Miracle-dz/UniFAR-FTUs huggingface dataset:
Peptide Binding to the Bacillus subtilis Oligopeptide-Binding Proteins OppA and AppA

The binding proteins of the two oligopeptide transport systems present in Bacillus subtilis, OppA and AppA, were expressed in a Lactococcus lactis strain that lacks the native oppA gene. Both OppABs and AppA were targeted to the cell surface, and shown to be functional in assays that monitor the binding of peptides by changes in intrinsic protein fluorescence. The specificities of the two proteins were shown to be different. An increase in fluorescence of OppABs was observed upon binding of the peptides RGG, GLGL and SLSQS. The peptides RDMPIQA, RPPGFSPFR and SLSQSKVLPVPQ did not produce such an increase in fluorescence. The only peptide that affected the intrinsic fluorescence of AppA was RPPGFSPFR. Our data indicate that OppABs has a relatively high affinity for tri-, tetra- and pentapeptides but does not bind longer peptides. The affinity of AppA seems to be targeted to a limited set of longer oligopeptides, but the protein still may bind short peptides with low affinity.
A Constitutive Model for the Simulation of the Deformation Behavior of TWIP Steels

Due to their high strength (tensile strength > 1GPa) in combination with an extreme ductility (failure strain 30-50%) TWinning Induced Plasticity–steels (TWIP-steels) can be considered as promising materials for the production of lightweight automotive components. The industrial application of TWIP-steels requires a fundamental experimental validation of the mechanical behavior as basis for an user-friendly but at the same time accurate constitutive framework and its implementation into commercial Finite Element codes. Related investigations and implementations in order to allow for the simulation of TWIP-steel forming processes are currently conducted within the research project “TWIP4EU”, executed as a cooperation of Fraunhofer - Institut für Werkstoffmechanik IWM in Freiburg (Germany), Salzgitter Mannesmann Forschung GmbH (Germany), Swerea KIMAB (Sweden), Faurecia Autositze GmbH (Germany / France), DYNAmore GmbH (Germany) and ESI GmbH Engineering System (Germany / France). The monotonic one-dimensional hardening behavior of TWIP-steels as a function of the twin volume fraction and dislocation density has been described by Bouaziz et al. (2008), Bouaziz et al. (2011). This model has been proven to be adequate for the description of the flow behavior of TWIP-steels and serves as basis for the constitutive model, presented here. This Bouaziz-model has been extended to a three-dimensional elasto-plastic formulation, including the influence of different loading conditions, anisotropy and kinematic hardening. The present paper deals with the implementation for solids and shells in the commercial Finite Element Code LS-DYNA® and appropriate validation simulations will be presented.
Internalization of Vectored Liposomes in a Culture of Poorly Differentiated Tumor Cells

Internalization of liposomal nanocontainers conjugated with monoclonal antibodies to VEGF, VEGFR2 (KDR), and proteins overproduced in the tumor tissue was studied in vitro on cultures of poorly differentiated tumor cells. Comparative analysis of accumulation of vectored liposomes in the tumor cells was performed by evaluating co-localization of labeled containers and cell organelles by laser scanning confocal microscopy. We observed nearly 2 times more active penetration and accumulation of liposomes vectored with antibodies in the tumor cells in comparison with non-vectored liposomes. Selective clathrin-dependent penetration of vectored liposomes into tumor cells was demonstrated by using pharmacological agents inhibiting endocytosis.
Generating diverse and representative image search results for landmarks

Can we leverage the community-contributed collections of rich media on the web to automatically generate representative and diverse views of the world's landmarks? We use a combination of context- and content-based tools to generate representative sets of images for location-driven features and landmarks, a common search task. To do that, we using location and other metadata, as well as tags associated with images, and the images' visual features. We present an approach to extracting tags that represent landmarks. We show how to use unsupervised methods to extract representative views and images for each landmark. This approach can potentially scale to provide better search and representation for landmarks, worldwide. We evaluate the system in the context of image search using a real-life dataset of 110,000 images from the San Francisco area.
Characterisation Of Receding Horizon Control For Constrained Linear Systems

This paper characterises the geometric structure of receding horizon control (RHC) of linear, discrete‐time systems, subject to a quadratic performance index and linear constraints. The geometric insights so obtained are exploited to derive a closed‐form solution for the case where the total number of constraints is less than or equal to the number of degrees of freedom, represented by the number of control moves. The solution is shown to be a partition of the state space into regions for which an analytic expression is given for the corresponding control law. Both the regions and the control law are characterised in terms of the parameters of the open‐loop optimal control problem that underlies RHC and can be computed off line. The solution for the case where the total number of constraints is greater than the number of degrees of freedom is addressed via an algorithm that iteratively uses the off‐line solution and avoids on‐line optimisation.
Solving convection-diffusion equations with mixed, Neumann and Fourier boundary conditions and measures as data, by a duality method

