gebhart/patrepeval huggingface dataset:
MEXPRESS update 2019 (2019)

The recent growth in the number of publicly available cancer omics databases has been accompanied by the development of various tools that allow researchers to visually explore these data. In 2015, we built MEXPRESS, an online tool for the integration and visualization of gene expression, DNA methylation and clinical data from The Cancer Genome Atlas (TCGA), a large collection of publicly available multi-omics cancer data. MEXPRESS addresses the need for an easy-to-use, interactive application that allows researchers to identify dysregulated genes and their clinical relevance in cancer. Furthermore, while other tools typically do not support integrated visualization of expression and DNA methylation data in combination with the precise genomic location of the methylation, MEXPRESS is unique in how it depicts these diverse data types together. Motivated by the large number of users MEXPRESS has managed to attract over the past 3 years and the recent migration of all TCGA data to a new data portal, we developed a new version of MEXPRESS (https://mexpress.be). It contains the latest TCGA data, additional types of omics and clinical data and extra functionality, allowing users to explore mechanisms of gene dysregulation beyond expression and DNA methylation.
Multi-fidelity Bayesian Optimisation with Continuous Approximations (2017)

Bandit methods for black-box optimisation, such as Bayesian optimisation, are used in a variety of applications including hyper-parameter tuning and experiment design. Recently, \emph{multi-fidelity} methods have garnered considerable attention since function evaluations have become increasingly expensive in such applications. Multi-fidelity methods use cheap approximations to the function of interest to speed up the overall optimisation process. However, most multi-fidelity methods assume only a finite number of approximations. In many practical applications however, a continuous spectrum of approximations might be available. For instance, when tuning an expensive neural network, one might choose to approximate the cross validation performance using less data $N$ and/or few training iterations $T$. Here, the approximations are best viewed as arising out of a continuous two dimensional space $(N,T)$. In this work, we develop a Bayesian optimisation method, BOCA, for this setting. We characterise its theoretical properties and show that it achieves better regret than than strategies which ignore the approximations. BOCA outperforms several other baselines in synthetic and real experiments.
Differential response of antioxidant compounds to salinity stress in salt‐tolerant and salt‐sensitive seedlings of foxtail millet (<i>Setaria italica</i>) (2000)

The modulation of antioxidant components was comparatively analysed in a salt‐tolerant (cv. Prasad) and salt‐sensitive (cv. Lepakshi) cultivar of foxtail millet ( Setaria italica L.) under different NaCl concentrations. Under conditions of salt stress, the salt‐tolerant cultivar exhibited increased total superoxide dismutase (SOD) and ascorbate peroxidase (APX) activity, whereas both enzyme activities decreased in acutely salt‐stressed seedlings of the sensitive cultivar. At 200 m M NaCl, the tolerant foxtail millet cultivar responded with induction of cytosolic Cu/Zn‐SOD and the Mn‐SOD isoform at the protein level. The induced accumulation of the cytosolic Cu/Zn‐SOD protein/activity is positively correlated with an elevated level of the cytosolic APX gene activity. The elevated cytosolic Cu/Zn‐SOD and cytosolic APX activity correlates with an induced accumulation of their transcripts. Tolerant 5‐day‐old seedlings grown during high salinity treatment (200 m M NaCl) contained a lower amount of Na + ions and showed a lower electrolyte leakage than sensitive seedlings. In conclusion, our comparative studies indicate that salt‐induced oxidative tolerance is conferred by an enhanced compartment‐specific activity of the antioxidant enzymes in response to compartment‐specific signals.
Aquatic Toxicology and Hazard Assessment: 10th Volume (1988)

Description The 10th volume in this series begins with a review of aquatic toxicology from its early dealing with acute problems, to its current statue as a mature field of science capable of dealing with long-term and sophisticated issues. The volume also features papers in two sections that address new aspects of aquatic toxicology: 1) bioengineering and aquatic environments and 2) application of paleoecological methodology.
Therapeutic effect of hepatocyte growth factor-overexpressing bone marrow-derived mesenchymal stem cells on CCl4-induced hepatocirrhosis. (2018)

