gebhart/patrepeval huggingface dataset:
A Novel Quorum-Quenching N -Acylhomoserine Lactone Acylase from Acidovorax sp. Strain MR-S7 Mediates Antibiotic Resistance (2017)

<i>N</i>-Acylhomoserine lactone acylase (AHL acylase) is a well-known enzyme responsible for disrupting cell-cell communication (quorum sensing) in bacteria. Here, we isolated and characterized a novel and unique AHL acylase (designated MacQ) from a multidrug-resistant bacterium, <i>Acidovorax</i> sp. strain MR-S7. The purified MacQ protein heterologously expressed in <i>Escherichia coli</i> degraded a wide variety of AHLs, ranging from C<sub>6</sub> to C<sub>14</sub> side chains with or without 3-oxo substitutions. We also observed that AHL-mediated virulence factor production in a plant pathogen, <i>Pectobacterium carotovorum</i>, was dramatically attenuated by coculture with MacQ-overexpressing <i>Escherichia coli</i>, whereas <i>E. coli</i> with an empty vector was unable to quench the pathogenicity, which strongly indicates that MacQ can act <i>in vivo</i> as a quorum-quenching enzyme and interfere with the quorum-sensing system in the pathogen. In addition, this enzyme was found to be capable of degrading a wide spectrum of β-lactams (penicillin G, ampicillin, amoxicillin, carbenicillin, cephalexin, and cefadroxil) by deacylation, clearly indicating that MacQ is a bifunctional enzyme that confers both quorum quenching and antibiotic resistance on strain MR-S7. MacQ has relatively low amino acid sequence identity to any of the known acylases (<39%) and has among the broadest substrate range. Our findings provide the possibility that AHL acylase genes can be an alternative source of antibiotic resistance genes posing a threat to human health if they migrate and transfer to pathogenic bacteria.<b>IMPORTANCE</b><i>N</i>-Acylhomoserine lactones (AHLs) are well-known signal molecules for bacterial cell-cell communication (quorum sensing), and AHL acylase, which is able to degrade AHLs, has been recognized as a major target for quorum-sensing interference (quorum quenching) in pathogens. In this work, we succeeded in isolating a novel AHL acylase (MacQ) from a multidrug-resistant bacterium and demonstrated that the MacQ enzyme could confer multidrug resistance as well as quorum quenching on the host organism. Indeed, the purified MacQ protein was found to be bifunctional and capable of degrading not only various AHL derivatives but also multiple β-lactam antibiotics by deacylation activities. Although quorum quenching and antibiotic resistance have been recognized to be distinct biological functions, our findings clearly link the two functions by discovering the novel bifunctional enzyme and further providing the possibility that a hitherto-overlooked antibiotic resistance mechanism mediated by the quorum-quenching enzyme may exist in natural environments and perhaps in clinical settings.
Investigation of thermoreversible polymer networks by temperature dependent size exclusion chromatography (2017)

We introduce a novel approach for studying thermoreversible Diels–Alder networks by Temperature Dependent SEC.
ChemInform Abstract: Synthesis of Alkenes by Wittig and Related Phosphorus‐Based Alkenations (2012)

Abstract Review: 528 refs.
Intrathoracic Impedance vs Daily Weight Monitoring for Predicting Worsening Heart Failure Events: Results of the Fluid Accumulation Status Trial (FAST) (2011)

The relative sensitivity and unexplained detection rate of changes in intrathoracic impedance has not been compared with standard heart failure (HF) monitoring using daily weight changes. The Fluid Accumulation Status Trial (FAST) prospectively followed 156 HF patients with implanted cardioverter-defibrillator or cardiac resynchronization therapy defibrillator devices modified to record daily changes in intrathoracic impedance in a blinded fashion for 537±312 days. Daily impedance changes were used to calculate a fluid index that could be compared with a prespecified threshold. True positives were defined as adjudicated episodes of worsening HF occurring within 30 days of a fluid index above threshold or an acute weight gain. Unexplained detections were defined as threshold crossings or acute weight gains not associated with worsening HF. Impedance measurements were performed on >99% of follow-up days, compared with only 76% of days for weight measurements. Sixty-five HF events occurred during follow-up (0.32/patient-year). Forty HF events were detected by impedance but not weight, whereas 5 were detected by weight but not impedance. Sensitivity was greater (76% vs 23%; P<.0001) and unexplained detection rate was lower (1.9 vs 4.3/patient-year; P<.0001) for intrathoracic impedance monitoring at the threshold of 60Ω days compared with acute weight increases of 3 lbs in 1 day or 5 lbs in 3 days and also over a wide range of fluid index and weight thresholds. The sensitivity and unexplained detection rate of intrathoracic impedance monitoring was superior to that seen for acute weight changes. Intrathoracic impedance monitoring represents a useful adjunctive clinical tool for managing HF in patients with implanted devices.
Analysis of CUSUM and Other Markov-Type Control Schemes by Using Empirical Distributions (1992)

