gebhart/patrepeval huggingface dataset:
Strand invasion promoted by recombination protein β of coliphage λ (2004)

Studies of phage lambda in vivo have indicated that its own recombination enzymes, beta protein and lambda exonuclease, are capable of catalyzing two dissimilar pathways of homologous recombination that are widely distributed in nature: single-strand annealing and strand invasion. The former is an enzymatic splicing of overlapping ends of broken homologous DNA molecules, whereas the latter is characterized by the formation of a three-stranded synaptic intermediate and subsequent strand exchange. Previous studies in vitro have shown that beta protein has annealing activity, and that lambda exonuclease, acting on branched substrates, can produce a perfect splice that requires only ligation for completion. The present study shows that beta protein can initiate strand invasion in vitro, as evidenced both by the formation of displacement loops (D-loops) in superhelical DNA and by strand exchange between colinear single-stranded and double-stranded molecules. Thus, beta protein can catalyze steps that are central to both strand annealing and strand invasion pathways of recombination. These observations add beta protein to a set of diverse proteins that appear to promote recognition of homology by a unitary mechanism governed by the intrinsic dynamic properties of base pairs in DNA.
Smart control of spinal alignment through active adjustment of mechanical bed properties during sleep (2013)

This study implements an algorithm for the autonomous control of spinal alignment during sleep by the active adjustment of mechanical bed characteristics according to the adopted sleep posture. Bed systems were used that allow active control of the m
Variable effects of maturity-onset-diabetes-of-youth (MODY)-associated glucokinase mutations on substrate interactions and stability of the enzyme (1995)

Mutations in the human glucokinase (GK) gene are thought to cause maturity-onset diabetes of youth (MODY) by leading to the production of enzymes with reduced catalytic activities and increased glucose Km values. However, in some cases the diabetic phenotype is more severe than might be predicted from these apparent kinetic effects alone. To determine whether these mutations might also effect other characteristics of the enzyme, nine MODY-associated mutants were expressed as fusion proteins with Schistosoma japonicum glutathione S-transferase (GST) and compared with three wild-type human GK isoforms that were also expressed in the same manner. Three GST-GK isoforms (liver 1, liver 2 and islet) were kinetically indistinguishable from each other and from purified rat liver GK. Noteworthy is a glucose-induced fit effect for the interaction of trinitrophenyl (TNP)-ATP with GST-GK, whereby glucose significantly increased the affinity of TNP-ATP binding to GST-GK without changing the stoichiometry of binding. The nine MODY-associated mutations studied either showed diminished catalytic activity, substrate affinities, allosteric regulation, or stability of the fusion enzyme. We conclude that: (1) Gly261 and Lys414 are important for ATP binding; (2) Val203 may be essential for a glucose-induced fit effect; and (3) the stability of fusion protein may be significantly reduced when Glu300 is replaced by Lys. These results suggest that, in addition to effects on the Km and Vmax. of GK, a decrease in the ATP-binding affinity or stability of the mutated enzyme may also contribute to a reduction of GK activity in individuals with GK-MODY. In the B-cell this would have the effect of blunting glucose-stimulated insulin release, thereby contributing to the diabetic phenotype.
LARGE SCALE IMAGE-BASED ADULT-CONTENT FILTERING (2006)

As more people start using the Internet and more content is placed online, the chances that individuals will encounter inappropriate or unwanted adult-oriented content increases.This paper presents a practical and scalable method to efficiently detect many adult-content images, specifically pornographic images.We currently use this system in a search engine that covers a large fraction of the images on the WWW.For each image, face detection is applied and a number of summary features are computed; the results are then fed to a support vector machine for classification.The results show that a significant fraction of adult-content images can be detected.
Relationships between job organisational factors, biomechanical and psychosocial exposures (2015)

The findings are based on a large number of subjects collected by three research teams in diverse US workplaces. Job rotation practices used in many workplaces may not be effective in reducing job biomechanical stressors for work-related musculoskeletal disorders. Overtime work is also associated with higher biomechanical stressors.
Filtration model for polydisperse aerosols in gas‐solid flow using granule‐resolved direct numerical simulation (2015)

