gebhart/patrepeval huggingface dataset:
Role of Toll-like receptor 2 (TLR2) in neutrophil activation: GM-CSF enhances TLR2 expression and TLR2-mediated interleukin 8 responses in neutrophils (2002)

In vitro studies as well as clinical trials indicate that the cytokines granulocyte-macrophage colony-stimulating factor (GM-CSF) and granulocyte colony-stimulating factor (G-CSF) enhance the ability of neutrophils (polymorphonuclear leukocytes) to eliminate microbial organisms. Toll-like receptor (TLR) proteins, homologs of the Drosophila protein Toll, have been found on the surface of mammalian cells and are important in the responses of macrophages to bacterial, viral, and fungal antigens. TLR4 is critical for the response to lipopolysaccharide (LPS) of gram-negative bacteria, while TLR2 is important for response to gram-positive bacteria, bacterial peptides, and yeast zymosan. We demonstrate that TLR2, but very little TLR4, is present on the surface of human neutrophils. In addition we demonstrate that GM-CSF and G-CSF dramatically up-regulate TLR2 and CD14 surface expression. GM-CSF treatment also up-regulates TLR2 and CD14 mRNA levels in neutrophils. In addition to increasing receptor expression, GM-CSF treatment enhanced the interleukin 8 (IL-8) secretion and superoxide priming responses of neutrophils to stimulation with TLR2 ligands, including zymosan, peptidoglycan, and lipoarabinomannan. The human monocyte response to crude bacterial LPS is composed of a TLR4-specific response to the pure LPS component and a TLR2-dependent response to associated lipopeptides. The removal of TLR2 lipopeptide components from LPS by phenol re-extraction substantially reduced both the IL-8 and superoxide response of the stimulated neutrophils, indicating that, unlike monocytes, the neutrophil response is preferentially directed to TLR2 ligands. Thus, our studies demonstrate that GM-CSF dramatically enhances the functional response of neutrophils to TLR2 ligands, including LPS-associated lipopeptides.
The interstellar wind - Mariner 10 measurements of hydrogen /1216 A/ and helium /584 A/ interplanetary emission (1978)

A set of unique observations of interplanetary emission at 1216 A and 584 A is presented which were made from Mariner 10 when that spacecraft was in interplanetary space on its way to Venus. The data provide simultaneous mapping of 1216-A hydrogen emission and 584-A helium emission, which allows a direct cross-correlation of these two aspects of the interstellar wind. The data are examined photometrically and compared with the principles of a simple model which provides a first-order understanding of the expected intensity variation over the celestial sphere. Hydrogen and helium sky maps are given which indicate the minima and maxima in emission intensity, a helium-focusing region in excess of 50 to 60 deg, and asymmetries in both emission profiles.
COMPLETE REGRESSION OF POSTTRANSPLANT LYMPHOPROLIFERATIVE DISEASE USING PARTIALLY HLA-MATCHED EPSTEIN BARR VIRUS-SPECIFIC CYTOTOXIC T CELLS1 (2001)

If this success is repeated in more PTLD patients, then stored CTL could be used for antiviral and antitumor therapies in immunocompromised patients.
Identification of multipotent progenitors in the embryonic mouse kidney by a novel colony-forming assay (2005)

Renal stem or progenitor cells with a multilineage differentiation potential remain to be isolated, and the differentiation mechanism of these cell types in kidney development or regeneration processes is unknown. In an attempt to resolve this issue, we set up an in vitro culture system using NIH3T3 cells stably expressing Wnt4 (3T3Wnt4) as a feeder layer, in which a single renal progenitor in the metanephric mesenchyme forms colonies consisting of several types of epithelial cells that exist in glomeruli and renal tubules. We found that only cells strongly expressing Sall1 (Sall1-GFP(high) cells), a zinc-finger nuclear factor essential for kidney development, form colonies, and that they reconstitute a three-dimensional kidney structure in an organ culture setting. We also found that Rac- and JNK-dependent planar cell polarity (PCP) pathways downstream of Wnt4 positively regulate the colony size, and that the JNK pathway is also involved in mesenchymal-to-epithelial transformation of colony-forming progenitors. Thus our colony-forming assay, which identifies multipotent progenitors in the embryonic mouse kidney, can be used for examining mechanisms of renal progenitor differentiation.
Caching less for better performance: balancing cache size and update cost of flash memory cache in hybrid storage systems (2012)

