Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to develop tools to evaluate risks for TB disease caused by M. bovis/M.caprae and for TB control in humans and animals.
Random suffix search trees

A random suffix search tree is a binary search tree constructed for the suffixes Xi = 0 · BiBi+1Bi+2… of a sequence B1, B2, B3, … of independent identically distributed random b‐ary digits Bj. Let Dn denote the depth of the node for Xn in this tree when B1 is uniform on ℤb. We show that for any value of b > 1, 𝔼Dn = 2 log n + O(log2log n), just as for the random binary search tree. We also show that Dn/𝔼Dn → 1 in probability. © 2003 Wiley Periodicals, Inc. Random Struct. Alg. , 2003
Wavelet-Based Audio Watermarking Using Adaptive Tabu Search

In this paper, we present an algorithm for robust audio watermarking in wavelet transform domain. Using Daubechies wavelet decomposition, we perform watermark embedding to wavelet coefficients of host audio signal. In enhance security, a pseudo-random permutation is performed to disperse the spatial relationship of the binary watermark image. In our watermark embedding algorithm, we search for the optimal intensity of watermark by using the adaptive tabu search (ATS). The watermark detection process can be performed without using the original audio signal. The experimental results demonstrate that watermark is inaudible and robust to many digital signal processing, such as resamplig, cropping, low pass filter, additive noise and lossy compression (MP3).
Science, Scientists, and Local Weather: Understanding Mass Perceptions of Global Warming

Objective To explore the effects of long-term climate trends and short-term weather fluctuations, evaluations of scientists and science, political predispositions, religious affiliation, the information environment, and demographic attributes on individuals’ views about whether global warming exists and, if so, whether it is a result of natural cycles or human activity. Methods We use data from the 2009 Pew General Public Science Survey, along with data on long- and short-term patterns of temperature and precipitation in individuals’ home communities. Results We find that long-term trends in summer temperatures influence perceptions of global warming. Individuals who reside in communities with long-term warming of summer temperatures that are coupled with long-term cooling of spring temperatures are significantly more likely to perceive that global warming exists and is due to human activity. We also find that Americans' attitudes toward scientists and science, political dispositions, evangelical religious affiliation, education, and some demographic attributes all have discernible effects on their perceptions of anthropogenic (man-made) global warming. Conclusion Individuals’ attitudes toward global warming are influenced by long-term temperature trends in their home communities, as well as a variety of attitudinal and demographic attributes.
Predicting drop-out from social behaviour of students

This paper focuses on predicting drop-out and school failure when student data has been enriched with data derived from students social behaviour. These data describe social dependencies gathered from e-mail and discussion boards conversation, among other sources. We describe an extraction of new features from both student data and behaviour data (or more precisely from social graph which we construct). Then we introduce a novel method for learning classier for student failure prediction that employs cost-sensitive learning to lower the number of incorrectly classified unsuccessful students. We show that a use of social behaviour data results in significant prediction accuracy increase.
Social skills characteristics of students with autism spectrum disorder

Objectives: This study examines differences in social skills among children with autism spectrum disorder (ASD). In order to investigate these differences, social skills were associated with variables like gender, age, intellectual disability, language development, and school type. Methods: For the purposes of the study a total of 63 students with ASD attending primary and secondary special education units were selected in Northern Greece. A structured questionnaire was filled in by their teachers. Results: The results showed major differences between children with ASD and intellectual disability and those without. Likewise, verbal children obtained higher scores than non-verbal. These higher scores indicate better social skills. Age, gender, and school type differentiated the scores of the groups only in a few factors of the questionnaire. Conclusion: Intellectual disability and language are variables that clearly influence the socialization of children with ASD.
Single Neuron Firing Properties Impact Correlation-Based Population Coding

