gebhart/patrepeval huggingface dataset:
Recent progress on the role of gut microbiota in the pathogenesis of inflammatory bowel disease (2013)

In recent years investigations of inflammatory bowel disease (IBD) have advanced rapidly with regard to the relationship between the host immune response and gut microbiota. Patients with IBD have been shown to have an abnormal composition of gut microbiota and host immune dysregulation. Abnormal components of gut microbiota, to which the host mounts aberrant immune responses in genetically vulnerable individuals, appear to play a critical role in the pathogenesis of IBD. Therefore, inappropriate innate and adaptive host immune responses to abnormal components of gut microbiota and their products form the basis of IBD pathogenesis. Modern molecular genetic methods should be utilized to help to illuminate the pathogenetic mechanism of IBD and to develop personalized therapeutic strategies for this disease.
Lysyl oxidase-like 2 inhibition ameliorates glomerulosclerosis and albuminuria in diabetic nephropathy (2018)

Diabetic nephropathy is characterised by the excessive amount of extracellular matrix in glomeruli and tubulointerstitial space. Lysyl oxidase-like 2 (LOXL2) is elevated in renal fibrosis and known to play key roles in ECM stabilisation by facilitating collagen cross-links, epithelial to mesenchymal transition and myofibroblast activation. Thus, targeting LOXL2 may prove to be a useful strategy to prevent diabetic nephropathy. We explored the renoprotective effect of a selective small molecule LOXL2 inhibitor (PXS-S2B) in a streptozotocin-induced diabetes model. Diabetic mice were treated with PXS-S2B for 24 weeks and outcomes compared with untreated diabetic mice and with telmisartan treated animals as comparator of current standard of care. Diabetic mice had albuminuria, higher glomerulosclerosis scores, upregulation of fibrosis markers and increased renal cortical LOXL2 expression. Treatment with PXS-S2B reduced albuminuria and ameliorated glomerulosclerosis. This was associated with reduced expression of glomerular fibronectin and tubulointerstitial collagen I. The renoprotective effects of both PXS-S2B and telmisartan were more marked in the glomerular compartment than in the tubulointerstitial space. The study reveals that LOXL2 inhibition was beneficial in preserving glomerular structure and function. Thus, LOXL2 may be a potential therapeutic target in diabetic nephropathy.
Electrostatic Confinement, Patterning, and Manipulation of Charged Nanoparticles by Combining Nanostructured Surfaces and Ionic Charge Regulation. (2016)

Electrostatic forces are amongst the most versatile when applied to mediate the interactions between nanostructured interfaces. Depending on the experimental conditions, these forces can be either attractive or repulsive, and their directionality can be controlled dynamically. In this dissertation, we employ these forces to confine and manipulate charged nanoparticles using nanostructured interfaces. The various methodologies discussed herein inform and complement each other while opening pathways for diversified applications. Electrostatic confinement of nanoscale species in solution has far-reaching effects in fields as diverse as biophysics, gene therapy, single-particle motion monitoring studies and bottom-up fabrication of nanostructures. We present a methodology to uniaxially confine charged nanoparticles on one-dimensional electrodes without the usage of geometrical barriers. An actively-tunable, engineered model system for electrostatic binding interactions is demonstrated and interaction characteristics are discussed in relation to mimicking the natural biological interaction between charged species. We further investigate the electrostatic interactions between nanoparticles and patterned sinusoidal-void structures. A size-selective nanoparticle confinement and patterning technique is demonstrated. In addition, ionic charge regulation in the electrical double layer, its ramifications and its applications are discussed. In many particle-fractionation applications, complementary geometries are critical for understanding confinement characteristics and so a novel methodology is introduced to detect and visualize relative size variations in pre-characterized nanoparticle ensembles. This capped particle optical-sizing methodology is easily accessible, has high-throughput, and is relatively facile when compared to existing size-characterization techniques. Finally, a nanoparticle-manipulation-based transparent display concept is demonstrated that has been supplemented by our enhanced understanding of the above mentioned confinement methodologies of electrostatically confining charged nanoparticles in solution.
Stereochemistry of the acetoxymercuration of alkynes. A synthesis of vinyl acetates (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry of the acetoxymercuration of alkynes. A synthesis of vinyl acetatesRobert D. Bach, Robert A. Woodard, Thomas J. Anderson, and Milton D. GlickCite this: J. Org. Chem. 1982, 47, 19, 3707–3712Publication Date (Print):September 1, 1982Publication History Published online1 May 2002Published inissue 1 September 1982https://pubs.acs.org/doi/10.1021/jo00140a024https://doi.org/10.1021/jo00140a024research-articleACS PublicationsRequest reuse permissionsArticle Views696Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Kinetic: verifiable dynamic network control (2015)

