Miracle-dz/UniFAR-FTUs huggingface dataset:
The Use of Advanced Mass Spectrometry to Dissect the Life-Cycle of Photosystem II

Photosystem II (PSII) is a photosynthetic membrane-protein complex that undergoes an intricate, tightly regulated cycle of assembly, damage, and repair. The available crystal structures of cyanobacterial PSII are an essential foundation for understanding PSII function, but nonetheless provide a snapshot only of the active complex. To study aspects of the entire PSII life-cycle, mass spectrometry (MS) has emerged as a powerful tool that can be used in conjunction with biochemical techniques. In this article, we present the MS-based approaches that are used to study PSII composition, dynamics, and structure, and review the information about the PSII life-cycle that has been gained by these methods. This information includes the composition of PSII subcomplexes, discovery of accessory PSII proteins, identification of post-translational modifications and quantification of their changes under various conditions, determination of the binding site of proteins not observed in PSII crystal structures, conformational changes that underlie PSII functions, and identification of water and oxygen channels within PSII. We conclude with an outlook for the opportunity of future MS contributions to PSII research.
Evaluating Test Suites and Adequacy Criteria Using Simulation-Based Models of Distributed Systems

Test adequacy criteria provide the engineer with guidance on how to populate test suites. While adequacy criteria have long been a focus of research, existing testing methods do not address many of the fundamental characteristics of distributed systems, such as distribution topology, communication failure, and timing. Furthermore, they do not provide the engineer with a means to evaluate the relative effectiveness of different criteria, nor the relative effectiveness of adequate test suites satisfying a given criterion. This paper makes three contributions to the development and use of test adequacy criteria for distributed systems: (1) a testing method based on discrete-event simulations; (2) a fault-based analysis technique for evaluating test suites and adequacy criteria; and (3) a series of case studies that validate the method and technique. The testing method uses a discrete-event simulation as an operational specification of a system, in which the behavioral effects of distribution are explicitly represented. Adequacy criteria and test cases are then defined in terms of this simulation-based specification. The fault-based analysis involves mutation of the simulation-based specification to provide a foil against which test suites and the criteria that formed them can be evaluated. Three distributed systems were used to validate the method and technique, including DNS, the domain name system.
Rheological Characterization of Blended Paving Asphalt

ABSTRACT Asphalt is processed in India through various means such as straight-run, air blown and blending. Production of asphalt for paving purposes in some of the refineries is carried out by blending the heavy extract with the PDA pitch. Since 60/70 or 80/100 penetration grade is predominantly used in India, appropriate proportions of PDA pitch and extract are determined to meet the penetration grade. Considering the current move in India towards viscosity grading and then to performance grading, a need was felt to observe the rheological properties of blended asphalt and the role of blending process on the final end product. This investigation reports the rheological characterization of various blends made with PDA pitch and heavy extract. Three blend proportions were manufactured by two different blending process and all the blends were subjected to short term aging in rolling thin film oven. The unaged and short term aged blends were tested for steady shear, creep and recovery and stress relaxation properties. The single point measurement of viscosity at a specific temperature cannot reveal the complex behaviour of asphalt. A complete and systematic rheological characterization is necessary. In fact, this investigation reports for the first time, stress overshoot in steady shear and measurement of first normal stress difference relaxation for blended asphalt. From the analysis of the experimental data it is shown that blends with higher proportion of PDA pitch are more temperature susceptible and the blending process tends to “homogenize” the mixture. One can use the data gathered from these experiments for designing asphalt blend with the required appropriate property. These experiments also underline the requirement to develop non-linear constitutive models for asphalt and asphalt blends.
Surface energy and wettability of polymers light-cured by two different systems

Objectives This study evaluated the surface energy and wettability of composite resins polymerized by different light-curing units to ascertain the good wetting of tooth surfaces to achieve adhesion. Material and Method Filtek Z350 (3M ESPE), Admira (VOCO) and Grandio (VOCO) resins were selected for the testing procedures. The resins were light cured using LED and Halogen devices. Contact angles were measured goniometrically (Ramé-Hart F100) using water and glycerol as test liquids. Surface energy values were calculated with a software program (DROPimage Standard) that uses the harmonic mean method applied to the acid-base theory. The data were analyzed statistically by ANOVA and Tukey's test with a significance of 0.05. Results and Conclusions No statistically significant differences were found between the values of surface energy. The measured wettability differed statistically in most combinations as a function of the type of composite resin, type of light-curing unit, and the test liquid.
Development and Characterization of Novel Films Based on Sulfonamide-Chitosan Derivatives for Potential Wound Dressing

