gebhart/patrepeval huggingface dataset:
Transcriptional Activation of the Rice Tungro Bacilliform Virus Gene Is Critically Dependent on an Activator Element Located Immediately Upstream of the TATA Box (2000)

To investigate the transcriptional mechanisms of rice tungro bacilliform virus, we have systematically analyzed an activator element located immediately upstream of the TATA box in the rice tungro bacilliform virus promoter and its cognate trans-acting factors. Using electrophoretic mobility shift assays, we showed that rice nuclear proteins bind to the activator element, forming multiple specific DNA-protein complexes via protein-protein interactions. Copper-phenanthroline footprinting and DNA methylation interference analysis indicated that multiple DNA-protein complexes share a common binding site located between positions -60 to -39, and the proteins contact the activator element in the major groove. DNA UV cross-linking assays further showed that two nuclear proteins (36 and 33 kDa), found in rice cell suspension and shoot nuclear extracts, and one (27 kDa), present in root nuclear extracts, bind to this activator element. In protoplasts derived from a rice (Oryza sativa) suspension culture, the activator element is a prerequisite for promoter activity and its function is critically dependent on its position relative to the TATA box. Thus, transcriptional activation may function via interactions with the basal transcriptional machinery, and we propose that this activation is mediated by protein-protein interactions in a position-dependent mechanism.
Pancreatic Islet Transplantation in Type 1 Diabetes Mellitus: An Update on Recent Developments (2013)

Type 1 diabetes mellitus is an autoimmune disease that is characterized by the destruction of the islets of Langerhans cells which produce insulin. The current gold standard treatment is exogenous insulin injection, but this is onerous for the patients, and can lead to severe complications. Another approach involves transplanting pancreatic islet cells in order to restore endogenous insulin production under physiologic regulation. Although there has been some success with this treatment plan, there have been several hurdles. The largest hurdle is improving the 5 year survival of the graft, which is currently at 10%. In order to do so, there has been research into better locations for the graft, better isolation techniques, alternate immune suppression regimens, and novel transplantation methodologies utilizing encapsulated grafts. Another hurdle for pancreatic islet transplantation is that current methodologies require islets from several pancreata in order to create one successful graft, which leads to difficulties since there is a limited supply. However, there has been research looking into single donor transplants and porcine xenografts to increase the supply and address this problem. In this article, we review the current state of research regarding pancreatic islet transplantation.
Involvement of IL-32 in activation-induced cell death in T cells (2006)

NK cell transcript 4 (NK4), now denoted as IL-32, was originally identified as a transcript whose expression was increased in activated NK cells. It has been very recently demonstrated that NK4 is secreted from several cells upon the stimulation of some inflammatory cytokines such as IL-18, IL-1beta, IFN-gamma and IL-12. Furthermore, NK4 induces production of tumor necrosis factor, macrophage inflammatory protein (MIP)-2 and IL-8 in monocytic cell lines, indicating that this factor would be involved in the inflammatory responses. Based on these findings, NK4 was renamed IL-32. However, the biological activities of IL-32 on other cell types remained undetermined. Furthermore, it was still argued whether IL-32 acts on cells from outside or inside the cells. In this article, we first report that expression of IL-32 was up-regulated in activated T cells and NK cells, and that IL-32beta was the predominantly expressed isoform in activated T cells. IL-32 was specifically expressed in T cells undergoing apoptosis and enforced expression of IL-32-induced apoptosis, whereas its down-regulation rescued the cells from apoptosis in HeLa cells. IL-32 existing in the supernatant would be derived from the cytoplasm of apoptotic cells. These results strongly indicated that IL-32 would be involved in activation-induced cell death in T cells, probably via its intracellular actions. Our present findings expand our understanding of the biological function of IL-32 and argue that IL-32 may act on cells, not only from the outside but also from the inside.
Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit (2008)

A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the "tip effect" in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method.
Novel Micropyrolyis Index (MPI) to Estimate the Sooting Tendency of Fuels (2008)

