gebhart/patrepeval huggingface dataset:
A Bioluminescent Transposon Reporter-Trap Identifies Tumor-Specific Microenvironment-Induced Promoters in Salmonella for Conditional Bacterial-Based Tumor Therapy (2012)

Salmonella, which often encounter acidic environments during classical host infection, may co-opt evolutionarily conserved pathways for tumor colonization in response to the acidic tumor microenvironment. We identified specific promoter sequences that provide a platform for targeted Salmonella-based tumor therapy in vivo.
Chymase Inhibitor as a Novel Therapeutic Agent for Non-alcoholic Steatohepatitis (2018)

Non-alcoholic steatohepatitis (NASH) is characterized by inflammation and fibrosis, in addition to steatosis, of the liver, but no therapeutic agents have yet been established. The mast cell protease chymase can generate angiotensin II, matrix metalloproteinase-9 and transforming growth factor-β, all of which are associated with liver inflammation or fibrosis. In animal models of NASH, augmented chymase has been observed in the liver. In histological analysis, chymase inhibitor prevented hepatic steatosis, inflammation, and fibrosis. Chymase inhibitor also attenuated the augmentation of angiotensin II, matrix metalloproteinase-9, and transforming growth factor-β observed in the liver of NASH. Oxidative stress, inflammatory markers, and collagen were attenuated by chymase inhibition. Moreover, chymase inhibitor showed a mitigating effect on established NASH, and survival rates were significantly increased by treatment with chymase inhibitor. In this review, we propose that chymase inhibitor has potential as a novel therapy for NASH.
Trading Precision for Throughput in XPath Processing (2009)

We present in this paper a system for rewriting user-specific XPath queries for higher sharing of common sub-expressions in a streaming environment. We rewrite these queries according to an extracted schema from a pre-processed stream and we apply the rewritten queries to a subsequent stream. We show that this rewriting yields a much higher throughput while keeping an error rate under control.
The technology of water separation and purification after anaerobic digestion of liquid manure, and biofertilizer production from organic sludge (2011)

In the wake of the man’s household activity, large quantities of organic waste are created and their accumulation leads to serious ecological and social problems. Even though in most cases organic waste can be reused in the household and energetics sectors, due to the variety of different chemical components, the complex technology of the waste management and recycling is yet not available in the market. One of the most universal ways to utilize the household and agricultural waste is anaerobic fermentation, which not only degrades waste, but provides the benefit of the energy from emitted bio-gas. However, this method does not completely solve the task of total waste reprocessing into an economically profitable product. Also, after the emission of bio-gas, liquid organic waste still occupies a large volume, has a foul smell and might have toxic substances and pathogenic microorganisms. In this study, the organic household and agricultural waste management technologies, used in the last decades, are discussed and summarized, the sequence of water separation and purification processes and the ways to degrade organic compounds and liquidate undesirable scents are suggested. The results of completed research are presented. During technological processes, water was separated from liquid manure and purified. After the treatment of slurry of concentrated organic components, the dry, sterile and odourless complex of organic and mineral compounds, that can be used for soil fertilization, has been obtained. Keywords: slurry, manure, separation, deodoration, biofertilizers, waste, utilization
Comparison of Erythrocytes for Individual Indications of Metabolism Changes in Parkinson’s and Alzheimer’s Diseases (2020)

Alzheimer’s and Parkinson’s diseases are neurodegenerative diseases where several biomarkers have suggested that a single measurement is not a sufficient biomarker. The observation of increased concentration of cadmium (Cd), lead (Pb), and silver (Ag) in erythrocytes by inductively coupled plasma mass spectrometry (ICP-MS) shows a need to look for new approaches to understand the complex synchronistic effects of the cell metabolism. We have used a simplified scheme to follow some of the effects by following a hierarchy of reactions simplified to monitor elements in peripheral blood cells, e.g., erythrocytes. Erythrocytes carry oxygen to cells and carbon dioxide and waste to the lungs and back when passing from different organs including the brain. Erythrocytes also have the capacity to carry metal ions, which may be transferred to other organs, e.g., brain, despite the blood-brain barrier (BBB) and choroid plexus filter. If transfer of Cd, Pb, and Ag is continued too long, the repair systems may not be sufficient, and epigenetic effects on DNA and RNA may begin. Peripheral blood cells, e.g., erythrocytes, may help get earlier individual indications of changes at the cell level by using ICP-MS.
Control Valve Cavitation, Damage Control (2007)

