gebhart/patrepeval huggingface dataset:
Identification of novel stage‐specific genetic requirements through whole genome transcription profiling of <i>Vibrio cholerae</i> biofilm development (2005)

Bacterial biofilm formation has been described as a developmental process. This process may be divided into three stages: the planktonic stage, the monolayer stage and the biofilm stage. Bacteria in the planktonic stage are not attached to each other or to a surface; bacteria in the monolayer stage are attached to surfaces as single cells; and bacteria in the biofilm stage are attached to surfaces as cellular aggregates. In a study limited to the Vibrio cholerae flaA, mshA and vps genes, we previously demonstrated that transcription in monolayer cells is distinct from that in biofilm cells and that the genetic requirements of monolayer formation are distinct from those of biofilm formation. In this work, we sought to identify additional stage-specific genetic requirements through microarray analysis of the V. cholerae transcriptome during biofilm development. These studies demonstrated unique patterns of transcription in the planktonic, monolayer and biofilm stages of biofilm development. Based on our microarray results, we selected cheY-3 as well as two previously uncharacterized genes, bap1 and leuO, for targeted mutation. The DeltacheY-3 mutant displayed a defect in monolayer but not biofilm formation, suggesting that chemotaxis plays a stage-specific role in formation of the V. cholerae monolayer. Mutants carrying deletions in bap1 and leuO formed monolayers that were indistinguishable from those formed by wild-type V. cholerae. In contrast, these mutants displayed greatly decreased biofilm accumulation. Our microarray analyses document modulation of the transcriptome of V. cholerae as it progresses through the stages in biofilm development. These studies demonstrate that microarray analysis of the transcriptome of biofilm development may greatly accelerate the discovery of novel targets for stage-specific inhibition of biofilm development.
Degradations due to stimulated Brillouin scattering in multigigabit intensity-modulated fiber-optic systems (1993)

The stimulated Brillouin scattering (SBS) process limits the maximum power that can be transmitted in low-loss optical fibers in multigigabit fiber optic systems. It is shown that recently observed large optical fluctuations resulting from SBS degrade the signal-to-noise ratio and consequently the system bit error rate. Since SBS has potentially the lowest power threshold of all fiber nonlinearities: it is critical that it be addressed. It is shown that the SBS threshold can be increased by providing a low frequency sine wave dither to the laser pre-bias current. It is found that a modulation index as low as 2% can quadruple the SBS threshold. Measurements with a 1.5- mu m externally modulated laser at 2.5 Gb/s indicate that this dither in no way degrades the performance in the presence of chromatic dispersion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cathode preparation method for molten carbonate fuel cell (1982)

A method of preparing a porous cathode structure for use in a molten carbonate fuel cell begins by providing a porous integral plaque of sintered nickel oxide particles. The nickel oxide plaque can be obtained by oxidizing a sintered plaque of nickel metal or by compacting and sintering finely divided nickel oxide particles to the desired pore structure. The porous sintered nickel oxide plaque is contacted with a lithium salt for a sufficient time to lithiate the nickel oxide structure and thus enhance its electronic conductivity. The lithiation can be carried out either within an operating fuel cell or prior to assembling the plaque as a cathode within the fuel cell.
Fine-tuning of the <i>Escherichia coli</i> σ<sup>E</sup> envelope stress response relies on multiple mechanisms to inhibit signal-independent proteolysis of the transmembrane anti-sigma factor, RseA (2004)

Proteolytic cascades are widely implicated in signaling between cellular compartments. In Escherichia coli, accumulation of unassembled outer membrane porins (OMPs) in the envelope leads to expression of sigma(E)-dependent genes in the cytoplasmic cellular compartment. A proteolytic cascade conveys the OMP signal by regulated proteolysis of RseA, a membrane-spanning anti-sigma factor whose cytoplasmic domain inhibits sigma(E)-dependent transcription. Upon activation by OMP C termini, the membrane localized DegS protease cleaves RseA in its periplasmic domain, the membrane-embedded protease RseP (YaeL) cleaves RseA near the inner membrane, and the released cytoplasmic RseA fragment is further degraded. Initiation of RseA degradation by activated DegS makes the system sensitive to a wide range of OMP concentrations and unresponsive to variations in the levels of DegS and RseP proteases. These features rely on the inability of RseP to cleave intact RseA. In the present report, we demonstrate that RseB, which binds to the periplasmic face of RseA, and DegS each independently inhibits RseP cleavage of intact RseA. Thus, the function of RseB, widely conserved among bacteria using the sigma(E) pathway, and the second role of DegS (in addition to RseA proteolysis initiation) is to improve the performance characteristics of this signal transduction system.
X-ray Phase Measurements with Talbot Interferometry and Its Applications (2010)

