gebhart/patrepeval huggingface dataset:
Sheaths: More complicated than you think (2005)

Sheaths in low temperature collisionless and weakly collisional plasmas are often viewed as simple examples of nonlinear physics. How well do we understand them? Closer examination indicates that they are far from simple. Moreover, many predicted sheath properties have not been experimentally verified and even the appropriate “Bohm velocity” for often encountered two-ion species plasma is unknown. In addition, a variety of sheathlike structures, e.g., double layers, can exist, and many two- and three-dimensional sheath effects have not been considered. Experimental studies of sheaths and presheaths in weakly collisional plasmas are described. A key diagnostic is emissive probes operated in the “limit of zero emission.” Emissive probes provide a sensitive diagnostic of plasma potential with a resolution approaching 0.1V and a spatial resolution of 0.1cm. Combined with planar Langmuir probes and laser-induced fluorescence, they have been used to investigate a wide variety of sheath, presheath, and sheathlike structures. Our experiments have provided some answers but have also raised more questions.
Thermodynamic Comparison of the Salt Dependence of Natural RNA Hairpins and RNA Hairpins with Non-Nucleotide Spacers (1996)

RNA hairpins with loops of either ten or eight nucleotides, or seven nucleotides with (ethylene glycol)n spacers, have been compared in experiments that measure the NaCl dependence of their thermodynamic properties. In 1 M NaCl, the eight-nucleotide RNA hairpin/loop has the most favorable folding free energy (delta G degree = -8.6 kcal/mol), while the RNAs containing the spacers are considerably more unstable (delta G degree = -5.2 to -5.7 kcal/mol); for these RNA/linker species, there are compensating reductions in favorable entropy and unfavorable enthalpy of the helix-coil transition. Preferential interaction coefficients (delta IN) determined from analyses of melting transitions as a function of NaCl concentration are compared to determine the effect of the ethylene glycol on differential ion association. While the difference in ion association to the helix and coil states of the fully RNA molecules follows prediction, the RNAs with linkers do not, indicating that the description of their native and/or denatured state has changed.
Production of Mice Deficient in Genes for Interleukin (IL)-1α, IL-1β, IL-1α/β, and IL-1 Receptor Antagonist Shows that IL-1β Is Crucial in Turpentine-induced Fever Development and Glucocorticoid Secretion (1998)

Interleukin (IL)-1 is a major mediator of inflammation and exerts pleiotropic effects on the neuro-immuno-endocrine system. To elucidate pathophysiological roles of IL-1, we have first produced IL-1alpha/beta doubly deficient (KO) mice together with mice deficient in either the IL-1alpha, IL-1beta, or IL-1 receptor antagonist (IL-1ra) genes. These mice were born healthy, and their growth was normal except for IL-1ra KO mice, which showed growth retardation after weaning. Fever development upon injection with turpentine was suppressed in IL-1beta as well as IL-1alpha/beta KO mice, but not in IL-1alpha KO mice, whereas IL-1ra KO mice showed an elevated response. At this time, expression of IL-1beta mRNA in the diencephalon decreased 1.5-fold in IL-1alpha KO mice, whereas expression of IL-1alpha mRNA decreased >30-fold in IL-1beta KO mice, suggesting mutual induction between IL-1alpha and IL-1beta. This mutual induction was also suggested in peritoneal macrophages stimulated with lipopolysaccharide in vitro. In IL-1beta KO mice treated with turpentine, the induction of cyclooxygenase-2 (EC 1.14.99.1) in the diencephalon was suppressed, whereas it was enhanced in IL-1ra KO mice. We also found that glucocorticoid induction 8 h after turpentine treatment was suppressed in IL-1beta but not IL-1alpha KO mice. These observations suggest that IL-1beta but not IL-1alpha is crucial in febrile and neuro-immuno-endocrine responses, and that this is because IL-1alpha expression in the brain is dependent on IL-1beta. The importance of IL-1ra both in normal physiology and under stress is also suggested.
Outcome and Predictors of Failure of Highly Active Antiretroviral Therapy: One‐Year Follow‐Up of a Cohort of Human Immunodeficiency Virus Type 1–Infected Persons (1999)

