gebhart/patrepeval huggingface dataset:
Initial increase in blood CD4+ lymphocytes after HIV antiretroviral therapy reflects redistribution from lymphoid tissues (1999)

Previous studies proposed a dynamic, steady-state relationship between HIV-mediated cell killing and T-cell proliferation, whereby highly active antiretroviral therapy (HAART) blocks viral replication and tips the balance toward CD4(+) cell repopulation. In this report, we have analyzed blood and lymph node tissues obtained concurrently from HIV-infected patients before and after initiation of HAART. Activated T cells were significantly more frequent in lymph node tissue compared with blood at both time points. Ten weeks after HAART, the absolute number of lymphocytes per excised lymph node decreased, whereas the number of lymphocytes in the blood tended to increase. The relative proportions of lymphoid subsets were not significantly changed in tissue or blood by HAART. The expression levels of mRNA for several proinflammatory cytokines (IFN-gamma, IL-1beta, IL-6, and macrophage inflammatory protein-1alpha) were lower after HAART. After therapy, the expression of VCAM-1 and ICAM-1 -- adhesion molecules known to mediate lymphocyte sequestration in lymphoid tissue -- was also dramatically reduced. These data provide evidence suggesting that initial increases in blood CD4(+) cell counts on HAART are due to redistribution and that this redistribution is mediated by resolution of the immune activation that had sequestered T cells within lymphoid tissues.
High activity of inclusion bodies formed in Escherichia coli overproducing Clostridium thermocellum endoglucanase D (1991)

The formation of cytoplasmic inclusion bodies by Escherichia coli overproducing Clostridium thermocellum endoglucanase D (EGD) was investigated. EGD was found in inclusion bodies as a 68 kDa form, whereas the size of the cytoplasmic form was 65 kDa. Upon solubilization with urea followed by dialysis, the 68 kDa form was converted to the 65 kDa species. Proteolysis occurred within the COOH-terminal, reiterated region of the 68 kDa form, which is conserved among most C. thermocellum endoglucanases, but is not required for catalytic activity. The specific activity of the enzyme embedded in inclusion bodies was close to that of the purified protein. Thus, inclusion body formation does not involve denaturation of the catalytic domain of EGD, but, more likely, the participation of the reiterated, conserved region in intermolecular interactions.
Arginin-Vasopressin im septischen und vasodilatatorischen Schock (2006)

Current therapy of septic/vasodilatory cardiovascular failure includes volume resuscitation and infusion of inotropic and vasopressor agents. Norepinephrine is the first-line vasoconstrictor, and can stabilize hemodynamic variables in most patients. Nonetheless, irreversible cardiovascular failure which is resistant to conventional hemodynamic therapies still is the main cause of death in patients with severe sepsis and septic shock. In such advanced, catecholamine-resistant shock states, arginine-vasopressin (AVP) has repeatedly caused an increase in mean arterial blood pressure, a decrease in toxic norepinephrine-dosages, as well as further beneficial hemodynamic, endocrinologic and renal effects. Although AVP exerted negative inotropic effects in previous clinical trials and in selected animal experiments, a continuous low-dose AVP infusion during advanced septic/vasodilatory shock caused a decrease in cardiac index only in patients with a hyperdynamic circulation. Adverse effects on gastrointestinal circulation and the systemic microcirculation can not be excluded, but have not yet been confirmed in clinical prospective trials. Negative side effects of a supplementary AVP therapy are an increase in total bilirubin concentrations, and a decrease in platelet count. A transient increase in hepatic transaminases during AVP infusion is most likely related to preceding hypotensive episodes. Important points which must be considered when using AVP as a "rescue vasopressor" in septic/vasodilatory shock states are: 1) AVP infusion only in advanced shock states that can not be adequately reversed by conventional hemodynamic therapy (e.g. norepinephrine >0,5-0,6 mug/kg/min), 2) presence of normovolemia, 3) AVP infusion only in combination with norepinephrine, 4) strict avoidance of bolus injections and dosages >4 IU/h. Effects of a supplementary AVP infusion in advanced vasodilatory shock on survival are currently examined in a large, prospective multicenter trial in North America and Australia.
Quantitative Assessment of Altered Rectal Mucosal Permeability Due to Rectally Applied Nonoxynol-9, Biopsy, and Simulated Intercourse (2013)

