gebhart/patrepeval huggingface dataset:
Pharmacoproteomics of a Metalloproteinase Hydroxamate Inhibitor in Breast Cancer Cells: Dynamics of Membrane Type 1 Matrix Metalloproteinase-Mediated Membrane Protein Shedding (2008)

Broad-spectrum matrix metalloproteinase (MMP) inhibitors (MMPI) were unsuccessful in cancer clinical trials, partly due to side effects resulting from limited knowledge of the full repertoire of MMP substrates, termed the substrate degradome, and hence the in vivo functions of MMPs. To gain further insight into the degradome of MMP-14 (membrane type 1 MMP) an MMPI, prinomastat (drug code AG3340), was used to reduce proteolytic processing and ectodomain shedding in human MDA-MB-231 breast cancer cells transfected with MMP-14. We report a quantitative proteomic evaluation of the targets and effects of the inhibitor in this cell-based system. Proteins in cell-conditioned medium (the secretome) and membrane fractions with levels that were modulated by the MMPI were identified by isotope-coded affinity tag (ICAT) labeling and tandem mass spectrometry. Comparisons of the expression of MMP-14 with that of a vector control resulted in increased MMP-14/vector ICAT ratios for many proteins in conditioned medium, indicating MMP-14-mediated ectodomain shedding. Following MMPI treatment, the MMPI/vehicle ICAT ratio was reversed, suggesting that MMP-14-mediated shedding of these proteins was blocked by the inhibitor. The reduction in shedding or the release of substrates from pericellular sites in the presence of the MMPI was frequently accompanied by the accumulation of the protein in the plasma membrane, as indicated by high MMPI/vehicle ICAT ratios. Considered together, this is a strong predictor of biologically relevant substrates cleaved in the cellular context that led to the identification of many undescribed MMP-14 substrates, 20 of which we validated biochemically, including DJ-1, galectin-1, Hsp90alpha, pentraxin 3, progranulin, Cyr61, peptidyl-prolyl cis-trans isomerase A, and dickkopf-1. Other proteins with altered levels, such as Kunitz-type protease inhibitor 1 and beta-2-microglobulin, were not substrates in biochemical assays, suggesting an indirect affect of the MMPI, which might be important in drug development as biomarkers or, in preclinical phases, to predict systemic drug actions and adverse side effects. Hence, this approach describes the dynamic pattern of cell membrane ectodomain shedding and its perturbation upon metalloproteinase drug treatment.
Comparative analysis of master-slave latches and flip-flops for high-performance and low-power systems (1999)

In this paper, we propose a set of rules for consistent estimation of the real performance and power features of the flip-flop and master-slave latch structures. A new simulation and optimization approach is presented, targeting both high-performance and power budget issues. The analysis approach reveals the sources of performance and power-consumption bottlenecks in different design styles. Certain misleading parameters have been properly modified and weighted to reflect the real properties of the compared structures. Furthermore, the results of the comparison of representative master-slave latches and flip-flops illustrate the advantages of our approach and the suitability of different design styles for high-performance and low-power applications.
Desquamative interstitial pneumonia (2010)

Desquamative interstitial pneumonia (DIP) is one of the rarest of the idiopathic interstitial pneumonias. It is characterized by the accumulation of macrophages in large numbers in the alveolar spaces associated with interstitial inflammation and/or fibrosis. The macrophages frequently contain light brown pigment, and because of their association with smoking have been called 'smoker's macrophages'. Lymphoid nodules are common, as is a sparse but distinct eosinophil infiltrate. Most cases of DIP are caused by cigarette smoking, but drugs and other inhaled agents, including marijuana smoke, can also produce the same disease. Although respiratory bronchiolitis-interstitial lung disease (RB-ILD) is a closely related process, there are prognostic reasons for continuing to separate it from DIP when possible. The proposed relationship of DIP to fibrotic non-specific interstitial pneumonia (NSIP) remains uncertain. The prognosis of DIP appears to be significantly better than that of fibrotic NSIP, so while there can be morphological overlap between the two, merging them into one disease may hide important prognostic information. Although the majority of DIP patients improve on treatment, some patients develop progressive irreversible fibrosis.
Tissue classification and segmentation of MR images (1993)

Previously reported classification or segmentation methods are reviewed, and some statistical approaches that may be capable of automatically classifying tissues and segmenting magnetic resonance (MR) images are discussed. The image segmentation methods reviewed are edge detection methods and region detection methods. The key feature of statistical approaches toward automatically classifying tissues and segmenting MR images is the determination of the number of image classes and the model parameters of these classes from the image data directly by a computer. Any free parameter requiring extensive user interactions should be avoided. Further research on the Gaussian Markov random field (GMRF) model and the MRF penalty term will push the statistical approaches further along the automatic track. As these approaches become more practical they will become more valuable.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ultrahigh Sensitivity Measurement of Doppler Shift with a Microchip Solid-State Laser (1993)

