Miracle-dz/UniFAR-FTUs huggingface dataset:
Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering

Next generation sequencing holds great promise for applications of phylogeography, landscape genetics, and population genomics in wild populations of nonmodel species, but the robustness of inferences hinges on careful experimental design and effective bioinformatic removal of predictable artifacts. Addressing this issue, we use published genomes from a tunicate, stickleback, and soybean to illustrate the potential for bioinformatic artifacts and introduce a protocol to minimize two sources of error expected from similarity-based de-novo clustering of stacked reads: the splitting of alleles into different clusters, which creates false homozygosity, and the grouping of paralogs into the same cluster, which creates false heterozygosity. We present an empirical application focused on Ciona savignyi, a tunicate with very high SNP heterozygosity (~0.05), because high diversity challenges the computational efficiency of most existing nonmodel pipelines while also potentially exacerbating paralog artifacts. The simulated and empirical data illustrate the advantages of using higher sequence difference clustering thresholds than is typical and demonstrate the utility of our protocol for efficiently identifying an optimum threshold from data without prior knowledge of heterozygosity. The empirical Ciona savignyi data also highlight null alleles as a potentially large source of false homozygosity in restriction-based reduced representation genomic data.
Cerebral mechanisms underlying orienting of attention towards auditory frequency changes

Brain mechanisms underlying detection of auditory frequency changes were studied with event-related potentials (ERPs) in 14 human subjects discriminating visual stimuli. Scalp-current density mapping revealed bilateral components of mismatch negativity (MMN) in frontal and auditory cortices. Deviance-related activations in frontal and temporal cortex began to be significant at 94 ms and 154 ms in the right hemisphere, and at 128 ms and 132 ms in the left hemisphere. The magnitude of MMN-neuroelectric currents from the left temporal cortex correlated significantly (r = −0.56, p < 0.05) with distraction caused by MMN-eliciting deviant tones. These results suggest a complex cerebral circuitry involved in frequency change detection and strongly support the role of this circuitry in driving attention involuntarily towards potentially relevant frequency changes in the acoustic environment.
Dissolution kinetics of a lateritic nickel ore in sulphuric acid medium

The dissolution kinetics of a lateritic nickel ore in the sulphuric acid solution were investigated. The shrinking core model was applied to the results of experiments. The effects of stirring speed (100–600 rpm), H2SO4 concentration (0.1–2 mol l), leaching temperature (40-96 °C) and the particle size of the ore were studied on the nickel dissolution rate. The correlation coefficients for each different parameters were calculated. The results indicated that the dissolution rate of Ni is controlled by diffusion. The activation energy (Ea) for the dissolution reaction was determined to be 68.66 kJ mol. The Arrhenius constant was calculated to be 8.2578 s. The order of reaction for the H2SO4 concentration and the particle size were also obtained. It was found that the stirring speed had no effect on the rate of nickel dissolution.
Learning outcomes of a work-based training programme : The significance of managerial support

Purpose – The purpose of this study was to explore the extent to which first-line managers' (FLMs') support of employee learning activities influence the learning outcomes and the transfer of training from a work-based vocational education and training (VET) programme. Design/methodology/approach – The study was designed as a multiple-case study including six service units in elder care. Data were collected through interviews with managers and care workers in the six units. Findings – The study demonstrated that the role of FLMs was a significant condition for the learning outcomes attained and for positive transfer of training. For care workers to attain benefits from training that went beyond the individual level, that is, benefits at the level of the work team or the organisation, a supportive FLM role appeared to be necessary. Research limitations/implications – The statistical generalisability of the study is limited by its character of a multiple-case study of six work units. At the same time, a str.
Investigating the role of healthcare in the construction of lay experience of physical disability : a multimethod qualitative study of people living with dystonia

