gebhart/patrepeval huggingface dataset:
The role of alterations in free radical metabolism in mediating cognitive impairments in Down’s syndrome (1992)

Down's syndrome (DS) is a genetic disorder involving an excess of chromosome 21 (trisomy 21) in approximately 96% of the cases and comprises approximately 15% of the population with mental retardation (Heller, 1969). In addition to the constitutional mental deficiencies associated with the syndrome many DS patients develop dementia associated with Alzheimer's disease (AD) in their later years of life (Thase et al., 1984). The genetic locus for Cu,Zn-superoxide dismutase (SOD1), a key enzyme in free radical metabolism, is located on chromosome 21, and the activity level of this enzyme is elevated by approximately 50% in a variety of cells of DS patients (see Kedziora and Bartosz, 1988; Sinet, 1982). Because alterations in free radical metabolism may be involved in neuronal death and may be associated with a number of pathological manifestations of DS, it is important to understand the role of free radical metabolism in cognitive impairments of DS, the topic discussed in this chapter.
13N ammonia myocardial imaging at rest and with exercise in normal volunteers. Quantification of absolute myocardial perfusion with dynamic positron emission tomography. (1989)

Positron emission tomography (PET) was applied to the measurement of myocardial perfusion using the perfusion tracer 13N-labeled ammonia. 13N ammonia was delivered intravenously to 13 healthy volunteers both at rest and during supine bicycle exercise. Dynamic PET imaging was obtained in three cross-sectional planes for 10 minutes commencing with each injection. The left ventricle was divided into eight sectors, and a small region of interest was assigned to the left ventricular blood pool to obtain the arterial input function. The net extraction of 13N ammonia was obtained for each sector by dividing the tissue 13N concentration at 10 minutes by the integral of the input function from the time of injection to 10 minutes. With this approach for calculating net extractions, rest and exercise net extractions were not significantly different from each other. To obviate possible overestimation of the true 13N ammonia input function by contamination by 13N-labeled compounds other than 13N ammonia or by spillover from myocardium into blood pool, the net extractions were calculated using only the first 90 seconds of the blood and tissue time-activity curves. This approach for calculating net extractions yielded significant differences between rest and exercise, with an average ratio of exercise to rest of 1.38 +/- 0.34. Nonetheless, the increase was less than predicted from the average 2.7-2.8-fold increase in double product at peak exercise or the 1.7-fold increase in double product at 1 minute after exercise. However, when the first 90 seconds of dynamic data were fit with a two compartment tracer kinetic model, average perfusion rates of 0.75 +/- 0.43 ml/min/g at rest and 1.50 +/- 0.74 ml/min/g with exercise were obtained. This average increase in perfusion of 2.2-fold corresponded to similar average increases in double product. Thus, the noninvasive technique of PET imaging with 13N ammonia shows promise for future applications in determining absolute flows in patients with coronary artery disease.
Limited value of preoperative serum analyses of matrix metalloproteinases (MMP-2, MMP-9) and tissue inhibitors of matrix metalloproteinases (TIMP-1, TIMP-2) in colorectal cancer. (2000)

Serum analyses of free MMP-2 the MMP-2/TIMP-2 complex and total amounts of MMP-9, TIMP-1 and TIMP-2 are of limited value for tumor staging and prognosis in colorectal cancer.
Liver regeneration is transiently impaired in urokinase-deficient mice (1998)

To test the hypothesis that urokinase-type plasminogen activator (uPA) plays an important role in liver regeneration in vivo, partial hepatectomy was performed on wild-type and uPA-deficient (uPA-/-) mice. Mice were studied at 24, 44, and 96 h and at 8 days and 4 wk post-partial hepatectomy for evidence of regeneration, as measured by mitotic indexes and [3H]thymidine incorporation. In wild-type mice, thymidine incorporation peaked at 44 h and this index was reduced by 47% in uPA-/- mice (P = 0.02). By 8 days, however, liver mass was comparable in both groups. Histological analysis revealed the presence of focal areas of fibrin deposition and cellular loss by 24 h that were more severe and prevalent in uPA-/- mice than in wild-type mice (62 and 23%, respectively; chi2 = 3.939, P = 0.047). In contrast, regeneration was not impaired in uPA receptor (uPAR)-deficient mice at 24 and 44 h. Taken together, these data indicate that uPA, independent of its interaction with the uPAR, plays an important role in liver regeneration in vivo.
Use of a cell-free system to identify the vaccinia virus L1R gene product as the major late myristylated virion protein M25 (1990)

