gebhart/patrepeval huggingface dataset:
Identification of SR2211: A Potent Synthetic RORγ-Selective Modulator (2012)

Nuclear receptors (NRs) are ligand-regulated transcription factors that display canonical domain structure with highly conserved DNA-binding and ligand-binding domains. The identification of the endogenous ligands for several receptors remains elusive or is controversial, and thus these receptors are classified as orphans. One such orphan receptor is the retinoic acid receptor-related orphan receptor γ (RORγ). An isoform of RORγ, RORγt, has been shown to be essential for the expression of Interleukin 17 (IL-17) and the differentiation of Th17 cells. Th17 cells have been implicated in the pathology of several autoimmune diseases, including multiple sclerosis (MS) and rheumatoid arthritis (RA). Genetic ablation of RORγ alone or in combination with RORα in mice led to impaired Th17 differentiation and protected the mice from development of experimental autoimmune encephalomyelitis (EAE), a mouse model of MS. Here we describe SR2211, a selective RORγ modulator that potently inhibits production of IL-17 in cells.
Renal phenotype of inwardly rectifying potassium channel Kcnj16 (Kir 5.1) knockout in the Dahl salt‐sensitive rats (893.16) (2014)

The inward‐rectifying channels play an important role in the control of resting membrane potential and tubular homeostasis in the kidney. To illuminate the importance of Kcnj16 (Kir 5.1) in the context of a disease state in vivo, we generated a Kcnj16 knockout rat model in Dahl salt‐sensitive (SS) background by using zinc finger nuclease (ZFN) technology. ZFN against Kcnj16 caused a 18‐bp in‐frame deletion that occurred in the second protein transmembrane domain. IHC analysis demonstrated highly specific expression of Kcnj16 on the basolateral membranes of cortical collecting ducts and distal convoluted tubules in the control kidneys of SS and Sprague Dawley rats, which was completely abolished in Kcnj16‐/‐ rats; thus, successful knock out of this protein and consequent degradation of the channel in renal tubules were shown. The mean arterial pressure was significantly lower in Kcnj16‐/‐ compared to wild type SS rats (91.3±1.8 to 104.7±5.5 mmHg) when animals were fed a low salt (0.4%) diet. BUN, potassium and magnesium plasma concentrations were significantly modulated in knock out rats. Urea electrolyte balance was also disturbed compared to wild type animals. Importantly, change of the diet to high salt (4%) chow resulted in mortality of KO rats within 1‐2 days. These data demonstrate critical role of Kcnj16 channels in renal salt handling and in the development of salt‐sensitive hypertension. Grant Funding Source : Supported by NIH HL108880 and ADA 1‐10‐BS‐168 to A.S., NHLBI 5RC2HL101681 to H.J.J
Experimental Validation of Energy Storage System Management Strategies for a Local DC Distribution System of More Electric Aircraft (2010)

The local DC power distribution system of More Electric Aircraft is one of the cores of the electric power transmission. Because the mechanical source (turbine engine) is unidirectional, the system is not totally reversible. Some storage and dissipation systems are necessary to store or/and dissipate the returned energy to maintain the dc bus voltage. Different power-management strategies are proposed and compared. The development of experimental test benches is necessary to validate these strategies. In this paper, we present a 3-kW test bench, emulating a unidirectional source that supplies a bidirectional load with the help of a hybrid system using supercapacitors and a dissipation system. The experimental validation of the power-management strategies is presented in this paper, too.
Electrooxidation of Organics in Waste Water (1990)

&lt;div class="htmlview paragraph"&gt;Electrooxidation is a means of removing organic solutes directly from waste waters without the use of chemical expendables. Research sponsored by NASA Johnson Space Center is currently being pursued at Texas A&amp;amp;M University to demonstrate the feasibility of the concept for oxidation of organic impurities common to urine, shower waters and space habitat humidity condensates. Electrooxidation of urine and waste water ersatz was experimentally demonstrated. This paper discusses the electrooxidation principle, reaction kinetics, efficiency, power, size, experimental test results and water reclamation applications. Process operating potentials and the use of anodic oxidation potentials that are sufficiently low to avoid oxygen formation and chloride oxidation are described. The design of a novel electrochemical system that incorporates a membrane-based electrolyte based on parametric test data and current fuel cell technology is presented.&lt;/div&gt;
Hydrolysis of Magnesium Methoxide. Effects of Toluene on Gel Structure and Gel Chemistry (2001)

