gebhart/patrepeval huggingface dataset:
Strategic Placement of Phasor Measurements for Parameter Error Identification (2012)

Previous work on parameter error identification based on normalized Lagrange multipliers has shown that the errors in parameters of branches constituting single- or double-edge cutsets could not be detected or identified without incorporating phasor measurements. In order to address this deficiency, a computationally efficient algorithm has been developed to identify all such cutsets and documented in a recent paper. This paper builds on that work and formulates a strategic phasor measurement placement problem whose objective is to ensure detectability and identifiability of all network parameters in a given system. A practical solution is developed for this problem and simulation results for IEEE 14-, 30- and 57-bus test systems are provided to illustrate its implementation.
Identification and Role of Thiols in Toxoplasma gondii Egress (2001)

The nucleoside triphosphate hydrolase of Toxoplasma gondii is a potent apyrase that is secreted into the parasitophorous vacuole where it appears to be essentially inactive in an oxidized form. Recent evidence shows that nucleoside triphosphate hydrolase can be activated by dithiothreitol in vivo. On reduction of the enzyme, there is a rapid depletion of host cell ATP. Previous results also demonstrate a dithiothreitol induced egress of parasites from the host cell with a concurrent Ca2+ flux, postulated to be a consequence of the release of ATP-dependent Ca2+ stores within the tubulovesicular network of the parasitophorous vacuole. Reduction of the nucleoside triphosphate hydrolase appears crucial for its activation; however, the exact mechanism of reduction/activation has not been determined. Using a variety of techniques, we show here that glutathione promoters activate a Ca2+ flux and decrease ATP levels in infected human fibroblasts. We further show the in vitro activation of nucleoside triphosphate hydrolase by endogenous reducing agents, one of which we postulate might be secreted into the PV by T. gondii. Our findings suggest that the reduction of the parasite nucleoside triphosphate hydrolase, and ultimately parasite egress, is under the control of the parasites themselves.
DNA methylation of interferon regulatory factors in gastric cancer and noncancerous gastric mucosae (2010)

Interferon regulatory factors (IRFs) are transcription factors known to play key roles in innate and adaptive immune responses, cell growth, apoptosis, and development. Their function in tumorigenesis of gastric cancer remains to be determined, however. In the present study, therefore, we examined epigenetic inactivation of IRF1-9 in a panel of gastric cancer cell lines. We found that expression of IRF4, IRF5, and IRF8 was frequently suppressed in gastric cancer cell lines; that methylation of the three genes correlated with their silencing; and that treating the cells with the demethylating agent 5-aza-2'-deoxycytidine (DAC) restored their expression. Expression of IRF5 in cancer cells was enhanced by the combination of DAC treatment and adenoviral vector-mediated expression of p53, p63, or p73. Interferon-gamma-induced expression of IRF8 was also enhanced by DAC. Moreover, treating gastric cancer cells with DAC enhanced the suppressive effects of interferon-alpha, interferon-beta, and interferon-gamma on cell growth. Among a cohort of 455 gastric cancer and noncancerous gastric tissue samples, methylation of IRF4 was frequently observed in both gastric cancer specimens and noncancerous specimens of gastric mucosa from patients with multiple gastric cancers, which suggests IRF4 methylation could be a useful molecular marker for diagnosing recurrence of gastric cancers. Our findings indicate that epigenetic IRF inactivation plays a key role in tumorigenesis of gastric cancer, and that inhibition of DNA methylation may restore the antitumor activity of interferons through up-regulation of IRFs.
How Do Charged End-Groups on the Steric Stabilizer Block Influence the Formation and Long-Term Stability of Pickering Nanoemulsions Prepared Using Sterically Stabilized Diblock Copolymer Nanoparticles? (2020)

