gebhart/patrepeval huggingface dataset:
Effects of Topical Application of Acidified Omeprazole on Acid Secretion and Transmucosal Potential Difference in Anesthetized Rat Stomachs (1988)

Effects of topical application of omeprazole on transmucosal potential difference (PD), luminal pH and histamine-stimulated acid secretion were examined in anesthetized rat stomachs, and they were compared with those of systemic administration. Omeprazole was suspended in 1% CMC with NaHCO3 (pH 9.0) or dissolved in 0.1 Ν HCl (pH 1.0). Both omeprazole (30 mg/kg, pH 9.0) and cimetidine (100 mg/kg), given i.d., increased the pH and inhibited acid secretion induced by histamine (8 mg/kg/hr, i.V.), while basal gastric PD was markedly elevated only by the former. Similar responses in PD, pH and acid output were obtained dose-dependently after brief exposure of the stomach (10 min) to omeprazole (0.3-30 mg/kg), even in acidic conditions, but the effects of acidified omeprazole disappeared depending upon the latency period in 0.1 Ν HCl. there was no effect when applied at more than 30 min after dissolution. Of interest, subsequent exposure of the stomach to a mercaptane compound (cysteine, 100 mg/kg) for 30 min significantly reversed the antisecretory effect of omeprazole (both i.d. and i.g.) but not of cimetidine. These results suggest that omeprazole has a local antisecretory action even in acidic stomachs, probably through an inhibition of the H+/K+ ATPase activity, and the increase of PD caused by omeprazole may be a characteristic phenomenon seen after the blockade of H+/K+ ATPase, but is not associated with acid inhibition itself.
Modulation of tumor angiogenesis by stem cell factor. (2000)

Mast cells accumulate within solid tumors and can release many angiogenic factors, suggesting that they may modulate vascularization of tumors. Stem cell factor (SCF) stimulates mast cell migration, proliferation, and degranulation and therefore may influence mast cell behavior within tumors. We investigated the contribution of SCF to tumor angiogenesis by manipulating its level in mammary tumors. Sense or antisense cDNA fragments of rat SCF were ligated into an episomal expression vector. Ethylnitrosourea-induced rat mammary tumor cell lines were transfected with vector containing either control (no insert, C-P), sense (S-P), or antisense (AS-P) SCF DNA. The functional nature of the transfectants was confirmed by measuring SCF in cell lysates and conditioned media. Immunohistochemical analysis of the tumors induced in Berlin-Druckrey rats by these transfected cells demonstrated that mast cell number and microvascular density were significantly higher in S-P tumors and significantly lower in AS-P tumors, compared with C-P tumors. The expression of von Willebrand factor, an endothelial cell marker, showed a similar pattern. AS-P tumors were significantly smaller than either C-P or S-P tumors. These data suggest that SCF modulates tumor growth and angiogenesis via the involvement of mast cells.
Bcl11a Causes p21Cip1 Down-Regulation and Transplantable Leukemia in Nf1-Deficient Mice. (2007)

Abstract Inactivation of the tumor suppressor gene, NF1, is associated with chronic and acute forms of myeloid diseases including juvenile myelomonocytic leukemia. Nf1-deficiency mouse models have shown some phenotypes reminiscent of those of the human disease. However, Nf1mutation in itself does not lead to leukemia. We reported the identification of 37 common proviral insertion sites, loci containing candidate genes whose mutation could cooperate with inactivation of Nf1 to result in BXH-2 AML. Among these candidate genes, Bcl11a, was able to cause leukemia/lymphoma in bone marrow transduction and transplantation assay using Nf1-deficient cells. In this report, we have found that transplantation of these leukemia cells induced secondary leukemia in syngeneic recipient mice. In patients, we previously reported that BCL11A was expressed in juvenile myelomonocytic leukemia and chronic myelomonocytic leukemia samples. Interestingly, high expression levels of BCL11A are also observed in two specific subsets of samples from a large cohort of patients with acute myelogenous leukemia. Moreover, these subsets of patients tended to have a worse outcome. Regarding the biochemical mechanisms underlying the oncogenicity of Bcl11a, we have recently found that p21Cip1 induction by doxorubicin is severely impaired in Bcl11a-expressing cells, while other cell-cycle regulatory proteins are not affected. Examination of BCL11A’s role in leukemia patients using both over-expression and shRNA knocking-down approaches is underway.
Endometrial Carcinoma Biomarker Discovery and Verification Using Differentially Tagged Clinical Samples with Multidimensional Liquid Chromatography and Tandem Mass Spectrometry (2007)