Hepatocirrhosis is one of the most severe complications of chronic hepatic disease in terms of medical intervention, and the available therapies are limited and not very successful. In this study, bone marrow-derived mesenchymal stem cells (BM-MSCs) from host rats were transduced with an adenoviral vector labelled with green fluorescent protein (EGFP) to overexpress hepatocyte growth factor (HGF). The therapeutic effect of these modified stem cells (HGF-BM-MSC group) transplanted intravenously into hepatocirrhosis model rats treated with CCl<sub>4</sub> was evaluated using serological, biochemical and histological approaches. We compared the rats in the HGF-BM-MSC group with those in the other groups (rats treated with BM-MSCs, rats treated with HGF and untreated rats (Controls)) in detail. The localisation of EGFP-tagged BM-MSCs in the injured liver was evaluated using a microscope, and the cells co-expressed hepatocyte nuclear factor 4α, albumin and cytokeratin 18. After treatment for 4 weeks, the HGF-BM-MSC, BM-MSC and HGF groups exhibited increased protein and mRNA levels of hepatocyte nuclear factor 4α, albumin and cytokeratin 18, but decreased levels of aspartate aminotransferase, alanine aminotransferase and total bilirubin. These findings indicate that BM-MSC transplantation and HGF application have great potential for the treatment of hepatocirrhosis.
Directional ground-fault indicator for high-resistance grounded systems (2003)

Locating ground faults is a difficult and challenging problem for low-voltage power systems that are ungrounded or have high-impedance grounding. Recent work in pilot signals has renewed efforts in developing fault location methodologies. This paper presents a method for directional ground-fault indication that utilizes the fundamental frequency voltages and currents. Although the ground-fault current is small and usually less than the load currents, the fault has zero-sequence components that distinguish it from the load. Signal processing techniques are used to identify and compare the fault signals to determine the fault direction. The process takes advantage of the currents flowing from the distributed grounding capacitance. An experimental microprocessor-based directional indicator unit is tested in an industrial power distribution system. Directional indication of ground faults is applied near tap-off branch circuit connections. Promising results from field test conducted in a harmonic-noisy setting are presented. Directional indicator units simplify the search process on large networks, thus reducing the time and effort necessary to locate and remove the fault, and thereby significantly reduces the probability of a second ground fault with its destructive currents.
Single-dose Live Oral Cholera Vaccine CVD 103-HgR Protects Against Human Experimental Infection With<i>Vibrio cholerae</i>O1 El Tor (2016)

NCT01895855.
dCache, the Commodity Cache. (2004)

The aim was to investigate potential targets and anti-inflammatory mechanisms of bicyclol, which has been extensively used in clinic for decades in China. Tar-Fis-Dock, virtual molecular docking system, showed that inosine 5'-monophosphate dehydrogenase II (IMPDH II) has the highest probability of binding to bicyclol. To investigate the possible role of IMPDH II in mechanisms of bicyclol, recombinant enzyme models, mice splenic lymphocytes, and human lymphocytes were used. Bicyclol (1-5 μM) significantly inhibited the proliferation of mice splenic lymphocytes stimulated by concanavalin A (conA). However, bicyclol did not show inhibitory effects on proliferation of human peripheral blood mononuclear cells (hPBMC) induced by phytohemagglutinin (PHA). IMPDH II enzyme kinetic model showed that bicyclol only had a slight regulatory effect on IMPDH II enzyme activity. These results revealed that bicyclol may be not a conventional inhibitor of IMPDH II. Further studies showed that bicyclol could promote recruitment of IMPDH II by active toll-like 2 receptor (TLR2) complex. Such effects lead to the reduction of nuclear factor κB (NF-κB) expression, increase in I-κB expression, and decrease in cytokine release, including tumor necrosis factor α (TNF-α) and interleukin 1β (IL-1β). It may be a new mechanism of bicyclol for its anti-inflammatory effect.
The interaction between HPV infection and estrogen metabolism in cervical carcinogenesis (1991)

Cancer of the genital tract is the final outcome of some infections with human papillomavirus (HPVs), and the most estrogen-sensitive cells are at greatest risk for the HPV-related cancers. Therefore we investigated relationships between HPVs and estrogen metabolism in cells of the genital tract. Increased conversion of estradiol to 16 alpha-hydroxyestrone, known to be a risk factor for cancer in some other estrogen-sensitive cells, was investigated in keratinocytes from the genital tract. Primary cells, particularly those explants from the transformation zone of the cervix, are able to 16 alpha-hydroxylate estradiol. Both cervical and foreskin cells immortalized with HPV-16 are greatly enhanced in the 16 alpha-hydroxylation of estradiol as compared with normal cells. We suggest a model whereby the combined action of 16 alpha-hydroxylation of estrogen and HPV work together to promote cell proliferation.
Stereoselective <i>P</i>‐Cyclisation and Diastereoisomeric Purification of 5‐Phenyl‐3‐(pyridin‐2‐yl)‐1,3,2‐oxazaphospholidine Formed from a Thermolabile Protecting Group (2016)

