gebhart/patrepeval huggingface dataset:
Characterisation of Potential Antimicrobial Targets in Bacillus spp. I. Aminotransferases and Methionine Regeneration in Bacillus subtilis (2002)

The aminotransferases involved in the final step of methionine recycling from methylthioadenosine have been examined in the gram-positive bacterium Bacillits subtilis. Homogenates of this bacterium were able to convert ketomethiobutyrate to methionine, utilising leucine, isoleucine, valine, phenylalanine, tyrosine, and alanine as preferred amino donors. Unlike other organisms examined to date in this context, B. subtilis was found to contain no aspartate aminotransferase or tyrosine aminotransferase sequences with structural homology to subfamily Ia aminotransferases. Instead, in B. subtills, the six putative homologues of aspartate aminotransferase were found to be members of the If subfamily. Five of these six sequences were cloned and expressed, with only the ykrV gene product capable of producing methionine from ketomethiobutyrate. However, this enzyme only catalysed the reaction using glutamine as an amino donor. Two putative branched-chain amino acid aminotransferases from family III were also cloned and expressed, and both were found to produce methionine from ketomethiobutyrate using branched-chain and aromatic amino acids. Of these two enzymes, the ybgE gene product was the most active and had kinetic constants consistent with it being the enzyme responsible for the majority of methionine regeneration in this organism. The ybgE gene product could be inhibited uncompetitively by the aminooxy compound canaline, with a Ki of 48 muM. In addition, canaline inhibited the in vitro growth of B. subtilis in minimal medium with an IC50 of 37 muM and an MIC of 500 muM. Growth inhibition in nutrient broth was negligible.
Performance and fault modeling with VHDL (1992)

Describes how VHDL can be used across the system design process, from specification to the development of maintenance strategies. The contributors provide advanced techniques, and detail how these can be adapted to improve the system development process, reducing time and cost.
( <i>R</i> )-2-Hydroxyglutarate Is Sufficient to Promote Leukemogenesis and Its Effects Are Reversible (2013)

Mutations in IDH1 and IDH2, the genes coding for isocitrate dehydrogenases 1 and 2, are common in several human cancers, including leukemias, and result in overproduction of the (R)-enantiomer of 2-hydroxyglutarate [(R)-2HG]. Elucidation of the role of IDH mutations and (R)-2HG in leukemogenesis has been hampered by a lack of appropriate cell-based models. Here, we show that a canonical IDH1 mutant, IDH1 R132H, promotes cytokine independence and blocks differentiation in hematopoietic cells. These effects can be recapitulated by (R)-2HG, but not (S)-2HG, despite the fact that (S)-2HG more potently inhibits enzymes, such as the 5'-methylcytosine hydroxylase TET2, that have previously been linked to the pathogenesis of IDH mutant tumors. We provide evidence that this paradox relates to the ability of (S)-2HG, but not (R)-2HG, to inhibit the EglN prolyl hydroxylases. Additionally, we show that transformation by (R)-2HG is reversible.
Preclinical Evaluation of Rapeseed, Raspberry, and Pine Bark Phenolics for Health Related Effects (2005)

Rapeseed, raspberry, and pine bark are promising bioactive sources of plant phenolics selected from among ca. 100 previously screened plant materials for in vitro preclinical evaluation of health related effects. Phenolic extracts and isolated fractions of the selected materials were investigated for antioxidant, antimicrobial, antiinflammatory, and antimutagenic properties as well as for cell permeability. It was shown that rapeseed and pine bark phenolics and raspberry anthocyanins were good or excellent antioxidants toward oxidation of phosphatidylcholine membrane (liposomes), rapeseed oil (crude) phenolics were effective radical scavengers (DPPH test), and both raspberry and pine bark phenolics inhibited LDL oxidation. Rapeseed oil phenolics, principally vinylsyringol, raspberry anthocyanins, and pinoresinol and matairesinol, the principal components of pine bark phenolic isolate, were effective against formation of the proinflammatory mediator, prostaglandin E(2). Raspberry ellagitannins inhibited the growth of Proteus mirabilis and Klebsiella oxytoca. Pine bark and rapeseed had minor effects on the permeability of model drugs in Caco-2 experiments. None of the tested extracts were mutagenic nor toxic to Caco-2 cells or macrophages. Thus, phenolic isolates from rapeseed, raspberry, and pine bark and are safe and bioactive for possible food applications including functional foods intended for health benefit.
Reciprocal leukemia-stroma VCAM-1/VLA-4-dependent activation of NF-κB mediates chemoresistance (2014)

