gebhart/patrepeval huggingface dataset:
I-CeuI fragment analysis of the Shigella species: evidence for large-scale chromosome rearrangement in S. dysenteriae and S. flexneri (2000)

I-CeuI fragments of four Shigella species were analyzed to investigate their taxonomic distance from Escherichia coli and to collect substantiated evidence of their genetic relatedness because their ribosomal RNA sequences and similarity values of their chromosomal DNA/DNA hybridization had proved their taxonomic identity. I-CeuI digestion of genomic DNAs yielded seven fragments in every species, indicating that all the Shigella species contained seven sets of ribosome RNA operons. To determine the fragment identities, seven genes were selected from each I-CeuI fragment of E. coli strain K-12 and used as hybridization probes. Among the four Shigella species, S. boydii and S. sonnei showed hybridization patterns similar to those observed for E. coli strains; each gene probe hybridized to the I-CeuI fragments with sizes similar to that of the corresponding E. coli fragment. In contrast, S. dysenteriae and S. flexneri showed distinct patterns; rcsF and rbsR genes that located on different I-CeuI fragments in E. coli, fragments D and E, were found to co-locate on a fragment. Further analysis using an additional three genes that located on fragment D in K-12 revealed that some chromosome rearrangements involving the fragments corresponding to fragments D and E of K-12 took place in S. dysenteriae and S. flexneri.
Interleukin‐29 uses a type 1 interferon‐like program to promote antiviral responses in human hepatocytes† (2006)

Interleukin-28A (IL-28A), IL-28B and IL-29 are a family of class II cytokines that stimulate antiviral responses through a heterodimeric receptor that is distinct from the type I interferon (IFN) receptor. To better understand how this newly described family of cytokines regulates the antiviral state, we compared various cellular responses elicited by IL-29 and IFN-alpha. Here we show that these cytokines stimulate similar patterns of signal transducer and activator of transcription 1 (STAT-1), -2, -3, and -5 phosphorylation and nearly identical patterns of gene expression when analyzed in two distinct cell types by microarray analysis. Interestingly, the IL-29 receptor is preferentially expressed on primary hepatocytes within normal liver and pegylated forms of IL-29 and IFN-alpha induced equivalent 2'5' oligoadenylate synthetase (OAS) and MX1 gene expression in this cell type. Pegylated IL-29 also produced a significant reduction in human hepatitis B and hepatitis C viral load in vitro and reduced the cytopathic effect caused by the fully replicating flavivirus, West Nile virus. In conclusion, IL-29 and IFN-alpha stimulate identical antiviral responses despite their utilization of different receptors. This fact, combined with significant receptor expression in hepatitis virus-infected livers, suggests that IL-29 may have therapeutic value against chronic viral hepatitis in human patients.
ChemInform Abstract: Improved Synthesis of 2‐Deoxy‐L‐ribose. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
GMPLS controlled ethernet: an emerging packet-oriented transport technology (2008)

Most of the world's traffic is now packet-based. While SONET/SDH transport technology continues to evolve, there are now major standardization efforts to develop a native packet-oriented transport technology. Ethernet, long dominant in the enterprise, is one of the fastest developing technologies for the transport layer. GMPLS, based on mature signaling and routing protocols, is gaining traction as a transport control plane, providing fast restoration and supporting automation of provisioning. We will briefly highlight recent Ethernet standardization and then introduce the concepts and standards work allowing GMPLS to control Ethernet.
WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations (2007)

WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at http://bioinfo.biotec.or.th/WASP.
The Weight-based Heparin Dosing Nomogram Compared with a Standard Care Nomogram (1993)

The weight-based heparin nomogram is widely generalizable and has proved to be effective, safe, and superior to one based on standard practice.
Overexpression of Pim‐1 is associated with poor prognosis in patients with esophageal squamous cell carcinoma (2010)

These findings demonstrate that Pim-1 may be used as molecular marker for predicting the prognosis of patients with ESCC.
Superconducting and normal-state properties of YBa2Cu3O7−δ -bicrystal grain boundary junctions in thin films (1998)