Plasma sampling after rectal radioisotope administration provided quantitative estimates of altered mucosal permeability after chemical and mechanical stresses. Permeability testing may provide a useful noninvasive adjunct to assess the mucosal effects of candidate microbicides. Clinical Trials Registration. NCT00389311.
Transformation of Neurospora crassa with the Cloned am (Glutamate Dehydrogenase) Gene (1984)

We used DNA containing the am gene of Neurospora crassa, cloned in the lambda replacement vector lambdaL-47 (this clone is designated lambdaC-10), and plasmid vector subclones of this DNA to transform am deletion and point mutant strains. By means of subcloning, all sequences required for transformation to am prototrophy and expression of glutamate dehydrogenase have been shown to reside on a 2.5-kilobase BamHI fragment. We also characterized several am+ strains that were obtained after transformation with lambdaC-10. These strains showed Mendelian segregation of the am+ gene, although less than 50% of the transformed strains showed the normal linkage relationship of am with inl. In all cases tested, the strains had incorporated lambda DNA as well. The lambda DNA also showed a Mendelian segregation pattern. In one case, the incorporation of am DNA in a novel position was associated with a mutagenic event producing a strain with a very tight colonial morphology. In all cases in which the am+ gene had become the resident of a new chromosome, glutamate dehydrogenase was produced to only 10 to 20% of the wild-type levels.
The leukocyte adhesion glycoprotein CD18 participates in HIV-1-induced syncytia formation in monocytoid and T cells. (1990)

mAb 60.3 and IB4 to CD18, the common beta-subunit of the human leukocytic cell adhesion molecule family, efficiently inhibit syncytium formation induced by the interaction of HIV type 1 (HIV-1)-infected monocytoid cells and CD4+ T cells. The antibodies also interfere with cellfree HIV-1 infection of U-937 clone 16 cells. Virus-induced aggregation of these cells and the subsequent syncytia formation leading to massive cell death are efficiently blocked, and the number of infected cells remains at a very low level, 2 to 5%, for the entire culture period. However, anti-CD18 mAb do not inhibit binding of the viral envelope glycoprotein gp120 to the cell surface receptor CD4. The results indicate participation of CD18, or of the protein complex CD11a-c/CD18, in addition to CD4, in the infection and cytopathic effect of HIV-1. They also suggest that intercellular adhesion contributes to virus transmission from cell to cell and may be an important mechanism for virus spreading.
Performance modelling of UPT networks (2002)

A general modelling framework for steady state performance analysis of Universal Personal Telecommunications (UPT) services in a multinetwork environment is presented in this paper. The investigated performance measures are related to service control points (SCPs) and databases. The proposed framework enables the modelling of UPT services described in the ITU Draft Rec. Q.76. This framework considers the presence of UPT and non-UPT users in a network, as well as the impact of users' reattempts to invoke UPT services. A UPT network is modelled as a set of clusters of one or more exchanges. The calculation of the SCP utilisation in a simple multinetwork UPT environment is performed using this framework.
Complex formation between 3;3´‐diethylthiacarbocyanine iodide and DNA and its investigation in aqueous solution (1999)

The binding of 3;3′‐diethylthiacarbocyanine iodide (DTCC) with molecules of DNA was investigated by different photochemical methods. Absorption spectra were investigated under various concentration of DNA. Isosbestic points observed in these spectra are attributable to existence of two different complexes DTCC with DNA. Equilibrium constants of the formation of complexes I and II were determined ( K 1 ≈ 10 6 M −1 , K 2 ≈ 5 × 10 4 M −1 accordingly). Differential absorption spectra of two photoisomers of DTCC were obtained by flash photolysis method; it was found that the quantum yield of the short‐lived photoisomer decreases and the quantum yield of the second long‐lived photoisomer builds up with the increase in the DNA concentration. Kinetics of interaction between the triplet state of the dye and oxygen were investigated under various concentration of DNA. The growth of the quantum yield of fluorescence and intersystem crossing was observed with the increase in the DNA concentration.
MRI Template and Atlas Toolbox for the C57BL/6J Mouse Brain (2005)

