gebhart/patrepeval huggingface dataset:
Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing (2014)

We analyzed the transcriptome of Escherichia coli K-12 by strand-specific RNA sequencing at single-nucleotide resolution during steady-state (logarithmic-phase) growth and upon entry into stationary phase in glucose minimal medium. To generate high-resolution transcriptome maps, we developed an organizational schema which showed that in practice only three features are required to define operon architecture: the promoter, terminator, and deep RNA sequence read coverage. We precisely annotated 2,122 promoters and 1,774 terminators, defining 1,510 operons with an average of 1.98 genes per operon. Our analyses revealed an unprecedented view of E. coli operon architecture. A large proportion (36%) of operons are complex with internal promoters or terminators that generate multiple transcription units. For 43% of operons, we observed differential expression of polycistronic genes, despite being in the same operons, indicating that E. coli operon architecture allows fine-tuning of gene expression. We found that 276 of 370 convergent operons terminate inefficiently, generating complementary 3' transcript ends which overlap on average by 286 nucleotides, and 136 of 388 divergent operons have promoters arranged such that their 5' ends overlap on average by 168 nucleotides. We found 89 antisense transcripts of 397-nucleotide average length, 7 unannotated transcripts within intergenic regions, and 18 sense transcripts that completely overlap operons on the opposite strand. Of 519 overlapping transcripts, 75% correspond to sequences that are highly conserved in E. coli (>50 genomes). Our data extend recent studies showing unexpected transcriptome complexity in several bacteria and suggest that antisense RNA regulation is widespread. Importance: We precisely mapped the 5' and 3' ends of RNA transcripts across the E. coli K-12 genome by using a single-nucleotide analytical approach. Our resulting high-resolution transcriptome maps show that ca. one-third of E. coli operons are complex, with internal promoters and terminators generating multiple transcription units and allowing differential gene expression within these operons. We discovered extensive antisense transcription that results from more than 500 operons, which fully overlap or extensively overlap adjacent divergent or convergent operons. The genomic regions corresponding to these antisense transcripts are highly conserved in E. coli (including Shigella species), although it remains to be proven whether or not they are functional. Our observations of features unearthed by single-nucleotide transcriptome mapping suggest that deeper layers of transcriptional regulation in bacteria are likely to be revealed in the future.
<title>Pulse-length dependence of absorptance and degradation rate of fused silica at 248 nm</title> (1997)

Optical components for industrial excimer laser applications such as semiconductor lithography steppers have to withstand more than 10<SUP>10</SUP> laser pulses without suffering from significant cumulative absorption increase due to color center formation. Lithography lasers are now approaching pulse durations of 10 ns and repetition rates of 1000 Hz, a domain unexplored in previous degradation studies. With the aid of an optical pulse-extension unit and a modified laser resonator, we measured absorptance and absorption changes in Suprasil 312 UV-grade fused silica calorimetrically at pulse lengths of 7-73 ns. At 100 mJ/cm<SUP>2</SUP>, no degradation was detectable even after 500,000 pulses, but there was slight evidence of an absorption decrease due to laser cleaning. At 400 mJ/cm<SUP>2</SUP>, both absorptance and degradation rate increased towards shorter pulses and hence higher intensities, but even over the full pulse-length range, the changes remained moderate. Furthermore, degradation at 300 Hz was lower than at 150 Hz, indicating that a simultaneous bleaching effect might be involved which favors future high- repetition rate applications.
Words, concepts, or both: optimal indexing units for automated information retrieval. (1992)

What is the best way to represent the content of documents in an information retrieval system? This study compares the retrieval effectiveness of five different methods for automated (machine-assigned) indexing using three test collections. The consistently best methods are those that use indexing based on the words that occur in the available text of each document. Methods used to map text into concepts from a controlled vocabulary showed no advantage over the word-based methods. This study also looked at an approach to relevance feedback which showed benefit for both word-based and concept-based methods.
<i>GCR1</i> , the putative <i>Arabidopsis</i> G protein-coupled receptor gene is cell cycle-regulated, and its overexpression abolishes seed dormancy and shortens time to flowering (2002)

Although signaling through heterotrimeric G proteins has been extensively studied in eukaryotes, there is little information about this important signaling pathway in plants. We observed that expression of GCR1, the gene encoding the only known (but still putative) G protein-coupled receptor of Arabidopsis thaliana, is modulated during the cell cycle and during plant development. Overexpression of GCR1 in tobacco (Nicotiana tabacum) BY-2 cells caused an increase in thymidine incorporation and in the mitotic index of aphidicolin synchronized cells. Overexpression of GCR1 in Arabidopsis caused two remarkable phenotypes: seed dormancy was abolished and time to flowering was reduced. Molecular markers of these two developmental processes (phosphatase PP2A and MYB65 in germination; LFY during flowering) were up-regulated in GCR1 overexpressors. These data are consistent with the hypothesis that GCR1 may be a regulator of the cell cycle and that this regulation underlies the developmental changes observed in the GCR1 transformants.
Oncolytic parvoviruses: from basic virology to clinical applications (2015)