The hydrolysis of magnesium methoxide in methanol or methanol−toluene solvents with a water-to-methoxide molar ratio of 2 has been studied. The gel obtained from the hydrolysis of magnesium methoxide appears to be polymeric based on the mass fractal dimensions and TEM micrographs. The presence of toluene accelerates the hydrolysis and gelation processes. The fractal dimensions of the wet gels obtained in the absence and in the presence of toluene were 2.22 and 1.80, respectively. Both of these observations indicate that the presence of toluene changes the fractal growth from a reaction-limited to a diffusion-limited growth. In either case, the hydrolysis is only completed partially and produces an intimate gel of MgO−Mg(OH)2−Mg(OH)(OCH3). The N2 BET surface area of the dry gel, obtained with a toluene to methanol volume ratio of 1.60, is 1011 m2/g, which is 1.74 times as large as that of the gel obtained in the absence of toluene.
A streptococcal effector protein that inhibits Porphyromonas gingivalis biofilm development (2010)

Dental plaque formation is a developmental process involving cooperation and competition within a diverse microbial community, approximately 70 % of which is composed of an array of streptococci during the early stages of supragingival plaque formation. In this study, 79 cell-free culture supernatants from a variety of oral streptococci were screened to identify extracellular compounds that inhibit biofilm formation by the oral anaerobe Porphyromonas gingivalis strain 381. The majority of the streptococcal supernatants (61 isolates) resulted in lysis of P. gingivalis cells, and some (17 isolates) had no effect on cell viability, growth or biofilm formation. One strain, however, produced a supernatant that abolished biofilm formation without affecting growth rate. Analysis of this activity led to the discovery that a 48&emsp14;kDa protein was responsible for the inhibition. Protein sequence identification and enzyme activity assays identified the effector protein as an arginine deiminase. To identify the mechanism(s) by which this protein inhibits biofilm formation, we began by examining the expression levels of genes encoding fimbrial subunits; surface structures known to be involved in biofilm development. Quantitative RT-PCR analysis revealed that exposure of P. gingivalis cells to this protein for 1&emsp14;h resulted in the downregulation of genes encoding proteins that are the major subunits of two distinct types of thin, single-stranded fimbriae (fimA and mfa1). Furthermore, this downregulation occurred in the absence of arginine deiminase enzymic activity. Hence, our data indicate that P. gingivalis can sense this extracellular protein, produced by an oral streptococcus (Streptococcus intermedius), and respond by downregulating expression of cell-surface appendages required for attachment and biofilm development.
Trust No One Else: Detecting MITM Attacks against SSL/TLS without Third-Parties (2012)

The security guarantees provided by SSL/TLS depend on the correct authentication of servers through certificates signed by a trusted authority. However, as recent incidents have demonstrated, trust in these authorities is not well placed. Increasingly, certificate authorities (by coercion or compromise) have been creating forged certificates for a range of adversaries, allowing seemingly secure communications to be intercepted via man-in-the-middle (MITM) attacks. A variety of solutions have been proposed, but their complexity and deployment costs have hindered their adoption. In this paper, we propose Direct Validation of Certificates (DVCert), a novel protocol that, instead of relying on third-parties for certificate validation, allows domains to directly and securely vouch for their certificates using previously established user authentication credentials. By relying on a robust cryptographic construction, this relatively simple means of enhancing server identity validation is not only efficient and comparatively easy to deploy, but it also solves other limitations of third-party solutions. Our extensive experimental analysis in both desktop and mobile platforms shows that DVCert transactions require little computation time on the server (e.g., less than 1 ms) and are unlikely to degrade server performance or user experience. In short, we provide a robust and practical mechanism to enhance server authentication and protect web applications from MITM attacks against SSL/TLS.
Quaternary Ammonium 3‐(Aminoethoxy)pyridines as Antinociceptive Agents. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Ionization dilatation effects in fused silica from 2 to 18-keV electron irradiation (1974)