A model, based on universal properties of high-Tc superconductors only, is presented for the transport characteristics of grain boundaries in these materials. The model accounts for the superconducting as well as for the normal-state transport properties observed in a comprehensive study of YBa2Cu3O7−δ [001]-tilt bicrystalline grain boundaries with varying misorientation angles and of two different symmetries.
Glycogen synthase kinase‐3β, mood stabilizers, and neuroprotection (2002)

Glycogen synthase kinase-3beta (GSK-3beta) is a central component in many critical intracellular signaling mechanisms. These include the phosphatidylinositol 3-kinase/Akt cell survival pathway, which inhibits GSK-3beta activity. GSK-3beta itself inhibits the activation of several transcription factors, which are important cell survival factors, such as heat shock factor 1. These factors likely contribute to the recent revelation that GSK-3beta is a pro-apoptotic enzyme. Recently, lithium has been identified as a selective and direct inhibitor of GSK-3beta. Based on these findings, we have proposed that part of the neuroprotectant properties of lithium is due to its ability to inhibit GSK-3beta, and thus block the facilitation of apoptosis produced by GSK-3beta. Since several anticonvulsants recently have been shown to be effective mood stabilizers, we examined if these agents are capable of protecting cells from GSK-3beta-facilitated apoptosis. In addition to lithium, both valproic acid and lamotrigine, but not carbamazepine, provided protection from GSK-3beta-facilitated apoptosis in human neuroblastoma SH-SY5Y cells. These results demonstrate that several drugs therapeutic for bipolar disorder can provide neuroprotection by inhibiting the pro-apoptotic effects of GSK-3beta, providing new evidence that dysregulation of GSK-3beta may contribute to the pathophysiology of bipolar disorder.
[Genetic diagnosis of viral diseases in nervous system]. (1997)

The rapid diagnosis of viral infection in nervous system is necessary for the effective treatment, since they progress so rapidly. The identification of infected virus can be achieved by amplifying DNA or RNA in virus, using polymerase chain reaction (PCR). Herpes simplex encephalitis is the most common and fruitful target for genetic diagnosis. Genetic diagnosis can also detect the presence of cytomegalovirus, EB virus, human herpes 6 virus, herpes zoster virus, HTLV-1 (human T-lymphotrophic virus type 1), measles virus, mumps virus, Japanese encephalitis virus, rubella virus, HIV (human immunodeficiency virus), and HCV (hepatitis C virus). However, the presence of the virus does not always mean a recent infection by the virus, nor a cause of the disease.
Intraepithelial CD8+tumor-infiltrating lymphocytes and a high CD8+/regulatory T cell ratio are associated with favorable prognosis in ovarian cancer (2005)

In a recent report, [Zhang et al. (2003) N. Engl. J. Med. 348, 203-213], the presence of CD3+ tumor-infiltrating lymphocytes (TILs) was found to correlate with improved survival in epithelial ovarian cancer. We performed immunohistochemical analysis for TILs and cancer testis antigens in 117 cases of epithelial ovarian cancer. The interrelationship between subpopulations of TILs and expression of cancer testis antigens was investigated, as well as between TILs and overall survival. The median follow-up of the patients was 31 months. Patients with higher frequencies of intraepithelial CD8+ T cells demonstrated improved survival compared with patients with lower frequencies [median = 55 versus 26 months; hazard ratio = 0.33; confidence interval (C.I.) = 0.18-0.60; P = 0.0003]. No association was found for CD3+ TILs or other subtypes of intraepithelial or stromal TILs. However, the subgroups with high versus low intraepithelial CD8+/CD4+ TIL ratios had median survival of 74 and 25 months, respectively (hazard ratio = 0.30; C.I. = 0.16-0.55; P = 0.0001). These results indicate that CD4+ TILs influence the beneficial effects of CD8+ TIL. This unfavorable effect of CD4+ T cells on prognosis was found to be due to CD25+ forkhead box P3 (FOXP3)+ regulatory T cells (Treg; suppressor T cells), as indicated by survival of patients with high versus low CD8+/Treg ratios (median = 58 versus 23 months; hazard ratio = 0.31; C.I. = 0.17-0.58; P = 0.0002). The favorable prognostic effect of intraepithelial CD8+ TILs did not correlate with concurrent expression of NY-ESO-1 or MAGE antigens. We conclude that intraepithelial CD8+ TILs and a high CD8+/Treg ratio are associated with favorable prognosis in epithelial ovarian cancer.
pS2 expression as a possible diagnostic marker of colorectal carcinoma in ulcerative colitis. (2000)

