gebhart/patrepeval huggingface dataset:
A method for allelic replacement in<i>Francisella tularensis</i> (2003)

A vector for mutagenesis of Francisella tularensis was constructed based on the pUC19 plasmid. By inserting the sacB gene of Bacillus subtilis, oriT of plasmid RP4, and a chloramphenicol resistance gene of Shigella flexneri, a vector, pPV, was obtained that allowed specific mutagenesis. A protocol was developed that allowed introduction of the vector into the live vaccine strain, LVS, of F. tularensis by conjugation. As a proof of principle, we aimed to develop a specific mutant defective in expression of a 23-kDa protein (iglC) that we previously have shown to be prominently upregulated during intracellular growth of F. tularensis. A plasmid designated pPV-DeltaiglC was developed that contained only the regions flanking the encoding gene, iglC. By a double crossover event, the chromosomal iglC gene was deleted. However, the resulting strain, denoted DeltaiglC1, still had an intact iglC gene. Southern blot analysis verified that LVS harbors two copies for the iglC gene. The mutagenesis was therefore repeated and a mutant defective in both iglC alleles, designated DeltaiglC1+2, was obtained. The DeltaiglC1+2 strain, in contrast to DeltaiglC1, was shown to display impaired intracellular macrophage growth and to be attenuated for virulence in mice. The developed genetic system has the potential to provide a tool to elucidate virulence mechanisms of F. tularensis and the specific F. tularensis mutant illustrates the critical role of the 23-kDa protein, iglC, for the virulence of F. tularensis LVS.
高新技术发展的政府“种子基金”构架—重庆高新技术产业发展的理论研究 (2002)

高新技术产业化发展是经济增长的火车头,发展高新技术产业已经成为当今世界经济发展的主旋律.而重庆强位弱势的高新技术产业,究其原因,其中之一在于麦克米伦缺口壁垒现象.为把重庆建设成为长江上游最大的高新技术产业基地,抢占高新技术产业发展制高点,构架发展重庆高新技术产业的政府种子基金,显得尤为重要.政府种子基金的主要形式有:政府担保、政府补贴、政府投资基金等.
[Scavenging effects of Astragalus and Gynostemma pentaphyllum with its product on O2-. and .OH]. (1999)

The scavenging effects of Astragalus and Gynostemma pentaphyllum with its products on O2-. (produced by the autoxidation of pyrogallol) and .OH (generated from the Fenton reaction) were investigated by electrochemical method. The results showed that they could scavenge the active oxygen free radicals effectively, however, their scavenge ability was different for O2-. and .OH. The inhibitory effect of Ginsenoside Rb1 and Astragaloside IV on O2-. and .OH was the most strongest. Their IC50 values were calculated respectively. The scavenging ability of Astragalus samples on O2-. was in the order of the following: astragaloside IV > crude radix astragali > mongolia radix astragali > hebei radix astragali > radix astragali > radix astragali mixfry with honey; and the scavenging effect on .OH was: astragaloside IV > hebei radix astragali > radix astragali mix-fry with honey > radix astragali > crude radix astragali > mongolia radix astragali. The scavenging activity of gynostemma samples on O2-. was: ginsenoside Rb1 > gynostemma jujube tea > tabellae Jiaogulanosidi > anguo market gynostemma > hebei qingxian gynostemma; while on .OH, the inhibitory ability was: ginsenoside Rb1 > gynostemma jujube tea > anguo market gynostemma > hebei qingxian gynostemma > tabellae Jiaogulanosidi.
Oncolytic Vaccinia Virotherapy of Anaplastic Thyroid Cancer <i>in Vivo</i> (2008)

GLV-1h68 efficiently infects, expresses transgenes within, and inhibits the growth of ATC in vivo. These promising findings support future clinical trials for patients with ATC.
Designing Image Compression Algorithms for Massively Parallel Processors (2016)