The run-length distribution of a cumulative sum control scheme, when the underlying distribution of the incoming observations is unknown, is discussed. Given a sample of size n from this distribution, the estimators related to various characteristics of the run length can be obtained by using the empirical cdf instead of the true cdf in the standard analysis procedure. The article discusses the properties of the resulting point estimators, as well as interval estimators obtained by using resampling techniques. Applications of the technique for the purpose of design and analysis of control schemes are also discussed. The proposed methodology can be easily adapted for other Markov-type control schemes.
Outlier faces detector via efficient cohesive subgraph identification (2016)

A personal or enterprise collection of a large set of face images may contain many types of tags used for querying the collection. Often the tags have many irrelevant content that may not reflect the image content in terms of the facial characteristics. In this paper, we propose a data curation method to filter out the irrelevant face images using a face recognition based subgraph identification. Results on retrievals from the Internet using popular celebrities show the efficacy of our approach after we cleanse the images collection retrieved and applying our algorithm to the collection.
Photo‐Conversion of Methane into Higher Hydrocarbons Using 355 NM Laser Radiation (2003)

Abstract A laser‐based technique for the conversion of methane into higher hydrocarbons and hydrogen has been developed. This technique involves the photo‐dissociation of methane using a high power pulsed ultraviolet laser at 355 nm. The reaction products, such as CH, CH2, C2H2, atomic and molecular hydrogen, are characterized by real‐time laser induced fluorescence for the first time, to our knowledge. In addition to this online fluorescence detection of the species, gas chromatography is also applied to analyze the stable hydrocarbon products generated due to photo‐dissociation of methane. Another interesting result of the laser excitation of methane is the observation of Stimulated Raman lines (Stokes and Antistokes) observed in the 150–850 nm region, which is a manifestation of the inherent characteristics of the laser radiation such as high directionality and high intensity. Keywords: Methane conversionMulti‐photon dissociationHydrocarbonsLaser photolysis Acknowledgments The support by the Research Institute and Physics Department of King Fahd University of Petroleum and Minerals is gratefully acknowledged. This work is a part of the Research Project # SABIC‐2000 /12 funded by Saudi Basic Industries (SABIC).
Partial Stereochemical Assignment of Quartromicins A3 and D3 (2002)

[structure: see text]. A partial stereochemical assignment of quartromicins A3 (R = alpha-D-galactosyl) and D3 (R = H, M+ = Na+, K+, Ca+) is presented.
The application of program verification techniques to hardware verification (1988)

Article Free Access Share on The application of program verification techniques to hardware verification Author: J. A. Darringer IBM Thomas J. Watson Research Center, Yorktown Heights, New York IBM Thomas J. Watson Research Center, Yorktown Heights, New YorkView Profile Authors Info & Claims 25 years of DAC: Papers on Twenty-five years of electronic design automationJune 1988 Pages 373–379https://doi.org/10.1145/62882.62926Online:01 June 1988Publication History 2citation174DownloadsMetricsTotal Citations2Total Downloads174Last 12 Months6Last 6 weeks3 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 SiteeReaderPDF
Lanthanum hexaboride hollow cathode for dense plasma production (1978)

A hollow tube cathode using lanthanum hexaboride as the electron emitter has been designed and constructed. Tests in both argon and hydrogen indicate that this cathode is capable of producing over 800 A of electron current continuously, corresponding to over 25 A/cm(2) from the LaB(6). The cathode has been operated for over 300 h and exposed to air more than 100 times with no deterioration in emission. Projected lifetime is in excess of 3500 h for the sintered LaB(6) piece tested in this configuration. Construction details, performance characteristics, and discussions of space charge limits on emission are described.
Hybridization and Selective Release of DNA Microarrays (2011)

DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.
Aluminum nitride grating couplers (2012)

Grating couplers in sputtered aluminum nitride, a piezoelectric material with low loss in the C band, are demonstrated. Gratings and a waveguide micromachined on a silicon wafer with 600 nm minimum feature size were defined in a single lithography step without partial etching. Silicon dioxide (SiO(2)) was used for cladding layers. Peak coupling efficiency of -6.6 dB and a 1 dB bandwidth of 60 nm have been measured. This demonstration of wire waveguides and wideband grating couplers in a material that also has piezoelectric and elasto-optic properties will enable new functions for integrated photonics and optomechanics.
Particle Image Velocimetry (PIV) Uncertainty Quantification Using Moment\n of Correlation (MC) Plane (2018)