In this paper, we prove, following [1], existence and uniqueness of the solutions of convection-diffusion equations on an open subset of R , with a measure as data and different boundary conditions: mixed, Neumann or Fourier. The first part is devoted to the proof of regularity results for solutions of convection-diffusion equations with these boundary conditions and data in (W 1,q(Ω))′, when q < N/(N − 1). The second part transforms, thanks to a duality trick, these regularity results into existence and uniqueness results when the data are measures.
Simulation Of Highly Heterogeneous Traffic Flow Characteristics

Simulation models are mathematical/logical representations of real-world systems. Microscopic traffic simulation models have been playing an important role in traffic engineering and particularly in cases, in which field studies, involving extensive data collection, over a wide range, is difficult or expensive to conduct. As the available simulation models can only replicate homogeneous traffic flow, a model of heterogeneous traffic flow, named, HETEROSIM was developed to simulate heterogeneous traffic flow. In this model, a dynamic stochastic type discrete event simulation is adopted in which the aspects of interest are analysed numerically with the aid of a computer program. The model was validated using field observed data of traffic flow. Then, the model was applied to measure one of the fundamental charactertistics of traffic flow, namely concentration. It is a broader term encompassing both density and occupancy. Occupancy takes into account the traffic composition and speed, and hence, occupancy is more meaningful than density. The concept of occupancy can not be directly applied under heterogeneous traffic conditions, as the traffic has no lane discipline. In this paper, a new concept named, ‘area-occupancy’ is proposed to measure traffic concentration.
Gaussian Message Passing Iterative Detection for MIMO-NOMA Systems with Massive Access

This paper considers a low-complexity Gaussian Message Passing Iterative Detection (GMPID) algorithm for Multiple-Input Multiple-Output systems with Non-Orthogonal Multiple Access (MIMO-NOMA), in which a base station with $N_r$ antennas serves $N_u$ sources simultaneously. Both $N_u$ and $N_r$ are very large numbers and we consider the cases that $N_u&#62;N_r$. The GMPID is based on a fully connected loopy graph, which is well understood to be not convergent in some cases. The large-scale property of the MIMO-NOMA is used to simplify the convergence analysis. Firstly, we prove that the variances of the GMPID definitely converge to that of Minimum Mean Square Error (MMSE) detection. Secondly, two sufficient conditions that the means of the GMPID converge to a higher MSE than that of the MMSE detection are proposed. However, the means of the GMPID may still not converge when $ N_u/N_r&#60; (\sqrt{2}-1)^{-2}$. Therefore, a new convergent SA- GMPID is proposed, which converges to the MMSE detection for any $N_u&#62; N_r$ with a faster convergence speed. Finally, numerical results are provided to verify the validity of the proposed theoretical results.
Performance Analysis and Enhancement of the DSRC for VANET's Safety Applications

An analytical model for the reliability of a dedicated short-range communication (DSRC) control channel (CCH) to handle safety applications in vehicular ad hoc networks (VANETs) is proposed. Specifically, the model enables the determination of the probability of receiving status and safety messages from all vehicles within a transmitter's range and vehicles up to a certain distance, respectively. The proposed model is built based on a new mobility model that takes into account the vehicle's follow-on safety rule to derive accurately the relationship between the average vehicle speed and density. Moreover, the model takes into consideration 1) the impact of mobility on the density of vehicles around the transmitter, 2) the impact of the transmitter's and receiver's speeds on the system reliability, 3) the impact of channel fading by modeling the communication range as a random variable, and 4) the hidden terminal problem and transmission collisions from neighboring vehicles. It is shown that the current specifications of the DSRC may lead to severe performance degradation in dense and high-mobility conditions. Therefore, an adaptive algorithm is introduced to increase system reliability in terms of the probability of successful reception of the packet and the delay of emergency messages in a harsh vehicular environment. The proposed model and the enhancement algorithm are validated by simulation using realistic vehicular traces.
On the application of least-commitment and heuristic search in temporal planning

Graphplan planning graphs are structures widely used in modern planners. The exclusion relations calculated in the planning graph extension provide very useful information, especially in temporal planning where actions have different duration. However, Graphplan backward search has some inefficiencies that impose limitations when dealing with large temporal problems. This paper presents a new search process for temporal planning to avoid these inefficiencies. This search uses the information of a planning graph and shows beneficial in the scalability of the planner. Moreover, our experiments show that a planner with this new search is competitive with other state-of-the-art planners w.r. t. the plan quality.
Time Series Analysis Using Geometric Template Matching

