gebhart/patrepeval huggingface dataset:
Molecular Diversity, Cultivation, and Improved Detection by Fluorescent In Situ Hybridization of a Dominant Group of Human Gut Bacteria Related toRoseburiaspp. orEubacterium rectale (2006)

Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eubacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.
CEA in activated macrophages. New diagnostic possibilities for tumor markers in early colorectal cancer. (2009)

CEACM combined with CRP appears to have diagnostic potential in early CRC.
Querying the World Wide Web (2002)

The World Wide Web is a large, heterogeneous, distributed collection of documents connected by hypertext links. The most common technology currently used for searching the Web depends on sending information retrieval requests to "index servers". One problem with this is that these queries cannot exploit the structure and topology of the document network. The authors propose a query language, WebSQL, that takes advantage of multiple index servers without requiring users to know about them, and that integrates textual retrieval with structure and topology-based queries. They give a formal semantics for WebSQL using a calculus based on a novel "virtual graph" model of a document network. They propose a new theory of query cost based on the idea of "query locality," that is, how much of the network must be visited to answer a particular query. Finally, they describe a prototype implementation of WebSQL written in Java.
Synthesis and preliminary evaluation in animals of carrier-free 11C-1-dopamine hydrochloride: X. (1973)

Carrier-free /sup 11/C-labeled dopamine hydrochloride was synthesized using carrier-free H/sup 11/CN as a precursor. Tissue distribution studies on five dogs showed a specific localization in the adrenal medu1la. Tissue distribution studies with /sup 11/C-labeled noradrenaline are in progress. (auth)
Functional genomics uncovers three glucosyltransferases involved in the synthesis of the major sweet glucosides of Stevia rebaudiana (2004)

Stevia rebaudiana leaves accumulate a mixture of at least eight different steviol glycosides. The pattern of glycosylation heavily influences the taste perception of these intensely sweet compounds. The majority of the glycosides are formed by four glucosylation reactions that start with steviol and end with rebaudioside A. The steps involve the addition of glucose to the C-13 hydroxyl of steviol, the transfer of glucose to the C-2' and C-3' of the 13-O-glucose and the addition of glucose to the hydroxyl of the C-4 carboxyl group. We used our collection of ESTs, an UDP-glucosyltransferase (UGT)-specific electronic probe and key word searches to identify candidate genes resident in our collection. Fifty-four expressed sequence tags (ESTs) belonging to 17 clusters were found using this procedure. We isolated full length cDNAs for 12 of the UGTs, cloned them into an expression vector, and produced recombinant enzymes in Escherichia coli. An in vitro glucosyltransferase activity enzyme assay was conducted using quercetin, kaempferol, steviol, steviolmonoside, steviolbioside, and stevioside as sugar acceptors, and (14)C-UDP-glucose as the donor. Thin layer chromatography was used to separate the products and three of the recombinant enzymes produced labelled products that co-migrated with known standards. HPLC and LC-ES/MS were then used to further define those reaction products. We determined that steviol UGTs behave in a regioselective manner and propose a modified pathway for the synthesis of rebaudioside A from steviol.
Role of Rac in controlling the actin cytoskeleton and chemotaxis in motile cells (2000)

We have used the chemotactic ability of Dictyostelium cells to examine the roles of Rho family members, known regulators of the assembly of F-actin, in cell movement. Wild-type cells polarize with a leading edge enriched in F-actin toward a chemoattractant. Overexpression of constitutively active Dictyostelium Rac1B(61L) or disruption of DdRacGAP1, which encodes a Dictyostelium Rac1 GAP, induces membrane ruffles enriched with actin filaments around the perimeter of the cell and increased levels of F-actin in resting cells. Whereas wild-type cells move linearly toward the cAMP source, Rac1B(61L) and Ddracgap1 null cells make many wrong turns and chemotaxis is inefficient, which presumably results from the unregulated activation of F-actin assembly and pseudopod extension. Cells expressing dominant-negative DdRac1B(17N) do not have a well-defined F-actin-rich leading edge and do not protrude pseudopodia, resulting in very poor cell motility. From these studies and assays examining chemoattractant-mediated F-actin assembly, we suggest DdRac1 regulates the basal levels of F-actin assembly, its dynamic reorganization in response to chemoattractants, and cellular polarity during chemotaxis.
Using a suppression subtractive library-based approach to identify tobacco genes regulated in response to short-term sulphur deficit (2005)