The outcome and predictors of virologic treatment failure of highly active antiretroviral therapy (HAART) were determined for 271 human immunodeficiency virus (HIV)-infected protease inhibitor-naive persons. During a follow-up of 48 weeks after the initiation of HAART, 6.3% of patients experienced at least one new AIDS-defining event, and 3.0% died. Virologic treatment failure occurred in 40% (indinavir, 27%; ritonavir, 30%; saquinavir, 59%; ritonavir plus saquinavir, 32%; chi2, P=.001). Risk factors for treatment failure were baseline plasma HIV-1 RNA (odds ratio [OR], 1.70 per log10 copies increase in plasma HIV-1 RNA), baseline CD4 cell count (OR, 1. 35 per 100 CD4 cells/mm3 decrease), and use of saquinavir versus other protease inhibitors (OR, 3.21). During the first year of treatment, 53% of all patients changed (part of) their original HAART regimen at least once. This was significantly more frequent for regimens containing saquinavir (62%; 27% for virologic failure) or ritonavir (64%; 55% for intolerance) as single protease inhibitor.
Out-of-order processing (2008)

Many stream-processing systems enforce an order on data streams during query evaluation to help unblock blocking operators and purge state from stateful operators. Such in-order processing (IOP) systems not only must enforce order on input streams, but also require that query operators preserve order. This order-preserving requirement constrains the implementation of stream systems and incurs significant performance penalties, particularly for memory consumption. Especially for high-performance, potentially distributed stream systems, the cost of enforcing order can be prohibitive. We introduce a new architecture for stream systems, out-of-order processing (OOP), that avoids ordering constraints. The OOP architecture frees stream systems from the burden of order maintenance by using explicit stream progress indicators, such as punctuation or heartbeats, to unblock and purge operators. We describe the implementation of OOP stream systems and discuss the benefits of this architecture in depth. For example, the OOP approach has proven useful for smoothing workload bursts caused by expensive end-of-window operations, which can overwhelm internal communication paths in IOP approaches. We have implemented OOP in two stream systems, Gigascope and NiagaraST. Our experimental study shows that the OOP approach can significantly outperform IOP in a number of aspects, including memory, throughput and latency.
CGRP receptor antagonist olcegepant (BIBN4096BS) does not prevent glyceryl trinitrate-induced migraine (2010)

The present study indicates that NO does not induce migraine by liberating CGRP. The most likely explanation for our findings is that CGRP has its effect higher than NO in the cascade of events leading to MO attacks.
Repeated peripheral stem cell mobilization in healthy donors: time‐dependent changes in mobilization efficiency (1999)

Mobilization of peripheral blood stem cells was analysed in 10 consecutive healthy donors undergoing repeated stem cell mobilization for allogeneic transplantation. Donors received recombinant G-CSF at a dose of 10 microg/kg/d for both mobilizations. Collection of stem cells was started on day 5 of G-CSF administration. To compare the efficiency of first and second mobilization, we determined the leucocyte and CD34+ cell counts in peripheral blood, and the yield of nucleated cells and CD34+ cell counts in the apheresis product. CD34+ cell numbers in peripheral blood were (median) 81.2 x 10(6)/l during the first and 50.4 x 10(6)/l during the second mobilization (P = 0.007). Likewise, CD34+ cells in the apheresis product decreased from 319.8 x 10(6) to 275.7 x 10(6) (P = 0.02). Decrease in CD34+ cell counts in peripheral blood and in the apheresis product was associated with the time interval between first and second mobilization. In a regression analysis there was a correlation between the ratios of CD34+ cell counts of first and second mobilization and the inverse of time interval between procedures (r2 = 0.51 peripheral blood; r2 = 0.74 apheresis product). Thus, stem cell yield is reduced when healthy donors receive repeated mobilization within a short time. Nevertheless, an adequate number of stem cells may repeatedly be mobilized within 2 months.
Unexpected Multivalent Display of Proteins by Temperature Triggered Self-Assembly of Elastin-like Polypeptide Block Copolymers (2012)

