Miracle-dz/UniFAR-FTUs huggingface dataset:
GriPhyN-2002-20 Pegasus : Planning for Execution in Grids

1 Motivation Grid computing has made great progress in the last few years. The basic mechanisms for accessing remote resources have been developed as part of the Globus Toolkit and are now widely deployed and used. Among such mechanisms are: § Information services, which allow for the discovery and monitoring of resources. The information provided can be used to find the available resources and select the resources which are the most appropriate for the task. § Security services, which allow users and resources to mutually authenticate and allows the resources to authorize users based on local policies. § Resource management, which allows for the scheduling of jobs on particular resources. § Data management services, which enable users and applications to manage large, distributed and replicated data sets. Some of the available services deal with locating particular data sets, others with efficiently moving large amounts of data across wide area networks. With the use of the above mechanisms, one can manually find out about the resources and schedule the desired computations and data movements. However, this process is time consuming and can potentially be complex. As the result it is becoming increasingly necessary to develop higher level services which can automate the process and provide an adequate level of performance and reliability.
Simulation and Research for Forward Neural Networks Modeling

This paper presents analysis and experiments for Forward Neural Networks (FNN) modeling based on software simulation. First, we illustrate this modeling method in detail. Then the algorithm flow charts of four learning algorithms, including Back Propagation (BP), Modified BP (MBP), Davidon Least Square based algorithm and Damping Least Square based algorithm are given. In addition, a simulation software for training and testing FNN is developed using these algorithms. In the last, we compare and analyze the performance of these four algorithms based on simulation experimental results.
A Virtual Environment for the Treatment of Chronic Combat-Related Post-Traumatic Stress Disorder

Post-traumatic stress disorder (PTSD) is one of the most disabling psychopathological conditions affecting the veteran population. An estimated 830,000 U.S. veterans currently have symptoms of chronic combat-related PTSD. No therapeutic approach has proven to be consistently effective in the management of combat-related PTSD. Behavior therapies with an exposure element have proven more effective than most other types of treatment, but a significant number of patients do not seem to benefit from them, possibly because of difficulties imagining, visualizing, or describing their traumatic experiences. In this article, we describe Virtual Vietnam, a set of two virtual environments we have developed for the treatment of combat-related PTSD, and its use as one component of a comprehensive treatment program.
Integrating Visual and Textual Cues for Query-by-String Word Spotting

In this paper, we present a word spotting framework that follows the query-by-string paradigm where word images are represented both by textual and visual representations. The textual representation is formulated in terms of character n-grams while the visual one is based on the bag-of-visual-words scheme. These two representations are merged together and projected to a sub-vector space. This transform allows to, given a textual query, retrieve word instances that were only represented by the visual modality. Moreover, this statistical representation can be used together with state-of-the-art indexation structures in order to deal with large-scale scenarios. The proposed method is evaluated using a collection of historical documents outperforming state-of-the-art performances.
Expression of Pseudomonas aeruginosa nitrite reductase in Pseudomonas putida and characterization of the recombinant protein.

Nitrite reductase from Pseudomonas aeruginosa has been successfully expressed in Pseudomonas putida. The purified recombinant enzyme contains haem c but no haem d1. Nonetheless, like the holoenzyme from Ps. aeruginosa, it is a stable dimer (molecular mass 120 kDa), and electron transfer to oxidized azurin is biphasic and follows bimolecular kinetics (k1 = 1.5 x 10(5) and k2 = 2.2 x 10(4) M-1.s-1). Unlike the chemically produced apoenzyme, recombinant nitrite reductase containing only haem c is water-soluble, stable at neutral pH and can be quantitatively reconstituted with haem d1, yielding a holoenzyme with the same properties as that expressed by Ps. aeruginosa (namely optical and c.d. spectra, molecular mass, cytochrome c551 oxidase activity and CO-binding kinetics).
Sleep, depression and anxiety: an epidemiological perspective

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Effects of Sleep on Memory Consolidation and Automaticity in Word Learning