Leukemia cells are protected from chemotherapy-induced apoptosis by their interactions with bone marrow mesenchymal stromal cells (BM-MSCs). Yet the underlying mechanisms associated with this protective effect remain unclear. Genome-wide gene expression profiling of BM-MSCs revealed that coculture with leukemia cells upregulated the transcription of genes associated with nuclear factor (NF)-κB signaling. Moreover, primary BM-MSCs from leukemia patients expressed NF-κB target genes at higher levels than their normal BM-MSC counterparts. The blockade of NF-κB activation via chemical agents or the overexpression of the mutant form of inhibitor κB-α (IκBα) in BM-MSCs markedly reduced the stromal-mediated drug resistance in leukemia cells in vitro and in vivo. In particular, our unique in vivo model of human leukemia BM microenvironment illustrated a direct link between NF-κB activation and stromal-associated chemoprotection. Mechanistic in vitro studies revealed that the interaction between vascular cell adhesion molecule 1 (VCAM-1) and very late antigen-4 (VLA-4) played an integral role in the activation of NF-κB in the stromal and tumor cell compartments. Together, these results suggest that reciprocal NF-κB activation in BM-MSCs and leukemia cells is essential for promoting chemoresistance in the transformed cells, and targeting NF-κB or VLA-4/VCAM-1 signaling could be a clinically relevant mechanism to overcome stroma-mediated chemoresistance in BM-resident leukemia cells.
Proximity-based assays for the detection of activated HER3, HER2/HER3 heterodimers and HER3/PI3K complexes in formalin-fixed, paraffin-embedded cell line controls and tumors. (2009)

Abstract Abstract #4040 Although kinase-defective, the role of the HER3 receptor in driving tumor growth through dimerization with other HER family members is well recognized. There is increasing interest in developing therapeutic strategies to interfere with signaling through this receptor, either directly or indirectly. At the same time, there is recognition that the activation of HER3 could be an important biomarker of drug response and resistance. In particular the HER2/HER3 heterodimer has been extensively studied and, among all the possible homo and heterodimers formed by HER receptors, is considered the most mitogenic because of the ability of HER3 to effectively couple to the pro-survival PI3K/Akt pathway.&#x2028; Using the VeraTag™ technology, we have developed a suite of assays designed to detect quantitatively the activation status of the HER3 receptor by measuring HER3-specific phosphorylation and formation of HER3 signaling complexes in formalin-fixed, paraffin-embedded (FFPE) cell line controls and tissue samples.These assays are dual antibody-based and measure complexes of proteins in close association since signal is generated only when the antibodies are bound to target-specific epitope sites proximal to one another. A capillary electrophoresis instrument equipped with laser-induced fluorescence provides a highly sensitive and quantitative read-out of the assay. We report data on assays which detect a ligand-induced, 2-5-fold change in HER2/HER3 heterodimer formation, a 10-20 fold change in phosphorylated HER3 signal and as high as a 10 fold change in HER3/PI3K complex formation in a series of cell line controls, spanning a wide range of HER2 and HER3 receptor levels. FFPE data were verified with results from co-immunoprecipitation using antibodies identical to those used in the VeraTag assay. The influence of the HER2 and HER3 levels on the formation of HER2/HER3 heterodimers and correlation with HER3 phosphorylation and formation of the PI3K adaptor complex will be discussed.&#x2028; In addition, we have used these assays to landscape HER3 activation in a number of tissues, including breast and ovarian tumors, focusing particularly on HER2 positive breast cancer, where the HER2/HER3 heterodimer is thought to play a particularly significant role. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 4040.
Fast and robust camera's auto exposure control using convex or concave model (2015)

