gebhart/patrepeval huggingface dataset:
Biochemical characterization of the Yersinia YopT protease: Cleavage site and recognition elements in Rho GTPases (2003)

The Gram-negative bacterial pathogen Yersinia delivers six effector proteins into the host cells to thwart the host innate immune response. One of the effectors, YopT, causes the disruption of the actin cytoskeleton and contributes to the inhibition of phagocytosis of the pathogen. YopT functions as a cysteine protease to cleave Rho family GTPases. We have analyzed the YopT cleavage products of Rho GTPases by TLC and determined their chemical structure by MS. Amino acid labeling experiments were performed to locate the exact site in RhoA where the YopT cleavage occurs. Our data unambiguously demonstrate that YopT cleaves N-terminal to the prenylated cysteine in RhoA, Rac, and Cdc42 and that the cleavage product of the GTPases is geranylgeranyl cysteine methyl ester. YopT cleaves GTP- and GDP-bound forms of RhoA equally, suggesting that the cleavage does not depend upon the conformation status of the GTPases. YopT also cleaves both farnesylated and geranylgeranylated forms of RhoA. The polybasic sequence in the C terminus of RhoA is essential for YopT substrate recognition and cleavage.
Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes (2018)

Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes the biosynthetic pathways for the main components of biomass-namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-α-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK and ACK enzymes are the most effective in increasing succinate production.
The Brain Tumor Cooperative Group NIH Trial 87-01: A Randomized Comparison of Surgery, External Radiotherapy, and Carmustine versus Surgery, Interstitial Radiotherapy Boost, External Radiation Therapy, and Carmustine (2002)

We conclude that there is no long-term survival advantage of increased radiation dose with (125)I seeds in newly diagnosed glioma patients.
Applications of Chitosan for the Elimination of Organochlorine Xenobiotics from Wastewater (2020)

Chitin and especially its deacetylated derivative, chitosan, have found numerous applications in industrial processes and especially in wastewater treatment and in potable water purification. Standard methods for water purification used in water-softening plants remain largely ineffective to remove these persistent xenobiotics. The high affinity of organochlorine hydrocarbons to chitin and chitosan, observed in vitro in the beginning of the 1980s, has instigated new research to develop effective polychlorinated biphenyls (PCB)-contaminated stream water treatment using these natural polymers. Pentachlorophenol (PCP) is a pesticide widely used in wood treatment against fungi. With time the PCP is slowly liberated from the wood and contaminates nearby water systems. The identification of the most useful adsorbent for PCP sorption was determined by the adsorption isotherms according to the Freundlich model. A PCP adsorption mechanism on the CHT-Glu-Red chitosan derivative based on a weak dipole-dipole interaction is suggested. Moreover, the nonwoven reactive filter K8WOT is a powerful and useful PCP and PCB adsorbent.
Technical Note (1988)

A simple technique is presented that allows determination of the degree of damping and the damped resonant frequency of catheter-transducer systems. From these data, the hydraulic sinusoidal frequency response, as well as the undamped (natural) frequency can be determined. The technique consists of suddenly releasing pressure in a bubble-free, fluid-filled catheter-transducer system while recording pressure with a stripchart recorder.
Glutamatergic—cholinergic interaction on memory consolidation in mice (1996)

NMRI mice were trained in a one-trial inhibitory avoidance task. They were injected immediately after training with the muscarinic cholinergic agonist oxotremorine, the muscarinic cholinergic antagonist atropine, the N-methyl-d-aspartate (NMDA) noncompetitive antagonist MK-801, or with a combination of MK-801 and one of the cholinergic agents. Oxotremorine improved, while atropine and MK-801 impaired, memory retention. In addition, oxotremorine attenuated, while atropine enhanced, the effect of MK-801. The results show the existence of a glutamatergic-cholinergic interaction in modulating memory consolidation of mice.
Transient behavior of regulated Brownian motion, I: Starting at the origin (1987)

