gebhart/patrepeval huggingface dataset:
Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data (2013)

Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6-40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources.
Repetitive sequences in<i>Mycobacterium leprae</i>and their impact on genome plasticity (2001)

About 2% of the genome of Mycobacterium leprae is composed of repetitive DNA. There are more than 26 extinct IS elements together with four families of dispersed repeats, present in five copies or more, RLEP (37 copies), REPLEP (15 copies), LEPREP (eight copies), and LEPRPT (five copies). Although there is no sequence similarity to known transposable elements, RLEP occurs predominantly at the 3'-end of genes and, in several cases, within pseudogenes, suggesting that it was capable of dissemination. Strikingly, on comparison of the genome sequences of M. leprae and the closely related tubercle bacillus, Mycobacterium tuberculosis H37Rv, many of these repetitive sequences were found at sites of discontinuity in gene order. Evidence is presented that loss of synteny, inversion and genome downsizing may have resulted from recombination between dispersed copies of these repetitive elements.
Wavelet transform and frequency domain kurtosis: application to assessment of hearing hazard from noise exposure (2002)

Research on the effects of noise on the auditory system has shown that the frequency domain kurtosis (FDK) statistic could be a useful metric in quantifying a noise environment for hearing conservation purposes. Joint time-frequency analytical methods used in signal processing may be of use in the extraction of such information from an exposure environment characterized by nonstationary signals. This paper shows that the FDK metric can be efficiently computed by applying the wavelet transform to the analysis of an acoustic signal.
Molecular methods to study the organization of microbial communities (1995)

This review describes the potentials and limitations of different molecular techniques which are nowadays used to determine the species composition of microbial communities, and to study the spatial distribution of their inhabitants.
Steam reforming of natural gas with intergrated hydrogen separation for hydrogen production (1987)

Abstract The development of heat resistant permeation membranes has opened up new possibilities for the conversion of fossil energy resources. In steam reforming of natural gas, such membranes even permit a direct production of hydrogen at high temperatures during the conversion of feed hydrocarbons. Further gas processing, such as required for reformer gas in existing hydrogen production processes, is not necessary. Due to continuous hydrogen discharge directly in the reformer tube, the chemical equilibrium of the occurring reactions becomes displaced towards the products, resulting in more favourable process conditions and, consequently, in improved by 36% utilization of the feed hydrocarbons. At the same time, the hydrogen yield increases by 44%. The heat required, which is provided by a high temperature reactor, is 17% in excess of that in conventional plants. It can be expected that the simplified process design will produce substantial cost advantages over the existing processes for the production of hydrogen.
A Novel Nonnucleoside Analogue That Inhibits Human Immunodeficiency Virus Type 1 Isolates Resistant to Current Nonnucleoside Reverse Transcriptase Inhibitors (2006)

Nonnucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are important components of current combination therapies for human immunodeficiency virus type 1 (HIV-1) infection. However, their low genetic barriers against resistance development, cross-resistance, and serious side effects can compromise the benefits of the two current drugs in this class (efavirenz and nevirapine). In this study, we report a novel and potent NNRTI, VRX-480773, that inhibits viruses from efavirenz-resistant molecular clones and most NNRTI-resistant clinical HIV-1 isolates tested. In vitro mutation selection experiments revealed that longer times were required for viruses to develop resistance to VRX-480773 than to efavirenz. RT mutations selected by VRX-480773 after 3 months of cell culture in the presence of 1 nM VRX-480773 carried the Y181C mutation, resulting in a less-than-twofold increase in resistance to the compound. A virus containing the double mutation V106I-Y181C emerged after 4 months, causing a sixfold increase in resistance. Viruses containing additional mutations of D123G, F227L, and T369I emerged when the cultures were incubated with increasing concentrations of VRX-480773. Most of the resistant viruses selected by VRX-480773 are susceptible to efavirenz. Oral administration of VRX-480773 to dogs resulted in plasma concentrations that were significantly higher than those required for the inhibition of wild-type and mutant viruses. These results warrant further clinical development of VRX-480773 for the treatment of HIV infection in both NNRTI-naive and -experienced patients.
Temozolomide delivered by intracerebral microinfusion is safe and efficacious against malignant gliomas in rats. (2000)