We report three applications of X‐ray grating interferometry, which employs X‐ray transmission gratings, to X‐ray phase imaging and phase tomography for weakly absorbing objects. The fusion with a normal X‐ray imaging microscope enabled phase‐sensitive microscopic observation. The operation with a white synchrotron light enabled high‐speed X‐ray imaging and furthermore four‐dimensional phase tomography. Finally, the development of a practical phase imaging technique using a conventional X‐ray generator is reported for future clinical applications.
RELIGIONS OF WESTERN ANTIQUITY (1984)

RELIGIONS OF WESTERN ANTIQUITY The Gospel According to Matthew. By Francis Wright Beare. Harper & Row, 1981. 550 pages. $29.95. Matthew: A Commentary on His Literary and Theological Art. By Robert H. Cundry. Eeerdmans, 1982. 652 pages. $24.95. Dennis E. Smith Dennis E. Smith Oklahoma State University Search for other works by this author on: Oxford Academic Google Scholar Journal of the American Academy of Religion, Volume LII, Issue 1, March 1984, Pages 171–172, https://doi.org/10.1093/jaarel/LII.1.171 Published: 01 March 1984
Plating Lambda Phage to Generate Plaques (1987)

This unit provides detailed protocols for isolating a single plaque by titering serial dilutions or streaking on a lawn of cells. A discussion of phage transfection and in vitro packaging is also included.
Genetic Variation in Odorant Receptors Contributes to Variation in Olfactory Behavior in a Natural Population of Drosophila melanogaster (2011)

Chemoreception is a principle modality by which organisms gain information from their environment, and extensive variation in odor-mediated behavior has been documented within and among species. To examine the mechanisms by which sensory systems mediate these responses, we ask to what extent variation in Drosophila melanogaster odorant receptor genes contributes to variation in odor-mediated behavior. Significant differences in behavioral responses to structurally similar odorants, methyl hexanoate and ethyl hexanoate, were found in a natural population. Polymorphisms in 3 genomic regions (Or22a/Or22b, Or35a, and Or47a) were identified and associated with variation in behavior to these esters. Overall similarity in association profiles for both odorants was observed, except for Or47a in which polymorphisms were associated solely with variation in responses to ethyl hexanoate. Our analyses were then extended to examine polymorphisms in 3 odorant receptors previously reported to contribute to variation in olfactory behavior for the chemically distinct odorants benzaldehyde and acetophenone. Two Or10a polymorphisms were associated with variation in response to ethyl hexanoate. Finally, differences in Or35a and Or47a expression were associated with variation in responses to ethyl hexanoate. These results demonstrate that the genetic variation at the peripheral sensory stage plays a role in mediating differences in odor-mediated behavior.
Chip Placement with Deep Reinforcement Learning (2020)

In this work, we present a learning-based approach to chip placement, one of the most complex and time-consuming stages of the chip design process. Unlike prior methods, our approach has the ability to learn from past experience and improve over time. In particular, as we train over a greater number of chip blocks, our method becomes better at rapidly generating optimized placements for previously unseen chip blocks. To achieve these results, we pose placement as a Reinforcement Learning (RL) problem and train an agent to place the nodes of a chip netlist onto a chip canvas. To enable our RL policy to generalize to unseen blocks, we ground representation learning in the supervised task of predicting placement quality. By designing a neural architecture that can accurately predict reward across a wide variety of netlists and their placements, we are able to generate rich feature embeddings of the input netlists. We then use this architecture as the encoder of our policy and value networks to enable transfer learning. Our objective is to minimize PPA (power, performance, and area), and we show that, in under 6 hours, our method can generate placements that are superhuman or comparable on modern accelerator netlists, whereas existing baselines require human experts in the loop and take several weeks.
Lithium(1+) extraction/insertion with spinel-type lithium manganese oxides. Characterization of redox-type and ion-exchange-type sites (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLithium(1+) extraction/insertion with spinel-type lithium manganese oxides. Characterization of redox-type and ion-exchange-type sitesQi Feng, Yoshitaka Miyai, Hirofumi Kanoh, and Kenta OoiCite this: Langmuir 1992, 8, 7, 1861–1867Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/la00043a029https://doi.org/10.1021/la00043a029research-articleACS PublicationsRequest reuse permissionsArticle Views1862Altmetric-Citations189LEARN 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-Alertsclose Get e-Alerts
Size dependence of magnetic parameters and surface disorder in magnetite nanoparticles (2009)