Compared to sleep studies on memory consolidation, there have been limited studies investigating effects of sleep on memory integration. Memory integration occurs when long-term associations between new and existing items are formed, leading to generalization of item knowledge across new contexts. Using semantic distance and size congruity effects as measures of automatic semantic access in integrated word representations, this thesis aimed to investigate the effects of sleep on declarative knowledge integration. By examining relationships between behavioural data and sleep architecture, this thesis also aimed to investigate if sleep plays an active role in knowledge integration. Experiment 1 revealed that participants who slept after learning exhibited significantly stronger semantic distance and size congruity effects for new second language words compared to participants who remained awake. Analysis of sleep polysomnography data also revealed that the strength of semantic distance and congruity effects were positively correlated with slow-wave sleep and sleep spindles respectively. Experiments 2 and 3 examined if selective factors such as training performance and encoding strength would modulate effects of sleep-dependent memory integration. Experiment 2 found that nap-associated gains in automaticity were stronger in participants who performed poorly during training. Experiment 3 also revealed that daytime-napping selectively benefitted integration of items that were more difficult to process. Experiment 4 explored the time-course required for automatic semantic access to emerge. Results highlighted that semantic distance effects emerge rapidly, whereas, size congruity effects that were considered a purer measure of automaticity only emerged after overnight consolidation. Finally, Experiment 5 studied if the sleep-associated findings from Experiments 1-4 would be similar for numeral learning. Compared to word learning, integration of new numerals required a shorter time-course and lower levels of sleep dependence. The thesis findings were evaluated against models of memory consolidation to gain theoretical understanding on the neural changes relating to knowledge integration.
Experimental Verification of Interference Mitigation Techniques for 5G Small Cells

Inter-cell interference is the main performance limiting factor in the dense deployment of small cells targeted by the upcoming 5th Generation (5G) radio access technology. In this paper, we present an experimental evaluation of inter-cell interference mitigation techniques in a real indoor office deployment with four cells, where each cell features one Access Point (AP) and one User Equipment (UE). In particular, we compare traditional Frequency Reuse Planning (FRP) with the recently proposed Maximum Rank Planning (MRP) technique, which relies on the degrees of freedom offered by the multi-antenna transceivers for suppressing a number of interfering streams. Different receiver types are also considered, namely Interference Rejection Combining (IRC) and the interference unaware Maximum Ratio Combining (MRC). Each node in our software defined radio (SDR) testbed features a 2 x 2 MIMO transceiver built with the USRP N200 hardware by Ettus Research. The experimental results in a fully loaded network reveal the capability of the MRP technique to achieve higher throughput performance than FRP for 90% of the cases when IRC receivers are used. Lower network loads lead to further performance improvements for MRP.
Work and Rest Patterns and Psychomotor Vigilance Performance of Crewmemebers of the USS Jason Dunham: A Comparison of the 3/9 and 6/6 Watchstanding Schedules

Abstract : This study compares the patterns of crew rest and sleep, psychomotor vigilance performance, and work demands/rest opportunities afforded by two different schedules, the 3-hour on/9-hour off ( 3/9 ) and the 6-hour on/6-hour off ( 6/6 ) watchstanding schedules. The study was conducted aboard the USS Jason Dunham, a U.S. Navy destroyer operating in the vicinity of the Persian Gulf during the months of November and December 2012. Of the 122 participants in the overall study, 52 were shift workers using either the 3/9 (n=41) or the 6/6 (n=11) schedules. These 52 individuals are the focus of the current analysis. Although sleep deprivation was evident in both watch schedules, results show that crewmembers on the 3/9 received more sleep than their peers on the 6/6, with 6.46 0.77 hours versus 5.89 0.87 hours, respectively. The 3/9 schedule, compared to the 6/6, was also better in terms of the distribution of sleep episodes across the day. Specifically, crewmembers on the 3/9 received more sleep during nighttime hours, whereas crewmembers on the 6/6 had to sleep during the day to compensate for their lack of sleep during nighttime hours. In terms of work demands, crewmembers on the 6/6 schedule have considerably long workdays, with, on average, 15 hours on duty, which corresponds to approximately 30% more time on duty than allocated in the Navy Standard Work Week criterion (on average, 105 hours compared to 81 hours weekly). The two schedules differed significantly in the variability of psychomotor vigilance performance; specifically, crewmembers on the 6/6 schedule had larger variability than those on the 3/9 in 11 of the 13 Psychomotor Vigilance Task (PVT) metrics analyzed (p0.05). The average value of the PVT scores was better on the 3/9 compared to the 6/6, but not at statistically significant levels.
220D-F2 from Rubus ulmifolius Kills Streptococcus pneumoniae Planktonic Cells and Pneumococcal Biofilms

