Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing Multiple Sequence Alignments Using Visual Tools

Bioinformatics and molecular evolutionary analyses most often start with comparing DNA or amino acid sequences by aligning them. Pairwise alignment, for example, is used to measure the similarities between a query sequence and each of those in a database in BLAST similarity search, the most used bioinformatics tool (Altschul et al., 1990; Camacho et al., 2009). Evolutionary history among sequences can be reflected better when more than two sequences are aligned, in a multiple sequence alignment (MSA). When building an MSA, we assume that the sequences compared are derived from a common ancestral sequence. Then the process of MSA building is to infer homologous positions between the input sequences and place gaps in the sequences in order to align these homologous positions. These gaps represent evolutionary events of their own. Gaps (also called indels) are caused by either insertions or deletions of characters (nucleotides or amino acids) on a particular lineage of sequences during the evolution. Building an MSA is, therefore, to reconstruct the evolutionary history of the sequences involved. While it is easy to understand that the quality of MSAs affects the quality of phylogenetic tree reconstruction, the effect of MSA quality reaches far beyond this. Some examples of bioinformatics methods that utilize information extracted from MSAs include: profile building in similarity search (e.g., PSIBLAST: Altschul et al., 1997), motif/profile recognition (e.g., PROSITE: Hulo et al., 2008), profile hidden Markov models for protein families/domains (e.g., Pfam: Finn et al., 2010), and protein secondary-structure prediction (for review, see Pirovano & Heringa, 2010). There are numerous bioinformatics and molecular evolutionary analyses that are affected by MSA quality and they can be benefited by having reliable MSAs. Despite the significance of having good MSAs, assessing MSA quality is far from straightforward. Measuring the quality of MSAs requires two components: a benchmark dataset and a scoring method. A benchmark dataset includes reference alignments. These alignments are considered to represent the evolutionary history of the sequences truthfully. The same set of sequences included in a reference alignment is then aligned using the MSA methods to be tested. The reconstructed MSA can be compared with the reference MSA using a scoring method and the quality of the reconstructed MSA is assessed compared to the
Compare Beamforming with Multiplexing for Mimo Relay Network in the Low SNR Regime

Given a multiple-antenna source and a multiple- antenna destination, a multiple-antenna relay between the source and the destination is desirable under useful circumstances. In this paper, a spatial multiplexing scheme and a cooperative beamforming scheme have been proposed for a non-regenerative MIMO relay system. In the spatial multiplexing scheme, the MIMO relay channel can be decomposed into several parallel channels each with the source to relay channel gain and the relay to destination channel gain. In the cooperative beamforming scheme, the transmitter uses all of its antennas to transmit one signal instead of multiplexing different signals simultaneously. It can be proved that the capacity of the spatial multiplexing scheme is smaller than that of the cooperative beamforming scheme in the low SNR regime. It is shown that for asymptotically large number of relays, the capacity of the spatial multiplexing scheme is converging to that of the beamforming scheme.
Identifying International Networks : Latent Spaces and Imputation

