gebhart/patrepeval huggingface dataset:
The function of the human homolog of <i>Saccharomyces cerevisiae REV1</i> is required for mutagenesis induced by UV light (2000)

In Saccharomyces cerevisiae, most mutations induced by a wide range of mutagens arise during translesion replication employing the REV1 gene product and DNA polymerase zeta. As part of an effort to investigate mammalian mutagenic mechanisms, we have identified cDNA clones of the human homologs of the yeast REV genes and examined their function in UV mutagenesis. Previously, we described the isolation of a human homolog of yeast REV3, the catalytic subunit of pol zeta, and here report the identification and sequence of a human homolog of yeast REV1. This gene was isolated by identifying an expressed sequence tag encoding a peptide with similarity to the C terminus of yeast Rev1p, followed by sequencing of the clone and retrieval of the remaining cDNA by 5' rapid amplification of cDNA ends. The human gene encodes an expected protein of 1,251 residues, compared with 985 residues in the yeast protein. The proteins share two amino-terminal regions of approximately 100 residues with 41% and 20% identity, a region of approximately 320 residues with 31% identity, and a central motif in which 11 of 13 residues are identical. Human cells expressing high levels of an hREV1 antisense RNA grew normally, and were not more sensitive to the cytotoxic effect of 254 nm UV radiation than cells lacking antisense RNA. However, the frequencies of 6-thioguanine resistance mutants induced by UV in the cells expressing antisense hREV1 RNA were significantly lower than in the control (P = 0.01), suggesting that the human gene has a function similar to that of the yeast homolog.
Low-energy error correction of NAND Flash memory through soft-decision decoding (2012)

The raw bit error rate of NAND Flash memory increases as the semiconductor geometry shrinks for high density, which makes it very necessary to employ a very strong error correction circuit. The soft-decision-based error correction algorithms, such as low-density parity-check (LDPC) codes, can enhance the error correction capability without increasing the number of parity bits. However, soft-decision error correction schemes need multiple precision data, which obviously increases the energy consumption in NAND Flash memory for more sensing operations as well as more data output. We examine the energy consumption of a NAND Flash memory system with an LDPC code-based soft-decision error correction algorithm. The energy consumed at multiple-precision NAND Flash memory as well as the LDPC decoder is considered. The output precision employed is 1.0, 1.4, 1.7, and 2.0 bits per data. In addition, we also propose an LDPC decoder-assisted precision selection method that needs virtually no overhead. The experiment was conducted with 32-nm 128-Gbit 2-bit multi-level cell NAND Flash memory and a 65-nm LDPC decoding VLSI.
Anatomy of the Replication Origin of Plasmid ColE2-P9 (2006)

The plasmid ColE2-P9 origin is a 32-bp region which is specifically recognized by the plasmid-specified Rep protein to initiate DNA replication. We analyzed the structural and functional organization of the ColE2 origin by using various derivatives carrying deletions and single-base-pair substitutions. The origin may be divided into three subregions: subregion I, which is important for stable binding of the Rep protein; subregion II, which is important for binding of the Rep protein and for initiation of DNA replication; and subregion III, which is important for DNA replication but apparently not for binding of the Rep protein. The Rep protein might recognize three specific DNA elements in subregions I and II. The relative transformation frequency of the autonomously replicating plasmids carrying deletions in subregion I is lower, and nevertheless the copy numbers of these plasmids in host bacteria are higher than those of the wild-type plasmid. Efficient and stable binding of the Rep protein to the origin might be important for the replication efficiency to be at the normal (low) level. Subregion II might be essential for interaction with the catalytic domain of the Rep protein for primer RNA synthesis. The 8-bp sequence across the border of subregions II and III, including the primer sequence, is conserved in the (putative) origins of many plasmids, the putative Rep proteins of which are related to the ColE2-P9 Rep protein. Subregion III might be required for a step that is necessary after Rep protein binding has taken place.
Virtual I/O scheduler (2007)