Abstract A one‐pot, two‐step synthesis of 5‐phenyl‐3‐(pyridin‐2‐yl)‐1,3,2‐oxazaphospholidine from linear precursor bis(diisopropylamino){2‐[(pyridin‐2‐yl)amino]‐1‐phenylethoxy}phosphine is achieved using a stereoselective intramolecular cyclisation. Application of a pure enantiomer {1‐phenyl‐2‐[(pyridin‐2‐yl)amino]ethanol} enabled partial diastereopurification by crystallisation. For all four diastereoisomers, the absolute configuration of the P ‐centre was determined using X‐ray crystallography and correlative 31 P NMR data. Stereochemically pure 5a was then used in nucleoside phosphitylation reactions with partial loss of stereopurity by retention of configuration on the phosphorus centre.
Immunological evaluation of a novel HLA-A2 restricted phosphopeptide of tumor associated Antigen, TRAP1, on cancer therapy (2019)

The tumor necrosis factor receptor associated protein 1 (TRAP1) is a mitochondria chaperon protein that has been previously implicated as a target for cancer therapy due to its expression level is linked to tumor progression. In this study, an immunodominant phosphopeptide of TRAP1 was identified from an HLA-A2 gene transfected mouse cancer cell line using mass spectrometry, and a synthetic phosphopeptide was generated to evaluate the potency on cancer immunotherapy. In the transporter associated with antigen processing (TAP) deficient cell, the conjugated phosphate group plays a critical role to enhance the binding affinity of phosphopeptide with HLA-A2 molecule. On the basis of immunological assay, immunization of synthetic phosphopeptide could induce a high frequency of IFN-γ-secreting CD8<sup>+</sup> T cells in HLA-A2 transgenic mice, and the stimulated cytotoxic T lymphocytes showed a high target specificity to lysis the epitope-pulsed splenocytes <i>in vivo</i> and the human lung cancer cell <i>in vitro</i>. In a tumor challenge assay, vaccination of the HLA-A2 restricted phosphopeptide appeared to suppress the tumor growth and prolong the survival period of tumor-bearing mice. These results suggest that novel phosphopeptide is naturally presented as a HLA-A2-restricted CTL epitope and capable of being a potential candidate for the development of therapeutic vaccine against high TRAP1-expressing cancers.
Effect of fluorine on the diffusion of through-oxide implanted boron in silicon (1991)

Annealing of boron through-oxide implanted silicon has been known to induce an incubated, oxygen-precipitation enhanced boron diffusion. In this letter, it is shown that annealing the ‘‘through-oxide’’ implants in a NF3-containing N2 ambient effectively reduces the incubated enhanced diffusion. The effect of fluorine is further demonstrated for boron plus fluorine through-oxide implants with pure N2 annealing. Comparing the boron diffusion between boron plus fluorine and boron plus neon implants suggests that fluorine does not have a chemical effect on capturing the point defects that cause the enhanced diffusion. Rather, fluorine is believed to be incorporated in the oxygen precipitates, which alters the point defect generation.
The scope of the strain gage principle (2003)

The 50-year-old strain-gage principle has found widespread application in the measurement of dynamometric quantities; i.e., sensors for force/mass, pressure, torque, or acceleration. It further plays an important role in the measurement of such geometric quantities as displacement and level. About 50% of all sensors (by value) rely on the strain-gage principle. A very important second application of strain gages is the experimental stress analysis of structural parts. The piezoresistive effect can be described by a gage factor k resulting from a geometric effect plus a stress-induced modulation of the electric-field charge transport. These gage factors range from near 2 in metals to more 100 in semiconductors. On this basis, a broad spectrum of sensors can be realized, reaching from the especially tailored super-precision transfer-load cell (maximum error 2*10/sup -5/, diameter 25 cm, price $25000) down to a mass-produced tiny monolithic silicon pressure sensor (error 1%, diameter 6 mm, price $5).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Virial Approximation for Load and Loss in High-Speed Journal Bearings Using Pressurized Gases (2019)

