both termini shared extensive similarities with those of bovine parvovirus. Four full-length molecular clones constructed with different orientations of the left-end terminus proved to be infectious in Walter Reed canine cell/3873D (WRD) canine cells. Both MVC infection and transfection of the infectious clone in WRD cells revealed an identical RNA transcription profile that was similar to that of bovine parvovirus. Mutagenesis of the infectious clone demonstrated that the middle open reading frame encodes the NP1 protein. This protein, unique to the genus Bocavirus, was essential for MVC DNA replication. Moreover, the phospholipase A2 motif in the VP1 unique region was also critical for MVC infection. Thus, our studies revealed important information about the genus Bocavirus that may eventually help us to clone the human bocavirus and study its pathogenesis.
Melanopsin Is Expressed in PACAP-Containing Retinal Ganglion Cells of the Human Retinohypothalamic Tract (2004)

Given the expression of melanopsin in PACAP-containing RGCs of the human RHT, this photoreceptor is a likely first base in the chain of events leading to photoentrainment of both normal and blind people.
Simplified quantification of Pittsburgh Compound B amyloid imaging PET studies: a comparative analysis. (2005)

Of the simplified methods for PIB analysis examined, CAR90 provided DVR measures that were most comparable to ART90; CER90 was the most reproducible and SUVR90 produced the largest effect size. All simplified methods were effective at distinguishing AD and control differences and may be effectively used in the analysis of PIB. SUVR60 data can be obtained with as little as 20 min of PET emission data collection. The relative strengths and limitations of each method must be considered for each experimental design.
Sputtered Cobalt‐Carbon‐Nitrogen Thin Films as Oxygen Reduction Electrocatalysts: I. Physical and Electrochemical Characterization (1998)

Thin films of amorphous Co‐C‐N mixtures which were co‐sputtered in vacuum showed good catalyst properties for oxygen reduction in alkaline solution. The optimal catalytic activity was . The oxygen reduction for these films proceeds via a four‐electron pathway and the redox couple is shown to be responsible for the oxygen reduction reaction. The performance is comparable to transition metal macrocycles in alkaline solutions. Evidently, intact structures of the macrocycles are not necessary for good catalyst activity.
Expression cloning of a human dual-specificity phosphatase. (1992)

Using an expression cloning strategy, we isolated a cDNA encoding a human protein-tyrosine-phosphatase. Bacteria expressing the kinase domain of the keratinocyte growth factor receptor (bek/fibroblast growth factor receptor 2) were infected with a fibroblast cDNA library in a phagemid prokaryotic expression vector and screened with a monoclonal anti-phosphotyrosine antibody. Among several clones showing decreased anti-phosphotyrosine recognition, one displayed phosphatase activity toward the kinase in vitro. The 4.1-kilobase cDNA encoded a deduced protein of 185 amino acids with limited sequence similarity to the vaccinia virus phosphatase VH1. The purified recombinant protein dephosphorylated several activated growth factor receptors, as well as serine-phosphorylated casein, in vitro. Both serine and tyrosine phosphatase activities were completely abolished by mutagenesis of a single cysteine residue conserved in VH1 and the VH1-related (VHR) human protein. These properties suggest that VHR is capable of regulating intracellular events mediated by both tyrosine and serine phosphorylation.
Integration of Bombyx mori R2 Sequences into the 28S Ribosomal RNA Genes of Drosophila melanogaster (2000)

R2 non-long-terminal-repeat retrotransposable elements integrate into a precise location in the 28S rRNA genes of arthropods. The purified protein encoded by R2 can cleave the 28S gene target site and use the 3' hydroxyl group generated by this cleavage to prime reverse transcription of its own RNA, a process called target-primed reverse transcription. An integration system is described here in which components from the R2 element of the silkmoth, Bombyx mori, are injected into the preblastoderm embryo of Drosophila melanogaster. Silkmoth R2 sequences were readily detected in the 28S rRNA genes of the surviving adults as well as in the genes of their progeny. The 3' junctions of these insertions were similar to those seen in our in vitro assays, as well as those from endogenous R2 retrotransposition events. The 5' junctions of the insertions originally contained major deletions of both R2 and 28S gene sequences, a problem overcome by the inclusion of upstream 28S gene sequences at the 5' end of the injected RNA. The resulting 5' junctions suggested a recombination event between the cDNA and the upstream target sequences. This in vivo integration system should help determine the mechanism of R2 retrotransposition and be useful as a delivery system to integrate defined DNA sequences into the rRNA genes of organisms.
Folate‐targeted imaging of activated macrophages in rats with adjuvant‐induced arthritis (2002)

Although EC20 is currently undergoing clinical evaluation for use in the imaging of ovarian carcinomas, the present results suggest that it may also be useful for assaying the participation of activated macrophages in inflammatory processes such as rheumatoid arthritis.
Augmented Reality adaptive web content (2016)