The objective of this study was to develop new films based on chitosan functionalized with sulfonamide drugs (sulfametoxydiazine, sulfadiazine, sulfadimetho-xine, sulfamethoxazol, sulfamerazine, sulfizoxazol) in order to enhance the biological effects of chitosan. The morphology and physical properties of functionalized chitosan films as well the antioxidant effects of sulfonamide-chitosan derivatives were investigated. The chitosan-derivative films showed a rough surface and hydrophilic properties, which are very important features for their use as a wound dressing. The film based on chitosan-sulfisoxazol (CS-S6) showed the highest swelling ratio (197%) and the highest biodegradation rate (63.04%) in comparison to chitosan film for which the swelling ratio was 190% and biodegradation rate was only 10%. Referring to the antioxidant effects the most active was chitosan-sulfamerazine (CS-S5) which was 8.3 times more active than chitosan related to DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging ability. This compound showed also a good ferric reducing power and improved total antioxidant capacity.
Dendritic Cells Pulsed with Live and Dead Legionella pneumophila Elicit Distinct Immune Responses1

Legionella pneumophila is the causative pathogen of Legionnaires’ disease, which is characterized by severe pneumonia. In regard to the pathophysiology of Legionella infection, the role of inflammatory phagocytes such as macrophages has been well documented, but the involvement of dendritic cells (DCs) has not been clarified. In this study, we have investigated the immune responses that DCs generate in vitro and in vivo after contact with L. pneumophila. Heat- and formalin-killed L. pneumophila, but not live L. pneumophila, induced immature DCs to undergo similar phenotypic maturation, but the secreted proinflammatory cytokines showed different patterns. The mechanisms of the DC maturation by heat- or formalin-killed L. pneumophila depended, at least in part, on Toll-like receptor 4 signaling or on Legionella LPS, respectively. After transfer to naive mice, DCs pulsed with dead Legionella produced serum Ig isotype responses specific for Legionella, leading to protective immunity against an otherwise lethal respiratory challenge with L. pneumophila. The in vivo immune responses required the Ag presentation of DCs, especially that on MHC class II molecules, and the immunity yielded cross-protection between clinical and environmental strains of L. pneumophila. Although the DC maturation was impaired by live Legionella, macrophages were activated by live as well as dead L. pneumophila, as evidenced by the up-regulation of MHC class II. Finally, DCs, but not macrophages, exhibited a proliferative response to live L. pneumophila that was consistent with their cell cycle progression. These findings provide a better understanding of the role of DCs in adaptive immunity to Legionella infection.
A new supervisory fault tolerant output regulation scheme for nonlinear systems

The fault tolerant output regulation problem for a class of nonlinear systems are considered from hybrid system point of view. The faults are generated by the exogenous systems that belong to a certain pre-specified set of models. The novelty is to design the fault tolerant control (FTC) scheme for the overall system process where different faults may occur respectively at different time instants of the process, which is called “the successional faulty case”. The proposed FTC framework only relies on a simple supervisory switching among a family of pre-computed candidate controllers without any additional model/filter or adaptive scheme. A DC motor example illustrates the efficiency of the proposed method.
Functionalised silica nanoparticles stable in serum-containing medium efficiently deliver siRNA targeting HIV-1 co-receptor CXCR4 in mammalian cells

The development of non-viral DNA delivery systems using nanomaterials has attracted much research interest for its potential in biomedicine. However, for these new nanocarriers to be successfully used in therapeutic applications they have to overcome many barriers. Here, we report the development and characterisation of polyethyleneimine-modified tetramethylrhodamine-doped silica nanoparticles as a vehicle to deliver siRNA in the presence of serum. We have demonstrated that polyethyleneiminemodified tetramethylrhodamine-doped silica nanoparticles bind and protect siRNA against nuclease degradation and facilitate cellular uptake and intracellular delivery of the siRNA in HeLa-derived TZM-bl cells. The nanoparticles can penetrate TMZ-bl cells at concentrations as low as 1 μg/mL and can escape the lysosomal and endosomal cavities. Following delivery, the nanoparticles release active siRNA targeting the co-receptor CXCR4 for HIV-1 to achieve reduction in the targeted mRNA and protein expression. These nanoparticles are also non-toxic for the cells and are capable of carrying out all of these functions in the presence of serum, a characteristic that is critical if such nanoparticles are to be employed in any type of in vivo application.
ADP ribosylation factor 6 is activated and controls membrane delivery during phagocytosis in macrophages