Reversible addition-fragmentation chain transfer (RAFT) solution polymerization is used to prepare well-defined poly(glycerol monomethacrylate) (PGMA) chains bearing carboxylic acid, tertiary amine, or neutral end-groups. Each of these PGMA precursors was then chain-extended in turn via RAFT aqueous emulsion polymerization of 2,2,2-trifluoroethyl methacrylate to form spherical nanoparticles as confirmed by transmission electron microscopy (TEM) analysis. Dynamic light scattering studies indicated an intensity-average diameter of approximately 25 nm. Aqueous electrophoresis measurements confirmed that the amine-functional nanoparticles became cationic at low pH owing to end-group protonation. In contrast, carboxylic acid-functional nanoparticles became appreciably anionic at pH 10 owing to end-group ionization. Finally, nanoparticles bearing neutral end-groups exhibited zeta potentials close to zero over a range of solution pH. High-shear homogenization of <i>n</i>-dodecane in the presence of such sterically stabilized nanoparticles led to the formation of oil-in-water Pickering <i>macroemulsions</i> with volume-average diameters of 20-30 μm. High-pressure microfluidization was then used to prepare the three corresponding Pickering <i>nanoemulsions</i>. Each Pickering nanoemulsion was characterized by analytical centrifugation and TEM studies of the dried nanoemulsion droplets confirmed their original nanoparticle superstructure. The nanoparticle adsorption efficiency at the oil-water interface was assessed by gel permeation chromatography (using a UV detector) for each nanoparticle type at both pH 3 and 7. Nanoparticles with charged end-groups exhibited relatively low adsorption efficiency, whereas up to 90% of the neutral nanoparticles were adsorbed onto the oil droplets. This observation was supported by small-angle X-ray scattering experiments, which indicated that the packing efficiency of neutral nanoparticles around oil droplets was higher than that of nanoparticles bearing charged end-groups. Analytical centrifugation was used to evaluate the colloidal stability of the aged Pickering nanoemulsions. Pickering nanoemulsions stabilized with nanoparticles bearing charged end-groups proved to be significantly less stable than those prepared using neutral end-groups.
Adsorption of plasma proteins and adhesion of platelets onto novel polyetherurethaneureas—relationship between denaturation of adsorbed proteins and platelet adhesion (1990)

Novel polyetherurethaneureas which have been synthesized by the present authors were chosen for the substrate polymers, on which adhesion of platelets was investigated. The number of adhered platelets and the amount of serotonin released from platelets adhered on the polymers and the protein-coated polymers were determined by radioisotope method. Both of them were enhanced with increasing content of urea linkages in the polyetherurethaneureas. The platelet adhesion was discussed in terms of the denaturation of plasma proteins upon adsorption, which was determined by Fourier-transform infrared spectroscopy. With increasing degree of protein denaturation, the platelet adhesion and the serotonin release were enhanced. This relationship was particularly evident in the case of albumin adsorption. It was shown that the surface properties of substrate polymers affect the protein adsorption, which in turn influences the adhesion of platelets.
Abstract 1247: Development of GRP78 scFv-Subtilase fusion proteins for sensitization of melanoma to chemotherapeutics. (2013)

Abstract GRP78 is an important molecular chaperone in the endoplasmic reticulum (ER). However, GRP78 is aberrantly expressed on the surface of melanoma cells. Our objective is to characterize cell-surface GRP78 in melanoma and determine whether immunoconjugates against GRP78 are a viable treatment strategy. We have demonstrated that cleavage of ER GRP78 by Subtilase (SubAB), a GRP78-specific protease, sensitizes melanoma cell lines of different genotypes to melphalan, vemurafenib, and temozolomide. Our data indicate that SubAB cleavage of GRP78 sensitizes melanoma cells to melphalan and vemurafenib. We then coupled the catalytic domain of SubAB, SubA, to GRP78-single chain variable fragments derived from anti-GRP78 mouse monoclonal antibodies. We have previously published that these antibodies target GRP78+ mouse melanomas in a syngeneic mouse melanoma model. These GRP78 scFv-SubA fusion proteins are internalized by cell-surface GRP78 and the SubA moiety cleaves ER GRP78 inside the cell, leading to tumor cell sensitization to chemotherapeutics, and in some instances, tumor cell death. To determine the mechanism by which ER GRP78 cleavage sensitizes melanoma cells to chemotherapeutics, the NH2-terminal 28 kDa and COOH-terminal 50 kDa SubA cleavage products were overexpressed in melanoma cells, and pull-down experiments were performed to identify binding partners. Microarray analyses were also performed on chemotherapy-treated and GRP78 scFv-SubA fusion protein-treated melanoma cells to obtain a broad view of cellular events that occurred subsequent to ER GRP78 cleavage by SubAB or GRP78 scFv-SubA fusion proteins. These fusion proteins will then be tested in mouse melanoma models to determine whether they sensitize cancer cells to chemotherapeutics in vivo. These results of these studies may lead to the development of novel melanoma therapeutics. Citation Format: Rupa Ray, Gustaaf de Ridder, Salvatore V. Pizzo. Development of GRP78 scFv-Subtilase fusion proteins for sensitization of melanoma to chemotherapeutics. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1247. doi:10.1158/1538-7445.AM2013-1247
Systematic Affiliation and Genome Analysis of Subtercola vilae DB165T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake (2019)