Network conditions are dynamic; unfortunately, current approaches to configuring networks. Network operators need tools to express how a network's data-plane behavior should respond to a wide range of events and changing conditions, ranging from unexpected failures to shifting traffic patterns to planned maintenance. Yet, to update the network configuration today, operators typically rely on a combination of manual intervention and ad hoc scripts. In this paper, we present Kinetic, a domain specific language and network control system that enables operators to control their networks dynamically in a concise, intuitive way. Kinetic also automatically verifies the correctness of these control programs with respect to user-specified temporal properties. Our user study of Kinetic with several hundred network operators demonstrates that Kinetic is intuitive and usable, and our performance evaluation shows that realistic Kinetic programs scale well with the number of policies and the size of the network.
Direct Observation of Polylysine Side-Chain Interaction with Smectites Interlayer Surfaces through<sup>1</sup>H−<sup>27</sup>Al Heteronuclear Correlation NMR Spectroscopy (2002)

International audience
Potential-Flow Modeling for Data Center Applications (2011)

Potential-flow-based airflow and heat transfer models have been proposed as a computationally efficient alternative to the Navier-Stokes Equations for predicting the three-dimensional flow field in data center applications. These models are simple, solve quickly, and capture much of the fluid flow physics, but ignore buoyancy and frictional effects, i.e., rotationality, turbulence, and wall friction. However, a comprehensive comparison of the efficiency and accuracy of these methods versus more sophisticated tools, like CFD, is lacking. The main contribution of this paper is a study of the performance of potential-flow methods compared to CFD in eight layouts inspired by actual data center configurations. We demonstrate that potential-flow methods can be helpful in data center design and management applications.
The BCL2 selective inhibitor venetoclax induces rapid onset apoptosis of CLL cells in patients via a TP53-independent mechanism (2016)

BCL2 blunts activation of the mitochondrial pathway to apoptosis, and high-level expression is required for chronic lymphocytic leukemia (CLL) survival. Venetoclax (ABT-199) is a small-molecule selective inhibitor of BCL2 currently in clinical trials for CLL and other malignancies. In conjunction with the phase 1 first-in-human clinical trial of venetoclax in patients with relapsed or refractory CLL (M12-175), we investigated the mechanism of action of venetoclax in vivo, explored whether in vitro sensitivity assays or BH3 profiling correlated with in vivo responses in patients, and determined whether loss of TP53 function affected responses in vitro and in vivo. In all samples tested, venetoclax induced death of CLL cells in vitro at concentrations achievable in vivo, with cell death evident within 4 hours. Apoptotic CLL cells were detected in vivo 6 or 24 hours after a single 20-mg or 50-mg dose in some patients. The extent of mitochondrial depolarization by a BIM BH3 peptide in vitro was correlated with percentage reduction of CLL in the blood and bone marrow in vivo, whereas the half lethal concentration derived from standard cytotoxicity assays was not. CLL cell death in vitro and the depth of clinical responses were independent of deletion of chromosome 17p, TP53 mutation, and TP53 function. These data provide direct evidence that venetoclax kills CLL cells in a TP53-independent fashion by inhibition of BCL2 in patients and support further assessment of BH3 profiling as a predictive biomarker for this drug.
The fringe distance measure: an easily calculated image distance measure with recognition results comparable to Gaussian blurring (1994)

