gebhart/patrepeval huggingface dataset:
Characterization of a Glyphosate-Tolerant Enzyme from Streptomyces svecius: A Distinct Class of 5-Enolpyruvylshikimate-3-phosphate Synthases (2021)

Natural and modified versions of the 5-enolpyruvylshikimate-3-phosphate synthase (<i>epsps</i>) gene have been used to confer tolerance to the broad-spectrum herbicide glyphosate in a variety of commercial crops. The most widely utilized trait was obtained from the <i>Agrobacterium tumefaciens</i> strain CP4 and has been commercialized in several glyphosate-tolerant crops. The EPSPS gene products are enzymes that have been divided into three classes based on sequence similarity, sensitivity to glyphosate, and steady-state catalytic parameters. Herein, we describe the informatics-guided identification and biochemical and structural characterization of a novel EPSPS from <i>Streptomyces sviceus</i> (DGT-28 EPSPS). The data suggest DGT-28 EPSPS and other closely related homologues exemplify a distinct new class (Class IV) of EPSPS enzymes that display intrinsic tolerance to high concentrations of glyphosate (<i>K<sub>i</sub></i> ≥ 5000 μM). We further demonstrate that <i>dgt-28 epsps</i>, when transformed into stable plants, provides robust (≥4× field rates) vegetative/reproductive herbicide tolerance and has utility in weed-control systems comparable to that of commercialized events.
LaSEWeb (2014)

We show how to programmatically model processes that humans use when extracting answers to queries (e.g., "Who invented typewriter?", "List of Washington national parks") from semi-structured Web pages returned by a search engine. This modeling enables various applications including automating repetitive search tasks, and helping search engine developers design micro-segments of factoid questions.
Towards low-power near-infrared modulators operating at telecom wavelengths: when graphene plasmons frustrate their metallic counterparts (2020)

A free-space electro-optic modulator device exploiting graphene’s surface plasmon polariton (SPP) at near-infrared frequencies is proposed and theoretically studied. The device is made up of two resonant structures, the first being a metallic SPP displaying broadband absorption, and the second graphene’s own SPP, which is shown to frustrate the metallic plasmon when excited, leading to a narrow reflectance peak. Doping of the graphene to achieve Fermi-level tuning is shown to shift the wavelength of the frustration phenomenon, thereby enabling the use of the device as a modulator. A reduction of 20% in the switching energy is expected due to the unique principle of operation which, crucially and contrary to most work in this field, does not rely on electroabsorption but electrorefraction changes in graphene. This coupled SPP resonator geometry also permits efficient channeling of optical energy from free space into graphene’s SPP at near-infrared frequencies.
Synthesis, structure, and reactivity of a zirconocene complex of cyclobutene (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, structure, and reactivity of a zirconocene complex of cyclobuteneRichard A. Fisher and Stephen L. BuchwaldCite this: Organometallics 1990, 9, 3, 871–873Publication Date (Print):March 1, 1990Publication History Published online1 May 2002Published inissue 1 March 1990https://pubs.acs.org/doi/10.1021/om00117a057https://doi.org/10.1021/om00117a057research-articleACS PublicationsRequest reuse permissionsArticle Views326Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Metformin for chemoprevention of lung cancer in high-risk overweight or obese individuals. (2023)

TPS10636 Background: Lung cancer is the most common cause of cancer-related deaths in the United States, with tobacco smoking being the most important risk factor. However, ~60% of individuals at a high risk for lung cancer or with early-stage lung cancer are either overweight or obese. Preliminary studies suggest that the diabetes drug metformin improves survival in high BMI lung cancer patients and inhibits lung cancer progression in preclinical models, likely through its effects on the obesity-triggered changes to the immune microenvironment of the lung, particularly, the regulatory T cells (Tregs) in the airway. Given the known dysregulation of Tregs in obesity and the importance of Tregs in lung carcinogenesis, we hypothesize that metformin therapy will reprogram the immune defense of obesity in directions that are consistent with the control of nascent lung tumor development. While more generalized lung cancer prevention approaches have to date shown limited effectiveness, the targeting of a specific subset of individuals at high risk for lung cancer provides a precision prevention approach, which is likely to be more effective. Methods: This is an open-label, randomized, wait-list control trial, where 50 non-diabetic obese/overweight former smokers with over 20 pack year smoking history and PLCOm2012 Lung Cancer Risk Prediction score above 1.34% will be enrolled. They will be equally randomized to either oral metformin or no treatment for 26 weeks followed by partial crossover, whereby no-treatment subjects will receive metformin for 26 weeks. The open-label, wait-list control design allows inclusion of a control group to assess stability of the primary biomarker in an untreated population while retaining the statistical power of 40 metformin-treated subjects (assuming 20% subject attrition) and will aid accrual since all trial participants will be treated. Treatment regimen is one daily dose of metformin at 500 mg for 1 week followed by 1000 mg for the second week and 2000 mg thereafter for a total of 24 weeks. Sampling for endpoint assessment include bronchoscopy with biopsy and bronchoalveolar lavage (BAL) and blood collection before and after completion of metformin treatment. The primary endpoint is to evaluate the effect of metformin treatment on the expression of PD-1, an immune checkpoint factor, on BAL Tregs. The secondary endpoints include stability of BAL Treg PD-1 expression over time and the impact of metformin on circulating immune cells. Trial sites include Roswell Park Comprehensive Cancer Center, the Rocky Mountain Regional Veterans Affairs Medical Center, and University of British Columbia, Vancouver. Since the trial opened to accrual in March 2022, 77 patients have been pre-screened and 19 were consented. Among them, 10 participants have been enrolled and randomized, 5 in each arm. We expect to complete accrual by April 2024. Clinical trial information: NCT04931017 .
An Improved Dynamic Compact Thermal Model for Non-Linear and Non-Homogeneous Heat Diffusion Problems (2020)