Correlated spiking has been widely observed, but its impact on neural coding remains controversial. Correlation arising from comodulation of rates across neurons has been shown to vary with the firing rates of individual neurons. This translates into rate and correlation being equivalently tuned to the stimulus; under those conditions, correlated spiking does not provide information beyond that already available from individual neuron firing rates. Such correlations are irrelevant and can reduce coding efficiency by introducing redundancy. Using simulations and experiments in rat hippocampal neurons, we show here that pairs of neurons receiving correlated input also exhibit correlations arising from precise spike-time synchronization. Contrary to rate comodulation, spike-time synchronization is unaffected by firing rate, thus enabling synchrony- and rate-based coding to operate independently. The type of output correlation depends on whether intrinsic neuron properties promote integration or coincidence detection: “ideal” integrators (with spike generation sensitive to stimulus mean) exhibit rate comodulation, whereas ideal coincidence detectors (with spike generation sensitive to stimulus variance) exhibit precise spike-time synchronization. Pyramidal neurons are sensitive to both stimulus mean and variance, and thus exhibit both types of output correlation proportioned according to which operating mode is dominant. Our results explain how different types of correlations arise based on how individual neurons generate spikes, and why spike-time synchronization and rate comodulation can encode different stimulus properties. Our results also highlight the importance of neuronal properties for population-level coding insofar as neural networks can employ different coding schemes depending on the dominant operating mode of their constituent neurons.
Effect of Pravastatin on Coronary Disease Events in Subgroups Defined by Coronary Risk Factors: The Prospective Pravastatin Pooling Project

BackgroundPrevious trials have had insufficient numbers of coronary events to address definitively the effect of lipid-modifying therapy on coronary heart disease in subgroups of patients with varying baseline characteristics. Methods and ResultsThe data from 3 large randomized trials with pravastatin 40 mg were pooled and analyzed with the use of a prospectively defined protocol. Included were 19 768 patients, 102 559 person-years of follow-up, 2194 primary end points (coronary death or nonfatal myocardial infarction), and 3717 expanded end points (primary end point, CABG, or PTCA). Pravastatin significantly reduced relative risk in younger (<65 years) and older (≥65 years) patients, men and women, smokers and nonsmokers, and patients with or without diabetes or hypertension. The relative effect was smaller, but absolute risk reduction was similar in patients with hypertension compared with those without hypertension. Relative risk reduction was significant in predefined categories of baseline lipid concentrations. Tests for interaction were not significant between relative risk reduction and baseline total cholesterol (5% to 95% range 177 to 297 mg/dL, 4.6 to 7.7 mmol/L), HDL cholesterol (27 to 58 mg/dL, 0.7 to 1.5 mmol/L), and triglyceride (74 to 302 mg/dL, 0.8 to 3.4 mmol/L) concentrations, analyzed as continuous variables. However, for LDL cholesterol, the probability values for interaction were 0.068 for the prespecified primary end point and 0.019 for the expanded end point. Relative risk reduction was similar throughout most of the baseline LDL cholesterol range (125 to 212 mg/dL, 3.2 to 5.5 mmol/L) with the possible exception of the lowest quintile of CARE/LIPID (<125 mg/dL) (relative risk reduction 5%, 95% CI 19% to −12%). ConclusionsPravastatin treatment is effective in reducing coronary heart disease events in patients with high or low risk factor status and across a wide range of pretreatment lipid concentrations.
Educational mobility trajectories and mobility barriers in the Norwegian social space

Presently three dominant theoretical frameworks for studies of social mobility can be singled out: Erik Olin Wright's marxist class model, John H. Goldthorpe's class scheme, and Pierre Bourdieu's notion of social space'. These frameworks are associated with uses of different statistical tools and techniques of data analysis. In this article we argue that combinations of such tools and techniques of data analysis, within the framework of'social space', may contribute to further development both of that framework and social mobility studies in general. The argument is substantiated through an analysis of intergenerational educational mobility trajectories and barriers in the Norwegian 'social space', based on data on four post-war cohorts.
A New Hierarchical Key AuthData Management Scheme for Trusted Platform

The purpose of TPM authorization mechanism is to authenticate the owner of a TPM or to authorize the use of an instance of a TPM capability. The TPM treats knowledge of the AuthData as complete proof of ownership of the entity. The main specification defines an authorized user must provide the parent key AuthData before loading its child key and provide the child key AuthData before using it. All users had to manage more and more AuthData values with the rapid increasing of keys. We have designed and analyzed a new hierarchical key AuthData management Scheme for trusted platform. In our scheme, each authorized user just needs to keep one single AuthData, and the computational requirement for generating or deriving an AuthData is just at the level of modular exponentiation and hash operation. Moreover, the lower level AuthData values can be easily derived from higher level AuthData along the same chain, but it is infeasible reversely. Even if more lower level AuthData values can’t be colluded to calculate the higher level AuthData. The result of performance evaluation and security analysis demonstrates that our proposed method is feasible and security.
Factors Affecting Two Types of Memory Specificity: Particularization of Episodes and Details

