gebhart/patrepeval huggingface dataset:
Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov. (2005)

A novel solvent-producing, anaerobic clostridium, strain P7(T), was isolated from sediment from an agricultural settling lagoon after enrichment with CO as the substrate. The metabolism of this Gram-positive, motile, spore-forming rod was primarily acetogenic. Acetate, ethanol, butyrate and butanol were the end-products of metabolism. Strain P7(T) grew on CO, H(2)/CO(2), glucose, galactose, fructose, xylose, mannose, cellobiose, trehalose, cellulose, starch, pectin, citrate, glycerol, ethanol, propanol, 2-propanol, butanol, glutamate, aspartate, alanine, histidine, asparagine, serine, betaine, choline and syringate as sole substrates. Growth was not supported by methanol, formate, D-arabinose, fucose, lactose, melibiose, amygdalin, gluconate, lactate, malate, arginine, glutamine or vanillate. Nitrate reduction, production of indole, gelatin hydrolysis and aesculin hydrolysis were not observed. Analysis of the 16S rRNA gene sequence of the isolate showed that it was closely related to Clostridium scatologenes ATCC 25775(T) (99.7% sequence similarity) and clostridial strain SL1(T) (99.8% sequence similarity). Strain SL1 had been classified as a strain of C. scatologenes. However, DNA-DNA reassociation analysis showed that both strain P7(T) and strain SL1 represented novel clostridial species. It is proposed that strain P7(T) (=ATCC BAA-624(T)=DSM 15243(T)) be classified as the type strain of Clostridium carboxidivorans sp. nov. and that strain SL1(T) (=ATCC BAA-623(T)=DSM 12750(T)) be reclassified as the type strain of Clostridium drakei sp. nov.
Regnase-1, a Ribonuclease Involved in the Regulation of Immune Responses (2013)

Zc3h12a is a lipopolysaccharide-inducible gene and has a CCCH-type zinc-finger domain. Zc3h12a knockout mice develop spontaneous autoimmune diseases accompanied by splenomegaly and by lymphadenopathy. Subsequent studies show that Zc3h12a is a nuclease involved in destabilization of interleukin (IL)-6 and IL-12 mRNA via the stem loop structure within the 3' UTR of these genes. Thus, we renamed it regulatory RNase-1 (Regnase-1) based on its function. IκB kinases phosphorylate and degrade Regnase-1 protein in macrophages in response to IL-1R/Toll-like receptor (TLR) stimulation. T-cell-specific deletion of Regnase-1 produces pathogenic T cells with hyperactivated phenotypes as well as autoimmune diseases. Regnase-1 protein is cleaved by Malt1 and inactivated in response to T-cell receptor stimulation. Thus, Regnase-1 is a key molecule in the regulation of immune responses.
The transmembrane domain of diphtheria toxin improves molecular conjugate gene transfer (1997)

Vectors based on the formation of a soluble DNA-polycation complex are being developed for the treatment of human diseases. These complexes are rapidly taken up by receptor-mediated endocytosis, but are inefficiently delivered to the nucleus owing to entrapment in membrane-bound vesicles. In this study we introduced the transmembrane domain of diphtheria toxin into a DNA-polycation conjugate complex in an effort to increase gene transfer by membrane perturbation. The transmembrane domain of diphtheria toxin was expressed in Escherichia coli as a maltose-binding protein fusion and chemically coupled to high-molecular-mass poly-L-lysine. Incorporation of this conjugate into a traditional complex formed with a luciferase-containing plasmid with an asialo-orosomucoid-polycation conjugate significantly increased transfection efficiency in vitro in a manner proportional to the amount of diphtheria toxin incorporated. The delivery of luciferase RNA transcript was similarly increased when complexed with similar polycation conjugates. This study uses the structural biology of a bacterial protein to improve polycation-based gene delivery.
CD40L Activation in Circulating Platelets in Patients with Acute Coronary Syndrome (1999)

