gebhart/patrepeval huggingface dataset:
Protein Disulfide Bond Formation in the Cytoplasm during Oxidative Stress (2004)

The majority of disulfide-linked cytosolic proteins are thought to be enzymes that transiently form disulfide bonds while catalyzing oxidation-reduction (redox) processes. Recent evidence indicates that reactive oxygen species can act as signaling molecules by promoting the formation of disulfide bonds within or between select redox-sensitive proteins. However, few studies have attempted to examine global changes in disulfide bond formation following reactive oxygen species exposure. Here we isolate and identify disulfide-bonded proteins (DSBP) in a mammalian neuronal cell line (HT22) exposed to various oxidative insults by sequential nonreducing/reducing two-dimensional SDS-PAGE combined with mass spectrometry. By using this strategy, several known cytosolic DSBP, such as peroxiredoxins, thioredoxin reductase, nucleoside-diphosphate kinase, and ribonucleotide-diphosphate reductase, were identified. Unexpectedly, a large number of previously unknown DSBP were also found, including those involved in molecular chaperoning, translation, glycolysis, cytoskeletal structure, cell growth, and signal transduction. Treatment of cells with a wide range of hydrogen peroxide concentrations either promoted or inhibited disulfide bonding of select DSBP in a concentration-dependent manner. Decreasing the ratio of reduced to oxidized glutathione also promoted select disulfide bond formation within proteins from cytoplasmic extracts. In addition, an epitope-tagged version of the molecular chaperone HSP70 forms mixed disulfides with both beta4-spectrin and adenomatous polyposis coli protein in the cytosol. Our findings indicate that disulfide bond formation within families of cytoplasmic proteins is dependent on the nature of the oxidative insult and may provide a common mechanism used to control multiple physiological processes.
Episodic weakness and Charcot–marie–tooth disease due to a mitochondrial MT‐ATP6 mutation (2017)

Mitochondrial DNA mutations should be considered in patients with a history of episodic weakness and axonal inherited neuropathy (CMT2). The episodic weakness is responsive to acetazolamide therapy, and electrophysiological testing for periodic paralysis with a long exercise protocol is negative in these cases. Muscle Nerve 55: 922-927, 2017.
Optical breakdown of multilayer thin-films induced by ultrashort pulses at MHz repetition rates (2013)

Multilayer coatings composed of TiO(2), Ta(2)O(5), HfO(2), or Al(2)O(3) as high-index materials and SiO(2) as low-index material were investigated for laser-induced damage using 1 ps, 5 µJ pulses generated by a mode-locked Yb:YAG thin-disk oscillator operating at a wavelength of 1030 nm and repetition rate of 11.5 MHz. Previously reported linear band gap dependence of damage threshold at kHz repetition rates was confirmed also for the MHz regime. Additionally, we studied the effect of electric field distribution inside of the layer stack. We did not observe any significant influence of thermal effects on the laser-induced damage threshold in this regime.
An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes (2016)

Mesenchymal (lamellipodial) migration is heterogeneous, although whether this reflects progressive variability or discrete, 'switchable' migration modalities, remains unclear. We present an analytical toolbox, based on quantitative single-cell imaging data, to interrogate this heterogeneity. Integrating supervised behavioral classification with multivariate analyses of cell motion, membrane dynamics, cell-matrix adhesion status and F-actin organization, this toolbox here enables the detection and characterization of two quantitatively distinct mesenchymal migration modes, termed 'Continuous' and 'Discontinuous'. Quantitative mode comparisons reveal differences in cell motion, spatiotemporal coordination of membrane protrusion/retraction, and how cells within each mode reorganize with changed cell speed. These modes thus represent distinctive migratory strategies. Additional analyses illuminate the macromolecular- and cellular-scale effects of molecular targeting (fibronectin, talin, ROCK), including 'adaptive switching' between Continuous (favored at high adhesion/full contraction) and Discontinuous (low adhesion/inhibited contraction) modes. Overall, this analytical toolbox now facilitates the exploration of both spontaneous and adaptive heterogeneity in mesenchymal migration.
Molecular genetic approaches to malaria research (2016)

Understanding of the basic biology, pathogenesis, and transmission of Plasmodium falciparum at the cellular and molecular levels has dramatically improved since methods to transfect parasites were first developed. Established during the 1990s and refined further ever since, the ability to introduce recombinant DNA into P. falciparum and other Plasmodium species, particularly those infecting rodents, has enabled us to modify endogenous gene loci to study their functions at different stages of the parasite's lifecycle. The ability to modify the expression of essential genes in a controlled manner, the conditional knockdown approach, offers the opportunity to understand the function of essential proteins in the disease-causing blood stage of the lifecycle. These approaches are still being developed, but even as they are they offer a great opportunity to understand the function of proteins that are essential to blood-stage growth, information that will help prioritize these proteins as targets for further drug and vaccine development.
The traffic light bougie: a study of a novel safety modification (2014)