A 25-kDa vaccinia virus (VV) virion protein, designated M25, is modified in vivo by covalent addition of myristic acid. The predicted amino acid sequences of all VV open reading frames which have been reported were searched for the sequence M-G-X-X-X-(S/T/A), which has been proposed to be the consensus recognition signal for cotranslational modification of proteins by N-myristyltransferase. This conserved signal was found at the amino terminus of a single locus, which corresponded to the leftmost rightward-reading open reading frame (L1R) initiating within the VV HindIII L DNA fragment. By using synthetic oligonucleotides in concert with polymerase chain reaction techniques, a chimeric gene consisting of open reading fram L1R fused to a bacteriophage T7 promoter was constructed and cloned into a plasmid vector. Transcripts derived from the wild-type expression plasmid (designated pL1G1) were translated in vitro in a wheat germ extract to yield a polypeptide with an apparent molecular mass of 25 kDa. This polypeptide was labeled with either [35S]methionine or [3H]myristic acid and comigrated with in vivo-labeled protein M25 on sodium dodecyl sulfate-polyacrylamide gels. Polyclonal antiserum generated in rabbits against a trpE:L1R fusion protein immunoprecipitated a 25-kDa protein labeled either in vitro (the L1R gene product, designated protein L1) or in vivo (from purified VV, protein M25), identifying the M25 protein as the gene product of open reading frame L1R. Chromatographic analysis of the protein L1-bound fatty acid moieties liberated after acid methanolysis resulted in recovery of greater than 99% of the fatty acid as myristate-associated label. Cell-free translation of proteins derived from a set of deletions from the carboxy terminus of the open reading frame L1R suggested that the site of myristylation maps near the amino terminus of protein L1. This hypothesis was supported by cell-free translation of mutant L1R transcripts in which the penultimate glycine codon had been altered by site-directed mutagenesis to encode either an aspartic acid (pL1D1) or alanine (pL1A1) residue. In both cases, the mutant transcripts were translated into a 25-kDa protein which could be labeled in vitro with [35S]methionine but not with [3H]myristic acid. These data demonstrate that VV open reading frame L1R encodes a myristylated protein and provide evidence that the site of modification of protein L1 is the amino-terminal glycine residue.
A Methodology for Product Family Ontology Development Using Formal Concept Analysis and Web Ontology Language (2005)

The use of ontologies for information sharing is well documented in the literature, but the lack of a comprehensive and systematic methodology for constructing product ontologies has limited the process of developing ontologies for design artifacts. In this paper we introduce the Product Family Ontology Development Methodology (PFODM), a novel methodology to develop formal product ontologies using the Semantic Web paradigm. Within PFODM, Formal Concept Analysis (FCA) is used first to identify similarities among a finite set of design artifacts based on their properties and then to develop and refine a product family ontology using Web Ontology Language (OWL). A family of seven one-time-use cameras is used to demonstrate the steps of the PFODM to construct such an ontology. The benefit of PFODM lies in providing a systematic and consistent methodology for constructing ontologies to support product family design. The resulting ontologies provide a hierarchical conceptual clustering of related design artifacts, which is particularly advantageous for product family design where parts, processes, and most important, information is intentionally shared and reused to reduce complexity, lead-time, and development costs. Potential uses of the resulting ontologies and FCA representations within product family design are also discussed.
Identifying Diabetic Patients at High Risk for Lower-Extremity Amputation in a Primary Health Care Setting: A prospective evaluation of simple screening criteria (1992)

These data suggest that the risk categorization described here may have a role in identifying patients at risk for lower extremity events who are followed in a primary-care setting.
Wnt signalling in lung development and diseases (2006)

