gebhart/patrepeval huggingface dataset:
Silver-alumina catalysts for lean NOx reduction (2014)

Introduction Combustion in oxygen excess, as in dieseland lean-burn engines, significantly improves the fuel-efficiency and thereby effectively reduces the CO2 emissions. However, the lean environment obstructs the NOx reduction ability of the three-way catalyst. One promising technique to reduce NOx in oxygen excess is hydrocarbon-assisted selective catalytic reduction (HC-SCR). In particular, Ag supported on alumina has shown high activity for this reaction, see e.g. [1,2]. Although numerous experimental studies have clarified issues concerning this system, the state and structure of the Ag-alumina system, as well as the reaction mechanism, remain elusive. This work presents an overview of our recent findings concerning lean NOx reduction over silver-alumina with various types of reducing agents, including hydrocarbons, oxygenates and commercial biodiesel [3-11]. Furthermore, the structure and chemical state of the silver sites will be discussed in relation to the catalytic performance and reaction mechanisms.
YouLighter: An Unsupervised Methodology to Unveil YouTube CDN Changes (2015)

YouTube relies on a massively distributed Content Delivery Network (CDN) to stream the billions of videos in its catalogue. Unfortunately, very little information about the design of such CDN is available. This, combined with the pervasiveness of YouTube, poses a big challenge for Internet Service Providers (ISPs), which are compelled to optimize end-users' Quality of Experience (QoE) while having no control on the CDN decisions. This paper presents YouLighter, an unsupervised technique to identify changes in the YouTube CDN. YouLighter leverages only passive measurements to cluster co-located identical caches into edge-nodes. This automatically unveils the structure of YouTube's CDN. Further, we propose a new metric, called Constellation Distance, that compares the clustering obtained from two different time snapshots, to pinpoint sudden changes. While several approaches allow comparison between the clustering results from the same dataset, no technique allows to measure the similarity of clusters from different datasets. Hence, we develop a novel methodology, based on the Constellation Distance, to solve this problem. By running YouLighter over 10-month long traces obtained from two ISPs in different countries, we pinpoint both sudden changes in edge-node allocation, and small alterations to the cache allocation policies which actually impair the QoE that the end-users perceive.
The SLC6A14 gene shows evidence of association with obesity (2003)

In our previous genome-wide scan of Finnish nuclear families, obesity was linked to chromosome Xq24.Here we analyzed this 15-Mb region by genotyping 9 microsatellite markers and 36 single nucleotide polymorphisms (SNPs) for 11 positional and functional candidate genes in an extended sample of 218 obese Finnish sibling pairs (sibpairs) (BMI > 30 kg/m 2 ).Evidence of linkage emerged mainly from the obese male sibpairs, suggesting a gender-specific effect for the underlying gene.By constructing haplotypes among the obese male sibpairs, we restricted the region from 15 Mb to 4 Mb, between markers DXS8088 and DXS8067.Regional functional candidate genes were tested for association in an initial sample of 117 cases and 182 controls.Significant evidence was observed for association for an SNP in the 3-untranslated region of the solute carrier family 6 member 14 (SLC6A14) gene (P = 0.0002) and for SNP haplotypes of the SLC6A14 gene (P = 0.0007-0.006).Furthermore, an independent replication study sample of 837 cases and 968 controls from Finland and Sweden also showed significant differences in allele frequencies between obese and non-obese individuals (P = 0.003).The SLC6A14 gene is an interesting novel candidate for obesity because it encodes an amino acid transporter, which potentially regulates tryptophan availability for serotonin synthesis and thus possibly affects appetite control.
Magnification‐driven B‐spline interpolation for cone‐beam projection and backprojection (2021)

Magnification-driven B-spline interpolation is shown to provide high-accuracy projection operators with good-quality adjoints for iterative reconstruction. It equally applies to backprojection for analytical reconstruction and detector data downsampling.
Stromal striae: a new insight into corneal physiology and mechanics (2017)