Most analyses of world politics and studies of national security policies recognize the interdependence among the salient actors across the salient issues. Traditionally, international politics has been defined as the scope and extent of the relations among independent countries, thought to be the most important elements in world politics. This means that actors as well as their actions are strategically interdependent (Signorino 1999). Ignoring the interdependence among these phenomena would appear to be a serious oversight that plague attempts to understand, let alone predict, the course of national security policy and world politics more generally. With very few exceptions, quantitative, systematic studies of international relations and national security have assumed that the major actors and actions that comprise world politics consist of unconnected actions and actors. Game theoretic models are legion, but rarely deal with more than two actors at a time. Some beginning attempts to model the interdependency in international relations have appeared in the literature (Ward and Kirby 1987; Gleditsch and Ward 2001; Gleditsch and Ward 2001; Ward and Gleditsch 2002; Gleditsch 2002; Lofdahl 2002), but as yet network models have yet be widely applied in scholarly or policy work on international politics. This is somewhat surprising, since it is evident at first blush that international politics is about the interdependence that appears around the world. Social network analysis is one technique that has been developed to map and measure the relationships and flows among agents. The nodes in the network are the individuals and groups and the links among them illustrate their interdependencies, both in terms of structure and in terms of the flows of information from one node to others. Since the development of the sociogram (Moreno 1934), sociologists among others have been interested in analyzing the linkages among individuals and groups. An interesting early example is found in the early work of Coleman, Katz and Menzel (1957). Most early theoretical advances were based on graph theory as developed and advanced by Frank Harary and his students and collaborators (Harary 1959; Harary 1969; Harary, Norman and Cartwright 1965). The so-called “Columbia school” worked throughout the 1960s and beyond to further advance the substantive findings in this arena of sociology (White 1963; White, Boorman and Breiger 1976). Broader dissemination of these ideas came much more recently with didactic writings (Knoke and Kuklinski 1982; Scott 1991) as well as early
IZA DP No . 2927 Competition , Cooperation , and Corporate Culture

Competition, Cooperation, and Corporate Culture Teamwork and cooperation between workers can be of substantial value to a firm, yet the level of worker cooperation often varies between individual firms. We show that these differences can be the result of labor market competition if workers have heterogeneous preferences and preferences are private information. In our model there are two types of workers: selfish workers who only respond to monetary incentives, and conditionally cooperative workers who might voluntarily provide team work if their co-workers do the same. We show that there is no pooling in equilibrium, and that workers self-select into firms that differ in their incentives as well as their resulting level of team work. Our model can explain why firms develop different corporate cultures in an ex-ante symmetric environment. Moreover, the results show that, contrary to first intuition, labor market competition does not destroy but may indeed foster within-firm cooperation. JEL Classification: D23, D82, L23, M54
Diabetes prevalence and risk factors among ethnic minorities.

BACKGROUND Ethnic minorities living in Western societies may have a higher prevalence of diabetes. We investigated whether the prevalence of diabetes among Turkish and Moroccan migrants differs from the indigenous urban population in the Netherlands, and whether these differences can be explained by differences in risk factors. METHODS In 2004 a general health survey, stratified by ethnicity and age, was carried out among the population of Amsterdam. The current study included 375 Turkish, 314 Moroccan and 417 Dutch individuals aged 18-70 years. Participants underwent a physical examination and a health interview. Diabetes was based on self-report, the use of anti-diabetic medicine, blood glucose levels and HbA1c. RESULTS The prevalence of diabetes in the Amsterdam population was significantly higher in Turkish (5.6%) and Moroccan (8.0%), compared to Dutch individuals (3.1%). These differences, which were much larger after adjustment for age, were only partly explained by the lower socioeconomic status and higher frequency of obesity among ethnic minorities. The difference between Dutch and Moroccan individuals remained significant even after adjustments for multiple risk factors. The typical age of onset of diabetes in both Turks and Moroccans is respectively one and two decades younger than in the indigenous population. CONCLUSION Diabetes is more prevalent among Turkish and Moroccan migrants as compared to the indigenous population. Only part of this difference can be explained by differences in demographic and lifestyle risk factors.
Mutation of wrb, a Component of the Guided Entry of Tail-Anchored Protein Pathway, Disrupts Photoreceptor Synapse Structure and Function