A fast and robust camera's auto exposure algorithm is proposed by modeling its luminance characteristics as a concave/convex function of a control parameter. A proper parameter value is computed using a modified secant algorithm with fast convergence. The superior performance of the proposed algorithm is confirmed by experimental results.
Machine Learning for Anomaly Detection: A Systematic Review (2021)

Anomaly detection has been used for decades to identify and extract anomalous components from data. Many techniques have been used to detect anomalies. One of the increasingly significant techniques is Machine Learning (ML), which plays an important role in this area. In this research paper, we conduct a Systematic Literature Review (SLR) which analyzes ML models that detect anomalies in their application. Our review analyzes the models from four perspectives; the applications of anomaly detection, ML techniques, performance metrics for ML models, and the classification of anomaly detection. In our review, we have identified 290 research articles, written from 2000-2020, that discuss ML techniques for anomaly detection. After analyzing the selected research articles, we present 43 different applications of anomaly detection found in the selected research articles. Moreover, we identify 29 distinct ML models used in the identification of anomalies. Finally, we present 22 different datasets that are applied in experiments on anomaly detection, as well as many other general datasets. In addition, we observe that unsupervised anomaly detection has been adopted by researchers more than other classification anomaly detection systems. Detection of anomalies using ML models is a promising area of research, and there are a lot of ML models that have been implemented by researchers. Therefore, we provide researchers with recommendations and guidelines based on this review.
Atorvastatin Treatment of Rats with Ischemia-Reperfusion Injury Improves Adipose-Derived Mesenchymal Stem Cell Migration and Survival via the SDF-1α/CXCR-4 Axis (2013)

Migration and survival of ASCs could be improved by atorvastatin under ischemia-reperfusion injury, which were ascribed to SDF-1α/CXCR-4 axis.
Hybrid Cascaded Neural Network for Liver Lesion Segmentation (2020)

Automatic liver lesion segmentation is a challenging task while having a significant impact on assisting medical professionals in the designing of effective treatment and planning proper care. In this paper, we propose a cascaded system that combines both 2D and 3D convolutional neural networks to segment hepatic lesions effectively. Our 2D network operates on a slice-by-slice basis in the axial orientation to segment liver and large liver lesions; while we use a 3D network to detect small lesions that are often missed in a 2D segmentation design. We employ this algorithm on the LiTS challenge obtaining a Dice score per subject of 68.1%, which performs the best among all non-pre-trained models and the second-best among published methods. We also perform two-fold cross-validation to reveal the over- and under-segmentation issues in the annotations of the LiTS dataset.
Understanding the Detection of View Fraud in Video Content Portals (2016)

While substantial effort has been devoted to understand fraudulent activity in traditional online advertising (search and banner), more recent forms such as video ads have received little attention. The understanding and identification of fraudulent activity (i.e., fake views) in video ads for advertisers, is complicated as they rely exclusively on the detection mechanisms deployed by video hosting portals. In this context, the development of independent tools able to monitor and audit the fidelity of these systems are missing today and needed by both industry and regulators.
A Survey of Security and Privacy Issues in ePassport Protocols (2016)

This article examines in great detail the most relevant security and privacy issues affecting the protocols used by contactless chips integrated in ePassports, and presents all relevant literature together with some new attacks and insights that could help in improving future standards and the next generations of ePassports.
Radar and vision sensors calibration for outdoor 3D reconstruction (2015)

