gebhart/patrepeval huggingface dataset:
Relationship between symptom pattern, assessed by the PAGI‐SYM© questionnaire, and gastric sensorimotor dysfunction in functional dyspepsia (2009)

The patient assessment of upper gastrointestinal symptom severity index (PAGI-SYM) questionnaire was recently developed and validated for the evaluation of therapeutic responsiveness in functional dyspepsia (FD). Functional dyspepsia is a heterogeneous disorder, with different pathophysiological mechanisms underlying the symptom pattern. The relationship between PAGI-SYM scores and putative pathophysiological mechanisms has not been studied. The aim of this study was to evaluate the relationship between PAGI-SYM subscales and gastric emptying, gastric sensitivity and gastric accommodation in FD. A total of 161 consecutive FD patients underwent Helicobacter pylori (HP), gastric barostat and standardized gastric emptying testing (n = 126), and completed the PAGI-SYM questionnaire. Relationships between scores for the six subscales (heartburn/regurgitation, nausea/vomiting, fullness/satiety, bloating, upper abdominal pain, lower abdominal pain) and gastric function were analysed using Pearson's linear correlation, multiple regression analysis, chi-square and Student's t-tests. Gastric emptying was significantly correlated with scores for heartburn/regurgitation (r = 0.26), nausea/vomiting (r = 0.19), fullness/satiety (r = 0.20), bloating (r = 0.21) and lower abdominal pain (r = 0.22; all P < 0.05). Patients with delayed emptying had significantly higher scores for each of these subscales (all P < 0.05). Discomfort volume during gastric distension was significantly correlated with scores for fullness/satiety (r = -0.27), bloating (r = -0.23), heartburn/regurgitation (r = -0.21), and upper abdominal pain (r = -0.20). Patients with hypersensitivity to distension had significantly higher scores for fullness/satiety (P < 0.05). At different cut-off levels of symptom severities, consistent associations were found between fullness/satiety and gastric discomfort volume, between preprandial volumes and upper abdominal pain, compliance and upper abdominal pain, and between bloating and gastric discomfort volume. Multiple regression analysis revealed that gastric emptying rate contributed significantly to models for the severity of these subscales. The importance of discomfort volume disappeared in favour of gender when sex was included in the model. No significant correlations were found with HP status or with gastric accommodation. PAGI-SYM scores are mainly correlated with gastric emptying rate and with gastric hypersensitivity. Multivariate analysis suggests that the questionnaire may be useful in the evaluation of gastroprokinetics. Its role in the evaluation of drugs that alter gastric sensitivity is less clear.
Redispersible Polymer Colloids Using Carbon Dioxide as an External Trigger (2011)

Polystyrene latexes prepared using a carbon dioxide switchable amidine surfactant and a switchable free radical initiator can be aggregated using only nitrogen and gentle heat and redispersed using carbon dioxide and sonication. The long-term colloidal stability of the redispersed latexes is excellent provided they are maintained under a carbon dioxide atmosphere. Redispersion of the particles is most effective when both the surfactant and the initiator contain switchable amidine moieties. The zeta potential of the original particles (with the switchable surfactant/initiator in their active form) decreases when the surfactant and initiator are converted to their inactive form upon addition of nitrogen and heat. Zeta potential is restored to its original value upon conversion of the surfactant and initiator to their active forms with carbon dioxide addition. This is the first report of redispersible polymer colloids that can be aggregated by reduction of surface charge, without requiring added acid or base solution. These switchable latexes demonstrate the future potential for switchable polymer colloids, capable of undergoing multiple reversible aggregation−redispersion cycles.
Improved Method for the Rapid Determination of Terpenoid Aldehydes in Cotton (2001)

A simple, rapid method for the extraction of cotton terpenoid aldehydes from green tissues and seed is described. Samples were treated by ultrasonification with acidified acetonitrile/water followed by centrifugation. The resulting extract was injected directly onto a C(18) HPLC column and no sample concentration or further cleanup steps were required. The level of gossypol, the most labile of the target analytes, decreased by only 2% after 12 h of storage at room temperature, thus enabling automated analysis of individual terpenoid aldehydes by HPLC. The method gives excellent reproducibility and enables large numbers of samples to be screened quickly and accurately.
Observed interannual oscillations of planetary wave forcing in the Northern Hemisphere winter (2002)

