gebhart/patrepeval huggingface dataset:
Palladium-catalyzed coupling of vinyl triflates with organostannanes. Synthetic and mechanistic studies (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPalladium-catalyzed coupling of vinyl triflates with organostannanes. Synthetic and mechanistic studiesWilliam J. Scott and J. K. StilleCite this: J. Am. Chem. Soc. 1986, 108, 11, 3033–3040Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://doi.org/10.1021/ja00271a037Request reuse permissionsArticle Views5232Altmetric-Citations436LEARN 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 InReddit PDF (1 MB) Get e-Alertsclose Get e-Alerts
THE TROUBLE WITH KIDNEYS DERIVED FROM THE NON HEART-BEATING DONOR: A SINGLE CENTER 10-YEAR EXPERIENCE1 (2000)

Machine perfusion and viability assessment of NHB kidneys in phase III of the program has increased our donor pool as well as improved the graft survival. This is particularly relevant for the use of the category II NHB donor where the incidence of primary nonfunction was high, illustrated by phase II where machine perfusion/viability assessment was not used.
Bacterial community analysis of shallow groundwater undergoing sequential anaerobic and aerobic chloroethene biotransformation (2007)

At Department of Energy Site 300, beneficial hydrocarbon cocontaminants and favorable subsurface conditions facilitate sequential reductive dechlorination of trichloroethene (TCE) and rapid oxidation of the resultant cis-dichloroethene (cis-DCE) upon periodic oxygen influx. We assessed the geochemistry and microbial community of groundwater from across the site. Removal of cis-DCE was shown to coincide with oxygen influx in hydrocarbon-containing groundwater near the source area. Principal component analysis of contaminants and inorganic compounds showed that monitoring wells could be differentiated based upon concentrations of TCE, cis-DCE, and nitrate. Structurally similar communities were detected in groundwater from wells containing cis-DCE, high TCE, and low nitrate levels. Bacteria identified by sequencing 16S rRNA genes belonged to seven phylogenetic groups, including Alpha-, Beta-, Gamma- and Deltaproteobacteria, Nitrospira, Firmicutes and Cytophaga-Flexibacter-Bacteroidetes (CFB). Whereas members of the Burkholderiales and CFB group were abundant in all wells (10(4)-10(9) 16S rRNA gene copies L(-1)), quantitative PCR showed that Alphaproteobacteria were elevated (>10(6) L(-1)) only in wells containing hydrocarbon cocontaminants. The study shows that bacterial community structure is related to groundwater geochemistry and that Alphaproteobacteria are enriched in locales where cis-DCE removal occurs.
Molecular Interactions between Dying Tumor Cells and the Innate Immune System Determine the Efficacy of Conventional Anticancer Therapies (2008)

The efficacy of anticancer treatments is mostly assessed by their ability to directly inhibit the proliferation of tumor cells. Recently, we showed that tumor cell death triggered by chemotherapy or radiotherapy initiates an immunoadjuvant pathway that contributes to the success of cytotoxic treatments. The interaction of high mobility group box 1 protein (HMGB1) released from dying tumor cells with Toll-like receptor 4 (TLR4) on dendritic cells was required for the crosspresentation of tumor antigens and the promotion of tumor specific cytotoxic T-cell responses. Breast cancer patients harboring the loss-of-function Asp299Gly polymorphism of TLR4 relapsed earlier after receiving anthracycline-based chemotherapy. These data suggests that HMGB1- and TLR4-dependent immune responses elicited by conventional cancer treatment may increase the probability to achieve a durable therapeutic success.
Inhibition of transcription by the TAR RNA of HIV-1 in a nuclear extract of HeLa cells (1997)

