Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystallographic Studies of the Escherichia coliQuinol-Fumarate Reductase with Inhibitors Bound to the Quinol-binding Site*

The quinol-fumarate reductase (QFR) respiratory complex of Escherichia coli is a four-subunit integral-membrane complex that catalyzes the final step of anaerobic respiration when fumarate is the terminal electron acceptor. The membrane-soluble redox-active molecule menaquinol (MQH2) transfers electrons to QFR by binding directly to the membrane-spanning region. The crystal structure of QFR contains two quinone species, presumably MQH2, bound to the transmembrane-spanning region. The binding sites for the two quinone molecules are termed QP and QD, indicating their positions proximal (QP) or distal (QD) to the site of fumarate reduction in the hydrophilic flavoprotein and iron-sulfur protein subunits. It has not been established whether both of these sites are mechanistically significant. Co-crystallization studies of the E. coli QFR with the known quinol-binding site inhibitors 2-heptyl-4-hydroxyquinoline-N-oxide and 2-[1-(p-chlorophenyl)ethyl] 4,6-dinitrophenol establish that both inhibitors block the binding of MQH2 at the QP site. In the structures with the inhibitor bound at QP, no density is observed at QD, which suggests that the occupancy of this site can vary and argues against a structurally obligatory role for quinol binding to QD. A comparison of the QP site of the E. coli enzyme with quinone-binding sites in other respiratory enzymes shows that an acidic residue is structurally conserved. This acidic residue, Glu-C29, in the E. coli enzyme may act as a proton shuttle from the quinol during enzyme turnover.
Potential Direct Regulators of the Drosophila yellow Gene Identified by Yeast One-Hybrid and RNAi Screens

The regulation of gene expression controls development, and changes in this regulation often contribute to phenotypic evolution. Drosophila pigmentation is a model system for studying evolutionary changes in gene regulation, with differences in expression of pigmentation genes such as yellow that correlate with divergent pigment patterns among species shown to be caused by changes in cis- and trans-regulation. Currently, much more is known about the cis-regulatory component of divergent yellow expression than the trans-regulatory component, in part because very few trans-acting regulators of yellow expression have been identified. This study aims to improve our understanding of the trans-acting control of yellow expression by combining yeast-one-hybrid and RNAi screens for transcription factors binding to yellow cis-regulatory sequences and affecting abdominal pigmentation in adults, respectively. Of the 670 transcription factors included in the yeast-one-hybrid screen, 45 showed evidence of binding to one or more sequence fragments tested from the 5′ intergenic and intronic yellow sequences from D. melanogaster, D. pseudoobscura, and D. willistoni, suggesting that they might be direct regulators of yellow expression. Of the 670 transcription factors included in the yeast-one-hybrid screen, plus another TF previously shown to be genetically upstream of yellow, 125 were also tested using RNAi, and 32 showed altered abdominal pigmentation. Nine transcription factors were identified in both screens, including four nuclear receptors related to ecdysone signaling (Hr78, Hr38, Hr46, and Eip78C). This finding suggests that yellow expression might be directly controlled by nuclear receptors influenced by ecdysone during early pupal development when adult pigmentation is forming.
Salinomycin as a Drug for Targeting Human Cancer Stem Cells

Cancer stem cells (CSCs) represent a subpopulation of tumor cells that possess self-renewal and tumor initiation capacity and the ability to give rise to the heterogenous lineages of malignant cells that comprise a tumor. CSCs possess multiple intrinsic mechanisms of resistance to chemotherapeutic drugs, novel tumor-targeted drugs, and radiation therapy, allowing them to survive standard cancer therapies and to initiate tumor recurrence and metastasis. Various molecular complexes and pathways that confer resistance and survival of CSCs, including expression of ATP-binding cassette (ABC) drug transporters, activation of the Wnt/β-catenin, Hedgehog, Notch and PI3K/Akt/mTOR signaling pathways, and acquisition of epithelial-mesenchymal transition (EMT), have been identified recently. Salinomycin, a polyether ionophore antibiotic isolated from Streptomyces albus, has been shown to kill CSCs in different types of human cancers, most likely by interfering with ABC drug transporters, the Wnt/β-catenin signaling pathway, and other CSC pathways. Promising results from preclinical trials in human xenograft mice and a few clinical pilote studies reveal that salinomycin is able to effectively eliminate CSCs and to induce partial clinical regression of heavily pretreated and therapy-resistant cancers. The ability of salinomycin to kill both CSCs and therapy-resistant cancer cells may define the compound as a novel and an effective anticancer drug.
Grid infrastructure development as support for e-science services

