Miracle-dz/UniFAR-FTUs huggingface dataset:
GOMIT: a generic and adaptive annotation algorithm based on gene ontology term distributions

We address the issue of providing highly informative annotations using information revealed by the structured vocabularies of gene ontology (GO). For a target, a set of candidate terms used to infer the target's property is collected and forms a unique distribution on the GO directed acyclic graph (DAG). We propose a generic and adaptive algorithm - GOMIT, which bases on term distributions and GO hierarchical characteristics to assign correct annotations for a target. We establish a quantitative model with parameters that can be framed for optimal performance for different applications. We propose several criteria for evaluating GOMIT's performance, and conducted three experiments involving a) automated functional annotations, b) biological annotations of microarray data clusters and c) protein family GO assignments. In these experiments, we used our proposed criteria to compare GOMIT with other algorithms. Results not only reflect GOMIT's generality and adaptability, but also suggest that GOMIT is better or comparable to other works for assigning correct annotations.
Approximate common divisors via lattices

We analyze the multivariate generalization of Howgrave-Graham's algorithm for the approximate common divisor problem. In the m-variable case with modulus N and approximate common divisor of size N^beta, this improves the size of the error tolerated from N^(beta^2) to N^(beta^((m+1)/m)), under a commonly used heuristic assumption. This gives a more detailed analysis of the hardness assumption underlying the recent fully homomorphic cryptosystem of van Dijk, Gentry, Halevi, and Vaikuntanathan. While these results do not challenge the suggested parameters, a 2^(n^epsilon) approximation algorithm with epsilon<2/3 for lattice basis reduction in n dimensions could be used to break these parameters. We have implemented our algorithm, and it performs better in practice than the theoretical analysis suggests. Our results fit into a broader context of analogies between cryptanalysis and coding theory. The multivariate approximate common divisor problem is the number-theoretic analogue of multivariate polynomial reconstruction, and we develop a corresponding lattice-based algorithm for the latter problem. In particular, it specializes to a lattice-based list decoding algorithm for Parvaresh-Vardy and Guruswami-Rudra codes, which are multivariate extensions of Reed-Solomon codes. This yields a new proof of the list decoding radii for these codes.
Evolutionary history and phylogeographic relationships of shrews from Sorex araneus group

Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species. These processes were additionally complicated by introgressions of mitochondrial DNA, which made the evolutionary history of this group quite complex and difficult to infer. To tackle the problem, we performed multi-method phylogenetic analyses based on mitochondrial cytochrome b that is considered a good molecular marker available for many representatives of Sorex. The results were compared with phylogenies based on chromosomal rearrangement data and put into temporal and spatial context using molecular dating and historical biogeography methods. We complemented the study with the estimation of diversification rates within the S. araneus group as well as comparing the results with paleontological records and climatic oscillations within the last 4 million years. Based on the gathered data, we proposed a hypothetical scenario for the evolution and geographic dispersion of species belonging to the S. araneus group. The shrews began to diversify about 2.7 million years ago in Eurasia and then migrated at least twice to North America. The evolution of shrews was driven by Pleistocene glacial and interglacial cycles, which increased their speciation rate and the emergence of new lineages. The migrations of populations were accompanied by introgressions of mitochondrial DNA into native shrews and occurred at least twice.
The 2 x 2 factorial design: its application to a randomized trial of aspirin and carotene in U.S. physicians.

The 2 x 2 factorial design calls for randomizing each participant to treatment A or B to address one question and further assignment at random within each group to treatment C or D to examine a second issue, permitting the simultaneous test of two different hypotheses. This design can increase the efficiency of large-scale clinical trials. The Physicians' Health Study, a randomized trial of aspirin and beta-carotene among U.S. physicians, illustrates some features and potential problems in the design and analysis of a factorial trial. The most common concern, interaction between treatments, is generally an advantage rather than a limitation of this design. Although such interactions are relatively uncommon, this design provides a means to measure an effect which otherwise might not be apparent. If the interaction is sufficiently severe, however, then loss of power is possible.
Representing Uncertainty, Profile and Movement History in Mobile Objects Databases

This paper presents a model of data for mobile objects. The model is represented by spatial-temporal classes with mobility aspects, and represents the route and the trajectories where the objects move. The problem of mobile databases inaccuracy is approached. A model of trajectory uncertainty for free route is considered, where spatial operators are defined to capture the uncertainty. Another important concept added by the model is the profile and historical movement, that is, an attempt to increase the precision of prevision for object positions not yet observed. Some simulations results are shown, presenting the efficiency of some techniques for calculating the uncertainty of the positioning prevision.
Contested Delineations: Planning, Law, and the Governance of Protected Areas

