gebhart/patrepeval huggingface dataset:
Integration of the pSLT Plasmid into the Salmonella Chromosome Results in a Temperature-Sensitive Growth Defect Due to Aberrant DNA Replication (2020)

A mutant of <i>Salmonella enterica</i> serovar Typhimurium was isolated that simultaneously affected two metabolic pathways as follows: NAD metabolism and DNA repair. The mutant was isolated as resistant to a nicotinamide analog and as temperature-sensitive for growth on minimal glucose medium. In this mutant, <i>Salmonella</i>'s 94-kb virulence plasmid pSLT had recombined into the chromosome upstream of the NAD salvage pathway gene <i>pncA</i> This insertion blocked most transcription of <i>pncA</i>, which reduced uptake of the nicotinamide analog. The pSLT insertion mutant also exhibited phenotypes associated with induction of the SOS DNA repair system, including an increase in filamentous cells, higher exonuclease III and catalase activities, and derepression of SOS gene expression. Genome sequencing revealed increased read coverage extending out from the site of pSLT insertion. The two pSLT replication origins are likely initiating replication of the chromosome near the normal replication terminus. Too much replication initiation at the wrong site is probably causing the observed growth defects. Accordingly, deletion of both pSLT replication origins restored growth at higher temperatures.<b>IMPORTANCE</b> In studies that insert a second replication origin into the chromosome, both origins are typically active at the same time. In contrast, the integrated pSLT plasmid initiated replication in stationary phase after normal chromosomal replication had finished. The gradient in read coverage extending out from a single site could be a simple but powerful tool for studying replication and detecting chromosomal rearrangements. This technique may be of particular value when a genome has been sequenced for the first time to verify correct assembly.
Ultrabright plasmonic fluor nanolabel-enabled detection of a urinary ER stress biomarker in autosomal dominant tubulointerstitial kidney disease (2021)

Autosomal dominant tubulointerstitial kidney disease (ADTKD)-uromodulin (<i>UMOD)</i> is the most common nonpolycystic genetic kidney disease, but it remains unrecognized due to its clinical heterogeneity and lack of screening test. Moreover, the fact that the clinical feature is a poor predictor of disease outcome further highlights the need for the development of mechanistic biomarkers in ADTKD. However, low abundant urinary proteins secreted by thick ascending limb cells, where UMOD is synthesized, have posed a challenge for the detection of biomarkers in ADTKD-<i>UMOD</i>. In the CRISPR/Cas9-generated murine model and patients with ADTKD-<i>UMOD</i>, we found that immunoglobulin heavy chain-binding protein (BiP), an endoplasmic reticulum chaperone, was exclusively upregulated by mutant UMOD in the thick ascending limb and easily detected by Western blot analysis in the urine at an early stage of disease. However, even the most sensitive ELISA failed to detect urinary BiP in affected individuals. We therefore developed an ultrasensitive, plasmon-enhanced fluorescence-linked immunosorbent assay (p-FLISA) to quantify urinary BiP concentration by harnessing the newly invented ultrabright fluorescent nanoconstruct, termed "plasmonic Fluor." p-FLISA demonstrated that urinary BiP excretion was significantly elevated in patients with ADTKD-<i>UMOD</i> compared with unaffected controls, which may have potential utility in risk stratification, disease activity monitoring, disease progression prediction, and guidance of endoplasmic reticulum-targeted therapies in ADTKD.<b>NEW & NOTEWORTHY</b> Autosomal dominant tubulointerstitial kidney disease (ADTKD)-uromodulin (<i>UMOD</i>) is an underdiagnosed cause of chronic kidney disease (CKD). Lack of ultrasensitive bioanalytical tools has hindered the discovery of low abundant urinary biomarkers in ADTKD. Here, we developed an ultrasensitive plasmon-enhanced fluorescence-linked immunosorbent assay (p-FLISA). p-FLISA demonstrated that secreted immunoglobulin heavy chain-binding protein is an early urinary endoplasmic reticulum stress biomarker in ADTKD-<i>UMOD</i>, which will be valuable in monitoring disease progression and the treatment response in ADTKD.
A Novel Energy-Conscious Access Point (eAP) System With Cross-Layer Design in Wi-Fi Networks for Reliable IoT Services (2022)