We uncover the significance of a previously unappreciated structural feature in corneal stroma, important to its biomechanics. Vogt striae are a known clinical indicator of keratoconus, and consist of dark, vertical lines crossing the corneal depth. However we detected stromal striae in most corneas, not only keratoconus. We observed striae with multiple imaging modalities in 82% of 118 human corneas, with pathology-specific differences. Striae generally depart from anchor points at Descemet's membrane in the posterior stroma obliquely in a V-shape, whereas in keratoconus, striae depart vertically from posterior toward anterior stroma. Optical coherence tomography shear wave elastography showed discontinuity of rigidity, and second harmonic generation and scanning electron microscopies showed undulation of lamellae at striae locations. Striae visibility decreased beyond physiological pressure and increased beyond physiological hydration. Immunohistology revealed striae to predominantly contain collagen VI, lumican and keratocan. The role of these regions of collagen VI linking sets of lamellae may be to absorb increases in intraocular pressure and external shocks.
Modulating transcriptional control of drug metabolism: A novel paradigm in drug therapeutics (2006)

893 Individual variation in drug metabolism is a major cause of treatment failures during cancer therapy. Because variations can lead to unpredictable and erratic drug side effects, there is a considerable need to modulate the pharmacodynamics of therapeutics to maximize efficacy and minimize side effects. Individual variations stem from differences in activity and abundance of drug metabolizing enzymes, including the cytochrome p450 family, whose expression is regulated at the level of transcription by orphan nuclear receptors. We have found that ketoconazole, a known inhibitor of p450 enzyme activity, represses the transcription of genes central to drug metabolism and transport by blocking the activation of nuclear receptors. Ketoconazole prevented the activation of endogenous as well as transiently transfected genes in cell lines and primary human and mouse hepatocytes. This inhibition was mediated by blocking the activation of nuclear receptors hPXR and CAR but not other nuclear receptors such as ERα or PPARγ. Ketoconazole disrupted the interaction between hPXR and co-activators in both mammalian two-hybrid assays and in co-activator dependent receptor ligand binding assays (CARLA). Furthermore, ketoconazole specifically inhibited PXR mediated gene transcription of cyp3a11, mdr1 and mrp2 in mice. Using LORR (Loss of Righting Reflex), we found that treatment of mice with ketoconazole inhibited the metabolism, and hence the functional consequences, of a CYP450 substrate-tribromoethanolamine. Finally, in wild type mice (n=6), we demonstrate that the pharmacokinetics of paclitaxel are normalized. Short term treatment with ketoconazole markedly reduces variation in treated population, and this effect coincides with decreased transcription of cyp3a11 and mrp2 in liver and mdr-1 in small bowel. These studies demonstrate for the first time that ketoconazole can inhibit the transcriptional activation of drug metabolism genes in vivo. Thus, ketoconazole has the potential to be used clinically to reduce individual variability in therapeutic responses.
Delayed CTLA-4Ig treatment of established acute allograft rejection successfully abrogates ongoing B cell responses (TRAN1P.950) (2015)

Abstract Once rejection is initiated, halting the immune response becomes much more difficult and effective therapies are necessary. Despite evidence that CTLA4Ig is ineffective at controlling memory T cell responses, we here report that CTLA4Ig is unexpectedly effective at controlling established B cell responses and treating established acute rejection. When C57BL/6 mice were sensitized with BALB/c splenocytes and treated with CTLA4Ig from 7d post-sensitization, B cell germinal center responses rapidly collapsed and alloantibody production was halted. In contrast, the effector CD4 and CD8 T cells response, which was monitored with seeded TCR-tg or endogenous allospecific cells, was not inhibited, and the extent of CD44 differentiation, IFNg production, and Tfh differentiation was similar to untreated controls. We also tested the effect of delayed CTLA-4Ig in established acute allograft rejection. In C57BL/6 recipients of BALB/c hearts, delayed treatment of CTLA4Ig till 6d post-transplant (just 2d before rejection) inhibited alloAb production and prevented acute rejection. 10 of 15 grafts survived to ≥ 30d post-transplant, despite significant T cell infiltration in the graft. Thus significant control of B cell responses and rejection can be achieved through delayed CTLA-4Ig treatment. This study raises the exciting possibility of using CLTA-4Ig therapeutically, not just prophylactically, in the clinic to control established B cell responses and established acute rejection.
Detection of Osseous Metastasis by 18F-NaF/18F-FDG PET/CT Versus CT Alone (2014)

