Miracle-dz/UniFAR-FTUs huggingface dataset:
c-Type Cytochrome Assembly Is a Key Target of Copper Toxicity within the Bacterial Periplasm

ABSTRACT In the absence of a tight control of copper entrance into cells, bacteria have evolved different systems to control copper concentration within the cytoplasm and the periplasm. Central to these systems, the Cu+ ATPase CopA plays a major role in copper tolerance and translocates copper from the cytoplasm to the periplasm. The fate of copper in the periplasm varies among species. Copper can be sequestered, oxidized, or released outside the cells. Here we describe the identification of CopI, a periplasmic protein present in many proteobacteria, and show its requirement for copper tolerance in Rubrivivax gelatinosus. The ΔcopI mutant is more susceptible to copper than the Cu+ ATPase copA mutant. CopI is induced by copper, localized in the periplasm and could bind copper. Interestingly, copper affects cytochrome c membrane complexes (cbb3 oxidase and photosystem) in both ΔcopI and copA-null mutants, but the causes are different. In the copA mutant, heme and chlorophyll synthesis are affected, whereas in ΔcopI mutant, the decrease is a consequence of impaired cytochrome c assembly. This impact on c-type cytochromes would contribute also to the copper toxicity in the periplasm of the wild-type cells when they are exposed to high copper concentrations. IMPORTANCE Copper is an essential cation required as a cofactor in enzymes involved in vital processes such as respiration, photosynthesis, free radical scavenging, and pathogenesis. However, copper is highly toxic and has been implicated in disorders in all organisms, including humans, because it can catalyze the production of toxic reactive oxygen species and targets various biosynthesis pathways. Identifying copper targets, provides insights into copper toxicity and homeostatic mechanisms for copper tolerance. In this work, we describe for the first time a direct effect of excess copper on cytochrome c assembly. We show that excess copper specifically affects periplasmic and membrane cytochromes c, thus suggesting that the copper toxicity targets c-type cytochrome biogenesis. Copper is an essential cation required as a cofactor in enzymes involved in vital processes such as respiration, photosynthesis, free radical scavenging, and pathogenesis. However, copper is highly toxic and has been implicated in disorders in all organisms, including humans, because it can catalyze the production of toxic reactive oxygen species and targets various biosynthesis pathways. Identifying copper targets, provides insights into copper toxicity and homeostatic mechanisms for copper tolerance. In this work, we describe for the first time a direct effect of excess copper on cytochrome c assembly. We show that excess copper specifically affects periplasmic and membrane cytochromes c, thus suggesting that the copper toxicity targets c-type cytochrome biogenesis.
Multiple path planning using wavefront collision

The concept of wavefront expansion was introduced in order to build a collision-free path between two points among obstacles, minimizing a criterion. In this paper, we propose a new concept, called wavefront collision, in order to do the same for all possible paths between n waypoints. It consists in expanding simultaneously one wavefront by waypoint, until they collide. Using this concept, all paths can be computed thanks to one multiple wavefront expansion instead of n - 1, hence dividing the computational effort by about 3.5.
From Frat to Fraternity: An Evolutionary Model for 21st Century Greek-Letter Organizations

Fraternities and sororities have been fixtures of American collegiate campuses since the founding of Phi Beta Kappa in 1776. Since that time the wants, needs, aspirations and desires of the college student has continually evolved. In an effort to keep up with the evolution of the student, Greek-letter organizations (GLOs) have needed to find ways of evolving as well. As we jump head-first into the 21 st century and beyond these great bastions of the collegiate experience are again in need of a face-lift to meet the needs of the latest generation of students. Now, more than ever, it is time for GLOs to get back to their true roots and find a way to accentuate the values that they represent. It is also important to work towards diminishing the negative aspects often associated with membership within these organizations, bringing congruence between their exposed and enacted values. This thesis presents a model designed to help GLOs evolve into hybrid organizations with close ties to living-learning communities, while still holding onto their individual identities.
Comparing the best maximum clique finding algorithms, which are using heuristic vertex colouring

In this paper two best known at the moment algorithms for finding the maximum clique is compared. A key technique that both algorithms rely on is using a heuristic vertex colouring. The only difference between those algorithms is a way of using vertex-colouring and this difference in the very important. The algorithms' approaches are divided in this paper into two classes: re-applying vertex colouring on each depth and re-using colour classes obtained before the start of the main part. Historical attempts to use the colour classes for the maximum clique finding are also reviewed. Those two algorithms were never compared so far as is not widely announced also. The comparison is essential information for finding further development ways.
The Safety and Pharmacokinetics of Cyanidin-3-Glucoside after 2-Week Administration of Black Bean Seed Coat Extract in Healthy Subjects