Using NCEP‐NCAR reanalysis data from 1958 to 1998, two interannual oscillations in the eddy forcing due to planetary waves (wavenumbers 1–3) are found in the Northern Hemisphere winter, called as the stratospheric interannual oscillation (SIO) and the tropospheric interannual oscillation (TIO). The temporal evolutions are different between the SIO and the TIO, suggesting different dynamic mechanisms. The planetary waves tend to be bent equatorward in the troposphere during a positive TIO phase, and in the mid‐ and upper stratosphere during a positive SIO phase. The result also suggests that upward propagation of planetary waves into the polar waveguide across the tropopause is closely associated with the TIO. Further regression and correlation analyses suggest that the TIO is closely linked to the Northern Annular Mode (NAM), whereas the SIO is closely associated with the El Niño/Southern Oscillation (ENSO).
107. Quinazolines. Part IV. Covalent hydration in the cations of substituted quinazolines (1962)

W. L. F. Armarego, J. Chem. Soc., 1962, 561 DOI: 10.1039/JR9620000561
Quantitative T cell repertoire analysis by deep cDNA sequencing of T cell receptor α and β chains using next-generation sequencing (NGS) (2014)

Immune responses play a critical role in various disease conditions including cancer and autoimmune diseases. However, to date, there has not been a rapid, sensitive, comprehensive, and quantitative analysis method to examine T-cell or B-cell immune responses. Here, we report a new approach to characterize T cell receptor (TCR) repertoire by sequencing millions of cDNA of TCR α and β chains in combination with a newly-developed algorithm. Using samples from lung cancer patients treated with cancer peptide vaccines as a model, we demonstrate that detailed information of the V-(D)-J combination along with complementary determining region 3 (CDR3) sequences can be determined. We identified extensive abnormal splicing of TCR transcripts in lung cancer samples, indicating the dysfunctional splicing machinery in T lymphocytes by prior chemotherapy. In addition, we found three potentially novel TCR exons that have not been described previously in the reference genome. This newly developed TCR NGS platform can be applied to better understand immune responses in many disease areas including immune disorders, allergies, and organ transplantations.
Idiotype-cytokine fusion proteins as cancer vaccines. Relative efficacy of IL-2, IL-4, and granulocyte-macrophage colony-stimulating factor. (1994)

Idiotypic determinants, antigenic sites expressed on the variable region of Ig molecules of malignant B cells, represent tumor-specific Ags but are weak immunogens. We have previously shown that the immunogenicity can be dramatically increased by fusing tumor Id to granulocyte macrophage (GM)-CSF. Here, we demonstrate that fusion proteins with IL-2 or IL-4 can also be highly immunogenic. Co-immunization of these fusion proteins with another Id demonstrated the importance of physical linkage between the cytokine and relevant Ag for this enhancement. All three fusion proteins are capable of eliciting significant levels of specific Abs against the Id without the use of carrier proteins or adjuvants, although the GM-CSF fusion protein appeared to be unique in its ability to induce higher titers of anti-Id Abs in the primary response. Furthermore, the Id-IL-2 fusion protein induced high titers of IgG2a and IgG3 anti-Id Abs, whereas the Id-IL-4 and Id-GM-CSF fusion proteins did not. Despite the differences, tumor protection was comparable in all mice having significant titers of anti-Id Abs, regardless of the fusion protein used. We concluded that Id-cytokine fusion proteins are potent immunogens that can elicit significant antitumor immunity. The general approach of fusing a cytokine to a potential Ag may be applicable to the design of vaccines for immunotherapy of other types of tumors as well as for other pathogens and disease states.
Effects of Technology Enhancements and Type of Teacher Support on Assessing Spanish-Speaking Children’s Oral Reading Fluency in Second Grade (2011)