We address the problem of generating Dynamic Compact Thermal Models for non-linear and non-homogeneous heat diffusion problems. We propose a novel Model Order Reduction technique that is based on i) a specifically designed discretization that properly models the non-linear behaviour of different materials, and ii) the introduction of an improved Hyper Reduction method that dramatically reduces the problem dimension. Our experiments show that our method performs similarly to full Finite Volume simulation in terms of accuracy, while being much more computationally efficient.
Amphiphilic Co-networks with Moisture-Induced Surface Segregation for High-Performance Nonfouling Coatings (2011)

Herein we report the design of a photocurable amphiphilic co-network consisting of perfluoropolyether and poly(ethylene glycol) segments that display outstanding nonfouling characteristics with respect to spores of green fouling alga Ulva when cured under high humidity conditions. The analysis of contact angle hysteresis revealed that the poly(ethylene glycol) density at the surface was enhanced when cured under high humidity. The nonfouling behavior of nonbiocidal surfaces against marine fouling is rare because such surfaces usually reduce the adhesion of organisms rather than inhibit colonization. We propose that the resultant surface segregation of these materials induced by high humidity may be a promising strategy for achieving nonfouling materials, and such an approach is more important than simply concentrating poly(ethylene glycol) moieties at an interface because the low surface energy has been maintained in our work.
Structure‐Based Evolution of G Protein‐Biased μ‐Opioid Receptor Agonists (2022)

The μ-opioid receptor (μOR) is the major target for opioid analgesics. Activation of μOR initiates signaling through G protein pathways as well as through β-arrestin recruitment. μOR agonists that are biased towards G protein signaling pathways demonstrate diminished side effects. PZM21, discovered by computational docking, is a G protein biased μOR agonist. Here we report the cryoEM structure of PZM21 bound μOR in complex with G<sub>i</sub> protein. Structure-based evolution led to multiple PZM21 analogs with more pronounced G<sub>i</sub> protein bias and increased lipophilicity to improve CNS penetration. Among them, FH210 shows extremely low potency and efficacy for arrestin recruitment. We further determined the cryoEM structure of FH210 bound to μOR in complex with G<sub>i</sub> protein and confirmed its expected binding pose. The structural and pharmacological studies reveal a potential mechanism to reduce β-arrestin recruitment by the μOR, and hold promise for developing next-generation analgesics with fewer adverse effects.
Numerical Study of Branched Turboprop Inlet Ducts Using a Multiple Block Grid Procedure (1991)

An important requirement in the design of an inlet duct of a turboprop engine is the ability to provide foreign object damage protection. A possible method for providing this protection is to include a bypass branch duct as an integral part of the main inlet duct. This arrangement would divert ingested debris away from the engine through the bypass. However, such an arrangement could raise the possibility of separated flow in the inlet, which in turn can increase pressure losses if not properly accounted for during the design. A fully elliptic three-dimensional body-fitted computational fluid dynamics (CFD) code based on pressure correction techniques has been developed that has the capability of performing multiple block grid calculations compatible with present day turboshaft and turboprop branched inlet ducts. Calculations are iteratively performed between sets of overlapping grids with one grid representing the main duct and a second grid representing the branch duct. Both the grid generator and the flow solver have been suitably developed to achieve this capability. The code can handle multiple branches in the flow. Using the converged flow field from this code, another program was written to perform a particle trajectory analysis. Numerical solutions were obtained on a supercomputer for a typical branched duct for which experimental flow and pressure measurements were also made. The flow separation zones predicted by the calculations were found to be in good agreement with those observed in the experimental tests. The total pressure recovery factors measured in the experiments were also compared with those obtained numerically. Within the limits of the grid resolution and the turbulence model, the agreement was found to be fairly good. In order to simulate the path of debris entering the duct, the trajectories of spherical particles of different sizes introduced at the inlet were determined.
SU‐FF‐I‐50: Whole Body and Distal Organ‐Specific Dosimetry Using Parallel SN Methods (2007)