A fast simple distance measure for calculating the degree of dissimilarity between binary images is presented. The new distance measure, called the fringe distance, gives the same degree of distortion tolerance as optimized Gaussian blurring, but can be calculated much more rapidly. Template matching using the fringe distance executes about six times as fast as Gaussian blurring template matching on an IBM AT with coprocessor, and more than three times as fast on a SUN SPARCStation I with floating point accelerator. The greater speed means more templates can be used in process time limited applications, increasing recognition accuracy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Role of Skeletal Muscle in The Pathogenesis of Altered Concentrations of Branched-Chain Amino Acids (Valine, Leucine, and Isoleucine) in Liver Cirrhosis, Diabetes, and Other Diseases (2021)

The article shows that skeletal muscle plays a dominant role in the catabolism of branched-chain amino acids (BCAAs; valine, leucine, and isoleucine) and the pathogenesis of their decreased concentrations in liver cirrhosis, increased concentrations in diabetes, and nonspecific alterations in disorders with signs of systemic inflammatory response syndrome (SIRS), such as burn injury and sepsis. The main role of skeletal muscle in BCAA catabolism is due to its mass and high activity of BCAA aminotransferase, which is absent in the liver. Decreased BCAA levels in liver cirrhosis are due to increased use of the BCAA as a donor of amino group to alpha-ketoglutarate for synthesis of glutamate, which in muscles acts as a substrate for ammonia detoxification to glutamine. Increased BCAA levels in diabetes are due to alterations in glycolysis, citric acid cycle, and fatty acid oxidation. Decreased glycolysis and citric cycle activity impair BCAA transamination to branched-chain keto acids (BCKAs) due to decreased supply of amino group acceptors (alpha-ketoglutarate, pyruvate, and oxaloacetate); increased fatty acid oxidation inhibits flux of BCKA through BCKA dehydrogenase due to increased supply of NADH and acyl-CoAs. Alterations in BCAA levels in disorders with SIRS are inconsistent due to contradictory effects of SIRS on muscles. Specifically, increased proteolysis and insulin resistance tend to increase BCAA levels, whereas activation of BCKA dehydrogenase and glutamine synthesis tend to decrease BCAA levels. The studies are needed to elucidate the role of alterations in BCAA metabolism and the effects of BCAA supplementation on the outcomes of specific diseases.
As restrições verticais e a análise econômica do direito (2006)

RELATIONAL AGREEMENTS USUALLY CAUSE A SAVING WITH CONNECTION TO THE TRANSACTION COSTS. THE POINT IS TO DETERMINE WHEN AND IN WHICH LEVEL SUCH ADVANTAGES OVERCOME THE NEGATIVE EFFECTS OF A POSSIBLE VERTICAL RESTRICTION. SUCH ANALYSIS SHALL BE PROCEEDED THROUGH THE APPRECIATION OF THE ECONOMICAL AND JURIDICAL RATIONALITY ADOPTED IN THE PERIOD. THUS, THE ANTITRUST LAW SHALL LIMIT THE INTEGRATIVE MOVEMENTS AND THE EFFICIENCY ANALYSIS SHALL CONSIDER THE SITUATIONS IN WHICH THE TRANSACTIONS PROCEEDED OUT OF THE FIRM ARE WORTHY FOR THE PLAYERS. IN ADDITION, IT SHALL ALSO BE CONSIDERED THE CONSUMERS AND THE SOCIETY’S INTERESTS INVOLVED, ONCE THE RESTRICTION WILL ONLY BE WORTHY IF THE HIGH TRANSACTION COSTS IMPOSE AN INSTABILITY OF THE MARKET’S PRICES, WHICH WOULD BE AVOIDED BY THE PERMISSION OF THE VERTICAL AGREEMENT.
A Complete and Efficient Algebraic Compiler for XQuery (2006)