Virtualized storage systems are required to service concurrently executing workloads, with potentially diverse data delivery requirements, that are running under multiple operating systems. Although a number of algorithms have been developed for I/O performance virtualization among operating system (OS) instances and their applications, none results in absolute performance virtualization. By absolute performance virtualization we mean that the performance experienced by applications of one operating system does not suffer due to variations in the I/O request stream characteristics of applications of other operating systems. Key requirements of I/O performance virtualization are fairness and performance isolation. In this paper, we present a novel virtual I/O scheduler (VIOS) that provides absolute performance virtualization by being fair in sharing I/O system resources among operating systems and their applications, and provides performance isolation in the face of variations in the characteristics of I/O streams. The VIOS controls the coarse grain allocation of disk time to the different operating system instances and is OS independent; optionally, a set of OS-dependent schedulers may determine the fine-grain interleaving of requests from the corresponding operating systems to the storage system.
Synthesis of <i>N</i>,<i>N</i>′‐bis(phenylsulfonyl)‐1,2‐bis(4‐pyridyl)ethylenediamines (1990)

Abstract Reaction of (4‐pyridylmethyl)amine (3) with benzenesulfonyl chlorides 2a—i affords the corresponding N ‐(4‐pyridylmethyl)benzenesulfonamides 4a—i which are converted into the N ‐oxides 5 by treatment with hydrogen peroxide and acetic acid. Treatment of compounds 4 with their N ‐oxides 5 in acetic anhydride results in dimerization to give the corresponding N , N ′‐bis(phenylsulfonyl)‐1,2‐bis(4‐pyridyl)ethylenediamines 6a – d , f . The mixed ethylenediamines 6e, g are similarly synthesized from differently substituted sulfonamides and N ‐oxides.
Evaluation of Phase-Diversity Techniques for Solar-Image Restoration (1996)

Phase-diversity techniques provide a novel observational method for overcoming the effects of turbulence and instrument-induced aberrations in ground-based astronomy. Two implementations of phase-diversity techniques that differ with regard to noise model, estimator, optimization algorithm, method of regularization, and treatment of edge effects are described. Reconstructions of solar granulation derived by applying these two implementations to common data sets are shown to yield nearly identical images. For both implementations, reconstructions from phase-diverse speckle data (involving multiple realizations of turbulence) are shown to be superior to those derived from conventional phase-diversity data (involving a single realization). Phase-diverse speckle reconstructions are shown to achieve near diffraction-limited resolution and are validated by internal and external consistency tests, including a comparison with a reconstruction using a well-accepted speckle-imaging method.
Synthesis of Narrow-Distribution, High-Molecular-Weight ROMP Polycyclopentene via Suppression of Acyclic Metathesis Side Reactions (2017)

Methods for the preparation of narrow-distribution ROMP polycyclopentene are developed to suppress the rate of acyclic metathesis: reaction between the active metal-carbene chain end and an acyclic olefin in the reaction medium. In particular, we investigate interchain metathesis, which generates linear polymers with "scrambled" chain lengths, and we demonstrate the formation of ring polymers by intrachain backbiting and quantify their content in the reaction product. By controlling the relative rates of propagation versus these side reactions, we prepare ROMP polycyclopentene with low dispersity to substantially higher molecular weights than have been reported previously. Polymerization kinetics are quantitatively described by a kinetic model, which accounts for the reversible binding of added trimethylphosphine to the active chain end.
Tests of linkage and/or association of the LEPR gene polymorphisms with obesity phenotypes in Caucasian nuclear families (2004)