Memory for repeated events is relevant to legal investigations about repeated occurrences. We investigated how two measures of specificity (number of events referred to and amount of detail reported about the events) were influenced by interviewees’ age, number of experienced events, interviewer, perceived unpleasantness, and memory rehearsal. Transcribed narratives consisting of over 40.000 utterances from 95 dental patients, and the corresponding dental records, were studied. Amount of detail was measured by categorizing the utterances as generic, specific, or specific-extended. We found that the two measures were affected differently by all five factors. For instance, number of experienced events positively influenced number of referred events but had no effect on amount of detail provided about the events. We make suggestions for future research and encourage reanalysis of the present data set and reuse of the material.
Renal Cancer Stem Cells: Characterization and Targeted Therapies

Renal cell carcinoma (RCC) is a major neoplasm with high incidence in western countries. Tumors are heterogeneous and are composed of differentiated cancer cells, stromal cells, and cancer stem cells (CSCs). CSCs possess two main properties: self-renewal and proliferation. Additionally, they can generate new tumors once transplanted into immunodeficient mice. Several approaches have been described to identify them, through the expression of cell markers, functional assays, or a combination of both. As CSCs are involved in the resistance mechanisms to radio- and chemotherapies, several new strategies have been proposed to directly target CSCs in RCC. One approach drives CSCs to differentiate into cancer cells sensitive to conventional treatments, while the other proposes to eradicate them selectively. A series of innovative therapies aiming at eliminating CSCs have been designed to treat other types of cancer and have not been experimented with on RCC yet, but they reveal themselves to be promising. In conclusion, CSCs are an important player in carcinogenesis and represent a valid target for therapy in RCC patients.
Discovery of a broad iron line in the black hole candidate Swift J1753.5−0127, and the disc emission in the low/hard state revisited

We analysed simultaneous archival XMM-Newton and Rossi X-ray Timing Explorer observations of the X-ray binary and black hole candidate Swift J1753.5-0127. In a previous analysis of the same data, a soft thermal component was found in the X-ray spectrum, and the presence of an accretion disc extending close to the innermost stable circular orbit was proposed. This is in contrast with the standard picture in which the accretion disc is truncated at large radii in the low/hard state. We tested a number of spectral models and found that several of them fit the observed spectra without the need of a soft disc-like component. This result implies that the classical paradigm of a truncated accretion disc in the low/hard state cannot be ruled out by these data. We further discovered a broad iron emission line between 6 and 7 keV in these data. From fits to the line profile we found an inner disc radius that ranges between similar to 6 and 16 gravitational radii, which can be in fact Much larger, LIP to similar to 250 gravitational radii, depending oil the model used to fit the continuum and the line. We discuss the implications of these results in the context of a fully or partially truncated accretion disc.
Mutations in Radial Spoke Head Genes and Ultrastructural Cilia Defects in East-European Cohort of Primary Ciliary Dyskinesia Patients