Accumulated evidence gathered over recent decades demonstrated that some members of the Parvoviridae family, in particular the rodent protoparvoviruses H-1PV, the minute virus of mice and LuIII have natural anticancer activity while being nonpathogenic to humans. These studies have laid the foundations for the launch of a first phase I/IIa clinical trial, in which the rat H-1 parvovirus is presently undergoing evaluation for its safety and first signs of efficacy in patients with glioblastoma multiforme. After a brief overview of the biology of parvoviruses, this review focuses on the studies which unraveled the antineoplastic properties of these agents and supported their clinical use as anticancer therapeutics. Furthermore, the development of novel parvovirus-based anticancer strategies with enhanced specificity and efficacy is discussed, in particular the development of second and third generation vectors and the combination of parvoviruses with other anticancer agents. Lastly, we address the key challenges that remain towards a more rational and efficient use of oncolytic parvoviruses in clinical settings, and discuss how a better understanding of the virus life-cycle and of the cellular factors involved in virus infection, replication and cytotoxicity may promote the further development of parvovirus-based anticancer therapies, open new prospects for treatment and hopefully improve clinical outcome.
Enhanced Biological Treatment of Leachates from Industrial Landfills (1984)

Hyde Park Landfill was used from 1953 to 1975 as a disposal site for chemi cal wastes, including chlorinated hydrocarbons. A compacted clay cover was installed in 1978 and a tile leachate collection system, in 1979. The present treatment of Hyde Park leachate by conventional activated carbon technology, although producing a suitable quality effluent, is unacceptable for economic and technical reasons. The cost forecast for purchase of carbon alone is 21 million dollars over the next ten years. In addition, carbon adsorption of compounds of interest is not efficient because of competition for adsorptive sites by less hazardous compounds. As a result, technologies were investigated which would remove these competing compounds. Biological waste treatment in a Sequencing Batch Reactor (SBR) was selected as the most cost effective alternative. Biological degradation of the lechate in the SBR was tested both with and without the addition of Occidental organism HCV. Between 85 and 95% of the total organic carbon (TOC) was removed by the SBR operating strategies investigated. Any increased TOC removal obtained from organism addition was small and will require additional research before the full potential can be evaluated. Nevertheless, use of biological waste treatment in the SBR is expected to result in substantial cost savings because of the extended life of the activated carbon beds.
TEM Study on the Evolution of Ge Nanocrystals in Si Oxide Matrix as a Function of Ge Concentration and the Si Reduction Process (2006)

Growth and evolution of germanium (Ge) nanocrystals embedded into a silicon oxide (SiO₂) system have been studied based on the Ge content of co-sputtered Ge-SiO₂ films using transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy. It was found that when the proportion of Ge relative to Ge oxide is 20%, TEM showed that annealing the samples at 800°C for 60 min resulted in the formation of a denuded region between the silicon/silicon oxide (Si/SiO₂) interface and a band of Ge nanocrystals towards the surface of the film. By introducing a 20nm thick thermal oxide barrier on top of the silicon (Si) substrate on which the film is deposited, no denuded region in the bulk of this sample is observed. It is proposed that this barrier is effective in reducing both Ge diffusion into the Si substrate and Si diffusion from the substrate into the film. Si diffusing from the Si substrate reduces the Ge oxide into Ge which can subsequently diffuse into the Si substrate. However, the oxide barrier is able to confine the Ge within the oxide matrix so that the denuded region in the bulk of the film cannot form. However the reduction in diffusion should be more significant for Ge as its diffusion coefficient is lower than Si due to its larger size. It is suggested that the denuded region consists of amorphous Ge diffusing towards the Si/SiO₂ interface. When the Ge content is increased to slightly more than 70%, TEM showed that Ge nanocrysyals formed after annealing at 800°C for only 30 min for samples with and without the oxide barrier. There is no denuded region between the Ge nanocrystals band and the Si/SiO₂ interface for both samples but it was observed that coarsening effects were more prominent in the film deposited on top of the oxide barrier. The reduction effect of Si on Ge oxide should not play a significant role in these samples as the Ge content is high.
Synthesis, Properties and Application of Nucleic Acids Containing Phosphorothiolate Linkages (2008)

