Miracle-dz/UniFAR-FTUs huggingface dataset:
DrugBank: a knowledgebase for drugs, drug actions and drug targets

DrugBank is a richly annotated resource that combines detailed drug data with comprehensive drug target and drug action information. Since its first release in 2006, DrugBank has been widely used to facilitate in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. The latest version of DrugBank (release 2.0) has been expanded significantly over the previous release. With ∼4900 drug entries, it now contains 60% more FDA-approved small molecule and biotech drugs including 10% more ‘experimental’ drugs. Significantly, more protein target data has also been added to the database, with the latest version of DrugBank containing three times as many non-redundant protein or drug target sequences as before (1565 versus 524). Each DrugCard entry now contains more than 100 data fields with half of the information being devoted to drug/chemical data and the other half devoted to pharmacological, pharmacogenomic and molecular biological data. A number of new data fields, including food–drug interactions, drug–drug interactions and experimental ADME data have been added in response to numerous user requests. DrugBank has also significantly improved the power and simplicity of its structure query and text query searches. DrugBank is available at http://www.drugbank. ca
Tip-of-the-Tongue Experiences Are Not Merely

Often when one answers a question, one feels or has a sense that one knows the answer, but it is not forthcoming. Examples of such instances are feeling-of-knowing (FOK) and tip-of-the-tongue (TOT) experiences. It is often assumed that TOT experiences are merely strong FOK experiences. In the present study, the authors examined this hypothesis. They observed that participants with deficient prefrontal cortex (PFC) functioning reported fewer and less accurate FOKs than did participants with intact PFC functioning (Experiment 1). In contrast, the authors observed no contribution of PFC functioning in the reporting of TOT experiences (Experiment 2). That is, the level of PFC functioning did not have an impact on the frequency or accuracy of TOT reports. These data support the assertion that TOTs are not merely strong FOKs but that the two experiences are qualitatively different phenomena.
An Analysis of Teacher Nominations and Student Performance in Gifted Programs

This study evaluated the relationship of teacher nomination instruments to later performance of students in a gifted program. Teacher nominations were based on two instruments, an instrument designed specifically to assess gifted behaviors of students from culturally divergent and/or low income populations and an instrument designed to assess gifted behaviors in the general population. Separate canonical correlation analyses between these two instruments and a gifted teacher rating of student performance resulted in significant findings indicating relationships between the teacher nominations and later school performance. Structure correlations showed nominations based on thinking abilities, general gifted behaviors, and special learning skills were related to later performance on creativity, group skills, and language abilities.
Application of word-level confidence measures in interactive statistical machine translation

In this paper, we will address the question of how to efficiently integrate word confidence measures into a state-of-the-art interactive statistical machine translation system and improve prediction performance. Different methods will be presented: the selection of words according to their confidence as well as the rejection which has not been investigated so far. Experimental evaluation with respect to prediction accuracy of the system and typing effort saved by a user will show the improved prediction quality. Additionally, we will describe novel methods exploiting knowledge about a correct prefix of the target sentence for confidence estimation. These further increase the interactive system's performance.
The experiences of migrant social work and social care practitioners in the UK: findings from an online survey

Over recent years there has been a growing interest in the role of migrants in the social care sector in the United Kingdom (UK) and beyond. This article reports on the findings of an online survey of migrant social care workers in the UK, undertaken to complement a larger scale qualitative study on the subject. The survey aimed to test hypothesised relationships between migrant workers’ characteristics, circumstances, experiences and future plans. The survey ran from February to May 2009 and was advertised widely. A total of 101 responses were received (73% of those sent a survey link). A focus group was held with seven newly appointed migrant social workers to discuss issues arising from their experiences. Survey respondents were aged 39 years on average and were predominantly (75%) women. They came from a wide range of countries and job roles, although almost half (47%) were social workers. Most mentioned financial needs and opportunity, in addition to altruistic motivations. Challenges, including bullying and mistreatment in the sector, were highlighted. These and other findings are discussed in the context of increased demand for social care workers in the developed world, and specific barriers and challenges facing different groups of migrant social care workers.
Current Projects in Languages of Military Interest at the Defense Language Institute

Recent US military events have produced a desperate need for language data in languages which have previously been given very little attention. Data resources for languages of military interest are often unavailable or insufficient to adequately develop new technologies. Realizing this need, the Defense Language Institute Foreign Language Center, has created a language data distribution center, which focuses on collecting and distributing data in languages of military interest. This paper outlines current projects and resources available at the Defense Language Institute (DLI).
A 400-Gb/s and Low-Power Physical-Layer Architecture for Next-Generation Ethernet

