gebhart/patrepeval huggingface dataset:
Nuclear and mitochondrial tRNA-lookalikes in the human genome (2014)

We are interested in identifying and characterizing loci of the human genome that harbor sequences resembling known mitochondrial and nuclear tRNAs. To this end, we used the known nuclear and mitochondrial tRNA genes (the "tRNA-Reference" set) to search for "tRNA-lookalikes" and found many such loci at different levels of sequence conservation. We find that the large majority of these tRNA-lookalikes resemble mitochondrial tRNAs and exhibit a skewed over-representation in favor of some mitochondrial anticodons. Our analysis shows that the tRNA-lookalikes have infiltrated specific chromosomes and are preferentially located in close proximity to known nuclear tRNAs (z-score ≤ -2.54, P-value ≤ 0.00394). Examination of the transcriptional potential of these tRNA-lookalike loci using public transcript annotations revealed that more than 20% of the lookalikes are transcribed as part of either known protein-coding pre-mRNAs, known lncRNAs, or known non-protein-coding RNAs, while public RNA-seq data perfectly agreed with the endpoints of tRNA-lookalikes. Interestingly, we found that tRNA-lookalikes are significantly depleted in known genetic variations associated with human health and disease whereas the known tRNAs are enriched in such variations. Lastly, a manual comparative analysis of the cloverleaf structure of several of the transcribed tRNA-lookalikes revealed no disruptive mutations suggesting the possibility that these loci give rise to functioning tRNA molecules.
EBSD for analysing the twinning microstructure in fine‐grained TWIP steels and its influence on work hardening (2009)

Summary A 22 Mn–0.6 C twinning induced plasticity steel with an average grain size of 2.6 μm was deformed in tension at room temperature. The electron backscattered diffraction technique was used to characterize the twinning structure in relation with the local texture evolution. For nanoscale analysis, additional transmission electron microscopy analysis was performed. Nanotwins were activated in the largest grains from the beginning of the deformation. They interacted with a well‐developed dislocation structure that induced detectable intragranular orientation variations. With increasing deformation, dense bundles of nanotwins preferentially developed in grains oriented close to the <111>//tensile direction fibre (promoted by the deformation) as well as medium to high angle sub‐boundaries. These key features of the twinned microstructure were finally related to the remarkably high strain hardening, which evolved according to different stages.
General anesthetics activate a nociceptive ion channel to enhance pain and inflammation (2008)

General anesthetics (GAs) have transformed surgery through their actions to depress the central nervous system and blunt the perception of surgical insults. Counterintuitively, many of these agents activate peripheral nociceptive neurons. However, the underlying mechanisms and significance of these effects have not been explored. Here, we show that clinical concentrations of noxious i.v. and inhalation GAs excite sensory neurons by selectively activating TRPA1, a key ion channel in the pain pathway. Further, these GAs induce pain-related responses in mice that are abolished in TRPA1-null animals. Significantly, TRPA1-dependent neurogenic inflammation is greater in mice anesthetized with pungent compared with nonpungent anesthetics. Thus, our results show that TRPA1 is essential for sensing noxious GAs. The pronociceptive effects of GAs combined with surgical tissue damage could lead to a paradoxical increase in postoperative pain and inflammation.
Robust Conjunctive Item–Place Coding by Hippocampal Neurons Parallels Learning What Happens Where (2009)

Previous research indicates a critical role of the hippocampus in memory for events in the context in which they occur. However, studies to date have not provided compelling evidence that hippocampal neurons encode event-context conjunctions directly associated with this kind of learning. Here we report that, as animals learn different meanings for items in distinct contexts, individual hippocampal neurons develop responses to specific stimuli in the places where they have differential significance. Furthermore, this conjunctive coding evolves in the form of enhanced item-specific responses within a subset of the preexisting spatial representation. These findings support the view that conjunctive representations in the hippocampus underlie the acquisition of context-specific memories.
Recombination activity of interstitial iron and other transition metal point defects in p- and n-type crystalline silicon (2004)