We analyzed the pharmacokinetics of C3G on data from twelve subjects, after 2-week multiple dosing of black bean (Phaseolus vulgaris, Cheongjakong-3-ho) seed coat extract, using the mixed effect analysis method (NONMEM, Ver. 6.2), as well as the conventional non-compartmental method. We also examined the safety and tolerability. The PK analysis used plasma concentrations of the C3G on day 1 and 14. There was no observed accumulation of C3G after 2-week multiple dosing of black bean seed coat extract. The typical point estimates of PK were CL (clearance)=3,420 l/h, V (volume)=7,280 L, Ka (absorption constant)=9.94 h-1, ALAG (lag time)=0.217 h. The black bean seed coat extract was well tolerated and there were no serious adverse events. In this study, we confirmed that a significant amount of C3G was absorbed in human after given the black bean seed coat extract.
Modeling of Suppliers' Learning Behaviors in a Market Environment

An important objective of electricity suppliers is to maximize their profits over a planning horizon and comply with the market rules. This objective requires suppliers to learn from their bidding experience and behave in an anticipatory way. With volatile Locational Marginal Prices (LMPs), ever-changing transmission grid conditions, and incomplete information about other market participants, decision making for a supplier is a complex task. A learning algorithm that does not require an analytical model of the complicated market but allows suppliers to learn from experience and act in an anticipatory way is a suitable approach to this problem. Q-Learning, an anticipatory reinforcement learning technique, has all these desired properties. Therefore, it is used in this research to model the learning behaviors of electricity suppliers in a Day-Ahead electricity market. The Day-Ahead electricity market is modeled as a multi-agent system with interacting agents including supplier agents, Load Serving Entities and a Market Operator. Simulation of the market clearing results under the scenario in which agents have learning capabilities is compared with the scenario where agents report true marginal costs. It is shown that, with Q- Learning, electricity suppliers are making more profits compared to the scenario without learning due to strategic gaming. As a result, the LMP at each bus is substantially higher.
Toward a common model and a markup language for personal gazetteers

Collecting human mobility data on a large spatial and temporal scales allows a wide variety of representations and models, as well as quantitative, qualitative, and hybrid analysis techniques, of such data. This work introduces a graph-theoretical model of personal mobility, a specification to facilitate interoperability between different models of personal mobility, collected by various techniques, and for different analytical purposes. Moreover, the work introduces a common markup language for personal gazetteers, based on the proposed model. A prototype showcase application shows the usability of the proposed model.
Consumer Stickiness : A longitudinal study

The growth in e-commerce has been mainly in B2B, while B2C is still facing major hurdles associated with consumer acquisition and retention. In the evaluation of B2C businesses, the focus is shifting from measures of visitor attraction such as pageviews and click-through ratios to measures of consumer retention such as stickiness. Most prior research focused on explaining/ predicting the intention to adopt and the usage of online shopping rather than repeated behavior such as repurchase. In this study, we develop and empirically validate a model explaining online consumer stickiness as measured by repurchase. The results provide strong support for the importance of satisfaction in explaining repurchase and for the moderating effect of online shopping habit on the relationship between satisfaction and repurchase. The implications of these findings for theory and practice are discussed.
Validating a geographical image retrieval system

This paper summarizes a prototype geographical image retrieval system that demonstrates how to integrate image processing and information analysis techniques to support large-scale content-based image retrieval. By using an image as its interface, the prototype system addresses a troublesome aspect of traditional retrieval models, which require users to have complete knowledge of the low-level features of an image. In addition we describe an experiment to validate the performance of this image retrieval system against that of human subjects in an effort to address the scarcity of research evaluating performance of an algorithm against that of human beings. The results of the experiment indicate that the system could do as well as human subjects in accomplishing the tasks of similarity analysis and image categorization. We also found that under some circumstances texture features of an image are insufficient to represent a geographic image. We believe, however, that our image retrieval system provides a promising approach to integrating image processing techniques and information retrieval algorithms.
0 31 10 21 v 1 7 N ov 2 00 3 Improving LLR Tests of Gravitational Theory