A new 400-Gb/s (100-Gb/s×4) physical-layer architecture for the next-generation Ethernet-using 100-Gb/s serial (optical single wavelength) transmission-is proposed. For the next-generation 400-Gb/s Ethernet, there are additional requirements from the market, such as power reduction and further compactization in addition to attaining even higher transmission speed. To meet these requirements, a 100-Gb/s×4 physical-layer architecture is proposed. This architecture uses a 100-Gb/s serial (optical single wavelength) transmission Ethernet and low-power control technologies, which include transmission-capacity-degeneracy control for multi-lane transmission Ethernet. These technologies were implemented on a 100-Gb/s serial (optical single wavelength) transmission Ethernet using a field-programmable gate array (FPGA). Experimental evaluation of this implementation demonstrates the feasibility of low-power and fault-tolerant 400-Gb/s Ethernet.
Distance and exposure dependent effective dielectric function

In an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (Deff) for a large number of atom pairs in a typical globular protein are calculated by continuum electrostatics. Plots of Deff versus the intercharge distance are in general sigmoidal with the characteristics of the curve depending on the distance of the two charges from the dielectric boundary and, secondarily, on the extent to which the area surrounding each charge is occupied by solvent (the “exposure”). The Deff values were fitted to an empirical, analytical function of these parameters that reproduces the data reasonably well, although considerable scatter exists in the range of Deff from 30 to 80. In the system used for parameterization, the mean square deviation of electrostatic interaction energies with this function is 0.48 kcal/mol, compared to 1.45 for an analytical Generalized Born model and 1.52 for the linear distance‐dependent dielectric model. When tested in other proteins of varying size and compactness, the present function is superior to both of the above models, except for a fully unfolded polypeptide chain, where the Generalized Born model is superior. © 2002 Wiley Periodicals, Inc. J Comput Chem 11: 1090–1099, 2002
iTRAQ-Based Identification of Proteins Related to Muscle Growth in the Pacific Abalone, Haliotis discus hannai

The abalone Haliotis discus hannai is an important aquaculture species that is grown for human consumption. However, little is known of the genetic mechanisms governing muscle growth in this species, particularly with respect to proteomics. The isobaric tag for relative and absolute quantitation (iTRAQ) method allows for sensitive and accurate protein quantification. Our study was the first to use iTRAQ-based quantitative proteomics to investigate muscle growth regulation in H. discus hannai. Among the 1904 proteins identified from six samples, 125 proteins were differentially expressed in large specimens of H. discus hannai as compared to small specimens. In the large specimens, 47 proteins were upregulated and 78 were downregulated. Many of the significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including these differentially expressed proteins, were closely related to muscle growth, including apoptosis, thyroid hormone signaling, regulation of the actin cytoskeleton, and viral myocarditis (p < 0.05). Our quantitative real-time polymerase chain reaction (qRT-PCR) analyses suggested that the alterations in expression levels observed in the differentially expressed proteins were consistent with the alterations observed in the encoding mRNAs, indicating the repeatability of our proteomic approach. Our findings contribute to the knowledge of the molecular mechanisms of muscle growth in H. discus hannai.
List Length and Organization in the Recall of Categorized Lists

60 subjects in a 2 × 3 factorial design learned and recalled categorized lists. Gains in recall from uncued to cued recall were examined as a function of list organization, either blocked or random, and list length, 5, 8, or 11 categories of 7 items each. Significantly greater gains were observed for the simple effects of both list organization and list length but not their interaction. The pattern was one of greater gains in both total word and categories recalled following blocked list organization and longer lists. Words per category recalled were not significantly affected.
MIG-15 and ERM-1 promote growth cone directional migration in parallel to UNC-116 and WVE-1

Neurons require precise targeting of their axons to form a connected network and a functional nervous system. Although many guidance receptors have been identified, much less is known about how these receptors signal to direct growth cone migration. We used Caenorhabditis elegans motoneurons to study growth cone directional migration in response to a repellent UNC-6 (netrin homolog) guidance cue. The evolutionarily conserved kinase MIG-15 [homolog of Nck-interacting kinase (NIK)] regulates motoneuron UNC-6-dependent repulsion through unknown mechanisms. Using genetics and live imaging techniques, we show that motoneuron commissural axon morphology defects in mig-15 mutants result from impaired growth cone motility and subsequent failure to migrate across longitudinal obstacles or retract extra processes. To identify new genes acting with mig-15, we screened for genetic enhancers of the mig-15 commissural phenotype and identified the ezrin/radixin/moesin ortholog ERM-1, the kinesin-1 motor UNC-116 and the actin regulator WVE-1 complex. Genetic analysis indicates that mig-15 and erm-1 act in the same genetic pathway to regulate growth cone migration and that this pathway functions in parallel to the UNC-116/WVE-1 pathway. Further, time-lapse imaging of growth cones in mutants suggests that UNC-116 might be required to stimulate protrusive activity at the leading edge, whereas MIG-15 and ERM-1 maintain low activity at the rear edge. Together, these results support a model in which the MIG-15 kinase and the UNC-116–WVE-1 complex act on opposite sides of the growth cone to promote robust directional migration.
Protocol for genomic DNA preparation from fresh or frozen serum for PCR amplification.