In this paper we present a design of an Augmented Reality (AR) browser that renders web pages without obstructing the view of the world when seen from an AR headset such as Oculus Rift, Gear VR or Google Cardboard. The browser overlays the contents of the web page transparently on the user's view and is capable of modifying font size, colors, and layout of the web page, such that it augments the user's view of the page. This approach is different from existing AR applications such as Amazon Flow, in that it is more flexible and acts as a real browser. In existing browsers, webpages are sandboxed and hence cannot access the capabilities of AR. We describe the design of Cascading Style Sheets (CSS) and JavaScript (JS) that leverages AR. Our approach processes the external data and generates different types of events through an event generator. Pages rendered on our browser can exploit these CSS and JS events to morph themselves. This enables content developers to provide custom layouts for the web page when viewed through the AR headset, in a way that centers the web objects on the user's field of view whose coordinates are sent to the content provider. The callbacks provided by the browser encapsulate required information like co-ordinates, dimensions and color of the actual web object instead of providing the video stream itself, thus sandboxing the web page yet allowing it to exploit AR capabilities. The actual data stream that the user is viewing is not sent, thus ensuring privacy. We provide details of the implementation and the method to integrate our approach with the Samsung Gear VR headset.
Zone Plates Produced Optically (1969)

The nature of optically produced zone plates is briefly discussed in contrast to the conventional type of Fresnel zone plate. A rather simple method for generating zone plates is described, and some of the experimental results are given.
Increased Co-localization of Connexin43 and ZO-1 in Dissociated Adult Myocytes (2001)

In the heart, the intercellular geometry of myocyte coupling by Connexin43-gap junctions (Cx43-gjs) is a determinant of normal and abnormal patterns of propagation of electrical excitation. ZO-1 has been suggested to play a role in determining the pattern of intercellular coupling between myocytes. We therefore investigated the co-distribution of Cx43 with ZO-1 in ventricular myocytes of the adult rat using quantitative immunoconfocal microscopy. Our data indicates that low-moderate levels of co-immunolocalization occur between Cx43 and ZO-1 in normal ventricular myocardium. However, rapid and significant increases in relative co-localization occur between Cx43 and ZO-1 following dissociation of myocytes from ventricular myocardium--a treatment inducing internalization of Cx43-gjs. This increased relative co-localization may represent an increase in Cx43-ZO-1 interaction, suggesting a role for ZO-1 in the remodeling of myocardial Cx43-gjs. A more comprehensive study, including immunoprecipitation and immunoelectron microscopy analyses has been carried out (Barker et al. Circ. Res., in press, 2002 and as presented to the 2001 International GJ Conference). This study further assesses the biological relevance of the increased association between ZO-1 and Cx43 accompanying internalization of Cx43-gjs.
Gene expression changes in HLA mismatched mixed lymphocyte cultures reveal genes associated with allorecognition (2015)

Human leucocyte antigen (HLA) compatibility is the main factor determining the occurrence of graft-vs-host disease (GVHD) in patients. It has also been shown that minor histocompatibility antigen differences as well as genetic polymorphisms that are not sequenced by standard methodology for HLA typing can play a role. We used mixed lymphocyte cultures (MLCs) as a functional cellular test and investigated gene expression changes driven by HLA incompatibility in an effort to better understand the mechanisms involved in the disease. Gene expression profile of HLA matched and HLA mismatched MLC identified differentially regulated genes and pathways. We found that a great number of genes related to immune function were differentially regulated; these genes were also found to be associated with GVHD and graft rejection. The majority of differentially regulated genes were interferon-gamma (IFNγ)-inducible genes and IFNγ neutralisation in MLCs abrogated their induction. The microRNA-155, a recently identified target for acute GVHD (aGVHD), was also found to be significantly induced in HLA mismatched MLC but not in the matched setting and its induction was not diminished by blocking IFNγ. In this proof-of-principle study we show gene expression changes in mismatched MLC that represent alloreactive responses, correlate with markers involved in GVHD and can potentially be useful in the study of the biological processes involved in this disease.
Semantic relations asserting the etiology of genetic diseases. (2003)

Considerable research is being directed at extracting molecular biology information from text. Particularly challenging in this regard is to identify relations between entities, such as protein-protein interactions or molecular pathways. In this paper we present a natural language processing method for extracting causal relations between genetic phenomena and diseases. After presenting the results of preliminary evaluation, we suggest the use of a graphical display application for viewing the semantic predications produced by the system.
Nitric oxide inhibition of respiration involves both competitive (heme) and noncompetitive (copper) binding to cytochromecoxidase (2006)

NO reversibly inhibits mitochondrial respiration via binding to cytochrome c oxidase (CCO). This inhibition has been proposed to be a physiological control mechanism and/or to contribute to pathophysiology. Oxygen reacts with CCO at a heme iron:copper binuclear center (a(3)/Cu(B)). Reports have variously suggested that during inhibition NO can interact with the binuclear center containing zero (fully oxidized), one (singly reduced), and two (fully reduced) additional electrons. It has also been suggested that two NO molecules can interact with the enzyme simultaneously. We used steady-state and kinetic modeling techniques to reevaluate NO inhibition of CCO. At high flux and low oxygen tensions NO interacts predominantly with the fully reduced (ferrous/cuprous) center in competition with oxygen. However, as the oxygen tension is raised (or the consumption rate is decreased) the reaction with the oxidized enzyme becomes increasingly important. There is no requirement for NO to bind to the singly reduced binuclear center. NO interacts with either ferrous heme iron or oxidized copper, but not both simultaneously. The affinity (K(D)) of NO for the oxygen-binding ferrous heme site is 0.2 nM. The noncompetitive interaction with oxidized copper results in oxidation of NO to nitrite and behaves kinetically as if it had an apparent affinity of 28 nM; at low levels of NO, significant binding to copper can occur without appreciable enzyme inhibition. The combination of competitive (heme) and noncompetitive (copper) modes of binding enables NO to interact with mitochondria across the full in vivo dynamic range of oxygen tension and consumption rates.