gebhart/patrepeval huggingface dataset:
Effect of Dietary Fatty Acids on Inflammatory Gene Expression in Healthy Humans (2009)

Over the past 100 years, changes in the food supply in Western nations have resulted in alterations in dietary fatty acid consumption, leading to a dramatic increase in the ratio of omega-6 (omega6) to omega3 polyunsaturated fatty acids (PUFA) in circulation and in tissues. Increased omega6/omega3 ratios are hypothesized to increase inflammatory mediator production, leading to higher incidence of inflammatory diseases, and may impact inflammatory gene expression. To determine the effect of reducing the omega6/omega3 ratio on expression of inflammatory pathway genes in mononuclear cells, healthy humans were placed on a controlled diet for 1 week, then given fish oil and borage oil for an additional 4 weeks. Serum and neutrophil fatty acid composition and ex vivo leukotriene B(4) production from stimulated neutrophils were measured at the start and end of the supplementation period and after a 2-week washout. RNA was isolated from mononuclear cells and expression of PI3K, Akt, NFkappaB, and inflammatory cytokines was measured by real-time PCR. A marked increase was seen in serum and neutrophil levels of long-chain omega3 PUFA concomitant with a reduction in the omega6/omega3 PUFA ratio (40%). The ex vivo capacity of stimulated neutrophils to produce leukotriene B(4) was decreased by 31%. Expression of PI3Kalpha and PI3Kgamma and the quantity of PI3Kalpha protein in mononuclear cells was reduced after supplementation, as was the expression of several proinflammatory cytokines. These data reveal that PUFA may exert their clinical effects via their capacity to regulate the expression of signal transduction genes and genes for proinflammatory cytokines.
Optical cross connect switch based on tip/tilt micromirrors in a white cell (2003)

We present a new approach to optical interconnections, based on microelectromechanical system tip/tilt mirror technology and the White cell. This is a free-space approach in which many beams circulate simultaneously in the device, each beam forming a unique spot pattern on the micromirror array. On each bounce, each beam can be switched to any of several White cells, each of which has a different effect on the spot pattern. By appropriate combinations of these White cells, any input beam can be directed to any output. A simple proof-of-concept prototype has been demonstrated, and output coupling loss addressed.
Cross-clade human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte responses in HIV-infected Zambians (1997)

We have examined cross-clade HIV-specific cytotoxic T-lymphocyte (CTL) activity in peripheral blood of eight Zambian individuals infected with non-B-clade human immunodeficiency virus type 1 (HIV-1). Heteroduplex mobility assay and partial sequence analysis of env and gag genes strongly suggests that all the HIV-infected subjects were infected with clade C HIV-1. Six of eight C-clade HIV-infected individuals elicited CTL activity specific for recombinant vaccinia virus-infected autologous targets expressing HIV gag-pol-env derived from B-clade HIV-1 (IIIB). Recognition of individual recombinant HIV-1 B-clade vaccinia virus-infected targets expressing gag, pol, or env was variable among the patients tested, indicating that cross-clade CTL activity is not limited to a single HIV protein. These data demonstrate that HIV clade C-infected individuals can mount vigorous HIV clade B-reactive CTL responses.
Type I and Type II GABA A -Benzodiazepine Receptors Produced in Transfected Cells (1989)

GABA A (γ-aminobutyric acid A)-benzodiazepine receptors expressed in mammalian cells and assembled from one of three different α subunit variants (α 1 , α 2 , or α 3 ) in combination with a β 1 and a γ 2 subunit display the pharmacological properties of either type I or type II receptor subtypes. These receptors contain high-affinity binding sites for benzodiazepines. However, CL 218 872, 2-oxoquazepam, and methyl β-carboline-3-carboxylate (β-CCM) show a temperature-modulated selectivity for α 1 subunit-containing receptors. There were no significant differences in the binding of clonazepam, diazepam, Ro 15-1788, or dimethoxy-4-ethyl-β-carboline-3-carboxylate (DMCM) to all three recombinant receptors. Receptors containing the α 3 subunit show greater GABA potentiation of benzodiazepine binding than receptors containing the α 1 or α 2 subunit, indicating that there are subtypes within the type II class. Thus, diversity in benzodiazepine pharmacology is generated by heterogeneity of the α subunit of the GABA A receptor.
Heart rate variability in an ageing population and its association with lifestyle and cardiovascular risk factors: results of the SAPALDIA study (2006)

