Miracle-dz/UniFAR-FTUs huggingface dataset:
An Individual-based Probabilistic Model for Fish Stock Simulation

We define an individual-based probabilistic model of a sole (Solea solea) behaviour. The individual model is given in terms of an Extended Probabilistic Discrete Timed Automaton (EPDTA), a new formalism that is introduced in the paper and that is shown to be interpretable as a Markov decision process. A given EPDTA model can be probabilistically model-checked by giving a suitable translation into syntax accepted by existing model-checkers. In order to simulate the dynamics of a given population of soles in different environmental scenarios, an agent-based simulation environment is defined in which each agent implements the behaviour of the given EPDTA model. By varying the probabilities and the characteristic functions embedded in the EPDTA model it is possible to represent different scenarios and to tune the model itself by comparing the results of the simulations with real data about the sole stock in the North Adriatic sea, available from the recent project SoleMon. The simulator is presented and made available for its adaptation to other species.
Wafer-scale epitaxial graphene on SiC for sensing applications

The epitaxial graphene-on-silicon carbide (SiC-G) has advantages of high quality and large area coverage owing to a natural interface between graphene and SiC substrate with dimension up to 100 mm. It enables cost effective and reliable solutions for bridging the graphene-based sensors/devices from lab to industrial applications and commercialization. In this work, the structural, optical and electrical properties of wafer-scale graphene grown on 2’’ 4H semi-insulating (SI) SiC utilizing sublimation process were systemically investigated with focus on evaluation of the graphene’s uniformity across the wafer. As proof of concept, two types of glucose sensors based on SiC-G/Nafion/Glucose-oxidase (GOx) and SiC-G/Nafion/Chitosan/GOx were fabricated and their electrochemical properties were characterized by cyclic voltammetry (CV) measurements. In addition, a few similar glucose sensors based on graphene by chemical synthesis using modified Hummer’s method were also fabricated for comparison.
Scalability of reliable group communication using overlays

This study provides some new insights into the scalability of reliable group communication mechanisms using overlays. These mechanisms use individual TCP connections for packet transfers between end-systems. End-systems store incoming packets and forward them to downstream nodes using different unicast TCP connections. In this paper we assume that buffers in end-systems are large enough for the transfers. It is shown that the throughput of the reliable overlay group communication scales in the sense that for all multicast tree sizes and topologies, the group throughput is strictly positive under natural conditions. This is in contrast with the IP supported multicast paradigm where reliable protocols have vanishing throughput when the group size tends to infinity. The scalability of packet delay and buffer occupancy is then investigated. In the absence of additional control, the occupancy of the buffer and the latency in the end-systems explodes with time. It is then shown that proactive rate throttle mechanism implemented at the source leads to finite packet latency and buffer occupancy in any end-system of the network provided certain moment conditions are satisfied by cross traffic in the routers.
The fifth subunit in α3β4 nicotinic receptor is more than an accessory subunit

The α3ß4 subtype is the predominant neuronal nicotinic acetylcholine receptor present in the sensory and autonomic ganglia and in a subpopulation of brain neurons. This subtype can form pentameric receptors with either 2 or 3 ß4 subunits that have different pharmacologic and functional properties. To further investigate the role of the fifth subunit, we coexpressed a dimeric construct coding for a single polypeptide containing the ß4and α3 subunit sequences, with different monomeric subunits. With this strategy, which allowed the formation of single populations of receptors with unique stoichiometry, we demonstrated with immunofluorescence and biochemical and functional assays that only the receptors with 3 ß4 subunits are efficiently expressed at the plasma membrane. Moreover, the LFM export motif of ß4 subunit in the fifth position exerts a unique function in the regulation of the intracellular trafficking of the receptors, their exposure at the cell surface, and consequently, their function, whereas the same export motif present in the ß4 subunits forming the acetylcholine binding site is dispensable. —Crespi, A. , Plutino, S. , Sciaccaluga, M. , Righi, M. , Borgese, N. , Fucile, S. , Gotti, C. , Colombo, S. F. The fifth subunit in α3ß4 nicotinic receptor is more than an accessory subunit. FASEB J. 32, 4190–4202 (2018). www.fasebj. org
Justification du modèle et caractère bien posé des équations primitives quasi-hydrostatiques

Ce travail a pour but de presenter et d'etudier les equations primitives quasi-hydrostatiques (QHPE). Ce modele, qui derive des equations completes de la mecanique des fluides geophysiques dans la limite d'un faible rapport d'aspect, est plus complet que le modele hydrostatique classique, car il s'abstrait de l'approximation dite traditionnelle qui consiste a negliger une partie de la force de Coriolis. Nous justifions dans cet article la derivation des QHPE avant de montrer leur caractere bien pose. ---Derivation and Well-Posedness of the Quasi-Hydrostatic Primitive Equations. This paper aims at introducing and studying the well-posedness of the quasi-hydrostatic primitive equations (QHPE). This model, that derives from the full non-hydrostatic model for geophysical uid dynamics in the zero-limit of the aspect ratio, is more realistic than the classical hydrostatic model, since the traditionnal approximation that consists in neglecting a part of the Coriolis force is relaxed. After justifying the derivation of the QHPE model, we give some well-posedness arguments.
Water-Current and IMU Aided AUV Localization in Deep MidWater