An analytical framework for calculating the filtration efficiency of polydisperse aerosols in a granular bed is developed for cases where inertial impaction and interception are the principal filtration mechanisms. This framework is used to develop a model for the polydisperse single‐collector efficiency from monodisperse single‐collector efficiency correlations. Conceptually, the polydisperse model is developed by transforming the probability density of particle radius into a probability density of particle Stokes number that is then used to weight the monodisperse single‐collector efficiency at a given Stokes number. An extension of this polydisperse filtration concept results in an analytical solution for the axial variation of polydisperse particle flux in a random three‐dimensional granule configuration. In order to verify the analytical results for polydisperse particle filtration, a granule‐resolved direct numerical simulation approach is coupled with Lagrangian particle tracking to simulate filtration of polydisperse aerosols in a granular bed. © 2015 American Institute of Chemical Engineers AIChE J , 61: 3594–3606, 2015
Developing workflow-based information integration (WII) with exception support in a Web services environment (2004)

Assembling a coherent view of distributed heterogeneous information and information processing resources is a challenging and important process for inter-organizational collaboration and service provision. We refer to this process as information integration. However, traditional information integration approaches do not consider human intervention and exceptions, such as obtaining access approvals from service providers. Therefore, we propose a workflow-based approach to address this problem. This is particularly suitable in a loosely coupled and autonomous Web services environment. In this paper, we propose an implementation framework of workflow-based information integration (WII) comprise four layers, namely, application layer, workflow layer, service layer, and message layer. In particular, our paper focuses on the workflow layer from the aspects of control-flows, data-flows and exception-flows by using the business process execution language for Web services (BPEL4WS), extended with our proposed data-integration and exception-handling assertions. Each service provider provides Web services at the service layer and BPEL4WS orchestrates them together in order to achieve workflow-based information integration plans. The message layer comprises SOAP message specifications. We map information into SOAP messages and link the proposed exception-handling assertions in BPEL4WS to SOAP-fault implementations. Lastly, we demonstrate the feasibility of our approach with a practical health administrative information integration case study at the application layer and examine some typical use cases of exceptions.
Cross-Species Functional Analysis of Cancer-Associated Fibroblasts Identifies a Critical Role for CLCF1 and IL-6 in Non–Small Cell Lung Cancer In Vivo (2012)

Cancer-associated fibroblasts (CAF) have been reported to support tumor progression by a variety of mechanisms. However, their role in the progression of non-small cell lung cancer (NSCLC) remains poorly defined. In addition, the extent to which specific proteins secreted by CAFs contribute directly to tumor growth is unclear. To study the role of CAFs in NSCLCs, a cross-species functional characterization of mouse and human lung CAFs was conducted. CAFs supported the growth of lung cancer cells in vivo by secretion of soluble factors that directly stimulate the growth of tumor cells. Gene expression analysis comparing normal mouse lung fibroblasts and mouse lung CAFs identified multiple genes that correlate with the CAF phenotype. A gene signature of secreted genes upregulated in CAFs was an independent marker of poor survival in patients with NSCLC. This secreted gene signature was upregulated in normal lung fibroblasts after long-term exposure to tumor cells, showing that lung fibroblasts are "educated" by tumor cells to acquire a CAF-like phenotype. Functional studies identified important roles for CLCF1-CNTFR and interleukin (IL)-6-IL-6R signaling in promoting growth of NSCLCs. This study identifies novel soluble factors contributing to the CAF protumorigenic phenotype in NSCLCs and suggests new avenues for the development of therapeutic strategies.
Semantics of asynchronous JavaScript (2017)

