gebhart/patrepeval huggingface dataset:
HRD1 and UBE2J1 target misfolded MHC class I heavy chains for endoplasmic reticulum-associated degradation (2011)

The assembly of MHC class I molecules is governed by stringent endoplasmic reticulum (ER) quality control mechanisms. MHC class I heavy chains that fail to achieve their native conformation in complex with β2-microglobulin (β2m) and peptide are targeted for ER-associated degradation. This requires ubiquitination of the MHC class I heavy chain and its dislocation from the ER to the cytosol for proteasome-mediated degradation, although the cellular machinery involved in this process is unknown. Using an siRNA functional screen in β2m-depleted cells, we identify an essential role for the E3 ligase HRD1 (Synoviolin) together with the E2 ubiquitin-conjugating enzyme UBE2J1 in the ubiquitination and dislocation of misfolded MHC class I heavy chains. HRD1 is also required for the ubiquitination and degradation of the naturally occurring hemochromatosis-associated HFE-C282Y mutant, which is unable to bind β2m. In the absence of HRD1, misfolded HLA-B27 accumulated in cells with a normal MHC class I assembly pathway, and HRD1 depletion prevented the appearance of low levels of cytosolic unfolded MHC I heavy chains. HRD1 and UBE2J1 associate in a complex together with non-β2m bound MHC class I heavy chains, Derlin 1, and p97 and discriminate misfolded MHC class I from conformational MHC I-β2m-peptide heterotrimers. Together these data support a physiological role for HRD1 and UBE2J1 in the homeostatic regulation of MHC class I assembly and expression.
Arabidopsis genes, AtNPR1, AtTGA2 and AtPR-5, confer partial resistance to soybean cyst nematode (Heterodera glycines) when overexpressed in transgenic soybean roots (2014)

Knowledge of the pathogen defense system gained from studies of the model system, Arabidopsis, can be directly translated to soybean through direct overexpression of Arabidopsis genes. When the genes, AtNPR1, AtGA2, and AtPR-5, encoding specific components involved in SA regulation, synthesis, and signaling, are overexpressed in soybean roots, resistance to SCN is enhanced. This demonstrates functional compatibility of some Arabidopsis genes with soybean and identifies genes that may be used to engineer resistance to nematodes.
SDN based Network Function Parallelism in Cloud (2018)

Network function virtualization (NFV) based service function chaining (SFC) allows the provisioning of various security and traffic engineering applications in a cloud network. Inefficient deployment of network functions can lead to security violations and performance overhead. In an OpenFlow enabled cloud, the key problem with current mechanisms is that several packet field match and flow rule action sets associated with the network functions are non-overlapping and can be parallelized for performance enhancement. We introduce Network Function Parallelism (NFP) SFC-NFP for OpenFlow network. Our solution utilizes network function parallelism over the OpenFlow rules to improve SFC performance in the cloud network. We have utilized the DPDK platform with an OpenFlow switch (OVS) for experimental analysis. Our solution achieves a 1.40-1.90x reduction in latency for SFC in an OpenStack cloud network managed by the SDN framework.
Regulation of Phagocytosis in Macrophages by Neuraminidase 1 (2009)

The differentiation of monocytes into macrophages and dendritic cells is accompanied by induction of cell-surface neuraminidase 1 (Neu1) and cathepsin A (CathA), the latter forming a complex with and activating Neu1. To clarify the biological importance of this phenomenon we have developed the gene-targeted mouse models of a CathA deficiency (CathA(S190A)) and a double CathA/Neu1 deficiency (CathA(S190A-Neo)). Macrophages of CathA(S190A-Neo) mice and their immature dendritic cells showed a significantly reduced capacity to engulf Gram-positive and Gram-negative bacteria and positively and negatively charged polymer beads as well as IgG-opsonized beads and erythrocytes. Properties of the cells derived from CathA(S190A) mice were indistinguishable from those of wild-type controls, suggesting that the absence of Neu1, which results in the increased sialylation of the cell surface proteins, probably affects multiple receptors for phagocytosis. Indeed, treatment of the cells with purified mouse Neu1 reduced surface sialylation and restored phagocytosis. Because Neu1-deficient cells showed reduced internalization of IgG-opsonized sheep erythrocytes whereas binding of the erythrocytes to the cells at 4 degrees C persisted, we speculate that the absence of Neu1 in particular affected transduction of signals from the Fc receptors for immunoglobulin G (FcgammaR). Indeed the macrophages from the Neu1-deficient mice showed increased sialylation and impaired phosphorylation of FcgammaR as well as markedly reduced phosphorylation of Syk kinase in response to treatment with IgG-opsonized beads. Altogether our data suggest that the cell surface Neu1 activates the phagocytosis in macrophages and dendritic cells through desialylation of surface receptors, thus, contributing to their functional integrity.
Homeopathic arnica for prevention of pain and bruising: randomized placebo-controlled trial in hand surgery (2003)