In this paper we introduce a new geometric calibration algorithm, and a geometric method of 3D reconstruction using a panoramic microwave radar and a camera. These two sensors are complementary, considering the robustness to environmental conditions and depth detection ability of the radar on one hand, and the high spatial resolution of a vision sensor on the other hand. This makes the approach well adapted for large scale outdoor cartography. Firstly, we address the global calibration problem which consists in finding the exact transformation between radar and camera coordinate systems. The method is based on the optimization of a non-linear criterion obtained from a set of radar-to-image target correspondences. Unlike existing methods, no special configuration of the 3D points is required, only the knowledge of inter-targets distance is needed. This makes the method flexible and easy to use by a non expert operator. Secondly, we present a 3D reconstruction method based on sensors geometry. Both methods have been validated with synthetic and real data.
Use of an organic template structure for the manipulation of nano-scale objects (2005)

In this paper, we report on a new method for the investigation and manipulation of single molecules by STM without the explicit need for experimentally challenging UHV techniques. The controlled manipulation of single molecules becomes possible, since an organic template preadsorbed on the substrate introduces a hexagonal grid of stable adsorption sites with a next nearest neighbor distance of approximately 1.6 nm.
Formula Tolerance in Postbreastfed and Exclusively Formula-fed Infants (1999)

The present clinical studies indicate that the composition and/or processing of milk-based powder iron-fortified infant formulas affect stool characteristics experienced by infants. The inclusion of palm olein oil in formula B may be the reason for the observed differences in stool characteristics. Palm olein is used in infant formulas to provide palmitic acid at a level similar to that found in breast milk. However, palmitic acid from palm olein is arranged differently from that in breast milk triglyceride and is poorly absorbed. Unabsorbed palmitic acid tends to react with calcium to form insoluble soaps, and the level of these soaps is correlated with stool hardness. The pattern of softer stools and greater frequency of stooling associated with formula A is similar to the stool pattern in the exclusively breastfed infant. Thus, the use of formula A may ease the transition from breast milk to formula feeding and ameliorate parents' perception that constipation is associated with iron-fortified formula.
Implication of OTX2 in Pigment Epithelium Determination and Neural Retina Differentiation (1997)

The expression pattern of Otx2, a homeobox-containing gene, was analyzed from the beginning of eye morphogenesis until neural retina differentiation in chick embryos. Early on, Otx2 expression was diffuse throughout the optic vesicles but became restricted to their dorsal part when the vesicles contacted the surface ectoderm. As the optic cup forms, Otx2 was expressed only in the outer layer, which gives rise to the pigment epithelium. This early Otx2 expression pattern was complementary to that of PAX2, which localizes to the ventral half of the developing eye and optic stalk. Otx2 expression was always observed in the pigment epithelium at all stages analyzed but was extended to scattered cells located in the central portion of the neural retina around stage 22. The number of cells expressing Otx2 transcripts increased with time, following a central to peripheral gradient. Bromodeoxyuridine labeling in combination with immunohistochemistry with anti-OTX2 antiserum and different cell-specific markers were used to determine that OTX2-positive cells are postmitotic neuroblasts undergoing differentiation into several, if not all, of the distinct cell types present in the chick retina. These data indicate that Otx2 might have a double role in eye development. First, it might be necessary for the early specification and subsequent functioning of the pigment epithelium. Later, OTX2 expression might be involved in retina neurogenesis, defining a differentiation feature common to the distinct retinal cell classes.
Communication over fading channels with finite buffer constraints"single user and multiple access cases (2002)

We consider communication over a fading channel where arriving data is stored in a buffer of size L until it is transmitted. Any data arriving when the buffer is full is discarded. The transmitter utilises a power and rate control policy that can depend on both the buffer occupancy as well as the channel state. The trade-off between minimizing transmission power and buffer overflow probability is analyzed in the asymptotic regime as L/spl rarr//spl infin/. Both single user and multi-access models are considered.
A new authentication mechanism for loosely coupled 3G-WLAN integrated networks (2005)