Among the <i>Microbacteriaceae</i> the species of <i>Subtercola</i> and <i>Agreia</i> form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species <i>Subtercola frigoramans</i> and <i>Subtercola vilae</i>, together with a larger number of isolates from various cold environments. Genomic evidence supports the separation of <i>Agreia</i> and <i>Subtercola</i> species. In order to gain insight into the ability of <i>S. vilae</i> to adapt to life in this extreme environment, we analyzed the genome with a particular focus on properties related to possible adaptation to a cold environment. General properties of the genome are presented, including carbon and energy metabolism, as well as secondary metabolite production. The repertoire of genes in the genome of <i>S. vilae</i> DB165<sup>T</sup> linked to adaptations to the harsh conditions found in Llullaillaco Volcano Lake includes several mechanisms to transcribe proteins under low temperatures, such as a high number of tRNAs and cold shock proteins. In addition, <i>S. vilae</i> DB165<sup>T</sup> is capable of producing a number of proteins to cope with oxidative stress, which is of particular relevance at low temperature environments, in which reactive oxygen species are more abundant. Most important, it obtains capacities to produce cryo-protectants, and to combat against ice crystal formation, it produces ice-binding proteins. Two new ice-binding proteins were identified which are unique to <i>S. vilae</i> DB165<sup>T</sup>. These results indicate that <i>S. vilae</i> has the capacity to employ different mechanisms to live under the extreme and cold conditions prevalent in Llullaillaco Volcano Lake.
Data Augmentation using Evolutionary Image Processing (2018)

In the machine learning community, data augmentation techniques have been widely used to make deep neural networks invariant to object transition. However, less attention has been paid to data augmentation in traditional classification methods. In this paper, we take a closer look at traditional classification methods and introduce a new data augmentation technique based on the concept of image transformation. Starting with a few existing examples, we add noise and generate new data points to reduce sparseness in a given feature space. Then, we generate images corresponding to the new data points, although this is usually an ill-posed problem. Herein, the novelty is in constructing an image transformation tree and generating new data from a small number of instances. This allows us to reduce sparseness in the feature space and build more robust classifiers. We evaluate our method on the Caltech-101 dataset to verify its potential. In the context of the situation where the amount of training data is limited, we demonstrate that the support vector machine-based classifiers trained with an augmented dataset using our method outperform classifiers trained with the original dataset in most cases.
Volume illustration for medicine and flows (2006)

This talk will start by describing general techniques and principles for effective computergenerated illustrations of volumetric datasets and review the state-of-the-art of volume illustration. It will then describe unique techniques and problems of both medical and flow data and discuss specific solution techniques for each class of data. An in-depth presentation of the work by Ebert's group in this area will be discussed next, including work on interactive stipple rendering, example-based volume illustration, and then Svakhine's system for interactive medical and flow illustration. The talk will conclude with a discussion of implementation and optimization techniques for interactive volume illustration by Svakhine as well as an interactive demonstration of the use of the system for medical education illustration, surgical simulation training, and analyzing three-dimensional fluid flow datasets, such as flow past spacecraft and convective flows.
Limitation of immune tolerance–inducing thymic epithelial cell development by Spi-B–mediated negative feedback regulation (2014)

Medullary thymic epithelial cells (mTECs) expressing the autoimmune regulator AIRE and various tissue-specific antigens (TSAs) are critical for preventing the onset of autoimmunity and may attenuate tumor immunity. However, molecular mechanisms controlling mTEC development remain elusive. Here, we describe the roles of the transcription factor Spi-B in mTEC development. Spi-B is rapidly up-regulated by receptor activator of NF-κB ligand (RANKL) cytokine signaling, which triggers mTEC differentiation, and in turn up-regulates CD80, CD86, some TSAs, and the natural inhibitor of RANKL signaling, osteoprotegerin (OPG). Spi-B-mediated OPG expression limits mTEC development in neonates but not in embryos, suggesting developmental stage-specific negative feedback regulation. OPG-mediated negative regulation attenuates cellularity of thymic regulatory T cells and tumor development in vivo. Hence, these data suggest that this negative RANKL-Spi-B-OPG feedback mechanism finely tunes mTEC development and function and may optimize the trade-off between prevention of autoimmunity and induction of antitumor immunity.
Chapter 9 In Vitro hESC Technology: State of the Art and Future Perspectives (2008)