The notion of ‘experiential knowledge’, or knowledge that is derived through and from people’s direct or indirect experience of a condition, has been elusively defined, particularly its relationship to biomedicine. While some researchers argue that this episteme exists independently of expert models of disease, others maintain that it develops alongside and/or through the pervasive hegemonic framework of biomedicine. This research makes a novel contribution to the aforementioned debates by analysing the various ways in which the relationship between experiential and medical knowledge can be both synergistic and epistemologically (dis)similar. This argument is developed through an exploration of the everyday experiences and experiences of healthcare of 42 individuals living with, and managing, the hyperkinetic movement disorder known as dystonia. In many cases of this condition, effective treatment options are limited and prognoses uncertain. Qualitative data were gathered through group and individual interviews and thematically analysed for patterns and relationships, as well as deviant cases. It was found that participants interpreted their experiential knowledge of dystonia in confluence with medical knowledge and their everyday realities. The dynamism of this interrelationship fluctuated in intensity according to the extent to which participants felt that biomedicine could provide them with a socially legitimated explanation of their visceral experiences across different contexts. For example, the negotiation of a diagnosis and/or treatment plan were sites where this interrelationship became particularly fraught resulting in varying dynamic synergies between the two forms of knowledge, which I have termed dissonant and resonant synergies. Through these novel concepts, I demonstrate how the relationship between experiential and medical knowledge transforms and shifts across the disease trajectory of a contested and complex condition like dystonia. In addition to these conceptual insights, a consideration of how health professionals could strive to resonate their knowledge with that of their patients’ is presented.
MODELING AND VISUALIZATION OF ABORIGINAL ROCK ART IN THE BAIAME CAVE

A technique to digitally document and thereby permanently preserve prehistoric rock art has been developed. Laser scanning and texture mapping from digital images were used. Methods involving texture mapping require the exact relationships between the image and geometrical sensors. For geological structures, such as caves, the distinctive features required for registering the texture with the geometric model are difficult to find and extract. The developed technique combines a photogrammetric bundle adjustment and surveying observations to specific detail points to register the images with the scanner data, rather than searching for individual corresponding points. The technique is implemented and tested on Aboriginal painting at the Baiame rock art cave in New South Wales, Australia. The result is an extremely realistic virtual tour of the cave and its important rock art.
Hessenberg varieties and hyperplane arrangements

Abstract Given a semisimple complex linear algebraic group G {{G}} and a lower ideal I in positive roots of G, three objects arise: the ideal arrangement 𝒜 I {\mathcal{A}_{I}} , the regular nilpotent Hessenberg variety Hess ⁡ ( N , I ) {\operatorname{Hess}(N,I)} , and the regular semisimple Hessenberg variety Hess ⁡ ( S , I ) {\operatorname{Hess}(S,I)} . We show that a certain graded ring derived from the logarithmic derivation module of 𝒜 I {\mathcal{A}_{I}} is isomorphic to H * ⁢ ( Hess ⁡ ( N , I ) ) {H^{*}(\operatorname{Hess}(N,I))} and H * ⁢ ( Hess ⁡ ( S , I ) ) W {H^{*}(\operatorname{Hess}(S,I))^{W}} , the invariants in H * ⁢ ( Hess ⁡ ( S , I ) ) {H^{*}(\operatorname{Hess}(S,I))} under an action of the Weyl group W of G. This isomorphism is shown for general Lie type, and generalizes Borel’s celebrated theorem showing that the coinvariant algebra of W is isomorphic to the cohomology ring of the flag variety G / B {G/B} . This surprising connection between Hessenberg varieties and hyperplane arrangements enables us to produce a number of interesting consequences. For instance, the surjectivity of the restriction map H * ⁢ ( G / B ) → H * ⁢ ( Hess ⁡ ( N , I ) ) {H^{*}(G/B)\to H^{*}(\operatorname{Hess}(N,I))} announced by Dale Peterson and an affirmative answer to a conjecture of Sommers and Tymoczko are immediate consequences. We also give an explicit ring presentation of H * ⁢ ( Hess ⁡ ( N , I ) ) {H^{*}(\operatorname{Hess}(N,I))} in types B, C, and G. Such a presentation was already known in type A and when Hess ⁡ ( N , I ) {\operatorname{Hess}(N,I)} is the Peterson variety. Moreover, we find the volume polynomial of Hess ⁡ ( N , I ) {\operatorname{Hess}(N,I)} and see that the hard Lefschetz property and the Hodge–Riemann relations hold for Hess ⁡ ( N , I ) {\operatorname{Hess}(N,I)} , despite the fact that it is a singular variety in general.
How Ready is the East African Community for Monetary Union? New Evidence From an Interest Rate Pass-Through Analysis

