gebhart/patrepeval huggingface dataset:
Host Cell Interactome of HIV-1 Rev Includes RNA Helicases Involved in Multiple Facets of Virus Production (2011)

The HIV-1 Rev protein plays a key role in the late phase of virus replication. It binds to the Rev Response Element found in underspliced HIV mRNAs, and drives their nuclear export by the CRM1 receptor pathway. Moreover, mounting evidence suggests that Rev has additional functions in viral replication. Here we employed proteomics and statistical analysis to identify candidate host cell factors that interact with Rev. For this we studied Rev complexes assembled in vitro with nuclear or cytosolic extracts under conditions emulating various intracellular environments of Rev. We ranked the protein-protein interactions by combining several statistical features derived from pairwise comparison of conditions in which the abundance of the binding partners changed. As a validation set, we selected the eight DEAD/H box proteins of the RNA helicase family from the top-ranking 5% of the proteins. These proteins all associate with ectopically expressed Rev in immunoprecipitates of cultured cells. From gene knockdown approaches, our work in combination with previous studies indicates that six of the eight DEAD/H proteins are linked to HIV production in our cell model. In a more detailed analysis of infected cells where either DDX3X, DDX5, DDX17, or DDX21 was silenced, we observed distinctive phenotypes for multiple replication features, variously involving virus particle release, the levels of unspliced and spliced HIV mRNAs, and the nuclear and cytoplasmic concentrations of these transcripts. Altogether the work indicates that our top-scoring data set is enriched in Rev-interacting proteins relevant to HIV replication. Our more detailed analysis of several Rev-interacting DEAD proteins suggests a complex set of functions for the helicases in regulation of HIV mRNAs. The strategy used here for identifying Rev interaction partners should prove effective for analyzing other viral and cellular proteins.
Cloning of the 1.4-kb mRNA species of human complement factor H reveals a novel member of the short consensus repeat family related to the carboxy terminal of the classical 150-kDa molecule (1991)

Abstract Three factor H mRNA species of 4.3 kb, 1.8 kb, and 1.4 kb are constitutively expressed in human liver. Having previously characterized full-length cDNA clones derived from the 4.3-kb and 1.8-kb factor mRNA, we report here the isolation and eucaryotic expression of full-length cDNA clones coding for the 1.4-kb mRNA species. The 1266-bp cDNA codes for a polypeptide of 330 amino acids and contains two polyadenylation signals and a short poly(A)+tail. The protein is composed of a leader peptide followed by five short consensus repeat domains. It shows a hybrid structure with the last three domains being almost identical to the carboxy-terminal of the classical 150-kDa factor H molecule and the two first domains representing unique short consensus repeat structures. Eucaryotic expression in COS7 cells revealed two polypeptides derived from one cDNA clone that are also found in human serum. Differences between the cDNA clones within the last three domains indicate two distinct, possibly allelic sequences that, in addition, differ from the authentic 150-kDa factor H sequence. Southern blot results support the notion that the 4.3-kb factor H and the 1.4-kb factor H-related mRNA are transcribed from two separate but highly homologous genes.
XAS Study on Oxygenated LaSrNiO4and La2NiO4+δ (1997)

XANES studies at Ni K-edge have been performed for LaSrNiO3.99, and La2NiO4+δ treated under various atmosphere conditions as well as chemical and electrochemical oxidation methods. XRD patterns of polycrystalline have shown a well crystallized single phase, and valence states of Ni were carefully determined by iodometric titration, resulting in δ=0.01-0.17. The oxidation from Ni(II) to Ni(III) is indicated by an absorption edge shift to higher energy side, which is in good agreement with the amount of excess oxygen determined by iodometric titration. XANES study suggests that the doped holes in nickelates are more localized on nickel sites than those in cuprate.
Elaboración de harina de yuca (Manihot esculenta Crantz) evaluando métodos de inhibición enzimática para la obtención de puré instantáneo. (2017)