Genetic variations in the leptin receptor (LEPR) gene have been conceived to affect body weight in general populations. In this study, using the tests implemented in the statistical package QTDT, we evaluated association and/or linkage of the LEPR gene with obesity phenotypes in a large sample comprising 1,873 subjects from 405 Caucasian nuclear families. Obesity phenotypes tested include body mass index (BMI), fat mass, percentage fat mass (PFM), and lean mass, with the latter three measured by dual-energy X-ray absorptiometry (DXA). Three single nucleotide polymorphisms (SNPs), namely Lys109Arg (A/G), Lys656Asn (G/C), Pro1019Pro (G/A), in the LEPR gene were analyzed. Significant linkage disequilibrium (0.394 < or = |D'| < or = 0.688, P < 0.001) was observed between pairs of the three SNPs. No significant population stratification was found for any SNP/phenotype. In single-locus analyses, evidence of association was observed for Lys656Asn with lean mass (P = 0.002) and fat mass (P = 0.015). The contribution of this polymorphism to the phenotypic variation of lean mass and fat mass was 2.63% and 1.15%, respectively. Subjects carrying allele G at the Lys656Asn site had, on average, 3.16% higher lean mass and 2.71% higher fat mass than those without it. In the analyses for haplotypes defined by the three SNPs, significant associations were detected between haplotype GCA (P = 0.005) and lean mass. In addition, marginally significant evidence of association was observed for this haplotype with fat mass (P = 0.012). No statistically significant linkage was found, largely due to the limited power of the linkage approach to detect small genetic effects in our data sets. Our results suggest that the LEPR gene polymorphisms contribute to variation in obesity phenotypes.
Hybrid ARQ receiver for packet communications over free-space optical channels (2006)

In this paper, we present receiver architectures for post-detection combining of multiple transmitted packets in direct-detection (DD) photon channels. It is assumed that the optical signal is intensity modulated (IM) and that the receiver operates under a shot-noise limit condition. Furthermore, it is assumed that the channel is free of atmospheric turbulence or turbulence is negligible enough so that it can be assumed away. An automatic-repeat-request (ARQ) mechanism is utilized with a time-out feature of M retransmissions. Maximum a posteriori (MAP) rule is considered here to arrive at optimal combining mechanism for the above scenarios. Performance is established in terms of average delay and probability of packet loss. Furthermore, the probability of successful transmission of a packet in q (<M) attempts is obtained. It is shown that the proposed technique offers a significant reduction in the number of attempts for successful transmission of a packet as compared with the conventional method.
Fibrillar Morphology in Shear-Induced Crystallization of Polypropylene (2014)

Crystallization of isotactic polypropylene during step shear rate experiments is carried out in a plate–plate geometry by means of a Linkam shearing cell. The evolution of crystalline structures is observed during the tests at a fixed radial position. The samples are then analyzed by optical microscopy and the radial position at which a transition between the spherulitic and fibrillar morphology took place is measured. The analysis of the samples allows detecting the critical shear rate at which, after a given shearing time, the fibrillar morphology overcomes the spherulitic structure. With the aim of giving a quantitative description of the conditions for the formation of a fibrillar structure, two different models are applied: one based on molecular stretch, the other one relying on specific work.
Cytohesin-1, a cytosolic guanine nucleotide-exchange protein for ADP-ribosylation factor (1997)

Cytohesin-1, a protein abundant in cells of the immune system, has been proposed to be a human homolog of the Saccharomyces cerevisiae Sec7 gene product, which is crucial in protein transport. More recently, the same protein has been reported to be a regulatory factor for the alphaLbeta2 integrin in lymphocytes. Overexpression of human or yeast ADP-ribosylation factor (ARF) genes rescues yeast with Sec7 defects, restoring secretory pathway function. ARFs, 20-kDa guanine nucleotide-binding proteins initially identified by their ability to stimulate cholera toxin ADP-ribosyltransferase activity and now recognized as critical components in intracellular vesicular transport, exist in an inactive cytosolic form with GDP bound (ARF-GDP). Interaction with a guanine nucleotide-exchange protein (GEP) accelerates exchange of GDP for GTP, producing the active ARF-GTP. Both soluble and particulate GEPs have been described. To define better the interaction between ARF and Sec7-related proteins, effects of cytohesin-1, synthesized in Escherichia coli, on ARF activity were evaluated. Cytohesin-1 enhanced binding of 35S-labeled guanosine 5'-[gamma-thio]triphosphate [35S]GTP[gammaS] or [3H]GDP to ARF purified from bovine brain (i.e., it appeared to function as an ARF-GEP). Addition of cytohesin-1 to ARF3 with [35S]GTP[gammaS] bound, accelerated [35S]GTP[gammaS] release to a similar degree in the presence of unlabeled GDP or GTP[gammaS] and to a lesser degree with GDP[betaS]; release was negligible without added nucleotide. Cytohesin-1 also increased ARF1 binding to a Golgi fraction, but its effect was not inhibited by brefeldin A (BFA), a drug that reversibly inhibits Golgi function. In this regard, it differs from a recently reported BFA-sensitive ARF-GEP that contains a Sec7 domain.
Factors Influencing Wheat Yield and Variability: Evidence from Manitoba, Canada (2009)