The utility of differentially expressed proteins discovered and identified in an earlier study (DeSouza, L., Diehl, G., Rodrigues, M. J., Guo, J., Romaschin, A. D., Colgan, T. J., and Siu, K. W. M. (2005) Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cleavable ICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 4, 377-386) to discriminate malignant and benign endometrial tissue samples was verified in a 40-sample iTRAQ (isobaric tags for relative and absolute quantitation) labeling study involving normal proliferative and secretory samples and Types I and II endometrial cancer samples. None of these proteins had the sensitivity and specificity to be used individually to discriminate between normal and cancer samples. However, a panel of pyruvate kinase, chaperonin 10, and alpha1-antitrypsin achieved the best results with a sensitivity, specificity, predictive value, and positive predictive value of 0.95 each in a logistic regression analysis. In addition, three new potential markers were discovered, whereas two other proteins showed promising trends but were not detected in sufficient numbers of samples to permit statistical validation. Differential expressions of some of these candidate biomarkers were independently verified using immunohistochemistry.
Modelling Clip: Some More Results (1990)

Abstract The modedling clip of the PHIGS ISO Standard is mathematically analysed. The most important result of this analysis is the fact that the projective image of a modding clip body (that is a not necessarily bounded convex body in space) is simply the union of two convex bodies. Furthermore, it will also be proved that in some cases one of these two bodies is empty. This fact makes the implementation of the modelling clip fairly straightforward and makes it also possible to use all already existing results on clipping against general convex bodies without change.
Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization (2009)

The ability to use lactate as a sole source of carbon and energy is one of the key metabolic signatures of Shewanellae, a diverse group of dissimilatory metal-reducing bacteria commonly found in aquatic and sedimentary environments. Nonetheless, homology searches failed to recognize orthologs of previously described bacterial d- or l-lactate oxidizing enzymes (Escherichia coli genes dld and lldD) in any of the 13 analyzed genomes of Shewanella spp. By using comparative genomic techniques, we identified a conserved chromosomal gene cluster in Shewanella oneidensis MR-1 (locus tag: SO_1522-SO_1518) containing lactate permease and candidate genes for both d- and l-lactate dehydrogenase enzymes. The predicted d-LDH gene (dld-II, SO_1521) is a distant homolog of FAD-dependent lactate dehydrogenase from yeast, whereas the predicted l-LDH is encoded by 3 genes with previously unknown functions (lldEGF, SO_1520-SO_1518). Through a combination of genetic and biochemical techniques, we experimentally confirmed the predicted physiological role of these novel genes in S. oneidensis MR-1 and carried out successful functional validation studies in Escherichia coli and Bacillus subtilis. We conclusively showed that dld-II and lldEFG encode fully functional d-and l-LDH enzymes, which catalyze the oxidation of the respective lactate stereoisomers to pyruvate. Notably, the S. oneidensis MR-1 LldEFG enzyme is a previously uncharacterized example of a multisubunit lactate oxidase. Comparative analysis of >400 bacterial species revealed the presence of LldEFG and Dld-II in a broad range of diverse species accentuating the potential importance of these previously unknown proteins in microbial metabolism.
Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons (2011)

Exon-intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon-intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3' and 5' splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery.
Circulating antibodies against c‐MYC oncogene product in sera of colorectal cancer patients (1990)

We developed a Western blot assay using purified human c-myc protein expressed in E. coli in order to look for circulating anti-c-myc antibodies in human sera. The presence of IgG antibodies against c-myc was observed in 25 out of 44 sera from patients with colorectal cancer diagnosed and treated at the Hôpital Curie in Paris, compared to the sera of 46 normal donors of which only 8 samples were positive (p = 0.001).
Unexpected effects of the severe combined immunodeficiency mutation on murine lymphomagenesis. (1992)

Strain C.B17 scid/scid (SCID) mice, which lack functional T and B lymphocytes, show heightened susceptibility to the induction of thymic lymphomas by x-irradiation. Susceptibility is highest in thymus-chimeric SCID-BL mice (thymectomized SCID mice bearing a C57BL thymus graft). All SCID-BL lymphomas originate in the cells of the thymic graft (C57BL type) and lack murine leukemia virus expression. Both SCID and SCID-BL lymphomas are phenotypically CD4-8+ and/or CD4+8+, but only the SCID-BL tumors express CD3. Injection of C57BL or BALB/c bone marrow into irradiated SCID-BL mice prevents lymphoma development, but SCID marrow is completely ineffective. The results suggest that the scid condition enhances the activity of a putative lymphomagenic agent induced in the bone marrow by x-irradiation and that C57BL thymic cells are highly sensitive targets. Moreover, the failure of SCID bone marrow to protect against lymphomagenesis vs. the efficacy of marrow from immunocompetent donors points to involvement of T or B lineage cells in this process.
Genomic Structure and Nucleotide Sequence Analysis of a New HIV Type 1 Subtype A Strain from Nigeria (1996)