We examined student-, classroom-, and school-level effects in predicting second-grade Spanish-speaking children’s oral reading fluency in Spanish. Teachers in 67 randomly selected urban schools administered the Tejas LEE to 1,537 first- and second-grade students. Oral reading fluency was measured in the passages students read for comprehension. Covariates were mean fluency in Grade 1, variability in fluency in Grade 1, degree of grouping in the school, and the proportion of second-grade students in the classroom and/or the school taking the Tejas LEE. Treatment effects were administration format (paper, desktop, handheld) and type of teacher support (no mentoring, web mentoring, and on-site plus web mentoring). Second-grade teachers positively affected students’ reading fluency when (a) they administered the Tejas LEE on paper with the associated paper reports in classrooms of bilingual students, and (b) they either received web mentoring and had relatively homogeneous classrooms or received on-site or no mentoring and had ability-grouped classes. Implications for interpreting assessment results are discussed in the context of the type of support provided to teachers and the grouping of bilingual students by language and/or by ability.
Complementary DNA and derived amino acid sequence of the .beta. subunit of human complement protein C8: identification of a close structural and ancestral relationship to the .alpha. subunit and C9 (1987)

A cDNA clone encoding the beta subunit (Mr 64,000) of the eighth component of complement (C8) has been isolated from a human liver cDNA library. This clone has a cDNA insert of 1.95 kilobases (kb) and contains the entire beta sequence [1608 base pairs (bp)]. Analysis of total cellular RNA isolated from the hepatoma cell line HepG2 revealed the mRNA for beta to be approximately 2.5 kb. This is similar to the message size for the alpha subunit of C8 and confirms the existence of different mRNAs for alpha and beta. This finding supports genetic evidence that alpha and beta are encoded at different loci. Analysis of the derived amino acid sequence revealed several membrane surface seeking segments that may facilitate beta interaction with target membranes during complement-mediated cytolysis. Determination of the carbohydrate composition indicated 1 or 2 asparagine-linked but no O-linked oligosaccharide chains. Comparison of the beta sequence to that reported for alpha in the preceding paper [Rao, A. G., Howard, O. M. Z., Ng, S. C., Whitehead, A. S., Colten, H. R. & Sodetz, J. M. (1987) Biochemistry (preceding paper in this issue)] and to that of human C9 revealed a striking homology between all three proteins. For beta and alpha, the overall homology is 33% on the basis of identity and 53% when conserved substitutions are allowed. For beta and C9, the values are 26% and 47%, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Isolation and functional characterization of regulatory CD25brightCD4+ T cells from the target organ of patients with rheumatoid arthritis (2003)

In the homeostasis of the immune system regulatory cells play a major role. Removal of one group of regulatory cells, the CD25(+)CD4(+) T cells, leads to autoimmune manifestations in experimental animal models, and reintroduction of this population prevents disease. This study addresses the role of such regulatory T cells in humans with an autoimmune disease, where we demonstrate the presence of CD25(bright)CD4(+) T cells in the target organ of patients with active rheumatoid arthritis. The patients displayed an enrichment of CD25(bright)CD4(+) T cells in synovial fluid as compared to peripheral blood. These cells are functional regulatory cells, as they were able to suppress in vitro proliferation of autologous T cells, both from synovial and peripheral blood origin. Although the frequency of CD25(bright)CD4(+) T cells varied between patients, it was found to be constant over time in any one joint during each relapse. Numbers were also comparable in two inflamed knee joints of one and the same patient, emphasizing the symmetry of the disease. In summary, it is striking that in addition to all activated, potentially pathological T cells the synovial fluid from RA patients also contains CD25-expressing CD4(+) T cells with a regulatory capacity.
Generation of a mouse strain that produces immunoglobulin kappa chains with human constant regions (1993)