Monitoring expression at the transcriptional level is an essential first step for the functional analysis of plant genes. Genes encoding proteins directly involved in sulphur metabolism constitute only a small fraction of all the genes affected by sulphur deficiency stress. Transcriptional responses to various periods of sulphur deprivation have been extensively studied in Arabidopsis thaliana; however, no corresponding data are available for Solanaceae sp. To address this problem, a subtractive library-based approach to search for tobacco genes regulated by a short-term sulphur starvation has been adopted. In this work, 38 genes were identified, of which 22 were regulated positively and 16 were regulated negatively. The transcript levels of the representative genes were monitored in four parts of the plants (mature and immature leaves, stems, and roots), which exhibited differential sulphur deficiency. Interestingly, some genes exhibit different regulation of expression in different parts of the plants. Database analysis allowed assignment of the potential function for many of the identified genes; however, the functions of a small number of genes strongly regulated by sulphur starvation remain unknown. The genes were grouped into nine functional categories, each including both up- and down-regulated genes. The possible links between the identified regulated genes and sulphur metabolism are considered, and compared where possible with expression patterns in Arabidopsis thaliana. Although no obvious regulatory genes were identified, the genes encoding proteins of unknown function remain as potential components of the regulatory processes.
9‐β‐D‐ribopyranosylhypoxanthine, a minor component produced by streptomyces antibioticus (1980)

Abstract 9‐β‐ d ‐Ribopyranosylhypoxanthine was isolated from fermentation broths of Streptomyces antibioticus. Its structure was proved by synthesis.
Structure of the murine lck gene and its rearrangement in a murine lymphoma cell line. (1988)

The lck gene encodes a lymphocyte-specific protein-tyrosine kinase that is implicated in neoplastic transformation. We have determined the germ line organization of the murine lck gene and have isolated and characterized a rearranged lck allele in the murine lymphoma cell line LSTRA. The overall exon-intron organization of the normal lck gene is almost identical to that of avian c-src. In LSTRA DNA, an internally rearranged Moloney murine leukemia virus genome is interposed between two distinct promoters that normally generate lck transcripts differing only in 5' untranslated regions. The rearrangement appears to have been selected to permit splicing of transcripts that initiate from the Moloney virus promoter to an acceptor site located within the first exon 3' to the downstream promoter, thus generating an lck mRNA with a novel 5' untranslated region that may be more efficiently translated.
Ferrite particles for bowel contrast in MR imaging: design issues and feasibility studies. (1987)

Diverse materials with varying physical and magnetic properties have been evaluated as gastrointestinal contrast agents for magnetic resonance (MR) imaging. Uniform marking of the small bowel remains the greatest challenge. Ferrites are magnetically active iron oxide particles that are miscible with water and cause loss of signal on MR images. The decrease in MR signal intensity produced by ferrites occurs with a wide range of iron concentrations (0.1-10 mM) and with both T1- and T2-weighted pulse sequences. These effects of ferrites are explained by predominant T2 shortening with negligible T1 effects. The ferrite preparation used in this study was stable in vitro, with little iron solubilized by acid. Intragastric administration of ferrite (5 mg of iron per kg in 6 ml) routinely marked the small bowel of rats. The authors conclude that ferrites represent a promising new class of contrast agents for gastrointestinal MR imaging.
Neuroprotective Effects of Intravitreal Mesenchymal Stem Cell Transplantation in Experimental Glaucoma (2010)