JavaScript code running in the Node.js runtime is a major platform for developers building cloud, mobile, or IoT applications. A fundamental concept in Node.js programming is the use of asynchronous callbacks and event loops to provide highly responsive applications. While conceptually simple, this programming model contains numerous subtleties and behaviors that are defined implicitly by the current Node.js implementation. This paper presents the first comprehensive formalization of the Node.js asynchronous execution model and defines a high-level notion of async-contexts to formalize fundamental relationships between asynchronous executions in an application. These formalizations provide a foundation for the construction of static or dynamic program analysis tools, support the exploration of alternative Node.js event loop implementations, and provide a high-level conceptual framework for reasoning about relationships between the execution of asynchronous callbacks in a Node.js application.
Mechanisms in CD4 antibody‐mediated transplantation tolerance: kinetics of induction, antigen dependency and role of regulatory T cells (1994)

CBA/Ca mice may be made tolerant to minor histoincompatible B10.BR skin grafts by treatment with a short course of non-depleting anti-mouse CD4 and CD8 monoclonal antibodies (mAb), during the transplantation period. We wished to determine when, in relation to antibody therapy, the T cells became tolerant. This was investigated by a series of adoptive transfer experiments in which mAb-treated cells were removed from therapeutic antibody at defined times after skin grafting, and exposed to fresh antigen in the absence of further mAb treatment. We show here that T cells do not become fully tolerant until 5 weeks after skin grafting. If antibody therapy is continued for the full 5 weeks, T cell tolerance can still be established, suggesting that antibody therapy does not prevent lymphocytes from registering the presence of antigen. Once the tolerant state is established, it is difficult to break that tolerance by lymphocyte infusions from normal donors. This "resistance" is mediated by T cells of the tolerant host. We show that the maintenance of both tolerance and "resistance" requires a continuous supply of antigen. When tolerant cells were "parked" in T cell-depleted mice, tolerance and "resistance" were eventually lost by 6 months. In contrast, "parked" cells exposed to fresh antigen at any time up to 4 months remained tolerant and "resistant" indefinitely. Finally, we wished to establish whether "resistance" was peculiar to this form of peripheral tolerance, or whether it might also be present in tolerance considered to be classically central. We observed resistance to be greater in the mAb-treated peripherally tolerant group, but noted that some of the centrally tolerant animals also exhibited a level of resistance above that of T cell-ablated controls. This suggests that a tolerance mechanism whose role is only minor in central tolerance may have a major role in antibody-mediated peripheral tolerance.
Selective determination of pyridine alkaloids in tobacco by PFTBA ions/analyte molecule reaction ionization ion trap mass spectrometry (2007)

The application of perfluorotributylamine (PFTBA) ions/analyte molecule reaction ionization for the selective determination of tobacco pyridine alkaloids by ion trap mass spectrometry (IT-MS) is reported. The main three PFTBA ions (CF(3)(+), C(3)F(5)(+), and C(5)F(10)N(+)) are generated in the external source and then introduced into ion trap for reaction with analytes. Because the existence of the tertiary nitrogen atom in the pyridine makes it possible for PFTBA ions to react smoothly with pyridine and forms adduct ions, pyridine alkaloids in tobacco were selectively ionized and formed quasi-molecular ion [M + H](+)and adduct ions, including [M + 69](+), [M + 131](+), and [M + 264](+), in IT-MS. These ions had distinct abundances and were regarded as the diagnostic ions of each tobacco pyridine alkaloid for quantitative analysis in selected-ion monitoring mode. Results show that the limit of detection is 0.2 microg/mL, and the relative standard deviations for the seven alkaloids are in the range of 0.71% to 6.8%, and good recovery of 95.6% and 97.2%. The proposed method provides substantially greater selectivity and sensitivity compared with the conventional approach and offers an alternative approach for analysis of tobacco alkaloids.
Effect of Modulator Bias Control in the Presence of a Finite Extinction Ratio in DQPSK Pre-Equalization Systems (2011)

The effect of the finite extinction ratio of a dual-parallel Mach-Zehnder modulator in 43-Gb/s differential quadrature phase-shift keying systems employing pre-equalization is reported. The degradation of the signal quality with 10000-ps/nm dispersion pre-equalization is 2.9 dB at an extinction ratio of 26 dB. We show that bias adjustment can improve the degradation due to a finite extinction ratio. The improvement at an extinction ratio of 26 dB is 2.2 dB. In practical pre-equalized systems, bias control is a key enabler for maintaining high signal quality.
The impact of demand response on rural island power system operation (2013)