We have used low-energy electron irradiations in conjunction with a bending-cantilever-plate technique to investigate the volume dilatations produced by ionization effects in fused silica. Our irradiations generally cause compaction in agreement with previous data from high-energy electron irradiations, but we consistently observe a slowly saturating compaction-dose relationship rather than the sublinear power-law relationship seen in the high-energy data. Our results show agreement with the apparent ionization compaction effect extracted from low-dose-rate 1H+-ion-implantation experiments. We find no dose-rate dependence in the electron ionization compaction effect, in marked contrast with the apparent ionization compaction effect in the implantation experiments. We therefore conclude that the enhancement of the apparent ionization compaction effect at high dose rates in the implantation experiments results from an interaction between the ionization and the atomic displacements accompanying the implanation. By probing to various depths at a constant dose and dose rate, we find that the electron irradiation compaction effect is generally enhanced within several hundred angstroms of the sample surface. There is no apparent threshold for onset of the compaction mechanism for incident electron energies between 2.2 and 18 keV. Finally, we observe the low-fluence expansion effect in impure fused silica as seen by other workers but establish here that it is primarily an ionization-stimulated phenomenon that occurs only when the irradiation current varies with time.
Unusual Local Recurrence with Distant Metastasis after Successful Endoscopic Submucosal Dissection for Colorectal Mucosal Cancer (2016)

Intramucosal colorectal cancer (CRC) is thought not to metastasize because the colonic lamina propria lacks lymphatics. Only a few recent case reports have suggested lymph node metastasis from intramucosal CRC, but there is no clear evidence supporting the metastatic potential of intramucosal CRC. Hence, endoscopic resection is regarded as curative treatment for intramucosal CRC. This report describes two cases of unusual local recurrence with distant metastasis in patients who had previously undergone successful endoscopic submucosal dissection for intramucosal CRC. The recurrent colorectal lesions developed at the site of the previous endoscopic submucosal dissection scars in a relatively short-term period, and the pathologic findings showed an "undermining" invasion pattern without surrounding mucosal change. Based on the clinical course and pathological findings, we concluded that the second colorectal lesions were recurrences rather than <i>de novo</i> cancers.
Spatio-Temporal Characterization of High-Power Few-Cycle Pulses by SEA-F-SPIDER and Time-Domain Ptychography (2018)

In recent years OPCPA and NOPCPA laser systems have shown the potential to supersede Ti: Sapphire plus nonlinear post-compression based laser systems to drive next generation attosecond light sources via direct amplification of few-cycle pulses to high pulse energies at high repetition rates. With the advent of these laser systems comes a need for improved pulse characterization technology. Due to the non-collinear interaction in NOPA based laser systems the amplified few-cycle pulses can suffer from spatio-temporal couplings. Most spatio-temporal pulse characterization techniques are based on separating spatial and temporal measurements in a test-plus reference-pulse scheme. Here we review two self-referencing techniques that are able to perform spatio-temporal pulse characterization of few-cycle pulses.
Generation of highly tunable microwave radiation via a relativistic ionization front (2002)

A novel method of continuously upshifting the frequency of an electromagnetic wave is presented. This technique utilizes a relativistically propagating ionization front to simultaneously upshift and compress the source radiation. Using existing technology, it is possible to apply this technique to obtain a single source that is tunable from the microwave (30 GHz) to the millimeter (300 GHz) regime. Peak powers in the kilowatt range with pulse durations of much less than 1 ns are feasible. This technique has been demonstrated in a proof-in-principle experiment by upshifting 34.8-GHz radiation to greater than 116 GHz, with the degree of upshift being continuously tunable. The experimental arrangement employed a microwave cavity filled with azulene vapour. It should be possible to scale the technique to higher frequencies and higher powers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Thin film mixed potential nitrogen oxide sensor development for stationary reciprocating engine applications. (2004)