Hybrid storage solutions use NAND flash memory based Solid State Drives (SSDs) as non-volatile cache and traditional Hard Disk Drives (HDDs) as lower level storage. Unlike a typical cache, internally, the flash memory cache is divided into cache space and overprovisioned space, used for garbage collection. We show that balancing the two spaces appropriately helps improve the performance of hybrid storage systems. We show that contrary to expectations, the cache need not be filled with data to the fullest, but may be better served by reserving space for garbage collection. For this balancing act, we present a dynamic scheme that further divides the cache space into read and write caches and manages the three spaces according to the workload characteristics for optimal performance. Experimental results show that our dynamic scheme improves performance of hybrid storage solutions up to the off-line optimal performance of a fixed partitioning scheme. Furthermore, as our scheme makes efficient use of the flash memory cache, it reduces the number of erase operations thereby extending the lifetime of SSDs.
Multifunctional nanofibrous scaffold for tissue engineering (2008)

In tissue engineering, scaffolds with multiscale functionality, especially with the ability to release locally multiple or specific bioactive molecules to targeted cell types, are highly desired in regulating appropriate cell phenotypes. In this study, poly (epsilon-caprolactone) (PCL) solutions (8% w/v) containing different amounts of bovine serum albumin (BSA) with or without collagen were electrospun into nanofibres. As verified by protein release assay and fluorescent labelling, BSA and collagen were successfully incorporated into electrospun nanofibres. The biological activity of functionalised fibres was proven in the cell culture experiments using human dermal fibroblasts. By controlling the sequential deposition and fibre alignment, 3D scaffolds with spatial distribution of collagen or BSA were assembled using fluorescently labelled nanofibres. Human dermal fibroblasts showed preferential adhesion to PCL nanofibres containing collagen than PCL alone. Taken together, multiscale scaffolds with diverse functionality and tunable distribution of biomolecules across the nanofibrous scaffold can be fabricated using electrospun nanofibres.
Inverted vibrational distributions from N2 recombination at Ru(001): Evidence for a metastable molecular chemisorption well (1999)

We have measured translational and internal state distributions for N2 desorbed from a Ru(001) surface following NH3 cracking at 900 K. Nitrogen is formed with a vibrational population inversion, P(v=1)/P(v=0)=1.4, but a subthermal rotational energy release, Trot(v=0)=630 K. The translational energy distributions show a peak at low energy with a tail extending up to ∼2 eV and a mean energy release of 0.62 eV for N2(v=0) and 0.61 eV for (v=1). The product state distributions indicate a preferential energy release into the N2 stretching coordinate with a relatively weak N2–surface repulsion. Density functional calculations for N2 dissociation on Ru(001) and Cu(111) have been performed to compare the shape of the potentials in the N2 stretching (d) and translational (Z) coordinates. These reveal a sharp curvature of the surface for Ru, the energy release occurring close to the surface over a narrow range of Z. We suggest that this behavior is the result of the presence of a metastable molecular state, bound close to the surface with a short N2 bond, as predicted by Mortensen et al. [J. Catalysis, 169, 85 (1997)]. We contrast the dynamics on Ru with that observed for N recombination on Cu(111) [Murphy et al., J. Chem. Phys. 109, 3619 (1998)], where the potential energy surface shows no evidence for a molecular chemisorption well. Detailed balance arguments predict that N2 dissociation on Ru(001) is highly activated, S(E) increasing by nine orders of magnitude between 0.1 and 2 eV translational energy. The vibrational population inversion implies that vibration promotes dissociation more efficiently than translational excitation, sticking having a vibrational efficacy of 1.3. The predicted S(E) are consistent with reports of a very low sticking probability (S&amp;lt;10−9) on Ru(001) at thermal energies but in disagreement with recent molecular beam adsorption measurements.
A 33-dBm 1.9-GHz silicon-on-insulator CMOS stacked-FET power amplifier (2009)

A single-stage stacked-FET power amplifier (PA) is demonstrated using a 0.28-mum silicon-on-insulator (SOI) CMOS technology. To overcome the low breakdown voltage limit of MOSFETs, a stacked-FET structure is employed, where four transistors are connected in series so that their output voltage swings are added in phase. The stacked-FET PA has been designed to withstand up to 9 V of supply voltage before reaching its breakdown limit. The measurement results show that, with a 6.5-V supply, the PA achieves a small-signal gain of 13.2 dB, a saturated output power of 33 dBm, and a maximum power-added-efficiency (PAE) of 47% at 1.9 GHz. This is the first reported stacked-FET PA in submicron SOI CMOS technology that delivers multi-Watt output power in the GHz range. It also maintains high power efficiency over a wide range of supply voltages.
Histidylated polylysine as a synthetic vector for gene transfer into immortalized cystic fibrosis airway surface and airway gland serous cells (2000)