This study was performed to evaluate the significance of pS2 and MUC1 expressions in ulcerative colitis (UC)-associated colorectal neoplasias. Tissues were collected from 6 patients with UC-associated colorectal neoplasias treated surgically. Specimens were 13 adenocarcinomas, 40 dysplasias (20 high-grade dysplasias, 20 low-grade dysplasias), and 60 normal mucosae. Tissues were also collected from patients without UC treated surgically or endoscopically. pS2, p53, and MUC1 expressions were examined immunohistochemically and compared. The K-ras codon 12 mutation was investigated by single-strand conformation polymorphism analysis. In patients with UC, the incidence of pS2 expression was significantly higher (p<0.01) in adenocarcinomas than it was in dysplasias, and no pS2 expression was seen in normal mucosae. p53 overexpression was detected in 50% (10/20) even in low-grade dysplasias. MUC1 expression was seen only in invasive carcinomas, but it was seen in 100% of cases (3/3). K-ras gene mutations were detected in 2 (20%) of 10 carcinomas. In low and high-grade dysplasias, the incidences of pS2 expression were significantly (p<0.01) lower than the incidences of p53 overexpression, however, in UC-associated carcinomas there was no significant difference; pS2 expression and p53 overexpression were detected in 13 of 13 (100%) cases and in 12 of 13 (92%) cases, respectively. These results suggest that p53 overexpression may be a diagnostic marker of neoplasia, and that pS2 expression may be a diagnostic marker of colorectal carcinoma in case of UC.
The release of pancreatic glucagon and inhibition of insulin in response to stimulation of the sympathetic innervation. (1975)

The changes in the concentration of glucagon and insulin in arterial plasma which occur in response to splanchnic nerve stimulation have been investigated in adrenalectomized dogs, cats and sheep. 2. In dogs, stimulation of both splanchnic nerves at a low frequency (2-0 c/s) for 10 min produced a small but statistically significant increase in plasma glucagon concentration and appeared to inhibit the release of insulin. Stimulation at a higher frequency (10-0 c/s) produced a much greater increase in plasma glucagon concentration, which was normally accompanied by a rise in plasma glucose concentration. 3. Qualitatively similar changes in plasma glucagon and insulin concentration were observed in both sheep and cats in response to adrenergic stimulation. 4. Intramesenteric infusions of glucagon at a dose of 5-0 ng kg-1 min-1 in dogs produced a comparable rise in plasma glucagon concentration to that elicited by splanchnic nerve stimulation at high frequency (10-0 c/s) and invariably caused a rise in plasma glucose concentration. 5. In dogs given exogenous glucose, release of glucagon in response to splanchnic nerve stimulation was unaffected by induced hyperglycaemia. Secretion of insulin was partially inhibited by stimulation at 2-0 c/s and completely suppressed at higher frequency (10-0c/s). 6. It is concluded that stimulation of the sympathetic innervation to the pancreatic islets, at frequencies within thephysiological range, stimulates the release of glucagon and inhibits that of insulin in each of these species.
Synthetic foldamers (2011)

Foldamers are artificial folded molecular architectures inspired by the structures and functions of biopolymers. This highlight focuses on important developments concerning foldamers produced by chemical synthesis and on the perspectives that these new self-organized molecular scaffolds offer. Progress in the field has led to synthetic objects that resemble small proteins in terms of size and complexity yet that may not contain any α-amino acids. Foldamers have introduced new tools and concepts to develop biologically active substances, synthetic receptors and novel materials.
Identification of the primary growth response gene, ST2/T1, as a gene whose expression is differentially regulated by different protein kinase C isozymes (1995)