Survey class Autonomous Underwater Vehicles (AUVs) typically rely on Doppler Velocity Logs (DVL) for precise navigation near the seafloor. In cases where the distance to the seafloor is greater than the DVL bottom lock range, localizing between the surface where GPS is available and the seafloor presents a localization problem, since both GPS and DVL are unavailable in the mid-water column. Previous work [3] [6] proposed a solution to navigation in the mid-water column that exploits the stability of the vertical water current profile in space over the minutes scale. With repeated measurements of these currents with the Acoustic Doppler Current Profiler (ADCP) mode of the DVL during vertical descent, along with sensor fusion of other low cost sensors, position error growth is constrained during the dive. Following DVL bottom lock, due to correlations in the joint vehicle and water current velocity estimation, the entire velocity history is further constrained. Previous work in this area includes [4] to generalize the ADCP-aided filter to horizontal motion, including using ADCP beam geometry and a water-volume grid approach for the water velocity state space. Furthermore, a number of extensions are developed in [5] to improve navigation performance during missions characterized by prolonged time-scales. In this paper, the ADCP-aided filter is applied to a 25 hour 5000m deep straight line mission, with the environmental effects considered. Also, the addition of IMU acceleration outputs from a navigation grade IMU for the prediction model as an alternative to the constant velocity (CV) model are implemented and analyzed. The re-acquisition of DVL bottom-lock at the end of the mission, simulating the vehicle lowering altitude to within range of the seafloor, is also investigated.
Action Classification via Concepts and Attributes

Classes in natural images tend to follow long tail distributions. This is problematic when there are insufficient training examples for rare classes. This effect is emphasized in compound classes, involving the conjunction of several concepts, such as those appearing in action-recognition datasets. In this paper, we propose to address this issue by learning how to utilize common visual concepts which are readily available. We detect the presence of prominent concepts in images and use them to infer the target labels instead of using visual features directly, combining tools from vision and natural-language processing. We validate our method on the recently introduced HICO dataset reaching a mAP of 31.54% and on the Stanford-40 Actions dataset, where the proposed method outperforms that obtained by direct visual features, obtaining an accuracy 83.12%. Moreover, the method provides for each class a semantically meaningful list of keywords and relevant image regions relating it to its constituent concepts.
Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields

Motivation: Incorporating gene interaction data into the identification of ‘hit’ genes in genomic experiments is a well‐established approach leveraging the ‘guilt by association’ assumption to obtain a network based hit list of functionally related genes. We aim to develop a method to allow for multivariate gene scores and multiple hit labels in order to extend the analysis of genomic screening data within such an approach. Results: We propose a Markov random field‐based method to achieve our aim and show that the particular advantages of our method compared with those currently used lead to new insights in previously analysed data as well as for our own motivating data. Our method additionally achieves the best performance in an independent simulation experiment. The real data applications we consider comprise of a survival analysis and differential expression experiment and a cell‐based RNA interference functional screen. Availability and implementation: We provide all of the data and code related to the results in the paper. Contact: sean.j.robinson@utu.fi or laurent.guyon@cea.fr Supplementary information: Supplementary data are available at Bioinformatics online.
Social Anhedonia and Romantic Relationship Processes.

OBJECTIVE Social anhedonia is a deficiency in the capacity to experience pleasure from social interactions. This study examined the implications of social anhedonia for romantic relationship functioning, including the association of social anhedonia with sentiments toward romantic partners that are central to relationship functioning (satisfaction, commitment, regard for the partner, and care for the partner's welfare) and analogous perceptions of the partner's sentiments. METHOD Data were collected from 281 participants who were involved in romantic relationships. RESULTS Social anhedonia predicted less satisfaction, regard, and care, and these effects were independent of attachment insecurity and self-esteem. In addition, social anhedonia had an indirect negative effect on commitment via attachment avoidance. Social anhedonia also predicted more negative perceptions of the partner's sentiments. CONCLUSIONS Results suggest that social anhedonia may undermine the functioning of romantic relationships by reducing positive sentiments toward partners and security in the partner's sentiments toward the self.
Isca, v1.0: a framework for the global modelling of the atmospheres of Earth and other planets at varying levels of complexity