This paper proposes a novel energy-conscious access point (<i>e</i>AP) system with cross-layer design to increase the energy efficiency of IoT devices in IEEE 802.11 Wi-Fi networks for reliable IoT services. The proposed <i>e</i>AP system controls the energy resources of IoT devices to extend the lifetime of the IoT device. For this purpose, we develop a new <i>e</i>AP system that considers a cross-layer design with a prompt TCP ACK transmit function, a caching-and-retransmit IoT data function, and a multiple IoT data aggregate function to improve the energy efficiency of the IoT device. In addition, the proposed <i>e</i>AP system has a device energy management module that precisely controls operating parameters, such as the transmission period of IoT packets, the delivery of traffic indication message (DTIM) value of IoT devices, and the transmitting power of IoT devices. These features extend the lifetime of the battery-powered IoT devices while satisfying service requirements for reliable IoT services. The long listening time of TCP ACK messages in receive mode (Rx) results in the high energy consumption of IoT devices due to the large round trip time. The proposed <i>e</i>AP system reduces the reception time of TCP ACK messages in the IoT device, using the prompt TCP ACK transmit function in the <i>e</i>AP. This reduces the long Rx mode time for TCP ACK reception, and increases the short sleep mode time, which results in increase of the energy efficiency of the IoT device. In the energy-saving analyses, we formulate an energy consumption model for the IoT device, and determine the energy-saving gain when the IoT device uses the <i>e</i>AP system model, compared to a legacy AP system model. Our performance evaluation results verify that the proposed <i>e</i>AP system achieves a maximum improvement in energy efficiency of approximately 88%, and 8.4 times improvement in the expected lifetime of the IoT device, compared to the legacy AP system model.
ChemInform Abstract: Synthesis of Heteroaryl Sulfonamides from Organozinc Reagents and 2,4,6‐Trichlorophenyl Chlorosulfate. (2015)

Abstract Aryl‐ and heteroarylzinc reagents react with 2,4,6‐trichlorophenyl chlorosulfate (TCPC) to afford sulfonyl chlorides which are in situ converted to the corresponding sulfonamides by rapid reaction with various amines.
Development of biphasic scaffolds with distinct mechanical properties for the regeneration of osteochondral interface (2016)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
Thermal modeling of zone-melting-recrystallization processing of silicon-on-insulator film structures (1991)

A numerical simulation model that considers changes in thermal and radiation properties during zone-melting-recrystallization processing of silicon-on-insulator film structures with a graphite strip heater was developed. A series of numerical experiments were conducted to investigate the conductive, convective, and radiative parameters affecting the process. The variability of the thermal conductivity of silicon as a function of temperature at the premelting stage and the variation in thermal conductivity due to the multilayer nature of the structure were found not to affect of the temperature distribution during processing. The convective heat losses induced by the inert gas in the processing chamber does not affect significantly the temperature profiles in the film structure, but can reduce the melt zone width by 10%–25%. The study of radiative effects focused on the effects of varying the width and height of the graphite strip and the distance between the graphite strip and the film structure. These parameters significantly affect the temperature distribution and the width of the melt zone. The relationships between the convection and radiation parameters and the resultant melt zone width are presented in graphical form for use in design optimization.
High Performance HF-VHF All Digital RF Receiver Tested at 20 GHz Clock Frequencies (2006)