Blood is the primary human tissue for clinical diagnosis. Serum may be stored in banks after diagnosis, and most of the specimens may have available corresponding clinical records. These serum samples can be important sources of genomic DNA for human genetic studies in the identification of disease-causing genes or the study of mutations in prenatal diagnosis (10,16), in the detection of tumor DNA from patients with pancreatic (12), lung (3), colorectal (1) and breast cancer (15). However, DNA isolation from serum is difficult because of the low content of DNA in serum and the small amounts of serum that may be available. Martin et al. (11) first described a procedure to isolate DNA for genotype analysis, and others have developed different methods for serum DNA isolation (6,14). Dixon et al. (4) have tested 13 currently available DNA extraction methods. We have also reported a method for DNA extraction from small amounts of serum (9). However, for DNA analysis on a larger scale, a simple, automation-amenable protocol is required. In the present study, we describe a simple protocol for DNA preparation from serum. It includes only two steps, alkaline lysis and neutralization, with two different solutions in one tube. Blood was collected in a red top Vacutainer (no additives) (Becton Dickinson, Franklin Lakes, NJ, USA) with a 22G1 needle and was allowed to clot at room temperature for at least 2 h. The clot was detached from the wall of the tube by a wooden applicator stick and then kept at 4°C overnight. It was centrifuged at 700× g for 5 min; the serum (supernatant) was collected and used for DNA extraction. For alkaline lysis, 10 μL serum were incubated with 1 μL 0.2 M KOH at 37°C for 20 min. During this treatment, various macromolecules in serum may be denatured or hydrolyzed (i.e., RNA) (7). To identify optimal conditions for the alkaline lysis, we tested different KOH concentrations (0.1 or 0.2 M) at different incubation temperatures (55°C, 45°C or 37°C). Ten microliters of serum were used, and the incubation time was 20 min. To neutralize the solution, 5 μL neutralization buffer (9 parts 1 M Tris, pH 8.3:1 part 2 M HCl) were added to the serum lysate and vortexed briefly. The final DNA solution volume was 16 μL, and 3 μL each condition were used for PCR amplification. In this study, the target DNA seBenchmarks
Miro1 regulates intercellular mitochondrial transport & enhances mesenchymal stem cell rescue efficacy

There is emerging evidence that stem cells can rejuvenate damaged cells by mitochondrial transfer. Earlier studies show that epithelial mitochondrial dysfunction is critical in asthma pathogenesis. Here we show for the first time that Miro1, a mitochondrial Rho‐GTPase, regulates intercellular mitochondrial movement from mesenchymal stem cells (MSC) to epithelial cells (EC). We demonstrate that overexpression of Miro1 in MSC (MSCmiroHi) leads to enhanced mitochondrial transfer and rescue of epithelial injury, while Miro1 knockdown (MSCmiroLo) leads to loss of efficacy. Treatment with MSCmiroHi was associated with greater therapeutic efficacy, when compared to control MSC, in mouse models of rotenone (Rot) induced airway injury and allergic airway inflammation (AAI). Notably, airway hyperresponsiveness and remodeling were reversed by MSCmiroHi in three separate allergen‐induced asthma models. In a human in vitro system, MSCmiroHi reversed mitochondrial dysfunction in bronchial epithelial cells treated with pro‐inflammatory supernatant of IL‐13‐induced macrophages. Anti‐inflammatory MSC products like NO, TGF‐β, IL‐10 and PGE2, were unchanged by Miro1 overexpression, excluding non‐specific paracrine effects. In summary, Miro1 overexpression leads to increased stem cell repair.
Connecting univariate smiles and basket dynamics: a new multidimensional dynamics for basket options