Purpose: To create a new methodology for dose computations applicable to general medical physics applications, based upon a direct deterministic solution of the (3‐D) Boltzmann transport equation (BTE). Method and Materials: Using the multigroup discrete ordinates (S N ) deterministic method in the PENTRAN‐MP (Parallel Environment Neutral‐particle TRANsport‐Medical Physics) code system, fluxes and corresponding doses were determined for a clinical test case using a UF Series B whole‐body voxelized pediatric patient phantom. With a 90 keV planar x‐ray source, we performed two sets of transport calculations based on the same phantom model, employing both the Monte Carlo (MC) and S N methods. S N calculations were performed using PENTRAN, and the MCNP5 code was used for MC calculations. Post processing in the PENTRAN‐MP code system includes seamless parallel data extraction using the PENDATA code, followed by application of the 3D‐DOSE code to compute dose in each phantom voxel, with dose‐volume histograms for critical organs of interest. Results: We demonstrate that the deterministic S N and MC solutions are, in the vicinity of the source region, completely in agreement; the largest statistical error of the MC simulation was &lt;5%, typically averaging &lt;2%. Moreover, the deterministic S N method also provided globally converged results in each voxel at sites distal to the source (in ∼3 hrs on 16 processors), where the MC results on the same computing platform had significant out of field error, and would require a significantly longer running time (estimated at &gt;2000 hrs) to produce meaningful results with an acceptable stochastic error to enable comparison with the well‐converged S N results. Conclusions: A new methodology for 3D dose calculations has been developed based on a parallel discrete ordinates (S N ) solution of the BTE. With the proper discretization applied, the S N method presents an accurate, fast solution yielding a complete 3‐D dose distribution without stochastic error.
In vitro study of the antioxydant properties of nonsteroidal anti-inflammatory drugs by chemiluminescence and electron spin resonance (ESR) (2000)

peer reviewed
Metabolism of a Plant Wax Paraffin (n-Nonacosane) by a Soil Bacterium (Micrococcus cerificans) (1968)

SUMMARY: Long-chain paraffins, such as nonacosane, reach the soil from plants and are degraded by micro-organisms. The ability of one soil organism, Micro-coccus cerificans, to grow on cabbage paraffin (n-nonacosane) was studied. Unlike the pattern seen with hexadecane, waxy esters were not produced when nonacosane was the sole carbon source, but esters were formed when a co-oxidation technique of [14C] n-nonacosane with hexadecane was employed. The alcohol and acid portions of the radioactive esters formed were primarily of chain length C16 C17 and C18; neither nonacosanol nor nonacosanoic acid were detected. Thus the nonacosanol and nonacosanoic acid which might have been produced from n-nonacosane must have been oxidized to shorter-chain compounds which in turn were incorporated into waxy esters as well as other lipids.
Degenerative ataxias, from genes to therapies (2016)

<h3>Objective:</h3> To review progress in spinocerebellar ataxias (SCAs) and novel approaches to treatment. <h3>Results and conclusions:</h3> Autosomal dominant ataxias are now referred to as SCAs, with polyglutamine expansion mutations constituting the most common cause of SCAs. Phenotypic variation in patients with SCA is remarkable even in patients with identical mutations. In patients with SCA2, cerebellar ataxia is typically associated with slowed saccadic eye movements. In addition to classic cerebellar and brainstem signs, however, SCA2 can also present as a parkinsonian syndrome or as amyotrophic lateral sclerosis. After identifying the <i>SCA2</i> gene (gene symbol <i>ATXN2</i>) in 1996, we generated several mouse models that recapitulated salient features of the human disease. In these models, behavioral and physiologic changes preceded cell death. Modified antisense oligonucleotides (ASOs) provide a unique tool to target mRNA transcripts in vivo with extended stability of ASOs and better activation of RNAse H. We generated methoxyethyl group–gapmer ASOs that reduced <i>ATXN2</i> expression &gt;80% in vitro and then progressed the lead ASO to in vivo testing in an SCA2 mouse model. Compared to intraventricular injection of saline, treatment with ASO resulted in significant knockdown of endogenous mouse and human transgenic <i>ATXN2</i>. In addition, progression of the motor phenotype was slowed and Purkinje cell firing in the acute cerebellar slice normalized. ASO-based therapies are underway in humans providing hope that this approach will also be applicable to patients with cerebellar degenerations.
Modeling Steam-Assisted Gravity Drainage With a Black-Oil Proxy (2013)