Highly-sensitive laser Doppler velocimetry featuring simultaneous measurement of different velocities of light-scattering objects and vibration sensing based on Doppler-shifted light-injection-induced intensity modulation in a self-mixing microchip solid-state laser are demonstrated.
Immune Cell Plasticity in Inflammation: Insights into Description and Regulation of Immune Cell Phenotypes (2022)

Inflammation is a life-saving immune reaction occurring in response to invading pathogens. Nonetheless, inflammation can also occur in an uncontrolled, unrestricted manner, leading to chronic disease and organ damage. Mechanisms triggering an inflammatory response, hindering such a response, or leading to its resolution are well-studied but so far insufficiently elucidated with regard to precise therapeutic interventions. Notably, as an immune reaction evolves, requirements and environments for immune cells change, and thus cellular phenotypes adapt and shift, leading to the appearance of distinct cellular subpopulations with new functional features. In this article, we aim to highlight properties of, and overarching regulatory factors involved in, the occurrence of immune cell phenotypes with a special focus on neutrophils, macrophages and platelets. Additionally, we point out implications for both diagnostics and therapeutics in inflammation research.
Natural amines inhibit activation of human plasmacytoid dendritic cells through CXCR4 engagement (2017)

Plasmacytoid dendritic cells (pDC) are specialized in secretion of type I interferon in response to pathogens. Here we show that natural monoamines and synthetic amines inhibit pDC activation by RNA viruses. Furthermore, a synthetic analogue of histamine reduces type I interferon production in a mouse model of influenza infection. We identify CXC chemokine receptor 4 (CXCR4) as a receptor used by amines to inhibit pDC. Our study establishes a functional link between natural amines and the innate immune system and identifies CXCR4 as a potential 'on-off' switch of pDC activity with therapeutic potential.
Framing the ethical and legal issues of human artificial gametes in research, therapy, and assisted reproduction: A German perspective (2018)

Recent results from studies on animals suggest that functional germ cells may be generated from human pluripotent stem cells, giving rise to three possibilities: research with these so-called artificial gametes, including fertilization experiments in vitro; their use in vivo for therapy for the treatment of human infertility; and their use in assisted reproductive technologies in vitro. While the legal, philosophical, and ethical questions associated with these possibilities have been already discussed intensively in other countries, the debate in Germany is still at its beginning. A systematic and detailed analysis of the legal framework in Germany is provided with regard to the three possibilities, including the applicable statutory laws as well as the constitutional law. The question emerges as to whether the statutory laws as well as the constitution justify a distinction to be made between embryos of artificial and natural origin. This question is subject to philosophical analysis, discussing the distinction between person and thing, dignity and price, personality and property, and nature and technique. As a result, the criterion of naturalness alone may not be sufficient to differentiate between embryos of natural and artificial origin, and other criteria need to be identified.
IC defect sensitivity for footprint-type spot defects (1992)

While it is important to exhaustively verify IC designs for their functional performance, it is equally important to verify their robustness against spot defects, that is, to foresee what will happen to the design when it is exposed to defect conditions in a real manufacturing environment. One such verification is done by extracting the layout sites where defects can induce a functional failure of the design. Initial attempts to perform this verification task were based on a 'critical area extraction' of one layer at a time, neglecting the electrical significance of interrelationships between layers. A novel method to construct deterministically multilayer critical areas is presented. These critical areas are established on the theoretical basis of defect semantics and on the new concept of 'susceptible sites'. A system comprising several algorithms which in principle maintain simultaneously as many scan lines as the number of layers, in such a way that it is possible to keep track of the vertical and horizontal effects of defects, is developed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ship diesel engine fault diagnosis based on the SVM and association rule mining (2016)

Ship diesel engine's structure is complex, and its fault has high coupling. For this reason, we study ship diesel engine fault diagnosis from two aspects. First of all, we divided ship diesel engine system into four parts according its basic structure and fault features, the fuel system, the lubrication system, the intake and exhaust system and the cooling system, and then analyzed the fault features for the each subsystem respectively. We used the support vector machine (SVM) algorithm to classify fault data for each subsystem of ship diesel engine. So that, we could implement the fault diagnosis for the each subsystem. It reduced the complexity of the whole system fault diagnosis. Secondly, Ship diesel engine fault often occurs between different the subsystems, and the occurrence of a fault is often accompanied by other fault. We could solve this high coupling by using association rule mining and then found out the implicit association rules of the fault in whole system.
A Surface Sol−Gel Process of TiO2 and Other Metal Oxide Films with Molecular Precision (1997)