A new approach to modelling and pricing derivative securities based on many underlying assets is developed, with the ultimate, practical aim to properly price such derivatives when each underlying shows a volatility smile/skew. We show that the proposed multidimensional model can indeed account for the observed implied volatility smiles for a range of single securities, when each single-asset volatility smile is modeled according to a density-mixture dynamical model. Extending in an intuitive way the model from the univariate to the multivariate setting, this theory allows to sample from an entirely new type of dynamics that still enjoys an internal consistency with the observed volatility surfaces for the individual securities. The computational implications have a strong impact on the calculation of prices of European options on baskets of securities. Operative proposals for the use of this model to deduce skews on baskets of many stocks/FX rates will be presented. A natural extension to the case of the Libor Market Model would allow computing in a quasianalytical fashion the swap rates’ smile given the smiles in the individual caplets. Introduction It is known that the Black–Scholes model [2] does not price all European options quoted on a given market in a consistent way. In fact, their model lies on the fundamental assumption that the asset price volatility is a constant. In reality, the implied volatility (i.e. the volatility parameter that, when plugged into the Black–Scholes formula, allows to reproduce the market price of an option) generally shows a dependence on both the option maturity and strike. If there were no dependence on strike one could extend the model in a straightforward fashion by allowing a deterministic dependence of the underlying’s instantaneous volatility on time, so that the dynamics could be represented by the following stochastic differential equation (SDE): (1) dSt = μStdt + σtStdWt, σt being the deterministic instantaneous volatility referred to above. In that case, reconstruction of the time dependence of σt would follow by considering that, if v(Ti) denotes the implied volatility for options maturing at time Ti, then (2) v(Ti) Ti = ∫ Ti 0 σ sds. Implied volatility however does indeed show a strike dependence; in the common jargon, this behaviour is described with the term smile whenever volatility has a minimum at the forward asset price level, or skew Corresponding author: e-mail francesco.rapisarda@bancaimi.it One of us (FR) deeply thanks the participants to the Fifteenth Annual Conference of the Financial Options Research Centre of the Warwick Business School and to the Workshop on Multiasset Options organized by Frontieres en Finance for useful discussions.
Reward modulates the effect of visual cortical microstimulation on perceptual decisions

Effective perceptual decisions rely upon combining sensory information with knowledge of the rewards available for different choices. However, it is not known where reward signals interact with the multiple stages of the perceptual decision-making pathway and by what mechanisms this may occur. We combined electrical microstimulation of functionally specific groups of neurons in visual area V5/MT with performance-contingent reward manipulation, while monkeys performed a visual discrimination task. Microstimulation was less effective in shifting perceptual choices towards the stimulus preferences of the stimulated neurons when available reward was larger. Psychophysical control experiments showed this result was not explained by a selective change in response strategy on microstimulated trials. A bounded accumulation decision model, applied to analyse behavioural performance, revealed that the interaction of expected reward with microstimulation can be explained if expected reward modulates a sensory representation stage of perceptual decision-making, in addition to the better-known effects at the integration stage. DOI: http://dx.doi. org/10.7554/eLife.07832. 001
Optical physics of imaging and interferometric phased arrays

Microwave, submillimetre-wave, and far-infrared phased arrays are of considerable importance for astronomy. We consider the behaviour imaging phased arrays and interferometric phased arrays from a functional perspective. It is shown that the average powers, field correlations, power fluctuations, and correlations between power fluctuations at the output ports of an imaging or interferometric phased array can be found once the synthesised reception patterns are known. The reception patterns do not have to be orthogonal or even linearly independent. It is shown that the operation of phased arrays is intimately related to the mathematical theory of frames, and that the theory of frames can be used to determine the degree to which any class of intensity or field distribution can be reconstructed unambiguously from the complex amplitudes of the travelling waves at the output ports. The theory can be used to set up a likelihood function that can, through Fisher information, be used to determine the degree to which a phased array can be used to recover the parameters of a parameterised source. For example, it would be possible to explore the way in which a system, perhaps interferometric, might observe two widely separated regions of the sky simultaneously.
Toward Exascale Resilience: 2014 update

Resilience is a major roadblock for HPC executions on future exascale systems. These systems will typically gather millions of CPU cores running up to a billion threads. Projections from current large systems and technology evolution predict errors will happen in exascale systems many times per day. These errors will propagate and generate various kinds of malfunctions, from simple process crashes to result corruptions.The past five years have seen extraordinary technical progress in many domains related to exascale resilience. Several technical options, initially considered inapplicable or unrealistic in the HPC context, have demonstrated surprising successes. Despite this progress, the exascale resilience problem is not solved, and the community is still facing the difficult challenge of ensuring that exascale applications complete and generate correct results while running on unstable systems. Since 2009, many workshops, studies, and reports have improved the definition of the resilience problem and provided refined recommendations. Some projections made during the previous decades and some priorities established from these projections need to be revised. This paper surveys what the community has learned in the past five years and summarizes the research problems still considered critical by the HPC community.
Dispositions to act in favor of the environment: Fatalism and readiness to make sacrifices in a cross-national perspective

This article hypothesizes that individuals' environmental attitudes depend not only on their knowledge, interests, emotions, and values but also on the social context in which they live. We test this hypothesis by analyzing the 2000/01 ISSP-II Survey on Environmental Attitudes; the data include respondents from 23 countries. Our findings show that individual characteristics influence both "pessimistic environmental orientations" and "the willingness to act in favor of the environment. " As for social context, the level of development and affluence, the degree of political centralization, the presence of green movements and parties, and the degree of objective pollution in a country are all important. However, their influences on fatalism and willingness vary.