In order to compare brain-imaging measurements from different subjects, brain-mapping algorithms are commonly used to register individual brain onto a standardized brain atlas. In this study, SPM99 was used to linearly and nonlinearly coregister a spatially standardized T2-weighted template of C57BL/6J to the atlas by Paxinos and Franklin (2001), local accuracy of between atlas and template was evaluated, and a toolbox was developed. This study provides a foundation for the region of interest analysis for mouse brain images
Special Edition Using Microsoft Excel 97 (1996)

Special Edition Using Microsoft Excel 97 is ideal for accomplished users, who will enjoy this complete reference to the best-selling Windows spreadsheet. The extensive index helps readers find information quickly, along with cross-indexing that shows how Excel features relate and work together. Expected to work seamlessly with the Internet, this edition is complete with special coverage of Internet enabling features. This title includes sections on techniques from the pros and integrating Excel with other Microsoft Office applications. It discusses everyday worksheet tasks, then guides the reader through managing lists and databases. It also provides helpful chapters on VBA and using Excel on a network.
Trehalose‐based thermosetting resins. I. Synthesis and thermal properties of trehalose vinylbenzyl ether (2003)

Abstract Trehalose vinylbenzyl ether was synthesized from trehalose and p ‐chloromethylstyrene (CMS) in DMSO in the presence of powdered NaOH. The structure of the product was characterized by IR and 1 H NMR spectroscopy. Degree of substitution (DS) on a trehalose unit calculated from the 1 H NMR spectrum varied from 2.4 to 3.2 by changing the feed ratio of p ‐chloromethylstyrene to trehalose. Thermal properties of the resin were analyzed by differential scanning calorimetry (DSC). DSC analysis revealed that the resin DS 2.4 has one exothermal peak at 132°C, whereas the resins DS 2.8 and 3.0 have two exothermal peaks. Furthermore, the resin DS 3.2 was found to have only one exothermal peak at 191°C. Dynamic mechanical analysis (DMA) and thermomechanical analysis (TMA) revealed that the cured resin has one transition, implying a glass transition. Biodegradability was assayed by the BOD method, and several percent of the cured resin was found to be degraded with activated sludge for 50 days. Further degradation, however, was not observed. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 91: 46–51, 2004
Sucrose Is a Nonaccumulated Osmoprotectant in Sinorhizobium meliloti (1998)

Intracellular accumulation of sucrose in response to lowered water activity seems to occur only in photosynthetic organisms. Here we demonstrate, for the first time, the potent ability of this common sugar, supplied exogenously, to reduce growth inhibition of Sinorhizobium meliloti cells in media of inhibitory osmolarity. Independently of the nature of the growth substrates and the osmotic agent, sucrose appears particularly efficient in promoting the recovery of cytoplasmic volume after plasmolysis. Surprisingly, sucrose is not accumulated by the bacteria at an osmotically efficient level. Instead, it strongly stimulates the accumulation of the main endogenous osmolytes glutamate and N-acetylglutaminylglutamine amide (NAGGN). Examining cell volume changes during the hyperosmotic treatment, we found a close correlation between the enhancement of the osmotically active solute pool and the increase in cell volume. Sucrose shares several features with ectoine, another nonaccumulated osmoprotectant for S. meliloti. Overall, osmoregulation in S. meliloti appears to be strongly divergent from that in most bacteria.
Changes in ganglioside composition of photoreceptors during postnatal maturation of the rat retina (1998)

To examine at which stage the unusual ganglioside composition observed in adult retinal photoreceptor cells was established, and to see whether ganglioside changes could be correlated to distinct maturational events, quantitative and qualitative variations in gangliosides within pure sheets of photoreceptors during postnatal differentiation and aging of retina were studied. Retinas were separated into their component layers, (particularly photoreceptor layers uncontaminated by other neuronal types) by exploiting a technique of mechanical separation by vibratome. We extracted lipids from the cell membranes and analyzed the ganglioside composition by high performance thin layer chromatography. The data show that from the earliest recordable postnatal age (6 days) until late in life (18 months), photoreceptors contain low quantities of lipid-bound N-acetyl neuraminic acid and a simplified ganglioside profile compared to inner retinal neurons. Specific ganglioside changes occur within photoreceptor cells during postnatal maturation and aging, with downregulation of a-pathway GM1 and overlapping upregulation of b-pathway GD1b taking place during the period corresponding to outer segment formation, correlating with the onset of retinal function.
Atlas of Fluorescence Spectra and Lifetimes of Dyes Attached to Protein (1985)