Homeopathic arnica is widely believed to control bruising, reduce swelling and promote recovery after local trauma; many patients therefore take it perioperatively. To determine whether this treatment has any effect, we conducted a double-blind, placebo-controlled, randomized trial with three parallel arms. 64 adults undergoing elective surgery for carpal tunnel syndrome were randomized to take three tablets daily of homeopathic arnica 30C or 6C or placebo for seven days before surgery and fourteen days after surgery. Primary outcome measures were pain (short form McGill Pain Questionnaire) and bruising (colour separation analysis) at four days after surgery. Secondary outcome measures were swelling (wrist circumference) and use of analgesic medication (patient diary). 62 patients could be included in the intention-to-treat analysis. There were no group differences on the primary outcome measures of pain (P=0.79) and bruising (P=0.45) at day four. Swelling and use of analgesic medication also did not differ between arnica and placebo groups. Adverse events were reported by 2 patients in the arnica 6C group, 3 in the placebo group and 4 in the arnica 30C group. The results of this trial do not suggest that homeopathic arnica has an advantage over placebo in reducing postoperative pain, bruising and swelling in patients undergoing elective hand surgery.
Discovery of lipid peroxidation products formed <i>in vivo</i> with a substituted tetrahydrofuran ring (isofurans) that are favored by increased oxygen tension (2002)

Free radicals have been implicated in the pathogenesis of an increasing number of diseases. Lipids, which undergo peroxidation, are major targets of free radical attack. We report the discovery of a pathway of lipid peroxidation that forms a series of isomers in vivo that are characterized by a substituted tetrahydrofuran ring structure, termed isofurans (IsoFs). We have proposed two distinct pathways by which IsoFs can be formed based on 18O2 and H2 18O labeling studies. Measurement of F2-isoprostanes (IsoPs), prostaglandin F2-like compounds formed nonenzymatically as products of lipid peroxidation, is considered one of the most reliable approaches for assessing oxidative stress status in vivo. However, one limitation with this approach is that the formation of IsoPs becomes limited at high oxygen tension. In contrast, the formation of IsoFs becomes increasingly favored as oxygen tension increases. IsoFs are present at readily detectable levels in normal fluids and tissues, and levels increase dramatically in CCl4-treated rats, an animal model of oxidant injury. The ratio of IsoFs to IsoPs in major organs varies according to normal steady-state tissue oxygenation. In addition, IsoFs show a marked increase early in the course of hyperoxia-induced lung injury, whereas IsoPs do not significantly increase. We propose that combined measurement of IsoFs and IsoPs should provide a more reliable index of oxidant stress severity than quantification of either alone because of the opposing modulation of the two pathways by oxygen tension, which can vary widely in different organs and disease states.
MEMS-based hemispherical resonator gyroscopes (2012)

This paper introduces a fabrication technique that uses planar MEMS micromachining processes to produce hemispherical resonating shells for gyroscopes. The hemispheres exhibit a quality factor in excess of 20,000 with resonant frequencies in the range of 20 kHz for the 4-node wineglass mode. The fabrication process enables production of almost perfect hemispheres (less than 1% asphericity near the pedestal) with an average surface roughness of 5nm. The high degree of sphericity contains the relative frequency mismatch Δf/f between the two degenerate modes to 0.02%. Simplicity of the fabrication process and the successful testing of the drive/sense mechanism in the resonator make it a good candidate for use as gyroscopes.
Tomographic techniques for the study of exceptionally preserved fossils (2008)