The CD40-CD40L interaction, which was initially shown to have important roles in the T cell-mediated activation of B cells during humoral immune responses, is now known to have roles in activation of endothelial cells, smooth muscle cells, and macrophages within atherosclerotic plaques. Recently, CD40L expression was found in activated platelets in the thrombus in vivo and CD40L was reported to be responsible for the platelet-mediated activation of endothelial cells in vitro. To investigate the activation status of platelets in coronary artery disease patients, we tested expression levels of CD40L, and platelet-endothelial cell adhesion molecule-1 (PECAM-1/CD31) in platelets isolated from peripheral blood, using flow cytometric analysis. Twenty-nine patients with acute coronary syndrome (10 acute myocardial infarction and 19 unstable angina patients) were compared with 14 normal subjects or 14 stable angina patients. In platelets isolated from normal subjects, the expression of CD40L was not detected in all subjects. In the patients with acute coronary syndrome, the average level of CD40L showed a significant increase (p = 0.0028), while stable angina patients did not have any increase when compared to normal subjects. Patients with more complex lesions or vessel occlusion tended to have a high platelet CD40L level compared to patients who do not. The expression levels of CD31 were increased in a small portion of the ACS patients. These data indicate that the rupture of plaque and subsequent formation of thrombus may lead to the activation of CD40L expression in circulating platelets of ACS patients.
Charge sharing concept and new clocking scheme for power efficiency and electromagnetic emission improvement of boosted charge pumps (2000)

A new power saving concept for boosted charge pumps is introduced, that combines two-step adiabatic switching, charge sharing and a simplified clocking scheme to double the power efficiency. Due to the charge charging the clock driver strengths can be reduced and therefore the peak value of the charging current is reduced by a factor of three. Further, the combination of tristate drivers and a new clocking scheme eliminates parasitic charge current peaks and together with the reduced current peaks the electromagnetic emission of the charge pump circuit is reduced significantly.
Naproxen incorporated lipid emulsions. I. Formulation and stability studies (1998)

Choice of emulsifier is the most important factor in the stability of the naproxen emulsions.
Bifurcation of insulin signaling pathway in rat liver: mTORC1 required for stimulation of lipogenesis, but not inhibition of gluconeogenesis (2010)

The livers of insulin-resistant, diabetic mice manifest selective insulin resistance, suggesting a bifurcation in the insulin signaling pathway: Insulin loses its ability to block glucose production (i.e., it fails to suppress PEPCK and other genes of gluconeogenesis), yet it retains its ability to stimulate fatty acid synthesis (i.e., continued enhancement of genes of lipogenesis). Enhanced lipogenesis is accompanied by an insulin-stimulated increase in the mRNA encoding SREBP-1c, a transcription factor that activates the entire lipogenic program. Here, we report a branch point in the insulin signaling pathway that may account for selective insulin resistance. Exposure of rat hepatocytes to insulin produced a 25-fold increase in SREBP-1c mRNA and a 95% decrease in PEPCK mRNA. Insulin-mediated changes in both mRNAs were blocked by inhibitors of PI3K and Akt, indicating that these kinases are required for both pathways. In contrast, subnanomolar concentrations of rapamycin, an inhibitor of the mTORC1 kinase, blocked insulin induction of SREBP-1c, but had no effect on insulin suppression of PEPCK. We observed a similar selective effect of rapamycin in livers of rats and mice that experienced an insulin surge in response to a fasting-refeeding protocol. A specific inhibitor of S6 kinase, a downstream target of mTORC1, did not block insulin induction of SREBP-1c, suggesting a downstream pathway distinct from S6 kinase. These results establish mTORC1 as an essential component in the insulin-regulated pathway for hepatic lipogenesis but not gluconeogenesis, and may help to resolve the paradox of selective insulin resistance in livers of diabetic rodents.
Identification of VceA and VceC, two members of the VjbR regulon that are translocated into macrophages by the Brucella type IV secretion system (2008)

Survival and replication inside host cells by Brucella spp. requires a type IV secretion system (T4SS), encoded by the virB locus. However, the identity of the molecules secreted by the T4SS has remained elusive. We hypothesized that proteins translocated by the T4SS would be co-regulated with the virB operon. The LuxR family regulator VjbR, known to regulate virB, bound a fragment of the virB promoter containing an 18 bp palindromic motif (virB promoter box), showing that VjbR regulated the virB operon directly. To identify virB co-regulated genes, we searched the Brucella suis 1330 and B. abortus 2308 genomes for genes with an upstream virB promoter box. One hundred and forty-four promoters in the two genomes contained the virB promoter box, including those of fliC encoding flagellin and cgs encoding cyclic beta-glucan synthetase. Thirteen of these proteins were tested for VirB-dependent translocation into macrophages using a beta-lactamase reporter assay. This analysis resulted in the identification of the proteins encoded by BAB1_1652 (VceA) and BR1038/BAB1_1058 (VceC) as novel protein substrates of the Brucella T4SS. VceC could also be translocated by the Legionella pneumophila Dot/Icm T4SS into host cells. Our results suggest that VjbR co-ordinates expression of the T4SS and at least two of its secreted substrates.
Creating Competitive Power Markets: The PJM Model (2001)