Streptococcus pneumoniae (pneumococcus) forms organized biofilms to persist in the human nasopharynx. This persistence allows the pneumococcus to produce severe diseases such as pneumonia, otitis media, bacteremia and meningitis that kill nearly a million children every year. While bacteremia and meningitis are mediated by planktonic pneumococci, biofilm structures are present during pneumonia and otitis media. The global emergence of S. pneumoniae strains resistant to most commonly prescribed antibiotics warrants further discovery of alternative therapeutics. The present study assessed the antimicrobial potential of a plant extract, 220D-F2, rich in ellagic acid, and ellagic acid derivatives, against S. pneumoniae planktonic cells and biofilm structures. Our studies first demonstrate that, when inoculated together with planktonic cultures, 220D-F2 inhibited the formation of pneumococcal biofilms in a dose-dependent manner. As measured by bacterial counts and a LIVE/DEAD bacterial viability assay, 100 and 200 µg/ml of 220D-F2 had significant bactericidal activity against pneumococcal planktonic cultures as early as 3 h post-inoculation. Quantitative MIC’s, whether quantified by qPCR or dilution and plating, showed that 80 µg/ml of 220D-F2 completely eradicated overnight cultures of planktonic pneumococci, including antibiotic resistant strains. When preformed pneumococcal biofilms were challenged with 220D-F2, it significantly reduced the population of biofilms 3 h post-inoculation. Minimum biofilm inhibitory concentration (MBIC)50 was obtained incubating biofilms with 100 µg/ml of 220D-F2 for 3 h and 6 h of incubation. 220D-F2 also significantly reduced the population of pneumococcal biofilms formed on human pharyngeal cells. Our results demonstrate potential therapeutic applications of 220D-F2 to both kill planktonic pneumococcal cells and disrupt pneumococcal biofilms.
Analysis of biomedical and health queries: Lessons learned from TREC and CLEF evaluation benchmarks

A large body of research work examined, from both the query side and the user behavior side, the characteristics of medical‐ and health‐related searches. One of the core issues in medical information retrieval (IR) is diversity of tasks that lead to diversity of categories of information needs and queries. From the evaluation perspective, another related and challenging issue is the limited availability of appropriate test collections allowing the experimental validation of medically task oriented IR techniques and systems. In this paper, we explore the peculiarities of TREC and CLEF medically oriented tasks and queries through the analysis of the differences and the similarities between queries across tasks, with respect to length, specificity, and clarity features and then study their effect on retrieval performance. We show that, even for expert oriented queries, language specificity level varies significantly across tasks as well as search difficulty. Additional findings highlight that query clarity factors are task dependent and that query terms specificity based on domain‐specific terminology resources is not significantly linked to term rareness in the document collection. The lessons learned from our study could serve as starting points for the design of future task‐based medical information retrieval frameworks.
INDO-1 Measurements of Absolute Resting and Light-Induced Ca2+ Concentration in DrosophilaPhotoreceptors