Purpose Tail-anchored (TA) proteins contain a single hydrophobic domain at the C-terminus and are posttranslationally inserted into the ER membrane via the GET (guided entry of tail-anchored proteins) pathway. The role of the GET pathway in photoreceptors is unexplored. The goal of this study was to characterize the zebrafish pinball wizard mutant, which disrupts Wrb, a core component of the GET pathway. Methods Electroretinography, optokinetic response measurements (OKR), immunohistochemistry, and electron microscopy analyses were employed to assess ribbon synapse function, protein expression, and ultrastructure in 5-day-old zebrafish larvae. Expression of wrb was investigated with real-time qRT-PCR and in situ hybridization. Results Mutation of wrb abolished the OKR and greatly diminished the ERG b-wave, but not the a-wave. Ribeye and SV2 were partially mislocalized in both photoreceptors and hair cells of wrb mutants. Fewer contacts were seen between photoreceptors and bipolar cells in wrb−/− mutants. Expression of wrb was observed throughout the nervous system and Wrb localized to the ER and synaptic region of photoreceptors. Morpholino knockdown of the cytosolic ATPase trc40, which targets TA proteins to the ER, also diminished the OKR. Overexpression of wrb fully restored contrast sensitivity in mutants, while overexpression of mutant wrbR73A, which cannot bind Trc40, did not. Conclusions Proteins Wrb and Trc40 are required for synaptic transmission between photoreceptors and bipolar cells, indicating that TA protein insertion by the TRC pathway is a critical step in ribbon synapse assembly and function.
' s personal copy Information fusion for robust ‘ context and driver aware ’ active vehicle safety systems q

Although there is currently significant development in active vehicle safety (AVS) systems, the number of accidents, injury severity levels and fatalities has not reduced. In fact, human error, low performance, drowsiness and distraction may account for a majority in all the accident causation. Active safety systems are unaware of the context and driver status, so these systems cannot improve these figures. Therefore, this study proposes a ‘context and driver aware’ (CDA) AVS system structure as a first step in realizing robust, human-centric and intelligent active safety systems. This work develops, evaluates and combines three sub-modules all employing a Gaussian Mixture Model (GMM)/Universal Background Model (UBM) and likelihood maximization learning scheme: biometric driver identification, maneuver recognition, and distraction detection. The resultant combined system contributes in three areas: (1) robust identification: a speaker recognition system is developed in an audio modality to identify the driver in-vehicle conditions requiring robust operation; (2) narrow the available information space for fusion: maneuver recognition system uses estimated driver identification to prune the selection of models and further restrict search space in a novel distraction detection system; (3) response time and performance: the system quickly produces a prediction of driver’s distracted behaviour for possible use in accident prevention/ avoidance. Overall system performance of the combined system is evaluated on the UTDrive Corpus, confirming the suitability of the proposed system for critical imminent accident cases with narrow time windows. 2010 Elsevier B.V. All rights reserved.
Relationship Between Executive Functioning and Activities of Daily Living in Patients With Relatively Mild Dementia

There is very little research regarding the relationship between tests of executive functioning and actual functional ability in patients with dementia. Thirty-three patients diagnosed with dementia and 35 age- and education-matched healthy controls were administered tests of executing functioning and an observation- and informant-based activities of daily living (ADL). As expected, the results revealed that the controls outperformed the dementia patients on the executive and ADL tests. Additionally, executive functioning correlated significantly with aspects of functional ability in patients with dementia. This relationship was strongest for tests of verbal fluency and a complex test of cognitive flexibility and reasoning ability (i.e., Wisconsin Card Sorting Test). These findings suggest that some executive function tests are more sensitive than others for predicting specific functional abilities and that they may be most useful to healthcare professionals for treatment planning.
Stability analysis and stabilization of systems presenting nested saturations

This note addresses the problems of stability analysis and stabilization of systems presenting nested saturations. Depending on the open-loop stability assumption, the global stability analysis and stabilization problems are considered. In the (local) analysis problem, the objective is the determination of estimates of the basin of attraction of the system. Considering the stabilization problem, the goal is to design a set of gains in order to enlarge the basin of attraction of the closed-loop system. Based on the modelling of the system presenting nested saturations as a linear system with dead-zone nested nonlinearities and the use of a generalized sector condition, linear matrix inequality (LMI) stability conditions are formulated. From these conditions, convex optimization strategies are proposed to solve both problems
Measuring Memory Hierarchy Performance of Cache-Coherent Multiprocessors Using Micro Benchmarks