V teto praci se zabývam paralelnim navrhem softwarove obrazove a video komprese a způsoby implementaci, ktere vedou k výkonu, který je potřebný pro vizualni aplikace pracujici s vysokou kvalitou obrazu. Soustřeďuji se na využiti paralelniho komoditniho hardware, jako jsou napřiklad soucasne CPU a GPU, pro ucely komprese. Aby bylo možne využit plneho potencialu těchto paralelnich procesorů je nezbytne, aby kompresni algoritmy byly paralelni. Řada kompresnich algoritmů a kompresnich kroků uvnitř těchto algoritmu je dnes vsak veskrze serialni. V praci proto zkoumam možnosti reformulace nebo změny v navrhu kompresnich algoritmů tak, aby bylo možne vyžit potencialu paralelnich komoditnich procesorů a dosahnout tak rychle softwarove komprese. Jednotlive kroky komprese rozděluji do tři kategorii: ty ktere jsou inherentně paralelni; ty ktere lze přeformulovat tak, aby vhodne pro paralelni zpracovani; a ty, ktere jsou inherentně serialni. V praci se zabývam reformulaci kompresnich algoritmů a optimalizaci serialnich algoritmů tak, aby využili co nejvice z dostupných paralelnich zdrojů. Za ucelem popisu možnosti paralelizace algoritmů rovněž srovnavam různe paralelni architektury využivane výrobci CPU a GPU. V teto praci demonstruji, že moderni paralelni komoditni architektury mohou být použity pro řadu praktických aplikaci v oblasti komprese v oblasti digitalniho videa a obrazu. Efektivni paralelni kompresni algoritmy urychli vývoj obrazove komprese, což povede k rychlejsimu vývoji v obrazove kvalitě. To v zasadě povede k věrnějsim dojmům z videa a obrazu.
Establishment and characterization of a human primary prostate carcinoma cell line, HH870 (2004)

We report the successful establishment and characterization of a new long-term primary human prostate tumor cell line HH870.
Development and potential of genetically engineered oilseeds (2005)

Oilseed crops are major sources of oils for human nutrition, and an increasing proportion is also being utilized for industrial purposes. Recent advances in our understanding of the basic biochemistry of seed oil biosynthesis, coupled with identification of genes for oilseed modification, have set the stage for the genetic engineering of oilseed crops that produce ‘designer’ plant seed oils tailored for specific applications. In this review we provide an overview of seed oil biosynthesis and highlight the enzymatic steps that have already been targeted for genetic manipulation, with the end goal of producing seed oils containing desired amounts of fatty acid components. Furthermore, we describe the identification of genes from various wild plant species that are capable of producing structurally diverse fatty acids, and how these advances open the door to the production of entirely novel oils in conventional oilseed crops. Transgenic oilseeds producing high amounts of these novel fatty acids represent renewable sources of raw materials that may compete with, and eventually replace, some petrochemicals that are derived from non-renewable crude oil.
Chemical Constituents from <i>Alnus formosana</i> Burk. II. Polar Constituents from the Leaves (2006)

This study was aimed to explore the n-BuOH soluble constituents of the leaves of Alnus formosana Burk. A total of 13 compounds were isolated and characterized. Of these, 2″'-cinnamoyloregonin is a new diaryl heptanoid glycoside. Ten of the remaining twelve known compounds, i.e. platyphylloside, aceroside VII, myzodendrone, quercetin, kaempferol-3-O-rhamnoside, quercetin-3-O-rhamnoside, quercetin-3-O-glucoside, rhamnetin-3-O-rhamnoside, inositol, and shikimic acid, are reported for the first time for an Alnus species. The structures were characterized by spectral analysis.
Papillomavirus E7 protein binding to the retinoblastoma protein is not required for viral induction of warts (1993)

Human papillomaviruses (HPVs) are the etiologic agents responsible for benign epithelial proliferative disorders including genital warts and are a contributory factor in the pathogenesis of cervical cancer. HPVs demonstrate strict species and cell-type specificity, which is manifested by the inability of these viruses to induce disease in any species other than humans. The natural history of HPV infection in humans is closely mimicked by cottontail rabbit papillomavirus (CRPV) infection in domestic laboratory rabbits. The CRPV E7 gene is known to play an essential role in virus-mediated induction of papillomas. We now show by mutational analysis that the CRPV E7 protein's biochemical and biological properties, including binding to the retinoblastoma suppressor protein (pRB), transcription factor E2F transactivation of the adenovirus E2 promoter, disruption of pRB-E2F complexes, and cellular transformation as measured by growth in soft agar, mimic those of the HPV E7 protein. Intradermal injection of CRPV DNA lacking E7 gene sequences critical for the binding of the CRPV E7 protein to pRB induced papillomas in rabbits. These studies indicate that E7 protein binding to pRB is not required in the molecular pathogenesis of virally induced warts and suggest that other properties intrinsic to the E7 protein are necessary for papilloma formation.
Wavefront diffusion and LMSR: algorithms for dynamic repartitioning of adaptive meshes (2001)