Intracerebral microinfusion (ICM) is an innovative technique of delivering therapeutic agents throughout large portions of the brain that circumvents the blood-brain barrier, minimizes systemic toxicity, and provides a homogeneous distribution of the infused agent. Temozolomide is a novel methylating agent with proven efficacy against malignant gliomas (MGs) after systemic administration but with dose-limiting myelotoxicity. Because MGs rarely metastasize, systemic drug delivery is unnecessary. Therefore, we evaluated the efficacy and toxicity of ICM with temozolomide in an athymic rat model of human MGs. Treatment of rats by ICM with temozolomide 3 days after intracerebral challenge with D54 human MG xenograft increased median survival by 128% compared with rats treated by ICM with saline, by 113% compared with rats treated with i.p. saline, and by 100% compared with rats treated with i.p. temozolomide (P < 0.001). Delay of treatment until 9 days after tumor challenge still resulted in a 23% increase in median survival in rats treated by ICM of temozolomide compared with rats treated with i.p. temozolomide. In addition, overall, 21.7% of rats treated by ICM with temozolomide survived for > 100 days without clinical or histological evidence of tumor. The dose of temozolomide delivered by ICM in this study was limited only by drug solubility, and no neurological or systemic toxicity could be attributed to ICM with temozolomide. Therefore, ICM of temozolomide may offer significant advantages in the treatment of MGs.
The Recovery of Vascular Changes Following Brief Noise Exposure (1985)

Histological measures of cochlear vasculature and blood flow were examined in 20 guinea pigs. Sixteen were exposed to octave band noise at 120 dB SPL for 30 min and then permitted to survive after the exposure for 6 h, 18 h, 48 h, or 4 weeks (N = 4 in each group). Control animals were exposed to the laboratory and apparatus but not to the noise and then sacrificed after 48 h (N = 2) or 4 weeks (N = 2). Statistically significant results indicate that the noise exposure resulted in reduced RBCs in the cochlea for animals permitted to survive 6 to 18 h after the noise exposure. These changes, however, were no longer apparent in animals which were permitted to survive 48 h or 4 weeks after the noise exposure. The vascular sequelae of 30 min exposure to 120 dB octave band noise appear to recover within a few days of the exposure.
The Fungi: 1, 2, 3 … 5.1 million species? (2011)

Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.
Editing of messenger RNA precursors and of tRNAs by adenosine to inosine conversion (1999)

The double-stranded RNA-specific adenosine deaminases ADAR1 and ADAR2 convert adenosine (A) residues to inosine (I) in messenger RNA precursors (pre-mRNA). Their main physiological substrates are pre-mRNAs encoding subunits of ionotropic glutamate receptors or serotonin receptors in the brain. ADAR1 and ADAR2 have similar sequence features, including double-stranded RNA binding domains (dsRBDs) and a deaminase domain. The tRNA-specific adenosine deaminases Tad1p and Tad2p/Tad3p modify A 37 in tRNA-Ala1 of eukaryotes and the first nucleotide of the anticodon (A 34) of several bacterial and eukaryotic tRNAs, respectively. Tad1p is related to ADAR1 and ADAR2 throughout its sequence but lacks dsRBDs. Tad1p could be the ancestor of ADAR1 and ADAR2. The deaminase domains of ADAR1, ADAR2 and Tad1p are very similar and resemble the active site domains of cytosine/cytidine deaminases.
Encapsulation of crosslinked penicillin G acylase aggregates in lentikats: Evaluation of a novel biocatalyst in organic media (2004)

The encapsulation of crosslinked enzyme aggregates (CLEA) of penicillin G acylase into a very rigid polymeric matrix based on polyvinyl alcohol (LentiKats) has been used successfully to improve the inadequate mechanical properties of CLEA. This encapsulation decreased CLEA activity by only around 40%. As compensation, a significant improvement in the stability of the CLEA in the presence of organic solvents was detected. This could be related to the highly hydrophilic environment inside the LentiKats biocatalysts: Partition experiments showed that the concentration of dioxane inside LentiKats was lower than in the reaction medium. In fact, thermal stability was about the same as in the corresponding CLEA. This permitted great improvement in the reaction rate for thermodynamically controlled synthesis of a model antibiotic (using phenylacetic acid and 7-amino-deacetoxycefalosporanic acid). Even more importantly, yields could be improved by using LentiKats-encapsulated CLEA, very likely by a favorable product/substrate partition. Thus, this very simple technique not only provides an efficient technique for solving the mechanical stability problem associated with CLEA, but also greatly improves the behavior of CLEA in organic media.
Promoting Native Vegetation and Diversity in Exotic Annual Grass Infestations (2009)