Accurate analysis of precision ranges to the Moon has provided several tests of gravitational theory including the Equivalence Principle, geodetic precession, parameterized postNewtonian (PPN) parameters γ and β, and the constancy of the gravitational constant G. Since the beginning of the experiment in 1969, the uncertainties of these tests have decreased considerably as data accuracies have improved and data time span has lengthened. We are exploring the modeling improvements necessary to proceed from cm to mm range accuracies enabled by the new Apache Point Observatory Lunar Laser-ranging Operation (APOLLO) currently under development in New Mexico. This facility will be able to make a significant contribution to the solar system tests of fundamental and gravitational physics. In particular, the Weak and Strong Equivalence Principle tests would have a sensitivity approaching 10, yielding sensitivity for the SEP violation parameter η of ∼ 3 × 10, v/c general relativistic effects would be tested to better than 0.1%, and measurements of the relative change in the gravitational constant, Ġ/G, would be ∼ 0.1% the inverse age of the universe. Having this expected accuracy in mind, we discusses the current techniques, methods and existing physical models used to process the LLR data. We also identify the challenges for modeling and data analysis that the LLR community faces today in order to take full advantage of the new APOLLO ranging station.
An Interactome-Centered Protein Discovery Approach Reveals Novel Components Involved in Mitosome Function and Homeostasis in Giardia lamblia

Protozoan parasites of the genus Giardia are highly prevalent globally, and infect a wide range of vertebrate hosts including humans, with proliferation and pathology restricted to the small intestine. This narrow ecological specialization entailed extensive structural and functional adaptations during host-parasite co-evolution. An example is the streamlined mitosomal proteome with iron-sulphur protein maturation as the only biochemical pathway clearly associated with this organelle. Here, we applied techniques in microscopy and protein biochemistry to investigate the mitosomal membrane proteome in association to mitosome homeostasis. Live cell imaging revealed a highly immobilized array of 30–40 physically distinct mitosome organelles in trophozoites. We provide direct evidence for the single giardial dynamin-related protein as a contributor to mitosomal morphogenesis and homeostasis. To overcome inherent limitations that have hitherto severely hampered the characterization of these unique organelles we applied a novel interaction-based proteome discovery strategy using forward and reverse protein co-immunoprecipitation. This allowed generation of organelle proteome data strictly in a protein-protein interaction context. We built an initial Tom40-centered outer membrane interactome by co-immunoprecipitation experiments, identifying small GTPases, factors with dual mitosome and endoplasmic reticulum (ER) distribution, as well as novel matrix proteins. Through iterative expansion of this protein-protein interaction network, we were able to i) significantly extend this interaction-based mitosomal proteome to include other membrane-associated proteins with possible roles in mitosome morphogenesis and connection to other subcellular compartments, and ii) identify novel matrix proteins which may shed light on mitosome-associated metabolic functions other than Fe-S cluster biogenesis. Functional analysis also revealed conceptual conservation of protein translocation despite the massive divergence and reduction of protein import machinery in Giardia mitosomes.
Performance Evaluation of Multiple Robots in aSearch and Retrieval

In this paper we study the performance of multiple robots at a search and retrieval task. The robots have all the same capabilities and perform the same task without any explicit communication. The sensing capabilities of the robots are quite limited, yet the robots succeed at performing the task. We show how the performance is aaected by the number of robots working in the same area, the distribution of the targets the robots are searching for, and the complexity of the environment. Introduction Cooperative multiple robots can often accomplish a task that is diicult, if not impossible, for a single robot. When approaching a problem involving coordinated behavior, the challenge arises out of determining the strategy that will maximize performance. Strategy considerations include: explicit versus implicit coordinated behavior, origin of control (central or decentralized), extent of communication, heterogeneous versus homogeneous abilities, and individual motivation (selfish or socialized). Despite the growing interest in multiple robots, only a handful of experimental studies exist which assess performance relative to cooperative and coordinative strategies. For performance evaluation relative to strategy, the research questions we address in this paper are: How does the complexity of the environment aaect performance? For instance, does the presence of extraneous obstacles suggest a diierent cooperation strategy? How does the number of robots operating in the same area aaect performance? For instance, how does an increase in population increase the chances of un-wanted interference. Mataric (Mataric 1995b) shows how the performance of a group of multiple robots performing a clean-up and collection task declines as the number of robots increases. How does the distribution of the targets in the environment aaect performance? For instance, do simple reactive behaviors work best with random distribution of targets? The tasks traditionally studied with multiple robots and behavior-based control include foraging which involves searching and retrieving items from a given area, box-pushing which involves moving an object between two locations, formation marching (Balch & Arkin 1995) which involves moving while maintaining a xed pattern, and various forms of military surveillance (Parker 1996). Another classic task involves janitorial services (Parker 1996) where robots clean a room of an unfamiliar building by emptying the garbage, dusting the furniture, and cleaning the oor. Here, we propose a task of search and retrieval whereby robots locate, collect, and return targets to a home base. Robots are homogeneous and perform independently with a localized goal of target retrieval without …
Evaluating PageRank methods for structural sense ranking in labeled tree data

