gebhart/patrepeval huggingface dataset:
Emerging Technologies in Hazardous Waste Management V (1995)

The process of development and application of many remedial alternatives has occurred largely in response to the mandates of "Superfund" (CERCLA and SARA), as well as other federal and state programs. Hence, an array of options have become available which can include an emerging concept with bench-scale testing, a field demonstration, a selection for site-specific remediation, and full-scale use and commercialization. For example, the state-of-technology development for options applicable to soils and ground waters has been described as indicated in Figure 1(1). Both ex situ and in situ techniques are evident, with dependence on the biological, physical and chemical sciences and engineering, either in separate or combined processes. When arrayed according to source matrix, technology applications for soils and ground waters have been or are being developed to destroy/detoxify, separate/recover, and/or immobilize contaminants(1,2). Although not as well developed, many of these same technologies may be similarly applied to sediments, sludges
Antiviral activity of α-helical stapled peptides designed from the HIV-1 capsid dimerization domain (2011)

These preliminary data serve as the foundation for designing small, stable, α-helical peptides and small-molecule inhibitors targeted against the CTD dimer interface. The observation that relatively weak CA binders, such as NYAD-201 and NYAD-202, showed specificity and are able to disrupt the CTD dimer is encouraging for further exploration of a much broader class of antiviral compounds targeting CA. We cannot exclude the possibility that the CA-based peptides described here could elicit additional effects on virus replication not directly linked to their ability to bind CA-CTD.
3Cnet: Pathogenicity prediction of human variants using knowledge transfer with deep recurrent neural networks (2020)

DATA UPDATE NOTICE: please see https://zenodo.org/record/6016720 Dataset needed to train and evaluate 3Cnet. See github repository for source code. https://github.com/KyoungYeulLee/3Cnet
Controlling of artificial neural network for fault diagnosis of photovoltaic array (2011)

High penetration of photovoltaic (PV) systems is expected to play important roles as power generation source in the near future. One of the typical deployments of PV systems is without supervisory mechanisms to monitor the physical conditions of cells or modules. In the longer term operation, the cells or modules may undergo fault conditions since they are exposure to the environment. Manually module checking is not recommended in this case because of time-consuming, less accuracy and potentially danger to the operator. Therefore, provision of early automatic diagnosis technique with quick and efficient responses is highly necessary. Since high accuracy is the important issue in the diagnosis problems, the paper present fault diagnosis method using three-layered artificial neural network. A single artificial neural network (ANN) is not suitable to provide precise solution for this fault identification. Therefore, several ANNs are developed, then automatic control based module voltage terminal is established. The proposed method is simple and accurate to detect the exact location of short-circuit condition of PV modules in array.
Loss of Serotonin Oxidation as a Component of the Altered Substrate Specificity in the Y444F Mutant of Recombinant Human Liver MAO A (2001)

To investigate the roles of tyrosyl residues located near the covalent 8alpha-S-cysteinyl FAD in monoamine oxidase A (MAO A) and to test the suggestion that MAO A and plant polyamine oxidase may have structural homology, tyrosyl to phenylalanyl mutants of MAO A at positions 377, 402, 407, 410, 419, and 444 were constructed and expressed in Saccharomyces cerevisiae. All mutant enzymes were expressed and exhibited lower specific activities as compared to WT MAO A using kynuramine as substrate. The lowest specific activities in this assay are exhibited by the Y407F and Y444F mutant enzymes. On purification and further characterization, these two mutants were found to each contain covalent FAD. Both mutant enzymes are irreversibly inhibited by the MAO A inhibitor clorgyline and exhibit binding stoichiometries of 0.54 (Y407F) and 0.95 (Y444F) as compared to 1.05 for WT MAO A. Y444F MAO A oxidizes kynuramine with a k(cat) <2% of WT enzyme and is greater than 100-fold slower in catalyzing the oxidation of phenylethylamine or of serotonin. In contrast, Y444F MAO A oxidizes p-CF(3)-benzylamine at a rate 25% that of WT enzyme. Steady state and reductive half-reaction stopped-flow data using a series of para-substituted benzylamine analogues show Y444F MAO A exhibits quantitative structure activity relationships (QSAR) properties on analogue binding and rates of substrate oxidation very similar to that exhibited by the WT enzyme (Miller and Edmondson (1999) Biochemistry 38, 13670): log K(d) = -(0.37 +/- ()()0.07)V(W)(x0.1) - 4.5 +/- 0.1; log k(red) = +(2.43 +/- 0.19)sigma + 0.17 +/- 0.05. The Y444F MAO A mutant also exhibits similar QSAR properties on the binding of phenylalkyl side chain amine analogues as WT enzyme: log K(i) = (4.37 +/- 0.51)E(S) + 1.21 +/- 0.77. These data show that mutation of Y444F in MAO A results in a mutant that has lost its ability to efficiently oxidize serotonin (its physiological substrate) but, however, exhibits unaltered quantitative structure-activity parameters in the binding and rate of benzylamine analogues. The mechanism of C-H abstraction is therefore unaltered. The suggestion that polyamine oxidase and monoamine oxidase may have structural homology appears to be valid as regards Y444 in MAO A and Y439 in plant polyamine oxidase.
Effects of Tea Polyphenols on Arachidonic Acid Metabolism in Human Colon (2003)