Exotic plant invasions are especially problematic because reestablishment of native perennial vegetation is rarely successful. It may be more appropriate to treat exotic plant infestations that still have some remaining native vegetation. We evaluated this restoration strategy by measuring the effects of spring burning, fall burning, fall applied imazapic, spring burning with fall applied imazapic, and fall burning with fall applied imazapic on the exotic annual grass, medusahead ( Taeniatherum caput‐medusae (L.) Nevski), and native vegetation at six sites in Oregon for 2 years post‐treatment. Medusahead infestations included in this study had some residual native perennial bunchgrasses and forbs. Burning followed by imazapic application provided the best control of medusahead and resulted in the greatest increases in native perennial vegetation. However, imazapic application decreased native annual forb cover the first year post‐treatment and density the first and second year post‐treatment. The spring burn followed by imazapic application produced an almost 2‐fold increase in plant species diversity compared to the control. The fall burn followed by imazapic application also increased diversity compared to the control. Results of this study indicate that native plants can be promoted in medusahead invasions; however, responses vary by plant functional group and treatment. Our results compared to previous research suggest that restoration of plant communities invaded by exotic annual grass may be more successful if efforts focus on areas with some residual native perennial vegetation. Thus, invasive plant infestations with some native vegetation remaining should receive priority for restoration efforts over near monocultures of invasive plant species.
A New Direct Anonymous Attestation Scheme from Bilinear Maps (2008)

The direct anonymous attestation scheme was proposed by Brickell, Jan Camenisch, Liqun Chen and was adopted by the trusted computing group in its specifications for trusted computing platforms. In this paper, We propose a new direct anonymous scheme from the bilinear maps based on the decisional Diffie-Hellman assumption and q-SDH assumption. The length of private keys and signatures in our scheme are much shorter than the lengths in the original DAA scheme, and has better computational performance. We analyze the security of the proposed scheme, it shows that the scheme meets the security requirements of unforgeability,variable anonymity and unlinkability. Our scheme gives a practical solution for ECC-based TPM on protecting the privacy of the TPM.
Regulatory Response to Carbon Starvation in Caulobacter crescentus (2011)

Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the regulatory response of C. crescentus to carbon starvation, based on combined high-throughput proteome and transcriptome analyses. Our results identify cell cycle changes in gene expression in response to carbon starvation that involve the prominent role of the FixK FNR/CAP family transcription factor and the CtrA cell cycle regulator. Notably, the SigT ECF sigma factor mediates the carbon starvation-induced degradation of CtrA, while activating a core set of general starvation-stress genes that respond to carbon starvation, osmotic stress, and exposure to heavy metals. Comparison of the response of swarmer cells and stalked cells to carbon starvation revealed four groups of genes that exhibit different expression profiles. Also, cell pole morphogenesis and initiation of chromosome replication normally occurring at the swarmer-to-stalked cell transition are uncoupled in carbon-starved cells.
Influence of structure on the behavior of flavonoids in capillary electrophoresis (1994)

In an attempt to elucidate the relation between structure and electrophoretic behavior, the effect of pH, surfactant and buffer on electrophoretic mobilities and resolution of several flavonoids, differing in structure, has been investigated. Ring-B substitution and the presence of a free hydroxy group at C7 of ring A play an important role, whereas O-methoxylation is less significant. Glycosylation also contributes in determining different degrees of complexation with borate, thus affecting the mobilities.
RF front-end of direct conversion receiver RFIC for cdma-2000 (2004)

We report on the front-end of a highly integrated dual-band direct-conversion receiver IC for cdma-2000 mobile handset applications. The RF front-end included a CELL-band low-noise amplifier (LNA), dual-band direct-conversion quadrature I/Q down-converters, and a local-oscillator (LO) signal generation circuit. At 2.7 V, the LNA had a noise figure of 1.2 dB and input third-order intermodulation product (IIP3) of 9 dBm. I/Q down-converters had a noise figure of 4-5 dB and IIP3 of 4-5 dBm and IIP2 of 55 dBm. An on-chip phase-locked loop and external voltage-controlled oscillator generated the LO signal. The receiver RFIC was implemented in a 0.35-/spl mu/m SiGe BiCMOS process and meets or exceeds all cdma-2000 requirements when tested individually or on a handset.
Synthesis, characterization, and fabrication of silicon carbide structural ceramics. [SiC-TiC-BN] (1982)