A new fuel quality indicator called micropyrolysis index (MPI) is proposed for quantifying sooting tendencies of fuels in research laboratories. The MPI has been designed with the following characteristics: (i) oxygen independence, since sooting tendencies can change dramatically with varying oxygen concentration, (ii) reduced sample volume that can be utilized on a laboratory scale, (iii) improved repeatability over traditional methods, and (iv) use of common laboratory equipment so that the method may easily be implemented in multiple laboratories. MPI measurements were conducted by pyrolyzing 20 µL of fuel across a bed of α-Al 2O 3 beads at a temperature of 850 °C. Subsequently, the carbon-containing beads were transferred to a clean reactor where the deposited carbon was burned via temperature programmed oxidation (TPO) in order to quantify the amount. The amount of deposited carbon provides an indication of the tendency of a particular fuel to form soot when pyrolyzed. The observed tendency is independent of operating conditions, such as flame temperature and stoichiometric oxygen/fuel ratios, which greatly affect the measurements in other techniques used to estimate sooting tendency. An MPI value of 5 was assigned to the amount of carbon deposited from n-octane, and a value of 20, to the value corresponding to decalin. These two compounds were used as reference. Repeatability tests showed that MPI measurements had a standard deviation of 1.02 MPI at MPI = 94.7 which scaled down to 0.11 at MPI = 3.3. MPI values of pure nonaromatic hydrocarbons were found to correlate well with traditional threshold soot index (TSI) values. However, MPI was found to be more differentiating than TSI among the different hydrocarbon families: n-alkanes, isoalkanes, and cycloalkanes. A quantitative structure−property relationship (QSPR) model was developed in order to predict the MPI of other pure compounds not measured experimentally and further expand the database. Blending issues with aromatics are discussed, as well as the effects of aromatic content in real feeds.
Proton pump inhibitors suppress absorption of dietary non-haem iron in hereditary haemochromatosis (2007)

Administration of a PPI to patients with HH can inhibit the absorption of non-haem iron from a test meal and the habitual diet.
Myb-Related <i>Schizosaccharomyces pombe</i>cdc5p Is Structurally and Functionally Conserved in Eukaryotes (1998)

Schizosaccharomyces pombe cdc5p is a Myb-related protein that is essential for G2/M progression. To explore the structural and functional conservation of Cdc5 throughout evolution, we isolated Cdc5-related genes and cDNAs from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens. Supporting the notion that these Cdc5 gene family members are functionally homologous to S. pombe cdc5(+), human and fly Cdc5 cDNAs are capable of complementing the temperature-sensitive lethality of the S. pombe cdc5-120 mutant. Furthermore, S. cerevisiae CEF1 (S. cerevisiae homolog of cdc5(+)), like S. pombe cdc5(+), is essential during G2/M. The location of the cdc5-120 mutation, as well as mutational analyses of Cef1p, indicate that the Myb repeats of cdc5p and Cef1p are important for their function in vivo. However, we found that unlike in c-Myb, single residue substitutions of glycines for hydrophobic residues within the Myb repeats of Cef1p, which are essential for maintaining structure of the Myb domain, did not impair Cef1p function in vivo. Rather, multiple W-to-G substitutions were required to inactivate Cef1p, and many of the substitution mutants were found to confer temperature sensitivity. Although it is possible that Cef1p acts as a transcriptional activator, we have demonstrated that Cef1p is not involved in transcriptional activation of a class of G2/M-regulated genes typified by SWI5. Collectively, these results suggest that Cdc5 family members participate in a novel pathway to regulate G2/M progression.
Early changes in biomarkers of skeletal metabolism and their association to the occurrence of osteochondrosis (OC) in the horse (2008)

Measuring osteocalcin concentrations during the first few weeks post partum may have potential value for the prediction of risk for OC development.
CO<sub>2</sub> Capture from Cement Plants and Steel Mills Using Membranes (2018)

Carbon dioxide capture, utilization, and storage (CCUS) has been identified as an effective method of mitigating anthropogenic CO2 emissions. To date, most research and development has centered on capturing CO2 emitted from coal power plants, as they are the largest point source emitters globally. However, cement and steel plants also emit large amounts of CO2 and are potentially easier targets for a CO2 capture process because the CO2 in their flue gas tends to be more concentrated. In this paper, the feasibility of capturing CO2 from cement and steel plants is examined using currently available membrane technology. Coal power plant flue gas contains 13–15% CO2; cement and steel plant flue gas contains 20–30% CO2; this higher CO2 concentration is useful for all separation technologies, but especially for membranes where separation is strongly dependent on the partial pressure driving force. Membrane-based systems can capture 80% of the CO2 emitted from cement or steel production processes at costs of $40 to $50/tonne of CO2 captured. Lower costs are possible if lower capture rates are considered. This makes CO2 capture from these gas streams an attractive first application for commercial membranes recently developed for flue gas treatment.
Head-Related Transfer Functions of Human Subjects (1995)