Combined 18F-NaF/18F-FDG PET/CT outperforms CT alone and is highly sensitive and specific for detection of osseous metastases. The concordantly interpreted false-positive cases demonstrate the difficulty of distinguishing degenerative from malignant disease, whereas the single case of metastasis seen on CT but not PET highlights the need for careful review of CT images in multimodality studies.
Charge transport and persistent conduction in high gain photoconductive semiconductor switches used in pulsed power applications (2000)

Summary form only given. High gain photoconductivity semiconductor switches (PCSS's) used in pulsed power applications usually have deep level impurities in high concentration that are normally utilized in the compensation processes that make the devices semi-insulating (SI). The overall resistivity of these switches is thus improved and the devices have higher hold-off voltages. Depending on the bias applied, the conduction mechanisms in these devices also vary. Some of these devices continue to conduct even after the elimination of the optical source. In this presentation we analyze the behavior of optically triggered high gain GaAs PCSS, and discuss the nature of conduction at high and very high bias conditions, presenting a model for the persistent conduction of the switches after the withdrawal of the trigger source. The analysis takes into account GaAs specific inter-valley charge transfer properties, negative resistivity, field-assisted charge trapping and de-trapping, and impact ionization to give a model that can explain the physical processes during conduction. Experimental and modeling results of PCSS's used in generating ultra wideband (UWB) high power microwaves (HPM) are used in our analysis. The devices analyzed consist of 1.2/spl times/1 cm opposed contact PCSS's that were fabricated from GaAs that has a high concentration of EL2 traps at the mid-gap level. The device I-V characteristics were generated at the AFRL Laboratories, while the simulation studies were carried out at the University of New Mexico using the SILVACO semiconductor simulation code. The GaAs PCSS used in the simulation was generated through an interface with the BLAZE module that simulates III-V semiconductor devices. Our study shows that the characteristics of the PCSS can be affected by the impurity concentration, specifically those at the deep level where the EL2 donor (>10/sup 16//cm/sup 3/) sites dominate.
ChemInform Abstract: Phosphonate vs. Phosphinate Elimination During Olefination of Aldehydes. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Monolithic optoelectronic integration: A new component technology for lightwave communications (1985)

We discuss recent advances in the field of optoelectronic device integration. Several problems and advantages associated with integration are illustrated by discussing in detail three device types which are currently undergoing intensive investigation: integrated laser transmitters, integrated p-i-n photodetector receivers, and arrays of individually addressable detectors and light emitters. Devices fabricated using either GaAs or InP-based material systems with application at wavelength of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.82-0.87 \mu</tex> m and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1.3-1.55 \mu</tex> m, respectively, are considered. It is concluded that the pursuit of optoelectronic integration will lead to an increase in device functionality, an improvement in performance, and a reduction in cost of the integrated device as compared with its hybrid counterpart.
Structure and Activity of Protegiun-1 in Model Lipid Membranes (1996)

Protegrin (PG)-1, an antimicrobial peptide from porcine leukocytes, mediated the release of encapsulated fluorescent dye from vesicles of simulated microbial lipids, suggesting that the peptide interacted strongly with membrane-mimetic ensembles. Circular dichroism measurements of PG-1 in membrane-lipid dispersions and liposomal systems indicated that the peptide assumed a predominantly β-sheet conformation in these environments. Fourier transform infrared measurements of the peptide in microbial lipid films showed that the P­ sheet component was oriented approximately parallel to the surface of the lipid film The ability of PG-1 to associate with and lyse model microbial-lipid membranes is likely to underlie its potent antibiotic properties.
Kallistatin: double-edged role in angiogenesis, apoptosis and oxidative stress (2017)