During last years the e-Infrastructure concept has been extensively elaborated and promoted as an essential pillar for the implementation of ERA (European Research Area). The main components of this infrastructure are the network for education and research and the Grid infrastructures. At the European level important efforts and resourced have been devoted to the development of both components, with joint financial support provided by Framework Programmes 6 and 7 of EU and national research programmes. At the national level, the high-speed communication network for education and research, and national grid infrastructure for research are included in the list of priority investment projects in the Information and Communications Technologies domain. The main financial support for the development of these projects is provided by the Sectorial Operational Programme "Increase of Economic Competitiveness". ICI Bucharest is among beneficiary organizations of this support. This paper presents the European context for e-Infrastructure development as support for e-Science concept implementation, the evolution and current status of Grid infrastructures at the European and national levels, a short review of the development of Grid computing at ICI Bucharest, the main objectives and activities of the structural funds grant awarded to the institute for a significant upgrade of the current grid site RO-01-ICI.
Image-Based Tactile Emojis: Improved Interpretation of Message Intention and Subtle Nuance for Visually Impaired Individuals

To enhance missing nonverbal cues in computer-mediated communication using text, those who can see often use emojis or emoticons. Although emojis for the sighted have transformed throughout the years to animated forms and added sound effects, emojis for visually impaired people remain underdeveloped. This study tested how tactile emojis based on visual imagery combined with the Braille system can enhance clarity in the computer-mediated communication environment for those with visual impairments. Results of this study confirmed three things: Visually impaired subjects were able to connect emotional emojis to the emotion they represented without any prior guidance, image-based (picture-based) and non-image-based (abstraction-based) tactile emoji were equally learnable, and the clarity of intended meaning was improved when an emoji was used with text (Braille). Thirty visually impaired subjects were able to match an average of 67% of emotions without prior guidance, and three of the four subjects who matched perfectly both before and after guidance were congenitally blind. The subjects had the most trouble discriminating the facial feature of “fear” between “sadness” or “surprised” for they shared similar traits. After guidance, the image-based tactile design elicited an average of 81% correct answers, whereas the non-image-based tactile design elicited an average of 37%, showing that the image-based tactile design was more effective for learning the meaning of emojis. The clarity of the sentence was also improved. This study shows that image-based tactile emojis can improve the texting experience of visually impaired individuals to a level where they can communicate subtle emotional cues through tactile imagery. This advance could minimize the service gap between sighted and visually impaired people and offer a much more abundant computer-mediated communication environment for visually impaired individuals.
Haplotype Inference by Entropy Minimization

The completion of the Human Genome Project and the identification of millions of SNPs in the human population has opened the way for large-scale association studies between genetic variation and susceptibility to common diseases. Constructing a haplotype map of the human population has become the next major target in genomics (http://www.hapmap.org/). The population haplotyping problem (PHP) is to infer the haplotypes from the genotypes of a large population; see [1, 2, 3] for recent surveys on computational methods for solving this problem. Recently, Halperin and Karp [4] introduced a novel approach to PHP based on the entropy minimization principle, which suggests that most common haplotypes are evenly distributed in large populations. They also proposed a simple greedy entropy minimization algorithm for missing allele imputation and haplotype inference. In this poster we show that a local improvement entropy minimization algorithm yields significantly higher phasing accuracy than the algorithm of [4], coming close to the phasing accuracy of the widely used but much slower PHASE algorithm [5].
MDA5 Can Be Exploited as Efficacious Genetic Adjuvant for DNA Vaccination against Lethal H5N1 Influenza Virus Infection in Chickens

Chickens lack the retinoic acid-inducible gene I (RIG-I) and sense avian influenza virus (AIV) infections by means of the melanoma differentiation-associated gene 5 product (chMDA5). Plasmid-driven expression of the N-terminal half of chMDA5 containing the caspase activation and recruitment domains [chMDA5(1-483)] triggers interferon-β responses in chicken cells. We hypothesized that mimicking virus infection by chMDA5(1-483) expression may enhance vaccine-induced adaptive immunity. In order to test this, the potential genetic adjuvant properties of chMDA5(1-483) were evaluated in vivo in combination with a suboptimal quantity of a plasmid DNA vaccine expressing haemagglutinin (HA) of H5N1 AIV. Co-administration of the HA plasmid with plasmid DNA for chMDA5(1-483) expression resulted in approximately 10-fold higher HA-specific antibody responses than injection of the HA plasmid mixed with empty vector DNA as control. Accordingly, compared with HA DNA vaccination alone, the chMDA5(1-483)-adjuvanted HA DNA vaccine mediated enhanced protection against a lethal H5N1 challenge infection in chickens, with reduced clinical signs and cloacal virus shedding. These data demonstrate that innate immune activation by expression of signaling domains of RIG-I-like receptors can be exploited to enhance vaccine efficacy.
Mixed Model-Based Hazard Estimation