We present a novel framework for analyzing univariate time series data. At the heart of the approach is a versatile algorithm for measuring the similarity of two segments of time series called geometric template matching (GeTeM). First, we use GeTeM to compute a similarity measure for clustering and nearest-neighbor classification. Next, we present a semi-supervised learning algorithm that uses the similarity measure with hierarchical clustering in order to improve classification performance when unlabeled training data are available. Finally, we present a boosting framework called TDEBOOST, which uses an ensemble of GeTeM classifiers. TDEBOOST augments the traditional boosting approach with an additional step in which the features used as inputs to the classifier are adapted at each step to improve the training error. We empirically evaluate the proposed approaches on several datasets, such as accelerometer data collected from wearable sensors and ECG data.
Quantum Number Tricks

Some results indicate that quantum information based on quantum physics is more powerful than classical one. In this paper, we propose new tricks based on quantum physics. Our tricks are methods inspired by the strategies of quantum game theory. In these tricks, magicians have the ability of quantum physics, but spectators have only classical one. We propose quantum tricks such that, by manipulating quantum coins and quantum cards, magicians guess spectators’ values.
Virulence and Draft Genome Sequence Overview of Multiple Strains of the Swine Pathogen Haemophilus parasuis

Haemophilus parasuis is the cause of Glässer's disease in swine, which is characterized by systemic infection resulting in polyserositis, meningitis, and arthritis. Investigation of this animal disease is complicated by the enormous differences in the severity of disease caused by H. parasuis strains, ranging from lethal systemic disease to subclinical carriage. To identify differences in genotype that could account for virulence phenotypes, we established the virulence of, and performed whole genome sequence analysis on, 11 H. parasuis strains. Virulence was assessed by evaluating morbidity and mortality following intranasal challenge of Caesarean-derived, colostrum-deprived (CDCD) pigs. Genomic DNA from strains Nagasaki (serotype 5), 12939 (serotype 1), SW140 (serotype 2), 29755 (serotype 5), MN-H (serotype 13), 84-15995 (serotype 15), SW114 (serotype 3), H465 (serotype 11), D74 (serotype 9), and 174 (serotype 7) was used to generate Illumina paired-end libraries for genomic sequencing and de novo assembly. H. parasuis strains Nagasaki, 12939, SH0165 (serotype 5), SW140, 29755, and MN-H exhibited a high level of virulence. Despite minor differences in expression of disease among these groups, all pigs challenged with these strains developed clinical signs consistent with Glässer's disease between 1–7 days post-challenge. H. parasuis strains 84-15995 and SW114 were moderately virulent, in that approximately half of the pigs infected with each developed Glässer's disease. H. parasuis strains H465, D74, and 174 were minimally virulent or avirulent in the CDCD pig model. Comparative genomic analysis among strains identified several noteworthy differences in coding regions. These coding regions include predicted outer membrane, metabolism, and pilin or adhesin related genes, some of which likely contributed to the differences in virulence and systemic disease observed following challenge. These data will be useful for identifying H. parasuis virulence factors and vaccine targets.
The joint Simon effect: a review and theoretical integration

The social or joint Simon effect has been developed to investigate how and to what extent people mentally represent their own and other persons' action/task and how these cognitive representations influence an individual's own behavior when interacting with another person. Here, we provide a review of the available evidence and theoretical frameworks. Based on this review, we suggest a comprehensive theory that integrates aspects of earlier approaches–the Referential Coding Account. This account provides an alternative to the social interpretation of the (joint) go-nogo Simon effect (aka the social Simon effect) and is able to integrate seemingly opposite findings on joint action.
Selective Inhibition of a Regulatory Subunit of Protein Phosphatase 1 Restores Proteostasis

Guanabenz, a small-molecule inhibitor, protects cells from lethal accrual of misfolded proteins in the endoplasmic reticulum. Many biological processes are regulated through the selective dephosphorylation of proteins. Protein serine-threonine phosphatases are assembled from catalytic subunits bound to diverse regulatory subunits that provide substrate specificity and subcellular localization. We describe a small molecule, guanabenz, that bound to a regulatory subunit of protein phosphatase 1, PPP1R15A/GADD34, selectively disrupting the stress-induced dephosphorylation of the α subunit of translation initiation factor 2 (eIF2α). Without affecting the related PPP1R15B-phosphatase complex and constitutive protein synthesis, guanabenz prolonged eIF2α phosphorylation in human stressed cells, adjusting the protein production rates to levels manageable by available chaperones. This favored protein folding and thereby rescued cells from protein misfolding stress. Thus, regulatory subunits of phosphatases are drug targets, a property used here to restore proteostasis in stressed cells.
Validating The Design Science Research Roadmap: Through The Lens Of "The Idealised Model For Theory Development"