Introduction In typical industrial process plants there are hundreds of process control loops. Most of these loops include a control valve as the final control element. Therefore, reliable system performance is directly associated with the control valve reliability. Because of the throttling process a control valve can be subjected to more severe conditions than other system components. In severe applications, control valves play a crucial role in safely controlling high process fluid energy levels to avoid valve and piping damage from acoustic noise, vibration, cavitation, and erosion. Designing valves to resist the deleterious effects of the throttling process fluid is only as effective as the valve sizing and selection process itself. A control valve designed with hardened trim material could last almost indefinitely on low pressure drop service conditions. This same valve used on a high pressure liquid letdown application could fail in a matter of hours. This paper outlines the application methods used by leading control valve manufacturers to avoid the damaging effect of cavitation on control valve performance and reliability.
Electric field enhanced phase separation and memory switching in amorphous arsenic triselenide (1972)

Electric field enhanced phase separation has been examined in amorphous As2Se3 and has been found to be a viable switching mechanism for this material. A simple theoretical analysis of this process is developed in which the formation of dispersed As clusters precedes the growth of an As filament. The analysis predicts that the switching behavior is field controlled and that devices biased below the point at which they switch instantly will switch at a later time. Measurements of the time for memory switching have been made for a large number of devices biased below ``threshold'' and the mean time for switching has been found to increase exponentially with decreasing applied field.
Silver Ion-Induced Grob Fragmentation of γ-Amino Iodides: Highly Stereoselective Synthesis of Polysubstituted Piperidines (2008)

A new concerted silver ion-mediated Grob fragmentation process is described in which a 1,2-dihydropyridinium ion is formed and trapped in situ with Grignard reagents in a highly regio- and diastereoselective fashion. Using this methodology, 2,3,6-trisubstituted piperidines were synthesized in good yields and further derivatized to polysubstituted indolizidine.
CD169+ lymph node macrophages have protective functions in mouse breast cancer metastasis (2021)

Although the contribution of macrophages to metastasis is widely studied in primary tumors, the involvement of macrophages in tumor-draining lymph nodes (LNs) in this process is less clear. We find CD169<sup>+</sup> macrophages as the predominant macrophage subtype in naive LNs, which undergo proliferative expansion in response to tumor stimuli. CD169<sup>+</sup> LN macrophage depletion, using an anti-CSF-1R antibody or clodronate-loaded liposomes, leads to increased metastatic burden in two mouse breast cancer models. The expansion of CD169<sup>+</sup> macrophages is tightly connected to B cell expansion in tumor-draining LNs, and B cell depletion abrogates the effect of CD169<sup>+</sup> macrophage absence on metastasis, indicating that the CD169<sup>+</sup> macrophage anti-metastatic effects require B cell presence. These results reveal a protective role of CD169<sup>+</sup> LN macrophages in breast cancer metastasis and raise caution for the use of drugs aiming at the depletion of tumor-associated macrophages, which might simultaneously deplete macrophages in tumor-draining LNs.
Neofunctionalisation of the Sli gene leads to self-compatibility and facilitates precision breeding in potato (2021)

Genetic gain in potato is hampered by the heterozygous tetraploid genome of cultivated potato. Converting potato into a diploid inbred-line based F1-hybrid crop provides a promising route towards increased genetic gain. The introduction of a dominant S-locus inhibitor (Sli) gene into diploid potato germplasm allows efficient generation of self-fertilized seeds and thus the development of potato inbred lines. Little is known about the structure and function of the Sli locus. Here we describe the mapping of Sli to a 12.6 kb interval on chromosome 12 using a recombinant screen approach. One of two candidate genes present in this interval shows a unique sequence that is exclusively present in self-compatible lines. We describe an expression vector that converts self-incompatible genotypes into self-compatible and a CRISPR-Cas9 vector that converts SC genotypes into SI. The Sli gene encodes an F-box protein that is specifically expressed in pollen from self-compatible plants. A 533 bp insertion in the promotor of that gene leads to a gain of function mutation, which overcomes self-pollen rejection.
Pharmacokinetics of subcutaneous morphine in the elderly postoperative patient (1990)