Magnetic properties of oleic acid/oleylamine coated magnetite nanoparticles of average diameter D=4, 6, 8, 10, and 12nm are reported. The samples were characterized by transmission electron microscopy and x-ray diffraction (XRD) with XRD showing increasing disorder with decreasing D. Magnetization M vs temperature T data show the blocking temperature TB decreasing with decreasing D from TB=38K for 12nm to TB=6.5K for D=4nm. The saturation magnetization Ms at 2K also decreases from Ms=62emu∕g for 12nm to Ms=17emu∕g for 4nm but the coercivity at 2K increases with a decrease in D. It is shown that Ms fits Ms=92(1−2d∕D)3 with d=0.68nm for D&gt;4nm and d=0.86 for D=4nm. This equation is derived assuming a core-shell model with shell of thickness d consisting of disordered spins not contributing to Ms.
Special Feature Chip-Level Simulation of Microprocessors (1980)

Chip-level simulation techniques represent a bridge between the old world of gate, flip-flop, and bit and the new world of the microprocessor.
Organic optoelectronic device fabrication using standard UV photolithography (2007)

Abstract The fabrication of organic optoelectronic devices requires patterning techniques that are compatible with organic semiconductor materials. Photolithography represents, by far, the dominant patterning approach for inorganic electronics and optoelectronics. High speed, parallel patterning capability, high resolution, and the availability of standard equipment make this technology also very attractive for applications in the field of organic semiconductor technology. In the present paper we present a successful implementation of photolithography to fabricate organic diodes. This process provides the basis for a future high‐resolution monolithic integration of organic optoelectronic and photonic devices into one photonic circuit. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Simple Flow Injection Spectrophotometric Determination of Iron Using Nitroso-R salt as complexing agent (2007)

Flow injection (FI) spectrophotometric method for iron (III) determination using Disodium-1-nitroso-2-naphthol-3,6disulphonate (nitroso-R salt) is performed. It is based on the measurement of Fe(III)-nitroso-R salt complex at 720 nm formed by the reaction between Fe(III) and nitroso-R salt in an acetate buffer solution pH 5. The FI parameters that affect the signal response have been optimized in order to get the better sensitivity and low standard deviation. The linear range for determination of iron in water samples was over the range of 0.05- 4.0 μg mL -1 with a correlation coefficient (r 2 ) of 0.9997. The limit of detection (3σ) was 0.011 μg mL −1 with sample throughput of 110 samples h -1 . The repeatability measured from three standard Fe (III) (0.1, 2.0 and 4.0 μg mL −1 ) were 1.42, 1.29 and 1.01% (n = 11) respectively. The proposed method was successfully applied to determination of Fe (III) in water samples and found to be in good agreement with those obtained by flame atomic absorption spectrophotometric (FAAS) method.
Investigation of a Modified Oscillating Capillary Nebulizer Design as an Interface for CE-ICP-MS (1998)

Performance of the New Single-Bore High-Pressure Pneumatic Nebulizer (SBHPPN) in Plasma Atomic Emission Spectrometry
Prostaglandin-stimulated recovery of the human duodenal epithelium: effects of misoprostol on ethanol damage. (1990)

This study was designed to determine whether prostaglandins can stimulate the repair of human duodenal epithelium. Ten healthy volunteers were given 50 ml 40% ethanol through an endoscope onto the duodenal mucosa 1-7 cm from the pyloric sphincter; 3 min later, misoprostol (200 micrograms) or inert vehicle (5 ml) was given locally in the same way. One and 5 h later, endoscopy was repeated to evaluate the damage. The conditions of the mucosa were evaluated by endoscopy and by scanning and transmission electron microscopy in biopsies taken at time 0 and 3 min, 1 and 5 h after ethanol. The study was double-blind with a cross-over balanced design. Three minutes after ethanol administration, the duodenal mucosa showed hyperemia with hemorrhagic lesions. Under the electron microscope, the lesions were caused by vascular engorgement or red blood cell extravasation into the submucosa; the epithelium underlining lesions showed loss of superficial cells and damage to the upper layer of the mucosa. One hour after ethanol, there was a striking difference between the two treatment groups, with a substantial recovery of the duodenal epithelium in the misoprostol-treated volunteers. Although spontaneous recovery was evident in the control group, there was also a significant difference at 5 h. Our results suggest that prostaglandins are able to stimulate the recovery of the duodenal epithelium after acute damage.
A market-based perspective on information systems development (2001)

article Share on A market-based perspective on information systems development Author: Steve Sawyer School of Information Sciences and Technology, Pennsylvania State University, State College, PA School of Information Sciences and Technology, Pennsylvania State University, State College, PAView Profile Authors Info & Claims Communications of the ACMVolume 44Issue 11Nov. 2001pp 97–102https://doi.org/10.1145/384150.384168Published:01 November 2001Publication History 67citation3,342DownloadsMetricsTotal Citations67Total Downloads3,342Last 12 Months101Last 6 weeks32 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Recombinant apolipoprotein A-I Milano reduces intimal thickening after balloon injury in hypercholesterolemic rabbits. (1994)

