Miracle-dz/UniFAR-FTUs huggingface dataset:
High-throughput single nucleotide polymorphism (SNP) discovery and validation through whole-genome resequencing of hundreds of individuals in Nile tilapia (Oreochromis niloticus)

Nile Tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world and so far, they are mainly based on conventional selection using genealogical and phenotypic information to estimate the genetic merit of breeders and make selection decisions. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to measure in the breeding goal. Thus, SNPs are required to investigate phenotype–genotype associations and determine the genomic basis of economically important traits. We performed de novo SNP discovery in three different populations of farmed tilapias. A total of 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After applying several filtering steps including removing SNP based on genotype and site quality, presence of Mendelian errors, and non unique position in the genome, a total of high quality 50,000 SNP were selected for validation purposes. These SNPs were highly informative in the three populations analyzed showing between 43,869 (94%) and 46,139 (99%) SNP in HWE; 37,843 (76%) and 45,171(90%) SNP with a MAF higher than 0.05 and; 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The final list of 50K SNPs will be very useful for the dissection of economically relevant traits, enhancing breeding programs through genomic selection as well as supporting genetic studies in farmed populations Nile tilapia using dense genome-wide information.
Attending and resident satisfaction with feedback in the emergency department.

OBJECTIVES Effective feedback is critical to medical education. Little is known about emergency medicine (EM) attending and resident physician perceptions of feedback. The focus of this study was to examine perceptions of the educational feedback that attending physicians give to residents in the clinical environment of the emergency department (ED). The authors compared attending and resident satisfaction with real-time feedback and hypothesized that the two groups would report different overall satisfaction with the feedback they currently give and receive in the ED. METHODS This observational study surveyed attending and resident physicians at 17 EM residency programs through web-based surveys. The primary outcome was overall satisfaction with feedback in the ED, ranked on a 10-point scale. Additional survey items addressed specific aspects of feedback. Responses were compared using a linear generalized estimating equation (GEE) model for overall satisfaction, a logistic GEE model for dichotomized responses, and an ordinal logistic GEE model for ordinal responses. RESULTS Three hundred seventy-three of 525 (71%) attending physicians and 356 of 596 (60%) residents completed the survey. Attending physicians were more satisfied with overall feedback (mean score 5.97 vs. 5.29, p < 0.001) and with timeliness of feedback (odds ratio [OR] = 1.56, 95% confidence interval [CI] = 1.23 to 2.00; p < 0.001) than residents. Attending physicians were also more likely to rate the quality of feedback as very good or excellent for positive feedback, constructive feedback, feedback on procedures, documentation, management of ED flow, and evidence-based decision-making. Attending physicians reported time constraints as the top obstacle to giving feedback and were more likely than residents to report that feedback is usually attending initiated (OR = 7.09, 95% CI = 3.53 to 14.31; p < 0.001). CONCLUSIONS Attending physician satisfaction with the quality, timeliness, and frequency of feedback given is higher than resident physician satisfaction with feedback received. Attending and resident physicians have differing perceptions of who initiates feedback and how long it takes to provide effective feedback. Knowledge of these differences in perceptions about feedback may be used to direct future educational efforts to improve feedback in the ED.
University of Alberta

Bacterial adhesion to inert surfaces in aquatic environments is highly dependent on the surface properties of the substratum, which could be altered significantly by the formation of conditioning films. The impacts of extracellular polymeric substances (EPS) and its several representative components of conditioning films on the initial adhesion of the wild type Pseudomonas aeruginosa PAO1 were investigated under four different conditions of ionic strength. Our results showed that bacterial adhesion to bare slides and slides coated with alginate or humic substances increased with the ionic strength. Conversely, BSA and extracted EPS coating enhanced bacterial adhesions only under low ionic strengths, but hindered their adhesion at higher ionic strengths. In addition, during the experiments using the components of P. aeruginosa PAO1 EPS, proteins seem to dominate the impact of EPS on bacterial adhesion. The extended Derjaguin-Landau-Verwey-Overbeek (DLVO) theory was applied to explain the adhesion of P. aeruginosa PAO1 to solid surfaces.
Low-income families: fertility in 1971-1972.