The five member countries of the East African Community (EAC), namely, Burundi, Kenya, Rwanda, Tanzania and Uganda have set the target of achieving a monetary union by 2012. The question that arises is: to what extent are they prepared for a monetary integration? Against this backdrop, this paper evaluates the current level of convergence amongst these East African countries by analysing whether the pass-through of monetary policy in the five countries has become similar over time. We use cointegration, error correction, and asymmetric error correction modelling frameworks and interest rate data over a ten year sample period, from 1999 to 2008, in the analysis. The results suggest that the degree of convergence amongst the countries remains low and that there are significant rigidities in the banking markets over time. While the pass-through of monetary policy has improved with respect to the banking loan markets, it has not done so in the deposit market. Overall the evidence suggests that implementing an EAC-wide monetary union will require more work to be done to stimulate the development of their financial systems and to harmonise their financial and monetary policies.
PROBLEMATIC ALCOHOL USE IN TEAM AND INDIVIDUAL EXERCISE SETTINGS

Background. The scholastic literature suggests that alcohol use may be a problem in team sports, but data on the general or average exercisers are lacking. This inquiry examined the prevalence of use and the level of problematic use of alcohol in a highly heterogeneous group of team and individual exercisers. Methods. Two-hundred exercising male (n = 79) and female (n = 121) participants (M age = 26.79 ± SD = 7.88 years) answered demographic questions and completed the Alcohol Use Disorder Identifcation Test (AUDIT). Results. The rate of alcohol drinkers did not diﬀer between the groups, but males exercising in team settings reported higher levels of alcohol drinking problems than individual exercisers in general. The fndings were similar for older (aged 25 years and over) adults too, as shown by a separate analysis of the latter group. The frequency and volume of exercise were unrelated to problematic alcohol use. Cases of high level of alcohol use problems were twice as many in team than in individual exercisers. Conclusions. The prevalence of alcohol use in team and individual exercisers is similar, but problematic alcohol use is greater in the former group. Increased alcohol use problems in team exercisers seem to be limited to men and it occurs in older adults too. Men drink more than women, but the behaviour may have a general social, rather than a sport-specifc, context.Keywords: dependence, drinking, physical activity, social, substance use.
Informal Work and the Diverse Economies of 'Post-Socialist' Europe

Introduction This chapter examines the development and role of ‘informal’ work in the ‘postsocialist’ economies of East-Central Europe. It argues that while there may have been some expansion of the role of ‘informal’ work as households and individuals have witnessed declining living standards and increasing social exclusion since the collapse of state socialism, it is not possible to ‘read off’ these activities from such wider contexts. Drawing upon research in Slovakia, along with a series of other studies, the chapter explores the ways in which ‘informal’ work – as a set of economic practices – is constituted through the articulation of ‘formal’ and ‘informal’ economies and ‘culture’ and ‘economy’. In this sense, such practices cannot easily be seen as the ‘survival strategies’ of the poor, but as complex cultural and socio-economic phenomena. The chapter highlights the importance of an historical and nuanced understanding of the constitution of such conventionally conceived ‘survival strategies’ in East-Central Europe. It argues that consideration of the almost mundane practices of ‘informal’ activity, everyday household production and reciprocity enables an opening of our conceptions of economic forms in post-socialist societies.
On the Autocorrelation Ergodic Properties of Sum-of-Cisoids Rayleigh Fading Channel Simulators