Use of a bougie is not without risk, and insertion too far may cause airway injury. We designed a new bougie with a 'traffic light' system to indicate depth of insertion. Forty anaesthetists were randomly assigned to insert either a conventional single-coloured bougie or a novel traffic light bougie. Depth of insertion was measured before and after railroading a tracheal tube. Participants were not informed as to the purpose of the colouring system. The median (IQR [range]) insertion depth of the traffic light bougie was 22 (21-24 [19-27]) cm and for the conventional bougie was 28 (21-32 [20-35]) cm (p = 0.011). Median (IQR [range]) insertion depth after railroading for the traffic light bougie was 25 (25-28 [21-34]) cm and for the conventional bougie was 30.5 (27-35 [23-40]) cm (p = 0.003). This simple colouring system appears to allow intuitive use and significantly reduced the depth of bougie insertion. This system could be also used with other airway exchange devices to improve safety.
Specific von Willebrand factor–cleaving protease in thrombotic microangiopathies: a study of 111 cases (2001)

Retrospective studies of patients with thrombotic microangiopathies (TMAs) have shown that a deficient activity of von Willebrand factor (vWF)-cleaving protease is involved in thrombotic thrombocytopenic purpura (TTP) but not in the hemolytic-uremic syndrome (HUS). To further analyze the relevance of this enzymatic activity in TMA diagnosis, a 20-month multicenter study of vWF-cleaving protease activity was conducted in adult patients prospectively enrolled in the acute phase of TMA. Patients with sporadic (n = 85), intermittent (n = 21), or familial recurrent (n = 5) forms of TMA (66 manifesting as TTP and 45 as HUS) were included. TMA was either idiopathic (n = 42) or secondary to an identified clinical context (n = 69). vWF-cleaving protease activity was normal in 46 cases (7 TTP and 39 HUS) and decreased in 65 cases (59 TTP and 6 HUS). A protease inhibitor was detected in 31 cases and was observed only in patients manifesting TTP with a total absence of protease activity. Among the 111 patients, mean vWF antigen levels were increased and the multimeric distribution of vWF was very heterogeneous, showing either a defect of the high-molecular-weight forms (n = 40), a normal pattern (n = 21), or the presence of unusually large multimers (n = 50). Statistical analysis showed that vWF-protease deficiency was associated with the severity of thrombocytopenia (P <.01). This study emphasizes that vWF-cleaving protease deficiency specifically concerns a subgroup of TMA corresponding to the TTP entity.
Entrapment and catalytic activity of gold nanoparticles in amine-functionalized MCM-41 matrices synthesized by spontaneous reduction of aqueous chloroaurate ions (2001)

There is tremendous current interest in the generation of nano-hybrid materials using silicate mesoporous materials. We describe herein a new process for the synthesis of gold nanoparticle–amine functionalized MCM-41 hybrid materials by the spontaneous reduction of chloroaurate ions within the silicate matrix. The gold nanoparticles thus formed are bound to the pores of the MCM-41 framework by amine functional groups and show excellent catalytic activity in hydrogenation reactions.
Ecofriendly Synthesis of Ceria Foam via Carboxymethylcellulose Gelation: Application for the Epoxidation of Chalcone (2015)

A simple and innovative process is described for the ecofriendly preparation of ceria foams via carboxymethylcellulose gelation by Ce4+ cations; heat treatment of the ensuing xerogels produces ceria foams. The influence of the concentration of cerium and of the calcination temperature of the xerogels is studied. Several characterization methods have been used and the obtained results demonstrate that this technique allows the controlled growth of ceria foams. The foamy structure apparently is responsible for UV absorption, and the ceria foam is basic enough to promote the epoxidation of chalcone; comparison of the catalytic activity of the ceria foam versus ceria prepared via a coprecipitation method shows that the ceria foam is most active as it promotes epoxidation of electron-deficient alkenes with dilute aqueous hydrogen peroxide.
Traceability Chain at KRISS from DC Quantum Hall Resistance to Farad Using Coaxial Bridges (2019)