Head-related transfer functions (HRTFs) were measured on 40 human subjects for 97 directions of sound incidence, covering the entire sphere.Individual HRTF data for the median, horizontal, and frontal planes are presented in the frequency domain.Measurements were made synchronously at both ears, thus making the time representations, that is, the head-related impulse responses (HRIRs), valid also when interaural time differences are considered.The measurements were made at the entrance to the blocked ear canal.Sound at this point contains full spatial information, and the interindividual variation is lower than at the open ear canal.
Standing wave analysis of SMB chromatography: Linear systems (1997)

Abstract The concept of standing concentration waves is introduced to derive design equations for continuous moving bed (CMB) processes. For linear isotherm systems, simple equations are derived from the analysis to link product purity and recovery to zone lengths, bed movement velocity, flow rates, column capacity factors, and mass‐transfer coefficients. Once product purity, recovery and feed flow rate are specified for a given system, the zone flow rates and bed movement velocity that provide the highest throughput and the lowest solvent consumption can be determined from the solutions. In a given system, there is a trade‐off between product purity and throughput. If bed volume and product purities are fixed, the longer the zone lengths, the higher the throughput. Simulations based on a linear driving force model that considers axial dispersion and lumped film and intraparticle diffusion are used to compare the column profiles and effluent histories of CMB and simulated moving bed (SMB). A numerical algorithm is introduced to allow simulation of both CMB and SMB operations using the same program. The comparison shows that the design equations derived for CMB systems are applicable to SMB systems. Finally, the standing wave solutions are used to analyze an experimental SMB system from the literature (Ching et al., 1991). Simulations agree closely with the data and the predictions of the theoretical analysis.
Controlling Morphology of Injection Molded Structural Foams by Mold Design and Processing Parameters (2007)

By the invention of foam processing techniques using physical blowing agents, the area of foam injection molding has caught the attention of product developers in industry as well as of researchers. Compared to conventional injection molding, the foaming approach delivers a great potential in the manufacturing as well as in the part itself, offering a monetary benefit, being vantages for example automotive and consumer goods producer (Hyde, L.J., Kishbaugh, L.A. and Katterman, J.A. (2002) [1]. How Microcellular Foam Molding Changes the Cost Structure of Injection Molded Automotive Components: A Review of the Process and Automotive Applications, SAE Technical Paper Series). The pros are facing several cons in the part quality, notably an impaired surface finish, an over-pronounced loss in mechanical strength and toughness or some uncertainties in subsequent processing steps like varnishing and plastic welding. Actual researchers are approaching those challenges in different ways (Dassow, J. (2003) [2]. Foamed Parts with Excellent Surface Quality, Kunststoffe-Plast Europe, 93(9): 65). On the one hand, the choice of the appropriate polymeric materials has a big impact on the morphologies and the properties of the obtained foam injection molded parts. The mold as well as the processing parameters have a big effect on the obtainable foam morphologies and thus the final part properties. This study presents some possibilities to control the morphology of structural foams at high-density reductions (>50%) by an intelligent mold and process design. Parameters affecting the morphology of the foamed part like the foaming temperature, the cavity pressure, and the expansion ratio are varied. Structural properties of the foamed part like surface finish, overall density, and skin layer-thickness as well as mechanical properties are examined.
Heat Transfer Enhancement in a Diffuser using Vortex Generators Placed on the Side Wall (2013)

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Effect of Trasina <sup>®</sup> , an Ayurvedic Herbal Formulation, on Experimental Models of Alzheimer's Disease and Central Cholinergic Markers in Rats (1997)