A natural model for stochastic flow systems is regulated or reflecting Brownian motion (RBM), which is Brownian motion on the positive real line with constant negative drift and constant diffusion coefficient, modified by an impenetrable reflecting barrier at the origin. As a basis for understanding how stochastic flow systems approach steady state, this paper provides relatively simple descriptions of the moments of RBM as functions of time. In Part I attention is restricted to the case in which RBM starts at the origin; then the moment functions are increasing. After normalization by the steady-state limits, these moment c.d.f.&amp;s (cumulative distribution functions) coincide with gamma mixtures of inverse Gaussian c.d.f.&amp;s. The first moment c.d.f. thus coincides with the first-passage time to the origin starting in steady state with the exponential stationary distribution. From this probabilistic characterization, it follows that the k th-moment c.d.f is the k -fold convolution of the first-moment c.d.f. As a consequence, it is easy to see that the ( k + 1)th moment approaches its steady-state limit more slowly than the kth moment. It is also easy to derive the asymptotic behavior as t →∞. The first two moment c.d.f.&amp;s have completely monotone densities, supporting approximation by hyperexponential ( H 2 ) c.d.f.&amp;s (mixtures of two exponentials). The H 2 approximations provide easily comprehensible descriptions of the first two moment c.d.f.&amp;s suitable for practical purposes. The two exponential components of the H 2 approximation yield simple exponential approximations in different regimes. On the other hand, numerical comparisons show that the limit related to the relaxation time does not predict the approach to steady state especially well in regions of primary interest. In Part II (Abate and Whitt (1987a)), moments of RBM with non-zero initial conditions are treated by representing them as the difference of two increasing functions, one of which is the moment function starting at the origin studied here.
Diclofenac prevents temporal increase of intraocular pressure after uneventful cataract surgery with longer operation time (2008)

Postoperative increase in IOP after cataract surgery was affected by total surgery time and EPT in the betamethasone-treated eye. The time for surgery and EPT is longer in complicated cases including patients with a hard nucleus or small pupils, and also longer for beginning surgeons and in older patients. In these cases, diclofenac in place of betamethasone as a postoperative topical antiinflammatory drug is recommended for the prevention of postoperative increase in IOP.
Numbered voices: how opinion polling has shaped American politics (1993)

Quantifying the American mood through opinion polls appear to be an unbiased means for finding out what people want. But in this study the author demonstrates that the way public opinion is measured affects the use that voters, legislators, and journalists make of it. Exploring the history of public opinion in the United States from the mid-19th century to the present day, Herbst shows how numbers served both instrumental and symbolic functions, not only conveying neutral information but creating a basis authority. Addressing how the quantification of public opinion has affected contemporary politics and the democratic process, Herbst asks fundamental questions about the workings of American politics.
Enantiomer separation using mobile and immobile cyclodextrin derivatives with electromigration (1994)

The principle of electrochromatography is applied to enantiomer separation with wall-coated capillaries of 50 microns (ID). As chiral stationary phase an immobilized polysiloxane containing chemically bonded monokis-6-O-octamethylene-permethyl-cyclodextrin (beta- or gamma-Chirasil-Dex) was used. The results are compared with the conventional method of adding cyclodextrin derivatives as chiral pseudostationary phase to the running buffer.
Comparison of Radiation Dose and Image Quality: 320-MDCT Versus 64-MDCT Coronary Angiography (2011)

Image quality was good for both 320- and 64-MDCT angiography. Overall radiation dose was significantly lower in 320-MDCT angiography when the heart rate was 65 beats/min or less. Every effort should be made to control heart rate to minimize radiation dose.
An Approach Guidance System for Side-Firing Tactical Aircraft (1970)

Abstract : The present approach guidance scheme is one of controlling the aircraft's velocity vector; however, this scheme has two major disadvantages: it's a difficult flying task for the pilot, and when the aircraft arrives tangent to the circular path, a violent maneuver is usually required to achieve the proper bank angle to stay on the desired circular path. An improved method for controlling the side firing AC-130 and AC-119 into circular attack geometry eliminates these disadvantages. Furthermore, with this improved system the bank angle rates never exceed 3 or 4 degrees per second. This control scheme was simulated on the analog computer and the results are presented graphically. The simulation showed that the bank angle, command-control scheme is effective for distances out to five circular orbit radii from the target and is effective for all aircraft headings (with one exception which is discussed in a stability study in the appendix). The initial test flight showed that the bank angle control scheme behaved very well, and its overall performance was near that predicted. Relatively minor modifications can incorporate this control scheme into existing analog computers on board the aircraft.
Ensemble of Deep Convolutional Neural Networks for Learning to Detect Retinal Vessels in Fundus Images (2016)

Vision impairment due to pathological damage of the retina can largely be prevented through periodic screening using fundus color imaging. However the challenge with large scale screening is the inability to exhaustively detect fine blood vessels crucial to disease diagnosis. In this work we present a computational imaging framework using deep and ensemble learning for reliable detection of blood vessels in fundus color images. An ensemble of deep convolutional neural networks is trained to segment vessel and non-vessel areas of a color fundus image. During inference, the responses of the individual ConvNets of the ensemble are averaged to form the final segmentation. In experimental evaluation with the DRIVE database, we achieve the objective of vessel detection with maximum average accuracy of 94.7\% and area under ROC curve of 0.9283.
Consistent Dialogue Generation with Self-supervised Feature Learning (2019)