Production functions to explain regional wheat yields have not been studied extensively in the Canadian prairies. The objective of this study is to employ a Just-Pope production function to examine the relationship between fertilizer inputs, soil quality, biodiversity indicators, cultivars qualifying for Plant Breeders' Rights (PBR), and climatic conditions on the mean and variance of spring wheat yields. Using regional-level wheat data from Manitoba, Canada, model results show nitrogen fertilizer, temporal diversity, and PBR wheat cultivars are associated with increased yield variance. Mean wheat yield is reduced by the proportion of land in wheat, the interaction of growing temperature and precipitation, and spatial diversity. By contrast, higher soil quality and PBR wheat cultivars increase mean yield. The wheat yield increases attributed to PBR range from 37.2 (1.4%) to 54.5 kg/ha (2.0%). Plant Breeders' Rights may have enhanced royalties from increased certified seed sales, but the benefits in terms of higher wheat yield or lower yield variability are limited. Future research is required to understand the interactive effects of fertilization practices, genetic diversity, and environmental conditions on regional wheat yield stability.
Biodegradation and biocompatibility of mechanically active magnetoelastic materials (2014)

Magnetoelastic (ME) materials have many advantages for use as sensors and actuators due to their wireless, passive nature. This paper describes the application of ME materials as biodegradable implants with controllable degradation rates. Experiments have been conducted to show that degradation rates of ME materials are dependent on the material compositions. In addition, it was shown that the degradation rates of the ME materials can be controlled remotely by applying a magnetic field, which causes the ME materials to generate low-magnitude vibrations that hasten their degradation rates. Another concern of ME materials for medical applications is biocompatibility. Indirect cytotoxicity analyses were performed on two types of ME materials: Metglas™ 2826 MB (FeNiMoB) and iron-gallium alloy. While results indicate Metglas is not biocompatible, the degradation products of iron-gallium materials have shown no adverse effects on cell viability. Overall, these results present the possibility of using ME materials as biodegradable, magnetically-controlled active implants. © 2014 IOP Publishing Ltd.
Dynamic binary neural networks and evolutionary learning (2010)

This paper studies the dynamic binary neural network having N bits input, N bits output and ternary weighting parameters of the hidden layer. Applying feedback from the output to the input, the network can generate dynamic binary sequence. We presents a simple learning algorithm that uses the genetic algorithm and reduces the number of hidden neurons efficiently. Performing a basic numerical experiment, the algorithm efficiency is confirmed. Application to switching power converters is also discussed.
Domain E of <i>Bacillus macerans</i> cyclodextrin glucanotransferase: An independent starch‐binding domain (1995)