As XQuery nears standardization, more sophisticated XQuery applications are emerging, which often exploit the entire language and are applied to non-trivial XML sources. We propose an algebra and optimization techniques that are suitable for building an XQuery compiler that is complete, correct, and efficient. We describe the compilation rules for the complete language into that algebra and present novel optimization techniques that address the needs of complex queries. These techniques include new query unnesting rewritings and specialized join algorithms that account for XQuery’s complex predicate semantics. The algebra and optimizations are implemented in the Galax XQuery engine, and yield execution plans that are up to three orders of magnitude faster than earlier versions of Galax.
FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates (2019)

The autophagy cargo receptor p62 facilitates the condensation of misfolded, ubiquitin-positive proteins and their degradation by autophagy, but the molecular mechanism of p62 signaling to the core autophagy machinery is unclear. Here, we show that disordered residues 326-380 of p62 directly interact with the C-terminal region (CTR) of FIP200. Crystal structure determination shows that the FIP200 CTR contains a dimeric globular domain that we designated the "Claw" for its shape. The interaction of p62 with FIP200 is mediated by a positively charged pocket in the Claw, enhanced by p62 phosphorylation, mutually exclusive with the binding of p62 to LC3B, and it promotes degradation of ubiquitinated cargo by autophagy. Furthermore, the recruitment of the FIP200 CTR slows the phase separation of ubiquitinated proteins by p62 in a reconstituted system. Our data provide the molecular basis for a crosstalk between cargo condensation and autophagosome formation.
Trust support for SDN controllers and virtualized network applications (2015)

The SDN paradigm allows networks to be dynamically reconfigurable by network applications. SDN is also of particular interest for NFV which deals with the virtualization of network functions. The network programmability offered by SDN presents then various advantages but it also induces various threats regarding potential attacks on the network. For instance, there is a critical risk that a hacker takes over the network control by exploiting this SDN network programmability (e.g., using the SDN API or tampering a network application running on the SDN controller). This paper proposes then an approach to deal with this possible lack of trust in the SDN controller or in their applications. This approach consists in not relying on a single controller but on several ‘redundant’ controllers that may also run in different execution environments. The network configuration requests coming from these controllers are then compared and, if deemed sufficiently consistent and then trustable, they are actually sent to the network. This approach has been implemented in an intermediary layer (based on a network hypervisor) inserted between the network equipments and the controllers. Experimentations have been performed showing the feasibility of the approach and providing some first evaluations of its impact on the network and the services.
Reaction Kinetics of the Lignin Conversion in Supercritical Water (2012)

The effect of temperature (390–450 °C) and residence time (0.5–10 s) at a pressure of 25 MPa was investigated for lignin conversion in supercritical water (SCW) using a continuous flow apparatus designed to rapidly heat the system to the desired reaction temperature. Conversion of lignin in SCW occurs rapidly, and complete depolymerization can be achieved within a 5 s residence time. A high degree of depolymerization is achieved from rapid heating to supercritical temperatures. In addition, supercritical conditions result in a high yield of solid that does not significantly change with an increase in temperature or residence time. To test the suggested hypothesis that the formation of low molecular weight fragments and cross-linking of these fragments forms higher molecular weight fragments, the yield of char, gaseous products, phenolic compounds (phenol, guaiacol, catechol, o-cresol, m-cresol, and catechol) and aromatic hydrocarbons (benzene, toluene, and naphthalene) were determined. The formation of phenolic compounds at short residence time indicates that ether bonds in lignin are easily degraded under supercritical conditions. A reaction network model was proposed, and the subsequent kinetic parameters for the conversion pathways were determined by assuming a first-order reaction. It is observed that the rate constant of overall lignin conversion obeys Arrhenius behavior. The individual rate constants of each reaction in the network are evaluated to determine conformity to Arrhenius behavior.
An Efficient Ultra-Wideband Bow-Tie Antenna (2001)