Abstract. Isca is a framework for the idealized modelling of the global circulation of planetary atmospheres at varying levels of complexity and realism. The framework is an outgrowth of models from the Geophysical Fluid Dynamics Laboratory in Princeton, USA, designed for Earth's atmosphere, but it may readily be extended into other planetary regimes. Various forcing and radiation options are available, from dry, time invariant, Newtonian thermal relaxation to moist dynamics with radiative transfer. Options are available in the dry thermal relaxation scheme to account for the effects of obliquity and eccentricity (and so seasonality), different atmospheric optical depths and a surface mixed layer. An idealized grey radiation scheme, a two-band scheme, and a multiband scheme are also available, all with simple moist effects and astronomically based solar forcing. At the complex end of the spectrum the framework provides a direct connection to comprehensive atmospheric general circulation models. For Earth modelling, options include an aquaplanet and configurable continental outlines and topography. Continents may be defined by changing albedo, heat capacity, and evaporative parameters and/or by using a simple bucket hydrology model. Oceanic Q fluxes may be added to reproduce specified sea surface temperatures, with arbitrary continental distributions. Planetary atmospheres may be configured by changing planetary size and mass, solar forcing, atmospheric mass, radiation, and other parameters. Examples are given of various Earth configurations as well as a giant planet simulation, a slowly rotating terrestrial planet simulation, and tidally locked and other orbitally resonant exoplanet simulations. The underlying model is written in Fortran and may largely be configured with Python scripts. Python scripts are also used to run the model on different architectures, to archive the output, and for diagnostics, graphics, and post-processing. All of these features are publicly available in a Git-based repository.
Effect of the School-Based Telemedicine Enhanced Asthma Management (SB-TEAM) Program on Asthma Morbidity: A Randomized Clinical Trial

Importance Poor adherence to recommended preventive asthma medications is common, leading to preventable morbidity. We developed the School-Based Telemedicine Enhanced Asthma Management (SB-TEAM) program to build on school-based supervised therapy programs by incorporating telemedicine at school to overcome barriers to preventive asthma care. Objective To evaluate the effect of the SB-TEAM program on asthma morbidity among urban children with persistent asthma. Design, Setting, and Participants In this randomized clinical trial, children with persistent asthma aged 3 to 10 years in the Rochester City School District in Rochester, New York, were stratified by preventive medication use at baseline and randomly assigned to the SB-TEAM program or enhanced usual care for 1 school year. Participants were enrolled at the beginning of the school year (2012-2016), and outcomes were assessed through the end of the school year. Data were analyzed between May 2017 and November 2017 using multivariable modified intention-to-treat analyses. Interventions Supervised administration of preventive asthma medication at school as well as 3 school-based telemedicine visits to ensure appropriate assessment, preventive medication prescription, and follow-up care. The school site component of the telemedicine visit was completed by telemedicine assistants, who obtained history and examination data. These data were stored in a secure virtual waiting room and then viewed by the primary care clinician, who completed the assessment and communicated with caregivers via videoconference or telephone. Preventive medication prescriptions were sent to pharmacies that deliver to schools for supervised daily administration. Main Outcomes and Measures The primary outcome was the mean number of symptom-free days per 2 weeks, assessed by bimonthly blinded interviews. Results Of the 400 enrolled children, 247 (61.8%) were male and 230 (57.5%) were African American, and the mean (SD) age was 7.8 (1.7) years. Demographic characteristics and asthma severity in the 2 groups were similar at baseline. Among children in the SB-TEAM group, 196 (98.0%) had 1 or more telemedicine visits, and 165 (82.5%) received supervised therapy through school. We found that children in the SB-TEAM group had more symptom-free days per 2 weeks postintervention compared with children in the enhanced usual care group (11.6 vs 10.97; difference, 0.69; 95% CI, 0.15-1.22; P = .01), with the largest difference observed at the final follow-up (difference, 0.85; 95% CI, 0.10-1.59). In addition, children in the SB-TEAM group were less likely to have an emergency department visit or hospitalization for asthma (7% vs 15%; odds ratio, 0.52; 95% CI, 0.32-0.84). Conclusions and Relevance The SB-TEAM intervention significantly improved symptoms and reduced health care utilization among urban children with persistent asthma. This program could serve as a model for sustainable asthma care among school-aged children. Trial Registration clinicaltrials.gov Identifier: NCT01650844
Neutrophil to lymphocyte ratio in patients with vitiligo