Kallistatin, via its two structural elements - an active site and a heparin-binding domain - displays a double-edged function in angiogenesis, apoptosis and oxidative stress. First, kallistatin has both anti-angiogenic and pro-angiogenic effects. Kallistatin treatment attenuates angiogenesis and tumor growth in cancer-bearing mice. Kallistatin via its heparin-binding site inhibits angiogenesis by blocking vascular endothelial growth factor (VEGF)-induced growth, migration and adhesion of endothelial cells. Conversely, kallistatin via the active site promotes neovascularization by stimulating VEGF levels in endothelial progenitor cells. Second, kallistatin inhibits or induces apoptosis depending on cell types. Kallistatin attenuates organ injury and apoptosis in animal models, and its heparin-binding site is essential for blocking tumor necrosis factor (TNF)-α-induced apoptosis in endothelial cells. However, kallistatin via its active site induces apoptosis in breast cancer cells by up-regulating miR-34a and down-regulating miR-21 and miR-203 synthesis. Third, kallistatin can act as an antioxidant or pro-oxidant. Kallistatin treatment inhibits oxidative stress and tissue damage in animal models and cultured cells. Kallistatin via the heparin-binding domain antagonizes TNF-α-induced oxidative stress, whereas its active site is crucial for stimulating antioxidant enzyme expression. In contrast, kallistatin provokes oxidant formation, leading to blood pressure reduction and bacterial killing. Kallistatin-mediated vasodilation is partly mediated by H2O2, as the effect is abolished by the antioxidant enzyme catalase. Moreover, kallistatin exerts a bactericidal effect by stimulating superoxide production in neutrophils of mice with microbial infection as well as in cultured immune cells. Thus, kallistatin's dual roles in angiogenesis, apoptosis and oxidative stress contribute to its beneficial effects in various diseases.
From a Federated to an Integrated Automotive Architecture (2009)

This paper describes an integrated system architecture for automotive electronic systems based on multicore systems-on-chips (SoCs). We integrate functions from different suppliers into a few powerful electronic control units using a dedicated core for each function. This work is fueled by technological opportunities resulting from recent advances in the semiconductor industry and the challenges of providing dependable automotive electronic systems at competitive costs. The presented architecture introduces infrastructure IP cores to overcome key challenges in moving to automotive multicore SoCs: a time-triggered network-on-a-chip with fault isolation for the interconnection of functional IP cores, a diagnostic IP core for error detection and state recovery, a gateway IP core for interfacing legacy systems, and an IP core for reconfiguration. This paper also outlines the migration from today's federated architectures to the proposed integrated architecture using an exemplary automotive E/E system.
A Laminar Flow Nebulizer for Aerosol MALDI (1997)

A laminar flow nebulizer was developed for use with aerosol matrix-assisted laser desorption/ionization mass spectrometry. The nebulizer consists of a glass pneumatic nebulizer combined with a laminar flow tube. Particles formed at the pneumatic nebulizer are entrained in an auxiliary gas stream that dries the particles in the laminar flow tube. The mass range of the reflectron time-of-flight mass spectrometer has been extended to greater than 5000 Da: a mass spectrum of bovine insulin is reported at a mass resolution of 100. Mass spectra of bovine insulin and the peptides bradykinin and angiotensin II contain features resulting from prompt analyte dissociation prior to ion acceleration.
Checkpoint Blockade with Neoantigen Cancer Vaccines for Personalized Immunotherapy (2015)