Data from the 1973 Current Population Survey is used to describe the fertility of women in the 6 poverty status classifications as determined by a threshold income for a nonfarm family of 4. Fertility for those below 125% of poverty (low income) declined 29% for the 1971-1972 period as compared with the 1960-1965 period. Fertility among women above 125% of poverty (marginal income) declined 28% during the same period. The greatest decline (35%) was among nonwhites below 125% of poverty. Another way of expressing this is that while the number of women classified as low or marginal income increased the average annual number of births decreased. It is felt that this decline is due in part to the impact of organized family planning programs. It is important that family planning programs do not restrict eligibility for their participation of women of low and marginal income.
Venus atmosphere profile from a maximum entropy principle

The variational method with constraints recently developed by Verkley and Gerkema to describe maximum-entropy atmospheric profiles is generalized to ideal gases but with temperature-dependent specific heats. In so doing, an extended and non standard potential temperature is introduced that is well suited for tackling the problem under consideration. This new formalism is successfully applied to the atmosphere of Venus. Three well defined regions emerge in this atmosphere up to a height of 100 km from the surface: the lowest one up to about 35 km is adiabatic, a transition layer located at the height of the cloud deck and finally a third region which is practically isothermal.
Computational Design of a Time-Dependent Histone Deacetylase 2 Selective Inhibitor

Development of isoform-selective histone deacetylase (HDAC) inhibitors is of great biological and medical interest. Among 11 zinc-dependent HDAC isoforms, it is particularly challenging to achieve isoform inhibition selectivity between HDAC1 and HDAC2 due to their very high structural similarities. In this work, by developing and applying a novel de novo reaction-mechanism-based inhibitor design strategy to exploit the reactivity difference, we have discovered the first HDAC2-selective inhibitor, β-hydroxymethyl chalcone. Our bioassay experiments show that this new compound has a unique time-dependent selective inhibition on HDAC2, leading to about 20-fold isoform-selectivity against HDAC1. Furthermore, our ab initio QM/MM molecular dynamics simulations, a state-of-the-art approach to study reactions in biological systems, have elucidated how the β-hydroxymethyl chalcone can achieve the distinct time-dependent inhibition toward HDAC2.
Improving the Performance of the Space Surveillance Telescope as a Function of Seeing Parameter

Abstract : This research paper investigates ways to improve the detection capability and predict the performance of the Space Surveillance Telescope (SST) system when it's relocated to Exmouth, Australia. The dataset collected by the SST observing the Geosynchronous Earth Orbit (GEO) satellite, ANIK-F1, entering the earth's eclipse is used to test the performance of the three existing and one new detection algorithm. The three existing algorithms are the point detection (Binary Hypothesis Test (BHT)), correlation detection (CD-BHT), and Multi-hypothesis Test using ten hypotheses (MHT10), and the new detection algorithm is the Multi-hypothesis Test using six hypotheses (MHT6). To improve the accuracy and validness of the comparison, a new method of obtaining the true atmospheric seeing parameter, terminator (point before the object entering the eclipse), and parameters used for the comparison are also investigated. It is found that the MHTs vastly outperform the BHTs, and the MHT6 offers a similar or improved performance over the MHT10, but requiring only half of the computing power.
User-Defined Privacy Grid System for Continuous Location-Based Services

Location-based services (LBS) require users to continuously report their location to a potentially untrusted server to obtain services based on their location, which can expose them to privacy risks. Unfortunately, existing privacy-preserving techniques for LBS have several limitations, such as requiring a fully-trusted third party, offering limited privacy guarantees and incurring high communication overhead. In this paper, we propose a user-defined privacy grid system called dynamic grid system (DGS); the first holistic system that fulfills four essential requirements for privacy-preserving snapshot and continuous LBS. (1) The system only requires a semi-trusted third party, responsible for carrying out simple matching operations correctly. This semi-trusted third party does not have any information about a user's location. (2) Secure snapshot and continuous location privacy is guaranteed under our defined adversary models. (3) The communication cost for the user does not depend on the user's desired privacy level, it only depends on the number of relevant points of interest in the vicinity of the user. (4) Although we only focus on range and k-nearest-neighbor queries in this work, our system can be easily extended to support other spatial queries without changing the algorithms run by the semi-trusted third party and the database server, provided the required search area of a spatial query can be abstracted into spatial regions. Experimental results show that our DGS is more efficient than the state-of-the-art privacy-preserving technique for continuous LBS.
An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave

The WaveForm DataBase (WFDB) Toolbox for MATLAB/Octave enables integrated access to PhysioNet’s software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox provides access over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by metadata such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet’s software and databases.
Increasing complexity in hydrologic modelling : an uphill route?