Three-dimensional fossils, especially those preserving soft-part anatomy, are a rich source of palaeontological information; they can, however, be difficult to work with. Imaging of serial planes through an object (tomography) allows study of both the inside and outside of three-dimensional fossils. Tomography may be performed using physical grinding or sawing coupled with photography, through optical techniques of serial focusing, or using a variety of scanning technologies such as neutron tomography, magnetic resonance imaging and most usefully X-ray computed tomography. This latter technique is applicable at a variety of scales, and when combined with a synchrotron X-ray source can produce very high-quality data that may be augmented by phase-contrast information to enhance contrast. Tomographic data can be visualized in several ways, the most effective of which is the production of isosurface-based 'virtual fossils' that can be manipulated and dissected interactively.
Positive and negative regulation of a sterol biosynthetic gene (<i>ERG3</i>) in the post‐squalene portion of the yeast ergosterol pathway (1996)

Regulation of sterol biosynthesis in the terminal portion of the pathway represents an efficient mechanism by which the cell can control the production of sterol without disturbing the production of other essential mevalonate pathway products. We demonstrate that mutations affecting early and late steps in sterol homeostasis modulate the expression of the ERG3 gene: a late step in sterol biosynthesis in yeast. Expression of ERG3 is increased in response to a mutation in the major isoform of HMG CoA reductase which catalyzes the rate-limiting step of sterol biosynthesis. Likewise, mutations in non-auxotrophic ergosterol biosynthetic genes downstream of squalene production (erg2, erg3, erg4, erg5, and erg6) result in an up-regulation of ERG3 expression. Deletion analysis of the ERG3 promoter identified two upstream activation sequences: UAS1 which when deleted reduces ERG3 gene expression 3-4-fold but maintains sterol regulation and UAS2, which when deleted further reduces ERG3 expression and abolishes sterol regulation. The recent isolation of two yeast genes responsible for the esterification of intracellular sterol (ARE1 and ARE2) has enabled us to directly analyze the relationship between sterol esterification and de novo biosynthesis. Our results demonstrate that the absence of sterol esterification leads to a decrease in total intracellular sterol and ERG3 is a target of this negative regulation.
Investigations In A Tactile Sensor Based On Fiber-Optic Interferometric Strain Gauges (1990)

A double-polarization interferometer with digital readout by fringe counting allows for discrimination between strain applied to the 'reference'- and 'signal'-arm respectively under transverse force induced fiber tension bending. This is utilized for laterally resolved displacement sensing by employing an array of interferometer arms placed under an elastic skin. Experimental results of the one-dimensional field of strain-displacement characteristics employing the four parallel arms of two Michelson interferometers are compared with the theoretically expected, to first order quadratic dependence of strain on displacement under transverse force.
The Helicobacter pylori VacA toxin is a urea permease that promotes urea diffusion across epithelia (2001)

Urease and the cytotoxin VacA are two major virulence factors of the human pathogen Helicobacter pylori, which is responsible for severe gastroduodenal diseases. Diffusion of urea, the substrate of urease, into the stomach is critically required for the survival of infecting H. pylori. We now show that VacA increases the transepithelial flux of urea across model epithelia by inducing an unsaturable permeation pathway. This transcellular pathway is selective, as it conducts thiourea, but not glycerol and mannitol, demonstrating that it is not due to a loosening of intercellular junctions. Experiments performed with different cell lines, grown in a nonpolarized state, confirm that VacA permeabilizes the cell plasma membrane to urea. Inhibition studies indicate that transmembrane pores formed by VacA act as passive urea transporters. Thus, their inhibition by the anion channel blocker 5-nitro-2-(3-phenylpropylamino) benzoic acid significantly decreases toxin-induced urea fluxes in both polarized and nonpolarized cells. Moreover, phloretin, a well-known inhibitor of eukaryotic urea transporters, blocks VacA-mediated urea and ion transport and the toxin's main biologic effects. These data show that VacA behaves as a low-pH activated, passive urea transporter potentially capable of permeabilizing the gastric epithelium to urea. This opens the novel possibility that in vivo VacA may favor H. pylori infectivity by optimizing urease activity.
RETRACTED: Detection of MLV-related virus gene sequences in blood of patients with chronic fatigue syndrome and healthy blood donors (2010)