Interstitial iron in crystalline silicon has a much larger capture cross section for electrons than holes. According to the Shockley–Read–Hall model, the low-injection carrier lifetime in p-type silicon should therefore be much lower that in n-type silicon, while in high injection they should be equal. In this work we confirm this modeling using purposely iron-contaminated samples. A survey of other transition metal impurities in silicon reveals that those which tend to occupy interstitial sites at room temperature also have significantly larger capture cross sections for electrons. Since these are also the most probable metal point defects to occur during high temperature processing, using n-type wafers for devices such as solar cells may offer greater immunity to the effects of metal contaminants.
Multi-scale Numerical Studies on Characterization of Shale Gas Reservoir Development (2018)

From three different perspectives, this thesis addresses one issue: how to reliably and objectively assess and forecast the shale reservoir performance with an advanced understanding of the shale reservoir specialty. With enhanced hydraulic characterization, Chapter 2 provides an advanced modelling scheme using the commercial platform to reduce history-match errors and forecast uncertainty. In Chapter 3, an integrated multi-scale numerical simulation platform is established. Based on the multi-scale characterization platform, the insights obtained at the micro-scale such as nanopore surface coverage evolution and induced heterogeneity can provide a better understanding of the macro reservoir performance, which leads to more reasonable and objective evaluation on the reservoir transient response. In Chapter 4, based on an integrated modelling workflow, the reservoir performance for carbon dioxide (CO2) sequestration in both dry and liquid-rich shale reservoirs is assessed. A more accurate shale reservoir model representing the most important features of shale formations is proposed. The objective of the work is to determine the most critical factors dominating the success of the CO2 sequestration and enhanced oil and gas recovery (EOR/EGR), which gives valuable guidance in field applications.
Creating and Assembling Virtual Exhibitions from Existing X3D Models (2011)

Abstract. Virtual visits on the Web are an important means to publicize a museum collection and attract visitors. Software applications for building virtual exhibitions, in addition to being tools to create content for virtual visits, may help the staff of a museum to conceive and mount exhibitions. This report presents the Virtual Exhibition Builder, an interactive software tool aimed at the creation of virtual exhibitions, given a 3D model of the physical environment of the museum described in an X3D file, and information about the artworks. The development of this tool involves inputs proposed by museum experts.
A Mild and Versatile Method for Palladium‐Catalyzed Cross‐Coupling of Aryl Halides in Water and Surfactants (2003)

Abstract Various aqueous surfactants proved to be excellent media for carrying out palladium‐catalyzed Suzuki−Miyaura cross‐coupling reactions under mild conditions. The dehalogenation side reaction, which is usually a drawback with the aqueous protocol, was not observed. The concentration of the surfactant in water played a pivotal role for the reaction outcome. Smooth cross‐coupling of iodoanisole and a variety of aryl bromides, including electron‐rich derivatives, with aryl boronic acids occurred at room temperature in high yields either with [Pd(PPh 3 ) 4 ] or Pd/C as catalyst. The water‐surfactant Pd/C system combines high activity under ambient conditions (air), easy separation and recyclability. Palladium acetate was found to be effective in cross‐coupling of the less reactive aryl chlorides at 100 °C. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Block Shanno constant modulus algorithm for wireless equalizations (2002)

We formulate a block processing objective function for the constant modulus algorithm (CMA) and present a nonlinear optimization strategy for its rapid minimization. The resulting algorithm is called the block Shanno constant modulus algorithm (BSCMA), which is applied in the simulation to equalize multipath fading channel models with a multi-antenna system. The results show that the algorithm can converge considerably faster than the steepest descent based CMA and the RLSCMA configured similarly.
Multi-Band Scheduler for Future Communication Systems (2007)

This paper presents a new concept for scheduling transmissions in a wireless radio system operating at multiple frequency bands: the multi-band scheduler (MBS). The MBS ensures transparency of the operation on multiple bands for the higher network layers. Special attention is paid to achieve low delay and latency when operating the system in the multi-band mode. Particularly we propose additions to the ARQ procedures to achieve this. Further, we work out in detail two deployment scenarios for multi-band scheduling. Firstly operation in a spectrum sharing context where multiple bands are used; one dedicated band for basic service and one shared extension band for extended services. Secondly we consider multi-band operation in a relay environment where the two bands have different propagation properties and relays provide extra coverage and capacity in the whole cell.
Mutational Analysis of Vpr-Induced G <sub>2</sub> Arrest, Nuclear Localization, and Cell Death in Fission Yeast (1999)