Generating responses that are consistent with the dialogue context is one of the central challenges in building engaging conversational agents. We demonstrate that neural conversation models can be geared towards generating consistent responses by maintaining certain features related to topics and personas throughout the conversation. Past work has required external supervision that exploits features such as user identities that are often unavailable. In our approach, topic and persona feature extractors are trained using a contrastive training scheme that utilizes the natural structure of dialogue data. We further adopt a feature disentangling loss which, paired with controllable response generation techniques, allows us to promote or demote certain learned topics and persona features. Evaluation results demonstrate the model's ability to capture meaningful topics and persona features. The incorporation of the learned features brings significant improvement in terms of the quality of generated responses on two dialogue datasets.
Epigenetic Alterations in Prescription Opioid Misuse: New Strategies for Precision Pain Management (2021)

Prescription opioids are used for some chronic pain conditions. However, generally, long-term therapy has unwanted side effects which may trigger addiction, overdose, and eventually cause deaths. Opioid addiction and chronic pain conditions have both been associated with evidence of genetic and epigenetic alterations. Despite intense research interest, many questions about the contribution of epigenetic changes to this typology of addiction vulnerability and development remain unanswered. The aim of this review was to summarize the epigenetic modifications detected in specific tissues or brain areas and associated with opioid prescription and misuse in patients who have initiated prescribed opioid management for chronic non-cancer pain. The review considers the effects of opioid exposure on the epigenome in central and peripheral tissues in animal models and human subjects and highlights the mechanisms in which opioid epigenetics may be involved. This will improve our current understanding, provide the basis for targeted, personalized pain management, and thus balance opioid risks and benefits in managing chronic pain.
The application of titanium dioxide, zinc oxide, fullerene, and graphene nanoparticles in photodynamic therapy (2017)

Nanoparticles (NPs) have been shown to have good ability to improve the targeting and delivery of therapeutics. In the field of photodynamic therapy (PDT), this targeting advantage of NPs could help ensure drug delivery at specific sites. Among the commonly reported NPs for PDT applications, NPs from zinc oxide, titanium dioxide, and fullerene are commonly reported. In addition, graphene has also been reported to be used as NPs albeit being relatively new to this field. In this context, the present review is organized by these different NPs and contains numerous research works related to PDT applications. The effectiveness of these NPs for PDT is discussed in detail by collecting all essential information described in the literature. The information thus assembled could be useful in designing new NPs specific for PDT and/or PTT applications in the future.
Mg–Ti–H thin films for smart solar collectors (2006)

Mg–Ti–H thin films are found to have very attractive optical properties: they absorb 87% of the solar radiation in the hydrogenated state and only 32% in the metallic state. Furthermore, in the absorbing state Mg–Ti–H has a low emissivity; at 400K only 10% of blackbody radiation is emitted. The transition between both optical states is fast, robust, and reversible. The sum of these properties highlights the applicability of such materials as switchable smart coatings in solar collectors.
Design Principles and Preliminary Clinical Performance of an Artificial Skin (1982)

We designed and successfully tested a novel family of polymeric membranes for treating patients with extensive skin loss. Stage 1 membranes consisted of a highly porous bottom layer of a covalently cross-linked collagen-glycosaminoglycan network and a top layer of a conventional silicone elastomer. Stage 2 membranes, studied so far only with guinea pigs, were prepared by seeding the bottom layer of Stage 1 membranes with autologous epidermal (basal) cells, prepared 4 h or less before grafting. Prompt and long-term closure of full-thickness skin wounds in guinea pigs and in humans occurred. Infection, exudation, and host-graft rejection were absent while synthesis of neoepidermal and neodermal tissue took place in the presence of the polymeric template.
Programming for Microscopy and Microanalysis (2013)

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.
Dynamic process location management in 5G (2019)