Design Science Research (DSR) has emerged as an important approach in Information Systems (IS) research. However, DSR is still in its genesis and has yet to achieve consensus on even the fundamentals, such as what methodology / approach to use for DSR. While there has been much effort to establish DSR methodologies, a complete, holistic and validated approach for the conduct of DSR to guide IS researcher (especially novice researchers) is yet to be established. Alturki et al. (2011) present a DSR ‘Roadmap’, making the claim that it is a complete and comprehensive guide for conducting DSR. This paper aims to further assess this Roadmap, by positioning it against the ‘Idealized Model for Theory Development’ (IM4TD) (Fischer & Gregor 2011). The IM4TD highlights the role of discovery and justification and forms of reasoning to progress in theory development. Fischer and Gregor (2011) have applied IM4TD’s hypothetico-deductive method to analyze DSR methodologies, which is adopted in this study to deductively validate the Alturki et al. (2011) Roadmap. The results suggest that the Roadmap adheres to the IM4TD, is reasonably complete, overcomes most shortcomings identified in other DSR methodologies and also highlights valuable refinements that should be considered within the IM4TD.
Automated web testing based on textual-visual UI patterns: the UTF approach

Automated software testing is the only resort for delivering quality software, since there are usually large test suites to be executed, especially for regression testing. Though many automated testing tools and techniques have been developed, they still do not solve all problems like cost and maintenance, and they can even be brittle in some situations, thus confining their adoption. To address these issues, we develop a pattern-based automated testing framework, called UTF (User-oriented Testing Framework), for Web applications. UTF encodes textual-visual information about and relationships between widgets into a domain specific language for test scripts based on the underlying invariant structural patterns in the DOM, which allows test scripts to be easily created and maintained. In addition, UTF provides flexible extension and customization capabilities to make it adaptable for various Web-application scenarios. Our experiences show UTF can greatly reduce the cost of adopting automated testing and facilitate its institutionalization.
Analysis of Self-Similar Workload on Real-Time Systems

Real-time systems used in media processing and transmission produce bursty workloads with highly variable execution and transmission times. To avoid the drawbacks of using the worst-case approach with these workloads, this paper uses a variation of the usual real-time task model where the WCET is replaced by a discrete statistical distribution. Using this approach, tasks are characterized by their processing time over a sampling period. We could expect that increasing the sampling period would smooth, in principle, the workload variability and the proposed analysis would provide more deterministic long- term results. However, we have surprisingly observed that this variability does not decreases with the sampling period: work- loads are bursty on many time scales. This property is known as self-similarity and is measured using the Hurst parameter.This paper studies how to properly model and analyze self- similar task sets showing the influence of the Hurst parameter on the schedulability analysis. It shows, through an analytical model and simulations, that this parameter may have a very negative impact on system performance. As a conclusion, it can be stated that this factor should be taken into account for statistical analysis of real-time systems, since simplistic workload models can lead to inaccurate results. It also shows that the negative effect of this parameter can be bounded using scheduling policies based on the bandwidth isolation principle.
Federal Reserve Credibility and the Term Structure of Interest Rates

In this paper, we show how the degree of central bank credibility influences the level, slope and curvature of the term structure of interest rates. In an estimated structural model, we find that historical yield curve data are best matched by the Federal Reserve conducting policy in a loose commitment framework, rather than the commonly used discretion and full commitment assumptions. The structural impulse responses indicate that the past history of realized shocks plays a crucial role in determining the dynamic effects of monetary policy on the yield curve. Finally, the regime-switching framework allows us to estimate likely re-optimization episodes which are found to impact the middle of the yield curve more than the short and long end.
Autophagosome Formation during Varicella-Zoster Virus Infection following Endoplasmic Reticulum Stress and the Unfolded Protein Response

ABSTRACT Autophagy is a recently recognized component of the life cycle of varicella-zoster virus (VZV). We have documented abundant autophagosome formation in skin vesicles (final site of virion assembly) from randomly selected cases of varicella and zoster. The fact that autophagy was an early event in the VZV replication cycle was documented by finding infected vesicle cells with the VZV IE62 protein confined to the nucleus. Next, we pursued studies in VZV-infected cultured cells to define whether autophagy was preceded by endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). First, we demonstrated that autophagosome formation in infected cells closely resembled that seen after treatment of cells with tunicamycin, a potent initiator of ER stress. Second, we demonstrated a marked expansion of ER size in both VZV-infected cells and cells transfected with the predominant VZV glycoprotein complex gE/gI. An enlarged ER is critical evidence of ER stress, which in turn is relieved by the UPR. To this end, we documented the UPR by detecting the alternatively spliced form of the XBP1 protein as well as CHOP (C/EBP homologous protein), both transcriptional activators of other UPR genes in an ER stress-dependent manner. Because VZV does not encode inhibitors of autophagy, the above results suggested that autophagy was a common event in VZV-infected cells and that it was provoked at least in part by ER stress secondary to overly abundant VZV glycoprotein biosynthesis, which led to UPR activation in an attempt to maintain cellular homeostasis.