In this paper we reflect on the relationship between planning and law. We analyse the Dutch interpretation and implementation of the European Union Habitats and Birds Directives by investigating the practices of delineation of protected areas. These directives provide a legislative framework for the designation of protected sites as well as for decision making about social and economic activities that might have negative effects on the conservation objectives. The formal boundaries of the protected area can have legal, political, and economic consequences and are therefore the subject of much debate. Using Niklas Luhmann's social systems theory, we analyse the debates concerning delineation and the potential for planning to reduce tensions and balance interests. It is argued that the irreducible differences between the economic, political, and legal perspectives, in combination with the Dutch path of a legalistic interpretation of EU directives, have produced a situation in which the role of planning is reduced and new forms of planning are hard to implement.
Hausdorff measure of p-Cantor sets.

In this paper we analyze Cantor type sets constructed by the removal of open intervals whose lengths are the terms of the p-sequence, {k−p}∞k=1. We prove that these Cantor sets are s-sets, by providing sharp estimates of their Hausdorff measure and dimension. Sets of similar structure arise when studying the set of extremal points of the boundaries of the so-called random stable zonotopes.
Direct Cortical Control of 3D Neuroprosthetic Devices

Three-dimensional (3D) movement of neuroprosthetic devices can be controlled by the activity of cortical neurons when appropriate algorithms are used to decode intended movement in real time. Previous studies assumed that neurons maintain fixed tuning properties, and the studies used subjects who were unaware of the movements predicted by their recorded units. In this study, subjects had real-time visual feedback of their brain-controlled trajectories. Cell tuning properties changed when used for brain-controlled movements. By using control algorithms that track these changes, subjects made long sequences of 3D movements using far fewer cortical units than expected. Daily practice improved movement accuracy and the directional tuning of these units.
Quantitative trait loci analysis for rice seed vigor during the germination stage

Seed vigor is an important characteristic of seed quality, and rice cultivars with strong seed vigor are desirable in direct-sowing rice production for optimum stand establishment. In the present study, the quantitative trait loci (QTLs) of three traits for rice seed vigor during the germination stage, including germination rate, final germination percentage, and germination index, were investigated using one recombinant inbred line (RIL) population derived from a cross between japonica Daguandao and indica IR28, and using the multiple interval mapping (MIM) approach. The results show that indica rice presented stronger seed vigor during the germination stage than japonica rice. A total of ten QTLs, and at least five novel alleles, were detected to control rice seed vigor, and the amount of variation (R2) explained by an individual QTL ranged from 7.5% to 68.5%, with three major QTLs with R2>20%. Most of the QTLs detected here are likely to coincide with QTLs for seed weight, seed size, or seed dormancy, suggesting that the rice seed vigor might be correlated with seed weight, seed size, and seed dormancy. At least five QTLs are novel alleles with no previous reports of seed vigor genes in rice, and those major or minor QTLs could be used to significantly improve the seed vigor by marker-assisted selection (MAS) in rice.
Smart Cities as an Application of Internet of Things: Experiences and Lessons Learnt in Barcelona

Internet of things is a ubiquitous technology that will be present everywhere. One of the first applications will be smart cities. Cities are growing in population and citizens demand better services from the administration without increasing taxes. The only way to attend this demand is to improve information and how this is treated to take decisions. In other words, we should make the city smart. Smart cities are a novel concept that defines new technologies but also reuses some of the existing ones. All novel solutions phase the same problem: the lack of standards and widely accepted solutions. The City of Barcelona with the collaboration from research centers and industrial partners has been testing the smart city concept with the double purpose to contribute to the creation of standards and providing in the interim a solution to cope with the heterogeneity of providers, in particular from the wireless sensor part. This work has been structured as a "Barcelona Intelligent City" project or BCI. BCI project considers all the steps of the data process from its capture by a sensor network to the processing to make it relevant (pointing events that requires attention) and rich (with context information). Conclusions from the pilots has started to be applied. One example is the sensoring in civil works control. This paper includes some lines about Avinguda de l'Estatut Civil Works Project and its conclusions.
Consistency and restructuring in learning cognitive procedural sequences.