Fabrication of metal oxide thin films with thickness control of nanometer precision is an important technology that leads to wide practical applications. The present study demonstrates that a surface sol−gel process, composed of chemisorption of alkoxide, rinsing, hydrolysis, and drying, is a superior technique for the preparation of ultrathin metal oxide films with molecular precision. The simplicity of this process should be a great advantage in commercial production of nanosized oxide films.
Absolute Quantitation of Stevioside and Rebaudioside A in Commercial Standards by Quantitative NMR (2012)

The extract prepared from the leaves of Stevia rebaudiana BERTONI (Asteraceae) contains sweet steviol glycosides, mainly stevioside and rebaudioside A. Highly purified stevia extracts have become popular worldwide as a natural, low-calorie sweetener. They contain various types of steviol glycosides, and their main components are stevioside and rebaudioside A. The content of each steviol glycoside is quantified by comparing the ratios of the molecular weights and the chromatographic peak areas of the samples to those of stevioside or rebaudioside A standards of the Food and Agriculture Organization of the United Nations (FAO)/World Health Organization (WHO) Joint Expert Committee on Food Additives (JECFA) and other specifications. However, various commercial standard reagents of stevioside and rebaudioside A are available. Their purities are different and their exact purities are not indicated. Therefore, the measured values of stevioside and rebaudioside A contained in a sample vary according to the standard used for the quantification. In this study, we utilized an accurate method, quantitative NMR (qNMR), for determining the contents of stevioside and rebaudioside A in standards, with traceability to the International System of Units (SI units). The purities of several commercial standards were determined to confirm their actual values.
Improvement of goat TSE discriminative diagnosis and susceptibility based assessment of BSE infectivity in goat milk and meat (2012)

In light of the known ability of the BSE agent to cross the animal/human species barrier, the evidence establishing the presence of BSE in goat is especially alarming, as it represents a potential risk of food-born contamination to human consumers of goat milk and meat products. The main objective has been to determine the tissue distribution of BSE after oral exposure of goats while simultaneously generating in dispensable data on genetic susceptibility in the most commonly used production breeds. Our approach integrates the predicted influence of PrP gene polymorphisms on scrapie and BSE susceptibility so that it could potentially be used for the control of field TSE outbreaks in goats. This proposal aims: - at providing data to allow evaluation of human risk associated with BSE passaged in goat; - at providing pathogenesis data and biologic al material from first and second passage BSE in goats; - at evaluating the possibility of BSE self-maintenance in goats by maternal/horizontal transmission; - at validating and improving our ability to detect and discriminate caprine BSE from goat scrapie.
Bolt-On Global Consistency for the Cloud (2018)

Web services that enable users in multiple regions to collaborate can increase availability and decrease latency by replicating data across data centers. If such a service spreads its data across multiple cloud providers---for the associated performance, cost, and reliability benefits---it cannot rely on cloud providers to keep the data globally consistent.
Parallel algorithms for visualising image surfaces (1989)

A parallel approach to processing and viewing image surfaces is presented. The approach incorporates a parallel SIMD solution to the visibility or hidden-surface, problem for perspective views, visibility maps and shadowing of image surfaces. The algorithm presented belongs to a more general class of techniques based on successive application of one-dimensional scan-line operations, in row and column directions, to appropriate intermediate spatial transformations of images. Data access requirements are regularised and independent of data values, and thus predictable, giving significant advantage on parallel and sequential machines.
Addition of divalent iron to electron donor mixtures for remediation of chlorinated ethenes: A study of 100 wells (2018)

Abstract The objective of this study is to assess the effects of adding soluble divalent iron (DVI) to emulsified electron donor mixtures to promote the biogeochemical destruction of four common chlorinated ethenes—perchloroethylene, trichloroethylene, cis‐1,2‐dichloroethylene, and vinyl chloride (VC)—as part of electron donor mixture enhanced reductive dechlorination treatments in groundwater. Twenty‐four project sites were studied, comprising 100 performance monitoring wells across the U.S. Wells that received DVI treatment showed increased dechlorination rates, improved contaminant reduction, and limited daughter product formation relative to the wells that did not receive DVI treatment. Following injection of electron donor treatments and DVI, the time required for a well to reach 90% reduction from a peak concentration was improved for the 25, 50, and 75% confidence intervals for the four chlorinated ethenes studied relative to an approach using electron donor mixture treatments alone. The total improvement in time to degrade chlorinated ethenes through VC was also improved. Daughter product formation was also less for wells where DVI was added to the electron donor mixture. The cost to add a DVI amendment was less than $3 per cubic yard as applied.
The Random Oracle Methodology, Revisited. (1998)