We present a new uncertainty estimation method for Particle Image Velocimetry\n(PIV), that uses the correlation plane as a model for the probability density\nfunction (PDF) of displacements and calculates the second order moment of the\ncorrelation (MC). The cross-correlation between particle image patterns is the\nsummation of all particle matches convolved with the apparent particle image\ndiameter. MC uses this property to estimate the PIV uncertainty from the shape\nof the cross-correlation plane. In this new approach, the Generalized\nCross-Correlation (GCC) plane corresponding to a PIV measurement is obtained by\nremoving the particle diameter contribution. The GCC primary peak represents a\ndiscretization of the displacement PDF, from which the standard uncertainty is\nobtained by convolving the GCC plane with a Gaussian function. Then a Gaussian\nleast-squares-fit is applied to the peak region, accounting for the stretching\nand rotation of the peak, due to the local velocity gradients and the effect of\nthe convolved Gaussian. The MC method was tested with simulated image sets and\nthe predicted uncertainties show good sensitivity to the error sources and\nagreement with the expected RMS error. Subsequently, the method was\ndemonstrated in three PIV challenge cases and two experimental datasets and was\ncompared with the published image matching (IM) and correlation statistics (CS)\ntechniques. Results show that the MC method has a better response to spatial\nvariation in RMS error and the predicted uncertainty is in good agreement with\nthe expected standard uncertainty. The uncertainty prediction was also explored\nas a function PIV interrogation window size, and the MC method outperforms the\nother uncertainty methods.\n
Multicanonical Sequential Monte Carlo Sampler for Uncertainty Quantification (2022)

In many real-world engineering systems, the performance or reliability of the system is characterised by a scalar parameter. The distribution of this performance parameter is important in many uncertainty quantification problems, ranging from risk management to utility optimisation. In practice, this distribution usually cannot be derived analytically and has to be obtained numerically by simulations. To this end, standard Monte Carlo simulations are often used, however, they cannot efficiently reconstruct the tail of the distribution which is essential in many applications. One possible remedy is to use the Multicanonical Monte Carlo method, an adaptive importance sampling scheme. In this method, one draws samples from an importance sampling distribution in a nonstandard form in each iteration, which is usually done via Markov chain Monte Carlo (MCMC). MCMC is inherently serial and therefore struggles with parallelism. In this paper, we present a new approach, which uses the Sequential Monte Carlo sampler to draw from the importance sampling distribution, which is particularly suited for parallel implementation. With both mathematical and practical examples, we demonstrate the competitive performance of the proposed method.
Large-signal compression measurements in high-current p-i-n photodiodes with +11 to +20 dBm output microwave power (2002)

We present comparisons between the small- and large-signal compression measurements for surface-illuminated p-i-n microwave photodetectors. The measured RF power provided by the photodiodes was +12, +17 and +20 dBm for bandwidths of 25, 3, and 1 GHz, respectively.
Omni-directional phase matching in integrated zero-index media (2020)

We experimentally demonstrate omni-directional phase matching via four-wave mixing in zero-index silicon waveguides exhibiting phase-free propagation in the infrared range. This property can be exploited to miniaturize integrated nonlinear devices.
An artificial intelligence–enabled ECG algorithm for comprehensive ECG interpretation: Can it pass the ‘Turing test’? (2021)

An AI-ECG algorithm outperforms an existing standard automated computer program and better approximates expert over-read for comprehensive 12-lead ECG interpretation.
Bottom‐up proteomics of envelope proteins extracted from spinach chloroplast via high organic content CE‐MS (2020)

A high organic content CE-MS/MS (HOCE-MS/MS) method was developed for the proteomic analysis of envelope proteins extracted from spinach leaves. Separation was performed in a 1-m long hydroxypropyl cellulose coated capillary, using 8% (v/v) formic acid in 70% (v/v) methanol and 22% water as the BGE. A flow-through microvial interface was used to couple the CE system with an Orbitrap Fusion Lumos mass spectrometer, and field-amplified sample stacking was used to improve the concentration sensitivity. Using this optimized method, 3579 peptides and 1141 proteins were identified using the Proteome Discoverer software with a 1% false discovery rate at the protein level. Relative to conventional aqueous CE, HOCE-MS did a better job of discovering hydrophobic peptides and provided more peptide and protein identifications. Relative to nano-LC-MS, it achieved comparable peptide and protein identification performance and detected peptides not identified by LC-MS: of the full set of peptides identified using the two techniques, 19% were identified only using HOCE-MS. It also outperformed nano-LC-MS with respect to the detection of low molecular weight peptides.
The challenge of studying perovskite solar cells’ stability with machine learning (2023)