Wireless applications would be less expensive, more flexible, and more robust if they had more digital and less analog circuitry. The problem is implementing digital signal processing at radio frequencies. Conventional data converters (ADCs and DACs) and digital circuits are simply not fast enough. However, superconductors can provide ultra fast mixed signal and digital circuits with the linearity and dynamic range required for true direct, digital-RF processing. These superconducting circuits are digital ICs based on Josephson junctions and "rapid-single-flux-quantum" logic (RSFQ), where switching speeds up to 750 GHz have been demonstrated enabling true digital-RF architecture at clock speeds eventually up to 160 GHz. This permits direct conversion between analog RF and digital baseband signals, replacing frequency and protocol-specific analog hardware with flexible digital processors. Data conversion in high frequency wireless applications at frequencies up to 50 GHz will soon become practical. Hypres recently delivered a HF-VHF all digital RF receiver (ADR) prototype to ONR. Testing of this ADR has demonstrated the superior performance of superconducting ICs in cryocooled systems. A US Navy laboratory is now evaluating the world's first complete prototype digital RF receiver capable of direct digitization from DC to 2 GHz
EUV Resist Chemical Analysis by Soft X-ray Absorption Spectroscopy for High Sensitivity Achievement (2014)

Simultaneous achievement of high sensitivity and low line edge roughness (LWR) is necessary in EUV resist. The chemical reaction analysis of EUV (Extreme Ultraviolet) chemical amplified (CA) resist and acid diffusion length evaluation was carried out. In order to achieve low LWR of the CA resist, the large chemical structure of the anion of photoacid generator (PAG) is required for shortening the acid diffusion length. On the other hand, in order to increase the sensitivity, on the basis of the chemical reaction analysis using the soft x-ray absorption spectroscopy, the decomposition reaction of the large chemical structure of the PAG anion should be taken in account in addition of ionization reaction. However, if the decomposition reaction occur, the acid diffusion length will become shorter than that as expected. It is found that the Imidate-type of anion of PAG has high sensitivity and short diffusion length. The chemical reaction analysis by the soft x-ray absorption spectroscopy using the synchrotron radiation with the combination analysis of the acid diffusion are useful method for the mitigation of high sensitivity and low LWR.
Synthesis and Structure of Asymmetric Zirconium‐Substituted Silicotungstates, [Zr6O2(OH)4(H2O)3 (β‐SiW10O37)3]14‐ and [Zr4O2(OH)2(H2O)4 (β‐SiW10O37)2]10‐. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
The Putative Neuroprotective Role of Neuropeptide Y in the Central Nervous System (2005)

Neuropeptide Y (NPY) is one of the most abundant and widely distributed neuropeptides in the mammalian central nervous system (CNS). An overview of the distribution of the G-protein coupled NPY receptor family (Y(1), Y(2), Y(4), Y(5) receptors) in the brain is described. The coexistence of NPY with other neurotransmitters and its wide distribution in several brain areas predict the high importance of NPY as a neuromodulator. Thus, the effect of NPY on the release of several neurotransmitters such as glutamate, gamma-aminobutyric acid (GABA), norepinephrine (NE), dopamine, somastotatin (SOM), serotonin (5-HT), nitric oxide (NO), growth hormone (GH) and corticotropin releasing factor (CRF) is reviewed. A neuroprotective role for NPY under physiological conditions and during hyperactivity such as epileptic-seizures has been suggested. We have shown previously that NPY inhibits glutamate release evoked from hippocampal nerve terminals and has a neuroprotective effect in rat organotypic hippocampal cultures exposed to an excitotoxic insult. Moreover, changes in NPY levels have been observed in different pathological conditions such as brain ischemia and neurodegenerative diseases (Huntington's, Alzheimer's and Parkinson's diseases). Taken together, these studies suggest that NPY and NPY receptors may represent pharmacological targets in different pathophysiological conditions in the CNS.
Critically Sampled and Oversampled Subband Structures (2009)

This chapter contains sections titled: Variants of critically sampled subband adaptive filters Oversampled and nonuniform subband adaptive filters Filter bank design Case study: Proportionate subband adaptive filtering Summary References
The Potential for Thermo-Electric Regeneration of Energy in Vehicles (2009)