Ss practiced mental arithmetic tasks that were consistent or varied at two levels: the sequence of operations and the data for those operations. Experiment 1 demonstrated separable benefits of sequence- and data-level consistency. In Experiment 2, sequence and data consistency varied within subjects, and the sequence of operations did not match the goal structure. Final performance benefited from consistent data but not from consistent sequence. In Experiment 3, sequence consistency varied between subjects. Sequence and data consistency had separable benefits
Natural prenylated resveratrol analogs arachidin-1 and -3 demonstrate improved glucuronidation profiles and have affinity for cannabinoid receptors

Rationale. The therapeutic promise of trans-resveratrol (tRes) is limited by poor bioavailability following rapid metabolism. We hypothesise that trans-arachidin-1 (tA1) and trans-arachidin-3 (tA3), peanut hairy root-derived isoprenylated analogs of tRes, will exhibit slower metabolism/enhanced bioavailability and retain biological activity via cannabinoid receptor (CBR) binding relative to their non-prenylated parent compounds trans-piceatannol (tPice) and tRes, respectively. Results. The activities of eight human UDP-glucuronosyltransferases (UGTs) toward these compounds were evaluated. The greatest activity was observed for extrahepatic UGTs 1A10 and 1A7, followed by hepatic UGTs 1A1 and 1A9. Importantly, an additional isoprenyl and/or hydroxyl group in tA1 and tA3 slowed overall glucuronidation. CBR binding studies demonstrated that all analogs bound to CB1Rs with similar affinities (5–18 µM); however, only tA1 and tA3 bound appreciably to CB2Rs. Molecular modelling studies confirmed that the isoprenyl moiety of tA1 and tA3 improved binding affinity to CB2Rs. Finally, although tA3 acted as a competitive CB1R antagonist, tA1 antagonised CB1R agonists by both competitive and non-competitive mechanisms. Conclusions. Prenylated stilbenoids may be preferable alternatives to tRes due to increased bioavailability via slowed metabolism. Similar structural analogs might be developed as novel CB therapeutics for obesity and/or drug dependency.
Non-functional Properties in Software Product Lines: A Taxonomy for Classification

In the recent years, the software product lines paradigm has gained interest in both industry and academia. As in traditional software development, the concept of quality is crucial for the success of software product line practices and both functional and nonfunctional characteristics must be involved in the development process in order to achieve a high quality software product line. Therefore, many efforts have been made towards the development of quality-based approaches in order to address non-functional properties in software product line development. In this paper, we propose a taxonomy that characterizes and classifies various approaches for employing non-functional properties in software product lines development. The taxonomy not only highlights the major concerns that need to be addressed in the area of quality-based software product lines, but also helps to identify various research gaps that need to be filled in future work in this area.
Life at the track: Country race clubs and social capital

The aim of this article is to report the findings of a study that explored both the contributions of country race clubs to social capital within rural and regional communities as well as their utilization of social capital. The article reviews the key concepts associated with social capital and their relationships to sport, and presents evidence of how country race clubs contribute to and benefit from social capital in their respective communities based on a series of interviews with individuals associated with race clubs and their communities. The final section of the article discusses the implications of these findings in relation to what we currently know of social capital and community level sport clubs.
Reliability and replicability of the Approaches to Studying Questionnaire

ABSTRACT The Approaches to Studying Questionnaire (ASQ) was devised to measure individual differences in terms of four major study orientations. It achieves satisfactory levels of reliability and the distinction between a meaning orientation and a reproducing orientation has been consistently demonstrated across a variety of student groups. However, the validity of the remaining study orientations and of the constituent subscales is open to question. A shorm form of the ASQ is described, based upon the eight subscales that have been consistently identified with meaning orientation and reproducing orientation. The reliability and replicability of this new questionnaire are considered in the light of a critical evaluation of the analytic methods employed in previous research. Satisfactory levels of internal consistency and test-retest reliability are demonstrated, and factor analysis successfully retrieves the two primary study orientations. While the validity of its constituent subscales is still rather un.
Intention Concepts and Brain-Machine Interfacing

Intentions, including their temporal properties and semantic content, are receiving increased attention, and neuroscientific studies in humans vary with respect to the topography of intention-related neural responses. This may reflect the fact that the kind of intentions investigated in one study may not be exactly the same kind investigated in the other. Fine-grained intention taxonomies developed in the philosophy of mind may be useful to identify the neural correlates of well-defined types of intentions, as well as to disentangle them from other related mental states, such as mere urges to perform an action. Intention-related neural signals may be exploited by brain-machine interfaces (BMIs) that are currently being developed to restore speech and motor control in paralyzed patients. Such BMI devices record the brain activity of the agent, interpret (“decode”) the agent’s intended action, and send the corresponding execution command to an artificial effector system, e.g., a computer cursor or a robotic arm. In the present paper, we evaluate the potential of intention concepts from philosophy of mind to improve the performance and safety of BMIs based on higher-order, intention-related control signals. To this end, we address the distinction between future-, present-directed, and motor intentions, as well as the organization of intentions in time, specifically to what extent it is sequential or hierarchical. This has consequences as to whether these different types of intentions can be expected to occur simultaneously or not. We further illustrate how it may be useful or even necessary to distinguish types of intentions exposited in philosophy, including yes- vs. no-intentions and oblique vs. direct intentions, to accurately decode the agent’s intentions from neural signals in practical BMI applications.
Cultural Difference in the Application of the Diagnosticity Principle to Schematic Faces