A largely historical survey is presented on the development of methods for the synthesis of oligonucleotides containing either 3??-S- or 5??-S-phosphorothiolate linkages. The properties of these modifications are discussed with emphasis on their specific cleavage and the use of a metal ion specificity switch for investigating the role of metal ions in enzyme- catalysed DNA/RNA cleavage processes. Finally, the effect of the 3??-S-phosphorothiolate modification on the structure of nucleic acids is described.
Electronics and process control systems (1957)

A brief history of the development of process control and instrumentation up to existing conventional pneumatic and electronics systems is given and the use of miniaturization, graphic panels and console desks discussed. Two possible future systems of process control are described, one whereby the plant is programmed by punched card input, and the second whereby the plant performance is continuously analysed and monitored by computer. Problems concerning maintenance, safety, choice of components, and other items of importance to process control are discussed.
Clustering algorithms and validity measures (2002)

Clustering aims at discovering groups and identifying interesting distributions and patterns in data sets. Researchers have extensively studied clustering since it arises in many application domains in engineering and social sciences. In the last years the availability of huge transactional and experimental data sets and the arising requirements for data mining created needs for clustering algorithms that scale and can be applied in diverse domains. The paper surveys clustering methods and approaches available in the literature in a comparative way. It also presents the basic concepts, principles and assumptions upon which the clustering algorithms are based. Another important issue is the validity of the clustering schemes resulting from applying algorithms. This is also related to the inherent features of the data set under concern. We review and compare clustering validity measures available in the literature. Furthermore, we illustrate the issues that are under-addressed by the recent algorithms and we address new research directions.
Determination of mycotoxins by gradient high-performance liquid chromatography using an alkylphenone retention index system (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of mycotoxins by gradient high-performance liquid chromatography using an alkylphenone retention index systemDennis W. Hill, Thomas R. Kelley, Karen J. Langner, and Kevin W. MillerCite this: Anal. Chem. 1984, 56, 13, 2576–2579Publication Date (Print):November 1, 1984Publication History Published online1 May 2002Published inissue 1 November 1984https://doi.org/10.1021/ac00277a068RIGHTS & PERMISSIONSArticle Views166Altmetric-Citations31LEARN 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 InReddit PDF (505 KB) Get e-Alerts Get e-Alerts
Evidence of the production of silver nanoparticles via pretreatment of Phoma sp.3.2883 with silver nitrate (2003)

Silver nanoparticles could be used in the oil industry as an important catalyst and in the field of human medicine as a bactericide. The fungus Phoma sp3.2883 is a potential biosorbent that could be used for the production of these silver nanoparticles, and may also be useful in waste detoxification and in silver recovery programmes.
Metabolism by Rat Hepatic Microsomes of Fluorinated Ether Anesthetics Following Isoniazid Administration (1980)

The possibility that enflurane defluorination is increased following treatment with isoniazid was investigated in male Fischer 344 rats. The effects of various isoniazid dosage regimens on the hepatic microsomal defluorination rates of enflurane were compared with those of several other ether anesthetics, and the conditions for production of maximal enflurane defluorination rates were determined. Seven to ten days of treatment with 50 mg/kg/day isoniazid (Nydrazid) resulted in maximal rates of defluorination of methoxyflurane, enflurane, isoflurane, and sevoflurane with no overt sign of toxicity. Compared with saline treatment of control rats, isoniazid increased defluorination of enflurane 370 per cent, methoxyflurane 259 per cent, sevoflurane 283 per cent, and isoflurane 168 per cent. Previous studies have shown that while the enzyme inducer phenobarbital increased in vitro rates of methoxyflurane defluorination approximately 1000 per cent, the rate of enflurane defluorination remained unchanged or increased by 100 per cent at most. In this study, enhanced hepatic microsomal defluorination was not associated with an increase in cytochrome P-450 per mg protein. Anesthetic defluorination rates were not altered by treatment with chlorobutanol, the preservative contained in Nydrazid.
A platform for functional assessment of large variant libraries in mammalian cells (2017)

Sequencing-based, massively parallel genetic assays have revolutionized our ability to quantify the relationship between many genotypes and a phenotype of interest. Unfortunately, variant library expression platforms in mammalian cells are far from ideal, hindering the study of human gene variants in their physiologically relevant cellular contexts. Here, we describe a platform for phenotyping variant libraries in transfectable mammalian cell lines in two steps. First, a landing pad cell line with a genomically integrated, Tet-inducible cassette containing a Bxb1 recombination site is created. Second, a single variant from a library of transfected, promoter-less plasmids is recombined into the landing pad in each cell. Thus, every cell in the recombined pool expresses a single variant, allowing for parallel, sequencing-based assessment of variant effect. We describe a method for incorporating a single landing pad into a defined site of a cell line of interest, and show that our approach can be used generate more than 20 000 recombinant cells in a single experiment. Finally, we use our platform in combination with a sequencing-based assay to explore the N-end rule by simultaneously measuring the effects of all possible N-terminal amino acids on protein expression.
Power reduction via macroblock prioritization for power aware H.264 video applications (2008)