These results suggest that histidylated polylysine may be an efficient non-viral vector for gene transfer into cystic fibrosis airway surface epithelial cells and airway gland serous cells.
Mammalian Mitochondrial and Cytosolic Folylpolyglutamate Synthetase Maintain the Subcellular Compartmentalization of Folates (2014)

Folylpoly-γ-glutamate synthetase (FPGS) catalyze the addition of multiple glutamates to tetrahydrofolate derivatives. Two mRNAs for the fpgs gene direct isoforms of FPGS to the cytosol and to mitochondria in mouse and human tissues. We sought to clarify the functions of these two compartmentalized isoforms. Stable cell lines were created that express cDNAs for the mitochondrial and cytosolic isoforms of human FPGS under control of a doxycycline-inducible promoter in the AUXB1 cell line. AUXB1 are devoid of endogenous FPGS activity due to a premature translational stop at codon 432 in the fpgs gene. Loss of folates was not measurable from these doxycycline-induced cells or from parental CHO cells over the course of three CHO cell generations. Likewise, there was no detectable transfer of folate polyglutamates either from the cytosol to mitochondria, or from mitochondria to the cytosol. The cell line expressing cytosolic FPGS required exogenous glycine but not thymidine or purine, whereas cells expressing the mitochondrial isoform required exogenous thymidine and purine but not glycine for optimal growth and survival. We concluded that mitochondrial FPGS is required because folate polyglutamates are not substrates for transport across the mitochondrial membrane in either direction and that polyglutamation not only traps folates in the cytosol, but also in the mitochondrial matrix.
Studies on steroids. CCLII. Separation and characterization of 3-oxobile acids in serum by high-performance liquid chromatography with fluorescence detection. (1991)

The separation of unconjugated and glycine- and taurine-conjugated bile acids with a C-3 oxo group has been carried out by high-performance liquid chromatography on a reversed-phase column. The chromatographic behaviour of these 3-oxobile acids was dependent on the number and positions of hydroxyl groups and the structure of the side-chain. The newly developed method has been applied to the characterization of 3-oxobile acids in biological fluids. The bile acid fraction was obtained from a serum specimen by passing it through a Sep-Pak C18 cartridge. 3-Oxobile acids were derivatized quantitatively to fluorescent oximes through the oxo group by treatment with O-(2-anthrylmethyl)hydroxylamine. The derivatives were separated into the unconjugated and glycine- and taurine-conjugated fractions by ion-exchange chromatography on a lipophilic gel, piperidinohydroxypropyl Sephadex LH-20. Subsequent resolution of each fraction into individual 3-oxobile acids was achieved by chromatography on a Nova-Pak Phenyl column using 3% methanol in 0.3% potassium phosphate buffer (pH 7.0)-acetonitrile (8:5, v/v) as the mobile phase. The derivatized 3-oxobile acids were monitored by fluorescence detection (excitation wavelength 260 nm and emission wavelength 405 nm), the limit of detection being 20 fmol. Glycine- and taurine-conjugated 7 alpha,12 alpha-dihydroxy- and 7 alpha-hydroxy-3-oxo-5 beta-cholanoic acids in human serum were unambiguously idenitified on the basis of their chromatographic behaviour using mobile phases of different pH values.
Ribosomal Acidic Phosphoproteins P1 and P2 Are Not Required for Cell Viability but Regulate the Pattern of Protein Expression in Saccharomyces cerevisiae (1995)

