gebhart/patrepeval huggingface dataset:
Adiponectin regulates the expression of genes associated with fatty acid synthesis and oxidation in primary pig adipocytes (2006)

Adiponectin has been implicated in the regulation of glucose uptake and fatty acid synthesis in adipocytes, and in the long‐term suppression of weight gain when over‐expressed in rodents by adenovirus associated virus vectors. The aim of this research was to determine whether adiponectin regulates the expression of genes associated with fatty acid oxidation in porcine adipocytes. Primary adipocytes were isolated from the dorsal subcutaneous adipose tissue of pigs (male castrates, n=5). Cells were incubated in DMEM with 3% BSA, in the presence and absence of recombinant porcine adiponectin (30 ìg/mL), and were harvested at 0, 30, 60, 120, 240 and 360 minutes. Total RNA was extracted for cDNA synthesis, and the abundance of selected transcripts determined by real time PCR analysis. Adiponectin transiently increased (2–6.5 fold, P < .05) the expression of acetyl Co‐A carboxylase (ACC), AMP activated kinase (AMPK), acyl Co‐A oxidase (ACO) and peroxisome proliferator activated receptor‐α (PPARα). After the initial increase in mRNA abundance, there was either a return to initial levels of expression (PPARα), a significant reduction (AMPK), or a cyclic pattern of expression (ACC, ACO). The abundance of the uncoupling protein‐3 (UCP3) transcript was not influenced by adiponectin until the final measure at 360 minutes, at which time it was increased 3.8‐fold (P < .05). Collectively, these data indicate that adiponectin acts through autocrine/paracrine signaling pathways to coordinately regulate lipid metabolism in the adipocyte, and may thus be a determinant of adipocyte size and overall lipid accumulation. Funding is USDA
Alpha interferon inhibits early stages of the human immunodeficiency virus type 1 replication cycle (1992)

In this study, we have analyzed the effect of human alpha interferon (IFN-alpha) on a single replication cycle of human immunodeficiency virus type 1 (HIV-1) infection in the lymphocytic cell line CEM-174, which is highly sensitive to the antiviral effects of IFN. Pretreatment of cells with 50 to 500 U of recombinant human IFN-alpha per ml resulted in a marked reduction in viral RNA and protein synthesis. The effect of IFN-alpha was dose dependent and was amplified in multiple infection cycles. IFN-induced inhibition of viral protein synthesis could be detected only when cells were treated with IFN-alpha prior to infection or when IFN-alpha was added up to 10 h postinfection, but not if IFN-alpha was added at the later stages of HIV-1 replication cycle or after the HIV-1 infection was already established. Analysis of the integrated HIV-1 provirus showed a marked decrease in the levels of proviral DNA in IFN-treated cells. Thus, in contrast to the previous studies on established HIV-1 infection in T cells, in which the IFN block appeared to be at the posttranslational level, during de novo infection, IFN-alpha interferes with an early step of HIV-1 replication cycle that occurs prior to the integration of the proviral DNA. These results indicate that the early IFN block of HIV-1 replication, which has been previously observed only in primary marcophages, can also be detected in the IFN-sensitive T cells, indicating that the early IFN block is not limited to macrophages.
Cognate CD4 T-Cell Licensing of Dendritic Cells Heralds Anti-Cytomegalovirus CD8 T-Cell Immunity after Human Allogeneic Umbilical Cord Blood Transplantation (2014)

Survival rates after stem cell transplantation are lowered by 25% when patients undergo reactivation of cytomegalovirus (CMV) that they harbor. Immune protection against CMV is mostly executed by white blood cells called killer T cells. We here show that for generation of optimally protective killer T-cell responses that respond to CMV, the early elicitation of help from a second branch of CMV-directed T cells, called helper T cells, is required.
Simple proof of the continued fraction algorithm for decoding Reed-Solomon codes (1978)

It was shown recently that BCH and RS codes can be implemented by Berlekamp's algorithm using continued fraction approximations. A simple transparent proof of Berlekamp's algorithm that uses such a development is given in this paper.
Noble Gas Hydride Compounds (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
AnAlgorithm forI/OPartitioning Targeting 3D Circuits and ItsImpact on 3D-Vias (2006)