&lt;div class="htmlview paragraph"&gt;The pursuit of improved fuel economy is becoming an increasingly important objective for automotive manufacturers. The field of thermo-electrics is highlighted as a promising technology. The figure of merit, Z is the primary measure of the effectiveness of a thermo-electric material, and the values now being offered by researchers have reached the level where new applications become attractive. It is feasible to consider such modules incorporated into a thermoelectric generator to recover waste heat from exhaust gas flow – an available energy stream that has traditionally been neglected as unusable. As a precursor to a costly experimental study it is desirable to accurately simulate the application of a thermo-electric system to a vehicle exhaust to understand both the feasibility and potential drawbacks.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A numerical model of a vehicle able to support transient analysis is presented Transient modelling of the exhaust flow is considered of considerable importance to the validity of the simulation study, an aspect that does not appear to have been considered in previous studies. An explicit time-marching numerical model has been developed to capture the transient performance of a thermo-electric generator. The heat exchange model is coupled with a quasi-static vehicle model to allow simulation of the effects on vehicles.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Initial studies indicate that with an output of around 1.3kW the alternator of a small passenger vehicle could be replaced.&lt;/div&gt;
Synthesis and Evaluation of 4-Halogeno-N-[4-[6-(isopropylamino)pyrimidin-4-yl]-1,3-thiazol-2-yl]-N-[11C]methylbenzamide for Imaging of Metabotropic Glutamate 1 Receptor in Melanoma (2015)

Metabotropic glutamate 1 (mGlu1) receptor is found not only in the brain but also in melanomas and breast cancers. mGlu1 is a promising target for molecular imaging-based diagnosis and treatment of melanoma because its overexpression induces melanocyte carcinogenesis. Here we developed three PET tracers: 4-halogeno-N-[4-[6-(isopropylamino)pyrimidin-4-yl]-1,3-thiazol- 2-yl]-N-[(11)C]methylbenzamide ([(11)C]4-6), which exhibited high uptake in target tumor and decreased uptake in nontarget brain tissues. In vitro binding assay indicated high to moderate binding affinities of 4-6 (Ki, 22-143 nM) for mGlu1 receptor. In vivo biodistribution studies in mice implanted with B16F10 melanoma cells confirmed high radioactive uptake in tumor and low uptake in blood, skin, and muscles. Inhibition of mGlu1 receptor using an mGlu1-selective ligand led to reduced radioactive uptake in the tumor. [(11)C]6 displayed the highest ratio of uptake between tumor and nontarget tissue and may prove useful as a PET tracer for mGlu1 imaging in melanoma.
Editorial on First-Time Disclosures of Clinical Candidates (2018)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTEditorial on First-Time Disclosures of Clinical CandidatesBruce E. MaryanoffBruce E. MaryanoffDepartment of Chemistry, The Scripps Research InstituteMore by Bruce E. Maryanoffhttp://orcid.org/0000-0003-3590-2357Cite this: J. Med. Chem. 2018, 61, 13, 5449Publication Date (Web):May 21, 2018Publication History Published online21 May 2018Published inissue 12 July 2018https://pubs.acs.org/doi/10.1021/acs.jmedchem.8b00739https://doi.org/10.1021/acs.jmedchem.8b00739editorialACS PublicationsCopyright © 2018 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2821Altmetric-Citations-LEARN 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 PDF (213 KB) Get e-AlertscloseSUBJECTS:Materials,Medicinal chemistry,Pharmaceuticals Get e-Alerts
Plasma-assisted thermal-cyclic atomic-layer etching of tungsten and control of its selectivity to titanium nitride (2022)

Plasma-assisted thermal-cyclic atomic-layer etching (ALE) of tungsten (W), the selectivity of which with respect to TiN can be tuned between highly selective and nonselective by changing infrared-heating time, has been demonstrated. It is a two-step process consisting of exposure to radicals generated in a CHF3/O2 or CH2F2/O2/Ar plasma followed by infrared heating. Analysis by in situ x-ray photoelectron spectroscopy confirmed that a WFx-based modified surface formed on the surface of a W film exposed to radicals at −22 °C. The modified surface on the W film is volatile at a heating temperature lower than that required for removing the modified surface on the TiN film. Cyclic etching of both W and TiN was performed by using the CH2F2/O2/Ar plasma and infrared heating in a 300-mm ALE apparatus. When the infrared-heating time was not long enough to remove the modified surface on TiN, the cyclic repetition etched only the W film. On the other hand, when the infrared-heating time was long enough to remove modified surfaces on both W and TiN, the cyclic repetition etched both W and TiN films. Therefore, both highly selective and nonselective ALEs for W and TiN were obtained by choosing an optimum infrared-heating time. This shows that material selectivity in plasma-assisted thermal-cyclic ALE can be controlled by changing the infrared-heating time.
ChemInform Abstract: A Bromine‐Catalyzed Free‐Radical Oxidation of Acetamides from Primary and Secondary Alkylamines by H2O2. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A new compound from the mushroom Tricholoma flavovirens (2014)