Regulation of transcription of human immunodeficiency virus type-1 (HIV-1) requires specific interaction of Tat protein with the trans-activation response region (TAR). Inhibition of replication of HIV-1 has previously been achieved with a TAR decoy, namely a short RNA oligonucleotide that corresponded to the sequence of the authentic TAR RNA. Since TAR RNA has the potential to interact with cellular factors, we examined the effect of TAR RNA on efficiency of transcription in nuclear of HeLa cell extracts. We performed an in vitro transcription assay in the presence of authentic TAR RNA using a template that was driven by the CMV (cytomegalovirus) early promoter in a HeLa nuclear extract and found, for the first time, that TAR RNA inhibited transcription by approximately 60-70% independently of the Tat-TAR interaction. Furthermore, we evaluated inhibition of transcription by variants of TAR RNA and found that the TAR RNA loop, bases surrounding the loop, the triple base bulge and the 'lower' stem region of TAR RNA were responsible for the inhibition of transcription. Taken together, earlier reports on proteins that bind to TAR RNA and the present results suggest that integrity of TAR RNA is important for efficient binding to cellular transcription factors. As judged from the significant inhibition observed in this study, the TAR decoy might sequester transcription factors and thus it might potentially be able to inhibit transcription of housekeeping genes that are unrelated to Tat function.
Regulatory T Cells and Infectious Disease (2007)

Various cell types that express regulatory function may influence the pathogenesis of most and perhaps all infections. Some regulatory cells are present at the time of infection whereas others are induced or activated in response to infection. The actual mechanisms by which different types of infections signal regulatory cell responses remain poorly understood. However a most likely mechanism is the creation of a microenvironment that permits the conversion of conventional T cells into cells with the same antigen specificity that have regulatory function. Some possible means by which this can occur are discussed. The relationship between regulatory cells and infections is complex especially with chronic situations. The outcome can either be of benefit to the host or damage the disease control process or in rare instances appears to be a component of a finely balanced relationship between the host and the infecting agent. Manipulating the regulatory cell responses to achieve a favorable outcome of infection remains an unfulfilled objective of therapeutic immunology.
Different modulation of steroidogenesis and prostaglandin production in frog ovary in vitro by ACE and ANG II (1997)

Our aim was to study the role of angiotensin-converting enzyme (ACE) and angiotensin II (ANG II) on ovarian steroidogenesis and prostaglandin production of amphibian. Hormonal effects of ACE, ACE inhibitors, synthetic bullfrog angiotensin I (ANG I), and [Val5]ANG II were compared on frog ovaries of postreproductive and prereproductive periods. Very high ACE activity was found in ovary of water frog (Rana esculenta) compared with other frog tissues, and this activity was inhibited by the typical ACE inhibitors, captopril and lisinopril. Frog ovary tissue in postreproductive and prereproductive periods was incubated in vitro in the presence of ACE (2.5 mU/ml), captopril (0.1 mM), lisinopril (0.1 mM), [Val5]ANG II (1 microM), and synthetic bullfrog ANG I (1 microM). Production of 17 beta-estradiol, progesterone, androgens, and prostaglandins E2 and F2 alpha was determined. The data showed a modulation of 17 beta-estradiol, progesterone, and prostaglandin E2 production by ovary ACE; on the other hand, [Val5]ANG II modulated the production of progesterone and prostaglandin F2 alpha, whereas androgen production was not influenced. The present in vitro studies suggest the existence of two pathways independently regulated by ACE and ANG II modulating ovarian steroidogenesis and prostaglandin production.
Practically Useful: What the R osetta Protein Modeling Suite Can Do for You (2010)