Trasina is a herbal formulation of some Indian medicinal plants classified in Ayurveda, the classic Indian system of medicine, as Medhyarasayanas or drugs reputed to improve memory and intellect. Earlier experimental and clinical investigations have indicated that the formulation has a memory-facilitating action. In this investigation, the effect of Trasina, after subchronic administration for 21 days, was assessed on two rodent models simulating some biochemical features known to be associated with Alzheimer's disease (AD). The models, in rats, included intracerebroventricularly (i.c.v.) administered colchicine (15 micrograms/rat) and lesioning of nucleus basalis magnocellularis (nbm) by ibotenic acid (10 micrograms/rat). Retention of an active avoidance response was used as the memory parameter. In addition, the effect of Trasina was evaluated on i.c.v. colchicine-induced depletion of acetylcholine (ACh) concentrations, reduction in choline acetyltransferase (ChAT) activity, and decrease in muscarinic cholinergic receptor (MCR) binding in rat brain frontal cortex and hippocampus. The behavioral and biochemical investigations were done 7, 14, and 21 days after colchicine or ibotenic acid lesioning. Trasina (200 and 500 mg/kg) was administered orally (p.o.) once daily for 21 days, the first drug administration being given just prior to lesioning. Colchicine and ibotenic acid induced marked retention deficit of active avoidance learning that was attenuated in a dose-dependent manner by Trasina after 14 and 21 days of treatment. Frontal cortical and hippocampal ACh concentrations, ChAT activity and MCR binding was significantly reduced after colchicine treatment. Trasina (200 and 500 mg/kg) reversed these deficits after 14 and 21 days of treatment. The findings indicate that the herbal formulation exerts a significant nootropic effect after subchronic treatment that may be due to reversal of perturbed cholinergic function.
Terrorism and War (2017)

Virginia Held is Distinguished Professor of Philosophy at Hunter College and the Graduate Center of the City University of New York. She is the author of Rights and Goods (University of Chicago Press, 1989), Feminist Morality (University of Chicago Press, 1993), The Ethics of Care (Oxford University Press, 2006), and How Terrorism Is Wrong (Oxford University Press, 2008), among others.
Valproic acid and butyrate induce apoptosis in human cancer cells through inhibition of gene expression of Akt/protein kinase B (2006)

Our study demonstrates that although the primary target of histone deacetylase inhibitors is transcription, it is the capacity of cells to maintain cellular survival networks that determines their fate of survival.
Itraconazole treatment of allergic bronchopulmonary aspergillosis in patients with cystic fibrosis (2002)

High dose itraconazole as monotherapy or in combination with systemic glucocorticosteroids seems effective in CF patients with ABPA. No hepatotoxicity was observed during long-term therapy.
Novel Airside Heat Transfer Surface Designs Using an Integrated Multi-Scale Analysis with Topology and Shape Optimization (2016)

The major limitation of air-to-refrigerant Heat eXchangers (HX) is the air side thermal resistance which can account for more than 90% of the overall thermal resistance. The current research on heat transfer augmentation extensively focuses on the secondary heat transfer surfaces (fins). The disadvantages of fins may include reduction of heat transfer potential due to temperature gradient, increased friction resistance, fouling and additional material consumption. On the other hand, fins contribute to reducing thermal resistance by adding significant secondary surface area. The heat transfer coefficient on the primary surfaces (tubes) is not high enough to minimize thermal resistance without significantly increasing the HX size. One contributing factor is the shape of the tube itself, which is generally limited to circular, oval, or flat. Another important aspect is the tube size; the reduction of the refrigerant flow channel significantly improves performance and compactness. This characteristic grants microchannel HXâ€™s (MCHX) a top position amongst the current state-of-the-art air-to-refrigerant HXâ€™s. Although the airside performance of MCHX is also improved, the need for fins has not yet been eliminated. In this paper we investigate three novel surface concepts, using NURBS and ellipse arcs, focusing on the airside tube shape with small flow channels aiming at the minimization or total elimination of fins. The study constitutes designing a 1.0kW air-to-water HX, using an integrated multi-scale analysis with topology and shape optimization methodology. Typically, such an optimization is unreasonably time consuming and computationally unaffordable. To overcome these limitations we leverage automated CFD simulations and Approximation Assisted Optimization (AAO), thus, significantly reducing the computational time and resources required for the overall analysis. The resulting optimum designs exhibit capacity similar to a baseline MCHX, with same flow rates and 20% reduced approach temperature, more than 20% reduction in pumping power, more than 20% reduction in size, while still reducing entropy generation. Experimental validation for a proof-of-concept design is conducted and the predicted heat capacity agrees within 5% of the measured values, whereas the air-side pressure drop agrees within 10%.
Monocular Architecture (2008)

A simplified angle-polytopic multiplexed holographic drive is presented. By putting both beams through one lens, using lens motion to achieve angle multiplexing, and using a grating to achieve phase conjugation, a holographic drive size and cost can be reduced dramatically.