Even with today's large caches, the increasing performance gap between processors and memory systems imposes a memory bottleneck for many important scientific and com mercial applications. This bottleneck is intensified in shared-memory multiprocessors by contention and the ef fects of cache coherency. Under heavy memory contention, the memory latency may increase two or three times. Nonethless, as more sophisticated techniques are used to hide latency and increase bandwidth, measuring memory performance has become increasingly difficult. Previous simple methods to measure memory performance can overestimate unipro cessor memory latency and underestimate bandwidth by tens of percent. We introduce a micro benchmark suite that measures memory hierarchy performance in light of both uniprocessor optimizations and the contention and coherence effects of multiprocessors. The benchmark suite has been used to improve the memory system performance of the SGI Origin multiprocessor.
Whose History? The Struggle for National Standards in American Classrooms

In the 1990s the debate over what history - and more importantly whose history - should be taught in American schools resonated through the halls of Congress, the national press, and the nation's schools. Politicians such as Lynne Cheney, Newt Gingrich, and Senator Slade Gorton, and pundits such as Rush Limbaugh, John Leo, and Charles Krauthammer fiercely denounced the findings of the National Standards for History which, subsequently, became a major battleground in the nation's ongoing struggle to define its historical identity. To help us understand what happened, Linda Symcox traces the genealogy of the National History Standards Project from its origins as a neo-conservative reform movement, through the 18 months of controversy and debate that ensued, and the aftermath - a fascinating account of a crucial moment in U.S. history. Broad in scope, this case study includes debates on social history, world history, multiculturalism, established canons, national identity, cultural history, and "liberal education. " This is ultimately the story of how a debate about our children's education became a struggle between competing political forces.
Bio-workflows with BizTalk: using a commercial workflow engine for eScience

Workflow is an important enabling technology for eScience. Research into workflow systems for eScience has yielded several specialized workflow engines. In this paper we investigate the nature of scientific workflow and describe how an existing business workflow engine, Microsoft's BizTalk, can be adapted to support scientific workflow, and some advantages of doing this. We demonstrate how BizTalk is able to support scientific workflow through the implementation of two real bioinformatics workflows. These workflows are enacted through a novel Web based interface making them widely accessible
An efficient method for recombineering GAL4 and QF drivers

Neural circuit mapping and manipulation are facilitated by independent control of gene expression in pre- and post-synaptic neurons. The GAL4/UAS and Q binary transcription systems have the potential to provide this capability. Of particular use in neural circuit mapping would be GAL4 and QF drivers specific for neurotransmitters and neurotransmitter receptors. Recently available Drosophila genomic BAC libraries make recombineering large genes including those specific for neurotransmitters and neurotransmitter receptors feasible. Here the functionality of cassettes that allow efficient recombineering of GAL4 and QF drivers based on kanamycin selection is demonstrated in Drosophila. The cassettes should, however, be generalizable for recombineering in other species.
Income and value measurement