Cell cycle G2 arrest, nuclear localization, and cell death induced by human immunodeficiency virus type 1 Vpr were examined in fission yeast by using a panel of Vpr mutations that have been studied previously in human cells. The effects of the mutations on Vpr functions were highly similar between fission yeast and human cells. Consistent with mammalian cell studies, induction of cell cycle G2 arrest by Vpr was found to be independent of nuclear localization. In addition, G2 arrest was also shown to be independent of cell killing, which only occurred when the mutant Vpr localized to the nucleus. The C-terminal end of Vpr is crucial for G2 arrest, the N-terminal alpha-helix is important for nuclear localization, and a large part of the Vpr protein is responsible for cell killing. It is evident that the overall structure of Vpr is essential for these cellular effects, as N- and C-terminal deletions affected all three cellular functions. Furthermore, two single point mutations (H33R and H71R), both of which reside at the end of each alpha-helix, disrupted all three Vpr functions, indicating that these two mutations may have strong effects on the overall Vpr structure. The similarity of the mutant effects on Vpr function in fission yeast and human cells suggests that fission yeast can be used as a model system to evaluate these Vpr functions in naturally occurring viral isolates.
Comparative effects of 7 beta-hydroxycholesterol towards murine lymphomas, lymphoblasts and lymphocytes: selective cytotoxicity and blastogenesis inhibition. (1986)

The effects of 7 beta-hydroxycholesterol on lymphoma cells in culture, on lymphocytes entering blastic transformation and on quiescent murine spleen lymphocytes have been investigated. The early events of blastogenesis as well as YAC-1, RDM-4 and EL-4 cells were shown to be very sensitive to this sterol at microM concentration, whereas constituted lymphoblasts and normal lymphocytes remained insensitive at 50 times higher concentration. The effect of some classical antitumor drugs (Adriamycin, Mitomycin-C, Methotrexate) on these lymphoma cells were of the same order of magnitude. However, the activity of 7 beta-hydroxycholesterol was closely related to the composition of the culture medium. Indeed, the cytotoxic effects of this compound were less in medium supplemented with foetal calf serum than in lipoprotein poor, Ultroser-G supplemented medium. The possible impairment of the same, or closely related, events occurring in blastic transformation and in rapid proliferation of cells is pointed out. Our results raise the question of the possible use of these compounds for an antitumor strategy.
Development of an ASIC macrocell design CAD system (2002)

An important factor in bringing a new product to market for a successful ASIC business is the generation of design data related to macrocells, such as graphic symbols, logic simulation models, input-to-output path delays, and timing parameters for the ASIC CAD system so that ASIC customers can begin designing with the new ASIC product. Logic model generation, transition from logic to circuit simulation, circuit design with estimated parasitics, circuit verification of physical layout, and encapsulation of the macrocell design CAD flow are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Lime-Soda Softening Process Modifications for Enhanced NOM Removal (2006)

In this research, a number of process modifications to the lime-soda softening process were examined, including utilization of high Mg-content lime, addition of MgCl2, and the recycling of softening sludge, in order to improve the removal of natural organic matter (NOM) and reduce the formation of disinfection byproducts (DBPs). Jar test results showed that dissolved organic carbon (DOC) removal increased and trihalomethane (THM) formation was reduced as the magnesium in hydrated lime increased, and was directly correlated with the amount of magnesium removed from the system. However, a dolomitic quick lime hydrated under atmospheric conditions resulted in less effective DOC removal due to a lack of available Mg, and subsequently, less co-precipitation of Mg(OH)2-NOM complexes. The addition of MgCl2 to the raw water also increased DOC removal and reduced THM formation in both the presence and absence of softening sludge, with DOC removal increasing as softening sludge and magnesium dosages increased. As high as 43% removal of DOC was achieved at the stoichoimetric lime-soda ash dose in the presence of 457 mg/L sludge and 7.5 mg/L MgCl2, as compared to only 13% removal in the absence of sludge and MgCl2. The recycling of softening sludge had little or no effect on the hardness and the level of inorganic elements in treated water. The results presented here provide new approaches for improving DBP precursor removal during lime-soda softening without significantly increasing lime and soda ash dosage or the generation of waste sludge.
Redoxschaltbarer, excitonengekoppelter Circulardichroismus: eine neue Strategie für die Entwicklung molekularer Schalter (1998)