Heart rate variability in a general population sample shows expected associations with all known cardiovascular risk factors, although not identically for all HRV domains. Together with our percentile estimates for HRV as a function of age, these findings could assist scientists in interpreting 24 h HRV values and factors influencing them in an ageing population.
Selective DNA amplification from complex genomes using universal double-sided adapters (2004)

There is a rapidly developing need for new technologies to amplify millions of different targets from genomic DNA for high throughput genotyping and population gene-sequencing from diverse species. Here we describe a novel approach for the specific selection and amplification of genomic DNA fragments of interest that eliminates the need for costly and time consuming synthesis and testing of potentially millions of amplicon-specific primers. This technique relies upon Type IIs restriction enzyme digestion of genomic DNA and ligation of the fragments to double-sided adapters to form closed-circular DNA molecules. The novel use of double-sided adapters, assembled through the combinatorial use of two small universal sets of oligonucleotide building blocks, provides greater selection capacity by utilizing both sides of the adapter in a sequence-specific ligation event. As demonstrated, formation of circular structures results in protection of the desired molecules from nuclease treatment and enables a level of selectivity high enough to isolate single, or multiple, pre-defined fragments from the human genome when digested at over five million sites. Priming sites incorporated into the adapter allows the utilization of a common pair of primers for the amplification of any adapter-captured DNA fragment of interest.
Plasma from women with severe pre-eclampsia increases microvascular permeability in an animal model in vivo (2004)

Pre-eclampsia results in oedema, hypertension and proteinuria, and is associated with increased vascular permeability. A number of studies have pointed to the existence of a circulating macromolecule that induces this endothelial dysfunction. To test whether this circulating factor could increase vascular permeability, we have measured the effect of dialysed human plasma from pregnant women with mild or severe pre-eclampsia (pre-eclamptic toxaemia). Plasma was collected from patients with mild or severe pre-eclampsia and from normotensive women. Plasma was dialysed against frog Ringer's solution using a 12-14 kDa molecular-mass cut-off dialysis tubing. pi c (colloid osmotic pressure) was measured with a modified Hansen oncometer. Lp (hydraulic conductivity) and sigma (oncotic reflection coefficient) were measured in individually perfused frog mesenteric microvessels using the Landis-Michel technique during perfusion with dialysed plasma. Perfusion of vessels with normal plasma or plasma from patients with mild pre-eclampsia did not alter either Lp or sigma. However, plasma from patients with severe pre-eclampsia resulted in a 3.8+/-0.3-fold increase in Lp and a reduction in sigma from 0.96+/-0.03 to 0.80+/-0.11. There was a significant correlation between the change in sigma and the change in Lp, suggesting that the increase in permeability was due to an increase in pore size in these vessels. A circulating macromolecule in human plasma in severe pre-eclampsia is therefore able to increase vascular permeability in an animal model. The nature of the circulating macromolecule is not known, except that it is, or is bound to, a molecule greater than 12 kDa.
Isolation and partial nucleotide sequence of a cDNA clone for human histocompatibility antigen HLA-B by use of an oligodeoxynucleotide primer. (1981)

We have isolated a cDNA clone for one of the HLA-B locus alloantigens by hybridization with a 30-nucleotide-long DNA probe. The probe was isolated from a reverse transcriptase (RNA-dependent DNA nucleotidyltransferase)-catalyzed cDNA synthesis reaction on poly(A)-mRNA in which an oligonucleotide (5'-32P)dC-T-T-C-T-C-C-A-C-A-TOH served as a primer and in which dideoxynucleoside triphosphates were used to reduce the size and heterogeneity of the cDNA products. The desired cDNA clone was isolated from a library of recombinant cDNA clones in the plasmid pBR322. The partial nucleotide sequence of the cDNA clone corresponds to the amino acid sequence of HLA-B7 antigen. The approach described in this paper is extremely sensitive and may be useful in cloning other genes for which the corresponding mRNA is present at low levels. This cDNA clone is nearly full length and can be used to isolate and to study the genes within the HLA region and to obtain expression of HLA-B peptides in cells.
Induction of apoptosis by sphingosine in human leukemic HL-60 cells: a possible endogenous modulator of apoptotic DNA fragmentation occurring during phorbol ester-induced differentiation. (1995)

