Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Analysis of the Octopus vulgaris Central Nervous System

Background Cephalopoda are a class of Mollusca species found in all the world's oceans. They are an important model organism in neurobiology. Unfortunately, the lack of neuronal molecular sequences, such as ESTs, transcriptomic or genomic information, has limited the development of molecular neurobiology research in this unique model organism. Results With high-throughput Illumina Solexa sequencing technology, we have generated 59,859 high quality sequences from 12,918,391 paired-end reads. Using BLASTx/BLASTn, 12,227 contigs have blast hits in the Swissprot, NR protein database and NT nucleotide database with E-value cutoff 1e−5. The comparison between the Octopus vulgaris central nervous system (CNS) library and the Aplysia californica/Lymnaea stagnalis CNS ESTs library yielded 5.93%/13.45% of O. vulgaris sequences with significant matches (1e−5) using BLASTn/tBLASTx. Meanwhile the hit percentage of the recently published Schistocerca gregaria, Tilapia or Hirudo medicinalis CNS library to the O. vulgaris CNS library is 21.03%–46.19%. We constructed the Phylogenetic tree using two genes related to CNS function, Synaptotagmin-7 and Synaptophysin. Lastly, we demonstrated that O. vulgaris may have a vertebrate-like Blood-Brain Barrier based on bioinformatic analysis. Conclusion This study provides a mass of molecular information that will contribute to further molecular biology research on O. vulgaris. In our presentation of the first CNS transcriptome analysis of O. vulgaris, we hope to accelerate the study of functional molecular neurobiology and comparative evolutionary biology.
Tetrachloroethene Dehalogenase from Dehalospirillum multivorans: Cloning, Sequencing of the Encoding Genes, and Expression of the pceA Gene in Escherichia coli

ABSTRACT The genes encoding tetrachloroethene reductive dehalogenase, a corrinoid-Fe/S protein, of Dehalospirillum multivorans were cloned and sequenced. The pceA gene is upstream ofpceB and overlaps it by 4 bp. The presence of a ς70-like promoter sequence upstream of pceA and of a ρ-independent terminator downstream of pceB indicated that both genes are cotranscribed. This assumption is supported by reverse transcriptase PCR data. The pceA and pceB genes encode putative 501- and 74-amino-acid proteins, respectively, with calculated molecular masses of 55,887 and 8,354 Da, respectively. Four peptides obtained after trypsin treatment of tetrachloroethene (PCE) dehalogenase were found in the deduced amino acid sequence of pceA. The N-terminal amino acid sequence of the PCE dehalogenase isolated from D. multivorans was found 30 amino acids downstream of the N terminus of the deduced pceA product. The pceAgene contained a nucleotide stretch highly similar to binding motifs for two Fe4S4 clusters or for one Fe4S4 cluster and one Fe3S4 cluster. A consensus sequence for the binding of a corrinoid was not found in pceA. No significant similarities to genes in the databases were detected in sequence comparisons. The pceB gene contained two membrane-spanning helices as indicated by two hydrophobic stretches in the hydropathic plot. Sequence comparisons of pceBrevealed no sequence similarities to genes present in the databases. Only in the presence of pUBS 520 supplying the recombinant bacteria with high levels of the rare Escherichia colitRNA4Arg was pceA expressed, albeit nonfunctionally, in recombinant E. coli BL21 (DE3).
Adding Temporal Dimension to Ontologies via OWL Reification

It has been pointed out recently by many researchers that it is difficult for languages such as OWL to incorporate time in their relations. As a result it is difficult to reason about the temporal ordering of events or about the temporal properties of relations that vary as a function of time. There are a number of methods that have been proposed in order to circumvent this difficulty. One technique that can be used for this purpose is reification. The advantage of this approach is that it does not require the introduction of additional constructs to the OWL language. In this work we investigate the types of queries that are possible with this mechanism and we conclude that is in fact possible to express many interesting and useful queries. Moreover, due to the use of standard OWL, existing reasoning tools are capable of handling these queries.
Discovering the Evolutionary Patterns in Local Topology of an E-Mail Social Network