We take a critical look at the relationship between the security of cryptographic schemes in the Random Oracle Model, and the security of the schemes that result from implementing the random oracle by so called “cryptographic hash functions”. The main result of this paper is a negative one: There exist signature and encryption schemes that are secure in the Random Oracle Model, but for which any implementation of the random oracle results in insecure schemes. In the process of devising the above schemes, we consider possible definitions for the notion of a “good implementation” of a random oracle, pointing out limitations and challenges.
Assembling Metal Complexes and Bridging Ligands for Photoactive Supramolecular Systems (1996)

Metal complexes and bridging ligands can provide useful building blocks for the design and construction of nanostructures and molecular devices capable of performing specific photoinduced functions. The choice of molecular components with appropriate structural and photophysical properties will be discussed and some multicomponent systems reviewed.
Vortex Breakdown and Global Modes in Swirling Combustor Flows with Axial Air Injection (2013)

Strongly swirling flows are used in the vast majority of gas turbine combustors. The complex flow field downstream of the vortex breakdown provides good flame stabilization but is also prone to self-excited large scale hydrodynamic instabilities. The role of these global modes, which usually manifest in a Precessing Vortex Core (PVC), for the combustion process is still an open question and influences on mixing processes and thermoacoustic oscillations have been proposed. In the current study the effect of axial air injection through a truncated center body on the type of the Vortex Breakdown (VB) and the global hydrodynamic mode is investigated using a combined experimental, numerical, and analytical approach. A parametric study of the isothermal flow field inside the combustion chamber and in the mixing tube upstream of the combustor is carried out in a water tunnel test facility. Selected configurations were further assessed under reacting conditions using methane fuel. Next, a Large Eddy Simulation (LES) was conducted and successfully validated with the experimental data. All results show a strong effect of the inflow parameters (axial injection rate and inlet swirl number) on the type of the vortexbreakdown and the frequency, amplitude, and shape of the global mode. The reacting cases show very similar results as the isothermal cases, proving the relevance of the isothermal investigation. Linear local hydrodynamic stability analyses, carried out on the time-average measured velocity data and the numerically obtained data, yield the absolutely unstable domain inside the flow field. Axial injection is shown to impede a zone of absolute instability near the combustor inlet while a a second zone further downstream remains. An excellent agreement of the measured to the calculated frequencies of the global modes is achieved over the whole range of investigated axial injection rates. The findings of this paper help to understand the mechanisms that are involved into the occurrence of global modes in swirling combustor flows and how they may be controlled by small flow field modifications. Furthermore, axial air injection is shown to provide a suitable flow field for flashback-proof combustor operation.
Nondominated sorting genetic algorithm for optimal phasor measurement placement (2004)

The paper considers a phasor measurement unit (PMU) placement problem requiring simultaneous optimization of two conflicting objectives, such as minimization of the number of PMUs and maximization of the measurement redundancy. The objectives are in conflict, since the improvement of one of them leads to the deterioration of another. Instead of unique optimal solution, it exists a set of best trade-offs between competing objectives, the so-called Pareto-optimal solutions. A specially tailored nondominated sorting genetic algorithm (NSGA) for PMU placement problem is proposed as a methodology to find these Pareto-optimal solutions. The algorithm is combined with the graph-theoretical procedure and a simple GA to reduce initial number of the PMU's candidate locations. The NSGA parameters are carefully set by performing a number of trial runs and evaluating the NSGA performances based on the number of distinct Pareto-optimal solutions found in the particular run and the distance of the obtained Pareto front from the optimal one. Illustrative results on the 39-bus and 118-bus IEEE systems are presented.
Species-Specific Detection of Vibrio anguillarum in Marine Aquaculture Environments by Selective Culture and DNA Hybridization (1996)

Methods for specific detection of Vibrio anguillarum in complex microbial communities within diverse marine aquaculture environments were evaluated. A system for the detection of culturable cells based on the combined use of a selective medium and a nonradioactively labeled oligodeoxynucleotide complementary to 16S rRNA was developed. Four hundred fourteen bacterial cultures were evaluated in order to assess the specificity of the method. When both the selective medium and the specific probe gave positive results, the cultures were always identified as V. anguillarum. The selectivity for colony hybridization was 1 V. anguillarum cell in 10,000 total bacterial cells in environmental samples. The utility of the method was also compared with detection by dot blot hybridization of either raw DNA purified from environmental samples or PCR-amplified DNA of 16S rRNA genes, using universal eubacterial primers. The post-PCR hybridization was more sensitive (8 x 10(sup2) cells) than direct hybridization of the whole purified DNA (10(sup6) cells). However, the selective medium-probe combined method was as sensitive as post-PCR hybridization, albeit more specific.