The present studies were undertaken to characterize the potential role of sphingosine in the regulation of apoptosis in HL-60 promyelocytic leukemia cells. A 6-h exposure of HL-60 cells to sphingosine or its methylated derivative, N,N-dimethylsphingosine, caused internucleosomal DNA fragmentation and stereotypical morphological changes characteristic of apoptosis (i.e., cell shrinkage, nuclear condensation, and the formation of apoptotic bodies), as well as that to pharmacological inhibitors of protein kinase C such as 1-(5-isoquinolinesulfonyl)-2-methylpiperazine and staurosporine. Apoptosis by sphingosine and N,N-dimethylsphingosine was measured using a flow cytometric method. The percentages of apoptotic cells in cultures treated with sphingosine (10 microM) and N,N-dimethylsphingosine (10 microM) for 6 h were 55.6 +/- 7.8% and 84.2 +/- 11.6%, respectively. HL-60 cells were induced to differentiate toward macrophages by treatment with 5 nM 4 beta-phorbol 12-myristate 13-acetate (PMA). Internucleosomal DNA fragmentation, which was a hallmark of apoptosis, was first detected after 10-h exposure to PMA and increased with longer treatment. Sphingosine concentrations in the cells increased concomitantly with the increasing proportion of apoptotic cells during cell differentiation. Sphingosine level in HL-60 cells differentiated by treatment with PMA for 48 h was about 3.3-fold greater than that in untreated cells. Differentiated HL-60 cells exhibited a markedly increased conversion of exogenously added [3H]ceramide to [3H]sphingosine, indicating elevation of ceramidase activity. Moreover, exposure to sphingosine resulted in down-regulation of c-myc mRNA. These observations suggest the possible role of sphingosine in induction of apoptotic DNA fragmentation during PMA-induced differentiation in myeloid leukemia cells. Sphingosine may function as an endogenous modulator mediating the apoptotic signal.
Monolithic Carbide-Derived Carbon Films for Micro-Supercapacitors (2010)

Microbatteries with dimensions of tens to hundreds of micrometers that are produced by common microfabrication techniques are poised to provide integration of power sources onto electronic devices, but they still suffer from poor cycle lifetime, as well as power and temperature range of operation issues that are alleviated with the use of supercapacitors. There have been a few reports on thin-film and other micro-supercapacitors, but they are either too thin to provide sufficient energy or the technology is not scalable. By etching supercapacitor electrodes into conductive titanium carbide substrates, we demonstrate that monolithic carbon films lead to a volumetric capacity exceeding that of micro- and macroscale supercapacitors reported thus far, by a factor of 2. This study also provides the framework for integration of high-performance micro-supercapacitors onto a variety of devices.
Application of the continuous-flow polyamide method to the solid-phase synthesis of a multiple antigen peptide (MAP) based on the sequence of a malaria epitope (1990)

Application of the ‘flow-polyamide’ method to the synthesis of the title compound, a high molecular weight (18947) branched peptide, was successful without requiring any deviation from the standard protocol.
Solubilization of particle-linked urate oxidase by different agents. (1975)

Urate oxidase was mostly recovered in a 40 000 g for 20 min subcellular fraction from conventional homogenated. Different agents were able to solubilize the sedimentable enzyme when tested on this crude peroxisomal fraction. The agents increased also total enzyme activity which was recovered in supernatants after centfiguation. If the possible effect of absorption to pellets is to be discounted, the enzyme was practically 100% extracted by six alternated freezing and thawing high alkaline pH, the detergent Hyamine 2389 and high ionic strength of calcium chloride. Triton X-100 was very effective in extracting proteins from the fraction, while it left most of the enzyme activity insoluble. It is suggested that the forces responsible for the integrity of the crystalloid, which was observed by other authors at the electron microscope, and to which the enzyme is believed to be related, are the electrostatic nature.
Characterization of a Highly Efficient Blue-shifted Channelrhodopsin from the Marine Alga Platymonas subcordiformis (2013)