We consider steady, laminar, compressible lubrication flows in a high-speed two-dimensional journal bearing governed by the appropriate Reynolds equation. The thermodynamic states correspond to pressurized gases and are in the single-phase regime. Simple explicit formulas for the load capacity, power loss, and attitude angle are derived by applying the virial (or small density) expansions of pressure and shear viscosity to results developed in previous studies. The present virial approximation was compared to the exact numerical solutions to the Reynolds equation. It was shown that the results based on our virial expansions are quite accurate at thermodynamic states corresponding to dense and supercritical gases. The first virial correction is seen to significantly improve predictions based on the ideal gas theory.
Dissipation of the Proton Electrochemical Potential in Intact and Lysed Chloroplasts (1991)

Effective ionophore:chlorophyll ratios were determined for various ionophores that decrease the electrical potential across thylakoid membranes in intact and hypo-osmotically lysed chloroplasts isolated from spinach (Spinacia oleracea). The efficacy of gramicidin D, valinomycin, carbonylcyanide m-chlorophenylhydrazone, and dicyclohexano-18-crown-6 in collapsing the electrical potential was determined spectrophotometrically by the decay half-time of the absorbance change at 518 nanometers induced by a saturating, single turnover flash. The results show that the effectiveness of the ionophores in collapsing the electrical potential in intact and lysed chloroplasts depends on the amount of ionophore-accessible membrane in the assay medium. Only gramicidin exhibited a significant difference in efficacy between intact and lysed chloroplasts. The ratio of gramicidin to chlorophyll required to collapse the electrical potential was more than 50 times higher in intact chloroplasts than in lysed chloroplasts. The efficacy of carbonylcyanide m-chlorophenylhydrazone was significantly reduced in the presence of bovine serum albumin. The other ionophores tested maintained their potency in the presence of bovine serum albumin. Valinomycin was the most effective ionophore tested for collapsing the electrical potential in intact chloroplasts, whereas gramicidin was the most potent ionophore in lysed chloroplasts. The significance of the ionophore:chlorophyll ratios required to collapse the electrical potential is discussed with regard to bioenergetic studies, especially those that examine the contribution of the transmembrane electrochemical potential to protein transport into chloroplasts.
Introduction (1996)

First, a few facts about my background. I was the eldest of three children of Cyril Emmet and Gertrude Weir. My father belonged to what is now probably an extinct species, the scholar country parson. We lived at West Hendred, a small village on the Berkshire Downs about 15 miles south of Oxford, in a vast vicarage, glorious in summer, bitterly cold in winter. It has now been renovated and sold as a gentleman’s residence with central heating installed. As children we had to take our turn in sawing logs for open fires and pumping water for baths. So life was fairly austere physically, but this was more than offset by the joys of the garden, meadow, orchard and unspoilt countryside.
DFT timing design methodology for at-speed BIST (2003)

Logic BIST is well known as an effective method for low cost testing. However, it is difficult to realize at-speed testing, as it requires a deliberate timing design in regard to logic design and layout of the chip. This paper presents a timing design methodology for at-speed BIST, using a multiple-clock domain scheme. Some experimental test results of large industrial designs using our custom fool "Singen", will also be shown.
Glycolipid activation of invariant T cell receptor <sup>+</sup> NK T cells is sufficient to induce airway hyperreactivity independent of conventional CD4 <sup>+</sup> T cells (2006)

Asthma is an inflammatory lung disease, in which conventional CD4+ T cells producing IL-4/IL-13 appear to play an obligatory pathogenic role. Here we show, in a mouse model of asthma, that activation of pulmonary IL-4/IL-13 producing invariant TCR+ CD1d-restricted natural killer T (NKT) cells is sufficient for the development of airway hyperreactivity (AHR), a cardinal feature of asthma, in the absence of conventional CD4+ T cells and adaptive immunity. Respiratory administration of glycolipid antigens that specifically activate NKT cells (alpha-GalactosylCeramide and a Sphingomonas bacterial glycolipid) rapidly induced AHR and inflammation typically associated with protein allergen administration. Naïve MHC class II-deficient mice, which lack conventional CD4+ T but have NKT cells, showed exaggerated baseline AHR and, when challenged with alpha-GalactosylCeramide, demonstrated even greater AHR. These studies demonstrate an expanded role for NKT cells, in which NKT cells not only produce cytokines that influence adaptive immunity but also function as critical effector cells that can induce AHR. These results suggest that NKT cells responding to glycolipid antigens, as well as conventional CD4+ T cells responding to peptide antigens, may be synergistic in the induction of AHR, although in some cases, each may independently induce AHR.
Entity Embedding-based Anomaly Detection for Heterogeneous Categorical\n Events (2016)