Absolute Ca2+ levels in dissociatedDrosophila photoreceptors were measured using the ratiometric indicator dye INDO-1 loaded via patch pipettes, which simultaneously recorded whole-cell currents. In wild-type photoreceptors, the ultraviolet (UV) excitation light used to measure fluorescence elicited a massive Ca2+ influx that saturated the dye (>10 μmCa2+), but lagged the electrical response by 2.8 msec. Resting Ca2+ levels in the dark, measured during the latent period before the response, averaged 160 nm in normal Ringer’s (1.5 mm Ca2+). Ca2+ increases in response to weak illumination were estimated (1) by using a weak adapting stimulus before the UV excitation light and measuring Ca2+ during the latent period; and (2) by using ninaE mutants with greatly reduced rhodopsin levels. Ca2+ rose linearly as a function of the time integral of the light-sensitive current with a slope of 2.7 nm/pC. In the transient receptor potential (trp) mutant, which lacks a putative light-sensitive channel subunit, the slope was only 1.1 nm/pC, indicating a 2.5-fold reduction in the fractional Ca2+ current. From these data, it can also be estimated that >99% of the Ca2+ influx is effectively buffered by the cell. In Ca2+-free Ringer’s, resting cytosolic Ca2+ was reduced (to 30–70 nm), but contrary to previous reports, significant light-induced increases (∼250 nm) could be elicited. This rise was reduced to <20 nm when extracellular Na+was replaced withN-methyl-d-glucamine, suggesting that it could be attributed to Na+ influx altering the Na/Ca exchanger equilibrium. It is concluded that any light-induced release from internal stores amounts to <20 nm.
SIRT1 regulates differentiation of mesenchymal stem cells by deacetylating β-catenin

Mesenchymal stem cells (MSCs) are multi‐potent cells that can differentiate into osteoblasts, adipocytes, chondrocytes and myocytes. This potential declines with aging. We investigated whether the sirtuin SIRT1 had a function in MSCs by creating MSC specific SIRT1 knock‐out (MSCKO) mice. Aged MSCKO mice (2.2 years old) showed defects in tissues derived from MSCs; i.e. a reduction in subcutaneous fat, cortical bone thickness and trabecular volume. Young mice showed related but less pronounced effects. MSCs isolated from MSCKO mice showed reduced differentiation towards osteoblasts and chondrocytes in vitro, but no difference in proliferation or apoptosis. Expression of β‐catenin targets important for differentiation was reduced in MSCKO cells. Moreover, while β‐catenin itself (T41A mutant resistant to cytosolic turnover) accumulated in the nuclei of wild‐type MSCs, it was unable to do so in MSCKO cells. However, mutating K49R or K345R in β‐catenin to mimic deacetylation restored nuclear localization and differentiation potential in MSCKO cells. We conclude that SIRT1 deacetylates β‐catenin to promote its accumulation in the nucleus leading to transcription of genes for MSC differentiation.
An Efficient Ciphertext-Policy Attribute-Based Access Control towards Revocation in Cloud Computing

Attribute-Based Encryption (ABE) is one of the new visions for fine- grained access control in cloud computing. Plenty of research work has been done in both academic and industrial communities. However, before ABE can be deployed in data outsourcing systems, efficient enforcement of authorization policies and policy updates are the main obstacles. Therefore, in order to solve this problem, efficient and secure attribute and user revocation should be proposed in original ABE scheme, which is still a challenge in existing work. In this paper, we propose a new ciphertext-policy ABE (CP-ABE) construction with efficient attribute and user revocation, which largely eliminates the overhead computation at data service manager and data owner. Besides, we present an efficient access control mechanism based on the CP-ABE construction with one outsourcing computation service provider.
Recovery of Avian Metapneumovirus Subgroup C from cDNA: Cross-Recognition of Avian and Human Metapneumovirus Support Proteins