Rhodopsin photosensors of phototactic algae act as light-gated cation channels when expressed in animal cells. These proteins (channelrhodopsins) are extensively used for millisecond scale photocontrol of cellular functions (optogenetics). We report characterization of PsChR, one of the phototaxis receptors in the alga Platymonas (Tetraselmis) subcordiformis. PsChR exhibited ∼3-fold higher unitary conductance and greater relative permeability for Na(+) ions, as compared with the most frequently used channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Photocurrents generated by PsChR in HEK293 cells showed lesser inactivation and faster peak recovery than those by CrChR2. Their maximal spectral sensitivity was at 445 nm, making PsChR the most blue-shifted channelrhodopsin so far identified. The λmax of detergent-purified PsChR was 437 nm at neutral pH and exhibited red shifts (pKa values at 6.6 and 3.8) upon acidification. The purified pigment undergoes a photocycle with a prominent red-shifted intermediate whose formation and decay kinetics match the kinetics of channel opening and closing. The rise and decay of an M-like intermediate prior to formation of this putative conductive state were faster than in CrChR2. PsChR mediated sufficient light-induced membrane depolarization in cultured hippocampal neurons to trigger reliable repetitive spiking at the upper threshold frequency of the neurons. At low frequencies spiking probability decreases less with PsChR than with CrChR2 because of the faster recovery of the former. Its blue-shifted absorption enables optogenetics at wavelengths even below 400 nm. A combination of characteristics makes PsChR important for further research on structure-function relationships in ChRs and potentially useful for optogenetics, especially for combinatorial applications when short wavelength excitation is required.
Soluble VEGFR‐2: an antilymphangiogenic variant of VEGF receptors (2010)

The vascular endothelial growth factor (VEGF) family of secreted proteins and their receptors are major regulators of blood vessel development (hemangiogenesis) and lymphatic vessel development (lymphangiogenesis). VEGF acts through a complex system of receptor tyrosine kinases, which can be membrane bound or soluble. New data concerning the receptor system are still emerging, thus contributing to the complexity of the system. Very recently a soluble form of VEGFR-2, termed sVEGFR-2, which is a result of alternative splicing, has been discovered. Earlier, it has been shown that a secreted/soluble form of VEGFR-1, termed sVEGFR-1, is produced by alternative splicing and exerts an antihemangiogenic effect by binding VEGF-A. The newly discovered spliced variant of sVEGFR-2 binds the lymphangiogenic growth factor VEGF-C and thus inhibits VEGF-C-induced activation of VEGFR-3, consequently inhibiting lymphatic endothelial cell proliferation. Its inactivation in murine embryos permits hyperplasia of dermal lymphatics and invasion of lymphatics into the cornea. Tumor lymphangiogenesis seems to influence the metastatic behavior of malignant cells. A correlation has been found between the downregulation of sVEGFR-2 and the malignant progression of neuroblastoma, which is characterized by lymphogenic metastases in progressed stages. Data show that lymphangiogenesis is regulated by both activators and inhibitors, and its balance is crucial in health and disease.
Stress Response of Prolactin‐Releasing Peptide Knockout Mice as to Glucocorticoid Secretion (2010)

Prolactin-releasing peptide (PrRP) is known to have functions in prolactin secretion, stress responses, cardiovascular regulation and food intake suppression. In addition, PrRP-knockout (KO) male mice show obesity from the age of 22 weeks and increase their food intake. The plasma concentrations of insulin, leptin, cholesterol and triglyceride are also increased in obese PrRP-KO mice. Fatty liver, hypertrophied white adipose tissue, decreased uncoupling protein 1 mRNA expression in brown adipose tissue and glucose intolerance were observed in obese PrRP-KO mice. As we reported previously, PrRP stimulates corticotrophin-releasing factor and regulates the hypothalamic-pituitary-adrenal axis. Therefore, it is speculated that PrRP regulates both food intake and metabolism as a stress responses. In the present study, we compared blood glucose and plasma glucocorticoid concentrations in PrRP-KO mice, and found that PrRP-KO mice showed higher concentrations of blood glucose and corticosterone compared to wild-type mice after restraint stress. By contrast, there were no difference in c-Fos expression in the paraventricular hypothalamic nucleus and plasma adrenocorticotrophic hormone concentrations between the two groups. These results suggest that the different stress responses as to glucocorticoid secretion may be induced by different responses of the adrenal glands between wild-type and PrRP-KO mice. Thus, we conclude that PrRP-KO mice become obese as a result of increased food intake, a change in metabolism, and abnormal stress responses as to glucose concentration and glucocorticoid secretion.
Regulation of nitrate and nitrite reductase expression in Nicotiana plumbaginifolia leaves by nitrogen and carbon metabolites (1993)