Engulfment of particles by phagocytes is induced by their interaction with specific receptors on the cell surface, which leads to actin polymerization and the extension of membrane protrusions to form a closed phagosome. Membrane delivery from internal pools is considered to play an important role in pseudopod extension during phagocytosis. Here, we report that endogenous ADP ribosylation factor 6 (ARF6), a small GTP-binding protein, undergoes a sharp and transient activation in macrophages when phagocytosis was initiated via receptors for the Fc portion of immunoglobulins (FcRs). A dominant-negative mutant of ARF6 (T27N mutation) dramatically affected FcR-mediated phagocytosis. Expression of ARF6-T27N lead to a reduction in the focal delivery of vesicle-associated membrane protein 3+ endosomal recycling membranes at phagocytosis sites, whereas actin polymerization was unimpaired. This resulted in an early blockade in pseudopod extension and accumulation of intracellular vesicles, as observed by electron microscopy. We conclude that ARF6 is a major regulator of membrane recycling during phagocytosis.
EMPIRICAL STUDY Concurrent Statistical Learning of Adjacent and Nonadjacent Dependencies

When children learn their native language, they have to deal with a confusing array of dependencies between various elements in an utterance. The dependent elements may be adjacent to one another or separated by intervening material. Prior studies suggest that nonadjacent dependencies are hard to learn when the intervening material has little variability, which may be due to a trade-off between adjacent and nonadjacent learning. In this study, we investigate the statistical learning of adjacent and nonadjacent dependencies under low intervening variability using a modified serial reaction time (SRT) task. Young adults were trained on mixed sets of materials comprising equally probable adjacent and nonadjacent dependencies. Offline tests administered after training showed better performance for adjacent than nonadjacent dependencies. However, online SRT data indicated that the participants developed sensitivity to both types of dependencies during training, with no significant differences between dependency types. The results demonstrate the value of online measures of learning and suggest that adjacent and nonadjacentlearningcanoccurtogetherevenwhenthereislowvariabilityintheintervening material.
A Fistful of Bitcoins Characterizing Payments Among Men with No Names

Damon McCoy is an assistant professor in the CS department at George Mason University. He obtained his PhD from the University of Colorado, Boulder, and his research includes work on anonymous communication systems, cyber-physical security, e-crime, and wireless privacy. damon.mccoy@gmail.com Geoffrey M. Voelker is a Professor of Computer Science at the University of California, San Diego. He works in computer systems, networking, and security. voelker@cs.ucsd. edu
Body schema acquisition through active learning

We present an active learning algorithm for the problem of body schema learning, i.e. estimating a kinematic model of a serial robot. The learning process is done online using Recursive Least Squares (RLS) estimation, which outperforms gradient methods usually applied in the literature. In addiction, the method provides the required information to apply an active learning algorithm to find the optimal set of robot configurations and observations to improve the learning process. By selecting the most informative observations, the proposed method minimizes the required amount of data. We have developed an efficient version of the active learning algorithm to select the points in real-time. The algorithms have been tested and compared using both simulated environments and a real humanoid robot.
High-performance focal plane array based on type-II InAs/GaSb superlattice heterostructures

Recent progress in growth techniques, structure design and processing has lifted the performances of Type-II InAs/GaSb superlattice photodetectors. A double heterostructure design, based on a low band gap (11 μm) active region and high band gap (5 μm) superlattice contacts, reduced the sensitivity of the superlattice to surface effects. The heterodiodes with an 11 µm cutoff, passivated with SiO2, presented similar performances to unpassivated devices and a one order of magnitude increase of the resistivity of the sidewalls, even after flip-chip bonding and underfill. Thanks to this new design and to the inversion of the polarity of the devices, a high performance focal plane array with an 11 μm cutoff was demonstrated. The noise equivalent temperature difference was measured as 26 mK and 19 mK for operating temperatures of 81 K and 67 K. At an integration time of 0.08 ms, the FPA presented a quantum efficiency superior to 50%.
Relational algorithms for multi-bulk-synchronous processors

Relational databases remain an important application infrastructure for organizing and analyzing massive volumes of data. At the same time, processor architectures are increasingly gravitating towards Multi-Bulk-Synchronous processor (Multi-BSP) architectures employing throughput-optimized memory systems, lightweight multi-threading, and Single-Instruction Multiple-Data (SIMD) core organizations. This paper explores the mapping of primitive relational algebra operations onto such architectures to improve the throughput of data warehousing applications built on relational databases.
A novel variable tap-length learning algorithm for low complexity, fast converging stereophonic acoustic echo cancellation