Tversky’s (1977) diagnosticity principle implies that categorization affects similarity, and that similarity in turn is based on context. However, Nisbett, Peng, Choi, and Norenzayan (2001) suggest that Chinese and Westerners differ in their sensitivity to context and categorization. Because of these differences, it is not clear whether Chinese should follow the diagnosticity principle. To explore these possibilities, we conducted a cross-cultural experiment using participants from Australia and China to repeat the experiment of Tversky (1977) using schematic faces as stimuli. Results showed that Australians, but not Chinese, made similarity judgments in a manner compatible with the diagnosticity principle. We suggest that: 1) the use of the diagnosticity principle depends upon contextualvariables for Chinese people; and 2) Chinese participants judged neutral schematic faces asmore positive than Western participants did
Prediction of Bioluminescent Proteins Using Auto Covariance Transformation of Evolutional Profiles

Bioluminescent proteins are important for various cellular processes, such as gene expression analysis, drug discovery, bioluminescent imaging, toxicity determination, and DNA sequencing studies. Hence, the correct identification of bioluminescent proteins is of great importance both for helping genome annotation and providing a supplementary role to experimental research to obtain insight into bioluminescent proteins’ functions. However, few computational methods are available for identifying bioluminescent proteins. Therefore, in this paper we develop a new method to predict bioluminescent proteins using a model based on position specific scoring matrix and auto covariance. Tested by 10-fold cross-validation and independent test, the accuracy of the proposed model reaches 85.17% for the training dataset and 90.71% for the testing dataset respectively. These results indicate that our predictor is a useful tool to predict bioluminescent proteins. This is the first study in which evolutionary information and local sequence environment information have been successfully integrated for predicting bioluminescent proteins. A web server (BLPre) that implements the proposed predictor is freely available.
The effects of quality improvement practices on team effectiveness: a mediational model

Researchers have been challenged to specify the processes that quality improvement (QI) practices could be expected to generate and to explain how they might contribute to organizational effectiveness. This research article meets that challenge through a study of 97 teams in the health care field. The authors developed a ‘Quality Improvement Practices Index’ and showed that QI practices could be differentiated from traditional team-level variables, and that such practices affect both directly and indirectly (through team-level variables) team effectiveness. Two models were tested using structural equation modelling. It was found that the perceptions of the impact of QI practices on team effectiveness varied depending on who was assessing the team's performance—members of the team or managers who were external to the team but responsible for the team's performance. The authors discuss the implications of these results both for researchers and practitioners. Copyright © 2002 John Wiley & Sons, Ltd.
Optimal Integrated Call Admission Control and Dynamic Pricing with Handoffs and Price-Affected Arrivals

Call admission control and dynamic pricing have been proposed as separate measures to reduce congestion in a network. In this paper, we integrate the call admission control and dynamic pricing problems, formulating them as a Markov decision problem (MDP), operating in a multiservice, resource-sharing cellular system. Our model incorporates price-affected behaviour of network users, considering effects on arrivals, retrials and substitutions among services and time. The network exercises admission control, to reject or accept a new connection requests, and price control to set a state-dependent price per bandwidth time with the objective to maximise the long-term revenue. The results show that the proposed method improves revenue and reduces congestion compared to other conventional sub-optimal policies
Attentional distraction and time perception in children

The purpose of the present study was to test the effect of attentional distraction on temporal bisection performance in 5- and 8-year-old children. During a first learning phase, children were trained to discriminate on a temporal bisection task a short standard duration (2 sec) from a long one (8 sec), presented as visual stimuli. Later, in a second testing phase, intermediate durations (3, 4, 5, 6, 7 s), including the standard durations, were presented. Children's task still was to report if it was a short standard duration or a long one. In addition, during the non-standard duration, a distracter either did or did not appear. Results showed increasing proportions of “it is the long standard duration” (response “long”) with increasing stimulus durations in both distracter and non-distracter conditions. However, psychophysical functions were flatter in the 5-year-olds than in the 8-year-olds, revealing their lower sensibility to time. Nevertheless, the 5-year-olds' proportion of long responses was higher.