The remarkable capacity of human embryonic stem cells (hESC) to transform into functional human tissues has captured the imagination of biologists and non-biologists alike. Unfortunately, the mechanisms of this transformation are still poorly understood and current methodology is inadequate to direct the forma- tion of many medically useful and safe cell therapies. This chapter provides an analysis of the state of the art of in vitro hESC research aimed at generating tissues suitable for the clinic. Discussed are laboratory techniques for controlling differen- tiation, for purifying homogenous populations, and for editing the genome of hESC. Also discussed are the strategies for ensuring the safety of hESC derived tissues for human patients, and an outlook on the future directions of hESC research.
Nonequiaxial Grain Growth and Polytype Transformation of Sintered α‐Silicon Carbide and β‐Silicon Carbide (2003)

α(6 H )‐ and β(3 C )‐SiC powders were sintered with the addition of AlB 2 and carbon. α‐SiC powder could be densified to ∼98% of the theoretical density over a wide range of temperatures from 1900° to 2150°C and with the additives of 0.67–2.7 mass% of AlB 2 and 2.0 mass% of carbon. Sintering of the β‐SiC powder required a temperature of &gt;2000°C for densification with these additives. Grains in the α‐SiC specimens grew gradually from spherical‐shaped to plate‐shaped grains at 2000°C; the 6 H polytype transformed mainly to 4 H . On the other hand, grains in the β‐SiC largely grew at &gt;2000°C; the 3 C polytype transformed to 4 H , 6 H , and 15 R . The stacking faults introduced in grains were denser in β‐SiC than in α‐SiC. The rapid grain growth in the β‐SiC specimen was attributed to polytype transformation from the unstable 3 C polytype at the sintering temperature.
ETARP: An Energy Efficient Trust-Aware Routing Protocol for Wireless Sensor Networks (2015)

This paper presents a new routing protocol called Secure and Energy Aware Routing Protocol (ETARP) designed for energy efficiency and security for wireless sensor networks (WSNs). ETARP attempts to deal with WSN applications operating in extreme environments such as the battlefield. The key part of the routing protocol is route selection based on utility theory. The concept of utility is a novel approach to simultaneously factor energy efficiency and trustworthiness of routes in the routing protocol. ETARP discovers and selects routes on the basis of maximum utility with incurring additional cost in overhead compared to the common AODV (Ad Hoc On Demand Distance Vector) routing protocol. Simulation results show that, in comparison to previously proposed routing protocols, namely, AODV-EHA and LTB-AODV (Light-Weight Trust-Based Routing Protocol), the proposed ETARP can keep the same security level while achieving more energy efficiency for data packet delivery.
Oxidation of methionine and 2-hydroxy 4-methylthiobutanoic acid stereoisomers in chicken tissues (1989)

International audience
Omega-3 Fatty Acids Augment the Actions of Nuclear Receptor Agonists in a Mouse Model of Alzheimer's Disease (2015)

Alzheimer's disease (AD) is a highly prevalent disorder for which there are no effective therapies. Accumulation of amyloid β (Aβ) peptides in the brain is associated with impaired cognition and memory, pronounced inflammatory dysregulation, and subsequent amyloid plaque deposition. Thus, drugs that promote the clearance of Aβ peptides and resolution of inflammation may represent viable therapeutic approaches. Agonists of nuclear receptors LXR:RXR and PPAR:RXR act to ameliorate AD-related cognitive impairment and amyloid accumulation in murine models of AD. The use of an agonist to the nuclear receptor RXR, bexarotene, as monotherapy against AD, presents potential challenges due to the metabolic perturbations it induces in the periphery, most prominently hypertriglyceridemia. We report that the ω-3 fatty acid docosahexaenoic acid (DHA), in combination with bexarotene, enhances LXR:RXR target gene expression of Abca1 and ApoE, reduces soluble forms of Aβ, and abrogates release of pro-inflammatory cytokines and mediators both in vitro and in a mouse model of AD. Moreover, DHA abrogates bexarotene-induced hypertriglyceridemia in vivo. Importantly, dual therapy promotes reductions in AD pathology and resultant amelioration of cognitive deficits. While monotherapy with either bexarotene or DHA resulted in modest effects in vitro and in vivo, combined treatment with both agents produced a significant additive benefit on associated AD-related phenotypes, suggesting that targeted combinatorial agents may be beneficial over single agents alone in treating AD.
133Cs Chemical Shielding Anisotropies and Quadrupole Couplings from Magic-Angle Spinning NMR of Cesium Salts (1996)