Primary ciliary dyskinesia (PCD) is a rare (1/20,000), multisystem disease with a complex phenotype caused by the impaired motility of cilia/flagella, usually related to ultrastructural defects of these organelles. Mutations in genes encoding radial spoke head (RSPH) proteins, elements of the ciliary ultrastructure, have been recently described. However, the relative involvement of RSPH genes in PCD pathogenesis remained unknown, due to a small number of PCD families examined for mutations in these genes. The purpose of this study was to estimate the involvement of RSPH4A and RSPH9 in PCD pathogenesis among East Europeans (West Slavs), and to shed more light on ultrastructural ciliary defects caused by mutations in these genes. The coding sequences of RSPH4A and RSPH9 were screened in PCD patients from 184 families, using single strand conformational polymorphism analysis and sequencing. Two previously described (Q109X; R490X) and two new RSPH4A mutations (W356X; IVS3_2–5del), in/around exons 1 and 3, were identified; no mutations were found in RSPH9. We estimate that mutations in RSPH4A, but not in RSPH9, are responsible for 2–3% of cases in the East European PCD population (4% in PCD families without situs inversus; 11% in families preselected for microtubular defects). Analysis of the SNP-haplotype background provided insight into the ancestry of repetitively found mutations (Q109X; R490X; IVS3_2–5del), but further studies involving other PCD cohorts are required to elucidate whether these mutations are specific for Slavic people or spread among other European populations. Ultrastructural defects associated with the mutations were analyzed in the transmission electron microscope images; almost half of the ciliary cross-sections examined in patients with RSPH4A mutations had the microtubule transposition phenotype (9+0 and 8+1 pattern). While microtubule transposition was a prevalent ultrastructural defect in cilia from patients with RSPH4A mutations, similar defects were also observed in PCD patients with mutations in other genes.
On the Evolution of the Temperature-Virial Mass Relation for Clusters of Galaxies

X-ray temperature measurements of clusters of galaxies are now reaching to redshifts high enough to constrain Ω0. A redshift-dependent relation that maps these X-ray temperatures to the virial masses of clusters is an essential ingredient when one is trying to determine cosmological parameters from cluster evolution. Most such relations assume that clusters form from top-hat perturbations that virialized just before the time at which we are observing them. The smaller Ω0 is, the less accurate these relations become. Here we derive a relation between virial mass and cluster temperature that allows for the fact that clusters form gradually and cease forming when the density of the universe drops well below the critical value. We show how sensitively the expected redshift distribution of clusters depends on the mass-temperature relation used and argue that one needs to use a relation that yields no evolution in the low-Ω0 limit.
Studying the evolution of open source systems at different levels of granularity: two case studies

This work presents a study of several evolutionary attributes of two open source software systems: the distributed file system Arla and the stable branch of the Web browser Mozilla. The attributes (size, activity rate and complexity) are visualized over releases using measures at various levels of granularity: folders, files and procedures. A number of hypotheses about the evolutionary behaviour of the systems are considered and, in general, supported by the data from the 2 systems.
Performance and reliability analysis of relevance filtering for scalable distributed interactive simulation

Achieving the real-time linkage among multiple, geographically-distant, local area networks that support distributed interactive simulation (DIS) requires tremendous bandwidth and communication resources. Today, meeting the bandwidth and communication requirements of DIS is one of the major challenges facing the design and implementation of large scale DIS training exercises. In this article, we discuss the DIS scalability problem, briefly overview the major bandwidth reduction techniques currently being investigated and implemented in contemporary DIS systems, and present a detailed analysis on the performance and reliability of relevance filtering—a promising technique to improve the scalability of distributed simulation. The idea of relevance filtering is to analyze the semantic contents of the state update messages of a simulated entity (vehicle) and transmit only the ones found to be relevant to other entities. We present our entity-based model for relevance filtering and discuss the implementation of filtering-at-transmission and filtering-at-reception. We introduce the concept of filtering reliability and present different methods to eliminate or reduce filtering errors. Methods that can ensure complete filtering reliability while providing significant bandwidth reduction are developed. Performance evaluation results of relevance filtering and of the filtering reliability methods are presented. The insight gained from our work and the challenges still facing the design of large scale DIS training exercises are discussed.
Does Hollywood Make Too Many R-Rated Movies?: Risk, Stochastic Dominance, and the Illusion of Expectation

We estimate the probability distributions of budgets, revenues, returns, and profits to G-, PG-, PG13-, and R-rated movies. The distributions are non-Gaussian and show a self-similar stable Paretian form with nonfinite variance and nonstationary mean. The profit distributions have asymmetric tails, which means that Hollywood could trim its "downside" risk while increasing its "upside" possibilities by shifting production dollars out of R-rated movies into G-, PG-, and PG13-rated movies. Stars who are willing to appear in edgy, counterculture R-rated movies for their prestige value may induce an "illusion of expectation" leading studios to "green-light" movies that have biased expectations.