Current multilevel repartitioning schemes tend to perform well on certain types of problems while obtaining worse results for other types of problems. We present two new multilevel algorithms for repartitioning adaptive meshes that improve the performance of multilevel schemes for the types of problems that current schemes perform poorly while maintaining similar or better results for those problems that current schemes perform well. Specifically, we present a new scratch-remap scheme called Locally-matched Multilevel Scratch-remap (or simply LMSR) for repartitioning of adaptive meshes. LMSR tries to compute a high-quality partitioning that has a large amount of overlap with the original partitioning. We show that LMSR generally decreases the data redistribution costs required to balance the load compared to current scratch-remap schemes. We present a new diffusion-based scheme that we refer to as Wavefront Diffusion. In Wavefront Diffusion, the flow of vertices moves in a wavefront from overweight to underweight subdomains. We show that Wavefront Diffusion obtains significantly lower data redistribution costs while maintaining similar or better edge-cut results compared to existing diffusion algorithms. We also compare Wavefront Diffusion with LMSR and show that these provide a trade-off between edge-cut and data redistribution costs for a wide range of problems. Our experimental results on a Gray T3E, an IBM SP2, and a cluster of Pentium Pro workstations show that both schemes are fast and scalable. For example, both are capable of repartitioning a seven million vertex graph in under three seconds on 128 processors of a Gray T3E. Our schemes obtained relative speedups of between nine and 12 when the number of processors was increased by a factor of 16 on a Gray T3E.
Effectiveness of Stepwise Current Wave Form in ULSI Copper Electroplating. (2002)

Copper electroplating is greatly interested in ULSI technology because of copper damascene process. We have already reported that void-free copper fill can be achieved by the selection of proper additives. However, inclusion of additives in copper deposit may cause deposit deterioration. A possibility of copper filling by the wave form control was examined using additive free bath. The void-free filling can be achieved by current density in stepwise current wave form by changing from lower to higher current.
The KAP parallelizer for DEC Fortran and DEC C programs (1994)

Associates, Inc. (KAI) is used on Digital Alpha systems to increase the performance of DEC Fortran and DEC C programs. KAP accomplishes this by restructuring fragments of code that are not efficient for the Alpha architecture. Essentially a superoptimizer, KAP performs optimizations at the source code level that augment those performed by the DEC Fortran or DEC C compilers.1 To enhance the performance of DEC Fortran and DEC C programs on Alpha systems, KAI engineers selected two challenging aspects of the Alpha architecture as KAP targets: symmetric multiprocessing (SMP) and cache memory. An additional design goal was to assist the compiler in optimizing source code for the reduced instruction set computer (RISC) instruction processing pipeline and multiple functional units. This paper discusses how the KAP preprocessor design was adapted to parallelize programs for SMP systems running under the DEC OSF/1 version 3.0 operating system. This version of the DEC OSF/1 system contains the DECthreads product, Digital’s POSIX-compliant multithreading library. The first part of the paper describes the process of mapping parallel programs to DECthreads. The paper then discusses the key techniques used in the KAP design. Finally, the paper presents examples of how KAP performs on actual code and mentions some remaining challenges. Readers with a compiler background may wish to explore Optimizing Supercompilers for Supercomputers for more details on KAP’s techniques.2 In this paper, the term directive is used interchangeably to mean directive, when referring to DEC Fortran programs, and pragma, when referring to DEC C programs. The term processor generally represents the system component used in parallel processing. In discussions in which it is significant to distinguish the operating system component used for parallel processing, the term thread is used.
SRAM Assist Techniques for Operation in a Wide Voltage Range in 28-nm CMOS (2012)

Reducing static random-access memory (SRAM) operational voltage (Vmin) can greatly improve energy efficiency, yet SRAM Vmin does not scale with technology due to increased process variability. Assist techniques have been shown to improve the operation of SRAM, but previous investigations of assist techniques at design time have either relied on static metrics that do not account for important transient effects or make specific assumptions about failure distributions. This paper uses importance sampling of dynamic failure metrics to quantify and analyze the effect of different assist techniques, array organization, and timing on Vmin at design time. This approach demonstrates that the most effective technique for reducing SRAM Vmin is the negative bitline write assist, resulting in a Vmin of 600 mV for a 28-nm LP process in the typical corner.
Glucose Variability: Timing, Risk Analysis, and Relationship to Hypoglycemia in Diabetes (2016)