La harina de yuca (Manihot esculenta Crantz) para pure instantaneo fue elaborada aplicando tres metodos de inactivacion enzimatica y evaluando la capacidad de rehidratacion del producto despues de haber sido sometido al secado. Los metodos utilizados para la inactivacion de la enzima polifenoloxidasa fueron: tratamiento termico en bano de Maria e inmersiones en solucion de acido citrico al 1 % y 0.5 %, siendo 
seleccionada la inmersion en acido citrico al 1 % por ofrecer el menor valor de b* en la comparacion de las coordenadas del color (L*, a* y b*) usando un colorimetro. La temperatura de secado fue a 80 °C, debido a que extrajo mayor humedad en comparacion con la deshidratacion a 60 °C y 70 °C. El producto cumplio con el standard de granulometria fina del CODEX STAN 176-1989 al ser el 92.55 % de sus particulas menor a 0.60 mm, y ademas presento valores de ceniza y grasa mayores a lo indicado por la Corporacion CLAYUCA, siendo estos 2.78 g y 1.55 g en 100 g de muestra, respectivamente. Las propiedades funcionales de poder de hinchamiento, indice de absorcion de agua e indice de solubilidad en agua medidas a 25 °C fueron de 8.61 (g gel/g muestra (BS)), 9.57 (g gel/g muestra (BS)) y 10.31 (g gel/g muestra (BS)) respectivamente; valores semejantes a los obtenidos en deshidratados de otras raices y tuberculos.
Human lupus autoantibodies against NMDA receptors mediate cognitive impairment (2006)

Neuropsychiatric systemic lupus erythematosus, which often entails cognitive disturbances and memory loss, has become a major complication for lupus patients. Previously, we developed a murine model of neuropsychiatric lupus based on Abs that cross-react with dsDNA and the NMDA receptor (NMDAR). We showed that these murine Abs impair cognition when they access the CNS through a breach in the blood-brain barrier (BBB) triggered by lipopolysaccharide. Because studies show that lupus patients possess anti-NMDAR Abs in their serum and cerebrospinal fluid, we decided to investigate whether these human Abs contribute to cognitive dysfunction. Here, we show that serum with reactivity to DNA and NMDAR extracted from lupus patients elicited cognitive impairment in mice receiving the serum intravenously and given lipopolysaccharide to compromise the BBB integrity. Brain histopathology showed hippocampal neuron damage, and behavioral testing revealed hippocampus-dependent memory impairment. To determine whether anti-NMDAR Abs exist in the brains of systemic lupus erythematosus patients, we eluted IgG from a patient's brain. The IgG bound DNA and NMDAR and caused neuronal apoptosis when injected into mouse brains. We examined four more brains of patients with neuropsychiatric lupus and found that they displayed endogenous IgG colocalizing with anti-NMDAR Abs. Our results indicate that lupus patients have circulating anti-NMDAR Abs capable of causing neuronal damage and memory deficit, if they breach the BBB, and that the Abs exist within patients' brains. Which aspects of neuropsychiatric lupus may be mediated by anti-NMDAR Abs, how often, and in which patients are now important clinical questions.
Site-specific Manipulation of Mitochondrial DNA by Artificial Restriction DNA Cutter (2019)

Site-specific gene manipulation using homologous recombination induced by a double-strand break in DNA is expected to be applied to mitochondrial genome manipulation. In this study, by using a chemistry-based DNA cutter, a double-strand break was formed in mitochondrial DNA. In highly purified mitochondrial extract, the scission mitochondrial DNA enhanced homologous recombination, confirming eminent activity of mitochondrial components for this important bioreaction. By using a chemistry-based DNA cutter, a double-strand break was formed in mitochondrial DNA. In highly purified mitochondrial extract, the mitochondrial DNA underwent homologous recombination, confirming eminent activity of mitochondrial components for this important bioreaction.
Organic photovoltaic materials and devices (2002)

Organic photovoltaic solar cells bere an important potential of development in the search for low-cost modules for the production of domestic electricity. We review the principles and techniques needed for their development: organic semiconductors, their transport properties and photophysical characteristics, photovoltaic molecule and polymer structures, device technologies, electrical and optical behaviour of the cells, state of the art, limitations and perspectives. Despite some recent record efficiencies, research on organic solar cells is still in its infancy when stability and efficiency have to be compared with the performances of silicon cells. A nominal 10% solar efficiency is the research target for the next few years.
SUPPRESSION OF HUMAN ANTI-PORCINE T-CELL IMMUNE RESPONSES BY MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II TRANSACTIVATOR CONSTRUCTS LACKING THE AMINO TERMINAL DOMAIN1 (1998)