Purpose. Retrograde neurotrophic factor transport blockade has been implicated in the pathophysiology of glaucoma. Stem cell transplantation appears to ameliorate some neurodegenerative conditions in the brain and spinal cord, in part by neurotrophic factor secretion. The present study was conducted to determine whether local or systemic bone marrow-derived mesenchymal stem cell (MSC) transplantation can confer neuroprotection in a rat model of laser-induced ocular hypertensive glaucoma. Methods. MSCs were isolated from the bone marrow of adult wild-type and transgenic rats that ubiquitously express green fluorescent protein. MSCs were transplanted intravitreally 1 week before, or intravenously on the day of, ocular hypertension induction by laser photocoagulation of the trabecular meshwork. Ocular MSC localization and integration were determined by immunohistochemistry. Optic nerve damage was quantified by counting axons within optic nerve cross-sections 4 weeks after laser treatment. Results. After intravitreal transplantation, MSCs survived for at least 5 weeks. Cells were found mainly in the vitreous cavity, though a small proportion of discrete cells migrated into the host retina. Intravitreal MSC transplantation resulted in a statistically significant increase in overall RGC axon survival and a significant decrease in the rate of RGC axon loss normalized to cumulative intraocular pressure exposure. After intravenous transplantation, MSCs did not migrate to the injured eye. Intravenous transplantation had no effect on optic nerve damage. Conclusions. Local, but not systemic, transplantation of MSCs was neuroprotective in a rat glaucoma model. Autologous intravitreal transplantation of MSCs should be investigated further as a potential neuroprotective therapy for glaucoma.
Pancreatic preproglucagon cDNA contains two glucagon-related coding sequences arranged in tandem. (1982)

We have constructed and cloned in bacteria recombinant plasmids containing DNA complementary to the mRNA encoding a pancreatic preproglucagon (Mr 14,500), a product of cell-free translation of angler fish islet mRNAs shown previously by immunoprecipitation analyses to be a precursor of glucagon. cDNAs of 630, 180, and 120 base pairs were isolated and correspond to most of the mRNA for the preproglucagon (650 bases). The cDNAs contain a protein coding sequence of 372 nucleotides and 5'- and 3'-untranslated regions of 58 and 206 nucleotides, respectively. From the coding sequence of the cDNAs, we find that the sequence of glucagon, identical to mammalian glucagon in 20 of 29 positions, resides in the preproglucagon of 124 amino acids flanked by NH2- and COOH-peptide extensions of 52 and 43 amino acids, respectively. The peptide extensions are linked to the glucagon by Lys-Arg sequences characteristic of the sites that are cleaved during the posttranslational processing of prohormones. Notable is the finding that, following the initial Lys-Arg sequence in the COOH-peptide extension is a pentapeptide. Ser-Gly-Val-Ala-Glu, followed by another Lys-Arg and a sequence of 34 residues that shows striking homology with glucagon and the other peptides of the glucagon family--gastric inhibitory peptide, vasoactive intestinal peptide, and secretin. Thus, the preproglucagon mRNA contains two glucagon-related coding sequences arranged in tandem. The finding of Lys-Arg sequences flanking the glucagon and glucagon-related sequences suggests that these two peptides and a pentapeptide are formed in vivo by posttranslational cleavages of a common precursor.
Tyrosine kinase inhibitors as potential drugs for B-cell lymphoid malignancies and autoimmune disorders (2012)

The use of TKIs, especially inhibitors of Btk, Syk, and Lyn, is a promising new strategy for targeted treatment of B-cell lymphoid malignancies, autoimmune disorders and allergic diseases. However, definitive data from ongoing and future clinical trials will aid in better defining the status of TKIs in the treatment of these disorders.
Phospholipase C-gamma 1 association with CD3 structure in T cells. (1992)