Tea has been suggested to be a possible cancer chemopreventive agent, and tea polyphenols are believed to be responsible for its anti-carcinogenic effect. Since modulation of arachidonic acid metabolism has been demonstrated to be an important target for cancer chemoprevention, the effects of green and black tea polyphenols on human colonic enzymes involved in arachidonic acid metabolism were investigated. At a concentration of 30 µg/mL, (-)-epigallocatechin-3-gallate (EGCG), (-)-epigallocatechin (EGC), and (-)-epicatechin-3-gallate (ECG) from green tea and theaflavins from black tea inhibited lipoxygenase (LOX)-dependent activity by 30 to 75%. Tea polyphenols (30 µg/mL) inhibited cyclooxygenae (COX)-dependent arachidonic acid metabolism in microsomes from normal colon mucosa by 37 to 62%. EGCG and ECG (50 µM) inhibited cytosolic phospholipase A2 (cPLA2) activity by 15 and 30%, respectively. Theaflavins (50 µM) inhibited cPLA2 activity by 10—45%. The inhibition of arachidonic acid metabolism at multiple levels by tea polyphenols may decrease the risk of human colon cancer.
Micellar catalysis for oxidation of nitric oxide (NO) in the multi‐phase systems in vivo (1999)

The equation of the dependence of the third-order reaction acceleration due to concentrating the reagents in a small volume of the hydrophobic phase on the partition coefficients of reagents (Q) and on the lipophilic phase fraction (x), [k(app)/ k2 = H(Q(NO),Q(O2),x)] was analyzed. It was demonstrated that the numeric value of dH/dx at x-->0 could not be used in order to calculate the efficiency of catalysis from the experimental data. It was shown that, unlike in two-phase systems (with an aqueous and a hydrophobic phase), the dependence of H on Q in multi-phase systems, that include all in vivo systems, is different. The multiple phase state of the systems has a determining role for a regulation of NO-dependent processes and in the realization of conditions of 'NO catastrophes'.
Alternative Nanostructures for Thermophones (2015)

Thermophones are highly promising for applications such as high-power SONAR arrays, flexible loudspeakers, and noise cancellation devices. So far, freestanding carbon nanotube aerogel sheets provide the most attractive performance as a thermoacoustic heat source. However, the limited accessibility of large-size freestanding carbon nanotube aerogel sheets and other even more exotic materials recently investigated hampers the field. We describe alternative materials for a thermoacoustic heat source with high-energy conversion efficiency, additional functionalities, environmentally friendly, and cost-effective production technologies. We discuss the thermoacoustic performance of alternative nanostructured materials and compare their spectral and power dependencies of sound pressure in air. We demonstrate that the heat capacity of aerogel-like nanostructures can be extracted by a thorough analysis of the sound pressure spectra. The study presented here focuses on engineering thermal gradients in the vicinity of nanostructures and subsequent heat dissipation processes from the interior of encapsulated thermoacoustic projectors. Applications of thermoacoustic projectors for high-power SONAR arrays, sound cancellation, and optimal thermal design, regarding enhanced energy conversion efficiency, are discussed.
Anonymous Identity-Based Encryption with Bounded Leakage Resilience (2015)