Mutated human CIITA constructs are potent suppressors of porcine MHC class II expression.
Cellular Cytoskeleton Dynamics Modulates Non-Viral Gene Delivery through RhoGTPases (2012)

Although it is well accepted that the constituents of the cellular microenvironment modulate a myriad of cellular processes, including cell morphology, cytoskeletal dynamics and uptake pathways, the underlying mechanism of how these pathways influence non-viral gene transfer have not been studied. Transgene expression is increased on fibronectin (Fn) coated surfaces as a consequence of increased proliferation, cell spreading and active engagement of clathrin endocytosis pathway. RhoGTPases mediate the crosstalk between the cell and Fn, and regulate cellular processes involving filamentous actin, in-response to cellular interaction with Fn. Here the role of RhoGTPases specifically Rho, Rac and Cdc42 in modulation of non-viral gene transfer in mouse mesenchymal stem (mMSCs) plated in a fibronectin microenvironment was studied. More than 90% decrease in transgene expression was observed after inactivation of RhoGTPases using difficile toxin B (TcdB) and C3 transferase. Expression of dominant negative RhoA (RhoAT19N), Rac1(Rac1T17N) and Cdc42 (Cdc42T17N) also significantly reduced polyplex uptake and transgene expression. Interactions of cells with Fn lead to activation of RhoGTPases. However, further activation of RhoA, Rac1 and Cdc42 by expression of constitutively active genes (RhoAQ63L, Rac1Q61L and Cdc42Q61L) did not further enhance transgene expression in mMSCs, when plated on Fn. In contrast, activation of RhoA, Rac1 and Cdc42 by expression of constitutively active genes for cells plated on collagen I, which by itself did not increase RhoGTPase activation, resulted in enhanced transgene expression. Our study shows that RhoGTPases regulate internalization and effective intracellular processing of polyplexes that results in efficient gene transfer.
A Dielectric Polymer with High Electric Energy Density and Fast Discharge Speed (2006)

Dielectric polymers with high dipole density have the potential to achieve very high energy density, which is required in many modern electronics and electric systems. We demonstrate that a very high energy density with fast discharge speed and low loss can be obtained in defect-modified poly(vinylidene fluoride) polymers. This is achieved by combining nonpolar and polar molecular structural changes of the polymer with the proper dielectric constants, to avoid the electric displacement saturation at electric fields well below the breakdown field. The results indicate that a very high dielectric constant may not be desirable to reach a very high energy density.
The temperature profile in weakly absorbing materials during irradiation (1994)

Irradiated materials that are weakly absorbing are heated by both diffusive and direct heating. This creates various internal heating patterns and introduces the possibility of developing hot spots in the specimen that are not detected by surface monitoring. These systems are investigated for a single instantaneous radiation pulse and for a chain of such pulses. Characteristic times are identified that describe various regimes in the temporal-spatial heating pattern in the specimen.
Synthesis and characterization of 19F NMR chelators for measurement of cytosolic free Ca (1987)

Fluorine 19 nuclear magnetic resonance (NMR) studies of intracellular fluorinated calcium chelators provide a useful strategy for the determination of cytosolic free calcium levels in cells and perfused organs. However, the fluorinated chelator with the highest affinity for calcium ions which has been described to date. 1,2-bis-(2-amino-5-fluorophenoxy)ethane-N,N,N',N'-tetraacetic acid (5FBAPTA), exhibits a dissociation constant (Kd) value 5- to 10-fold greater than the intracellular calcium concentration levels in most cell types, thus limiting the ability of fluorine NMR to report these concentrations reliably. We have consequently designed and synthesized several fluorinated calcium chelators with higher affinity for calcium. The best of these, 2-(2-amino-4-methyl-5-fluorophenoxy)-methyl-8 aminoquinidine-N,N,N',N'-tetraacetic acid (quinMF), has a Kd value approximately 10 times lower than that of 5FBAPTA. Several of the newly synthesized indicators have different chemical shifts for the calcium complexed and uncomplexed chelators to allow the simultaneous use of two indicators. In addition to providing information about the level of cytosolic free calcium, chelators containing a quinoline ring exhibit considerable sensitivity to magnesium levels and hence have potential application for the determination of cytosolic-magnesium concentrations. Application of these chelators is illustrated by determination of the cytosolic-free calcium level in erythrocytes. Use of quinMF, the chelator with the lowest Kd value, gives a calcium value of 25-30 nM.
Forward link unbalancing power control based on channel modulation scheme for wireless multimedia CDMA systems (2002)