This article proposes a new method for estimation of the hazard function from a set of censored failure time data, with a view to extending the general approach to more complicated models. The approach is based on a mixed model representation of penalized spline hazard estimators. One payoff is the automation of the smoothing parameter choice through restricted maximum likelihood. Another is the option to use standard mixed model software for automatic hazard estimation.
From Languages to Systems: Understanding Practical Application Development in Security-typed Languages

Security-typed languages are an evolving tool for implementing systems with provable security guarantees. However, to date, these tools have only been used to build simple "toy" programs. As described in this paper, we have developed the first real-world, security-typed application: a secure email system written in the Java language variant Jif. Real-world policies are mapped onto the information flows controlled by the language primitives, and we consider the process and tractability of broadly enforcing security policy in commodity applications. We find that while the language provided the rudimentary tools to achieve low-level security goals, additional tools, services, and language extensions were necessary to formulate and enforce application policy. We detail the design and use of these tools. We also show how the strong guarantees of Jif in conjunction with our policy tools can be used to evaluate security. This work serves as a starting point-we have demonstrated that it is possible to implement real-world systems and policy using security-typed languages. However, further investigation of the developer tools and supporting policy infrastructure is necessary before they can fulfil their considerable promise of enabling more secure systems
Perceived Benefits, Privacy Risks, and Perceived Justice in Location Information Disclosure: a Moderated Mediation Analysis

Previous studies on information disclosure have heavily relied on the justice theory to explain how users balance the benefits and privacy risks (e.g., privacy calculus) induced by the information disclosure behavior. However, the specific mechanism of privacy calculus (or the role of justice) and the boundary conditions under which the privacy calculus works have been rarely empirically investigated. To fill this research gap, we propose a moderated mediation model to examine the mediating role of justice and the conditions under which the mediating mechanism applies. Based on a field survey from the users of location-based social networks in China, we find that (1) privacy risks weaken the relationship between perceived benefits and perceived justice but strengthen the relationship between perceived justice and information disclosure intention, (2) privacy risks weaken the direct effect of perceived benefits on intention while strengthen the indirect effect of perceived benefits on intention via perceived justice, and (3) the total effect of perceived benefits on intention is stronger when privacy risks are lower than when they are higher. This paper contributes to the information disclosure literature by highlighting the moderated mediation mechanism of the key factors identified in previous research.
The Roles of Mental Animations and External Animations in Understanding Mechanical Systems

The effects of computer animations and mental animation on people's mental models of a mechanical system are examined. In 3 experiments, students learned how a mechanical system works from various instructional treatments including viewing a static diagram of the machine, predicting motion from static diagrams, viewing computer animations, and viewing static and animated diagrams accompanied by verbal commentaries. Although students' understanding of the system was improved by viewing both static and animated diagrams, there was no evidence that animated diagrams led to superior understanding of dynamic processes compared to static diagrams. Comprehension of diagrams was enhanced by asking students questions that required them to predict the behavior of the machine from static diagrams and by providing them with a verbal description of the dynamic processes. This article proposes that predicting motion from static diagrams engages students' mental animation processes, including spatial visualization, and provides them with information about what they do and do not understand about how the machine works. Verbal instruction provides information that is not easily communicated in graphics and directs students' attention to the relevant information in static and animated diagrams. The research suggests that an understanding of students' mental animation abilities is an important component of a theory of learning from external animations.
The influence of segmentation on individual gait recognition

The quality of the extracted gait silhouettes can hinder the performance and practicability of gait recognition algorithms. In this paper, we analyse the influence of silhouette quality caused by segmentation disparities, and propose a feature fusion strategy to improve recognition accuracy. Specifically, we first generate a dataset containing gait silhouette with various qualities generated by different segmentation algorithms, based on the CASIA Dataset B. We then project data into an embedded subspace, and fuse gallery features of different quality levels. To this end, we propose a fusion strategy based on Least Square QR-decomposition method. We perform classification based on the Euclidean distance between fused gallery features and probe features. Evaluation results show that the proposed fusion strategy attains important improvements on recognition accuracy.
On Reducing Mesh Delay for Peer-to-Peer Live Streaming