Saccharomyces cerevisiae strains with either three inactivated genes (triple disruptants) or four inactivated genes (quadruple disruptants) encoding the four acidic ribosomal phosphoproteins, YP1 alpha, YP1 beta, YP2 alpha, and YP2 beta, present in this species have been obtained. Ribosomes from the triple disruptants and, obviously, those from the quadruple strain do not have bound P proteins. All disrupted strains are viable; however, they show a cold-sensitive phenotype, growing very poorly at 23 degrees C. Cell extracts from the quadruple-disruptant strain are about 30% as active as the control in protein synthesis assays and are stimulated by the addition of free acidic P proteins. Strains lacking acidic proteins do not have a higher suppressor activity than the parental strains, and cell extracts derived from the quadruple disruptant do not show a higher degree of misreading, indicating that the absence of acidic proteins does not affect the accuracy of the ribosomes. However, the patterns of protein expressed in the cells as well as in the cell-free protein system are affected by the absence of P proteins from the particles; a wild-type pattern is restored upon addition of exogenous P proteins to the cell extract. In addition, strains carrying P-protein-deficient ribosomes are unable to sporulate but recover this capacity upon transformation with one of the missing genes. These results indicate that acidic proteins are not an absolute requirement for protein synthesis but regulate the activity of the 60S subunit, affecting the translation of certain mRNAs differently.
Identification of EBNA1 amino acid sequences required for the interaction of the functional elements of the Epstein-Barr virus latent origin of DNA replication (1993)

Epstein-Barr nuclear antigen 1 (EBNA1) activates DNA replication from the Epstein-Barr virus latent origin, oriP. This activation involves the direct interaction of EBNA1 dimers with multiple sites within the two noncontiguous functional elements of the origin, the family of repeats (FR) element and the dyad symmetry (DS) element. The efficient interaction of EBNA1 dimers bound to these two elements in oriP results in the formation of DNA loops in which the FR and DS elements are bound together through EBNA1. In order to elucidate the mechanism by which EBNA1 induces oriP DNA looping, we have investigated the DNA sequences and EBNA1 amino acids required for EBNA1-mediated DNA looping. Using a series of truncation mutants of EBNA1 produced in baculovirus and purified to apparent homogeneity, we have demonstrated that the EBNA1 DNA binding and dimerization domain is not sufficient to mediate oriP DNA looping and that an additional region(s) located between amino acids 346 and 450 is required. Single EBNA1-binding sites, separated by 930 bp of plasmid DNA, were also shown to support EBNA1-mediated looping, indicating that the formation of large EBNA1 complexes, such as those observed on oriP FR and DS elements, is not a requirement for looping.
Angiotensin-Converting Enzyme Inhibitor Enhances Liver Regeneration Following Partial Hepatectomy: Involvement of Bradykinin B2 and Angiotensin AT1 Receptors (2007)

Angiotensin-converting enzyme (ACE) inhibitor enhances the liver regeneration in rats after partial hepatectomy (PH), though the precise mechanisms are unknown. To determine the roles of bradykinin and angiotensin II in the ACE inhibitor-induced enhancement of liver regeneration, we investigated effects of lisinopril (ACE inhibitor), candesartan and losartan (angiotensin II type 1 (AT1) receptor antagonists) and icatibant (bradykinin B2 receptor antagonist) on the hepatic regenerative response to 70% PH in the rat. The liver regeneration was evaluated by measuring the frequency of 5-bromo-2'-deoxyuridine (BrdU) incorporation into hepatocyte nuclei 48 h after PH. We found that administration of candesartan or losartan, as well as lisinopril, enhanced BrdU incorporation after PH, and the lisinopril-induced enhancement was inhibited in part (40%) by icatibant. PH induced the expression of hepatocyte growth factor (HGF) mRNA in remnant liver, and this PH-induced up-regulation of HGF mRNA was further enhanced not only by lisinopril but also by candesartan and losartan. Administration of icatibant inhibited up to 40% of the lisinopril-induced up-regulation of HGF mRNA. These results suggest that the blockade of the renin-angiotensin system by either ACE inhibitor or AT1 receptor antagonist enhances the hepatic regenerative response to PH, probably through an augmentation of hepatic HGF production. In addition to this mechanism, the activation of B2 receptors may also be involved in the ACE inhibitor-induced enhancement of hepatic regenerative response.
Fabrication of a modular tissue construct in a microfluidic chip (2008)

By combining microfluidics and soft-lithographic molding of gels containing mammalian cells, a device for three-dimensional (3D) culture of mammalian cells in microchannels was developed. Native components of the extracellular matrix, including collagen or Matrigel, made up the matrix of each molded piece (module) of cell-containing gel. Each module had at least one dimension below approximately 300 microm; in modules of these sizes, the flux of oxygen, nutrients, and metabolic products into and out of the modules was sufficient to allow cells in the modules to proliferate to densities comparable to those of native tissue (10(8)-10(9) cells cm(-3)). Packing modules loosely into microfluidic channels and chambers yielded structures permeated with a network of pores through which cell culture medium could flow to feed the encapsulated cells. The order in the packed assemblies increased as the width of the microchannels approached the width of the modules. Multiple cell types could be spatially organized in the small microfluidic channels. Recovery and analysis of modules after 24 h under constant flow of medium (200 microL h(-1)) showed that over 99% of encapsulated cells survived this interval in the microfluidic chamber.
Acceleration of recombinant tissue-type plasminogen activator-induced thrombolysis and prevention of reocclusion by the combination of heparin and the Arg-Gly-Asp-containing peptide bitistatin in a canine model of coronary thrombosis. (1990)