A novel compound (1) and a known one (2) were isolated from the fruiting bodies of Tricholoma flavovirens. Their structures were determined by the interpretation of spectroscopic data. Both compounds showed inhibition effects on the growth of hypocotyl of lettuce with significant differences. In addition, compound 1 showed a promotion effect on the growth of root with significant differences and 2 had the similar tendency to promote the growth.
Asymmetric beampatterns with circular differential microphone arrays (2017)

Circular differential microphone arrays (CDMAs) facilitate compact superdirective beamformers whose beampatterns are nearly frequency invariant, and allow perfect steering for all azimuthal directions. Herein, we eliminate the inherent limitation of symmetric beampatterns associated with a linear geometry, and introduce an analytical asymmetric model for Nth-order CDMAs. We derive the theoretical asymmetric beampattern, and develop the asymmetric supercardioid. In addition, an Nth-order CDMAs design is presented based on the mean-squared-error (MSE) criterion. Experimental results show that the proposed model yields optimal performance in terms of white noise gain, directivity factor, and front-to- back ratio, as well as more flexible nulls design for the interfering signals.
New Fault-Resistance Estimation Algorithm for Rotor-Winding Ground-Fault Online Location in Synchronous Machines With Static Excitation (2014)

This paper presents a new algorithm for estimating the ground-fault resistance value in rotor windings. This new algorithm is an improvement of an online ground-fault location method previously presented. This location method is suitable for synchronous generators with static excitation, whose excitation field winding is fed by controlled rectifiers through an excitation transformer. The estimation of the fault resistance is obtained through the comparison between the third-harmonic voltage measured in a grounding resistance placed in the neutral of the excitation transformer and the third-harmonic voltage calculated by the algorithm. This latter variable is obtained with the dc component of the output voltage of the controlled rectifier and the ac supply voltage of this converter. The fault resistance value is used in the novel technique of online ground-fault location, and it allows improving the accuracy of the location of the defect. This new algorithm, integrated in the complete location method, has been tested with satisfactory results in a 5-kVA laboratory synchronous generator and in a 106-MVA hydro-generating unit.
Layout-Aware Embedding for Quantum Annealing Processors. (2019)

Due to the physical limit in connectivity between qubits in Quantum Annealing Processors (QAPs), when sampling from a problem formulated as an Ising graph model, it is necessary to embed the problem onto the physical lattice of qubits. A valid mapping of the problem nodes into qubits often requires qubit chains to ensure connectivity.
Photon-limited bounds for phase retrieval (2021)

We show that the optimal Cramér-Rao lower bound on the mean-square error for the estimation of a coherent signal from photon-limited intensity measurements is equal to the number of signal elements, or the number of signal elements minus one when we account for the unobservable reference phase. Whereas this bound is attained by phase-quadrature holography, we also show that it can be attained through a phase-retrieval system that does not require a coherent reference. We also present the bounds for classic phase-retrieval and ptychography, and show that practical coding strategies can approach optimal performance.
Supplementary Table 2 from Progressive Chromatin Repression and Promoter Methylation of <i>CTNNA1</i> Associated with Advanced Myeloid Malignancies (2023)

Supplementary Table 2 from Progressive Chromatin Repression and Promoter Methylation of &lt;i&gt;CTNNA1&lt;/i&gt; Associated with Advanced Myeloid Malignancies