ABSTRACT Avian metapneumovirus (AMPV) causes an acute respiratory disease in turkeys and is associated with “swollen head syndrome” in chickens, contributing to significant economic losses for the U.S. poultry industry. With a long-term goal of developing a better vaccine for controlling AMPV in the United States, we established a reverse genetics system to produce infectious AMPV of subgroup C entirely from cDNA. A cDNA clone encoding the entire 14,150-nucleotide genome of AMPV subgroup C strain Colorado (AMPV/CO) was generated by assembling five cDNA fragments between the T7 RNA polymerase promoter and the autocatalytic hepatitis delta virus ribozyme of a transcription plasmid, pBR 322. Transfection of this plasmid, along with the expression plasmids encoding the N, P, M2-1, and L proteins of AMPV/CO, into cells stably expressing T7 RNA polymerase resulted in the recovery of infectious AMPV/CO. Characterization of the recombinant AMPV/CO showed that its growth properties in tissue culture were similar to those of the parental virus. The potential of AMPV/CO to serve as a viral vector was also assessed by generating another recombinant virus, rAMPV/CO-GFP, that expressed the enhanced green fluorescent protein (GFP) as a foreign protein. Interestingly, GFP-expressing AMPV and GFP-expressing human metapneumovirus (HMPV) could be recovered using the support plasmids of either virus, denoting that the genome promoters are conserved between the two metapneumoviruses and can be cross-recognized by the polymerase complex proteins of either virus. These results indicate a close functional relationship between AMPV/CO and HMPV.
Functional characterisation of mycobacterial DNA gyrase: an efficient decatenase.

A rapid single step immunoaffinity purification procedure is described for Mycobacterium smegmatis DNA gyrase. The mycobacterial enzyme is a 340 kDa heterotetrameric protein comprising two subunits each of GyrA and GyrB, exhibiting subtle differences and similarities to the well-characterised Escherichia coli gyrase. In contrast to E.coli gyrase, the M.smegmatis enzyme exhibits strong decatenase activity at physiological Mg2+ concentrations. Further, the enzymes exhibited marked differences in ATPase activity, DNA binding characteristics and susceptibility to fluoroquinolones. The holoenzyme showed very low intrinsic ATPase activity and was stimulated 20-fold in the presence of DNA. The DNA-stimulated ATPase kinetics revealed apparent K0.5 and kcat of 0.68 mM and 0.39 s(-1), respectively. The dissociation constant for DNA was found to be 9.2 nM, which is 20 times weaker than that of E.coli DNA gyrase. The differences between the enzymes were further substantiated as they exhibited varied sensitivity to moxifloxacin and ciprofloxacin. In spite of these differences, mycobacterial DNA gyrase is a functionally and mechanistically conserved enzyme and the variations in activity seem to reflect functional optimisation for its physiological role during mycobacterial genome replication.
BodyGuards: A Clairvoyant Location Predictor Using Frequent Neighbors and Markov Model

The prediction of future locations is of enormous research interest, partly due to the fast growing number of users of pervasive devices, as well as the tons of spatiotemporal data generated by such devices. In this paper, we propose a novel enhanced Next Location prediction technique which utilizes a trajectory model called Time Mobility Context Correlation Pattern (TMC-Pattern) and sequence alignment to mine correlations between an object and its nearest neighbors. Hidden mobility patterns drawn from such correlations are utilized in the synthesis of weighted trees called TMC-Footprint trees. The weighted TMC-Footprint trees are used together with a Markov model to predict the next location of an object with an elevated accuracy of 14,3% when compared to a state-of-the-art work. Furthermore, prediction accuracy of existing next location predictors plummets rapidly if an object suddenly takes a new next location which is absent from its trajectory history. Our technique harnesses this problem using a novel notion of Surprise Path.
Institutional Knowledge at Singapore Management University The Determination of Natural Frequencies of Rectangular Plates with Mixed Boundary Conditions by Discrete Singular Convolution

This paper introduces the discrete singular convolution algorithm for vibration analysis of rectangular plates with mixed boundary conditions. A uni4ed scheme is proposed for the treatment of simply supported, clamped and transversely supported (with nonuniform elastic rotational restraint) boundary conditions. The robustness and reliability of the present approach are tested by a number of numerical experiments. All results agree well with those in the literature. 2001 Elsevier Science Ltd. All rights reserved.