A national traceability chain from dc quantum Hall resistance (QHR) to capacitance has been established at Korea Research Institute of Standards and Science using various impedance standards and coaxial bridges. An ac–dc calculable resistance standard of nominal value of 12.9 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{k}\Omega $ </tex-math></inline-formula> was used as a transfer standard from dc to ac at the frequency of 1.541 kHz. Two ac coaxial bridges, developed by INRiM, were employed: a ratio bridge, linking the 103- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{k}\Omega $ </tex-math></inline-formula> ac resistor to the 12.9- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{k}\Omega $ </tex-math></inline-formula> ac–dc calculable resistor calibrated in terms of the dc QHR and a quadrature bridge, calibrating the 1000 pF capacitors versus the 103- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{k}\Omega $ </tex-math></inline-formula> ac resistors. The ratio bridge defines the 103- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{k}\Omega $ </tex-math></inline-formula> resistor as a two-terminal-pair (2TP) standard and the 12.9- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{k}\Omega $ </tex-math></inline-formula> resistor as a four-terminal-pair standard; a cable correction was applied to the 2TP defined standard. The stability of all standards has been monitored for more than 3 years to be within a few parts in 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> . The capacitance value, obtained with the new traceability chain, shows an agreement (a few parts in 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> ) in a comparison with the reference values, traced from the National Institute for Standards and Technology (USA).
Analysis of Asphalt Pavement Materials and Systems (2007)

Proceedings of the Symposium on the Mechanics of Flexible Pavements, held at the 15th U.S. National Congress of Theoretical and Applied Mechanics in Boulder, Colorado, June 25-30, 2006, Sponsored by Pavement Committee of the Geo-Institute of ASCE; the Inelastic Committee and the Granular Materials Committee of the Engineering Mechanics Division of ASCE.
Self-assembly with fluorescence readout in a free base dipyrrin–polymer triggered by metal ion binding in aqueous solution (2019)

Profound morphological and fluorogenic changes ensue upon binding of a zinc ion by two polymers, each of which bears a single dipyrrin at one terminus, forming the bis(dipyrrinato)Zn(<sc>ii</sc>) complex.
Effect of Dipyridamole and Aspirin on Late Vein-Graft Patency after Coronary Bypass Operations (1984)

To study the prevention of occlusion of aortocoronary-artery bypass grafts, we concluded a prospective, randomized, double-blind trial comparing long-term administration of dipyridamole (begun two days before operation) plus aspirin (begun seven hours after operation) with placebo in 407 patients. Results at one month showed a reduction in the rate of graft occlusion in patients receiving dipyridamole and aspirin. At vein-graft angiography performed in 343 patients (84 per cent) 11 to 18 months (median, 12 months) after operation, 11 per cent of 478 vein-graft distal anastomoses were occluded in the treated group, and 25 per cent of 486 were occluded in the placebo group. The proportion of patients with one or more distal anastomoses occluded was 22 per cent of 171 patients in the treated group and 47 per cent of 172 in the placebo group. All grafts were patent within a month of operation in 94 patients in the placebo group and 116 patients in the treated group; late development of occlusions was reduced from 27 per cent in the placebo group to 16 per cent in the treatment group. The results show that dipyridamole and aspirin continue to be effective in preventing vein-graft occlusion late after operation, and we believe that such treatment should be continued for at least one year.
Estrogen Receptor-β Agonist Diarylpropionitrile: Biological Activities of R- and S-Enantiomers on Behavior and Hormonal Response to Stress (2008)

Estrogens have been shown to have positive and negative effects on anxiety and depressive-like behaviors, perhaps explained by the existence of two distinct estrogen receptor (ER) systems, ERalpha and ERbeta. The ERbeta agonist, diarylpropionitrile (DPN) has been shown to have anxiolytic properties in rats. DPN exists as a racemic mixture of two enantiomers, R-DPN and S-DPN. In this study, we compared R-DPN and S-DPN for their in vitro binding affinity, ability to activate transcription in vitro at an estrogen response element, and in vivo endocrine and behavioral responses. In vitro binding studies using recombinant rat ERbeta revealed that S-DPN has a severalfold greater relative binding affinity for ERbeta than does R-DPN. Furthermore, cotransfection of N-38 immortalized hypothalamic cells with an estrogen response element-luc reporter and ERbeta revealed that S-DPN is a potent activator of transcription in vitro, whereas R-DPN is not. Subsequently, we examined anxiety-like behaviors using the open-field test and elevated plus maze or depressive-like behaviors, using the forced swim test. Ovariectomized young adult female Sprague Dawley rats treated with racemic DPN, S-DPN, and the ERbeta agonist, WAY-200070, showed significantly decreased anxiety-like behaviors in both the open-field and elevated plus maze and significantly less depressive-like behaviors in the forced swim test compared with vehicle-, R-DPN-, or propylpyrazoletriol (ERalpha agonist)-treated animals. In concordance with the relative binding affinity and transcriptional potency, these results demonstrate that the S-enantiomer is the biologically active form of DPN. These studies also indicate that estrogen's positive effects on mood, including its anxiolytic and antidepressive actions, are due to its actions at ERbeta.
Experimental and numerical investigation on in-plane behaviour of hollow concrete block masonry panels (2012)