Humanized antibodies are highly efficient as immunotherapeutic reagents and have many advantages over rodent antibodies. A mouse strain was generated by gene targeting to replace the mouse kappa light chain constant (C) region gene with the human C kappa gene. Mice homozygous for the replacement mutation (C kappa R) produced normal concentrations of serum antibodies, most of which carry chimeric kappa light chains, and mounted normal immune responses to hapten-protein conjugates. This technology provides a feasible option for the generation of high-affinity humanized antibodies by means of the powerful somatic hypermutation-selection mechanism.
Conditional gene manipulation: Cre-ating a new biological era (2012)

To solve the problem of embryonic lethality in conventional gene knockouts, site-specific recombinase (SSR) systems (Cre-loxP, Flp-FRT, and ΦC31) have been used for tissue-specific gene knockout. With the combination of an SSR system and inducible gene expression systems (tetracycline and tamoxifen), stage-specific knockout and transgenic expression can be achieved. The application of this "SSR+inducible" conditional tool to genomic manipulation can be extended in various ways. Alternatives to conditional gene targeting, such as conditional gene trapping, multipurpose conditional alleles, and conditional gene silencing, have been developed. SSR systems can also be used to construct precise disease models with point mutations and chromosomal abnormalities. With these exciting achievements, we are moving towards a new era in which the whole genome can be manipulated as we wish.
Profiling Carbohydrate-Receptor Interaction with Recombinant Innate Immunity Receptor-Fc Fusion Proteins (2009)

The recognition of bacteria, viruses, fungi, and other microbes is controlled by host immune cells, which are equipped with many innate immunity receptors, such as Toll-like receptors, C-type lectin receptors, and immunoglobulin-like receptors. Our studies indicate that the immune modulating properties of many herbal drugs, for instance, the medicinal fungus Reishi (Ganoderma lucidum) and Cordyceps sinensis, could be attributed to their polysaccharide components. These polysaccharides specifically interact with and activate surface receptors involved in innate immunity. However, due to the complexity of polysaccharides and their various sources from medicinal fungi, quantitative analysis of medicinal polysaccharide extracts with regard to their functions represents a major challenge. To profile carbohydrate-immune receptor interactions, the extracellular domains of 17 receptors were cloned as Fc-fusion proteins, such that their interactions with immobilized polysaccharides could be probed in an enzyme-linked immunosorbent assay. The results show that several innate immune receptors, including Dectin-1, DC-SIGN, Langerin, Kupffer cell receptor, macrophage mannose receptor, TLR2, and TLR4, interact with the polysaccharide extracts from G. lucidum (GLPS). This analysis revealed distinct polysaccharide profiles from different sources of medicinal fungi, and the innate immune receptor-based enzyme-linked immunosorbent assay described here can serve as a high-throughput profiling method for the characterization and quality control of medicinal polysaccharides. It also provides a means to dissect the molecular mechanism of medicinal polysaccharide-induced immunomodulation events.
Cyclization of Isothiocyanates as a Route to Phthalic and Homophthalic Acid Derivatives1,2 (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclization of Isothiocyanates as a Route to Phthalic and Homophthalic Acid Derivatives1,2Peter A. S. Smith and Robert O. KanCite this: J. Org. Chem. 1964, 29, 8, 2261–2265Publication Date (Print):August 1, 1964Publication History Published online1 May 2002Published inissue 1 August 1964https://pubs.acs.org/doi/10.1021/jo01031a037https://doi.org/10.1021/jo01031a037research-articleACS PublicationsRequest reuse permissionsArticle Views487Altmetric-Citations84LEARN 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
Tumor-promoting phorbol diester-induced specific changes in cell surface glycoprotein profile of K562 human leukemic cells. (1981)