Mixed potential sensors using thin film Mg-doped LaCrO{sub 3} working electrodes, Pt counter electrodes, and thin film YSZ electrolytes on Al{sub 2}O{sub 3} polycrystalline substrates were prepared and studied at 600 and 650 C in 10.4% O{sub 2}/N{sub 2} balance and in air atmospheres for NO, NO{sub 2}, CO, and hydrocarbon responses. The lanthanum chromite-based sensors showed preferential sensitivity to NO{sub 2} with cross sensitivity to CO and nonmethane hydrocarbons such as C{sub 3}H{sub 6} and C{sub 3}H{sub 8}. In contrast, sensors with spinel NiCr{sub 2}O{sub 4} working electrodes show minimal sensitivity to NO{sub 2}. The use of a heated Pt black pre-catalyst upstream to the sensor was demonstrated and the use of this pre-catalyst effectively removed the CO and hydrocarbon response however more work needs to be done to understand the NO/NO{sub 2} chemistry post catalyst. Studies conducted for up to 800 hrs at 600 C show minimal aging in these devices.
Hive Transplantation Has Minimal Impact on the Core Gut Microbiome of the Australian Stingless Bee, Tetragonula carbonaria (2023)

Bacteria residing in the guts of pollinating insects play a key role in nutrient acquisition, digestion, and resistance to pests and diseases. Imbalances in microbial flora in response to environmental change and stress can therefore impact insect health and resilience. This study is aimed at defining the core gut microbiome of the Australian native stingless bee, Tetragonula carbonaria, and exploring the impact of colony transplantation on gut health. The gut microbiomes of nine forager bees from natural (log) and manufactured (box) hives were examined via 16S rRNA gene amplicon sequencing. Some differences were observed at the ASV level between the microbiomes of log and box hive bees. However, a core microbiome, dominated by Lactobacillus spp., unclassified Acetobacteraceae spp., and Bombella spp., was maintained. Further, the inferred functional potential of the microbiomes was consistent across all individuals. This study highlights that although hive transplantation has an impact on the overall diversity of stingless bee gut microbiomes, it is unlikely to have a significant negative impact on the overall health and resilience of the colony.
The Race To Find Antivirals for Zika Virus (2017)

Zika virus (ZIKV), a flavivirus transmitted by mosquitoes, was an almost neglected pathogen until its introduction in the Americas in 2015 and its subsequent explosive spread throughout the continent, where it has infected millions of people. The virus has caused social and sanitary alarm, mainly due to its association with severe neurological disorders (Guillain-Barré syndrome and microcephaly in fetuses and newborns). Nowadays, no specific antiviral therapy against ZIKV is available. However, during the past months, a great effort has been made to search for antiviral candidates using different approaches and methodologies, ranging from testing specific compounds with known antiviral activity to the screening of libraries with hundreds of bioactive molecules. The identified antiviral candidates include drugs targeting viral components as well as cellular ones. Here, an updated review of what has been done in this line is presented.
Can shared leadership enhance clinical team management? A systematic review (2019)

Although studies have acknowledged the relevance of SL in healthcare service and delivery, a systematic, evidence-based and robust evaluation of behavioural patterns and the benefits of SL in this field is still missing.
Ruthenium Tetroxide as a Phase Transfer Catalyst in Biphasic System and Its in situ Electrochemical Regeneration: Oxidation of Aromatic Primary Alcohol and Aldehydes (1995)

The application of ruthenium tetroxide as a phase transfer catalyst in a biphasic system comprised of carbon tetrachloride and saturated aqueous sodium chloride at platinised titanium anode, for the regeneration of spent oxidant, for the oxidation of benzyl alcohol, benzaldehyde and p-anisaldehyde has been investigated.
Colorless optical sources for fiber-optic access networks of new generation (2014)