Chronic fatigue syndrome (CFS) is a serious systemic illness of unknown cause. A recent study identified DNA from a xenotropic murine leukemia virus-related virus (XMRV) in peripheral blood mononuclear cells (PBMCs) from 68 of 101 patients (67%) by nested PCR, as compared with 8 of 218 (3.7%) healthy controls. However, four subsequent reports failed to detect any murine leukemia virus (MLV)-related virus gene sequences in blood of CFS patients. We examined 41 PBMC-derived DNA samples from 37 patients meeting accepted diagnostic criteria for CFS and found MLV-like virus gag gene sequences in 32 of 37 (86.5%) compared with only 3 of 44 (6.8%) healthy volunteer blood donors. No evidence of mouse DNA contamination was detected in the PCR assay system or the clinical samples. Seven of 8 gag-positive patients tested again positive in a sample obtained nearly 15 y later. In contrast to the reported findings of near-genetic identity of all XMRVs, we identified a genetically diverse group of MLV-related viruses. The gag and env sequences from CFS patients were more closely related to those of polytropic mouse endogenous retroviruses than to those of XMRVs and were even less closely related to those of ecotropic MLVs. Further studies are needed to determine whether the same strong association with MLV-related viruses is found in other groups of patients with CFS, whether these viruses play a causative role in the development of CFS, and whether they represent a threat to the blood supply.
A predictive network resource allocation technique for cognitive wireless networks (2010)

Future wireless networks are evolving towards a heterogeneous cooperative and cognitive architecture to support broadband communication needs of different types of traffic. Future wireless networks will allocate network resources based on cooperative techniques. Resource controllers will apply the cognitive principle to find out status of various networks. We propose a predictive resource allocation strategy where we employ adaptive algorithms to predict the network loading. These algorithms can detect changes in the traffic characteristics, and adapt automatically. To validate our claim, we present the results of applying these adaptive algorithms on real-world network traffic traces.
Efficient checker processor design (2000)

The design and implementation of a modern microprocessor creates many reliability challenges. Designers must verify the correctness of large complex systems and construct implementations that work reliably in varied (and occasionally adverse) operating conditions. In our previous work, we proposed a solution to these problems by adding a simple, easily verifiable checker processor at pipeline retirement. Performance analyses of our initial design were promising, overall slowdowns due to checker processor hazards were less than 3%. However, slowdowns for some outlier programs were larger.
Experimentation and self learning in continuous database marketing (2003)

We present a method for continuous database marketing that identifies target customers for a number of marketing offers using predictive models. The algorithm then selects the appropriate offer for the customer. Experimental design principles are encapsulated to capture more information that will be used to monitor and refine the predictive models. The updated predictive models are then used for the next round of marketing offers.
Does the geometric design of centrioles imply their function? (1981)

The paper suggests several principles of construction of a microscopically small device for locating the directions of signal sources in microscopic dimensions. It appears that the simplest and smallest device that is compatible with the scrambling influence of thermal fluctuations as are demonstrated by Brownian motion is a pair of cylinders oriented at right angles to each other. Nine equally spaced blades run in a pitched fashion along the mantle of each cylinder. The blades have a concave cross-section and bend around the circumference of the cylinder in a certain rotational pattern. Considering the striking similarity of this hypothetical device with centrioles, the paper puts forward the conjecture that centrioles locate the direction of hypothetical signals inside cells.
Psychomotor, Cognitive, Extrapyramidal, and Affective Functions of Healthy Volunteers During Treatment With an Atypical (Amisulpride) and a Classic (Haloperidol) Antipsychotic (1999)