Intensive chiroptische Eigenschaften und hervorragende Reversibilität der chemischen Redoxcyclen empfehlen das CuI/CuII-Komplexpaar 1/2 als Basis für die Entwicklung eines molekularen Schalters. Reduziert wird mit Ascorbinsäure, oxidiert mit Ammoniumpersulfat.
Study on Synthesis and Characterization of Anion Exchange Membrane Based on Poly (Vinyl Alcohol) modified by free-radical polymerization (2020)

In this study, poly(vinyl alcohol) (PVA) has been modified by free-radical polymerization (PVA-PVA). The formation of products were confirmed by nuclear magnetic resonance spectra (13C NMR). The anion exchange membranes based on modified PVA were fabricated in this work. The ionic conductivity, ion-exchange capacity, water uptake of membranes as a function of alkaline concentration and the thermal stability of electrolyte were studied. The obtained membranes have good conductivity (>1 mS/cm), high anion exchange capacity (>2 mmol/g), and stable at over 100°C, meeting the criteria for the anion-exchange membrane for alkaline fuel cell.
Investigation of SOI-like I-V characteristics for a 64-Mb DRAM SCC MOSFET with a buried drain (1992)

The MOSFET structure of a surrounding-high-capacitance cell (SCC) trench cell with a buried drain scaled down for 64-Mb DRAM applications has been studied using the device simulator MINIMOS. For this cell design, the depletion zones of the buried drain can pinch off the substrate at a sufficiently high drain bias. The resulting floating substrate causes sharply increased avalanche carrier generation similar to (but more severe than) the kink effects found in SOI structures. These effects limit the utility of this structure for small-geometry DRAM structures. The mechanism for the enhanced avalanche generation and its dependence on bias conditions and geometry have been studied, and pertinent design rules for punchthrough and pinchoff by the buried drain have been established.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Water‐Swollen Hydrogels with Pendant Terthiophenes (2003)

Abstract A chemically cross‐linked and water‐swollen poly(AA3T‐ co ‐AA) gel having pendant terthiophenes was synthesized by radical copolymerization of [(2,2′:5′,2″‐terthiophen‐5‐yl‐)methyl acrylate] (AA3T) and acrylic acid (AA), and its swelling, dissociation, and doping behaviors were studied. The gel swells in high pH solution, which is associated with the dissociation and, hence, electrostatic repulsion of the AA units, and the pH value at which the swelling starts increases with increasing AA3T composition. The dissociation of the gels is suppressed, presumably due to the incorporation of the hydrophobic AA3T unit, and, once started, the dissociation could be promoted by AA3T in the low pH region. Poly(AA3T‐ co ‐AA) copolymers and gels can be easily electrochemically and chemically doped. The volume change of the gels is observed during doping/undoping and the maximum volume change reached was about 50%. The pH dependence of the degree of swelling, q , for poly(AA3T‐ co ‐AA) gels with various F at 25 °C. (•) F = 0.11, DCL = 20%; (▪) F = 0.05, DCL = 20%; (▴) F = 0, DCL = 10%. image The pH dependence of the degree of swelling, q , for poly(AA3T‐ co ‐AA) gels with various F at 25 °C. (•) F = 0.11, DCL = 20%; (▪) F = 0.05, DCL = 20%; (▴) F = 0, DCL = 10%.
Soluble Polymer Complexes Having AlQ<sub>3</sub>‐Type Pendent Groups (2004)