An advanced low complexity, fast converging variable tap-length VT learning algorithm for stereophonic acoustic echo cancellation SAEC based on multiple sub-filters MSF approach is designed and analysed in this paper. The proposed algorithm retains advantage of both VT different error algorithm DEA and common error algorithm CEA. A systematic procedure is presented to set key variables that affect the structure adaptation to provide the best performance when compared to the existing stereophonic echo cancellers. The convergence performance of the MSF-based parallel structure is studied, for the designed dynamic structure and improvements are addressed over the VT-single long filter, VT-CEA, VT-DEA. A VT-selective coefficient update method to reduce the computational cost of adaptive design is discussed in context with the proposed design. It leads to the closest possible performance to the full update algorithm. Simulated results are shown to make a comparison of the proposed design with existing SAEC algorithms.
Mining Associations in Text in the Presence of Background Knowledge

This paper describes the FACT system for knowledge discovery from text. It discovers associations - patterns of co-occurrence -amongst keywords labeling the items in a collection of textual documents. In addition, FACT is able to use background knowledge about the keywords labeling the documents in its discovery process. FACT takes a query-centered view of knowledge discovery, in which a discovery request is viewed as a query over the implicit set of possible results supported by a collection of documents, and where background knowledge is used to specify constraints on the desired results of this query process. Execution of a knowledge-discovery query is structured so that these background-knowledge constraints can be exploited in the search for possible results. Finally, rather than requiring a user to specify an explicit query expression in the knowledge-discovery query language, FACT presents the user with a simple-to-use graphical interface to the query language, with the language providing a well-defined semantics for the discovery actions performed by a user through the interface.
Silencing the HaAK Gene by Transgenic Plant-Mediated RNAi Impairs Larval Growth of Helicoverpa armigera

Insect pests have caused noticeable economic losses in agriculture, and the heavy use of insecticide to control pests not only brings the threats of insecticide resistance but also causes the great pollution to foods and the environment. Transgenic plants producing double-stranded RNA (dsRNA) directed against insect genes have been is currently developed for protection against insect pests. In this study, we used this technology to silence the arginine kinase (AK) gene of Helicoverpa armigera (HaAK), encoding a phosphotransferase that plays a critical role in cellular energy metabolism in invertebrate. Transgenic Arabidopsis plants producing HaAK dsRNA were generated by Agrobacterium-mediated transformation. The maximal mortality rate of 55% was reached when H. armigera first-instar larvae were fed with transgenic plant leaves for 3 days, which was dramatically higher than the 18% mortality recorded in the control group. Moreover, the ingestion of transgenic plants significantly retarded larval growth, and the transcript levels of HaAK were also knocked down by up to 52%. The feeding bioassays further indicated that the inhibition efficiency was correlated with the integrity and concentration of the produced HaAK dsRNA in transgenic plants. These results strongly show that the resistance to H. armigera was improved in transgenic Arabidopsis plants, suggesting that the RNAi targeting of AK has the potential for the control of insect pests.
Optimizing the idle task and other MMU tricks

In highly cached and pipelined machines, operating system performance, and aggregate user/system performance, is enormously sensitive to small changes in cache and TLB hit rates. We have implemented a variety of changes in the memory management of a native port of the Linux operating system to the PowerPC architecture in an effort to improve performance. Our results show that careful design to minimize the OS caching footprint, to shorten critical code paths in page fault handling, and to otherwise take full advantage of the memory management hardware can have dramatic effects on performance. Our results also show that the operating system can intelligently manage MMU resources as well or better than hardware can and suggest that complex hardware MMU assistance may not be the most appropriate use of scarce chip area. Comparative benchmarks show that our optimizations result in kernel performance that is significantly better than other monolithic kernels for the same architecture and highlight the distance that micro-kernel designs will have to travel to approach the performance of a reasonably efficient monolithic kernel.
Outage Performance of Opportunistic Cooperation in Amplify-and-Forward Relaying Systems with Relay Selection

Opportunistic cooperation (OC) dynamically switches between a cooperative mode (CM, using direct and relayed links) and a non-cooperative mode (NM, using only the direct link). In this letter, we consider OC in amplify-and-forward (AF) relaying systems where a best relay is selected as an active relay if CM is selected. The OC is shown to have the same full diversity order as the CM. In terms of asymptotic outage probability, we show that the power gain (sometimes also referred to coding gain) achieved from using the OC compared to the CM is -10/(K+1) log10 (1-((2R)/(2R +1))K+1) dB where R is the data rate used for outage threshold. The result says that the power gain is always positive (in dB) and it increases when the data rate increases or the number of relays decreases. Numerical results are provided to verify the analysis and to give insights on the outage performance of the OC.