We have isolated and characterized a new HIV-1 variant (HIV-1IbNg) from the peripheral blood mononuclear cells (PBMCs) of an inhabitant of Nigeria. This virus is highly cytopathic to PBMCs in culture, replicates in primary human T cells and macrophages/monocytes as well as in established human T cell and monocytic cell lines (i.e., it has a wide host range), and it does not induce syncytia in MT-2 cells.1 Because of these unusual infectivity parameters in vitro, we analyzed the genetic structure of the entire genome. Using cytoplasmic RNA from HIV-1IbNg-infected PBMCs, five overlapping DNA fragments were amplified by the reverse transcriptase-polymerase chain reaction (RT-PCR) technique and cloned into pBluescript II SK(+). DNA sequencing of these fragments indicated that the entire HIV-1IbNg genome consisted of 9201 nucleotides and phylogenetic analysis of its env gene sequence revealed that this virus clustered with HIV-1 strains belonging to clade "A". In this article we present several genetic features unique to this virus, including (1) the presence of a 16-bp insert within the primer-binding site, (2) a large Rev open reading frame, (3) a Rev-responsive element that is predicted to form a different secondary structure than described for clade "B" viruses, (4) the potential to encode a heavily glycosylated Env protein, and (5) a frameshift, resulting in a stop codon, in the tat gene. This represents the first detailed analysis of the genetic structure of an HIV-1 strain from Nigeria.
The Squalestatins: Synthesis and Biological Activity of Some C3-Modified Analogs; Replacement of a Carboxylic Acid or Methyl Ester with an Isoelectronic Heterocyclic Functionality (1995)

A series of squalestatins modified at the C3-position with a heterocyclic functionality was prepared and evaluated in vitro as inhibitors of squalene synthase (SQS). Structure-activity relationships for compounds with the 4,6-dimethyloctenoate at C6(S1 analogues) were different from those for analogues lacking the C6 ester (H1 analogues), with a greater dependence on the nature of the C3-substituent for the H1 series. Potent SQS inhibitory activity equivalent to that of H1 is retained by a C3-(tetrazol-5-yl) analogue, i.e., a carboxylic acid mimetic. The C3-methyl ester derivative is 10-fold less active than H1, and SQS inhibitory activity similar to that of the methyl ester was retained only in those C3-heterocycle-substituted H1 analogues for which electrostatic potential maps of the C3-substituent were closely similar to that of a methyl ester.
Multistep sequential batch assembly of three-dimensional ferromagnetic microstructures with elastic hinges (2005)

In this paper, we have developed a process for multistep sequential batch assembly of complex three-dimensional (3-D) ferromagnetic microstructures. The process uses the magnetic torque generated by an external magnetic field perpendicular to the substrate to lift hinged structures. We found that a dimensionless factor that depends on the volume of the magnetic material and the stiffness of the hinges determines the sensitivity of the hinged microstructures to a magnetic field. This factor was used as a criterion in designing a process for sequential batch assembly, i.e., for setting appropriate differences in sensitivity. Using a dimensionless factor in the design of the sequential assembly simplified the assembly process, which requires only placing the structures on a permanent magnet, and which can be used to carry out multistep sequential batch assembly. We fabricated hinged microstructures, which consist of 4.5-/spl mu/m-thick electroplated Permalloy plates and 200-nm-thick nickel elastic hinges of various sizes. In an experiment, four plates (600 /spl mu/m/spl times/800 /spl mu/m) were lifted sequentially and out-of-plane microstructures were assembled in a four-step process. Assembly of more complex out-of-plane microstructures (e.g., regular tetrahedrons, 800 /spl mu/m long on one side) was also shown to be feasible using this method of sequential batch assembly. [1351].
Response to Draft Recommendations for Health System Reform (1996)

The final report of the Maine Health Care Reform Commission (MHCRC) was submitted to Governor Angus King in November, 1995. Given the complexity of what we call the healthcare system as well as the moving targets of federal and state incentives for reform, the report accomplished a great deal in a short period of time. Commission members were "mandated to offer a single payer universal coverage bill, a multiple payer universal coverage bill, and a bill to achieve reform through incremental changes to the existing system, emphasizing cost containment, managed care, and improved access. The commission was also mandated to cost out its recommendations" Reactions to the MHCRC report were invited from individuals who represent constituencies which often have an influential role in healthcare. Five commentaries address pros and cons of particular elements of the commission’s report. Dale Gordon and Kim Boothby-Ballantyne offer a nursing perspective in this commentary.
Yeast Carbon Catabolite Repression (1998)