Anomaly detection plays an important role in modern data-driven security\napplications, such as detecting suspicious access to a socket from a process.\nIn many cases, such events can be described as a collection of categorical\nvalues that are considered as entities of different types, which we call\nheterogeneous categorical events. Due to the lack of intrinsic distance\nmeasures among entities, and the exponentially large event space, most existing\nwork relies heavily on heuristics to calculate abnormal scores for events.\nDifferent from previous work, we propose a principled and unified probabilistic\nmodel APE (Anomaly detection via Probabilistic pairwise interaction and Entity\nembedding) that directly models the likelihood of events. In this model, we\nembed entities into a common latent space using their observed co-occurrence in\ndifferent events. More specifically, we first model the compatibility of each\npair of entities according to their embeddings. Then we utilize the weighted\npairwise interactions of different entity types to define the event\nprobability. Using Noise-Contrastive Estimation with "context-dependent" noise\ndistribution, our model can be learned efficiently regardless of the large\nevent space. Experimental results on real enterprise surveillance data show\nthat our methods can accurately detect abnormal events compared to other\nstate-of-the-art abnormal detection techniques.\n
A batch process micromachined thermoelectric energy harvester: fabrication and characterization (2010)

Micromachined thermopiles are considered as a cost-effective solution for energy harvesters working at a small temperature difference and weak heat flows typical for, e.g., the human body. They can be used for powering autonomous wireless sensor nodes in a body area network. In this paper, a micromachined thermoelectric energy harvester with 6 μm high polycrystalline silicon germanium (poly-SiGe) thermocouples fabricated on a 6 inch wafer is presented. An open circuit voltage of 1.49 V and an output power of 0.4 μW can be generated with 3.5 K temperature difference in a model of a wearable micromachined energy harvester of the discussed design, which has a die size of 1.0 mm × 2.5 mm inside a watch-size generator. © 2010 IOP Publishing Ltd.
A phase I study assessing the safety, clinical response, and pharmacokinetics of an experimental infliximab formulation for subcutaneous or intramuscular administration in patients with rheumatoid arthritis. (2006)

OBJECTIVE: To assess safety, clinical response, and pharmacokinetics of subcutaneous (SC) and intramuscular (IM) doses of an experimental formulation of infliximab [including experimental SC doses following administration of commercially-formulated intravenous (IV) infliximab] in patients with rheumatoid arthritis (RA) refractory to methotrexate.\nMETHODS: In this randomized, open-label, 3-stage design, 43 subjects were enrolled in 7 dose groups. In Stage I, 15 subjects received single SC doses of 0.5, 1.5, or 3.0 mg/kg. In Stage II, 21 subjects received one of 3 regimens: 100 mg SC every 2 weeks (3 injections); 3 mg/kg commercially-formulated IV infliximab every 2 weeks (2 infusions) followed by 100 mg SC every 2 weeks (3 injections); or 100 mg IM every 2 weeks (3 injections). In Stage III, 7 subjects received 100 mg SC every 4 weeks (3 injections).\nRESULTS: No treatment-related serious adverse events were observed, and there were no serious injection site reactions. A low-titer infliximab antibody response was detected in 27% of subjects receiving single SC doses, 5% receiving multiple SC doses, and 43% receiving IM doses. SC administration yielded roughly dose-proportional increases in Cmax and AUC. American College of Rheumatology 20% response (ACR20) was achieved 2 weeks after the last injection by 86.7% of subjects receiving single SC doses, 85.7% receiving SC doses every 2 weeks, 85.7% receiving both IV and SC doses, 57.1% receiving multiple IM doses, and 80.0% receiving SC doses every 4 weeks.\nCONCLUSION: SC and IM treatment with this experimental infliximab formulation was well tolerated and was associated with a favorable ACR response.