The effect of tissue-type plasminogen activator (t-PA) alone or in combination with heparin, the Arg-Gly-Asp-containing peptide bitistatin, or both heparin and bitistatin was evaluated on thrombolysis time and acute reocclusion in a canine model of coronary thrombosis. Thrombus formation was elicited by electrolytic injury with a needle electrode to the endothelial surface of the circumflex coronary artery in the open-chest, anesthetized dog in the presence of a flow-limiting critical stenosis. Thirty minutes after spontaneous coronary artery occlusion, t-PA (1 mg/kg i.v. over 90 minutes) was administered. Group 1 was given t-PA alone; reperfusion occurred at 78.2 +/- 5.6 minutes with a reperfusion incidence of 60% (6/10). Group 2 received t-PA plus heparin (100 units/kg plus 50 units/kg/hr); reperfusion occurred at 61.9 +/- 9.1 minutes with a reperfusion incidence of 90% (9/10). Group 3 received t-PA plus heparin plus bitistatin (30 micrograms/kg plus 3 micrograms/kg/min); reperfusion occurred at 47.3 +/- 7.6 minutes (p less than 0.05 versus group 1) with a reperfusion incidence of 90% (9/10). Group 4 received t-PA plus bitistatin, and reperfusion occurred at 51.8 +/- 8.5 minutes; however, the reperfusion incidence was only 60% (6/10). In groups 1, 2, and 4, acute reocclusion occurred in more than 80% of the reperfused dogs, whereas in group 3 reocclusion occurred in 22% (2/9) of the reperfused dogs (p less than 0.05 versus group 1). The dose of heparin used in this study increased activated partial thromboplastin times 1.5-2.0-fold over control.(ABSTRACT TRUNCATED AT 250 WORDS)
FIDELITY MECHANISMS IN DNA REPLICATION (1991)

BASE INSERTION SELECTIVITY BY DNA POL YMERASES . The Base 1''lSertion Pathway . Structural Aspects to Base Selection by DNA Polymerases . Polymerase Insertion Errors . Fidelity Assays and Major Conclusions . Error Avoidance in Base Insertion----General Conclusions ..... .
Part I: Minimum Quality Threshold in Preclinical Sepsis Studies (MQTiPSS) for Study Design and Humane Modeling Endpoints (2018)

Preclinical animal studies are mandatory before new treatments can be tested in clinical trials. However, their use in developing new therapies for sepsis has been controversial because of limitations of the models and inconsistencies with the clinical conditions. In consideration of the revised definition for clinical sepsis and septic shock (Sepsis-3), a Wiggers-Bernard Conference was held in Vienna in May 2017 to propose standardized guidelines on preclinical sepsis modeling. The participants conducted a literature review of 260 most highly cited scientific articles on sepsis models published between 2003 and 2012. The review showed, for example, that mice were used in 79% and euthanasia criteria were defined in 9% of the studies. Part I of this report details the recommendations for study design and humane modeling endpoints that should be addressed in sepsis models. The first recommendation is that survival follow-up should reflect the clinical time course of the infectious agent used in the sepsis model. Furthermore, it is recommended that therapeutic interventions should be initiated after the septic insult replicating clinical care. To define an unbiased and reproducible association between a new treatment and outcome, a randomization and blinding of treatments as well as inclusion of all methodological details in scientific publications is essential. In all preclinical sepsis studies, the high standards of animal welfare must be implemented. Therefore, development and validation of specific criteria for monitoring pain and distress, and euthanasia of septic animals, as well as the use of analgesics are recommended. A set of four considerations is also proposed to enhance translation potential of sepsis models. Relevant biological variables and comorbidities should be included in the study design and sepsis modeling should be extended to mammalian species other than rodents. In addition, the need for source control (in case of a defined infection focus) should be considered. These recommendations and considerations are proposed as "best practices" for animal models of sepsis that should be implemented.