The objective in this research was to analyze the influence of adding complexity on model performance and possibly find an optimum complexity considering model performance. The different complexities were analyzed for their influence on model performance, first using a comparison between complexity steps with equal parameter values. This showed the influence of the added complexity as other factors were kept constant. Secondly, calibration parameter values were optimized using an optimization algorithm after which a validation run was done on which model performance was based. This result was used as best possible simulation with the given complexity. Model performance was based on the capability of the model to reproduce measured discharges and spatially distributed phreatic groundwater heads. The different complexity steps are composed of a very simple lumped model consisting of 1 reservoir to a, as most complex step, spatially distributed model composed of a geological fault, 2 aquifers and detailed description of the surface water system with first-order coupling to the groundwater domain. Due to time restrictions it was not possible to test more complex models including unsaturated zone, van Genuchten, equations and an overland flow domain.
Super-efficient Electron Acceleration by an Isolated Magnetic Reconnection

Magnetic reconnection—the process typically lasting for a few seconds in space—is able to accelerate electrons. However, the efficiency of the acceleration during such a short period is still a puzzle. Previous analyses, based on spacecraft measurements in the Earth’s magnetotail, indicate that magnetic reconnection can enhance electron fluxes up to 100 times. This efficiency is very low, creating an impression that magnetic reconnection is not good at particle acceleration. By analyzing Cluster data, we report here a remarkable magnetic reconnection event during which electron fluxes are enhanced by 10,000 times. Such acceleration, 100 times more efficient than those in previous studies, is caused by the betatron mechanism. Both reconnection fronts and magnetic islands contribute to the acceleration, with the former being more prominent.
Structural and Electronic Properties of Cu2MnSnS4 from Experiment and First‐Principles Calculations

Cu2MnSnS4 shares several promising properties with the widely investigated Cu2ZnSnS4 for photovoltaic applications such as containing only earth abundant and non‐toxic elements, and suitable absorption characteristics for absorber materials. Thin film Cu2MnSnS4 samples with various cation compositions are co‐sputtered reactively followed by a high temperature anneal. Formation of Cu2MnSnS4 and co‐existence of several secondary phases is verified by XRD and Raman. Our investigation of the crystal structure based on first‐principles DFT confirms that stannite crystal structure is preferred over kesterite, although, further verification considering cation disorder is needed. The direct band gap of Cu2MnSnS4 is calculated as 1.52 eV (1.62 eV) for stannite (kesterite), which coincides with the range of the measured band gaps from spectrophotometry of 1.42–1.59 eV. After further annealing treatments below 240 °C, the absorption shows reversible changes: the band gap blue‐shifts and the Urbach tail energy is reduced. It is concluded that, just like Cu2ZnSnS4, disorder also occurs in Cu2MnSnS4. The implications of our findings are discussed and related to the current understanding of cation disorder in Cu2ZnSnS4 and related compounds. Furthermore, for the first time first‐principles DFT investigations are presented for the thiospinel Cu2MnSn3S8 which is observed experimentally as a secondary phase in Sn‐rich Cu2MnSnS4 thin films.
Economics of Climate Change in the Arab World: Case Studies from the Syrian Arab Republic, Tunisia and the Republic of Yemen

This Economics of Climate Change in the Arab World is presents detailed case studies on the impacts of climate change in the Syrian Arab Republic, Tunisia, and the Republic of Yemen that were summarized. The Arab region is already being impacted by climate change through more frequent cyclones, floods, and prolonged droughts. Thousands of rural producers have seen their crops and herds devastated by extreme conditions, and have been forced to abandon their traditional way of life and migrate to crowded urban areas. Those who stay behind in rural areas struggle to cope with shortages of food and water. Climate change affects countries' economies and households through a variety of channels. Rising temperatures and changes in rainfall patterns affect agricultural yields of both rainfed and irrigated crops, and thus global and local food markets. Adaptation is a process that will take place over decades as new information makes policy makers reevaluate their climate vulnerabilities. Still, by seizing the opportunity to act now and act together, the Arab region can not only meet the immense challenges of climate change but advance the development of its entire people.
Management Plan for Antarctic Specially Protected Area No . 165 EDMONSON

Edmonson Point (74°20’ S, 165°08’ E, 5.49 km2), Wood Bay, Victoria Land, Ross Sea, is proposed as an Antarctic Specially Protected Area (ASPA) by Italy on the grounds that it has outstanding ecological and scientific values which require protection from possible interference that might arise from unregulated access. The Area includes ice-free ground and a small area of adjacent sea at the foot of the eastern slopes of Mount Melbourne (2732 m), which is of limited extent and is the subject of ongoing and long-term scientific research.
Establishing monthly rainfall synthetic series by using artificial neural networks for the East Central Region of Madagascar