There are several signalling pathways involved in lung organogenesis including Notch, TGFbeta/BMP, Sonic hedgehog (Shh), FGF, EGF, and Wnt. Despite the widely acknowledged significance of Wnt signalling in embryonic lung development, the role of different Wnt pathways in lung pathologies has been slow to emerge. In this review, we will present a synopsis of current Wnt research with particular attention paid to the role of Wnt signals in lung development and in pulmonary diseases.
Proteins Specified by bovine herpesvirus 1 (infectious bovine rhinotracheitis virus) (1981)

An electrophoretic analysis of radioactively labeled, purified, "empty" and DNA-containing infectious bovine rhinotracheitis virions revealed the presence of 25 to 33 structural (virion) polypeptides. A total of 11 of these polypeptides could be labeled with [3H]glucosamine and were identified as glycoproteins. In addition to the 25 structural polypeptides, infectious bovine rhinotracheitis virus infected cells also contained at least 15 nonstructural (nonvirion) polypeptides that were not present in purified virions. Expression of the viral polypeptides in infected cells was controlled temporally. Thus, most viral polypeptides could be categorized as "alpha" (immediate early), "beta" (early), or "gamma" (late) on the basis of their order of appearance in infected cells and whether their syntheses were dependent upon prior viral protein or DNA synthesis. None of the glycoproteins belongs to the alpha class, although at least one (GVP11) was synthesized in the absence of viral DNA synthesis. Serum from a cow in which infectious bovine rhinotracheitis virus lesions were reactivated by dexamethasone precipitated both structural and nonstructural polypeptides.
Facile synthesis of concentrated gold nanoparticles with low size-distribution in water: temperature and pH controls (2011)

The citrate reduction method for the synthesis of gold nanoparticles (GNPs) has known advantages but usually provides the products with low nanoparticle concentration and limits its application. Herein, we report a facile method to synthesize GNPs from concentrated chloroauric acid (2.5 mM) via adding sodium hydroxide and controlling the temperature. It was found that adding a proper amount of sodium hydroxide can produce uniform concentrated GNPs with low size distribution; otherwise, the largely distributed nanoparticles or instable colloids were obtained. The low reaction temperature is helpful to control the nanoparticle formation rate, and uniform GNPs can be obtained in presence of optimized NaOH concentrations. The pH values of the obtained uniform GNPs were found to be very near to neutral, and the pH influence on the particle size distribution may reveal the different formation mechanism of GNPs at high or low pH condition. Moreover, this modified synthesis method can save more than 90% energy in the heating step. Such environmental-friendly synthesis method for gold nanoparticles may have a great potential in large-scale manufacturing for commercial and industrial demand.
Participation of lysine 516 and phenylalanine 530 of diphtheria toxin in receptor recognition. (1994)

To identify amino acid residues within diphtheria toxin that participate in receptor recognition, we made alanine replacements for each of 12 solvent-accessible residues within a loop (residues 516-530) of the toxin's R domain, which prominently extends from the main surface of the domain. Amino acid replacements were generated in an enzymatically attenuated form of the toxin (in compliance with regulations for cloning in Escherichia coli), and the mutant toxins were purified and assayed for toxicity on Vero cells. The largest effects were seen with K516A and F530A, which caused approximately 22- and approximately 10-fold increases, respectively, in the toxin concentration required for half-maximal inhibition of protein synthesis (IC50). Smaller effects were seen at certain other sites and no effect at still others. K516A caused approximately 500-fold reduction in ability to compete with radiolabeled wild-type toxin for receptors, and F530A gave approximately 100-fold reduction. The small differences in IC50 with the mutants, compared with differences in receptor binding, are attributable to nonlinearity in the cytotoxicity assay with the enzymatically attenuated toxin. K516A and F530A also inhibited the receptor-blocking activity of the isolated R domain. Neither mutation caused a change in the circular dichroism spectrum of the R domain. These results indicate important roles for Lys-516 and Phe-530 in receptor recognition. In addition, on the basis of cytotoxicity data, four other residues (Tyr-514, Val-523, Asn-524, and Lys-526) are proposed play roles in receptor binding. These findings support the notion that the toxin's receptor binds to the solvent-exposed face of the R domain opposite the catalytic domain.
Surface Plasmon Resonance Imaging Measurements of Electrostatic Biopolymer Adsorption onto Chemically Modified Gold Surfaces (1997)