We present a new approach to the quantifying changes in an email social network illustrated by the data from the Enron dataset). The Triad Transition Matrix containing the probabilities of transitions between triads is defined, then we show how it can help to discover the dynamic patterns of network evolution. The compatibility of the TTM approach with the existing methods of characterizing the local topology (network motifs) is discussed as well.
Model-based telerobotics with vision

We describe an implemented model-based telerobotic system designed to investigate assembly and other tasks involving contact and manipulation of known objects. Key features of our system include ease of maintaining a world model at the operator site and a task-centric operator interface. Our system incorporates gray-scale model-based vision to assist in building and maintaining the local model. The local model is used to provide a task-centric operator interface, emphasizing the natural and direct manipulation of objects, with the robot's presence indicated in a more abstract fashion. The operator interface is designed to work with widely available and inexpensive desktop computers with low DOF input devices (such as a mouse). We also describe experimental results to date, which include performing assembly-like tasks over the Internet.
Reaction Time to Onset and Termination of Lights and Sounds

An experiment was conducted which measured the RT of 40 adult Ss to the onset and termination of rapid rise and decay lights and sounds which had been equated for subjective intensity. Onset RT was faster than termination for both sense modes, and auditory RT was faster than visual for both onset and termination. The results are compared with previous intersensory and onset-termination RT research and with another auditory-visual difference in the judgment of duration.
Heuristics for the Minimum Linear Arrangement Problem

The linear arrangement minimization problem consists of finding a labeling or arrangement of the vertices of a graph that minimizes the sum of the absolute values of the differences between the labels of adjacent vertices. This is a well-known NP-hard problem that presents a challenge to solution methods based on heuristic optimization. Many linear arrangement reduction algorithms have recently been developed and applied to structural engineering, VLSI and software testing. We undertake the development of different heuristic procedures with the goal of uncovering the most effective designs to tackle this difficult but important problem. Specifically, we consider the adaptation of constructive, local search, GRASP and Path Relinking methods for the linear arrangement minimization. We perform computational experiments with previously reported instances to first study the effects of changes in critical search parameters and then to compare the efficiency of our proposal with previous solution procedures.
Tackling the remaining attainment gap between students with and without immigrant background: an investigation into the equivalence of SES constructs

In England, students with immigrant background exhibit lower educational attainment than those without immigrant background. Family socioeconomic status (SES) helps explain differences in educational attainment, but a gap remains that differs in size for students with different immigrant backgrounds. While the explanatory repertoire for the remaining gap is broad, it has been neglected to comprehensively investigate whether family SES constructs are equivalent across students with different immigrant backgrounds. Using data from the first wave of the Children of Immigrants Longitudinal Survey in Four European Countries (CILS4EU) for England (n = 4,315), the paper applies exploratory structural equation modelling (ESEM) to evaluate measurement invariance of family background constructs across students without and with immigrant background, specifically Pakistani/Bangladeshi immigrant background. Results suggest differences in the structure of family SES indicators across groups and in their association with educational attainment. Complementary variables are suggested to enhance family SES indicators. Findings are relevant to researchers investigating educational inequalities related to immigrant background.
A Density Turán Theorem

Let F be a graph that contains an edge whose deletion reduces its chromatic number. For such a graph F, a classical result of Simonovits from 1966 shows that every graph on n>n0(F) vertices with more than χ(F)−2χ(F)−1·n22 edges contains a copy of F. In this article we derive a similar theorem for multipartite graphs. For a graph H and an integer ℓ≥v(H) , let dℓ(H) be the minimum real number such that every ℓ‐partite graph whose edge density between any two parts is greater than dℓ(H) contains a copy of H. Our main contribution in this article is to show that dℓ(H)=χ(H)−2χ(H)−1 for all ℓ≥ℓ0(H) sufficiently large if and only if H admits a vertex‐coloring with χ(H)−1 colors such that all color classes but one are independent sets, and the exceptional class induces just a matching. When H is a complete graph, this recovers a result of Pfender (Combinatorica 32 (2012), 483–495). We also consider several extensions of Pfender's result.
Behaviour of NMDA and AMPA receptor‐mediated miniature EPSCs at rat cortical neuron synapses identified by calcium imaging