Memory attacks, inspired by recent realistic physical attacks, have broken many cryptographic schemes which were considered secure. In this paper, we consider the memory leakage resilience in anonymous identity-based encryption schemes. We construct a leakage-resilient anonymous identity based encryption scheme based on dual system encryption. Inspired by Lewko et al.'s techniques, our scheme is built in composite order groups which have four prime order subgroups and blind the public parameters and cipher texts using the random elements of same subgroup to achieve the anonymity. Moreover, we analyze the security of our scheme in the full adaptive-ID model rather than the selective-ID model.
Effect of regular ingestion of <i>Saccharomyces boulardii</i> plus inulin or <i>Lactobacillus acidophilus</i> LB in children colonized by <i>Helicobacter pylori</i> (2005)

S. boulardii seems promising as an agent that interferes with Hp in colonized individuals. More studies are needed to confirm these results and to elucidate the mechanisms by which Sb inhibits Hp.
Lung transplant outcomes: a review of survival, graft function, physiology, health-related quality of life and cost-effectiveness (2004)

The success of lung transplantation has improved over time as evidenced by better long-term survival and functional outcomes. Despite the success of this procedure, there are numerous problems and complications that may develop over the life of a lung transplant recipient. With proper monitoring and treatment, the frequency and severity of these problems can be decreased. However, significant improvement for the overall outcomes of lung transplantation will only occur when better methods exist to prevent or effectively treat chronic rejection.
Synthesis of well-defined copper nanocubes by a one-pot solution process (2006)

A simple one-pot solution-phase method was developed to synthesize well-defined copper nanocubes with an edge length in the range of 100 ± 25 nm. Copper nanocubes were produced by using ascorbic acid as a reducing agent and poly(vinylpyrrolidone) (PVP) as a capping agent. X-ray diffraction (XRD), UV–vis spectroscopy (UV–vis), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) as well as selected-area electron diffraction (SAED) were used to characterize the resulting nanoparticles. The influence of concentration, temperature and additives on the formation of Cu nanoparticles was investigated. Some nano-polyhedra and nanospheres were also fabricated. Shape-controlled synthesis of copper nanoparticles was partially achieved.
Growth inhibition of MCF-7 breast cancer cells by stable expression of an insulin-like growth factor I receptor antisense ribonucleic acid. (1995)

Insulin-like growth factors (IGFs) play an important role in cellular proliferation, and IGF action appears to be involved in tumorigenesis. To determine the role of the IGF-I receptor in breast cancer cell growth, we stably transfected MCF-7 breast cancer cells with a construct encoding an antisense RNA complementary to the region surrounding the translation initiation site of the IGF-I receptor messenger RNA (mRNA). Control cells were transfected with vector alone. Clones expressing the antisense RNA exhibited a 30% reduction in endogenous IGF-I receptor mRNA levels and a significant reduction in receptor protein levels, as measured by both ligand binding assays and Western blot analysis. Antisense-expressing clones expressed approximately 30,000 receptors/cell compared with approximately 48,000-58,000 receptors/cell in control (neo) cells (P < 0.05). Although endogenous RNA:RNA hybrids were demonstrable in antisense-expressing cells, our results suggest that the major effect of the antisense may be the reduction in mRNA levels and not via an inhibition of translation. The reduction in receptor expression reduced both IGF-I- and serum-stimulated cellular proliferation. The maximum cell number reached at 96 h in the presence of IGF-I (100 ng/ml) was significantly reduced in antisense-expressing clones (22,000-30,000) compared with that in control (neo) cells (39,000-42,000). Furthermore, IGF-I-induced c-fos gene expression was reduced by 30% in the clones expressing the antisense RNA. These results strongly support a role for the IGF-I receptor in the proliferation of human breast cancer cells and suggest that strategies using this type of technology may prove useful in cancer therapy.
Design and Implementation of a Real-Time Wireless Sensor Network (2007)