This paper proposes a forward link unbalancing power control algorithm which is based on a channel modulation scheme for wireless multimedia CDMA mobile systems. The forward channel adopts dual orthogonal spreading codes and a multicode modulation scheme to meet different data rate traffic requirements. The proposed power control algorithm is the integration of a priority scheme and forward link power allocation and adjustment. The numerical results show that the unbalancing power control can guarantee the QoS requirements of traffic with higher priority even for the condition of heavy traffic.
Micron‐sized membrane reactors: Multicompartment semipermeable polymer particles containing palladium nanoparticles (2015)

ABSTRACT Multicompartment polymer microparticles are prepared encapsulating palladium nanoparticles within closed‐shell compartments, using a double‐emulsion (W 1 /O/W 2 ), evaporative limited coalescence process. The encapsulation efficiency in some cases is as high as 99%, and very little Pd leaches from the particles. The Pd nanoparticles dispersed in an aqueous environment within the closed‐shell compartments of the microparticles catalyze hydrogenation reactions of low molar mass substrates in water at substantial rates. The microparticle walls serve as semipermeable membranes, permitting diffusion of small molecules into the compartments while retaining the larger metal nanoparticles. The microparticles can be reused after simple filtration. The catalytic activity increases on recycling, possibly because of plasticization of polymer walls by the reactant and products, resulting in increased diffusion. In a second demonstration of catalytic activity, the microparticles efficiently decompose hydrogen peroxide. These nanoparticle‐containing microparticles serve as convenient, reusable catalyst carriers, and prevent inadvertent human and environmental contact with nanoparticles. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132 , 42021.
Reinforcement learning for robots using neural networks (1992)

Reinforcement learning agents are adaptive, reactive, and self-supervised. The aim of this dissertation is to extend the state of the art of reinforcement learning and enable its applications to complex robot-learning problems. In particular, it focuses on two issues. First, learning from sparse and delayed reinforcement signals is hard and in general a slow process. Techniques for reducing learning time must be devised. Second, most existing reinforcement learning methods assume that the world is a Markov decision process. This assumption is too strong for many robot tasks of interest, This dissertation demonstrates how one can possibly overcome the slow learning problem and tackle non-Markovian environments, making reinforcement learning more practical for realistic robot tasks.
Roles of 14-3-3 and calmodulin binding in subcellular localization and function of the small G-protein Rem2 (2005)

kir/Gem, Rad, Rem and Rem2 comprise the RGK (Rad/Gem/kir) family of Ras-related small G-proteins. Two important functions of RGK proteins are the regulation of the VDCC (voltage-dependent Ca2+ channel) activity and cell-shape remodelling. RGK proteins interact with 14-3-3 and CaM (calmodulin), but their role on RGK protein function is poorly understood. In contrast with the other RGK family members, Rem2 has been reported to bind neither 14-3-3 nor induce membrane extensions. Furthermore, although Rem2 inhibits VDCC activity, it does not prevent cell-surface transport of Ca2+ channels as has been shown for kir/Gem. In the present study, we re-examined the functions of Rem2 and its interaction with 14-3-3 and CaM. We show that Rem2 in fact does interact with 14-3-3 and CaM and induces dendrite-like extensions in COS cells. 14-3-3, together with CaM, regulates the subcellular distribution of Rem2 between the cytoplasm and the nucleus. Rem2 also interacts with the beta-subunits of VDCCs in a GTP-dependent fashion and inhibits Ca2+ channel activity by blocking the alpha-subunit expression at the cell surface. Thus Rem2 shares many previously unrecognized features with the other RGK family members.
Molecular Modeling Studies of the Novel Inhibitors of DNA Methyltransferases SGI-1027 and CBC12: Implications for the Mechanism of Inhibition of DNMTs (2013)