1 Simultaneous recording of intracellular calcium concentration at a synapse and synaptic currents from the cell body allows mapping of miniature excitatory postsynaptic currents (mEPSCs) to single synapses. 2 In the absence of extracellular Mg2+, 77% of synapses had mEPSCs with fast and slow components, attributed to AMPA‐ and NMDA‐type glutamate receptors, respectively. The remainder of synapses (23%) had mEPSCs that lacked a fast component; these responses were attributed to NMDA receptors. 3 A strong positive correlation between the amplitude of the calcium transient and the NMDA receptor‐mediated mEPSC was observed, indicating that the mEPSCs originate from an identified synapse. 4 At synapses that had both mEPSC components, the AMPA receptor component was positively correlated with charge influx mediated by NMDA receptors during repeated synaptic events. No periodic failure in the AMPA receptor mEPSC was observed at synapses expressing both receptor components. 5 A significant positive correlation between the mean amplitudes of NMDA and AMPA receptor components of mEPSCs is observed across different synapses. 6 We suggest that factors effecting both receptor classes, such as the amount of transmitter in synaptic vesicles, might contribute to the variation in mEPSC amplitude during repeated miniature events at a single synapse. Although the average postsynaptic response at different synapses can vary in amplitude, there appears to be a mechanism to keep the ratio of each receptor subtype within a narrow range.
Phase III results of Boceprevir in treatment naïve patients with chronic hepatitis C genotype 1

Chronic hepatitis C virus infection affects approximately 2% of the world population and can result in cirrhosis and hepatocellular carcinoma. Until 2011, the standard of care (SOC) has been therapy with pegylated interferon alfa and ribavirin (PEG‐IFN/RBV). Sustained virologic response rates (SVR) after SOC in patients infected with genotype 1 have been 40–50%. The development of new direct antiviral agents (DAA) is vital. The first drugs that specifically target the HCV protease have been approved in 2011. This review summarizes the results of SPRINT‐2, a phase III double blind, placebo controlled study in which the efficacy and safety of Boceprevir, a new HCV protease inhibitor, was compared to SOC.
Stress among general practitioners and their spouses: a qualitative study.

BACKGROUND Although research has been carried out on stress in general practitioners, little is known about the stresses experienced by their spouses. AIM This study was undertaken to identify specific pressures at work and at home experienced by general practitioners and their spouses and to highlight their coping strategies. METHOD In-depth interviews were conducted with 25 general practitioners and their spouses in the north-west of England. RESULTS The doctors' increased workload and decreased interest in their family are important stressors for the entire family unit. Other stressors include time pressure, out-of-hours on-call, lack of support and amount of paperwork. General practitioners work late in the surgery, bring work home and spend time away from home at meetings. Family life is constantly interrupted by telephone calls. Role conflict was one of the major sources of stress for women general practitioners. Doctors' wives expressed concern regarding their husbands' excessive commitment to work and problems with communication. CONCLUSION Recent changes to contractual working conditions have caused general practitioners to focus their energies on their practice instead of paying attention to the needs of their family. Male general practitioners leave the bulk of responsibility for running the family and household to their wives, but women general practitioners appear to maintain domestic responsibility while spending as much time in medical practice as their male colleagues. This is only an exploratory study based on a small sample, and so the findings cannot be generalized; however, it provides in-depth information on stress among general practitioners and their spouses.
Calculation of Magnetic Field in the Reactor of RF Magnetized Plasma