Nitrate (NR) and nitrite reductase (NiR) catalyse the reduction of nitrate to ammonium. The regulation of NR and NiR gene expression by carbohydrates (C) and nitrogen (N) metabolites was studied using detached leaves. In the dark, glucose fructose and sucrose supplied to detached green leaves of dark-adapted Nicotiana plumbaginifolia plants resulted in NR mRNA and protein accumulation and the loss of circadian rhythmicity in the size of the transcript pool. The characterization of transgenic plants expressing either a NR cDNA controlled by the 35S CaMV promoter or a transcriptional fusion between the tobacco nia1 (NR structural gene) promoter and the beta-glucuronidase reporter gene, led us to conclude that C metabolite control is taking place at the transcriptional level. Under low light conditions (limiting photosynthetic conditions), the supply of glutamine or glutamate resulted in a drop in the level of NR mRNA. Exogenously supplied carbohydrates partially antagonized this inhibitory effect suggesting that the availability of N and C metabolites affects the expression of the NR gene. The effects of carbohydrates and glutamine on NiR expression were also studied. NiR mRNA levels in the dark were relatively insensitive to feeding with glucose. Glutamate and glutamine were less efficient at decreasing NiR mRNA than NR mRNA levels. In contrast to NR, NiR mRNA levels were significantly increased by light treatments, indicating that NiR display regulatory characteristics reminiscent of photosynthetic genes such as the small subunit of ribulose bisphosphate carboxylase than to NR.
TTRAP, a Novel Protein That Associates with CD40, Tumor Necrosis Factor (TNF) Receptor-75 and TNF Receptor-associated Factors (TRAFs), and That Inhibits Nuclear Factor-κB Activation (2000)

CD40 belongs to the tumor necrosis factor (TNF) receptor family. CD40 signaling involves the recruitment of TNF receptor-associated factors (TRAFs) to its cytoplasmic domain. We have identified a novel intracellular CD40-binding protein termed TRAF and TNF receptor-associated protein (TTRAP) that also interacts with TNF-R75 and CD30. The region of the CD40 cytoplasmic domain that is required for TTRAP association overlaps with the TRAF6 recognition motif. Association of TTRAP with CD40 increases profoundly in response to treatment of cells with CD40L. Interestingly, TTRAP also associates with TRAFs, with the highest affinity for TRAF6. In transfected cells, TTRAP inhibits in a dose-dependent manner the transcriptional activation of a nuclear factor-kappaB (NF-kappaB)-dependent reporter mediated by CD40, TNF-R75 or Phorbol 12-myristate 13-acetate (PMA) and to a lesser extent by TRAF2, TRAF6, TNF-alpha, or interleukin-1beta (IL-1beta). TTRAP does not affect stimulation of NF-kappaB induced by overexpression of the NF-kappaB-inducing kinase (NIK), the IkappaB kinase alpha (IKKalpha), or the NF-kappaB subunit P65/RelA, suggesting it acts upstream of the latter proteins. Our results indicate that we have isolated a novel regulatory factor that is involved in signal transduction by distinct members of the TNF receptor family.
Fiber optic sensors for use in monitoring flow front in vacuum resin transfer molding processes (1997)

A distributed fiber optic sensor array developed for use in vacuum resin transfer molding systems is described. The sensor is placed in the mold and can be used to monitor resin infiltration even in complicated parts because of its small size and flexibility. The sensor components themselves are low cost and become incorporated in the part during the molding process. Careful design of the sensor elements is necessary to avoid sensitivity to mechanical stresses associated with the resin infiltration process.
Optimization of Layered Cathode Material with Full Concentration Gradient for Lithium-Ion Batteries (2013)

Li[NixCoyMn1–x–y]O2 cathode materials were synthesized with varying concentration gradients of Ni and Co ions from the particle center (0.62–0.74 mol % for Ni and 0.05 mol % for Co) to the surface (0.48–0.62 mol % for Ni and 0.18 mol % for Co), i.e., full concentration gradient (FCG) with fixed Mn concentrations. In particular, the Mn concentration (20, 25, and 33 mol %) was controlled to optimize electrode performance. The average chemical compositions of lithiated products were Li[NixCo0.16Mn0.84–x]O2 (x = 0.64, 0.59, 0.51). These cathode materials with concentration gradients followed the general performance trend of conventional layered materials; an increase in Ni content improved the capacity, whereas a higher amount of Mn delivered better capacity retention and thermal properties at the expense of capacity. As a result, we determined an optimal level of Mn concentration among the tested FCG cathodes, which maximized the discharge capacity of 188 mAh g–1 and had an excellent capacity retention of 96% over 100 cycles operated up to 4.3 V at 25 °C, with a composition of FCG Li[Ni0.59Co0.16Mn0.25]O2.