Peer-to-peer (P2P) technology has emerged as a promising scalable solution for live streaming to large group. In this paper, we address the design of overlay which achieves low source-to-peer delay, is robust to user churn, accommodates of asymmetric and diverse uplink bandwidth, and continuously improves based on existing user pool. A natural choice is the use of mesh, where each peer is served by multiple parents. Since the peer delay in a mesh depends on its longest path through its parents, we study how to optimize such delay while meeting a certain streaming rate requirement. We first formulate the minimum delay mesh problem and show that it is NP-hard. Then we propose a centralized heuristic based on complete knowledge which serves as our benchmark and optimal solution for all the other schemes under comparison. Our heuristic makes use of the concept of power in network given by the ratio of throughput and delay. By maximizing the network power, our heuristic achieves very low delay. We then propose a simple distributed algorithm where peers select their parents based on the power concept. The algorithm makes continuous improvement on delay until some minimum delay is reached. Simulation results show that our distributed protocol performs close to the centralized one, and substantially outperforms traditional and state-of-the-art approaches.
From Social Sensor Data to Collective Human Behaviour Patterns - Analysing and Visualising Spatio-Temporal Dynamics in Urban Environments

The digital traces that people continuously leave behind – voluntarily or not – while using communication devices such as mobile phones or interacting with social media platforms reflect their behaviour in great detail. In this paper we show examples of the spatiotemporal patterns of collective human dynamics, which we derived from ‘social sensor’ data. We used user-generated data in mobile networks and voluntarily published information at social media platforms, which both served as proxies for human activity and mobility. Results show collective human activity and mobility hotspots in selected European urban environments and thus provide additional insights into how collective social activity shape urban systems. We used different geo-visualisation techniques to effectively communicate the urban inherent spatial and temporal dynamics. Especially for education related purposes, this allows a better general understanding of collective human behaviour in urban environments.
Leveraging semantic signatures for bug search in binary programs

Software vulnerabilities still constitute a high security risk and there is an ongoing race to patch known bugs. However, especially in closed-source software, there is no straightforward way (in contrast to source code analysis) to find buggy code parts, even if the bug was publicly disclosed. To tackle this problem, we propose a method called Tree Edit Distance Based Equational Matching (TEDEM) to automatically identify binary code regions that are "similar" to code regions containing a reference bug. We aim to find bugs both in the same binary as the reference bug and in completely unrelated binaries (even compiled for different operating systems). Our method even works on proprietary software systems, which lack source code and symbols. The analysis task is split into two phases. In a preprocessing phase, we condense the semantics of a given binary executable by symbolic simplification to make our approach robust against syntactic changes across different binaries. Second, we use tree edit distances as a basic block-centric metric for code similarity. This allows us to find instances of the same bug in different binaries and even spotting its variants (a concept called vulnerability extrapolation). To demonstrate the practical feasibility of the proposed method, we implemented a prototype of TEDEM that can find real-world security bugs across binaries and even across OS boundaries, such as in MS Word and the popular messengers Pidgin (Linux) and Adium (Mac OS).
Surveillance System with MegaPixel Scalable Transcoder

This paper presents a video surveillance system that displays mega-pixel streams effectively, while traansmitting and processing the streams efficiently with limited resources such as bandwidth, computing power and display resolution. The proposed system stores high-resolution and high-quality video data and associated object metadata, which includes ROI (Region-ofInterest)information. To satisfy such resource constraints and display important parts in detail without missing the overall scene context, the stored images are efficiently transcoded in the compressed-domain based on the ROI information, display resolution and available bandwidth. Simulation results confirm the effectiveness of the proposed system in terms of objective measures and subjective evaluation. SPIE Conference on Visual Communications and Image Processing (VCIP) This work may not be copied or reproduced in whole or in part for any commercial purpose. Permission to copy in whole or in part without payment of fee is granted for nonprofit educational and research purposes provided that all such whole or partial copies include the following: a notice that such copying is by permission of Mitsubishi Electric Research Laboratories, Inc.; an acknowledgment of the authors and individual contributions to the work; and all applicable portions of the copyright notice. Copying, reproduction, or republishing for any other purpose shall require a license with payment of fee to Mitsubishi Electric Research Laboratories, Inc. All rights reserved. Copyright c ©Mitsubishi Electric Research Laboratories, Inc., 2007 201 Broadway, Cambridge, Massachusetts 02139
Fault Diagnosis for Reciprocating Air Compressor Valve Using P-V Indicator Diagram and SVM

This paper presents a method of fault diagnosis for the reciprocating air compressor valve based on the indicator diagram and the support vector machine (SVM). This paper strikes 7 invariant moments of the indicator diagram of reciprocating air compressor, using image processing methods, according to the same moment theory. Then the method can be used to extract effective features as feature vectors for training the support vector machine, and achieve fault diagnosis for reciprocating air compressor valve. Finally, the paper simulate 5 kinds of working conditions of valve to identify using the fault monitoring system of reciprocating compressor valve, in order to verify the feasibility and effectiveness of the method.