Abstract Summary: Polymethacrylate having a pendent 8‐hydroxyquinoline moiety was prepared using Kelex‐100 (7‐(4‐ethyl‐1‐methyloctyl)‐8‐hydroxyquinoline) as a starting material. A soluble polymer having tris(8‐hydroxyquinolinato)aluminum (Al Q 3 )‐type side chains was obtained through the complexation of the polymer with Me 3 Al in the presence of a monomeric Kelex‐100. The polymer complex was applied to an organic light‐emitting diode (OLED) device through a spin‐cast process. Structure of the tris(8‐hydroxyquinolinato)aluminum‐type pendent group bound to polymethacrylate giving rise to the first soluble polymer of its kind. image Structure of the tris(8‐hydroxyquinolinato)aluminum‐type pendent group bound to polymethacrylate giving rise to the first soluble polymer of its kind.
Automated Evaluation of Kikuchi Patterns by Means of Radon and Fast Fourier Transformation, and Verification by an Artificial Neural Network (2003)

Automated crystal orientation measurement (ACOM) in the SEM by interpreting backscatter Kikuchi patterns (see Figure) has become a standard tool of quantitative texture analysis in materials science during the last decade. A Radon transformation of the diffraction pattern, in combination with a 1D fast Fourier transformation, enables the fast extraction of the positions of Kikuchi bands. The high‐frequency coefficients of the 1D FFT are used to define pattern quality as a measure of lattice imperfection and residual stress of the real crystal structure.
The bouquet of grapevine (<i>Vitis vinifera</i>L. cv. Cabernet Sauvignon) flowers arises from the biosynthesis of sesquiterpene volatiles in pollen grains (2009)

Terpenoid volatiles are important information molecules that enable pollinators to locate flowers and may protect reproductive tissues against pathogens or herbivores. Inflorescences of grapevine (Vitis vinifera L.) are composed of tiny green flowers that produce an abundance of sesquiterpenoid volatiles. We demonstrate that male flower parts of grapevines are responsible for sesquiterpenoid floral scent formation. We describe temporal and spatial patterns of biosynthesis and release of floral volatiles throughout the blooming of V. vinifera L. cv. Cabernet Sauvignon. The biosynthesis of sesquiterpene volatiles, which are emitted with a light-dependent diurnal pattern early in the morning at prebloom and bloom, is localized to anthers and, more specifically, within the developing pollen grains. Valencene synthase (VvValCS) enzyme activity, which produces the major sesquiterpene volatiles of grapevine flowers, is present in anthers. VvValCS transcripts are most abundant in flowers at prebloom stages. Western blot analysis identified VvValCS protein in anthers, and in situ immunolabeling located VvValCS protein in pollen grains during bloom. Histochemical staining, as well as immunolabeling analysis by fluorescent microscopy and transmission electron microscopy, indicated that VvValCS localizes close to lipid bodies within the maturing microspore.
Severity of innate immune-mediated colitis is controlled by the cytokine deficiency-induced colitis susceptibility-1 ( <i>Cdcs1</i> ) locus (2011)

Genetic modifier loci influence the phenotypic expression of many Mendelian traits; insight into disease pathogenesis gained from their identification in animal disease models may impact the treatment of human multigenic disorders. We previously described an innate immune-driven model of spontaneous ulcerative colitis in T-bet(-/-).Rag2(-/-) double-deficient mice that resembles human ulcerative colitis. On a BALB/c background, this disease is highly penetrant and results in the development of colorectal cancer. However, we observed that colitis in T-bet(-/-).Rag2(-/-) mice on a C57BL/6 background was significantly less severe. Quantitative trait locus analysis using an N2 backcross strategy revealed a single major quantitative trait locus on chromosome 3 that mapped to the Cdcs1 (cytokine deficiency-induced colitis susceptibility-1) locus previously identified in the Il10(-/-) and Gnai2(-/-) colitis models. Congenic introduction of the susceptible Cdcs1 interval from C3H/He into the C57BL/6 background restored colitis severity. Bone marrow reconstitution experiments further mapped the effect of host genetics on disease severity to the hematopoietic compartment. There were distinct differences in the expression of several Cdcs1 genes in bone marrow-derived dendritic cells from Cdcs1 congenic mice. We conclude that the Cdcs1 locus controls colitis severity in T-bet(-/-).Rag2(-/-) mice through innate immune cells.
Decreased spontaneous and lipopolysaccharide stimulated production of interleukin 8 by polymorphonuclear neutrophils of patients with active systemic lupus erythematosus. (1995)

These results suggest that decreased IL-8 production is one of the defects of PMN in patients with active SLE, which might predispose SLE patients to infection.