The objective of this review is to enable researchers to use the software package Rosetta for biochemical and biomedicinal studies. We provide a brief review of the six most frequent research problems tackled with Rosetta. For each of these six tasks, we provide a tutorial that illustrates a basic Rosetta protocol. The Rosetta method was originally developed for de novo protein structure prediction and is regularly one of the best performers in the community-wide biennial Critical Assessment of Structure Prediction. Predictions for protein domains with fewer than 125 amino acids regularly have a backbone root-mean-square deviation of better than 5.0 A. More impressively, there are several cases in which Rosetta has been used to predict structures with atomic level accuracy better than 2.5 A. In addition to de novo structure prediction, Rosetta also has methods for molecular docking, homology modeling, determining protein structures from sparse experimental NMR or EPR data, and protein design. Rosetta has been used to accurately design a novel protein structure, predict the structure of protein-protein complexes, design altered specificity protein-protein and protein-DNA interactions, and stabilize proteins and protein complexes. Most recently, Rosetta has been used to solve the X-ray crystallographic phase problem.
Genetic status of cell cycle regulators in squamous cell carcinoma of the oesophagus: the CDKN2A (p16INK4a and p14ARF ) and p53 genes are major targets for inactivation (2002)

We determined inactivation of the CDKN2A (p16(INK4a) and p14(ARF)) gene in 21 cases of oesophageal squamous cell carcinoma (OSCC). The tumours were also analysed for mutations in exons 5-8 and allelic losses in the p53 gene. In addition, we screened the CDKN2B (p15 INK4b), CDKN2C (p18 INK4c), CDK4 and p53R2 genes for mutations in the tumour tissues. Besides concomitant alterations in the CDKN2A and p53 loci in more than half of the cases, our results showed that in 18 OSCC (86%) the CDKN2A (p16(INK4a) and p14(ARF) ) gene was affected through mutations, homozygous/hemizygous deletions and promoter hypermethylation. Eight out of 10 tumours with mutations or promoter hypermethylation specific to the CDKN2A/p16 INK4a gene showed loss of the wild-type allele. One tumour with a single base deletion in the N-terminus (codon 8) of the CDKN2A/p16(INK4a) gene carried a novel germ-line mutation or a rare polymorphism (Ile51Met) in exon 2 of the CDK4 gene. Promoter hypermethylation in the CDKN2A/p14 ARF gene was detected in 11 tumours. In the p53 gene 15 mutations were detected in 14 tumours. We detected an inverse relationship between CDKN2A/p16 INK4a inactivation and frequency of loss of heterozygosity at the p53 locus (OR 0.09, 95% CI 0.01-0.98; Fisher exact test, P-value approximately 0.03). Screening of nine exons of the p53R2 [Human Genome Organisation (HUGO) official name RRM2B] gene resulted in identification of a novel polymorphism in the 5' untranslated region, which was detected in four cases. Our results suggest that the CDKN2A (p16(INK4a) and p14(ARF) ) and p53 genes involved in the two cell cycle pathways are major and independent targets of inactivation in OSCC.
Randomised controlled trial of azathioprine withdrawal in ulcerative colitis. (1992)

Azathioprine maintenance treatment in ulcerative colitis is beneficial for at least two years if patients have achieved remission while taking the drug. Demonstration of the relapse preventing properties of azathioprine has implications for a large number of patients with troublesome ulcerative colitis, who may benefit from treatment with azathioprine.
Quantum Dots as Multimodal Photoacoustic and Photothermal Contrast Agents (2008)

Quantum dots (QDs) have primarily been developed as fluorescent probes with unique optical properties. We herein demonstrate an extension of these QD utilities to photoacoustic (PA) and photothermal (PT) microscopy, using a nanosecond pulse laser excitation (420-900 nm, 8 ns, 10(-3)-10 J/cm(2)). The laser-induced PA, PT and accompanying bubble formation phenomena were studied with an advanced multifunctional microscope, which integrates fluorescence, PA, PT imaging, and PT thermolens modules. It was demonstrated that QDs, in addition to being excellent fluorescent probes, can be used as PA and PT contrast agents and sensitizers, thereby providing an opportunity for multimodal high resolution (300 nm) PA-PT-fluorescent imaging as well as PT therapy. Further improvements for this technology are suggested by increasing the conversion of laser energy in PT, PA, and bubble phenomena in hybrid multilayer QDs that have optimized absorption, thermal, and acoustic properties.
CAPILLARY ELECTROPHORESIS (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCAPILLARY ELECTROPHORESISAndrew G. Ewing, Ross A. Wallingford, and Teresa M. OlefirowiczCite this: Anal. Chem. 1989, 61, 4, 292A–303APublication Date (Print):February 15, 1989Publication History Published online30 May 2012Published inissue 15 February 1989https://pubs.acs.org/doi/10.1021/ac00179a722https://doi.org/10.1021/ac00179a722research-articleACS PublicationsRequest reuse permissionsArticle Views1132Altmetric-Citations210LEARN 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
Testing the Role of P2X7 Receptors in the Development of Type 1 Diabetes in Nonobese Diabetic Mice (2011)