In this paper, we analyze the autocorrelation prop- erties of seven fundamental classes of stochastic sum-of-cisoids (SOC) simulation models for narrowband mobile Rayleigh fading channels. The purpose of this analysis is to determine which classes of SOC models are autocorrelation ergodic (AE), i.e., for which classes of simulation models the time autocorrelation function (TACF) equals the autocorrelation function (ACF) of the ensemble. This information is of practical relevance, since an AE channel simulator allows to accurately emulate the channel's ACF in a single realization, making it possible to bypass the time- consuming computation of the ensemble average. The obtained results conclusively demonstrate that only the class of SOC mod- els defined by cisoids with constant gains, constant frequencies, and random phases possesses the desired AE property. The findings presented in this paper can be used as guidelines for the design of efficient SOC channel simulators that generate Rayleigh fading waveforms with specified autocorrelation properties in each simulation run.
Whose Gym Is It? Gendered Perspectives on Middle and Secondary School Physical Education

This study is the result of an action research project between a large, urban public school system and the faculty in a physical education teacher preparation (PETP) program in the same city. This collaboration led to the creation of a survey, administered to over 5000 students, to collect data about attitudes toward physical education. The data were analyzed for gender differences, and while boys and girls responded similarly on many items, there were some significant differences based on gender. Boys and girls differed on activity preferences as well as responses to environmental and social obstacles. Girls were more interested in cooperative activities, fitness, and dance than boys. Girls also cited logistical issues, such as discomfort with showering and changing, as barriers to participation at higher rates than boys. Physical educators need to consider the differing needs of girls and boys when planning and implementing the curriculum if they are to be successful in attracting and retaining the interest and participation of all their students.
The Shear Testing Programme – I. Weak lensing analysis of simulated ground-based observations

The Shear Testing Programme (STEP) is a collaborative project to improve the accuracy and reliability of all weak lensing measurements in preparation for the next generation of wide-field surveys. In this first STEP paper, we present the results of a blind analysis of simulated ground-based observations of relatively simple galaxy morphologies. The most successful methods are shown to achieve percent level accuracy. From the cosmic shear pipelines that have been used to constrain cosmology, we find weak lensing shear measured to an accuracy that is within the statistical errors of current weak lensing analyses, with shear measurements accurate to better than 7 per cent. The dominant source of measurement error is shown to arise from calibration uncertainties where the measured shear is over or underestimated by a constant multiplicative factor. This is of concern as calibration errors cannot be detected through standard diagnostic tests. The measured calibration errors appear to result from stellar contamination, false object detection, the shear measurement method itself, selection bias and/or the use of biased weights. Additive systematics (false detections of shear) resulting from residual point-spread function anisotropy are, in most cases, reduced to below an equivalent shear of 0.001, an order of magnitude below cosmic shear distortions on the scales probed by current surveys. Our results provide a snapshot view of the accuracy of current ground-based weak lensing methods and a benchmark upon which we can improve. To this end we provide descriptions of each method tested and include details of the eight different implementations of the commonly used Kaiser, Squires & Broadhurst method (KSB+) to aid the improvement of future KSB+ analyses.
Gender behavior in betting markets

We extend gender research on risk behavior to betting markets. Our data set consists of all 5,136,660 bets in New Zealand from 2006 to 2009 and allows assigning each bet to individ-ual bettors. Women are much more prone to the favorite-longshot bias and suffer higher losses. Usually, betting on longshots is associated with higher variance of return, but we find that bet sizes are disproportionally decreasing in odds. Hence, the average risk when betting on longshots is in fact lower. This observation reconciles our findings with gender research on risk preferences and leads to new insights on the favorite-longshot bias.
Vitality of Enterococcus faecalis inside dentinal tubules after five root canal disinfection methods