Recently, several authentication protocols have been proposed for wireless local area networks (WLANs) to improve security in hotspot public access and corporate networks, and some have been proposed for integrated 3G-WLAN networks. These authentication protocols are based on the extensible authentication protocol and have been directly applied to wireless networks based on their widespread use in wired networks. Depending on the 3G-WLAN architecture and how the WLAN is tied to the 3G network, these protocols could have large latency. Moreover, they do not have mechanisms for authenticating the usage time of a mobile in a WLAN. We first discuss these issues related to existing authentication protocols for a 3G-WLAN integrated network. Then, we propose a new authentication mechanism based on the dual signature concept used in secure electronic transactions that can be used in a loosely coupled architecture. Finally, we present a preliminary evaluation of the energy performance and latency of the existing and proposed protocols.
Experimental comparison of single-shot broadband vibrational and dual-broadband pure rotational coherent anti-Stokes Raman scattering in hot air (1996)

Broadband vibrational and dual-broadband pure rotational coherent anti-Stokes Raman scattering (CARS) have been compared in a high-temperature oven, in which the accuracy and single-shot precision of gas temperature and relative O(2)- and N(2)-concentration measurements in hot air were probed over a temperature range that is typical for many combustion processes. To ensure a realistic comparison, we used nearly the same experimental setup for both CARS techniques. Besides temperature information, dual-broadband pure rotational CARS offers the possibility of achieving simultaneous single-shot concentration measurements. The comparison shows that this technique also has significant advantages in temperature evaluation over a large temperature range in comparison with vibrational CARS.
Spin transport and dynamics in all-oxide perovskite <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>La</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mo>/</mml:mo><mml:mn>3</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi>Sr</mml:mi><mml:mrow><mml:mn>1</mml:mn><mml:mo>/</mml:mo><mml:mn>3</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi>MnO</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:mrow><mml:mo>/</mml:mo><mml:msub><mml:mi>SrRuO</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:math> bilayers probed by ferromagnetic resonance (2016)

Thin films of perovskite oxides offer the possibility of combining emerging concepts of strongly correlated electron phenomena and spin current in magnetic devices. However, spin transport and magnetization dynamics in these complex oxide materials are not well understood. Here, we experimentally quantify spin transport parameters and magnetization damping in epitaxial perovskite ferromagnet/paramagnet bilayers of ${\mathrm{La}}_{2/3}{\mathrm{Sr}}_{1/3}{\mathrm{MnO}}_{3}/{\mathrm{SrRuO}}_{3}$ (LSMO/SRO) by broadband ferromagnetic resonance spectroscopy. From the SRO thickness dependence of the Gilbert damping, we estimate a short spin diffusion length of $\ensuremath{\lesssim}1$ nm in SRO and an interfacial spin-mixing conductance comparable to other ferromagnet/paramagnetic-metal bilayers. Moreover, we find that anisotropic non-Gilbert damping due to two-magnon scattering also increases with the addition of SRO. Our results demonstrate LSMO/SRO as a spin-source/spin-sink system that may be a foundation for examining spin-current transport in various perovskite heterostructures.
A Platinized Titanium Anode for Chromium Electroplating (1986)

Une anode de titane platinee chargee d'un catalyseur IrO 2 resiste a la corrosion, mais l'aptitude a l'oxydation des ions chromiques en ions chromate est faible dans une solution fraiche de bain de Sergent. Les ions chromiques dans l'electrolyte contenant du fluorosilicate sont oxydes facilement a la surface de l'anode. La courbe de polarisation anodique est egalement fortement affectee par les ions fluosilicate pour les densites de courant >10 mA/cm 2
<title>Fabrication issues in micromachined tunable optical filters</title> (1995)

Prototypes of micromachined tunable infrared optical filters are being produced. Micromachining silicon for use in these filters requires the integration of multilayer dielectric optical coatings such as ZnSe/ThF<SUB>4</SUB>. These coatings are novel materials for integration with microlithographic processing. Devices were engineered and a process flow was developed to avoid contaminating processing tools with the coating. A method for patterning the coating was developed. Low-temperature bonding techniques have been explored and tested. Fabrication issues for these micromachined devices are discussed.