Although P2rx7 has been proposed as a type 1 diabetes (T1D) susceptibility gene in NOD mice, its potential pathogenic role has not been directly determined. To test this possibility, we generated a new NOD stock deficient in P2X(7) receptors. T1D development was not altered by P2X(7) ablation. Previous studies found CD38 knockout (KO) NOD mice developed accelerated T1D partly because of a loss of CD4(+) invariant NKT (iNKT) cells and Foxp3(+) regulatory T cells (Tregs). These immunoregulatory T cell populations are highly sensitive to NAD-induced cell death activated by ADP ribosyltransferase-2 (ART2)-mediated ADP ribosylation of P2X(7) receptors. Therefore, we asked whether T1D acceleration was suppressed in a double-KO NOD stock lacking both P2X(7) and CD38 by rescuing CD4(+) iNKT cells and Tregs from NAD-induced cell death. We demonstrated that P2X(7) was required for T1D acceleration induced by CD38 deficiency. The CD38 KO-induced defects in homeostasis of CD4(+) iNKT cells and Tregs were corrected by coablation of P2X(7). T1D acceleration in CD38-deficient NOD mice also requires ART2 expression. If increased ADP ribosylation of P2X(7) in CD38-deficient NOD mice underlies disease acceleration, then a comparable T1D incidence should be induced by coablation of both CD38 and ART2, or CD38 and P2X(7). However, a previously established NOD stock deficient in both CD38 and ART2 expression is T1D resistant. This study demonstrated the presence of a T1D resistance gene closely linked to the ablated Cd38 allele in the previously reported NOD stock also lacking ART2, but not in the newly generated CD38/P2X(7) double-KO line.
Practical Value Models (2007)

. Many complex decision problems require value judgments, and it is often useful to build formal models of these value judgments. Several models and assessment procedures exist for this task ranging from simple rating and weighting techniques to sophisticated multiattribute utility models that incorporate tradeoffs and risk attitudes. In this chapter, we argue that the choice of a value model and assessment procedure depends on the decision context, the purpose of the model, the quality of available value judgments, time, and other factors. We propose the notion of a practical value model that is useful for a given decision context and purpose, using simplifications and approximations, when appropriate. We then discuss practical considerations when choosing a value model, for example, when deciding whether a value model is additive over attributes or not. We also consider practical issues when choosing an assessment procedure, for example, when selecting equivalent-cost procedures versus rating and weighting procedures. We discuss several topics related to interacting with decision makers when constructing value models, and we conclude with the description of two generic practical value models that we have found useful in many past applications.
Multiple nucleotide cofactor use by yeast ligase in tRNA splicing. Evidence for independent ATP- and GTP-binding sites. (1993)