We report herein the unexpected temperature triggered self-assembly of proteins fused to thermally responsive elastin-like polypeptides (ELPs) into spherical micelles. A set of six ELP block copolymers (ELP(BC)) differing in hydrophilic and hydrophobic block lengths were genetically fused to two single domain proteins, thioredoxin (Trx) and a fibronectin type III domain (Fn3) that binds the α(v)β(3) integrin. The self-assembly of these protein-ELP(BC) fusions as a function of temperature was investigated by UV spectroscopy, light scattering, and cryo-TEM. Self-assembly of the ELP(BC) was unexpectedly retained upon fusion to the two proteins, resulting in the formation of spherical micelles with a hydrodynamic radius that ranged from 24 to 37 nm, depending on the protein and ELP(BC). Cryo-TEM images confirmed the formation of spherical particles with a size that was consistent with that measured by light scattering. The bioactivity of Fn3 was retained when presented by the ELP(BC) micelles, as indicated by the enhanced uptake of the Fn3-decorated ELP(BC) micelles in comparison to the unimer by cells that overexpress the α(v)β(3) integrin. The fusion of single domain proteins to ELP(BC)s may provide a ubiquitous platform for the multivalent presentation of proteins.
New Generation of Liposomal Drugs for Cancer (2006)

This review is focused on liposomes as a delivery system for anticancer agents and more specifically on the advantages of using liposomes as drug nanocarrier in cancer chemotherapy. The main advantages of liposomal drugs over the non-encapsulated drugs include: (1) improved pharmacokinetics and drug release, (2) enhanced intracellular penetration, (3) tumor targeting and preventing adverse side effects and (4) ability to include several active ingredients in one complex liposomal drug delivery system (DDS). The review also includes our recent data on advanced liposomal anticancer drug delivery systems. As a conclusion we propose a novel liposomal DDS which includes inhibitors of pump resistance combined in one liposomal drug delivery system with an inhibitor of antiapoptotic cellular defense, an apoptosis inducer (a traditional anticancer drug) and a targeting moiety. The proposed drug delivery system utilizes a novel three tier approach, simultaneously targeting three molecular targets: (1) extracellular receptors or antigen expressed on the surface of plasma membrane of cancer cells in order to direct the whole system specifically to the tumor, preventing adverse side effects on healthy tissues; (2) drug efflux pumps in order to inhibit them and enhance drug retention by cancer cells, increasing intracellular drug accumulation and thereby limiting the need for prescribed high drug doses that cause adverse drug side effects; and (3) intracellular controlling mechanisms of apoptosis in order to suppress cellular antiapoptotic defense.
Tor, a Phosphatidylinositol Kinase Homologue, Controls Autophagy in Yeast (1998)

Autophagy is a bulk protein degradation process that is induced by starvation. The control mechanism for induction of autophagy is not well understood. We found that Tor, a phosphatidylinositol kinase homologue, is involved in the control of autophagy in the yeast, Saccharomyces cerevisiae. When rapamycin, an inhibitor of Tor function, is added, autophagy is induced even in cells growing in nutrient-rich medium. A temperature-sensitive tor mutant also leads to induction of autophagy at a nonpermissive temperature. These results indicate that Tor negatively regulates the induction of autophagy. Tor is the first molecule that is identified as a pivotal player in the starvation-signaling pathway of autophagy. Furthermore, we found that a high concentration of cAMP is inhibitory for induction of autophagy. APG gene products are involved in autophagy induced by starvation. Autophagy was not induced in apg mutants in the presence of rapamycin, indicating that the site of action of Tor is upstream of those of Apg proteins. In nutrient-rich medium, Apg proteins are involved also in the transport of aminopeptidase I from the cytosol to the vacuole. Tor may act to switch Apg function between autophagy and transport of aminopeptidase I.
Isolation and Characterization of Mumps Virus Strains in a Mumps Outbreak with a High Incidence of Aseptic Meningitis (1996)

In 1993, mumps with a high incidence of aseptic meningitis became prevalent in Akita prefecture, Japan. Three mumps virus isolates obtained from the nonvaccine-associated cases lacked the BamHI restriction cleavage site of the P gene, like the Urabe strain (Yamada, A. et al, Vaccine 8: 553-557). However, four additional nucleotide substitutions were found in the determined region of 157 bp. Fourteen of 19 cases from which mumps virus showing the Urabe-like RFLP profile was detected were complicated with symptomatic meningitis, whereas there were only four cases of meningitis among 23 individuals infected with the wild type showing no Urabe-like RFLP profile (non-"Urabe-like" wild-type). The incidence of meningitis was over 70% among patients infected with the "Urabe-like" wild-type virus. The "Urabe-like" wild-type. disappeared after February 1994 in the epidemic area and was replaced by the non-"Urabe-like" wild-type. Patients infected with the "Urabe-like" wild-type lived in a closed colony, in which there were two instances of transmission between siblings. Thus this outbreak was transient and narrowly localized.
Midkine inhibitors: application of a simple assay procedure to screening of inhibitory compounds (2010)