As the importance of multimedia applications in hand-held devices increases, the computational strain and corresponding demand for energy in such devices continues to grow. Portable multimedia devices with inherently limited energy supplies face tight energy constraints and require optimization for energy conservation. Power-aware applications give their users flexibility to prioritize and trade between performance and battery-life.
TasA-tasB, a new putative toxin-antitoxin (TA) system from Bacillus thuringiensis pGI1 plasmid is a widely distributed composite mazE-doc TA system (2006)

In this work, we showed that the pGI1 plasmid of B. thuringiensis H1.1 harbours genes resembling a toxin-antitoxin system, named tasA-tasB for thuringiensis addiction system. This system appeared to be functional but unregulated in E. coli. Bioinformatics studies showed that the tasAB system is present on plasmids or chromosomes of a large variety of microorganisms. Moreover, the association between TasA antitoxin with toxins other than TasB (and vice versa) revealed the composite and modular nature of bacterial TA systems.
Theoretical Study on Photophysical Properties of Ambipolar Spirobifluorene Derivatives as Efficient Blue-Light-Emitting Materials (2009)

The aim of this work is to provide an in-depth interpretation of the optical and electronic properties of a series of spirobifluorene derivatives. These materials show great potential for application in organic light-emitting diodes as efficient blue-light-emitting materials due to the tuning of the optical and electronic properties by the use of different electron donors (D) and electron acceptors (A). The geometric and electronic structures of the molecules in the ground state are studied with density functional theory (DFT) and ab initio HF, whereas the lowest singlet excited states are optimized by ab initio CIS. The energies of the lowest singlet excited states are calculated by employing time-dependent density functional theory (TD-DFT). The results show that the HOMOs, LUMOs, energy gaps, ionization potentials, electron affinities, reorganization energies, and exciton binding energies for these complexes are affected by different D and A moieties. Also, it has obtained that these blue-light-emitting materials have improved charge transport rate and charge transfer balance performance and can be used as efficient ambipolar-transporting materials in organic light-emitting diodes.
A new hepatocyte stimulating factor: cardiotrophin‐1 (CT‐1) (1995)

Recently, a novel cytokine, cardiotrophin-1 (CT-1), was cloned and found to induce cardiac myocyte hypertrophy in vitro. Amino acid sequence similarity showed CT-1 to be a member of the IL-6/LIF/CNTF/OSM/IL-11 cytokine family. Since all known members of the IL-6 cytokine family induce an hepatic acute phase protein (APP) gene expression, we investigated the ability of CT-1 to induce a liver acute phase response. Upon stimulation of rat hepatoma cells, CT-1 and LIF induced the strongest rat fibrinogen mRNA expression, OSM and IL-6 induced a less pronounced response. When human hepatoma cells and primary rat hepatocytes were stimulated with CT-1, the expression of human haptoglobin and rat alpha 2-macroglobulin mRNA was induced. The induction of the acute phase response was dose- and time-dependent. In this study we demonstrate that CT-1, a novel cytokine belonging to the IL-6 cytokine family, is a hepatocyte stimulating factor.
Infant acute lymphoblastic leukemia with MLL gene rearrangements: outcome following intensive chemotherapy and hematopoietic stem cell transplantation (2004)

Forty-four infants with acute lymphoblastic leukemia (ALL) characterized by MLL gene rearrangements were treated on a protocol of intensive chemotherapy followed by hematopoietic stem cell transplantation (HSCT) between November 1998 and June 2002. The remission induction rate was 91.0%, and the 3-year overall survival and event-free survival (EFS) rates, with 95% confidence intervals, were 58.2% (43.5%-72.9%) and 43.6% (28.5%-58.7%), respectively. Univariate analysis of EFS by presenting features indicated a poorer outcome in patients younger than 6 months of age with high white blood cell counts (>/= 100 x 10(9)/L; EFS rate, 9.4% versus 55.1% for all others, P = .0036) and in those with central nervous system invasion (EFS rate, 10.0% versus 56.9% for all others, P = .0073). The 3-year posttransplantation EFS rate for the 29 patients who underwent HSCT in first remission was 64.4% (46.4%-82.4%). In this subgroup, only the timing of HSCT (first remission versus others) was a significant risk factor by multivariate analysis (P < .0001). These results suggest that early introduction of HSCT, possibly with a less toxic conditioning regimen, may improve the prognosis for infants with MLL(+) ALL. Identification of subgroups or patients who respond well to intensified chemotherapy alone should have a high priority in future investigations.