Glucose control, glucose variability (GV), and risk for hypoglycemia are intimately related, and it is now evident that GV is important in both the physiology and pathophysiology of diabetes. However, its quantitative assessment is complex because blood glucose (BG) fluctuations are characterized by both amplitude and timing. Additional numerical complications arise from the asymmetry of the BG scale. In this Perspective, we focus on the acute manifestations of GV, particularly on hypoglycemia, and review measures assessing the amplitude of GV from routine self-monitored BG data, as well as its timing from continuous glucose monitoring (CGM) data. With availability of CGM, the latter is not only possible but also a requirement-we can now assess rapid glucose fluctuations in real time and relate their speed and magnitude to clinically relevant outcomes. Our primary message is that diabetes control is all about optimization and balance between two key markers-frequency of hypoglycemia and HbA1c reflecting average BG and primarily driven by the extent of hyperglycemia. GV is a primary barrier to this optimization, including to automated technologies such as the "artificial pancreas." Thus, it is time to standardize GV measurement and thereby streamline the assessment of its two most important components-amplitude and timing.
Role of protein kinase C in the phosphorylation of cardiac myosin light chain 2 (1993)

The role of protein kinase C (PKC) in the phosphorylation of myosin light chain 2 (MLC2) in adult rat heart cells has been investigated. PKC-mediated phosphorylation of MLC2 in adult rat cardiac myofibrils in vitro occurs with a stoichiometry (0.7 mol of phosphate/mol of protein) similar to that mediated by myosin light chain kinase (MLCK). Two-dimensional tryptic phosphopeptide mapping of MLC2 following phosphorylation by PKC or MLCK in vitro yields the same major phosphopeptides for each protein kinase. These sites are also 32P-labelled in situ when isolated cardiomyocytes are incubated with [32P]P(i). 32P labelling of MLC2 in cardiomyocytes is increased by 5-fold in 10 min upon incubation with the phosphatase inhibitor calyculin A, demonstrating the existence of a rapidly turning over component of MLC2 phosphorylation in these cells. 32P label is completely removed from MLC2 when myocytes are exposed to 2,3-butanedione monoxime, an inhibitor of cardiac contraction known to desensitize the myofilaments to activation by Ca2+. 32P labelling of MLC2 is also decreased by 50-100% following exposure to the PKC-selective inhibitors calphostin C and chelerythrine, suggesting that PKC, and not MLCK, is primarily responsible for incorporation of rapidly turning over phosphate into MLC2 in situ. Taken together, these data implicate PKC in the phosphorylation of MLC2 in heart cells and support the hypothesis that phosphorylation of cardiac MLC2 has a role in determining myofibrillar Ca2+ sensitivity.
Optimal Frequency-Hopping Sequences Via Cyclotomy (2005)

Using cyclotomic numbers, a simple construction is presented for frequency-hopping (FH) sequences having optimal autocorrelation with respect to the well-known Lempel-Greenberger bound. Some optimal families of FH sequences are constructed. The simplicity of this technique makes it attractive for practical use.
Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure (2005)

Previously, we observed that without using prior information about individual sampling locations, a clustering algorithm applied to multilocus genotypes from worldwide human populations produced genetic clusters largely coincident with major geographic regions. It has been argued, however, that the degree of clustering is diminished by use of samples with greater uniformity in geographic distribution, and that the clusters we identified were a consequence of uneven sampling along genetic clines. Expanding our earlier dataset from 377 to 993 markers, we systematically examine the influence of several study design variables--sample size, number of loci, number of clusters, assumptions about correlations in allele frequencies across populations, and the geographic dispersion of the sample--on the "clusteredness" of individuals. With all other variables held constant, geographic dispersion is seen to have comparatively little effect on the degree of clustering. Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side. Thus, analysis of the 993-locus dataset corroborates our earlier results: if enough markers are used with a sufficiently large worldwide sample, individuals can be partitioned into genetic clusters that match major geographic subdivisions of the globe, with some individuals from intermediate geographic locations having mixed membership in the clusters that correspond to neighboring regions.
Stokes shift spectroscopy highlights differences of cancerous and normal human tissues (2012)