We present recent advances in the development of self-seeded colorless WDM-PON optical links employing modulation averaging. Modulation-averaging, employed as a reflector at the remote node, improves the link margin and allows for a wider range of bias conditions at the transmitter. The modulation-averaging reflector is a passive optical device and therefore the remote nodes in our proposed WDM-PON system remain passive, with no power needed to accomplish this improvement. The suitability of proposed architecture for next-generation optical access is demonstrated by transmission over 60 km at 1.25 GBaud line rate.
Transport of bacteria in porous media: II. A model for convective Transport and growth (1994)

A model is presented for the coupled processes of bacterial growth and convective transport of bacteria has been modeled using a fractional flow approach. The various mechanisms of bacteria retention can be incorporated into the model through selection of an appropriate shape of the fractional flow curve. Permeability reduction due to pore plugging by bacteria was simulated using the effective medium theory. In porous media, the rates of transport and growth of bacteria, the generation of metabolic products, and the consumption of nutrients are strongly coupled processes. Consequently, the set of governing conservation equations form a set of coupled, nonlinear partial differential equations that were solved numerically. Reasonably good agreement between the model and experimental data has been obtained indicating that the physical processes incorporated in the model are adequate. The model has been used to predict the in situ transport and growth of bacteria, nutrient consumption, and metabolite production. It can be particularly useful in simulating laboratory experiments and in scaling microbial-enhanced oil recovery or bioremediation processes to the field. (c) 1994 John Wiley & Sons, Inc.
A staggered-grid lowrank finite-difference method for elastic wave extrapolation (2020)

Elastic wave extrapolation in the time domain is significant for an elastic wave equation-based processing. To improve the simulation reliability and accuracy of decoupled elastic P- and S- waves, we propose the staggered-grid lowrank finite-difference method based on the elastic wave decomposition. For elastic wave propagation, a lowrank finite-difference method based on the staggered grid is derived to improve the accuracy. Regarding the application of the decoupled elastic wave equation, we derive the finite-difference scheme coefficients which are dependent on velocity. Based on the elastic wave decomposition and plane wave theories, we formulate the elastic wave-extrapolation operators, which contain trigonometric adjustment factors. Accordingly, by applying the lowrank method to approximating the operators, the finite- difference scheme is designed to discretize the decoupled wave equation. The derivation processing implies the combination of elastic wave-mode decomposition and extrapolation. The proposed method enables elastic P- and S-waves to extrapolate in the time-space domain separately and produces accurate P-and S-wave components simultaneously. Dispersion analysis suggests that our proposed method is reliable and accurate in a wide range of wavenumber. Numerical simulation tests on a simple model and the Marmousi2 model validate the accuracy and effectiveness of the method, showing its ability in handling complex structures. Although the operators are accurate only when the medium is homogeneous, they are of high accuracy when the velocity gradient is quite small and are applicable when the velocity gradient is large. The subsequent results of reverse time migration for the Marmousi2 model also suggest that the proposed method is enough to serve as an extrapolator in elastic reverse time migration.
A Course-Based Undergraduate Research Experience in CRISPR-Cas9 Experimental Design to Support Reverse Genetic Studies in Arabidopsis thaliana (2021)

Gene-editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene-editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a 5-week period. In the remote-learning version, students performed homology searches, designed guide RNAs (gRNAs) and primers, and learned the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as during closures that have occurred in response to the COVID-19 pandemic. In person, students designed gRNAs, cloned CRISPR-Cas9 constructs, and performed genetic transformation of Arabidopsis thaliana. Students learned how to design effective gRNA pairs targeting their assigned gene with an 86% success rate. Final exams tested students' ability to apply knowledge of an unfamiliar genome database to characterize gene structure and to properly design gRNAs. Average final exam scores of ∼73% and ∼84% for in-person and remote-learning CUREs, respectively, indicated that students met learning outcomes. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of sections. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be adapted readily to other organisms or projects that employ gene editing.