Morphine is a widely used opioid for treatment of moderate to severe pain, but large interindividual variability in patient response and no clear guidance on how to optimise morphine dosage regimen complicates treatment strategy for clinicians. Population pharmacokinetic–pharmacodynamic models can be used to quantify dose–response relationships for the population as well as interindividual and interoccasion variability. Additionally, relevant covariates for population subgroups that deviate from the typical population can be identified and help clinicians in dose optimisation.This review provides a detailed overview of the published human population pharmacokinetic–pharmacodynamic studies for morphine analgesia in addition to basic drug disposition and pharmacological properties of morphine and its analgesic active metabolite, morphine-6-glucuronide, that may help identify future covariates.Furthermore, based on simulations from key pharmacokinetic–pharmacodynamic models, the contribution of morphine-6-glucuronide to the analgesic response in patients with renal insufficiency was investigated. Simulations were also used to examine the impact of effect-site equilibration half-life on time course of response. Lastly, the impact of study design on the likelihood of determining accurate pharmacodynamic parameters for morphine response was evaluated.
Ferroelectric PbZr0.2Ti0.8O3 thin films on epitaxial Y-Ba-Cu-O (1991)

We have fabricated epitaxial ferroelectric PbZr0.2Ti0.8O3/YBa2Cu3O7−x heterostructures on single crystalline [001] LaAlO3. Only the (00l) peaks of the PbZr0.2Ti0.8O3 (PZT) film are observed, indicating that the epitaxial, c-axis oriented YBCO film is a good structural template for the heteroepitaxial growth of PZT films, in addition to being a metallic bottom electrode. A saturation polarization and remanence as high as 38 and 26.5 μC/cm2 (at 7.5 V, 0.5 kHz), respectively, have been achieved. The coercive field is about 100 kV/cm.
Antioxidant and antigenotoxic properties of CeO2NPs and cerium sulphate: Studies withDrosophila melanogasteras a promisingin vivomodel (2014)

Although in vitro approaches are the most used for testing the potential harmful effects of nanomaterials, in vivo studies produce relevant information complementing in vitro data. In this context, we promote the use of Drosophila melanogaster as a suitable in vivo model to characterise the potential risks associated to nanomaterials exposure. The main aim of this study was to evaluate different biological effects associated to cerium oxide nanoparticles (Ce-NPs) and cerium (IV) sulphate exposure. The end-points evaluated were egg-to-adult viability, particles uptake through the intestinal barrier, gene expression and intracellular reactive oxygen species (ROS) production by haemocytes, genotoxicity and antigenotoxicity. Transmission electron microscopy images showed internalisation of Ce-NPs by the intestinal barrier and haemocytes, and significant expression of Hsp genes was detected. In spite of these findings, neither toxicity nor genotoxicity related to both forms of cerium were observed. Interestingly, Ce-NPs significantly reduced the genotoxic effect of potassium dichromate and the intracellular ROS production. No morphological malformations were detected after larvae treatment. This study highlights the importance of D. melanogaster as animal model in the study of the different biological effects caused by nanoparticulated materials, at the time that shows its usefulness to study the role of the intestinal barrier in the transposition of nanomaterials entering via ingestion.
The human amniotic fluid stem cell secretome effectively counteracts doxorubicin-induced cardiotoxicity (2016)