Recently, we and others have reported tyrosine phosphorylation of phospholipase C-gamma 1 (PLC gamma 1) enzyme after CD3 activation of T cells, and have proposed that PLC gamma 1 mediates signal transduction through the T cell receptor (TCR/CD3). Here, using immunoblotting and immune complex PLC assays, we show that CD3 stimulation of Jurkat cells induces the association of PLC gamma 1 enzyme with CD3 complex. PLC activity is also found to co-precipitate with the CD3 zeta chain from activated cells. In addition, in vitro PLC assays show that CD3 activation leads to about 10-fold stimulation of PLC gamma 1 activity. These results, along with the observation that Jurkat cells preferentially express PLC gamma 1, indicate that PLC gamma 1 participates in CD3 signaling.
Antithrombin, heparin, and heparan sulfate (2002)

Antithrombin has complex interactions with host coagulopathic and systemic inflammatory responses under physiologic conditions and in sepsis. The impact of these interactions in critically ill patients and the therapeutic implications of administration of antithrombin, and various doses and types of heparin in such patients, need further clarification.
Reducing energy and delay using efficient victim caches (2003)

In this paper, we investigate methods for improving the hit rates in the first level of memory hierarchy.Particularly, we propose victim cache structures to reduce the number of accesses to more power consuming structures such as level 2 caches.We compare the proposed victim cache techniques to increasing the associativity or the size of the level 1 data cache and show that the enhanced victim cache technique yield better energy-delay and energy-delay-area products.We also propose techniques that predict the hit/miss behavior of the victim cache accesses and bypass the victim cache when a miss can be determined quickly.We report simulation results obtained from SimpleScalar/ARM modeling a representative Network Processor architecture.The simulations show that the victim cache is able to reduce the energy consumption by as much as 17.6% (8.6% on average) while reducing the execution time by as much as 8.4% (3.7% on average) for a set of representative applications.
Electrochemical properties of carbon nanofiber web as an electrode for supercapacitor prepared by electrospinning (2003)

Poly(acrylonitrile) solutions in dimethylformamide were electrospun to be webs consisting of 300 nm ultrafine fibers. The webs were oxidatively stabilized and activated by steam resulting in activated carbon nanofibers (ACNFs). The specific surface area of the ACNF activated at 700 °C was the highest but mesopore volume fraction of that was lowest. On the other hand, the ACNFs activated at 800 °C showed opposite trends to those activated at 700 °C. The high specific surface area, mainly due to the micropores, introduced maximum specific capacitance at low current density (173 F/g at 10 mA/g). The elevated volume fraction of mesopores gave maximum specific capacitance at high current density (120 F/g at 1000 mA/g). The behavior is explained on the basis of ion mobility in the pores.
Determining Optimal Cytotoxic Activity of Human Her2neu Specific CD8 T cells by Comparing the Cr51 Release Assay to the xCELLigence System (2012)

Cytotoxic CD8 T cells constitute a subgroup of T cells that are capable of inducing the death of infected or malignant host cells. These cells express a specialized receptor, called the T cell receptor (TCR), which can recognize a specific antigenic peptide bound to HLA class I molecules. Engagement of infected cells or tumor cells through their HLA class I molecule results in production of lytic molecules such as granzymes and perforin resulting in target cell death. While it is useful to determine frequencies of antigen-specific CD8 T cells using assays such as the ELIspot or flow cytometry, it is also helpful to ascertain the strength of CD8 T cell responses using cytotoxicity assays. The most recognizable assay for assessing cytotoxic function is the Chromium Release Assay (CRA), which is considered a standard assay. The CRA has several limitations, including exposure of cells to gamma radiation, lack of reproducibility, and a requirement for large numbers of cells. Over the past decade, there has been interest in adopting new strategies to overcome these limitations. Newer approaches include those that measure caspase release , BLT esterase activity and surface expression of CD107. The impedance-based assay, using the Roche xCelligence system, was examined in the present paper for its potential as an alternative to the CRA. Impedance or opposition to an electric current occurs when adherent tumor cells bind to electrode plates. Tumor cells detach following killing and electrical impedance is reduced which can be measured by the xCelligence system. The ability to adapt the impedance-based approach to assess cell-mediated killing rests on the observation that T cells do not adhere tightly to most surfaces and do not appear to have much impact on impedance thus diminishing any concern of direct interference of the T cells with the measurement. Results show that the impedance-based assay can detect changes in the levels of antigen-specific cytotoxic CD8 T cells with increased sensitivity relative to the standard CRA. Based on these results, impedance-based approaches may be good alternatives to CRAs or other approaches that aim to measure cytotoxic CD8 T cell functionality.
A matrix‐assisted laser desorption time‐of‐flight mass spectrometer based on a 600ps, 1.2 mJ nitrogen laser (1991)