This paper presents an analysis of the impact of demand response on island power system operation. Demand responsive HVACs and battery storages are taken as an example of rural grid demand response participant. Day-ahead and real-time scheduling of a rural island grid are discussed. Day-ahead scheduling handles the problem of rural island grid electricity market day-ahead clearance, and an iterative algorithm is presented to solve the problem. Real-time scheduling aims to respond to real-time forecasted deviation in renewable generation and system load, and is solved by minimizing system real-time line loss. Real-time scheduling at different temporal scales respond to real-time rural grid situation using different sets of demand responsive loads. Results from case study show that demand response is able to make a considerable contribution to local integration of renewable energy, and stabilize electricity price effectively in rural island power systems.
Extraction of surface‐active polymers from the compost of olive processing waste (2021)

Abstract Polysaccharides and proteins with potential use as emulsifiers and thickeners are extracted at pH 5, 7, and 9 from olive processing wastes, from the onset to the end of a full compost cycle (6 months). The aim is to monitor the temporal evolution of parameters which are related to the emulsifying ability, such as surface tension, macromolecular populations distribution, and chemical composition of the produced materials. The products are characterized using size exclusion chromatography (SEC–MALLS/UV), Fourier‐transform infra‐red spectroscopy (FTIR), and equilibrium surface tension. The initial extracts comprise of a large array of macromolecules; following 2 months of composting, the polysaccharides are considerably smaller than the ones at the onset of the composting. During the subsequent months, disintegration of the olive matrix enhances the extraction. At pH 7, a variety of proteins is produced as compared to the equivalent process at pH 5, which is attributed to the charge of proteins, while parts of the cellulosic matrix and some peptidic entities are only released from the humus at the end of the composting. At pH 9 the extraction of polysaccharides is enhanced due to the charged side chains and the elimination of positive charges. These are confirmed from FTIR. The oil (miglyol)–water interfacial tension is higher at the low‐pH extracts, leaving interesting room for adjusting the emulsification capacity (favored at low pH) and the extract composition (macromolecules favored at high pH). This makes for a promising source of valuable additives from the by‐products of the olive processing industry. Practical Applications In this work, we reclaim surface‐active polysaccharides and proteins with potential use as emulsifiers and thickeners, from olive processing wastes, as these undergo a 6‐months composting cycle. The products are characterized for their composition and oil–water interface activity, a key parameter for their performance as emulsifiers. We highlight the evolution of the extracts composition and their properties as they are reclaimed at different stages of the composting process. This work can provide information on the valorization of highly polluting food processing waste as precursors of high added value food ingredients, with the relevant impact on the environment, the local economy, and the green labeling of foods.
Numerical Analysis of Radiative Effects on Natural Convection in Vertical Convergent and Symmetrically Heated Channels (2006)

ABSTRACT Natural convection in a convergent channel with finite-thickness principal walls at uniform heat flux is investigated numerically. Heat conduction in the walls and the effects of walls emissivity are taken into account. Laminar two-dimensional steady-state conditions are assumed. Results in terms of wall dimensionless temperature profiles as a function of convergence angle, channel spacing, and heat flux are given for various values of wall emissivity. Wall temperatures decrease significantly, passing from δ = 0° to 2° at the lowest channel spacing. Streamlines and temperature fields show a recirculating region in the channel for large values of L w/b min and for δ equal to 5° and 10°. Correlations between Nusselt numbers and Rayleigh numbers are proposed. Dimensionless parameters are in the following ranges: 4.4 ≤ Ra′bmin ≤ 1.5 × 105, 10 ≤ L w /b min ≤ 58, 0.0 ≤ ϵ ≤ 1.0, and 0° ≤ δ ≤ 10°. Numerical predictions are in very good agreement with experimental data. This work was supported by Ministero dell'Istruzione, dell'Università e della Ricerca with a 2003–2005 Progetto di Ricerca d'Interesse Nazionale grant and Seconda Università degli Studi di Napoli with 2003 and 2005 research grants. Notes UWT: Uniform Wall Temperature. UWHF: Uniform Wall Heat Flux.
Applying Powder Characterization to Develop New Materials (1988)