Inthispaperwe discuss themigration ofa 2D netlist withpre-placed I/Osto3Dcircuits. Forthat, wepresent analgorithm toperform thepartitioning oftheI/Opinsinto varioustierstargeting at I/Obalancing and 3D-Vias minimization. We formulate thenetlist migration constrained withrespect tothepreservation ofsomeoriginal netlist properties. TheI/Opartitioning algorithm isbasedonthelogic distance betweenI/Os.Sincethereisno literature on I/O partitioning for3D circuits we compared ouralgorithm with twosimplistic approaches thattargeted balance andmin-cut respectively. Experimental results showthatouralgorithm can reduce thenumberof3D-Vias compared tobothalgorithms, whilebalance iskeptclose tooptimal. Mostimportantly, we showedthatperforming I/Opartitioning separately we can reducethenumberof3D-Viasevenmore thanexisting solutions in theliterature forthenetlist partitioning. Additionally, we studied theareaimpactofthe3D-Vias resulted fromthethreealgorithms targeting twodifferent technologies for3Dcircuits. We observed thatspecially inthe Bulkbasedtechnologies the3D-Viapenalty ishuge,favoring ouralgorithm.
Modeling and analysis of return-current paths for microstrip-to-microstrip via transitions (2008)

In this contribution, the return-current paths for single-ended microstrip-to-microstrip via transitions in conventional layer stack-ups are modeled and analyzed. Electromagnetic reliability (EMR) problems which occur in these layer stack-ups, because the return-currents are not properly managed are discussed. Finally, a layer stack-up with well defined return-current paths, which overcomes the limitations of traditional layer stack-ups, is proposed.
Research Translocation of bacterial NOD2 agonist and its link with (2009)

Introduction The gut is often considered as the motor of critical illness through bacterial translocation, which amplifies the inflammatory response and alters the immune status. However, systemic bacterial translocation was rarely proven and endotoxin measurement only reflects translocation of Gramnegative-derived products. The process could be more frequently identified if peptidoglycan, derived from both Gramnegative and Gram-positive bacteria, was measured. Methods We developed a new tool to detect circulating peptidoglycan-like structure using a NOD2-transfected cell line. We also measured plasma and cell-associated endotoxin and different plasma markers of inflammation. We studied 21 patients undergoing abdominal aortic surgery (AAS), and 21 patients undergoing carotid artery surgery (CAS) were included as negative controls. Patients were sampled during surgery until two days post-surgery. Results In 90.5% of the AAS patients, a NOD2 agonist peak was detected in plasma before aortic clamping, but after gut manipulation by the surgeon, and persisted after blood reperfusion. As expected, no peak was detected in plasma from CAS patients (P = 0.003). Leukocyte-bound endotoxin appeared after blood reperfusion in 71% of the AAS patients, and circulating endotoxin was detected for 57% of them. The levels of interleukin (IL)-6, IL-10 and of inflammatory markers (Creactive protein, procalcitonin) were maximal at postoperative day 1 or 2 in AAS patients. The levels of circulating NOD2 agonist positively correlated with those of cortisol and IL-10. Conclusions The measurement of circulating NOD2 agonist gives a higher informative tool than that of circulating endotoxin for early and sensitive detection of the translocation of bacterial products. The data suggest that circulating NOD2 agonist contributes to further enhance the stress response following surgery.
Cellular uptake of beta2M and AGE-beta2M in synovial fibroblasts and macrophages (2002)

Our results suggest that beta(2)M and AGE-beta(2)M are endocytosed via different mechanisms in human synovial fibroblasts and monocytes/macrophages. These results may offer a potential explanation of differences observed in cell culture experiments.
PAPER 133: INFLUENCE OF SACRAL MORPHOLOGY IN DEVELOPMENTAL SPONDYLOLISTHESIS (2010)

Purpose: To determine the relationship between sacral morphology and developmental L5/S1 spondylolisthesis in children and adolescent.

Method: A radiographic study was conducted to investigate sacral morphology in developmental L5/S1 spondylolisthesis in a pediatric and adolescent population. The lateral standing radiographs of 131 subjects, aged 6 to 20 years old with developmental L5-S1 spondylolisthesis (91 low grade and 40 high grade) were analyzed with a dedicated software allowing to measure the following parameters, which were analyzed for each subject by the same individual and compared to an age and sex-matched cohort of 120 asymptomatic subjects: the sacral table index (STI), the sacral table angle (STA), the sacral kyphosis (SK), S1 superior angle, S2 inferior angle, and grade of spondylolisthesis. Student t tests were used to compare the parameters between the curve types.