This comprehensive model of the nation's largest, most technically advanced and forward-thinking power pool - Pennsylvania, Jersey, Maryland (PJM) - provides a window on state-of-the-art solutions to complex, organizational, managerial, technical, and regulatory issues that cut across the entire industry in transition. With full cooperation from PJM, nationally recognized energy lawyer Jeremiah D. Lambert compares and contrasts PJM with other ISOs on key issues such as governance, structure and transmission pricing. Lambert's expert comparison will help readers: Successfully structure RTO or ISO projects Follow legal/ regulatory guidelines Develop the best-practice standards in all areas of the RTO/ISO structure.
Emerging Signalling and Protein Interactions Mediated Via Metabotropic Glutamate Receptors (2003)

Metabotropic glutamate receptors (mGlu) are GTP-binding (G) protein-coupled receptors (GPCRs) that are involved in learning and memory, cardiovascular control and motor function. Their structure and pharmacology has been reviewed recently in Current Drug Targets: CNS and Neurological Disorders (Vol. 1, Issue 3) where their roles in a variety of neurological disorders were highlighted. The present review focuses on the emerging evidence for interactions of mGlu receptors with other GPCRs in the CNS at the membrane interface and amongst signaling cascades in the cytosol (e.g. intracellular Ca(2+), cAMP and scaffolding proteins). While initially non-selective activity was thought to be responsible for many atypical responses, increasing evidence points to GPCR interactions in neurons and glia, with adrenoceptors, adenosine receptors, dopamine receptors and muscarinic receptors. For example, group II mGlu receptors were found to be required for group I mGlu receptor induction of long-term potentiation at the postsynaptic terminal. Increasing evidence demonstrates the intimate interaction of adenosine receptors and mGlu receptors, particularly in the regulation of neurotransmitter release. While adenosine itself can be released from astrocytes by co-activation of group II mGlu and beta-adrenergic receptors. Given the complexity of neurological disorders such as ischemic stroke, Alzheimer's disease and epilepsy, exploitation mGlu receptor-associated GPCR interactions may prove efficacious in the treatment of such disorders.
Effects of hyperammonaemia on brain function (1998)

Neuropsychiatric symptoms of hyperammonaemia include alterations of mood and personality, cognitive impairment, ataxia, convulsions and coma. The nature and severity of CNS dysfunction depend upon the aetiology and degree of hyperammonaemia, its acuteness of onset and the age of the patient. Neuropathological studies reveal Alzheimer type II astrocytosis in the adult hyperammonaemic patient, whereas hyperammonaemia in the infant resulting from congenital urea cycle disorders or Reye syndrome is accompanied by cerebral atrophy, neuronal loss and cerebral oedema. Several electrophysiological and biochemical mechanisms have been proposed to explain the deleterious effects of ammonia on CNS function. Such mechanisms include direct effects of the ammonium ion on excitatory and inhibitory neurotransmission and a deficit in cerebral energy metabolism due to ammonia-induced inhibition of alpha-ketoglutarate dehydrogenase. In addition, ammonia has been shown to interfere with normal processes of uptake, storage and release of various neurotransmitters. Ammonia disrupts monoamine storage, inhibits the high-affinity uptake of glutamate by both astrocytic and neuronal elements and activates 'peripheral-type' benzodiazepine receptors leading to the potential synthesis of neuroactive steroids in brain. On the basis of these actions, it has been proposed that ammonia disrupts neuron-astrocyte trafficking of amino acids and monoamines in brain. The increased formation of brain glutamine in hyperammonaemic syndromes could be responsible for the phenomenon of brain oedema in these disorders. Therapies aimed at either decreasing ammonia production in the gastrointestinal tract or increasing ammonia removal by liver or skeletal muscle are the mainstay in the prevention and treatment of the CNS consequences of hyperammonaemia. New therapeutic approaches aimed at correction of the neurotransmitter and cerebral energy deficits in these syndromes could hold promise for the future.
Contributions of polyol pathway to oxidative stress in diabetic cataract (1999)