BACKGROUNDSeveral epidemiological studies have shown an inverse relation between high-density lipoprotein (HDL) cholesterol levels and coronary heart disease. Recently, observational studies have suggested a similar inverse relation between HDL and restenosis after coronary balloon angioplasty. Despite these observations, it is unclear whether this inverse relation reflects a direct vascular protective effect of HDL or apolipoprotein (apo) A-I, the major apolipoprotein component of HDL. Therefore, to determine whether HDL directly influences neointima formation, we investigated the effect of recombinant apo A-I Milano (apo A-I M), a mutant of human apo A-I with Arg-173 to Cys substitution, on intimal thickening after balloon injury in cholesterol-fed rabbits.METHODS AND RESULTSCholesterol feeding was initiated 18 days before injury and continued until the time of death. Eight rabbits received intravenous injections of 40 mg of apo A-I M linked to a phospholipid carrier on alternate days, beginning 5 days ...
System for large scale production of small RNAs through their in vivo expression within 5S rRNA‐derived scaffold. (2009)

A stable system for manufacturing large quantity of small RNAs embedded into a 5S rRNA‐derived scaffold is under development. An RNA of interest will be incorporated into Bst aRNA, a deletion mutant of Vibrio proteolyticus 5S rRNA using standard molecular biological methods. The resulting chimeric RNA is expressed in Escherichia coli from either T7 or ribosomal P1/P2 promoters. The primary transcript is processed in vivo in the same way as endogenous 5S rRNA precursors but is not incorporated into E. coli ribosomes. As a result, the matured chimeric RNA accumulates to high levels in the bacterial cytoplasm. The RNA chimera can then be isolated, and the embedded RNA can be excised in vitro by appropriate enzymes. This system will provide a valuable and economic approach to produce defined small RNAs (such as siRNAs) in large quantity. Furthermore, the same system may be useful for the selection of novel small RNAs from a library of random RNA sequences incorporated into the 5S rRNA scaffold. The described approach will be of immediate interest in RNA pharmacological screening and drug development, and may ultimately find wider application.
The Role of Aquaporins in Root Water Uptake (2002)

The capacity of roots to take up water is determined in part by the resistance of living tissues to radial water flow. Both the apoplastic and cell-to-cell paths mediate water transport in these tissues but the contribution of cell membranes to the latter path has long been difficult to estimate. Aquaporins are water channel proteins that are expressed in various membrane compartments of plant cells, including the plasma and vacuolar membranes. Plant aquaporins are encoded by a large multigene family, with 35 members in Arabidopsis thaliana, and many of these aquaporins show a cell-specific expression pattern in the root. Mercury acts as an efficient blocker of most aquaporins and has been used to demonstrate the significant contribution of water channels to overall root water transport. Aquaporin-rich membranes may be needed to facilitate intense water flow across root tissues and may represent critical points where an efficient and spatially restricted control of water uptake can be exerted. Roots, in particular, show a remarkable capacity to alter their water permeability over the short term (i.e. in a few hours to less than 2-3 d) in response to many stimuli, such as day/night cycles, nutrient deficiency or stress. Recent data suggest that these rapid changes can be mostly accounted for by changes in cell membrane permeability and are mediated by aquaporins. Although the processes that allow perception of environmental changes by root cells and subsequent aquaporin regulation are nearly unknown, the study of root aquaporins provides an interesting model to understand the regulation of water transport in plants and sheds light on the basic mechanisms of water uptake by roots.
Association of Atrial Fibrillation and Obstructive Sleep Apnea (2004)

The novel finding of this study is that a strong association exists between OSA and AF, such that OSA is strikingly more prevalent in patients with AF than in high-risk patients with multiple other cardiovascular diseases. The coinciding epidemics of obesity and AF underscore the clinical importance of these results.
Phosphorylation of rhodopsin in bovine photoreceptor membranes. Dark reaction after illumination (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhosphorylation of rhodopsin in bovine photoreceptor membranes. Dark reaction after illuminationHermann Kuehn, James H. Cook, and William J. DreyerCite this: Biochemistry 1973, 12, 13, 2495–2502Publication Date (Print):June 1, 1973Publication History Published online1 May 2002Published inissue 1 June 1973https://pubs.acs.org/doi/10.1021/bi00737a020https://doi.org/10.1021/bi00737a020research-articleACS PublicationsRequest reuse permissionsArticle Views88Altmetric-Citations115LEARN 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-Alertsclose Get e-Alerts