Individual protein kinase C isozymes have been shown to play different roles in mediating proliferation, differentiation and transformation, but it is not known to what extent these effects involve induction of expression of particular genes. To explore the differential gene expression that might be induced by activation of different PKC isozymes, we stably transfected NIH 3T3 cells with expression vectors that encode the isozymes PKC-alpha, -beta II, -gamma, -delta, -epsilon, -sigma and -eta. Using differential display-reverse transcription-polymerase chain reaction we isolated a small cDNA that encodes a portion of the primary response gene, ST2 (also referred to as T1 or DER4), and we confirmed by RNA blot studies that ST2/T1 expression is differentially regulated by PKC isozymes. ST2/T1 mRNA is undetectable in the unstimulated parental NIH 3T3 cells that express only the alpha isozyme of PKC, but it can be induced by phorbol ester treatment. Clones that overexpress PKC-alpha, -delta or -epsilon similarly do not express ST2/T1 until they are stimulated with phorbol esters, which induces expression of ST2/T1 with kinetics similar to wild-type NIH 3T3 but to different extents. In contrast, ST2/T1 mRNA is already present in unstimulated cells that overexpress PKC-beta II, -gamma, -sigma and -eta, but phorbol ester greatly enhances ST2/T1 expression in these cells. These results suggest a differential role for PKC isozymes in mediating the ST2/T1 expression that is induced by growth stimuli.
Monoacylglycerols Activate Capsaicin Receptor, TRPV1 (2008)

Transient receptor potential vanilloid subtype 1 (TRPV1) is known as capsaicin (CAP) receptor and activated by CAP. Activation of TRPV1 by CAP increases energy expenditure and thermogenesis in rodents or human. Therefore, TRPV1 may be target for energy expenditure enhancement and thermogenesis. To search for novel TRPV1 agonist, we screened 19 types of foods by using TRPV1-expressing HEK293 cells. TRPV1 was activated by hexane extract of wheat flour, and its functional compounds were 1-monoacylglycerols containing oleic, linoleic, and alpha-linolenic acids. Their potencies (EC50) were about 50 times larger than that of CAP and their efficacies (maximal response) were about half of that of CAP. TRPV1 was activated by 1-monoacylglycerols (MGs) having C18 and C20 unsaturated and C8-C12 saturated fatty acid (FA). Moreover, 2-MGs having C18 and C20 unsaturated FA acted on TRPV1 with the same potency. On the other hand, no activation of TRPV1 was induced by MGs having C16 and C18 saturated FA, di- or triacylglycerols of C18:1 FA. Pain-relating aversive responses were induced when TRPV1-activating 1-monoacylglycerols (50 mM) was administered subcutaneously into rat hind paw. These effects were inhibited by the co-injection of capsazepine (10 mM) which is a TRPV1 competitive antagonist. These results suggested that these 1-monoacylglycerols activate TRPV1 in vitro and in vivo.
Validation of the Infectious Diseases Society of America's Diabetic Foot Infection Classification System (2007)

In this longitudinal study of 1666 persons with diabetes, there was an observed trend toward an increased risk for amputation (chi(2) test for trend, 108.0; P<.001), higher-level amputation (chi(2) test for trend, 113.3; P<.001), and lower extremity-related hospitalization (chi(2) test for trend, 118.6; P<.001) with increasing infection severity. The Infectious Diseases Society of America's foot infection classification system may be a useful tool for grading foot infections.
Optimization of the Hairpin Polyamide Design for Recognition of the Minor Groove of DNA (1996)

In order to optimize the hairpin design for ligands which bind the minor groove of DNA, a series of four pyrrole−imidazole polyamides substituted at the C-terminus with aliphatic amino acids have been prepared using solid phase synthetic methodology. Addition of a C-terminal β-alanine residue is found to enhance both the DNA binding affinity and sequence specificity, while addition of a C-terminal glycine residue is found to reduce DNA binding affinity and sequence specificity. These effects are modulated by the addition of an N-terminal acetyl group. Insertion of a C-terminal aliphatic amino acid residue makes the hairpin polyamide motif compatible with solid phase synthetic methods, allowing the rapid design of new polyamides for high-affinity specific recognition of a broad sequence repertoire in the minor groove of DNA.
Determination of gas oil cetane number and cetane index using near-infrared Fourier-transform Raman spectroscopy (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of gas oil cetane number and cetane index using near-infrared Fourier-transform Raman spectroscopyKenneth P. J. Williams, Rupert E. Aries, David J. Cutler, and David P. LidiardCite this: Anal. Chem. 1990, 62, 23, 2553–2556Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/ac00222a008https://doi.org/10.1021/ac00222a008research-articleACS PublicationsRequest reuse permissionsArticle Views399Altmetric-Citations27LEARN 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
Molecular Oxygen-Sensitive Fluorescent Lipobeads for Intracellular Oxygen Measurements in Murine Macrophages (2001)