The anthracycline doxorubicin (Dox) is widely used in oncology, but it may cause a cardiomyopathy with bleak prognosis that cannot be effectively prevented. The secretome of human amniotic fluid-derived stem cells (hAFS) has previously been demonstrated to significantly reduce ischemic cardiac damage. Here it is shown that, following hypoxic preconditioning, hAFS conditioned medium (hAFS-CM) antagonizes senescence and apoptosis of cardiomyocytes and cardiac progenitor cells, two major features of Dox cardiotoxicity. Mechanistic studies with mouse neonatal ventricular cardiomyocytes (mNVCM) reveal that hAFS-CM inhibition of Dox-elicited senescence and apoptosis is associated with decreased DNA damage, nuclear translocation of NF-kB, and upregulation of the NF-kB controlled genes, Il6 and Cxcl1, promoting mNVCM survival. Furthermore, hAFS-CM induces expression of the efflux transporter, Abcb1b, and Dox extrusion from mNVCM. The PI3K/Akt signaling cascade, upstream of NF-kB, is potently activated by hAFS-CM and pre-treatment with a PI3K inhibitor abrogates NF-kB accumulation into the nucleus, modulation of Il6, Cxcl1 and Abcb1b, and prevention of Dox-initiated senescence and apoptosis in response to hAFS-CM. These results support the concept that hAFS are a valuable source of cardioprotective factors and lay the foundations for the development of a stem cell-based paracrine treatment of chemotherapy-related cardiotoxicity.
Iraq Crude Oil Exports – November, December 2017 and January 2018 (2019)

Table (1) Iraq Crude Oil Exports – November 2017&#x0D; Table (2) Iraq Crude Oil Exports – December 2017&#x0D; Table (3) Iraq Crude Oil Exports –January 2018
Multiphase Modeling of Flow, Transport, and Biodegradation in a Mesoscale Landfill Bioreactor (2002)

The need to control gas and leachate production and minimize refuse volume in municipal solid waste landfills has motivated the development of landfill simulation models to predict and design optimal treatment processes. We have developed a multiphase and multicomponent nonisothermal module called T2LBM for the three-dimensional TOUGH2 flow and transport simulator. T2LBM can be used to simulate aerobic or anaerobic biodegradation of municipal solid waste and the associated flow and transport of gas and liquid through the refuse mass. Acetic acid is used as a proxy for all biodegradable substrates in the refuse. T2LBM incorporates a Monod kinetic rate law for the biodegradation of acetic acid by either aerobic or anaerobic microbes as controlled by the local oxygen concentration. We have verified the model against published data, and applied it to our own mesoscale laboratory aerobic landfill bioreactor experiments. We observe spatial variability of flow and biodegradation consistent with permeability heterogeneity and the geometry of the radial grid. The model is capable of matching results of a shut-in test where the respiration of the system is measured over time.
A new architecture for OGSA-based grid information service (2004)

The grid information service (GIS), which is mainly used for resource discovery and monitoring, plays an important role in grid systems. Although many GIS systems have been proposed, e.g. MDS2, no appropriate solutions exist for the OGSA-based grid systems today. The architecture for OGSA-based GIS, i.e. FOSIS (forest structured information service), is proposed in this paper. FOSIS is featured by its forest structure, which is composed of multiple trees of GIS.
3D to 2D approximation effect on propagation modeling, impact on scintillation indices in polar region (2016)

International audience
Hg(II) Removal from Aqueous Solution by Dead Fungal Biomass of MarineAspergillus niger: Kinetic Studies (2008)

Abstract Mercury removal from wastewater is a recognized pollution control challenge today. In the present investigation, the biosorption of Hg(II) onto the dead biomass of four different species of marine Aspergillus, prepared by alkaline treatment, was studied. Among the cultures studied, A. niger was found to be the most efficient for Hg(II) removal. The effects of initial Hg(II) concentration, contact time, pH, temperature, and biosorbent dosage on biosorption were also investigated. It was observed that biosorption equilibriums were established in about 2 h. Under the optimum conditions (pH: 3.0, Hg(II) concentration: 250 mg/L, biomass dose: 0.8 g/L, temperature: 40°C and contact time: 2 h), 40.53 mg Hg(II) was biosorbed per gram of dead biomass of A. niger. Kinetic studies based on fractional power, zero order, first order, pseudo first order, Elovich, second order, and second order rate expressions have also been carried out where the pseudo second order model exhibited best fit to experimental data. The intra‐particle diffusion study revealed that film diffusion is the rate‐limiting sorption process for Hg(II) on A. niger. The nature of the possible cell–metal ion interactions was evaluated by FTIR, SEM, and EDAX analysis. These examinations indicated the involvement of ‐OH and ‐NH2 + groups in the biosorption process present on the surface of the dead fungal biomass. Here, Hg(II) ions were deposited on the surface of the biomass as a film like structure.
Vortexing Methods to Reduce Secondary Losses in a Low Reaction Industrial Turbine (2015)