There is strong evidence to show that diabetes is associated with increased oxidative stress. However, the source of this oxidative stress remains unclear. Using transgenic mice that overexpress aldose reductase (AR) in their lenses, we found that the flux of glucose through the polyol pathway is the major cause of hyperglycemic oxidative stress in this tissue. The substantial decrease in the level of reduced glutathione (GSH) with concomitant rise in the level of lipid peroxidation product malondialdehyde (MDA) in the lens of transgenic mice, but not in the nontransgenic mice, suggests that glucose autoxidation and nonenzymatic glycation do not contribute significantly to oxidative stress in diabetic lenses. AR reduction of glucose to sorbitol probably contributes to oxidative stress by depleting its cofactor NADPH, which is also required for the regeneration of GSH. Sorbitol dehydrogenase, the second enzyme in the polyol pathway that converts sorbitol to fructose, also contributes to oxidative stress, most likely because depletion of its cofactor NAD+ leads to more glucose being channeled through the polyol pathway. Despite a more than 100% increase of MDA, oxidative stress plays only a minor role in the development of cataract in this acute diabetic cataract model. However, chronic oxidative stress generated by the polyol pathway is likely to be an important contributing factor in the slow-developing diabetic cataract as well as in the development of other diabetic complications.--Lee, A. Y. W., Chung, S. S. M. Contributions of polyol pathway to oxidative stress in diabetic cataract. FASEB J. 13, 23-30 (1999)
Towards a universal disulphide stabilised single chain Fv format: importance of interchain disulphide bond location and vL-vH orientation (2012)

Engineered introduction of interface interchain disulphide bonds is perceived to be a simple method to increase the stability of single chain Fv (scFv). Six disulphide bond locations have been cited within the literature but the potential for the broad use of each has not been examined. Five of these disulphide bond locations were introduced into one scFv in order to compare their relative effects on expression, thermal stability, percent monomer formation and retention of antigen binding. The disulphide bond position vH44-vL100 was observed to enable the most favourable balance of biophysical properties. The vH44-vL100 disulphide bond was introduced into five additional scFv in both vL-vH and vH-vL orientations in order to investigate its general applicability. Data are presented to show the relative influence of scFv sequence, v-region organisation and interchain disulphide bond on expression yield, thermal stability and percent monomer. Introduction of the vH44-vL100 disulphide bond typically resulted in no or little increase in thermal stability and no change in percent monomer but did confer the benefit of permanently fixing monomer:dimer ratios during purification and analysis.
Influence of Soil Temperature and Matric Potential on Sugar Beet Seedling Colonization and Suppression of Pythium Damping-Off by the Antagonistic Bacteria Pseudomonas fluorescens and Bacillus subtilis (2004)

ABSTRACT Pseudomonas fluorescens B5 and Bacillus subtilis MBI 600 colonized sugar beet seedlings at matric potentials of -7 x 10(3), -140 x 10(3), and -330 x 10(3) Pa and under five temperature regimes ranging from 7 to 35 degrees C, with diurnal fluctuations of 5 to 22 degrees C. No interaction between matric potential and temperature was observed. In situ bioluminescence indicated physiological activity of Pseudomonas fluorescens B5. Colonization of the root at >/=4 cm below the seed decreased at very low matric potential (-330 x 10(3) Pa). Total population size of Pseudomonas fluorescens B5 per seedling was significantly increased at -140 x 10(3) Pa. However, matric potential had no significant effect on the population density of Pseudomonas fluorescens per gram of root fresh weight and did not affect the distribution of the population down the root. Total population size per seedling and downward colonization by Pseudomonas fluorescens B5 were significantly reduced at high temperatures (25 to 35 degrees C). Maximum colonization down the root occurred at intermediate temperature (15 degrees C) at both matric potentials (-7 x 10(3) and -140 x 10(3) Pa). Addition of B. subtilis MBI 600 to the seed had no effect on rhizosphere populations of Pseudomonas fluorescens B5. Populations of B. subtilis MBI 600, which consisted largely of spores, were slightly reduced at lower matric potentials and were not affected by temperature. Survival and dry weight of plants in soils infested with Pythium spp. decreased with increasing soil temperature and matric potential, indicating an increase in disease pressure. However, there was no significant interaction between the two factors. At -330 x 10(3) Pa, soil dryness but not Pythium infection was the limiting factor for plant emergence. At temperatures of 7 to 25 degrees C and matric potentials of -7 x 10(3) to 120 x 10(3) Pa, treatment with Pseudomonas fluorescens B5 increased plant survival and dry weight. At 7 degrees C and -120 x 10(3) Pa, there was almost complete emergence of seeds treated with Pseudomonas fluorescens B5. Antagonistic activity of Pseudomonas fluorescens B5 decreased with increasing soil temperature and decreasing matric potential. At 25 to 35 degrees C and -7 x 10(3) Pa, no effect was observed. In regimes with different day and night temperatures, the maximum (day) temperature was decisive for disease development and antagonistic activity. B. subtilis MBI 600 displayed no significant antagonistic effect against Pythium ultimum and did not influence the performance of Pseudomonas fluorescens B5 in combined inocula.
Decreased HCRP1 expression is associated with poor prognosis in breast cancer patients. (2014)