Intracellular oxygen concentration is of primary importance in determining numerous physiological and pathological processes in biological systems. This paper describes the development and application of micrometer-sized oxygen-sensitive fluorescence lipobeads for intracellular measurements of molecular oxygen in J774 murine macrophages. A ruthenium diimine complex [Ru(bpy-pyr)(bpy)2]C12 (bpy = 2,2'-bipyridine, bpy-pyr = 4-(1"-pyrenyl)-2,2'-bipyridine) is used as the oxygen indicator. The indicator exhibits high chemical and photostability and high sensitivity to oxygen. The indicator molecules are immobilized in a phospholipid membrane that coats polystyrene microparticles. The fluorescence of the lipobeads is effectively quenched by molecular oxygen. The fluorescence intensity of the oxygen-sensitive lipobeads is 3 times higher in a nitrogenated solution than in an oxygenated solution. The lipobeads are internalized by murine macrophages through phagocytosis. They maintain their spectral properties for 24 h in living cells when the cells are stored in phosphate-buffered saline at pH 7.4. The photostability, reversibility, and effect of hypoxia, hyperoxia, and oxidative stress on the intracellular level of oxygen in J774 murine macrophages are described.
EGFR Intron 1 polymorphism in asian populations and its correlation with EGFR gene expression and amplification in breast tumour tissues (2006)

Our results show that the frequency of alleles encoding for short CA dinucleotide repeats is common in Asian populations. EGFR expression and amplification levels were also higher in Asian breast tumor tissues with short CA dinucleotide repeats. These findings suggest that the EGFR intron 1 polymorphism may influence response to treatment with tyrosine kinase inhibitors in breast cancer patients and further studies are warranted.
Characterization of the plasmid pVS809 from Bifidobacterium globosum. (1994)

A plasmid from a B. globosum strain was cut with 38 restriction enzymes and a physical map was constructed. Out of a total of 121 clones from curing experiments, plasmid was lost in 58% and 100% for acridine orange and ethidium bromide curing agent respectively. The plasmid does not exist as a chromosomal integrated form. An attempt to determine phenotypic characters encoded by the plasmid was made by electrophoretic analyses of the total proteins.
Space-time diversity systems based on linear constellation precoding (2003)

We present a unified approach to designing space-time (ST) block codes using linear constellation precoding (LCP). Our designs are based either on parameterizations of unitary matrices, or on algebraic number-theoretic constructions. With an arbitrary number of N/sub t/ transmit- and N/sub r/ receive-antennas, ST-LCP achieves rate 1 symbol/s/Hz and enjoys diversity gain as high as N/sub t/N/sub r/ over (possibly correlated) quasi-static and fast fading channels. As figures of merit, we use diversity and coding gains, as well as mutual information of the underlying multiple-input-multiple-output system. We show that over quadrature-amplitude modulation and pulse-amplitude modulation, our LCP achieves the upper bound on the coding gain of all linear precoders for certain values of N/sub t/ and comes close to this upper bound for other values of N/sub t/, in both correlated and independent fading channels. Compared with existing ST block codes adhering to an orthogonal design (ST-OD), ST-LCP offers not only better performance, but also higher mutual information for N/sub t/>2. For decoding ST-LCP, we adopt the near-optimum sphere-decoding algorithm, as well as reduced-complexity suboptimum alternatives. Although ST-OD codes afford simpler decoding, the tradeoff between performance and rate versus complexity favors the ST-LCP codes when N/sub t/, N/sub r/, or the spectral efficiency of the system increase. Simulations corroborate our theoretical findings.