Link analysis methods like the popular PageRank are increasingly being applied to lexical knowledge bases to deal with a number of natural language processing problems, including unsupervised word sense ranking and disambiguation. Compared to plain-text, the topic of sense ranking in semistructured data has been however studied marginally. This paper aims to bridge PageRank-based word sense ranking and tree-structured data. We propose PageRank-style methods for the structural sense ranking problem, which take into account tree structural relations as well as semantic relatedness in the constituents of tree data. The proposed methods are comparatively evaluated with existing Page-Rank methods for word sense disambiguation. Effectiveness and efficiency of PageRank methods have been assessed on various data with different domain vocabularies.
Prostaglandin I2 Signaling Drives Th17 Differentiation and Exacerbates Experimental Autoimmune Encephalomyelitis

Background Prostaglandin I2 (PGI2), a lipid mediator currently used in treatment of human disease, is a critical regulator of adaptive immune responses. Although PGI2 signaling suppressed Th1 and Th2 immune responses, the role of PGI2 in Th17 differentiation is not known. Methodology/Principal Findings In mouse CD4+CD62L+ naïve T cell culture, the PGI2 analogs iloprost and cicaprost increased IL-17A and IL-22 protein production and Th17 differentiation in vitro. This effect was augmented by IL-23 and was dependent on PGI2 receptor IP signaling. In mouse bone marrow-derived CD11c+ dendritic cells (BMDCs), PGI2 analogs increased the ratio of IL-23/IL-12, which is correlated with increased ability of BMDCs to stimulate naïve T cells for IL-17A production. Moreover, IP knockout mice had delayed onset of a Th17-associated neurological disease, experimental autoimmune encephalomyelitis (EAE), and reduced infiltration of IL-17A-expressing mononuclear cells in the spinal cords compared to wild type mice. These results suggest that PGI2 promotes in vivo Th17 responses. Conclusion The preferential stimulation of Th17 differentiation by IP signaling may have important clinical implications as PGI2 and its analogs are commonly used to treat human pulmonary hypertension.
User-assisted cloud storage system: Opportunities and challenges

1. Introduction Cloud storage has recently attracted a substantial amount of attention from both industry and academia. Notable commercial cloud storage services include Amazon S3, Google Drive, Dropbox, Microsoft Skydrive, and Apple's iCloud. Compared with traditional storage systems, cloud storage offers several desirable advantages, including high data availability, high data reliability, and dynamic storage space.
Semiparametric Regression Using Student  $t$ Processes

In this paper, we propose a latent factor regression model, in which priors are assigned to both the latent regression vector and the error term, by using reproducing kernels. The resulting regression function follows a stochastic process known as a student process. The model is attractive because its implementation is based on a tractable posterior predictive distribution and a simple expectation-maximization (EM) estimation algorithm. In addition, treating the transductive inference as a missing data problem, we devise the EM algorithm to deal with the parameter estimation as well as the response prediction in a single paradigm. The model is also elaborated for multivariate-response regression problems. For this purpose, we present a generalization of multivariate models and some of its properties. Experimental results show our approaches to be effective.
Indoor and outdoor channel simulator based on ray tracing

An efficient algorithm that dynamically calculates all possible ray paths in outdoor (macro- and micro-cells and land mobile satellite, LMS) and indoor environments is presented in this paper. The algorithm is based on the sweep line technique. Additionally a quadtree (bounding box (Athanasiadou, 1995)) division of the study environment is used to reduce search time. For indoor and microcellular environments wall reflections and transmissions as well as diffractions on vertical edges are considered up to the order specified by the user. 2D ray-path search algorithms have been extended to 3D in order to model macrocellular and land mobile satellite environments. For such cases, apart from multiple reflections, transmissions and vertical diffractions, the propagation simulator also takes into account single diffractions on horizontal edges and corners directly visible both from the transmitter and the receiver. Combinations of propagation mechanisms have also been considered in the simulator.
Multiclass Vehicle Type Recognition System using an Oriented Points Set based Model

This paper presents a framework for multiclass vehicle type identification based on oriented contour points. The decision process combines four classifiers: three voting algorithms and a distance error. This method have been tested on a realistic data set obtaining similar results for equivalent recognition frameworks with different features selections [11]. A confidence criterion is also calculated to validate the system results. The system also show to be robust to partial occlusions. Keywords— Pattern Recognition, Multiclass Classification, Oriented Contour Poins, Voting Algorithm.