Summary This paper describes an alternative approach to model steam-assisted gravity drainage (SAGD) with an isothermal black-oil (BO) reservoir simulator. The oil-viscosity reduction caused by heating in the actual SAGD process is emulated by a tuned saturated pseudo-oil viscosity relation in which solution gas/oil ratio (Rs) is used as a “proxy for temperature.” In the BO formulation, fully saturated oil viscosity (μo*) at reservoir pressure equals μo that would be attained at steam-chamber temperature (T*) in the actual SAGD process; initial oil viscosity (μoi) with initial Rs = 0 represents initial oil viscosity at reservoir temperature; and BO gas properties represent steam at T*. After careful analysis of the SAGD process, one finds that oil flows only along a narrow zone along the outer edge of the steam chamber—the “edge oil-flow zone.” The temperature gradient within this narrow zone is perpendicular to the oil-flow direction and is practically impossible to model with any precision because of the large temperature variation and dynamic steam-chamber shape over time. The BO-model solubility gradient also varies, analogous to temperature in a thermal model, from zero to fully saturated (Rs*) with an associated drop in oil viscosity from μoi to μo*. SAGD design requires many hundreds of runs to find operational conditions that maximize economic value (e.g., injector and producer location, rates, pattern spacing, and steam-chamber temperature T*). The proposed BO proxy model runs several times faster than a thermal model while maintaining similar performance behavior. The proxy-model saturated pseudo-oil viscosity μo(p) relation used is found by history matching a full-physics thermal-model performance prediction of oil rate, bottomhole flowing pressure, and cumulative oil for a 2D homogeneous model. We have found a single-constant μo(p) equation that yields a good match to thermal SAGD performance. The tuned pseudo-oil viscosity relation honors the measured initial reservoir and fully heated (at T*) oil viscosities. Its dependence on Rs is not physical, but reflects the use of Rs as a transform variable for temperature, capturing the strong spatial variation of temperature and oil viscosity within the localized steam/oil boundary region in which oil has been mobilized. The pseudo-oil viscosity relation, defined by a single empirical best-fit constant n—for a given T* and a set of thermal properties—appears to be applicable for a wide range of reservoir heterogeneity, injection and production rates, and well placement. Consequently, it should be possible to use the BO proxy model for SAGD optimization of T*, control rates, and injector/producer vertical-depth difference. We also see the potential of using the BO proxy model for solvent-based SAGD, with the pseudo-oil viscosity model depending on both T* and solvent; thermal compositional modeling is yet even slower and less suitable for optimization.
<title>Recent progress in flexible OLED displays</title> (2001)

Organic light emitting device (OLED) technology has recently been shown to demonstrate excellent performance and cost characteristics for use in numerous flat panel display (FPD) applications. OLED displays emit bright, colorful light with excellent power efficiency, wide viewing angle and video response rates. OLEDs are also demonstrating the requisite environmental robustness for a wide variety of applications. OLED technology is also the first FPD technology with the potential to be highly functional and durable in a flexible format. The use of plastic and other flexible substrate materials offers numerous advantages over commonly used glass substrates, including impact resistance, light weight, thinness and conformability. Currently, OLED displays are being fabricated on rigid substrates, such as glass or silicon wafers. At Universal Display Corporation (UDC), we are developing a new class of flexible OLED displays (FOLEDs). These displays also have extremely low power consumption through the use of electrophosphorescent doped OLEDs. To commercialize FOLED technology, a number of technical issues related to packaging and display processing on flexible substrates need to be addressed. In this paper, we report on our recent results to demonstrate the key technologies that enable the manufacture of power efficient, long-life flexible OLED displays for commercial and military applications.
An Analytical Investigation of the Impact of Design Parameters on the Performance of Centrifugal Pendulum Vibration Absorbers (2019)

Abstract A generalized nonlinear time-varying, planar dynamic model of bifilar centrifugal pendulum vibration absorbers (CPVA) is proposed. This dynamic model enables fast prediction of vibration reduction performance of any CPVA design considering the impact of absorber rollers, gravity, end stops and translational motion of the system. The modeling framework provides comparative, simultaneous simulation results for numerous different design possibilities, and thus can be used to optimize CPVA designs. The dynamic model is generic and can handle N individually designed absorbers on a rotor with numerous path options ranging from circular to cycloid. Absorbers can be designed to be equally or unequally spaced. In this study, first the dynamic model of the bifilar CPVAs is derived. Then, case studies are provided to showcase the capabilities of the modeling framework. Initially, maximum applicable dynamic torque to a CPVA and vibration reduction performance are investigated by considering the effect of tuning order and different absorber path options for different operating speeds. Then, impact of different modelling features on system frequency response and limit dynamic torque is investigated. Interactions between the important design parameters are highlighted. Finally, the influence of end stop positioning on the CPVA dynamic response is illustrated.
Molecular Design of Processable High Tg Thermoplastic Matrix Resins and Structural Adhesives (1993)

International audience