Aim: To compare the vitality of Enterococcus faecalis within dentinal tubules after subjected to five root canal disinfection methods. Materials and Methods: Dentin blocks (n = 60) were colonized with E. faecalis. After 4 weeks of incubation, the dentin blocks were divided into one control and five test groups (n = 10 each). The root canals of test groups were subjected to one of the disinfection methods, namely, normal saline (NS), sodium hypochlorite (NaOCl), chlorhexidine digluconate (CHX), neodymium-doped yttrium aluminum garnet (Nd: YAG) laser, and diode laser. The effect of disinfection methods was assessed by LIVE/DEAD BacLight stain under the confocal laser scanning microscopy to determine the “zone of dead bacteria” (ZDB). Mean values were calculated for ZDB and the difference between groups was established. Results: Penetration of E. faecalis was seen to a depth of >1000 μm. Viable bacteria were detected with NS irrigation. NaOCl and CHX showed partial ZDB. When the root canals were disinfected with Nd: YAG and diode lasers, no viable bacteria were found. Conclusion: E. faecalis has the ability to colonize inside dentinal tubules to a depth of >1000 μm. In contrast to conventional irrigants, both Nd: YAG and diode lasers were effective in eliminating the vitality of E. faecalis. NS, NaOCl, and CHX showed viable bacteria remaining in dentinal tubules.
Pulsar rotation measures and the magnetic structure of our Galaxy

We have obtained 63 rotation measures (RMs) from polarization observations of southern pulsars, of which 54 are new measurements and three are varied from previous values. The new pulsar RM data at high Galactic latitudes are mostly consistent with the antisymmetric RM distribution found previously. For the Galactic disc, evidence for a field reversal near the Perseus arm, and possibly another beyond it, is presented. Inside the Solar Circle, in addition to the two known field reversals in or near the Carina–Sagittarius arm and the Crux–Scutum arm, a further reversal in the Norma arm is tentatively identified. These reversals, together with the pitch angle derived from pulsar RM and stellar polarization distributions, are consistent with bisymmetric spiral models for the large-scale magnetic field structure in the disc of our Galaxy. However, discrimination between models is complicated by the presence of smaller scale irregularities in the magnetic field, as well as uncertainties in the theoretical modelling.
Severe Starvation-Induced Hepatocyte Autophagy as a Cause of Acute Liver Injury in Anorexia Nervosa: A Case Report

Introduction. Mild elevation of transaminase may be observed in anorexia nervosa, but acute liver injury is uncommon. A complex programmed cell death in response to starvation, called autophagy, has been described in experimental and human studies. Case Presentation. A 24-year-old woman suffering from anorexia nervosa was hospitalized for severe malnutrition. At admission, there were biological signs of acute liver injury but no electrolytic imbalance. After having ruled out the most common causes of liver injury, the patient was carefully refed. As liver tests remained abnormal, liver biopsy was performed. At histology and electron microscopy, numerous signs suggestive of starvation-induced hepatocyte autophagy were found. Discussion. Severe starvation can be associated with acute liver injury that is slowly reversible with careful enteral nutrition. In this clinical situation, profound hepatic glycogen depletion in association with autophagy appears as the leading cause of liver injury.
Investigating On-Screen Gamepad Designs for Smartphone-Controlled Video Games

On-screen gamepads are increasingly used as controllers for video games on distant screens, yet lack the typical tactile feedback known from hardware controllers. We conducted a comparative lab study to investigate four smartphone gamepads inspired by traditional game controllers and mobile game controls (directional buttons, directional pad, floating joystick, tilt control). The study consisted of both completing a formal control test as well as controlling two popular video games of different genres (Pac-Man and Super Mario Bros.). The results indicate that the directional buttons require the most attention of the user, however, work precisely for direction-restricted navigational tasks. Directional pad and joystick showed a similar performance, yet they encourage drifting and unintended operations when the user is focused on the remote screen. While currently unfamiliar to many users, the floating joystick can reduce the glances at the device. Tilt turned out to be not sufficiently precise and quick for the investigated tasks. The article concludes with derived design guidelines with easily realizable measures for typical contexts such as casual gaming at home or spontaneous gaming on public displays.