Introduction. 1. Nature and Relationship of Income, Capital and Value The nature of income The nature of capital The relationship of income and capital The separate roles of valuation and capital maintenance The price-level problem, Capital maintenance and income Summary 2. The Income Measurement function Purposes and reasons for income measurement Criteria for income measurement Alternative income models The transactions basis 3. Economic Concepts of Income and Value Economic income as consumption Economic income as consumption plus saving ideal income Income ex ante Income ex post A comparative analysis Underlying assumptions of economic income Summary Economic income as an entity concept 4. The Traditional Accounting Concept of Income. Nature and purpose of accounting income The transactions basis The primary measurement principles The conventional wisdom of accounting The defence for traditional accounting income Arguments against traditional accounting income Accounting and economic incomes 5. Current Value Concepts of Income Introduction Arguments for current value income Arguments against current value income The alternative current vale models difficulties of current valuation Current values an price-level restatement 6. Current Entry Values and Business Income The case for entry values The concept of business income Business income in practice The treatment of holding gains as income Advantages and disadvantageous of replacement cost 7. Current Exit Values and Realizable Income 8 Mixed Value and Current Cost Income The case for exit values The concept of realizable income Realizable income in practice Business income and realizable income Holding gains as realizable income The case against realizable income . 9. Current Value Income and Economic Income 10. The Price-Level Problem The nature of the price-level problem General, specific and realistic price restatement Restatement of economic income Restatement of current value income Price-level restatement and current value accounting Advantages of price-level restatement The index problem The appropriateness of price-level restatement 11. The Validity of the Income Concept Introduction The elusive concept of income Differing concepts of income Flexibility of accounting principles The problem of subjective judgment Significant resource omission The meaning of income Information needs of investors and others An alternative to income Selected bibliography Index
Strongly equivalent logic programs

A logic program Π1 is said to be equivalent to a logic program Π2 in the sense of the answer set semantics if Π1 and Π2 have the same answer sets. We are interested in the following stronger condition: for every logic program, Π, Π1, ∪ Π has the same answer sets as Π2 ∪ Π. The study of strong equivalence is important, because we learn from it how one can simplify a part of a logic program without looking at the rest of it. The main theorem shows that the verification of strong equivalence can be accomplished by cheching the equivalence of formulas in a monotonic logic, called the logic of here-and-there, which is intermediate between classical logic and intuitionistic logic.
Comparison between Direct-On-Line , Star-Delta and Autotransformer Induction Motor Starting Method in terms of Power Quality

induction motor starting method in terms of power quality. The purpose of this research is to find out the most reliable and practical starting method which has the less power quality problems. These three basic starting methods which differ in their respective wiring connection are the most applicable and widely-used starting method in the industrial area due to its economic reasons. This research is done by analyzing the existed power quality events during the motor starting by using the Fluke Power Quality Analyzer to capture the waveforms of the events. After the experiments, the three different starting method are being compared to conclude the most suitable and applicable starting method which causes the least severe power quality events.
A Hybrid Approach of Hazard Estimation for Chemical Hazard Installations

A hybrid approach of hazard estimation was proposed to estimate the real hazard rankings of chemical hazard installations. 4 popular methods were selected to synthesize the hybrid approach by AHP, including Critical factor (CF), Consequence Analysis (CA), Dow’ s Index and Mond’ s Index. A hierarchy structure was built to estimate the relative credibility of the selected methods. Next, Hazard Index (HI) was proposed as the new criterion to rank hazard levels under different assessment systems. Each method’ s result was translated into hazard index based on the mappings between them. And then a weighted average of all hazard indexes was calculated, which was taken as the only criterion to rank hazard levels of CHIs. A case study in Weinan City of China shows that the proposed method provides more reasonable estimation results than the traditional way.
Rossi XTE monitoring of 4U 1636–53 – I. Long-term evolution and kHz quasi-periodic oscillations

We have monitored the atoll-type neutron star low-mass X-ray binary 4U1636-53 with the Rossi X-ray Timing Explorer (RXTE) for more than 1.5yr. Our campaign consisted of short (~2ks) pointings separated by 2d, regularly monitoring the spectral and timing properties of the source. During the campaign we observed a clear long-term oscillation with a period of ~30-40d, already seen in the light curves from the RXTE All-Sky Monitor, which corresponded to regular transitions between the hard (island) and soft (banana) states. We detected kilohertz (kHz) quasi-periodic oscillations (QPOs) in about a third of the observations, most of which were in the soft (banana) state. The distribution of the frequencies of the peak identified as the lower kHz QPO is found to be different from that previously observed in an independent data set. This suggests that the kHz QPOs in the system shows no intrinsically preferred frequency.