A combination of in situ and ex situ surface plasmon resonance (SPR) imaging experiments is used to characterize the differential electrostatic adsorption of proteins and synthetic polypeptides onto photopatterned monolayers at gold surfaces. The nonspecific electrostatic adsorption of proteins onto negatively charged self-assembled monolayers (SAMs) of 11-mercaptoundecanoic acid (MUA) is found to depend on the protein pI, solution ionic strength, and solution pH. The pH dependence of the electrostatic adsorption of the protein avidin onto a MUA SAM indicates that a full monolayer adsorbs at a solution pH greater than 5.0, and an "effective pK(a)" of 3.6 is determined for the avidin adsorption. This effective pK(a) is a combination of the pK(a) of the MUA monolayer and the ion pairing adsorption coefficient for the avidin. Additional SPR imaging experiments show that the electrostatic adsorption of the synthetic polypeptide poly-l-lysine (PL) onto a MUA SAM varies with molecular weight, forming a full PL monolayer for polypeptides with more than 67 lysine residues.
Relative abilities of bis(ethyl) derivatives of putrescine, spermidine, and spermine to regulate polyamine biosynthesis and inhibit L1210 leukemia cell growth. (1987)

It has been shown previously (Porter et al., Cancer Res., 45: 2050-2057, 1985) that the N1,N8-bis(ethyl) derivative of spermidine has significant antiproliferative activity which appears to derive from its regulatory effects on the polyamine biosynthetic pathway, particularly on ornithine decarboxylase activity. In the present study, N1,N4-bis(ethyl)putrescine (BEP) and N1,N12-bis(ethyl)spermine (BESm) were compared with N1,N8-bis(ethyl)spermidine (BES) in their ability to inhibit cell growth and regulate polyamine biosynthesis. With cultured L1210 murine leukemia cells, the IC50 values at 48 h were approximately 2 mM for BEP, 30 microM for BES, and 1 microM for BESm making the latter the most effective polyamine inhibitor or analogue thus far identified. At concentrations which approximated IC50 values and yielded similar intracellular concentrations at 48 h (1500-2000 pmol/10(6) cells), the effects of the analogues on polyamine biosynthesis generally correlated with their antiproliferative activity. BEP, at 1 mM, exerted relatively minor effects on polyamine biosynthesis. By contrast, 100 microM BES totally eliminated ornithine decarboxylase activity, depleted putrescine and spermidine pools, and decreased spermine pools by 40%. AdoMet decarboxylase activity was lowered slightly. The most impressive effects were obtained with 10 microM BESm which decreased ornithine and AdoMet decarboxylase activities by 99 and 84%, respectively; depleted putrescine and spermidine pools; and decreased spermine pools by 73%. None of the analogues, at 1 or 3 mM, had significant direct inhibitory effects on the decarboxylase activities from untreated cells with the exception of BESm which inhibited ornithine but not AdoMet decarboxylase activity. Thus, the effects of the analogues on these enzymes in treated cells are presumed to be mainly mediated by regulatory mechanisms. In this regard, BESm was superior to BES since both ornithine and AdoMet decarboxylase activities were suppressed. Given its unique activities, BESm would seem to have potential as both an antiproliferative agent and also as an experimental probe for studying regulation of the polyamine pathway, particularly AdoMet decarboxylase.
Extracellular and surface-exposed polysaccharides of non-tuberculous mycobacteria (1996)