Results: This study demonstrated that STA is significantly smaller (p<0.01) in children and adolescents with L5-S1 spondylolisthesis compared to a similar control group. Furthermore, STA is significantly smaller in high grade spondylolisthesis when compared to subjects with low grade. There is also a significant difference in segmental sacral morphology (S1 and S2 anatomy) in the spondylolisthesis group. Increasing sacral kyphosis is also found to be significantly associated with spondylolisthesis.

Conclusion: The sagittal sacral morphology is a constant anatomic variable specific to each normal individual. The anatomy of the sacrum in children and aldolescentss with L5-S1 spondylolisthesis is particular and different from a control group. This study suggests that sacral anatomy may have a direct influence on the development of spondylolisthesis: a lower STA and higher sacral kyphosis may be two factors predisposing to vertebral slip in developmental spondylolisthesis.
Validation of the Large-Signal Klystron (2004)

We demonstrate the effectiveness of the Tele- graphist's Equations Solution for Linear-beam Amplifiers code for simulation of a range of klystron amplifier designs. Simulation results are compared to both particle-in-cell (PIC) simulations and experimental data, with good agreement obtained in each case. Specific features and optimizations included in the model are discussed and shown to allow a significant reduction in simulation times over the general PIC approach. Index Terms—Klystrons, microwave amplifiers, simulation.
Infrared and Raman studies show that poly(dA).cntdot.poly(dT) and d(AAAAATTTTT)2 exhibit a heteronomous conformation in films at 75% relative humidity and a B-type conformation at high humidities and in solution (1987)

The decadeoxynucleotide d(AAAAATTTTT)2 in duplex form and the double-helical polynucleotide poly(dA).poly(dT) have been studied by Raman and infrared (IR) spectroscopy under a variety of environmental conditions. The IR spectra have been taken of cast films and compared to the IR spectra of the alternating poly(dA-dT), which shows clear B-genus and A-genus vibrational spectra under conditions of high (greater than 92%) and low (75%) relative humidity (RH). From the IR data, it is shown that d-(AAAAATTTTT)2 and poly(dA).poly(dT) adopt a B-genus conformation in films with high water content. When the relative humidity of the film is decreased, the IR spectra reflect a gradual evolution of the geometry of both d(AAAAATTTTT)2 and poly(dA).poly(dT) into a form intermediate between the B genus and A genus, but the IR spectrum of a pure A genus has not been obtained. In these DNAs at 75% RH, the IR bands of adenosine have the same frequencies as those found in poly(dA-dT) at 75% RH where the local furanose conformation is C3' endo/anti, but the thymidine frequencies do not resemble those of poly(dA-dT) at 75% RH but rather those of poly(dA-dT) at high humidities. It is concluded that both poly(dA).poly(dT) and d(AAAAATTTTT)2 adopt a fully heteronomous duplex geometry in cast films at low humidity. For studies in aqueous solution the Raman effect was employed. As a model for the heteronomous conformation in solution, the duplex poly(rA).poly(dT) was used.(ABSTRACT TRUNCATED AT 250 WORDS)
Development of a Novel, Remote‐Controlled Artificial Bowel Sphincter Through Microsystems Technology (2006)

An artificial sphincter prototype has been developed, specifically designed for comfortable remote control by fecally incontinent patients. The artificial sphincter includes a fluid reservoir, an occlusive cuff, and a micropump based on piezo-technology in a single unit. Continence and implantation management were evaluated around isolated porcine anal canals and in vivo. The design of the prosthesis reduces the occlusion pressure and allows low inflation volumes (6.5-16 mL). Operating pressures between 24 and 58 mm Hg indicate a minor risk of ischemic injury to the bowel. The operation time is estimated at about 7 days with no recharging of the battery. The novel prototype is a highly integrated prosthesis for placement around the anal canal or lower rectum, effecting continence with comfortable control.
Cleavage oxygenases for the biosynthesis of trisporoids and other apocarotenoids in <i>Phycomyces</i> (2011)