The starch-binding domains of glucoamylase I (SBD of GA-I) from Aspergillus awamori and of cyclodextrin glucanotransferase (domain E of CGTase) from Bacillus macerans were fused to the C-terminus of beta-galactosidase (beta-gal) The majority of the fusion proteins produced in Escherichia coli were found as inclusion bodies. Active fusion proteins were purified by partial solubilization of the inclusion bodies with 2 M urea followed by affinity chromatography. Adsorption isotherms of purified fusion proteins on corn starch and cross-linked amylose were generated. The beta-gal fusion proteins had similar affinities for cross-linked amylose and corn starch but significantly different saturation capacities on corn starch. The adsorption and elution data from the potato starch column as well as the adsorption isotherms of p-gal-domain E fusion protein (BDE109) on corn starch and cross-linked amylose demonstrated that domain E of CGTase is an independent domain, which retained its starch-binding activity when separated from the other four (A-D) domains in CGTase. (c) 1995 John Wiley & Sons Inc.
Texture and Microstructure Development of RF Sputter-Deposited Polycrystalline Lithium Transition Metal Oxide Thin Films (2003)

Deposition of polycrystalline lithium transition metal oxide thin films has been performed using radio frequency magnetron sputter deposition on indium tin oxide substrates. Different substrate temperatures, up to 500°C, were applied during deposition. The films deposited at elevated temperature exhibited a strong texture (or preferred orientation). It was found that varying the substrate temperature resulted in changing film texture. As the substrate temperature increased, the film structure changed from noncrystalline to polycrystalline with enhanced texture. The film texture and crystallography were examined using X-ray diffraction and transmission electron microscopy. The cross section and surface morphology were observed using scanning electron microscopy. The compositions of the targets and films were characterized by inductively coupled plasma spectroscopy. The deposition technique was used to prepare textured and thin films. The change of texturing can be interpreted by volume strain energy and surface energy minimization. Film texture of lithium transition metal oxide thin films can be controlled by the substrate temperature. © 2003 The Electrochemical Society. All rights reserved.
Low-Dose Metronomic Paclitaxel Chemotherapy Suppresses Breast Tumors and Metastases in Mice (2009)

This study investigated the use of low-dose metronomic (LDM) chemotherapy with paclitaxel in a highly metastatic mouse model of 4T1 breast cancers, and compared it with the maximum tolerable dose (MTD) therapy. LDM therapy displayed a stronger anti-tumor activity in suppressing primary and metastatic breast tumors with less degree of side effects, and stronger anti-angiogenic and anti-lymphangiogenic activities than MTD therapy. But MTD therapy showed stronger pro-apoptotic and anti-proliferative activities in situ. Paclitaxel therapy downregulated expression of vascular endothelial growth factor receptor-2 (VEGFR2) and up-regulated expression of thrombospondin-1. The results support the application of paclitaxel LDM therapy to treat advanced breast cancer.
Hormone Replacement Therapy and Cardiovascular Disease (2004)

Observational studies in humans and experimental studies in animals and isolated cells supported the widely held belief that hormone replacement therapy protects the cardiovascular system from disease. To nearly everyone's astonishment, the Women's Health Initiative Study and the Heart and Estrogen/Progestin Replacement Study overturned the conclusion that hormone replacement therapy protects the cardiovascular system and, in fact, supported the opposite view that such therapy may actually increase the risk of cardiovascular disease. This review addresses 2 questions: what went wrong and where do we go from here?
Percutaneous balloon-assisted thrombectomy: preliminary in vivo results with an expandable vascular sheath system. (1998)

Percutaneous transcatheter balloon-assisted embolectomy is feasible with the expandable vascular sheath system.
Microfabricated Lamb wave device based on PZT sol-gel thin film for mechanical transport of solid particles and liquids (1997)

The fabrication using silicon micromachining and characterization of an acoustic Lamb wave actuator is presented. The intended use of the device is for mass transport and sensor applications. The device consists of dual interdigitated transducers patterned on a thin-film composite membrane of silicon nitride, platinum, and a sol-gel-derived piezoelectric ceramic (PZT) thin film. The acoustic properties of the device are presented along with preliminary applications to mechanical transport and liquid delivery systems. Improved acoustic signals and improved mass transport are achieved with PZT over present Lamb wave devices utilizing ZnO or AlN as the piezoelectric transducer.