Abstract Fluorescence spectra and lifetimes of ovalbumin labeled with a variety of fluorescent reagents have been measured. The peak positions of the emission spectrum and the long wavelength band of the excitation spectrum as well as the fluorescence lifetimes, are tabulated. Heterogeneity of binding sites is shown by the broadness of some emisison spectra and the presence of multiexponential decay. The atlas may serve as a guide to the properties of these dyes attached to proteins in general.
The 5′ end group of tobacco mosaic virus RNA is m7G5′ppp5′Gp (1975)

RNA extracted from CsC1-purified virions of tobacco mosaic virus is shown to give rise to an unusual nucleotide on digestion which RNAase T2, in addition to the four major nucleotides. This minor component has the electrophoretic characteristics of a phosphorylated end group, but is partially resistant to bacterial alkaline phosphatase. It is, however, a substrate for venom phosphodiesterase or nucleotide pyrophosphatase, yielding products which imply the structure m7G5'ppp5'Gp. TMV RNA, like many animal cellular and viral mRNAs recently examined, therefore has a 5' terminus blocked by a methylated nucleotide inverted with respect to the rest of the chain.
Getting computers to talk like you and me : discourse context, focus, and semantics : (an ATN model) (1985)

Getting a computer to understand our everyday language may be a long way off; the computer has to know how to think as well as follow the rules of a particular language. This book makes an important contribution to the study of pragmatics and discourse by presenting an explicit and precise computational approach to the complex problem of the structure of discourse.As Professor Stephen Pinker of MIT notes, has laudably chosen to inject some precision into a field much in need of it.The book first looks at extended person-machine communication, beginning with person-person communication and focusing in particular on the conversational flow itself - what makes for coherent discourse? It then describes a computer model that describes this phenomenon as an augmented transition network (ATN).Rachel Reichman is Professor, Department of Electrical Engineering and Computer Science, University of California, San Diego.
Clinical Features, Treatment, and Outcome of Macrophage Activation Syndrome Complicating Systemic Juvenile Idiopathic Arthritis: A Multinational, Multicenter Study of 362 Patients (2014)

This study provides information on the clinical spectrum and current management of systemic JIA-associated MAS through the analysis of a very large patient sample. MAS remains a serious condition, as a sizeable proportion of patients required admission to the ICU or died.
DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data (2013)

Abstract Summary: For heterogeneous tissues, measurements of gene expression through mRNA-Seq data are confounded by relative proportions of cell types involved. In this note, we introduce an efficient pipeline: DeconRNASeq, an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It adopts a globally optimized non-negative decomposition algorithm through quadratic programming for estimating the mixing proportions of distinctive tissue types in next-generation sequencing data. We demonstrated the feasibility and validity of DeconRNASeq across a range of mixing levels and sources using mRNA-Seq data mixed in silico at known concentrations. We validated our computational approach for various benchmark data, with high correlation between our predicted cell proportions and the real fractions of tissues. Our study provides a rigorous, quantitative and high-resolution tool as a prerequisite to use mRNA-Seq data. The modularity of package design allows an easy deployment of custom analytical pipelines for data from other high-throughput platforms. Availability: DeconRNASeq is written in R, and is freely available at http://bioconductor.org/packages. Contact: tinggong@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
Treatment mechanisms: traditional and new antipsychotic drugs (2000)

The first generation of antipsychotic drugs was discovered in the 1960s and 1970s, These agents were effective in treating psychosis, but were accompanied by significant side effects, including severe parkinsonism and akathisia. Second-generation antipsychotics were introduced in the 1990s, These drugs have at least equal efficacy to their predecessors, but far fewer side effects. Some data suggest a broader efficacy profile. Clozapine remains the only superior antipsychotic in terms of the magnitude of psychotic symptom reduction. Clinical and animal studies are consistent in suggesting that the antipsychotic component of antidopaminergic treatments is initiated by dopamine receptor blockade in the striatum and that the signal is transmitted to the neocortex through the established basal ganglia-thalamo-cortical neuronal circuits. Other neurotransmitter actions (eg, antiserotonergic) can be exerted locally, in the neocortex. Defining tissue targets of drug action may suggest additional strategies for developing new antipsychotic drugs.
IL-9 and IL-13 Production by Activated Mast Cells Is Strongly Enhanced in the Presence of Lipopolysaccharide: NF-κB Is Decisively Involved in the Expression of IL-9 (2001)