In this paper, a transient bow-tie antenna for Ground Penetrating Radar applications is discussed. This antenna exhibits good efficiency and an ultra-wideband property due to a combination of a tapered capacitive and a resistive loading. The tapered capacitive loading is realized by constructing an array of slots on the antenna surface and the resistive loading is obtained by making use of microwave absorber blocks placed on the slotted surface of the antenna. Using a 0.8-ns monocycle as input pulse, the amplitude of its transmit waveform is 70% higher than that of a conventional bow-tie antenna of equal dimension. The transmit waveform is a nearly symmetrical triplet with a late-time ringing level of lower than -33 dB.
Defining the p53 DNA‐binding domain/Bcl‐x<sub>L</sub>‐binding interface using NMR (2004)

p53 exerts its tumor suppressor activity through both transcription-dependent and transcription-independent processes. Although the transcription-dependent activity of p53 has been extensively studied, the mechanism for transcription-independent p53-mediated tumor suppression is less well known. Recently, it was reported that p53 can directly induce mitochondrial permeabilization and promote apoptosis. This occurs through complexation of the DNA-binding region of p53 with the anti-apoptotic proteins Bcl-x(L) and Bcl-2 (Mihara, M. et al. (2003) Mol. Cell 11, 577-590). Using nuclear magnetic resonance (NMR) spectroscopy we show that the interaction surface on p53 involves the same region that is used by the protein to contact DNA. The p53-binding site on Bcl-x(L) consists of the carboxy-terminus of the first alpha-helix, the loop between alpha3 and alpha4, and the loop between alpha5 and alpha6 of Bcl-x(L). Furthermore, the interaction of p53 with Bcl-x(L) is blocked by the binding of a 25-residue peptide derived from the BH3 region of the pro-apoptotic protein referred to as Bad.
Magnetic Field-Induced Spectroscopy of Forbidden Optical Transitions with Application to Lattice-Based Optical Atomic Clocks (2006)

We develop a method of spectroscopy that uses a weak static magnetic field to enable direct optical excitation of forbidden electric-dipole transitions that are otherwise prohibitively weak. The power of this scheme is demonstrated using the important application of optical atomic clocks based on neutral atoms confined to an optical lattice. The simple experimental implementation of this method--a single clock laser combined with a dc magnetic field--relaxes stringent requirements in current lattice-based clocks (e.g., magnetic field shielding and light polarization), and could therefore expedite the realization of the extraordinary performance level predicted for these clocks. We estimate that a clock using alkaline-earth-like atoms such as Yb could achieve a fractional frequency uncertainty of well below 10(-17) for the metrologically preferred even isotopes.
Palm oil and palm kernel oil as raw materials for basic oleochemicals and biodiesel (2007)

Abstract The palm oil‐ and palm kernel oil‐producing countries in South East Asia are becoming the dominant producers of fatty acids and fatty alcohols. The large and very efficient palm oil plantations are giving the local producers of basic oleochemicals a decisive competitive advantage. The production of fatty acid methyl esters for use as biodiesel is expanding all around the world. In tropical countries, the preferred raw material for biodiesel is palm oil, Europe uses mostly low‐erucic rapeseed oil and the USA soya oil. To a large extent, the growth of biodiesel depends on direct or indirect subsidies for the agriculture and on tax exemptions. The rapid growth of biodiesel has created an excess of glycerine, which cannot be absorbed by existing markets. The price for glycerine will probably remain low for the next years and therefore attract investments in new applications.
[Usefulness of the microscopic examination for the diagnosis of gonorrhea]. (1987)

Necessite d'une technique rapide et simple telle que la coloration des secretions uretrales pour un diagnostic precoce de la gonococcie