This paper describes the development of wireless sensor network prototype that gathers biometrical data and posture information from several wearable sensor networks and sends it in real-time to a personal computer where the information is monitored and stored. The wireless sensor network is based on a low power real-time MAC protocol that was designed and implemented in the MICAz platform. This paper also presents some analytical results and several experimental results regarding the behavior of the developed system.
Microscale patterning of hydrogel stiffness through light-triggered uncaging of thiols (2014)

Mammalian cell behavior is strongly influenced by physical and chemical cues originating from the extracellular matrix (ECM). In vivo, ECM signals are displayed in a spatiotemporally complex fashion, often composed as gradients and in concentration profiles that change in time. Most in vitro models to study the role of ECM signals in regulating cell behavior are limited in capturing this microenvironmental complexity, as they are static and homogeneous. In order to achieve a dynamic control of the physical properties of a hydrogel network, we here designed a chemical scheme to control poly(ethylene glycol) (PEG) hydrogel stiffness in space, time and intensity. Specifically, we combined caging chemistry and Michael-type addition to enable the light-triggered local control of hydrogel crosslinking density. Thiol moieties of one of the reactive PEG macromers undergoing crosslinking were equipped with caging groups to prevent their susceptibility to the counter-reactive vinyl sulfone groups on the termini of the complementary PEG macromers. Thus, the crosslinking density of the hydrogel network could be tuned by uncaging with light which directly translated into differential patterns of hydrogel stiffness. Using this approach, user-defined stiffness patterns in a range of soft tissue microenvironments (i.e. between 3-8 kPa) were obtained and shown to influence the migratory behavior of primary human mesenchymal stem cells (hMSC). Stiffness gradients in the higher range (5.5-8 kPa) were able to elicit durotaxis towards the more densely crosslinked regions, whereas those in the lower range (3-5.5 kPa) showed no significant directional preference in hMSC migration. Our patterning tool should be useful for the manipulation of cell fate in various other contexts.
Reflectance confocal microscopy as a new tool in the<i>in vivo</i>evaluation of desquamative gingivitis: patterns in mucous membrane pemphigoid, pemphigus vulgaris and oral lichen planus (2012)

We propose that RCM is a useful tool to help distinguish between the three most common causes of desquamative gingivitis.
Liquids: The Holy Grail of Microfluidics Modeling (2006)

Interest in microelectromechanical systems (MEMS) has experienced explosive growth during the past few years. Such small devices typically have characteristic size ranging from 1 mm down to 1 micron, and may include sensors, actuators, motors, pumps, turbines, gears, ducts and valves. Microdevices often involve mass, momentum and energy transport.Modeling gas and liquid flows through MEMS may necessitate including slip, rarefaction, compressibility, intermolecular forces and other unconventional effects. The continuum-based Navier-Stokes equations with either the traditional no-slip or slip-flow boundary conditions work only for a limited range of Knudsen numbers above which alternative models must be sought. These include molecular dynamics simulations (MD), Boltzmann equation, Direct Simulation Monte Carlo (DSMC), and other deterministic/probabilistic molecular models. The kinetic theory of gases defines well the boundaries for which the no-slip Navier-Stokes equations can accurately model the flow of a dilute gas. The same cannot be said about dense-gas and liquid flows where intermolecular interactions play a dominant role. Neither type of fluid has a well-advanced molecular-based theory, as is the case for dilute gases. The concept of mean free path is not very useful for liquids and the conditions under which a liquid flow fails to be in quasi-equilibrium state are not well defined. Such complex fluids can only be treated via hybrid continuum-molecular approaches, which approaches are still far from satisfactory at the present time. The present talk will address such issues and outline a blueprint for future developments.
Using Machine Teaching to Identify Optimal Training-Set Attacks on Machine Learners (2015)