Mast cells, due to their ability to produce a large panel of mediators and cytokines, participate in a variety of processes in adaptive and innate immunity. Herein we report that in primary murine bone marrow-derived mast cells activated with ionomycin or IgE-Ag the bacterial endotoxin LPS strongly enhances the expression of IL-9 and IL-13, but not IL-4. This costimulatory effect of LPS is absent in activated mast cells derived from the LPS-hyporesponsive mouse strain BALB/c-LPS(d), although in these cells the proinflammatory cytokine IL-1 can still substitute for LPS. The enhanced production of mast cell-derived IL-13 in the presence of IL-1 is a novel observation. Coactivation of mast cells with LPS leads to a synergistic activation of NF-kappa B, which is shown by an NF-kappa B-driven reporter gene construct. In the presence of an inhibitor of NF-kappa B activation, the production of IL-9 is strongly decreased, whereas the expression of IL-13 is hardly reduced, and that of IL-4 is not affected at all. NF-kappa B drives the expression of IL-9 via three NF-kappa B binding sites within the IL-9 promoter, which we characterize using gel shift analyses and reporter gene assays. In the light of recent reports that strongly support critical roles for IL-9 and IL-13 in allergic lung inflammation, our results emphasize the potential clinical importance of LPS as an enhancer of mast cell-derived IL-9 and IL-13 production in the course of inflammatory reactions and allergic diseases.
Sensitivity differences of SA and AV node to vagal stimulation: attenuation of vagal effects at SA node (1981)

The present study sought to characterize vagally induced desensitization at the sinoatrial (SA) node of the intact dog and to determine whether these findings could be extended to atrioventricular (AV) Nodal conduction. Autonomically decentralized anesthetized dogs were instrumented to record electrocardiograms, arterial pressure, and electrograms from the SA node, right atrium, right ventricle, and His bundle. During right- or left-vagal stimulation for 60 s, cycle length (CL) increased initially, followed by a gradual recovery toward control during stimulation; atrio-His (AH) interval remained prolonged throughout the stimulation. Atrial drive increased AH interval during stimulation, but AH prolongation was maintained throughout the stimulation period. To rule out acetylcholine (ACh) depletion, ACh was administered before and during vagal stimulation. Although control CL and AH interval were lengthened by ACh, no significant CL increases occurred when ACh was given during stimulation, but the AH interval became longer. Propranolol increased control CL and AH interval but did not alter the relationship between vagal stimulation and CL or AH interval. Thus the negative chronotropic effect of ACh at the SA node is diminished upon prolonged vagal stimulation, whereas the negative dromotropic effect upon AV nodal conduction remains unaltered. These results suggest differences in muscarinic receptor behavior at the SA and AV nodes.
Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease (2005)

The inflammatory bowel diseases (IBDs), Crohn's disease (CD) and ulcerative colitis, are chronic inflammatory disorders of the digestive tract. The pathogenesis of IBD is complicated, and it is widely accepted that immunologic, environmental and genetic components contribute to its etiology. To identify genetic susceptibility factors in CD, we performed a genome-wide association study in Japanese patients and controls using nearly 80,000 gene-based single nucleotide polymorphism (SNP) markers and investigated the haplotype structure of the candidate locus in Japanese and European patients. We identified highly significant associations (P = 1.71 x 10(-14) with odds ratio of 2.17) of SNPs and haplotypes within the TNFSF15 (the gene encoding tumor necrosis factor superfamily, member 15) genes in Japanese CD patients. The association was confirmed in the study of two European IBD cohorts. Interestingly, a core TNFSF15 haplotype showing association with increased risk to the disease was common in the two ethnic groups. Our results suggest that the genetic variations in the TNFSF15 gene contribute to the susceptibility to IBD in the Japanese and European populations.