The tumor-promoting phorbol ester, 12-O-tetradecanoylphorbol-13-acetate (TPA), induced specific changes in the cell surface glycoprotein profile of K562 human leukemic cells. TPA-treated K562 cells were examined by cell surface labeling followed by immunoprecipitation with anti-glycophorin antiserum or anti-K562 antiserum. TPA-treated K562 cells lost glycophorin and glycoprotein with a molecular weight of 105,000, which are specific to later stages of erythroid cell differentiation, and retained glycoprotein with a molecular weight of 95,000, which is specific to early stages of erythroid cell differentiation. On the other hand, 4 alpha-phorbol-12,13-didecanoate, which is inactive as a tumor promoter, induced no significant changes in cell surface glycoproteins of K562 cells. In parallel, TPA induced morphological changes of K562 cells as their growth was inhibited, whereas 4 alpha-phorbol-12,13-didecanoate had no effect on these two characteristics. Thus, the tumor promoter induced specific changes in the cell surface glycoprotein profile of K562 human leukemic cells, which appeared to be induced into a retrodifferentiated stage.
RISK ASSESSMENT OF VIRUS-RESISTANT TRANSGENIC PLANTS (2002)

Virus-resistant transgenic plants (VRTPs) hold the promise of enormous benefit for agriculture. However, over the past ten years, questions concerning the potential ecological impact of VRTPs have been raised. In some cases, detailed study of the mode of action of the resistance gene has made it possible to eliminate the source of potential risk, notably the possible effects of heterologous encapsidation on the transmission of viruses by their vectors. In other cases, the means of eliminating likely sources of risk have not yet been developed. When such residual risk still exists, the potential risks associated with the VRTP must be compared with those associated with nontransgenic plants so that risk assessment can fully play its role as part of an overall analysis of the advantages and disadvantages of practicable solutions to the problem solved by the VRTP.
Chemoprevention of chemically-induced mammary carcinogenesis by indole-3-carbinol. (1995)

Indole-3-carbinol, a component of cruciferous vegetables, was evaluated for it efficacy in the prevention of chemically-induced mammary tumors using three different protocols. Because this compound was unstable, it was administered by gavage rather than in the diet. A preliminary dose range study revealed that dose levels of 100 and 50 mg/day, 5x/week, were not toxic to female Sprague-Dawley rats. Initial studies in the DMBA model showed that administering indole-3-carbinol during the initiation and promotion phases were highly effective chemopreventive methods (91-96% reduction in cancer multiplicity). Subsequent studies showed that the administration of indole-3-carbinol only during the initiation phase (7 days prior to until 7 days post DMBA) was also highly effective as a chemopreventive agent. Determination of enzyme levels in the livers of animals treated long-term with indole-3-carbinol showed high levels of induction of various phase I and phase II drug metabolizing enzymes. Finally, indole-3-carbinol when administered both prior to and after MNU (a direct acting carcinogen) caused a significant decrease (65%) in mammary tumor multiplicity. These results support previous studies that indole-3-carbinol can prevent mammary carcinogenesis by direct and indirect acting carcinogens. Therefore, indole-3-carbinol might be a good candidate for chemoprevention of breast cancer in women.
A new class of Escherichia coli recBC mutants: implications for the role of RecBC enzyme in homologous recombination. (1984)

Mutants of Escherichia coli sensitive to phage T4 gene 2 mutants were obtained following ethyl methanesulfonate mutagenesis. By mapping and complementation analysis, the mutations in each of the six mutants are in recB and recC. By both in vivo and in vitro analyses, the nuclease activity of RecBC enzyme is undetectable in these mutants. However, by several other criteria, such as proficiency in recombination, relative resistance to UV radiation, and viability of the cells in the culture, these mutants are almost identical to their recBC+ parent. The properties of these mutants indicate that the ATP-dependent double-stranded DNA exonuclease activity of RecBC enzyme is not required for recombination. Chi recombinational hotspots, which stimulate recombination by the RecBC pathway, have no detectable activity in the mutants. This result suggests that the nuclease activity of RecBC enzyme is required for Chi activity and is consistent with the hypothesis that Chi stimulates recombination by directing RecBC enzyme to cut DNA at or near Chi.
Information distance and its application in time series (2008)

In this paper a new method is introduced for studying time series of complex systems. This method is based on using the concept of entropy and Jensen-Shannon divergence. In this paper this method is applied to time series of billiard system and heart signals. By this method, we can diagnose the healthy and unhealthy heart and also chaotic billiards from non chaotic systems . The method can also be applied to other time series.