: An Artificial Neural Network (ANN) model trained by the back-propagation algorithm is proposed for establishing synthetic rainfall scenarios to the Alaotra Region, East-Central Madagascar. This region suffers from irregular rainfalls, which are mostly concentrated between the months of November and April. In this study, 18 years of historical rainfall data were used for calibrating the ANN model and new 18-year synthetic series were generated. Statistics of the ANN synthetic series were compared with those from the historical series. The results showed that the ANN model proved to be capable of preserving the main statistical characteristics of the historical series. These findings suggest that the ANN model may produce reliable synthetic series and hence consistent support for the planning and management of the water resources in the Alaotra Region.
Diffusion ellipsoids of anisotropic porous rocks calculated by X‐ray computed tomography‐based random walk simulations

Water molecules and contaminants migrate in water‐saturated porous strata by diffusion in systems with small Péclet numbers. Natural porous rocks possess the anisotropy for diffusive transport along the percolated pore space. An X‐ray computed tomography (CT) based approach is presented to quickly characterize anisotropic diffusion in porous rocks. High‐resolution three‐dimensional (3‐D) pore images were obtained for a pumice and three sandstones by microfocus X‐ray CT and synchrotron microtomography systems. The cluster‐labeling process was applied to each image set to extract the 3‐D image of a single percolated pore cluster through which diffusing species can migrate a long distance. The nonsorbing lattice random walk simulation was performed on the percolated pore cluster to obtain the mean square displacement. The self‐diffusion coefficient along each direction in the 3‐D space was calculated by taking the time derivative of the mean square displacement projected on the corresponding direction. A diffusion ellipsoid (i.e., polar representation of the direction‐dependent normalized self‐diffusivity) with three orthogonal principal axes was obtained for each rock sample. The 3‐D two‐point autocorrelation was also calculated for the percolated pore cluster of each rock sample to estimate the pore diameter anisotropy. The autocorrelation ellipsoids obtained by the ellipsoid fitting to the high correlation zone were prolate or oblate in shape, presumably depending on the eruption‐induced deformation of magma and regional stress during sandstone diagenesis. The pore network anisotropy was estimated by calculating the diffusion ellipsoid for uniaxially elongated or compressed rock images. The degree and direction of the geological deformation of the samples estimated by the pore diameter anisotropy analysis agreed well with those estimated by the pore network anisotropy analysis. We found that the direction of the geological deformation coincided with the direction of the major (or minor) principal axis of the prolate (or oblate) diffusion ellipsoid for each sample. Thus, it can be concluded that the deformation‐induced pore structure anisotropy is responsible for the anisotropy of the diffusive transport properties.
Imagination and Reactance in a Psi Task Using the Imagery Cultivation Model and a Fuzzy Set Encoded Target Pool

— A psi-conducive altered state of consciousness can be induced through a shamanic-like journeying protocol in accordance with the Imagery Cultivation (IC) model proposed by Storm and Rock (2009a). Storm and Rock (2009b) found that the protocol helped cultivate psi-related mental imagery . Alternatively, it is hypothesized that individuals who do not believe in psi or paranormal phenomena (i.e. ‘goats’) are prone to so-called reactance (Brehm 1966). Reactance is a motivational state aimed at restoring one’s sense of freedom when one feels threatened (Silvia 2005). A reactance treatment in the form of an opinionated communication (perceived as a threat to freedom) can raise reactance, which remains high if no outlet is provided. This induced effect can result in a noncompliant attitude and response, purely as a knee-jerk reaction to the threat. It is hypothesized that higher noncompliant behavior (e.g., psi-missing) can be induced in goats. Storm, Ertel, and Rock (2013) and Storm and Rock (2014) found support for the reactance hypothesis. IC and Reactance principles were used in the present study to manipulate psi in positive and negative directions, respectively. Four groups (total N = 240) were formed: (i) IC/Reactance, (ii) IC/No-Reactance; (iii) No-IC/Reactance, and (iv) No-IC/No-Reactance. The IC treatment produced a non-significant but slightly higher psi effect than the control condition. The reactance treatment had a stronger psychological effect on goats compared with sheep, indicated by a significantly greater discrepancy in goats over the opinionated communication. Significant reactance effects were not found, but specific effects were in the directions expected, with reversals of effects probably due to goats and ‘indecisives’ (mid-range scorers on paranormal belief) in the No-IC/Reactance group. A marginally significant sheep–goat effect was found. Replication attempts would be worthwhile that include refinements to the various IC conditions, and a less persuasive (more challenging) reactance communication.
Sustainability of current account deficits in small states

This article applies the inter-temporal budget constraint framework and panel cointegration tests to examine the sustainability of current account deficits in 17 small states over the period 1980-2017. The findings show the existence of cointegration between real exports and real imports, but with the magnitude of the long-run coefficient being less than one, which support a “weak” form of current account sustainability in small states.