Mixed cultures of strains of opposite sex of the Mucorales produce trisporic acids and other compounds arising from cleavage of β-carotene, some of which act as signals in the mating process. The genome of Phycomyces blakesleeanus contains five sequences akin to those of verified carotenoid cleavage oxygenases. All five are transcribed, three of them have the sequence traits that are considered essential for activity, and we have discovered the reactions catalysed by the products of two of them, genes carS and acaA. The transcripts of carS became more abundant in the course of mating, and its expression in β-carotene-producing Escherichia coli cells led to the formation of β-apo-12'-carotenal, a C₂₅ cleavage product of β-carotene. Joint expression of both genes in the same in vivo system resulted in the production of β-apo-13-carotenone, a C₁₈ fragment. In vitro, AcaA cleaved β-apo-12'-carotenal into β-apo-13-carotenone and was active on other apocarotenoid substrates. According to these and other results, the first reactions in the apocarotenoid pathway of Phycomyces are the cleavage of β-carotene at its C11'-C12' double bond by CarS and the cleavage of the resulting C₂₅-fragment at its C13-14 double bond by AcaA.
DISRUPTION OF INFLUENZA VIRUS (1954)

1. The hemagglutinating capacity, enzymic activity, and infectivity of several influenza viruses were destroyed by repeated freezing and thawing of dialyzed allantoic fluids containing them. 2. Influenza virus degraded by freezing and thawing, by treatment with 5 M urea, or by heating at 65 degrees C. still combined with homologous antibody and was demonstrable by blocking of the hemagglutination-inhibition and virus neutralization reactions. 3. After 50 cycles of freezing and thawing, much of the blocking antigen activity was not sedimented by centrifugation at 120,000 g for 2 hours, and electron microscopy showed complete disruption of the virus particles. So called soluble blocking antigen was obtained from four strains of influenza A, the Lee strain of influenza B, mumps, and Newcastle disease viruses. 4. Soluble blocking antigens from influenza A viruses were highly strain-specific; gave little or no reaction in complement-fixation tests; stimulated but little antibody production in rabbits and did not induce immunity in mice; caused reactivation of infective virus in neutral mixtures of homologous virus and immune serum. 5. Repeatedly frozen and thawed influenza virus preparations did not interfere with the propagation of infective virus in the allantoic sac. The blocking antigen activity they contained was precipitated by half saturated ammonium sulfate, destroyed by trypsin, chymotrypsin, or heating at 56 degrees C. for 30 minutes, but was unaffected by desoxyribonuclease or ribonuclease. 6. These findings are in accord with the view that soluble blocking antigen obtained from influenza virus particles on disruption by repeated freezing and thawing is protein in nature and represents the essential antigenic material of the intact virus.
Neuronal expression of nuclear and mitochondrial genes for cytochrome oxidase (CO) subunits analyzed by in situ hybridization: comparison with CO activity and protein (1991)

Cytochrome oxidase (CO) is a mitochondrial energy-generating enzyme of the oxidative phosphorylation pathway. In neurons, CO activity varies among different cells and compartments (perikarya, dendrites, axons, and terminals) according to their physiological activity and metabolic requirements. Regulation of enzyme protein levels, rather than enzyme turnover number, largely accounts for local variations in CO activity (Hevner and Wong-Riley, 1989, 1990). In the present study, we examined how CO activity and protein levels are related to mitochondrial DNA (mtDNA) and CO subunit mRNA levels in neurons and neuronal compartments. Mammalian CO comprises 13 subunits (Kadenbach et al., 1983), of which three are encoded in mtDNA and 10 in nuclear genes. We studied one mitochondrial-encoded mRNA [subunit I (COI)], two nuclear-encoded mRNAs (COIV, COVIII), and mtDNA, using in situ hybridization to determine their distributions in monkey hippocampus, cerebellum, and primary visual cortex. We compared their distributions with those of CO activity and protein, determined by histochemistry and immunohistochemistry, respectively. In all regions, the local content of mtDNA was similar, but not identical, to the activity and amount of CO. Expression of COI mRNA was not proportional to mtDNA abundance or CO activity and protein, but instead was highest in cell bodies, lower in dendrites, and undetectable in axon terminals. COIV and COVIII mRNAs were detected exclusively in perikarya and proximal dendrites. Thus, the nuclear-encoded subunits of CO are probably translated mainly in neuronal cell bodies and allocated to other compartments posttranslationally. Regulation of CO was studied in two monkeys treated by monocular tetrodotoxin (TTX) injection, a procedure that blocks impulses from one eye. In those animals, cortical changes in CO activity were correlated with changes in mtDNA and in COI, COIV, and COVIII mRNA. Our results suggest that neuronal CO is synthesized and assembled mainly in cell bodies and indicate that both nuclear and mitochondrial CO subunit genes are regulated by neuronal activity.
Colossal magnetoresistance in La0.7Ba0.3MnO3 thin films prepared by spray pyrolysis (2000)