Summary 5G, as the next generation of wireless networks, promises very high throughput and low latency to mobile users that calls for a substantial innovation in computing management platforms to attend QoS metrics. Thanks to emerging technologies such as software‐defined networking (SDN)/network function virtualization (NFV), many features are available in 5G design to detect and control two types of latency caused by computation and communication. In this paper, taking features of caching mechanisms and SDN into the account, a platform is proposed to minimize latency in 5G via caching big flows intelligently and avoiding bottlenecks that may cause by virtualized computing components. First, the pioneering idea of compromising between the cloud radio access network (CRAN) and mobile edge computing (MEC)/information‐centric network (ICN) via dynamic processing location management platform is investigated. Accordingly, a mathematical optimization problem to minimize the average latency is formulated. Due to the problem complexity, a heuristic algorithm is proposed to treat the latency via dynamic orchestration of processing functionalities. Through numerical results, the performance of the proposed algorithm is analyzed, and the simulations corroborate our analytical results and illustrate the superior performance of the proposed algorithm with acceptable optimality gap.
Spin Conversion versus Antiferromagnetic Interaction in Iron(II) Trinuclear Species. Crystal Structures and Magnetic Properties of [Fe3(p-MeOptrz)8(H2O)4](BF4)6 and [Fe3(p-MeOprtz)6(H2O)6](tos)6 [p-MeOptrz = 4-(p-Methoxyphenyl)-1,2,4-triazole, tos = tosylate] (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpin Conversion versus Antiferromagnetic Interaction in Iron(II) Trinuclear Species. Crystal Structures and Magnetic Properties of [Fe3(p-MeOptrz)8(H2O)4](BF4)6 and [Fe3(p-MeOprtz)6(H2O)6](tos)6 [p-MeOptrz = 4-(p-Methoxyphenyl)-1,2,4-triazole, tos = tosylate]Martina Thomann, Olivier Kahn, Jean Guilhem, and Francois VarretCite this: Inorg. Chem. 1994, 33, 26, 6029–6037Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published inissue 1 December 1994https://pubs.acs.org/doi/10.1021/ic00104a010https://doi.org/10.1021/ic00104a010research-articleACS PublicationsRequest reuse permissionsArticle Views426Altmetric-Citations75LEARN 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
Optical Properties of Hybrid Inorganic/Organic Thin Film Encapsulation Layers for Flexible Top-Emission Organic Light-Emitting Diodes (2015)

Inorganic/organic hybrid thin film encapsulation layers consist of a thin Al2O3 layer together with polymer material. We have investigated optical properties of thin film encapsulation layers for top-emission flexible organic light-emitting diodes. The transmittance of hybrid thin film encapsulation layers and the electroluminescent spectrum of organic light-emitting diodes that were passivated by hybrid organic/inorganic thin film encapsulation layers were also examined as a function of the thickness of inorganic Al203 and monomer layers. The number of interference peaks, their intensity, and their positions in the visible range can be controlled by varying the thickness of inorganic Al2O3 layer. On the other hand, changing the thickness of monomer layer had a negligible effect on the optical properties. We also verified that there is a trade-off between transparency in the visible range and the permeation of water vapor in hybrid thin film encapsulation layers. As the number of dyads decreased, optical transparency improved while the water vapor permeation barrier was degraded. Our study suggests that, in top-emission organic light-emitting diodes, the thickness of each thin film encapsulation layer, in particular that of the inorganic layer, and the number of dyads should be controlled for highly efficient top-emission flexible organic light-emitting diodes.
CHARACTERIZATION OF BIOPHYSICAL PROPERTIES OF BABOON LIPOPRDTEINS: MODULATION BY DIETARY FAT AND CHOLESTEROL (1984)

The serum lipoproteins of pedigreed and non-pedigreed baboons (Papio cynocephalus) fed diets containing differing types and amounts of fat and varying amounts of cholesterol were examined by analytic ultracentrifugation, gradient gel c
Gremlin -mediated BMP antagonism induces the epithelial-mesenchymal feedback signaling controlling metanephric kidney and limb organogenesis (2004)

Epithelial-mesenchymal feedback signaling is the key to diverse organogenetic processes such as limb bud development and branching morphogenesis in kidney and lung rudiments. This study establishes that the BMP antagonist gremlin (Grem1) is essential to initiate these epithelial-mesenchymal signaling interactions during limb and metanephric kidney organogenesis. A Grem1 null mutation in the mouse generated by gene targeting causes neonatal lethality because of the lack of kidneys and lung septation defects. In early limb buds, mesenchymal Grem1 is required to establish a functional apical ectodermal ridge and the epithelial-mesenchymal feedback signaling that propagates the sonic hedgehog morphogen. Furthermore, Grem1-mediated BMP antagonism is essential to induce metanephric kidney development as initiation of ureter growth, branching and establishment of RET/GDNF feedback signaling are disrupted in Grem1-deficient embryos. As a consequence, the metanephric mesenchyme is eliminated by apoptosis, in the same way as the core mesenchymal cells of the limb bud.