Methods for harnessing the exquisite specificity of the immune system to eliminate tumors have been under development since the start of the 20th century, with numerous studies in animal models and trials in humans. Despite accumulating evidence, there has been widespread skepticism in the cancer community about whether tumors could be controlled by spontaneous immunity, and whether effective immunotherapy would be feasible to develop. However, the field has now passed an inflection point as new results have quelled these doubts, including: (i) several large clinical studies that have identified infiltrating CD8+ T cells as one of the best predictors of overall survival in human cancers, with strong validation in a large study of colorectal cancers; (ii) adoptive T cell therapy that effectively eradicates some types of B cell leukemias and (iii) novel checkpoint blockade (CPB) therapies inducing unprecedented long-term cures for patients with solid tumors, and more recently with blood malignancies. With the availability of these novel immunologic agents, the priority has shifted to understanding the mechanisms of and predicting responses to each treatment. Fundamental to this endeavor is the understanding of the crosstalk between tumor cells and immune cell populations within the tumor microenvironment and the selective pressure they mutually exert on each other. At the heart of cancer and host immune cell coevolution is the tumor antigen and host antigen-specific T cell interaction. The cytotoxic T cell-cognate antigen interaction forms the mechanistic basis for immune-mediated recognition and the killing of malignant cells, and provides selective pressure on the cancer cell to evolve. While the search for immunogenic tumor antigens has been the subject of decades-long studies, multiple lines of evidence have convincingly demonstrated tumor neoantigens as an important class of immunogenic tumor antigens. Neoantigens arise from amino acid changes encoded by somatic mutations in the tumor cell and have the potential to bind to and be presented by personal HLA molecules. With the recent availability of next-generation sequencing, systematic approaches to identify mutations leading to amino acid changes have become feasible. This development, together with the improved sensitivity of well-validated neural network/machine learning-based algorithms that predict binding to class I MHC, has enabled the implementation of neoantigen discovery pipelines. Recent studies by us and others in humans and mice have leveraged these tools to demonstrate evidence of protective immunity when targeting tumor neoantigens. We have further incorporated this approach to discover antigen targets to generate a multi-epitope personalized therapeutic cancer vaccine, that we are now testing in phase I clinical trials. Altogether, effective targeting of tumor neoantigens occurs spontaneously and during CPB, and offers prospects of a powerful, new immunotherapy. Disclosures No relevant conflicts of interest to declare.
Solubilization at high pH results in improved recovery of proteins from inclusion bodies of E. coli (2008)

Abstract BACKGROUND: Solubilization of inclusion bodies using high concentration of chaotropes followed by suboptimal refolding results in lower recovery of bioactive proteins from E. coli . Growing evidence indicates that aggregation of expressed proteins into inclusion bodies is molecular specific in nature and proteins in inclusion bodies have native‐like secondary structure. Protecting these pre‐existing native‐like secondary structures of proteins using mild solubilization conditions is one of the key steps in improved recovery of bioactive protein from inclusion bodies of E. coli . RESULTS: Inclusion bodies of seven proteins (hGH, oGH, Pyk, PKS, aldolase, enolase and superoxide dismutase) were solubilized at pH 12 in the presence of 2 mol L −1 urea and were subsequently refolded and purified. Enrichment of inclusion bodies after cell lysis, mild solubilization at alkaline pH and pulsatile refolding resulted in lower aggregation of protein during refolding and improved the final recovery of protein from inclusion bodies of E. coli . The efficiency of protein recovery from inclusion bodies was 30–40% for most of the proteins. This was almost two times higher than that achieved when inclusion bodies were solubilized in 8 mol L −1 urea and subsequently refolded. Purified hGH and Pyk were functionally active in respective in vitro assays. CONCLUSION: Non‐denaturing solubilization of inclusion body proteins at alkaline pH is a viable alternative to the use of high molar concentration chaotropes for efficient recovery of inclusion body proteins. Mild solubilization and pulsatile refolding contribute synergistically to reduce the extent of aggregation during refolding and result in high throughput recovery of bioactive proteins from inclusion bodies of E. coli. Copyright © 2008 Society of Chemical Industry
Modular Squalene-based Nanosystems (2017)

In a recent paper we have discussed the innovative and original concept the &ldquo;squalenoylation&rdquo; of nanoparticles. This method may be used in the nanoparticle-based formulation of a wide range of drug molecules (both hydrophilic and lipophilic). The "squalenoylation" approach is based on the covalent linkage between the squalene, a natural and biocompatible lipid belonging to the terpenoid family, and a drug, in order to increase its pharmacological efficacy. Fundamentally, the dynamically folded conformation of squalene triggers the resulting squalene-drug bioconjugates to self-assemble as nanoparticles of 100&ndash;300 nm. In general, these nanoparticles showed long blood circulation times after intravenous administration and improved pharmacological activity with reduced side effects and toxicity. This flexible and generic technique opens exciting perspectives in the drug delivery field. Ref: Curr Top Med Chem 2017, https://www.ncbi.nlm.nih.gov/pubmed/28730957