We have examined multiple cofactor usage by yeast tRNA ligase in splicing in vitro. The ligase mechanism of action requires expenditure of two molar equivalents of nucleotide cofactor per mole of tRNA product. Recent evidence (Westaway, S.K., Belford, H.G., Apostol, B.L., Abelson, J., and Greer, C.L. (1993) J. Biol. Chem. 268, 2435-2443) demonstrated that the ligase-associated kinase activity is more efficient with GTP as cofactor than with ATP. Employing a ligase fusion construct with dihydrofolate reductase (Apostol, B.L., Westaway, S.K., Abelson, J., and Greer, C.L. (1991) J. Biol. Chem. 266, 7445-7455) for purposes of enzyme purification, we performed joining assays demonstrating that ATP and GTP are the most effective combination of cofactors. ATP was essential to the joining reaction, while UTP, CTP, or ATP replaced GTP inefficiently. Specific and functionally independent binding sites were confirmed for ATP and GTP by direct binding measurement. A third site was implicated in UTP- and CTP-ligase interactions. Comparison of binding constants with Kapp values determined for nucleotide-dependent joining suggested both that nucleotide triphosphate binding may be limiting in tRNA joining and that tRNA ligation occurs most efficiently using GTP for the kinase reaction and ATP as the adenylylate synthetase cofactor.
Immobilization Technologies in Probiotic Food Production (2013)

Various supports and immobilization/encapsulation techniques have been proposed and tested for application in functional food production. In the present review, the use of probiotic microorganisms for the production of novel foods is discussed, while the benefits and criteria of using probiotic cultures are analyzed. Subsequently, immobilization/encapsulation applications in the food industry aiming at the prolongation of cell viability are described together with an evaluation of their potential future impact, which is also highlighted and assessed.
Streptococcal infection in young pigs. V. An immunogenic polysaccharide from Streptococcus suis type 2 with particular reference to vaccination against streptococcal meningitis in pigs (1980)

Of 17 pigs vaccinated with STreptococcus suis type-2 capsular polysaccharide plus Freund's Incomplete Adjuvant, all developed opsonizing antibody against Str. suis type 2. Of 14 pigs vaccinated with type-2 polysaccharide alone, 4 (possibly 6) developed opsonizing antibody. It is possible that some pigs vaccinated with polysaccharide plus Freund's Incomplete Adjuvant developed opsonizing antibody in response to a 'booster' injection of polysaccharide alone. Of 21 unvaccinated control pigs, late bleeding from 3 showed opsonizing activity against Str. suis type 2.
Development of a Sustained-Release Biodegradable Polymer Delivery System for Site-Specific Delivery of Oligonucleotides: Characterization of P(LA-GA) Copolymer MicrospheresIn Vitro (1998)

Development of a Sustained-Release Biodegradable Polymer Delivery System for Site-Specific Delivery of Oligonucleotides: Characterization of P(LA-GA) Copolymer Microspheres In Vitro Antisense oligodeoxynucleotides (ODNs) can selectively inhibit individual gene expression provided they gain access to and remain stable at the target site for a sufficient period of time. Biodegradable sustained-release delivery systems may facilitate site-specific delivery and also prevent degradation of ODNs by nucleases whilst delivering the nucleic acid in a controlled manner to the desired site of action. In this study, we have characterized biodegradable poly (lactide-co-glycolide) (P(LA-GA)) 50:50 microspheres for the potential delivery of antisense oligonucleotides in vivo. Phosphodiester (PO) oligonucleotides complementary to either c-myc proto-oncogene or the tat gene in HIV-RNA were adequately incorporated within P(LA-GA) microspheres with entrapment efficiencies up to 60% depending on particles size. In vitro release profiles of antisense nucleic acids from 10-20 microm size microspheres over 56 days in physiological buffer were triphasic. Profiles were characterised by an initial burst effect during the first 48 hours (phase 1) of release followed by a more sustained release (phase 2) with an additional increased release (phase 3) being observed after 25 days which corresponded with bulk degradation of the copolymer matrix. The release profiles were influenced by microsphere size, copolymer molecular weight, ODN loading, ODN length and by the pH of release medium used. The serum stability of PO ODNs was significantly improved when entrapped within P(LA-GA) microspheres and the hybridization capability, as assessed by duplex melting (Tm) measurements, of released ODN was not impaired by the double-emulsion microsphere fabrication procedure used. Thus, P(LA-GA) microspheres appear to be promising candidates for improving site-specific delivery profiles for ODNs and are worthy of further evaluation in vivo.