The assay procedure is helpful in screening midkine inhibitors. All reagents described here might become mother material to develop clinically effective midkine inhibitors.
Microgels as Stimuli-Responsive Stabilizers for Emulsions (2008)

Temperature- and pH-sensitive microgels from cross-linked poly(N-isopropylacrylamide)-co-methacrylic acid are utilized for emulsion stabilization. The pH- and temperature-dependent stability of the prepared emulsion was characterized. Stable emulsions are obtained at high pH and room temperature. Emulsions with polar oils, like 1-octanol, can be broken by either addition of acid or an increase of temperature, whereas emulsions with unpolar oils do not break upon these stimuli. However, complete phase separation, independent of oil polarity, can be achieved by successive acid addition and heating. This procedure also offers a way to recover and recycle the microgel from the sample. Interfacial dilatational rheology data correlate with the stimuli sensitivity of the emulsion, and a strong dependence of the interfacial elastic and loss moduli on pH and temperature was found. The influence of the preparation method on the type of emulsion is demonstrated. The mean droplet size of the emulsions is characterized by means of flow particle image analysis. The type of emulsion [water in oil (w/o) or oil in water (o/w)] depends on the preparation technique as well as on the microgel content. Emulsification with high shear rates allows preparation of both w/o and o/w emulsions, whereas with low shear rates o/w emulsions are the preferred type. The emulsions are stable at high pH and low temperature, but instable at low pH and high temperature. Therefore, we conclude that poly(N-isopropylacrylamide)-co-methacrylic acid microgels can be used as stimuli-sensitive stabilizers for emulsions. This offers a new and unique way to control emulsion stability.
The primary structure of thioredoxin from Chromatium vinosum determined by high-performance tandem mass spectrometry (1987)

The primary structure of thioredoxin, a redox protein isolated from Chromatium vinosum, was determined by high-performance tandem mass spectrometry, which permitted sequencing of the 14 peptides (ranging in length from 2 to 18 amino acids) generated by digestion with trypsin and of several peptides produced by Staphylococcus aureus protease. The mass spectrometrically determined molecular weights of the peptides from the latter digest were used to properly align the tryptic peptides, which could also be accomplished on the basis of the considerable homology with Escherichia coli thioredoxin. Finally, the molecular weight of the Chromatium thioredoxin was determined by mass spectrometry and found to be 11,748.0, in good agreement with 11,750.2 calculated for the proposed sequence. Although it was difficult to establish by mass spectrometry, five leucines and three isoleucines could be identified, leaving only eight undifferentiated.
DNA vaccination in combination or not with lamivudine treatment breaks humoral immune tolerance and enhances cccDNA clearance in the duck model of chronic hepatitis B virus infection (2008)

This study used a duck hepatitis B virus (DHBV) model to evaluate whether a novel DNA vaccination protocol alone or associated with antiviral (lamivudine) treatment was able to clear the intrahepatic covalently closed, circular viral DNA (cccDNA) pool responsible for persistence of infection. DHBV carriers received DNA vaccine (on weeks 6, 10, 13, 14, 28 and 35) targeting the large envelope and/or core proteins alone or combined with lamivudine treatment (on weeks 1-8) or lamivudine monotherapy. After 10 months of follow-up, a dramatic decrease in viraemia and liver DHBV cccDNA (below 0.08 cccDNA copies per cell) was observed in 9/30 ducks (30 %) receiving DNA mono- or combination therapy, compared with 0/12 (0 %) from lamivudine monotherapy or the control groups, suggesting a significant antiviral effect of DNA immunization. However, association with the drug did not significantly improve DHBV DNA vaccine efficacy (33 % cccDNA clearance for the combination vs 27 % for DNA monotherapy), probably due to the low antiviral potency of lamivudine in the duck model. Seroconversion to anti-preS was observed in 6/9 (67 %) ducks showing cccDNA clearance, compared with 1/28 (3.6 %) without clearance, suggesting a significant correlation (P<0.001) between humoral response restoration and cccDNA elimination. Importantly, an early (weeks 10-12) drop in viraemia was observed in seroconverted animals, and virus replication did not rebound following the cessation of immunotherapy, indicating a sustained effect. This study provides the first evidence that therapeutic DNA vaccination is able to enhance hepadnaviral cccDNA clearance, which is tightly associated with a break in humoral immune tolerance. These results also highlight the importance of antiviral drug potency and an effective DNA immunization protocol for the design of therapeutic vaccines against chronic hepatitis B.
Blunted Proarrhythmic Effect of Nicorandil in a Langendorff‐Perfused Phase‐2 Myocardial Infarction Rabbit Model (2012)