Our results suggest that HCRP1 may play an important role in EGFR regulation and that its decreased expression is an independent predictor of breast cancer, especially in TNBC patients.
BGP-LS extensions for Segment Routing BGP Egress Peer Engineering (2019)

Segment Routing (SR) leverages source routing. A node steers a packet
through a controlled set of instructions, called segments, by
prepending the packet with an SR header. A segment can represent any
instruction, topological or service-based. SR segments allow steering
a flow through any topological path and service chain while
maintaining per-flow state only at the ingress node of the SR domain.
This document describes an extension to BGP Link-State (BGP-LS) for
advertisement of BGP Peering Segments along with their BGP peering
node information so that efficient BGP Egress Peer Engineering (EPE)
policies and strategies can be computed based on Segment Routing.
Peripheral antinociceptive effects of inhibitors of monoacylglycerol lipase in a rat model of inflammatory pain (2010)

BACKGROUND AND PURPOSE The endocannabinoid 2-arachidonoylglycerol (2-AG) is degraded primarily by monoacylglycerol lipase (MGL). We compared peripheral antinociceptive effects of JZL184, a novel irreversible MGL inhibitor, with the reversible MGL-preferring inhibitor URB602 and exogenous 2-AG in rats. EXPERIMENTAL APPROACH Nociception in the formalin test was assessed in groups receiving dorsal paw injections of vehicle, JZL184 (0.001-300 µg), URB602 (0.001-600 µg), 2-AG (ED(50)), 2-AG + JZL184 (at their ED(50)), 2-AG + URB602 (at their ED(50)), AM251 (80 µg), AM251 + JZL184 (10 µg), AM630 (25 µg) or AM630 + JZL184 (10 µg). Effects of MGL inhibitors on endocannabinoid accumulation and on activities of endocannabinoid-metabolizing enzymes were assessed. KEY RESULTS Intra-paw administration of JZL184, URB602 and 2-AG suppressed early and late phases of formalin pain. JZL184 and URB602 acted through a common mechanism. JZL184 (ED(50) Phase 1: 0.06 ± 0.028; Phase 2: 0.03 ± 0.011 µg) produced greater antinociception than URB602 (ED(50) Phase 1: 120 ± 51.3; Phase 2: 66 ± 23.9 µg) or 2-AG. Both MGL inhibitors produced additive antinociceptive effects when combined with 2-AG. Antinociceptive effects of JZL184, like those of URB602, were blocked by cannabinoid receptor 1 (CB(1)) and cannabinoid receptor 2 (CB(2)) antagonists. JZL184 suppressed MGL but not fatty-acid amide hydrolase or N-arachidonoyl-phosphatidylethanolamine phospholipase D activities ex vivo. URB602 increased hind paw 2-AG without altering anandamide levels. CONCLUSIONS AND IMPLICATIONS MGL inhibitors suppressed formalin-induced pain through peripheral CB(1) and CB(2) receptor mechanisms. MGL inhibition increased paw skin 2-AG accumulation to mediate these effects. MGL represents a target for the treatment of inflammatory pain.