Introduction There are a few studies showing an increased risk of insulin resistance, metabolic syndrome, and oxidative stress in patients with vitiligo. Aim To investigate whether systemic inflammation is increased in vitiligo patients in a case-control study design. Material and methods Nonsegmental vitiligo patients who had been followed at the outpatient dermatology clinic of a university-affiliated teaching hospital, and healthy controls were enrolled in the study. Patients who were receiving systemic treatments and having a systemic disease such as diabetes mellitus and thyroiditis were excluded. Demographic features were recorded and peripheral blood samples were taken from all participants to study serum whole blood count, creatinine, and C-reactive protein (CRP). Results Fifty patients with localized vitiligo, 43 patients with generalized vitiligo, and 50 healthy volunteers were enrolled in the study. Neutrophil to lymphocyte ratio and serum CRP levels were significantly higher in patients who have generalized vitiligo than those with localized vitiligo and healthy controls. However, there was no significant difference regarding neutrophil to lymphocyte ratio (NLR) and CRP between localized vitiligo and control groups. Conclusions Patients with generalized vitiligo seem to have increased systemic inflammation compared with localized vitiligo and control subjects in our cohort. To the best of our knowledge, this is the first study in the literature showing increased NLR values in generalized vitiligo patients. Further studies with cardiovascular disease markers are required to elicit this association better.
The Property Value Impacts of Groundwater Contamination: Agricultural Runoff and Private Wells

There are few studies examining the impacts of groundwater quality on residential property values. Using a unique dataset of groundwater well tests, we link residential transactions to home-specific contamination levels and undertake a hedonic analysis of homes in Lake County, Florida; where groundwater pollution concerns stem primarily from agricultural runoff. We find that testing and contamination yield a 2% to 6% depreciation, an effect that diminishes after the situation is resolved. Focusing specifically on nitrogen-based contamination, we find prices decline mainly at concentrations above the regulatory health standard, suggesting up to a 15% deprecation at levels twice the standard.
Mustguseal: a server for multiple structure-guided sequence alignment of protein families

Motivation Comparative analysis of homologous proteins in a functionally diverse superfamily is a valuable tool at studying structure-function relationship, but represents a methodological challenge. Results The Mustguseal web-server can automatically build large structure-guided sequence alignments of functionally diverse protein families that include thousands of proteins basing on all available information about their structures and sequences in public databases. Superimposition of protein structures is implemented to compare evolutionarily distant relatives, whereas alignment of sequences is used to compare close homologues. The final alignment can be downloaded for a local use or operated on-line with the built-in interactive tools and further submitted to the integrated sister web-servers of Mustguseal to analyze conserved, subfamily-specific and co-evolving residues at studying a protein function and regulation, designing improved enzyme variants for practical applications and selective ligands to modulate functional properties of proteins. Availability and implementation Freely available on the web at https://biokinet.belozersky.msu.ru/mustguseal. Contact vytas@belozersky.msu.ru. Supplementary information Supplementary data are available at Bioinformatics online.
Extrapair Fertilizations and the Potential for Sexual Selection in a Socially Monogamous Songbird

ABSTRACT. Variation in mating success among individuals is the basis for sexual selection and the evolution of elaborate secondary sexual traits. In socially monogamous species, variation in mating success is generally thought to be small, but a skewed adult sex ratio, differences in female fecundity, and extrapair fertilizations that arise from matings outside the social pair bond can increase variance in reproductive success. We investigated how these factors generate the opportunity for sexual selection in the socially monogamous White-crowned Sparrow (Zonotrichia leucophrys pugetensis). We found a 38% increase in the standardized actual variance in reproductive success compared to the apparent standardized variance of males because of the contribution of extrapair fertilizations to total reproductive success. However, partitioning variance into within-pair and extrapair components showed that the majority of variance in male reproductive success was attributable to within-pair success and a skewed adult sex ratio. Finally, reproductive success increased significantly with the number of mates in males but not in females, which suggests a stronger potential for sexual selection in males than in females in this population. Our results confirm that social mating success may increase the variance in reproductive success more than extrapair fertilizations in some monogamous species. Thus, the evolution of sexual ornaments may be influenced equally or more by the number of available mates and their fecundity than by extrapair matings.
Robust Stereo Visual Inertial Odometry for Fast Autonomous Flight

In recent years, vision-aided inertial odometry for state estimation has matured significantly. However, we still encounter challenges in terms of improving the computational efficiency and robustness of the underlying algorithms for applications in autonomous flight with microaerial vehicles, in which it is difficult to use high-quality sensors and powerful processors because of constraints on size and weight. In this letter, we present a filter-based stereo visual inertial odometry that uses the multistate constraint Kalman filter. Previous work on the stereo visual inertial odometry has resulted in solutions that are computationally expensive. We demonstrate that our stereo multistate constraint Kalman filter (S-MSCKF) is comparable to state-of-the-art monocular solutions in terms of computational cost, while providing significantly greater robustness. We evaluate our S-MSCKF algorithm and compare it with state-of-the-art methods including OKVIS, ROVIO, and VINS-MONO on both the EuRoC dataset and our own experimental datasets demonstrating fast autonomous flight with a maximum speed of $\text{17.5}$ m/s in indoor and outdoor environments. Our implementation of the S-MSCKF is available at https://github.com/KumarRobotics/msckf_vio.