Five processes of SiC powder synthesis were investigated: chemical vapor decomposition, high-temperature rotary-furnace reactions, gel synthesis of precursors followed by carbothermic reduction, pyrolysis of polymeric precursors, and the Acheson process. Exploratory powder synthesis experiments were conducted on the gel process involving gelation of colloidal silica and petroleum pitch in toluene, or polymerization of methyltrimethoxysilane and resin in alcohol. The ..beta..-SiC powders synthesized by these gel processes have specific surface areas (SSA) exceeding 20 m/sup 2//g and round or polyhedral particle shape. These materials have excellent pressure sintering capability. SiC powder made by the rotary-furnace process consists of fine ..beta..-SiC particles with a round morphology and about 10 m/sup 2//g SSA. The rotary-furnace SiC powders with BN dopants were hot pressed to 95% dense. A commercial polycarbosilane prepared from dechlorination and polymerization reactions of vinyl and chloromethyl silanes was pyrolyzed and hot pressed without BN to 79% dense. In terms of pressureless sintering, the best result (96+% dense) is obtained with the Starck-SiC powder by doping with 0.8 wt % B and 2 wt % phenolic resin and sintering under argon in a graphite furnace for 2 h at 2050/sup 0/C. An SiC-TiC-BN composite was hot pressed to 97+% dense withmore » an indentation toughness nearly double that of sintered ..beta..-SiC. 10 figures, 6 tables.« less
One-dimensional topography underlies three-dimensional fibrillar cell migration (2009)

Current concepts of cell migration were established in regular two-dimensional (2D) cell culture, but the roles of topography are poorly understood for cells migrating in an oriented 3D fibrillar extracellular matrix (ECM). We use a novel micropatterning technique termed microphotopatterning (microPP) to identify functions for 1D fibrillar patterns in 3D cell migration. In striking contrast to 2D, cell migration in both 1D and 3D is rapid, uniaxial, independent of ECM ligand density, and dependent on myosin II contractility and microtubules (MTs). 1D and 3D migration are also characterized by an anterior MT bundle with a posterior centrosome. We propose that cells migrate rapidly through 3D fibrillar matrices by a 1D migratory mechanism not mimicked by 2D matrices.
Concise, Improved Procedure for the Synthesis of Brassinolide and Some Novel Side-Chain Analogues (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTConcise, Improved Procedure for the Synthesis of Brassinolide and Some Novel Side-Chain AnaloguesThomas G. Back, Denise L. Baron, Weide Luo, and Suanne K. NakajimaView Author Information Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4 Cite this: J. Org. Chem. 1997, 62, 4, 1179–1182Publication Date (Web):February 21, 1997Publication History Received30 September 1996Published online21 February 1997Published inissue 1 February 1997https://pubs.acs.org/doi/10.1021/jo961854yhttps://doi.org/10.1021/jo961854ybrief-reportACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views404Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Anions,Mixtures,Plants,Transfer reactions Get e-Alerts
Engineering Properties of Alkali-Activated Fly Ash Concrete (2006)

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Una propiedad del número de Todd de las matrices normales obtenidas en la compensación por el método de los mínimos cuadrados (1977)

The purpose of this study was to provide a thorough description of lumbar surface integrated electromyography (EMG) in pain-free normals during a standardized assessment protocol of static isometric and unresisted dynamic tasks. It has been proposed that in pain-free normals, symmetrical tasks that bend the trunk forward or extend the trunk backward produce symmetrical paraspinal EMG activity, and asymmetrical tasks that rotate or laterally bend the trunk produce asymmetrical paraspinal EMG activity. In addition, it has been observed that lumbar EMG assessment during static tasks has been more consistent than tasks involving dynamic activities. Twenty-eight pain-free normals were assessed during symmetrical and asymmetrical tasks in both static and dynamic activities in a counterbalanced manner. The assessment of paraspinal EMG patterns was conducted while subjects were secured in a triaxial dynamometer, which provided standardization of body position and concurrent measurement of torque, range of motion, and velocity. The results provided experimental evidence for the above-stated propositions. An implication derived from this research is that clinicians may be better served utilizing local norms when using EMG for classification purposes.
Bilateral deep brain stimulation of the globus pallidus internus in tardive dystonia (2008)

Tardive dystonia is a disabling movement disorder as a consequence of exposure to neuroleptic drugs. We followed 6 patients with medically refractory tardive dystonia treated by bilateral globus pallidus internus (GPi) deep brain stimulation (DBS) for 21 +/- 18 months. At last follow-up, the Burke-Fahn-Marsden Dystonia Rating Scale (BFMDRS) motor score improved by 86% +/- 14%, and the BFMDRS disability score improved by 80% +/- 12%. Bilateral GPi-DBS is a beneficial therapeutic option for the long-term relief of tardive dystonia.