K(ATP) expression is down-regulated in phase-2 MI hearts. Nicorandil restores APD, increases the rate of Ca(i) reuptake, and flattens CV restitution to suppress spatially discordant alternans induction, which ameliorates its proarrhythmic effects during phase-2 MI.
Emerging strategies for exploiting cannabinoid receptor agonists as medicines (2009)

Medicines that activate cannabinoid CB(1) and CB(2) receptor are already in the clinic. These are Cesamet (nabilone), Marinol (dronabinol; Delta(9)-tetrahydrocannabinol) and Sativex (Delta(9)-tetrahydrocannabinol with cannabidiol). The first two of these medicines can be prescribed to reduce chemotherapy-induced nausea and vomiting. Marinol can also be prescribed to stimulate appetite, while Sativex is prescribed for the symptomatic relief of neuropathic pain in adults with multiple sclerosis and as an adjunctive analgesic treatment for adult patients with advanced cancer. One challenge now is to identify additional therapeutic targets for cannabinoid receptor agonists, and a number of potential clinical applications for such agonists are mentioned in this review. A second challenge is to develop strategies that will improve the efficacy and/or the benefit-to-risk ratio of a cannabinoid receptor agonist. This review focuses on five strategies that have the potential to meet either or both of these objectives. These are strategies that involve: (i) targeting cannabinoid receptors located outside the blood-brain barrier; (ii) targeting cannabinoid receptors expressed by a particular tissue; (iii) targeting up-regulated cannabinoid receptors; (iv) targeting cannabinoid CB(2) receptors; or (v) 'multi-targeting'. Preclinical data that justify additional research directed at evaluating the clinical importance of each of these strategies are also discussed.
Detection of Restriction Enzyme–Digested Target DNA by PCR Amplification Using a Stem-Loop Primer: Application to the Detection of Hypomethylated Fetal DNA in Maternal Plasma (2007)

Detection of restriction enzyme-digested hypomethylated placental DNA molecules in maternal plasma by the use of a stem-loop primer represents a novel approach in fetal epigenetic marker detection. The analytical approach may also be generally applicable to the detection of restriction enzyme-digested nucleic acid fragments.
Contact insensitivity of a subpopulation of normal human fetal kidney epithelial cells and of human carcinoma cell lines. (1987)

Early passage normal human fetal kidney epithelial cells were inoculated on top of a confluent monolayer of X-ray lethally irradiated human fibroblasts to determine the colony-forming ability of these epithelial cells. The results indicate that the great majority of the epithelial cells did not have the clonogenic ability on the fibroblast cell mat, although they were capable of colony formation on plastic surface without the cell mat. A small subpopulation of these epithelial cells, however, was able to proliferate on the cell mat. These contact-insensitive fetal epithelial cells were found to be deficient in gap junction-mediated intercellular communication, to contain keratin and gamma-glutamyl transpeptidase but not fibronectin. These contact-insensitive cells appear to have greater proliferative potential than the parental cell population and to exist transiently in early passage but not in late passage culture. The ability of proliferation on cell mat was found to be shared by 22 different human carcinoma cell lines that were tested. This unique clonogenic ability of normal contact-insensitive and human carcinoma cells on the cell mat could provide a selection method for presumptive normal stem and tumor cells and for an assay for screening potential antitumor drugs and assessing the efficacy of chemotherapeutic drugs against a given tumor.
Continuous Micromixer with Pulsatile Micropumps (2000)

A continuous microfluidic mixer utilizing pulsatile flow micropumps has been created using an SOI process. While individual MEMS mixers, pumps, and valves have been developed, this work presents an integrated, planar system utilizing novel mixing, valving, and bonding processes in order to deliver well mixed fluids at controllable flow rates.
NUCLEASE HYPERSENSITIVE SITES IN CHROMATIN (1988)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More