Perovskite solar cells are the most dynamic emerging photovoltaic technology and attracts the attention of thousands of researchers worldwide. Recently, many of them are targeting device stability issues–the key challenge for this technology–which has resulted in the accumulation of a significant amount of data. The best example is the “Perovskite Database Project,” which also includes stability-related metrics. From this database, we use data on 1,800 perovskite solar cells where device stability is reported and use R andom Forest to identify and study the most important factors for cell stability. By applying the concept of learning curves, we find that the potential for improving the models’ performance by adding more data of the same quality is limited. However, a significant improvement can be made by increasing data quality by reporting more complete information on the performed experiments. Furthermore, we study an in-house database with data on more than 1,000 solar cells, where the entire aging curve for each cell is available as opposed to stability metrics based on a single number. We show that the interpretation of aging experiments can strongly depend on the chosen stability metric, unnaturally favoring some cells over others. Therefore, choosing universal stability metrics is a critical question for future databases targeting this promising technology.
Early Modulation of Circulating MicroRNAs Levels in HER2-Positive Breast Cancer Patients Treated with Trastuzumab-Based Neoadjuvant Therapy (2020)

Circulating microRNA (ct-miRNAs) are able to identify patients with differential response to HER2-targeted therapy. However, their dynamics are largely unknown. We assessed 752 miRNAs from 52 NeoALTTO patients with plasma pairs prior and two weeks after trastuzumab. Increased levels of ct-miR-148a-3p and ct-miR-374a-5p were significantly associated with pathological complete response (pCR) (<i>p</i> = 0.008 and 0.048, respectively). At a threshold ≥ the upper limit of the 95%CI of the mean difference, pCR resulted 45% (95%CI 24%-68%), and 44% (95%CI 22%-69%) for ct-miR-148a-3p and ct-miR-374a-5p, respectively. Notably, ct-miR-148a-3p retained its predictive value (OR 3.42, 95%CI 1.23-9.46, <i>p</i> = 0.018) in bivariate analysis along with estrogen receptor status. Combined information from ct-miR-148a-3p and ct-miR140-5p, which we previously reported to identify trastuzumab-responsive patients, resulted in greater predictive capability over each other, with pCR of 54% (95%CI 25%-81%) and 0% (95%CI 0%-31%) in ct-miR-148a/ct-miR-140-5p high/present and low/absent, respectively. GO and KEGG analyses showed common enriched terms between the targets of these ct-miRNAs, including cell metabolism regulation, AMPK and MAPK signaling, and HCC progression. In conclusion, early modulated ct-miR-148-3p may inform on the functional processes underlying treatment response, integrate the information from already available predictive biomarkers, and identify patients likely to respond to single agent trastuzumab-based neoadjuvant therapy.
High-Specific Impulse Operation of the BPT-4000 Hall Thruster for NASA Science Missions (2010)

To meet the propulsive requirements, cost constraints, and scientific objectives of NASA deep-space missions, high-performance, low-cost electric propulsion (EP) options are needed. Commercial EP technology has matured sufficiently that ion and Hall thrusters are now leading candidates for many of these missions. A commercial Hall thruster system is as much as 50% less expensive than an equivalent ion thruster system, but the maximum specific impulse of commercial, flight-qualified Hall thrusters is presently 2000 s. Extending the specific impulse to 2500-3000 s would increase the Hall thruster mission capture to include nearly all of the missions where EP was applicable. To assess the suitability of extending the specific impulse range of a candidate commercial Hall thruster, a test campaign designed to assess the performance and plasma properties of Aerojet’s BPT-4000 during high-specific impulse operation was executed. An inverted-pendulum thrust stand was used for performance measurements. An RPA, ExB probe, and emissive probe were used to measure the ion energy, ion species’ current fractions, and plasma potential, respectively, in the far-field plume. For operating conditions spanning 500-800 V discharge voltage and 2.5-5.5 kW discharge power, thrust varied from 134-288 mN, specific impulse from 1980-2720 s, and efficiency from 0.50-0.59. It was concluded that operating the BPT4000 at specific impulses of 2600 s and 4.5 kW discharge power was within the existing capabilities of the magnetic circuit, thermal margins, and voltage isolation. Based on these results, a delta-qualification for high specific impulse operation and higher propellant throughput via additional testing of the qualification thruster is recommended in order to ready the thruster for near-term infusion into NASA science missions.