Vortexing methods implemented on an industrial steam turbine vane in order to reduce secondary losses are discussed. Three vortexing methods presented are prismatic blade design, inverse vortex and parabolic forced vortex. Baseline industrial vane considered for study is a prismatic blade design. Modifications are analysed numerically using commercial code CFX. Modified vanes along with baseline rotor as a complete stage is considered for analysis. Steady state Reynolds averaged Navier Stokes equations are solved. Total pressure loss (TPL) is used as target functions to monitor reduction in secondary losses. Rotor considered for the study is the baseline industrial rotor for all design modifications of vane.
Hydride Transfer Made Easy in the Reaction of Alcohol Oxidation Catalyzed by Flavin-dependent Oxidases (2008)

Choline oxidase (E.C. 1.1.3.17; choline-oxygen 1-oxidoreductase) catalyzes the two-step, four-electron oxidation of choline to glycine betaine with betaine aldehyde as enzyme-associated intermediate and molecular oxygen as final electron acceptor. Biochemical, structural, and mechanistic studies on the wild-type and a number of mutant forms of choline oxidase from Arthrobacter globiformis have recently been carried out, allowing for the delineation at molecular and atomic levels of the mechanism of alcohol oxidation catalyzed by the enzyme. First, the alcohol substrate is activated to its alkoxide species by the removal of the hydroxyl proton in the enzyme-substrate complex. The resulting activated alkoxide is correctly positioned for catalysis through electrostatic and hydrogen bonding interactions with a number of active site residues. After substrate activation and correct positioning are attained, alcohol oxidation occurs in a highly preorganized enzyme-substrate complex through quantum mechanical transfer of a hydride ion from the alpha-carbon of the chelated, alkoxide species to the N(5) atom of the enzyme-bound flavin. This mechanism in its essence is shared by another class of alcohol oxidizing enzymes that utilize a catalytic zinc to stabilize an alkoxide intermediate and NAD(P)(+) as the organic cofactor that accepts the hydride ion, whose paradigm example is alcohol dehydrogenase. It will be interesting to experimentally evaluate the attractive hypothesis of whether the mechanism of choline oxidase can be extended to other flavin-dependent enzymes as well as enzymes that utilize cofactors other than flavins in the oxidation of alcohols.
Erbb Is Linked to the Alpha-Globin Locus on Mouse Chromosome 11 (1985)

A fragment of the human gene for c-erb-B was used to map homologous sequences in mice. Analysis of somatic cell hybrids and recombinant inbred and congenic mouse strains indicated that this gene, designated Erbb, is closely linked to the gene for alpha-globin on mouse chromosome 11. Several genes controlling hematopoietic differentiation map to mouse chromosome 11.
SIMULATION OF TIDAL CURRENTS AND DIFFUSION TAKING INTO DENSITY STRATIFICATION AROUND VERY LARGE FLOATING STRUCTURES (2000)

The object of this paper is to construct the numerical model for tidal currents and diffusion at the season progressed the density stratification in semi-enclosed bay within very large floating structure, and then discuss the effects on the density stratification and existing the structures. The simulation of this paper was applied the stratified function to the 3-dimensional multi-level model for considering the effects on the density stratification. Here, the stratified function compute the vertical eddy viscosity and vertical eddy diffusivity as the function of Richardson number. As the results, good reproduction was obtained on the tidal currents, the salinity and the water-temperature by simulation in case of without structure in the bay, and then the predicting simulations were done in the stratified season within very large floating structure.
Regio- and Stereoselective Synthesis of Functionalized Cyclopentene Derivatives via Mizoroki–Heck Reactions (2017)

Pd(0)-catalyzed Mizoroki-Heck alkenylations and arylations of protected aminocyclopentenes, prepared in a few steps from Vince lactam, afforded functionalized cyclopentenes in high yields and stereoselectivities. DFT calculations were performed to rationalize the high diastereoselectivities. Functionalized cyclopentene products were transformed into valuable chiral building blocks, such as cyclic γ-amino acids and carbocyclic nucleoside precursors.