We studied the outermost constituents of the cell envelopes, which are involved in the interaction between the bacilli and the host cells, of five pathogenic and non-pathogenic mycobacterial species for comparison with those we have previously characterized from M. tuberculosis . The extracellular materials (ECMs) were isolated by ethanol precipitation and compared to the surface-exposed materials (SXMs) extracted by mechanical means. The materials from both sources were composed almost exclusively of polysaccharides and proteins. Two groups of mycobacteria were clearly distinguishable. The first group comprised the pathogenic species M. kansasii which produced large amounts of ECM, the glycosyl composition of which was similar to that of the SXM. The second group comprised M. avium and the non-pathogenic strains of M. gastri, M. phlei and M. smegmatis which produced small amounts of ECM. This latter group could be subdivided into those which produced carbohydrate-rich ECM ( M. avium and M. gastri ) and those forming protein-rich ECM ( M. phlei and M. smegmatis ), a classification that correlated with the difference in the growth rate of the two subgroups. The glycosyl composition of the ECM of a given species was qualitatively similar to that of the SXM, except for M. avium and M. phlei whose SXM were devoid of arabinose. In addition to glucose, mannose and arabinose, xylose was detected in the hydrolysis products of the ECM and SXM of M. smegmatis , the SXM of M. phlei and the ECM of some batches of M. avium . The polysaccharide constituents of the ECM and SXM of the different mycobacteria were purified by anion-exchange and gel-filtration chromatography; all were found to be neutral compounds devoid of acyl substituents. The extracellular polysaccharides consisted of high-molecular-mass glycogen-like glucans, arabinomannans and mannans, structurally similar to the corresponding substances previously characterized from the capsule of M. tuberculosis . The same types of polysaccharides were characterized from the SXM of all the strains, except M. avium and M. phlei which were devoid of arabinomannans. This study questions the unique and universal representation of the mycobacterial cell envelope and the existence of the so-called acidic polysaccharide-rich outer layer.
Selective carbon-carbon bond formation by cross-coupling of Grignard reagents with organic halides. Catalysis by nickel-phosphine complexes (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective carbon-carbon bond formation by cross-coupling of Grignard reagents with organic halides. Catalysis by nickel-phosphine complexesKohei Tamao, Koji Sumitani, and Makoto KumadaCite this: J. Am. Chem. Soc. 1972, 94, 12, 4374–4376Publication Date (Print):June 1, 1972Publication History Published online1 May 2002Published inissue 1 June 1972https://pubs.acs.org/doi/10.1021/ja00767a075https://doi.org/10.1021/ja00767a075research-articleACS PublicationsRequest reuse permissionsArticle Views16875Altmetric-Citations1098LEARN 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
Specific peptides identified by mass spectrometry in placental tissue from pregnancies complicated by early onset preeclampsia attained by laser capture dissection (2007)

Preeclampsia is a common pregnancy-specific syndrome that is diagnosed by the appearance of both increased blood pressure and proteinuria. Preeclampsia is associated with significant fetal and maternal morbidity and mortality. Although the etiology of preeclampsia is unknown, it is evident that abnormal placentation and trophoblast metabolism plays an important role. We therefore analyzed, identified, and verified specific proteins of villous trophoblast and villous stroma in small numbers of microdissected cells (approximately 125 cells) from seven placentas of women with pregnancies complicated by preeclampsia (cases) and seven uncomplicated pregnancies (controls). Tryptic peptide profiling by MALDI-TOF MS was used for comparison and identification of significantly expressed peptides. The data were analyzed by ClinProTools (Bruker Daltonics) and by principal component analysis. Subsequently, a subset of placental tissues were homogenized and separated on a NanoLC system to obtain sequencing information (MS/MS spectra). We identified specific peptide patterns in the different cell types: villous stroma and trophoblast cells and differences in these cells of placentas from women with pregnancies complicated by early compared to late onset preeclampsia (<34 and >34 wk gestation, respectively) and controls. Principal component analysis revealed significant differences between the groups. The comparison with placental tissue after preterm delivery with unknown cause revealed that placental peptide patterns in early onset preeclampsia could not be explained by preterm delivery per se. Subsequently, specific, discriminating proteins for early onset preeclampsia compared to controls were identified including calcyclin, surfeit locus protein, and choriomammotropin A precursor. The expression of calcyclin was verified in early onset preeclamptic placental sections by immunohistochemistry. These data suggest that in early onset preeclampsia trophoblastic choriomammotropin regulation is abnormal, possibly through abnormal calcyclin expression and regulation.