DNA methylation is an epigenetic modification that regulates gene expression by DNA methyltransferases (DNMTs). Inhibition of DNMTs is a promising approach for cancer therapy. Recently, novel classes of the quinolone-based compound, SGI-1027, and RG108-procainamide conjugates, CBC12, have been identified as potent DNMT inhibitors. In this work, we report comprehensive studies using induced-fit docking of SGI-1027 and CBC12 with human DNMT1 and DNMT3A. The docking was performed in the C-terminal MTase catalytic domain, which contains the substrate and cofactor binding sites, in the presence and absence of other domains. Induced-fit docking predicts possible binding modes of the ligands through the appropriate structural changes in the receptor. This work suggests a hypothesis of the inhibitory mechanisms of the new inhibitors which is in agreement with the reported autoinhibitory mechanism. The insights obtained in this work can be used to design DNMT inhibitors with novel scaffolds.
Organization of the gene coding for human protein C inhibitor (plasminogen activator inhibitor-3). Assignment of the gene to chromosome 14 (1991)

Protein C inhibitor (plasminogen activator inhibitor-3) is a plasma glycoprotein and a member of the serine proteinase inhibitor superfamily. In the present study, the human gene for protein C inhibitor was isolated and characterized from three independent phage that contained overlapping inserts coding for the entire gene. The genomic DNA was isolated and studied by restriction mapping, polymerase chain reaction analysis, and DNA sequencing. The gene was 11.5 kilobases in length and consisted of five exons separated by four introns. In addition, 0.8 kilobases of DNA from the 5'-flanking region were sequenced. The exon-intron boundaries all observed the "GT-AG" rule. The gene for protein C inhibitor was assigned to chromosome 14 by polymerase chain reaction analysis of human/hamster hybrid cell lines. The organization of the gene for protein C inhibitor is similar to the genes coding for alpha 1-antitrypsin and alpha 1-antichymotrypsin. The genes for these two proteins are also localized on chromosome 14 suggesting a recent evolution of the genes for these three proteins from a common ancestor.
ZnO Nanowires: Synthesis Approaches and Electrical Properties (2014)

In the present chapter we aim to overview the synthesis techniques and growth mechanism of zinc oxide (ZnO) nanowires and their related properties. In particular, here we review both wet and dry synthesis techniques reported in the literature, such as hydrothermal and sol-gel routes, template-assisted growth, electrodeposition process, chemical vapor deposition (CVD), pulsed laser deposition and RF magnetron sputtering. According to each synthesis technique, the chapter reports not only the detailed procedure, but also the advantages and disadvantages, analyzing in particular the properties of ZnO nanowires related to their microstructural and morphological features. The functional properties of ZnO nanostructures are also overviewed with a particular attention to their electrical properties and the related potential applications, exploiting either the semiconductive and piezoelectric behavior of ZnO nanowires. A comprehensive review is here focused on their use as field effect transistor, energy nanogenerators, pH and gas sensors, as well as the use of ZnO nanowires for energy conversion, like photovoltaic cells and water splitting photoelectrochemical cells.
ChemInform Abstract: Modified Sol—Gel Based Approaches for Synthesizing Borophosphosilicates Glasses and Glass‐Ceramics. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Association of Mallampati scoring on airway outcomes in women undergoing general anesthesia with Supreme™ laryngeal mask airway in cesarean section (2019)

This study was registered at http://www.clinicaltrials.gov , identifier: NCT02026882 , retrospectively registered. Date of registration: December 31, 2013.
Resonant Ultrasound Spectroscopy for Irregularly-Shaped Samples and its Application to Uranium Ditelluride (2023)

Resonant ultrasound spectroscopy (RUS) is a powerful technique for measuring the full elastic tensor of a given material in a single experiment. Previously, this technique was limited to regularly-shaped samples such as rectangular parallelepipeds, spheres, and cylinders. We demonstrate a new method for determining the elastic moduli of irregularly-shaped samples, extending the applicability of RUS to a much larger set of materials. We apply this new approach to the recently-discovered unconventional superconductor UTe$_2$ and provide its elastic tensor at both 300 and 4 kelvin.
Evaluation of surface depletion effects in single-crystal test structures for reference materials applications (1998)

Monocrystalline silicon test structures are being investigated for critical dimension (CD) reference materials applications. The goal of this work is to produce samples which do not exhibit the phenomenon of “methods divergence,” where the measurement of a single sample, fabricated in an electrical conductor, by multiple techniques leads to results that differ from one another by more than the total known error budgets of the measurements. In this paper, measurements are described to determine the sources of differences observed between electrical and other measurements.