Barium–lanthanum–manganite (La0.7Ba0.3MnO3) thin films that exhibit a colossal magnetoresistance (CMR) effect have been prepared by spray pyrolysis of solutions of aqueous nitrates. Structural, optical, and magnetotransport properties of the films were studied as a function of growth conditions and postgrowth treatments. In a magnetic field of 600 mT, the maximum CMR effect amounted to a 15% decrease in resistivity relative to zero field value. Instead of decreasing at lower temperature, the value of the CMR continued to increase as the temperature decreased to 100 K. This behavior is attractive for practical applications.
Light propagation in tissue during fluorescence spectroscopy with single-fiber probes (2001)

Fluorescence spectroscopy systems designed for clinical use commonly employ fiberoptic probes to deliver excitation light to a tissue site and collect remitted fluorescence. Although a wide variety of probes have been implemented, there is little known about the influence of probe design on light propagation and the origin of detected signals. In this study, we examined the effect of optical fiber diameter, probe-tissue spacing and numerical aperture on light propagation during fluorescence spectroscopy with a single-fiber probe. A Monte Carlo model was used to simulate light transport in tissue. Two distinct sets of excitation-emission wavelength pairs were studied (337/450 nm and 400/630 nm). Simulation results indicated that increasing fiber diameter or fiber-tissue spacing increased the mean excitation-emission photon pair pathlength and produced a transition from high selectivity for superficial fluorophores to a more homogeneous probing with depth. Increasing numerical aperture caused an increase in signal intensity, but axial emission profiles and pathlengths were not significantly affected for numerical aperture values less than 0.8. Tissue optics mechanisms and implications for probe design are discussed. This study indicates that single-fiber probe parameters can strongly affect fluorescence detection and should be considered in the design of optical diagnostic devices.
Validating use-cases with the AsmL test tool (2003)

The Abstract State Machine Language supports use-case oriented modeling in a faithful way. In this paper, we discuss how the AsmL test tool, a new component of the AsmL tool environment, is used to generate finite state machines from use-case models which can be used for validation purposes or for testing.
Van Hove excitons and high-Tc superconductivity: VIIIC. Dynamic Jahn-Teller effects versus spin-orbit coupling in the LTO phase of La2−χSrχCuO4 (1993)

Abstract The possible role of the van Hove singularity (vHS) in stabilizing the low-temperature orthorhombic (LTO) phase transition in La2−χSrχCuO4 (LSCO) is discussed. It is found that the vHS can drive a structural distortion in two different ways, either due to spin-orbit coupling or to dynamic Jahn-Teller (JT) effects. This paper discusses the latter effect in some detail. It is shown that a model hamiltonian introduced earlier to describe the coupled electron-octahedral tilt motions (“cageons”) has a series of phase transitions, from a high-temperature disordered JT phase (similar to the high-temperature tetragonal phase of LSCO) to an intermediate temperature dynamic JT phase, of average orthorhombic symmetry (the LTO phase) to a low-temperature static JT phase (the low-temperature tetragonal phase). For some parameter values, the static JT phase is absent.
Methotrexate: An Effective Agent for Treating Cancer and Building Careers. The Polyglutamate Era (1996)

This paper chronicles developments in the laboratory of Dr. Bruce Chabner during the period 1978-1981. Initial work demonstrated that methotrexate is taken up by human breast cancer cells by a high-affinity, carrier-mediated, energy-dependent transport system similar to that described in murine leukemia cells. Conversion of methotrexate to a high molecular weight polyglutamate metabolite was also demonstrated to occur in human breast cancer cells. Polyglutamates became the predominant form of intracellular drug, both free in the cytosol and bound to dihydrofolate reductase, during a 24 h exposure to clinically achievable methotrexate concentrations. Intracellular retention of polyglutamates led to prolonged suppression of thymidine synthesis and loss of cell viability after removal of extracellular drug. This work identified methotrexate polyglutamates as biologically active enzyme inhibitors in human tumor cells and launched a series of investigations on the interaction of these derivatives with folate-requiring enzymes.