The design and performance of a short-pulse UV laser desorption time-of-flight mass spectrometer is described. The instrument combines the advantages of a 600 ps, 337 nm pulsed nitrogen laser with a compact, high-voltage extraction linear time-of-flight analyzer. A number of peptides and proteins have been analyzed to demonstrate sensitivity, high mass range, resolution and mixture analysis.
Influence of Cheyne-Stokes Respiration on Cardiovascular Oscillations in Heart Failure (2003)

In patients with congestive heart failure, Cheyne-Stokes respiration is accompanied by oscillations in blood pressure and heart rate at a very low frequency. It is not known whether these cardiovascular oscillations are primarily related to oscillations in ventilation or oxyhemoglobin saturation. We hypothesized that abolition of the ventilatory oscillations of Cheyne-Stokes respiration by CO2 inhalation would eliminate accompanying oscillations in blood pressure and heart rate but that elimination of hypoxic dips by supplemental O2 would not. We studied 10 subjects with heart failure and Cheyne-Stokes respiration during sleep using frequency spectral analysis. During Cheyne-Stokes respiration, heart rate and blood pressure oscillated in association with respiratory oscillations at very low frequency. Inhalation of CO2 abolished Cheyne-Stokes respiration and associated oscillations in both blood pressure and heart rate. In contrast, inhalation of O2 sufficient to eliminate hypoxic dips had no significant effect on Cheyne-Stokes respiration, blood pressure (n = 6), or heart rate (n = 5). We conclude that ventilatory oscillations during Cheyne-Stokes respiration rather than oscillations in oxygenation per se powerfully induce heart rate and blood pressure oscillations. Cheyne-Stokes respiration is therefore one of the mechanisms that contributes to the very low-frequency oscillations in heart rate and blood pressure observed in patients with heart failure.
ON THE RELATION OF CHRONIC INTERSTITIAL PANCREATITIS TO THE ISLANDS OF LANGERHANS AND TO DIABETES MELUTUS (1901)

(1) Congenital syphilitic pancreatitis retards the development of the glandular acini but does not affect the islands of Langerhans. Embedded in the stroma, but not invaded by it, the latter maintain their continuity with the small ducts and acini with which they have a common origin. (2) Two types of chronic interstitial inflammation affecting the developed pancreas are distinguishable: (a) Interlobular Pancreatitis.-In the interlobular variety the inflammatory process is localized chiefly at the periphery of the lobule and implicates the islands of Langerhans only when the sclerotic process has reached a very advanced grade. When pancreatitis has followed obstruction of the ducts, the islands long remain unaltered though embedded in dense scar-like tissue. (b) Interacinar Pancreatitis.-In the interacinar type the process is diffuse, invading the lobules and separating individual acini. The inflammatory change invades the islands of Langerhans. (3) A relationship has been observed between lesions of the islands of Langerhans and the occurrence of diabetes mellitus. (a) In one of eleven cases of interlobular panereatitis diabetes of mild intensity occurred. The sclerosis, which in this case followed obstruction of the ducts by calculi, was far advanced and affected the islands of Langerhans. (b) In two of three cases of interacinar pancreatitis, diabetes was present. The third case was associated with a condition, haemochromatosis, which at a later stage is associated with diabetes, the result of pancreatic lesion. (c) In a fourth case of diabetes, hyaline deposit between the capillaries and the parenchymatous cells had so completely altered the islands of Langerhans that they were no longer recognizable.