This paper presents the details of studies conducted on hollow concrete block masonry (HCBM) units and wall panels. This study includes, compressive strength of unit block, ungrouted and grouted HCB prisms, flexural strength evaluation, testing of HCBM panels with and without opening. Non-linear finite element (FE) analysis of HCBM panels with and without opening has been carried out by simulating the actual test conditions. Constant vertical load is applied on the top of the wall panel and then lateral load is applied in incremental manner. The in-plane deformation is recorded under each incremental lateral load. Displacement ductility factors and response reduction factors have been evaluated based on experimental results. From the study, it is observed that fully grouted and partially reinforced HCBM panel without opening performed well compared to other types of wall panels in lateral load resistance and displacement ductility. In all the wall panels, shear cracks originated at loading point and moved towards the compression toe of the wall. The force reduction factor of a wall panel with opening is much less when compared with fully reinforced wall panel with no opening. The displacement values obtained by non-linear FE analysis are found to be in good agreement with the corresponding experimental values. The influence of mortar joint has been included in the stress-strain behaviour as a monolith with HCBM and not considered separately. The derived response reduction factors will be useful for the design of reinforced HCBM wall panels subjected to lateral forces generated due to earthquakes.
The Session Description Protocol (SDP) Grouping Framework (2010)

In this specification, we define a framework to group &amp;quot;m &amp;quot; lines in the Session Description Protocol (SDP) for different purposes. This framework uses the &amp;quot;group &amp;quot; and &amp;quot;mid &amp;quot; SDP attributes, both of which are defined in this specification. Additionally, we specify how to use the framework for two different purposes: for lip synchronization and for receiving a media flow consisting of several media streams on different transport addresses. This document obsoletes RFC 3388.
Utilizing contrastive learning for graph-based active learning of SAR data (2023)

Automatic target recognition with synthetic aperture radar (SAR) data is a challenging image classification problem due to the difficulty in acquiring the large labeled training sets required for conventional deep learning methods. Recent work1 addressed this problem by utilizing powerful tools in graph-based semi-supervised learning and active learning, and achieved state of the art results on the Moving and Stationary Target Acquisition and Recognition (MSTAR) dataset with less labeled data compared to existing techniques. A key part of the previous work was the use of unsupervised deep learning, in particular, a convolutional variational autoencoder, to embed the MSTAR images into a meaningful feature space prior to constructing the similarity graph. In this paper, we develop a contrastive SimCLR framework for feature extraction from MSTAR images by using data augmentations specific to SAR imagery. We show that our contrastive embedding results in improved performance over the variational autoencoder similarity graph method in automatic target recognition on the MSTAR dataset. We also perform a comparative study of the quality of the autoencoder and contrastive embeddings by training support vector machines (SVM) at various label rates, applying spectral clustering, and evaluating graph-cut energies, all of which show that the contrastive learning embedding is superior to the autoencoder embedding.
Power system stabilising features from wind power plants augmented with energy storage (2014)

This paper describes a wind power plant augmented with energy storage, configured to provide ancillary services (primary reserve, inertial response, power<br/>oscillation damping) for enhancement of power system stability. Energy storage can complement wind power plants thus reducing the need for any overload or curtailment to allow active power modulation. A 12MW + 1.6MW augmented plant is used for demonstration of representative performance of the particular ancillary service control algorithms
Molecular Dynamics Simulations of CYP2E1 (2012)

CYP2E1, as a member of the cytochrome P450s (CYPs) super-family, is in charge of six percent drug metabolism involving a diversity of drugs distinct in structures and chemical properties, such as alcohols, monocyclic compounds (e.g., acetaminophen, benzene, p-nitrophenol), bicyclic heterocycles (e.g., coumarin, caffeine) and even fatty acids. The aromatic molecules form a vital species catalyzed by CYP2E1. To investigate the mechanism of metabolizing a diversity of aromatic molecules, five representative aromatic substrates were selected: (1) benzene, the non-polar simple ring; (2) aniline, the monocyclic substrate with smallest substitution on the phenyl ring; (3) acetaminophen, a large monocyclic substrate with highly active reactivity; (4) chlorzoxazone, and (5) theophylline, the bicyclic substrates with low or high catalytic activities. They were docked into X-ray structure of CYP2E1, after which all-atom molecular dynamics simulations of 5 ns were performed on each model. It was found that the active site interact with the aromatic substrates mainly through π-π stacking, supplied by five hydrophobic phenylalanines in the active site. Our simulations also illustrated the specific movement of different kinds of aromatic substrates in the pocket. Small monocyclic substrates show highly frequent self-rotation and limited translation movement. Substrates with single catalytic position are less movable in the pocket than substrates with multiple products. All these findings are quite useful for understanding the catalytic mechanism of CYP2E1, stimulating novel strategies for conducting further mutagenesis studies for specific drug design.