"Applying Powder Characterization to Develop New Materials." Materials and Processing Report, 2(11), pp. 8–9
Software Simulation of a Self-Organizing Learning Array System (2002)

A neural network paradigm named Self-Organizing Learning Array system has been simulated in software. Hardware implementation limitations are considered in this simulation. Simulation is performed based on a benchmark classification problem, the Australian Credit Card problem. The system behavior is observed and the learning algorithm is examined. The correct classification rate has been compared with some existing classification methods. Although not particularly designed for solving this type of classification problem, this system still shows very good performance. The system will be implemented in FPGA and SOC.
Scattered data modeling (1993)

A variety of methods for modeling scattered data are discussed, with an emphasis on two types of data: volumetric and spherical. To demonstrate the performance of the various methods, results from an empirical study using trivariate scattered data are presented. The author's objective is to provide information to aid in selecting a type of method or to form the basis for customizing a method for a particular application.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analysis of diffraction gratings by the mortar-element method (2014)

In this paper the development of a full-wave simulator of the scattering from a surface-relief diffraction grating is described. The general case of skew incidence, which leads to a vector differential problem, is addressed. First, the general mathematical formulation of the discretization scheme is introduced; then, a comparison with results obtained by the mode matching method is presented.
A framework for the analysis of damage and recovery characteristics of asphalt mixtures (2020)

This study presents two approaches for evaluating damage and recovery characteristics of asphalt mixtures. The first approach focuses on determining damage by extracting recoverable viscoelastic strain that has no damage and comparing it with the strain response of a material that has damage. The second approach is based on identifying the capacity of asphalt mixtures to recover some of the damage that may occur during creep loading. The advantage of these approaches is that they utilise experimental data to extract damage and recovery responses, without detailed mathematical modelling of material behaviour. The developed approaches are used to analyse the behaviours of fine aggregate mixtures (FAM) incorporating warm mix additives. The results show that these mixtures vary in their damage and recovery characteristics. For example, Sasobit FAM experienced the highest damage among mixtures, but it also had the highest recovery. Ageing was found to reduce the differences among mixtures in terms of resistance to damage, but it had less effect on the differences in their healing potential.
The proteasome inhibitor NPI-0052 is a more effective inducer of apoptosis than bortezomib in lymphocytes from patients with chronic lymphocytic leukemia (2006)

Proteasome inhibitors are potent inducers of apoptosis in isolated lymphocytes from patients with chronic lymphocytic leukemia (CLL). However, the reversible proteasome inhibitor bortezomib (PS-341; Velcade) did not display substantial antitumor activity in CLL patients. Here, we compared the effects of bortezomib and a new irreversible proteasome inhibitor (NPI-0052) on 20S chymotryptic proteasome activity and apoptosis in isolated CLL cells in vitro. Although their steady-state (3 hours) IC(50)s as proteasome inhibitors were similar, NPI-0052 exerted its effects more rapidly than bortezomib, and drug washout experiments showed that short exposures to NPI-0052 resulted in sustained (> or =24 hours) 20S proteasome inhibition, whereas 20S activity recovered in cells exposed to even 10-fold higher concentrations of bortezomib. Thus, brief (15 minutes) pulses of NPI-0052 were sufficient to induce substantial apoptosis in CLL cells, whereas longer exposure times (> or =8 hours) were required for commitment to apoptosis in cells exposed to equivalent concentrations of bortezomib. Commitment to apoptosis seemed to be related to caspase-4 activation, in that cells exposed to bortezomib or NPI-0052 could be saved from death by addition of a selective caspase-4 inhibitor up to 8 hours after drug exposure. Our results show that NPI-0052 is a more effective proapoptotic agent than bortezomib in isolated CLL cells and suggest that the chemical properties of NPI-0052 might also make it an effective therapeutic agent in CLL patients.