Magnitudes and relative orientations of 133Cs quadrupole coupling and chemical shielding tensors have been accurately determined from 133Cs magic-angle spinning (MAS) NMR spectra of the central and satellite transitions for four powdered cesium salts. Effects of small 133Cs chemical shielding anisotropies on the spectral appearance are observed in highly stabilized low-speed 133Cs MAS NMR spectra and analyzed by iterative fitting and numerical error analysis of the complete manifolds of spinning sidebands. 133Cs MAS NMR spectra of the single Cs site for CsVO3 and CsClO4, recorded at different spinning speeds, give consistent values for the parameters describing the two tensor interactions, while numerical error analysis of the spectra demonstrates that high levels of accuracy can be obtained for all parameters employing low-speed MAS NMR. The performance of the method for powders containing multiple sites is demonstrated by the 133Cs MAS spectra of Cs2CrO4 and Cs2SO4. The error limits for the 133Cs MAS NMR data for Cs2CrO4 are similar to those reported in a recent single-crystal NMR study. Quadrupole coupling parameters and isotropic chemical shifts are reported for Cs2CO3 from a high-speed 133Cs MAS spectrum. A linear correlation between 133Cs quadrupole tensor elements and estimated EFG tensor elements from point-charge calculations, employing effective oxygen charges, is reported and used to assign the NMR parameters for the two different crystallographic sites in Cs2CrO4, Cs2SO4, and Cs2CO3.
Antiproliferative and apoptosis-inducing activity of nobiletin against three subtypes of human breast cancer cell lines. (2014)

The predominant anticancer activity of nobiletin in MDA-MB-468 cells suggests a potential role of nobiletin for the prevention of triple-negative breast cancer.
An extremely heat‐stable extracellular proteinase (aeropyrolysin) from the hyperthermophilic archaeon Aeropyrum pernix K1 (1997)

An extracellular metalloproteinase, which we had designated aeropyrolysin, from the aerobic marine hyperthermophilic archaeon Aeropyrum pernix K1 (JCM 9820), was purified by ammonium sulfate precipitation, anionic exchange chromatography, and gel filtration chromatography. The purified enzyme was composed of a single polypeptide chain with a molecular mass of 52 kDa as determined by SDS-PAGE. The proteinase had a broad pH optimum (pH 5-9) with a maximal activity at pH 6-8 for azocasein hydrolysis. The optimum temperature for enzyme activity was 100 degrees C in the absence of 1 mM CaCl2 and 110 degrees C in the presence of 1 mM CaCl2. The enzyme activity was completely inhibited by EDTA and EGTA, indicating that it was a metalloproteinase. The enzyme was highly resistant to the denaturing reagents urea, guanidine-HCl, dithiothreitol, 2-mercaptoethanol and SDS. The enzyme also showed a high activity with the metalloproteinase specific substrate MOCAc-Pro-Leu-Gly-Leu-A2pr(Dnp)-Ala-Arg-NH2. The enzyme was extremely thermostable showing half-lives of 2.5 h at 120 degrees C and 1.2 h at 125 degrees C in the presence of 1 mM CaCl2. These results indicate that this enzyme is one of the most thermostable extracellular proteinases reported to date.
Detection of topographic characteristics in digital images approximated by triangular surfaces (2001)

This paper presents a new method for extracting topographic features from images approximated by triangular meshes. Peaks, pits, passes, ridges, valleys, and flat regions are defined by considering the topological and geometric relationship between the triangular elements. The approach is suitable for several computer-based recognition tasks, such as geographic information systems, rapid prototyping, computer graphics, and reverse engineering. The method has been applied to a wide range of images, producing a good compromise between accuracy and time requirements.