Glucose and related sugars repress the transcription of genes encoding enzymes required for the utilization of alternative carbon sources; some of these genes are also repressed by other sugars such as galactose, and the process is known as catabolite repression. The different sugars produce signals which modify the conformation of certain proteins that, in turn, directly or through a regulatory cascade affect the expression of the genes subject to catabolite repression. These genes are not all controlled by a single set of regulatory proteins, but there are different circuits of repression for different groups of genes. However, the protein kinase Snf1/Cat1 is shared by the various circuits and is therefore a central element in the regulatory process. Snf1 is not operative in the presence of glucose, and preliminary evidence suggests that Snf1 is in a dephosphorylated state under these conditions. However, the enzymes that phosphorylate and dephosphorylate Snf1 have not been identified, and it is not known how the presence of glucose may affect their activity. What has been established is that Snf1 remains active in mutants lacking either the proteins Grr1/Cat80 or Hxk2 or the Glc7 complex, which functions as a protein phosphatase. One of the main roles of Snf1 is to relieve repression by the Mig1 complex, but it is also required for the operation of transcription factors such as Adr1 and possibly other factors that are still unidentified. Although our knowledge of catabolite repression is still very incomplete, it is possible in certain cases to propose a partial model of the way in which the different elements involved in catabolite repression may be integrated.
Effects of Botulinum a Toxin on Detrusor-Sphincter Dyssynergia in Spinal Cord Injury Patients (1988)

We evaluated the ability of low doses of botulinum A toxin, an inhibitor of acetylcholine release at the neuromuscular junction, to denervate and relax the spastic rhabdosphincter in 11 men with spinal cord injury and detrusor-sphincter dyssynergia. Toxin concentration, injection volume, percutaneous versus cystoscopic injection of the sphincter and number of injections were evaluated in 3 treatment protocols. All 10 patients evaluated by electromyography after injection showed signs of sphincter denervation. Bulbosphincteric reflexes in the 10 patients evaluated after injection were more difficult to obtain, and they showed a decreased amplitude and normal latency. The urethral pressure profile in the 7 patients in whom it was measured before and after treatment decreased an average of 27 cm. water after toxin injections. Post-void residual urine volume decreased by an average of 146 cc after the toxin injections in 8 patients. In the 8 patients for whom it could be determined toxin effects lasted an average of 50 days. The toxin also decreased autonomic dysreflexia in 5 patients.
Activation of molecular oxygen: rhodium-catalyzed oxidation of olefins (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTActivation of molecular oxygen: rhodium-catalyzed oxidation of olefinsHubert Mimoun, M. Mercedes Perez Machirant, and Irenee Seree de RochCite this: J. Am. Chem. Soc. 1978, 100, 17, 5437–5444Publication Date (Print):August 1, 1978Publication History Published online1 May 2002Published inissue 1 August 1978https://pubs.acs.org/doi/10.1021/ja00485a031https://doi.org/10.1021/ja00485a031research-articleACS PublicationsRequest reuse permissionsArticle Views1204Altmetric-Citations135LEARN 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
Direct Imprinting of Porous Substrates: A Rapid and Low-Cost Approach for Patterning Porous Nanomaterials (2010)

This work describes a technique for one-step, direct patterning of porous nanomaterials, including insulators, semiconductors, and metals without the need for intermediate polymer processing or dry etching steps. Our process, which we call "direct imprinting of porous substrates (DIPS)", utilizes reusable stamps with micro- and nanoscale features that are applied directly to a porous material to selectively compress or crush the porous network. The stamp pattern is transferred to the porous material with high fidelity, vertical resolution below 5 nm, and lateral resolution below 100 nm. The process is performed in less than one minute at room temperature and at standard atmospheric pressure. We have demonstrated structures ranging from subwavelength optical components to microparticles and present exciting avenues for applications including surface-enhanced Raman spectroscopy (SERS), label-free biosensors, and drug delivery.
-globin mRNAs capped with m7G, m22.7G or m32.2.7G differ in intrinsic translation efficiency (1988)

We examined the intramolecular effect of altered cap structures on translation efficiency of artificial beta-globin mRNAs. For these studies, synthetic dinucleotides of the form X(5')ppp(5')G [X = 7-methyl guanosine (m7G), 2,7-dimethyl guanosine (m2(2,7)G) or 2,2,7-trimethyl guanosine (m3(2,2,7)G)], were transcriptionally incorporated into mRNAs, containing rabbit beta-globin coding sequences, using T7 RNA polymerase and a beta-globin cDNA template. These synthetic mRNAs were assayed in reticulocyte lysate for activity relative to m7G-capped mRNA. m2(2,7)G-Capped mRNA was found to be 1.5-fold more active than m7G-capped mRNA. Messenger RNA capped with m3(2,2,7)G was less active with activity of 0.24 relative to its m7G-capped counterpart (activity = 1.0). These data suggest that m7G-capped mRNAs become more active as translation templates after addition of a single N2 methyl moiety, which is especially pertinent to gene expression in togaviridae. The latter are observed to synthesize m2(2,7)G and m3(2,2,7)G-capped mRNAs in addition to m7G-capped templates during the course of infection in animal cells.