The Stokes shift spectroscopy (S3) offers a simpler and better way to recognize spectral fingerprints of fluorophores in complex mixtures. The efficiency of S3 for cancer detection in human tissue was investigated systematically. The alterations of Stokes shift spectra (S3) between cancerous and normal tissues are due to the changes of key fluorophores, e.g., tryptophan and collagen, and can be highlighted using optimized wavelength shift interval. To our knowledge, this is the first time to explicitly disclose how and why S3 is superior in comparison with other conventional spectroscopic techniques.
Magnetic Properties of Ferromagnetic Thin Films Prepared by Ion Plating (1977)

Thin films of Fe, Co and their alloys were prepared by ion plating. Metals were evaporated in the argon gas atmosphere of about 0.01 Torr, by applying a dc electric field of 2 kV/15 cm between the substrate and the evaporation source. Since evaporated metal atoms, which were given large kinetic energies by the gas plasma, impinged on the surface of the substrate, a strong adhesion between the ferromagnetic thin films and the substrate could be obtained. Due to the granular structure of the thin film, a higher coercive force and the squareness ratio could be obtained: i.e. by changing the Ar gas pressure, the coercive force and the squareness ratio could be controlled up to 500 Oe and 0.6, respectively, and also they were controlled by choosing the constituents of the mother alloys.
The effects of diets containing raw soya-bean flour on the vitamin B<sub>12</sub> status of rats (1973)

1. There were statistically-significant relationships between the concentrations of vitamin B 12 in the livers of rats and their urinary excretion of methylmalonic acid, both before and after the intraperitoneal injection of sodium propionate. 2. The effects of diets based on raw and heated soya-bean flour (SBF) on the growth rates, urinary excretion of methylmalonate and hepatic vitamin B 12 were compared in normal and vitamin B 12 -depleted rats. 3. When female weanling vitamin B 12 -deficient rats were put on to the raw SBF diet they lost weight and became moribund after 3 weeks, even when the diet was supplemented with vitamin B 12 . Male adult vitamin B 12 -deficient rats lost weight but showed no other signs of severe vitamin B 12 deficiency. 4. Stock weanling male rats were fed on raw SBF diets with or without added vitamin B 12 . The diets were given alone and supplemented with either methionine or a mixture of methionine, valine, threonine and tyrosine. The rats still did not grow as well as those fed on diets containing heated SBF. However, there was some evidence of increased methylmalonate excretion and lower hepatic concentrations of vitamin B 12 in the rats fed on the raw SBF diets.
Smoothing of Si Trench Sidewall Surface by Chemical Dry Etching and Sacrificial Oxidation (1998)

By combining the effects of chemical dry etching (CDE) and sacrificial oxidation, a smooth trench sidewall surface with a root-mean-square (Rms) roughness of less than 1 nm was obtained. The possibility of obtaining a smooth surface such as that of a planar metal-oxide-semiconductor (MOS) by increasing both the CDE etching time and the oxide thickness of sacrificial oxidation appears likely.
Preliminary design of rowing simulator for in-door skill training (2008)

In this paper we report on the preliminary design of a rowing simulator to be integrated in a VR sport training system for rowing. The proposed simulator aims at bringing in an indoor location the specifc features and situations of outdoor rowing, by means of an enhanced Virtual Environment (VE) tha
Radiation Dermatitis: Recognition, Prevention, and Management. (2017)

Radiation therapy (RT) is a frequently used modality for cancer treatment. Acute and/or chronic skin changes may occur and carry risk of influencing quality of life during and after completion of RT. Radiation reactions may lead to delays in treatment, diminished cosmesis, and functional deficits. Lifestyle factors, treatment modalities, topical agents, and, in some cases, wound dressings may be utilized to help prevent or ameliorate radiation-induced skin reactions. While rigorous evidence supporting specific interventions may be lacking or contradictory, this article summarizes the current knowledge of the etiology, manifestations, and interventions available for prevention and management of radiation dermatitis. Further well-designed studies are needed to confirm the efficacy of current recommendations and facilitate development of novel strategies for optimal care of patients with radiation dermatitis.
Improved Synthesis of 2,2‘-Bipyrimidine (2002)

A high-yield synthesis was developed for the preparation of 2,2'-bipyrimidine (1) using the Ullmann coupling of 2-iodopyrimidine. The new procedure was also used for the preparation of 4,4',6,6'-tetramethyl-2,2'-bipyrimidine (2) and 5,5'-dibromo-2,2'-bipyrimidine (3).