The primary objective of this study was to compare the objective and subjective effects of amisulpride with those of a classic antipsychotic, haloperidol, when both were given to healthy volunteers in representative therapeutic doses over 5 days. The secondary objective was to compare the effects of relatively low and high doses of amisulpride to confirm the suspected duality of its pharmacologic activity. Twenty-one subjects participated in the four-way, randomized, double-blind, crossover study with repeated daily doses of amisulpride 50 mg, amisulpride 400 mg, haloperidol 4 mg, and placebo. Subjects were institutionalized during treatment periods and were under 24-hour medical supervision. They underwent a series of psychomotor and cognitive tests 1 hour before and 3 and 6 hours after dosing on days 1 and 5. Their extrapyramidal disturbances and drug-related feelings were assessed at the end of each replication. Psychiatric interviews and ratings of depression, subjective well-being, and negative symptoms occurred on day 4. Amisulpride 50 mg had no significant effect on any parameter. Amisulpride 400 mg had several adverse effects on psychomotor and, although less severe, on cognitive performance on the fifth day only. Amisulpride 400 mg produced no significant extrapyramidal disturbances in the group as a whole, although it may have in some individual subjects. Also, it produced no signs of mental disturbances on clinical rating scales or during a structured psychiatric interview. Haloperidol ubiquitously impaired psychomotor and cognitive performance in a similar fashion after the first and the final doses. It produced extrapyramidal disturbances in nearly every subject, the most common being akathisia and the most severe, in the case of one individual, being acute dystonia. Unlike amisulpride, haloperidol produced a number of mental disturbances, the most noteworthy being negative symptoms. Amisulpride seems to be a well-tolerated drug. Its side effects should be much less troublesome to patients using the drug on a long-term basis than those of classic antipsychotics, like haloperidol.
Recent Translational Research in HIV/AIDS (2011)

The collective efforts of HIV/AIDS research scientists from over 16 countries in the world are included in the book. This 27-chapter Open Access book well covers HIV/AIDS translational researches on pathogenesis, diagnosis, treatment, prevention, and also those beyond conventional fields. These are by no means inclusive, but they do offer a good foundation for the development of clinical patient care. The translational model forms the basis for progressing HIV/AIDS clinical research. When linked to the care of the patients, translational researches should result in a direct benefit for HIV/AIDS patients.
New process for screen cutting: water-jet guided laser (2005)

Today's OLED manufacturers need high-precision, fast tools to cut the metal screens used to deposit the electroluminescent layers onto the substrate. Conventional methods -tching and dry laser cutting - are not satisfying regarding the demands of high-definition OLED displays. A new micro machining technology, the water jet guided laser - a hybrid of laser and water jet technologies that has been actively used in recent years in the electronic and semiconductor field - is now available to OLED manufacturers. This technology represents a significant improvement in screen, mask and stencil cutting, as it combines high precision and high speed. It is able to cut small apertures with totally clean edges (no dross or slag), as the water jet removes the particles and a thin water film is maintained on the material surface during the process. Because the water jet cools the material between the laser pulses, the cut material is free of any thermal stress. The water jet guided laser is also a very fast process: as an example, rectangular slots can be cut in 30 to 50 microns thick stainless steel or nickel at a rate between 25'000 and 30'000 holes per hour.
Maternal-fetal pH difference and fetal scalp pH as predictors of neonatal outcome. (1986)

The purpose of this study was to determine if interpretation of fetal scalp pH values would be enhanced by concurrent measurement of maternal venous pH. The last fetal capillary pH obtained before delivery was compared with simultaneous maternal-fetal pH difference as predictors of neonatal outcome assessed by five-minute Apgar scores. Fetal scalp pH and maternal-fetal pH difference were significantly correlated with r = -0.72 (P less than .0001). The acidotic fetuses born to acidotic mothers had low maternal-fetal pH differences, and all were nondepressed at birth. A 33% reduction in false negatives was found using maternal-fetal pH difference instead of scalp pH alone. Errors in interpretation of fetal scalp pH can be reduced by the use of maternal-fetal pH difference.