In this paper, we present an analytical method for calculating the axial and radial components of the magnetic field created by a permanent magnet in the form of a ring used in a magnetron radio frequency (RF) reactor. The calculation is based on the symmetric integral of the first kind; it was performed under a Linux 64-bit operating system. This analytical method allows us to accurately assess the magnetic field, and it allows us to reduce the computational time. Finally, in order to validate the results, they are successfully compared with the results obtained by a numerical method based on finite-difference method.
Path planning for a mobile robot using fuzzy logic controller tuned by GA

This paper presents a fuzzy logic controller tuned by genetic algorithm (GA) for path planning near the optimal time to avoid obstacles in unknown environments. A GA is applied to modify the input and output membership functions of the fuzzy controller. A Matlab application, Kiks II, is used to simulate a Khepera II robot. Also, this approach is implemented by Khepera II robot. It is also shown that the proposed method outperforms the FLC approach.
Foundations of Dominant Strategy Mechanisms

Wilson (1987) criticizes the existing literature of game theory as relying too much on common-knowledge assumptions. In reaction to Wilson's critique, the recent literature of mechanism design has started to employ stronger solution concepts such as dominant strategy incentive compatibility, and restrict attention to simpler mechanisms such as dominant strategy mechanisms. However, there has been little theory behind this approach. In particular, it has not been made clear why employing simpler mechanisms, instead of more complicated ones, is the correct way to address Wilson's critique. This paper aims at filling this void. We propose a potential theory, known as the {\it maxmin} theory, which postulates that a {\it cautious} mechanism designer, facing uncertainty over which (common-knowledge) assumptions are valid and which are not, would indeed rationally choose simpler mechanisms such as dominant strategy mechanisms. In this paper, we summarize our progress in proving this theory, explore other possible theories, and discuss related theoretical questions that will be of interest in other areas
A web platform for the evaluation of vernacular place names in automatically constructed gazetteers

Vernacular place names pose a research challenge in geographic information retrieval. There is a long standing demand from investigators for a reference collection to train their methods and evaluate their models and data. However no large collection of informal place names associated with type and footprint data is currently available to the GIR community. The present contribution discusses the implementation of a web platform to collect such an evaluation data set. Design considerations of the user interface are addressed and we present first results of a nationwide attempt to collect the vernacular place names of Great Britain. Our result will aid further research in automatic gazetteer construction, considering vernacular place names.
Quality of Consumption: The Friendlier Side of Quality of Service

Cloud services today are increasingly built using functionality from other running services. In this paper, we question whether legacy Quality of Services (QoS) metrics and enforcement techniques are sufficient as they are producer centric. We argue that, similar to customer rating systems found in banking systems and many sharing economy apps (e.g., Uber and Airbnb), Quality of Consumption (QoC) should be introduced to capture different metrics about service consumers. We show how the combination of QoS and QoC, dubbed QoX, can be used by consumers and providers to improve the security and management of their infrastructure. In addition, we demonstrate how sharing information among other consumers and providers increase the value of QoX. To address the main challenge with sharing information, namely sybil attacks and mis-information, we describe how we can leverage cloud providers as vouching authorities to ensure the integrity of information. We present initial results in prototyping the appropriate abstractions and interfaces in a cloud environment, focusing on the design impact on both service providers and consumers.
On-line continuous-time music mood regression with deep recurrent neural networks

This paper proposes a novel machine learning approach for the task of on-line continuous-time music mood regression, i.e., low-latency prediction of the time-varying arousal and valence in musical pieces. On the front-end, a large set of segmental acoustic features is extracted to model short-term variations. Then, multi-variate regression is performed by deep recurrent neural networks to model longer-range context and capture the time-varying emotional profile of musical pieces appropriately. Evaluation is done on the 2013 MediaEval Challenge corpus consisting of 1000 pieces annotated in continous time and continuous arousal and valence by crowd-sourcing. In the result, recurrent neural networks outperform SVR and feedforward neural networks both in continuous-time and static music mood regression, and achieve an R2 of up to . 70 and . 50 with arousal and valence annotations.
Prevalence and Predictors of Cyberbullying Perpetration by High School Seniors