We investigate a problem at the intersection of machine learning and security: training-set attacks on machine learners. In such attacks an attacker contaminates the training data so that a specific learning algorithm would produce a model profitable to the attacker. Understanding training-set attacks is important as more intelligent agents (e.g. spam filters and robots) are equipped with learning capability and can potentially be hacked via data they receive from the environment. This paper identifies the optimal training-set attack on a broad family of machine learners. First we show that optimal training-set attack can be formulated as a bilevel optimization problem. Then we show that for machine learners with certain Karush-Kuhn-Tucker conditions we can solve the bilevel problem efficiently using gradient methods on an implicit function. As examples, we demonstrate optimal training-set attacks on Support VectorMachines, logistic regression, and linear regression with extensive experiments. Finally, we discuss potential defenses against such attacks.
Intraoperative Imaging-Guided Cancer Surgery: From Current Fluorescence Molecular Imaging Methods to Future Multi-Modality Imaging Technology (2014)

Cancer is a major threat to human health. Diagnosis and treatment using precision medicine is expected to be an effective method for preventing the initiation and progression of cancer. Although anatomical and functional imaging techniques such as radiography, computed tomography (CT), magnetic resonance imaging (MRI) and positron emission tomography (PET) have played an important role for accurate preoperative diagnostics, for the most part these techniques cannot be applied intraoperatively. Optical molecular imaging is a promising technique that provides a high degree of sensitivity and specificity in tumor margin detection. Furthermore, existing clinical applications have proven that optical molecular imaging is a powerful intraoperative tool for guiding surgeons performing precision procedures, thus enabling radical resection and improved survival rates. However, detection depth limitation exists in optical molecular imaging methods and further breakthroughs from optical to multi-modality intraoperative imaging methods are needed to develop more extensive and comprehensive intraoperative applications. Here, we review the current intraoperative optical molecular imaging technologies, focusing on contrast agents and surgical navigation systems, and then discuss the future prospects of multi-modality imaging technology for intraoperative imaging-guided cancer surgery.
Contextual combinatorial cascading bandits (2016)

We propose the contextual combinatorial cascading bandits, a combinatorial online learning game, where at each time step a learning agent is given a set of contextual information, then selects a list of items, and observes stochastic outcomes of a prefix in the selected items by some stopping criterion. In online recommendation, the stopping criterion might be the first item a user selects; in network routing, the stopping criterion might be the first edge blocked in a path. We consider position discounts in the list order, so that the agent's reward is discounted depending on the position where the stopping criterion is met. We design a UCB-type algorithm, C3-UCB, for this problem, prove an n-step regret bound O(√n) in the general setting, and give finer analysis for two special cases. Our work generalizes existing studies in several directions, including contextual information, position discounts, and a more general cascading bandit model. Experiments on synthetic and real datasets demonstrate the advantage of involving contextual information and position discounts.
C–Cl/Si–H Exchange catalysed by P,N-chelated Pt(<scp>ii</scp>) complexes (2002)

Alkyl chlorides R-Cl are dehalogenated by HSiMe2Ph in the presence of catalytic amounts of the complex [(kappa 2-P,N)-Ph2PCH2CH2NMe2]PtMeCl to give R-H and ClSiMe2Ph.
A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq (2011)

Many questions about the regulation, functional specialization, computational prediction, and evolution of genomic imprinting would be better addressed by having an exhaustive genome-wide catalog of genes that display parent-of-origin differential expression. As a first-pass scan for novel imprinted genes, we performed mRNA-seq experiments on embryonic day 17.5 (E17.5) mouse placenta cDNA samples from reciprocal cross F1 progeny of AKR and PWD mouse strains and quantified the allele-specific expression and the degree of parent-of-origin allelic imbalance. We confirmed the imprinting status of 23 known imprinted genes in the placenta and found that 12 genes reported previously to be imprinted in other tissues are also imprinted in mouse placenta. Through a well-replicated design using an orthogonal allelic-expression technology, we verified 5 novel imprinted genes that were not previously known to be imprinted in mouse (Pde10, Phf17, Phactr2, Zfp64, and Htra3). Our data suggest that most of the strongly imprinted genes have already been identified, at least in the placenta, and that evidence supports perhaps 100 additional weakly imprinted genes. Despite previous appearance that the placenta tends to display an excess of maternally expressed imprinted genes, with the addition of our validated set of placenta-imprinted genes, this maternal bias has disappeared.