Cyberbullying is the deliberate and repeated misuse of communication technology by an individual or group to threaten or harm others. Guided largely by the communication skills deficiency model and previous research on cyberbullying, this study examins the effects of several predictor variables (i.e., verbal aggression, sex, risky behaviors, parental monitoring, parental limits, technology use, and scope of Internet activities) on cyberbullying perpetration. A total of 1,606 incoming freshmen at a large southwestern university completed an online survey measuring all predictor and dependent variables under investigation. Overall, 35% of these individuals reported that they had cyberbullied at least one person during their senior year of high school. Results indicated that verbal aggression, risky behaviors, and cyberbullying victimization emerged as significant predictors of cyberbullying perpetration. These results have important theoretical and practical implications for those interested in developing cyberbullying prevention interventions.
Electron-beam lithographed metamaterial devices operating in the terahertz region

Direct electron-beam lithography (EBL) was exploited to fabricate metamaterial devices operating in the terahertz (THz) region. Simulation show that, in order to reach the required frequency range, optimized metallic structures deposited on silicon must have submicron features. The effect of an external parameter, such as the substrate doping, is also studied.
Surface and edge information for spatial integration : A saccadic-selection search task

Three experiments are described that investigate visual integration across space using a saccade selection paradigm. Subjects saccaded to a vertical target in the presence of a number of horizontal distractor items. Both horizontal and vertical items were composed of two identical elements, so, in order to locate the target, subjects had to integrate the pairs of elements together. We measured saccade accuracy, the proportion of saccades directed to the vertical target, together with saccade latency following display appearance. In Experiment 1 we found that saccade accuracy was improved by the items having either common surface properties or collinear edges. These effects were not a resultof increased display heterogeneity (Experiment 2), or a result of the introduction of a strong internal contour between the items (Experiment 3). These results show that for saccadic selection both surface and edge properties of items are processed. This in turn suggests thatearly visual processing encodes and exploits .
Determinants of macular thickness using spectral domain optical coherence tomography in healthy eyes: the Singapore Chinese Eye study.

PURPOSE We determined ocular and systemic factors influencing macular thickness measured by spectral-domain optical coherence tomography (SD-OCT) in a population-based sample of healthy eyes. METHODS We recruited 490 healthy Chinese adults, aged 40 to 80 years, from the Singapore Chinese Eye Study, a population-based survey. All participants underwent a comprehensive eye examination and a standardized interview. The SD-OCT (Cirrus HD-OCT, software version 6.0) was used to measure a range of macular thickness parameters (central foveal subfield thickness, average inner macular thickness, average outer macular thickness, overall average macular thickness, and overall macular cube volume). Linear regression analyses were performed to examine the effects of various ocular and systemic factors on macular thickness. RESULTS The mean (standard deviation) age of the subjects was 53.17 (6.14) years and 50.0% of them were male. The mean central foveal subfield, average inner, and average outer macular thicknesses were 250.38 (20.58), 319.33 (14.40), and 276.67 (11.94) μm, respectively. The overall average macular thickness was 280.25 (11.42) μm and overall macular cube volume was 10.09 (0.41) mm(3). Sex, age, and axial length (AL) are the factors that influenced macular thicknesses. Thinner overall average macular thickness was associated with female sex (4.46 μm thinner compared to males, P < 0.001), older age (0.38 μm decrease per each year increase in age, P < 0.001), and longer AL (2.34-μm decrease per each mm increase in AL, P < 0.001), whereas thinner central foveal subfield thickness was associated with female sex (13.5 μm thinner compared to males, P < 0.001) and shorter AL (3.33-μm decrease per each mm increase in AL, P < 0.001). CONCLUSIONS Female sex, older age, and longer AL were associated independently with thinner overall average macular thickness, whereas female sex and shorter AL were associated with thinner central foveal thickness in ethnic Chinese. These factors should be taken into consideration when interpreting macular thickness measurements with SD-OCT.