Miracle-dz/UniFAR-FTUs huggingface dataset:
How frugal is mother nature with haplotypes?

MOTIVATION Inference of haplotypes from genotype data is crucial and challenging for many vitally important studies. The first, and most critical step, is the ascertainment of a biologically sound model to be optimized. Many models that have been proposed rely partially or entirely on reducing the number of unique haplotypes in the solution. RESULTS This article examines the parsimony of haplotypes using known haplotypes as well as genotypes from the HapMap project. Our study reveals that there are relatively few unique haplotypes, but not always the least possible, for the datasets with known solutions. Furthermore, we show that there are frequently very large numbers of parsimonious solutions, and the number increases exponentially with increasing cardinality. Moreover, these solutions are quite varied, most of which are not consistent with the true solutions. These results quantify the limitations of the Pure Parsimony model and demonstrate the imperative need to consider additional properties for haplotype inference models. At a higher level, and with broad applicability, this article illustrates the power of combinatorial methods to tease out imperfections in a given biological model.
Swift contribution to our understanding of Ultraluminous X-ray Sources

In the coming years a significant improvement in our understanding of Ultraluminous X-ray Sources (ULXs) is expected to come from the study of their long term X-ray variability and from the discovery and follow up of the still largely unknown population of transient sources. This requires a flexible and fast scheduling strategy to monitor ULXs and observe them in 'ToO' mode. Swift has shown to be the best suited X-ray facility for this purpose, capable to do effectively both things for bright ULXs. After a short summary on the properties of ULXs and the recent advances made in this field, I will focus on the contribution given by Swift, reviewing the main results obtained by this extraordinarily successful mission.
A characterization of the semisimplity of Lie-type algebras through the existence of certain linear bases

The class of Lie-type algebras contains the ones of associative algebras, Lie algebras and Leibniz algebras among other classes of algebras. We show that a Lie-type algebra , of arbitrary dimension and over an arbitrary base field, is semisimple if and only if it has zero annihilator and admits a weak-division linear basis. As a corollary, the simplicity of is also characterized.
Using Intervention Mapping to Develop and Facilitate Implementation of a Multifaceted Behavioural Intervention Targeting Physical Activity and Sedentary Behaviour in Stroke Survivors: Physical Activity Routines After Stroke (PARAS)

BackgroundThe benefits of increased physical activity for stroke survivors include improved walking ability, balance and mood. However, less than 30% achieve recommended levels of physical activity, and high levels of sedentary behaviour are reported. We engaged stroke survivors, informal carers and healthcare professionals (HCPs) in a co-design process to develop an evidence-informed behavioural intervention targeting physical activity and sedentary behaviour for use by stroke rehabilitation teams. MethodsIntervention Mapping was used as a framework for intervention development. Step 1 involved a systematic review, focus group discussions and a review of existing care pathways. Step 2 involved identification of social cognitive determinants of behavioural change and behavioural outcomes of the intervention. Step 3 involved linking the determinants of behavioural outcomes with specific behaviour change techniques to target the behaviours of interest. Step 4 involved the development of the intervention informed by steps 1 to 3. Subsequently, an implementation plan was developed (Step 5) followed by an evaluation plan (Step 6). ResultsSystematic review findings informed selection of nine ‘promising’ behaviour change techniques (e.g. goal setting-behaviour; problem-solving). Focus groups with stroke survivors (n=18) and HCPs (n=24) identified the need for an intervention that could be delivered at different time points within the rehabilitation pathway, tailored to individual needs and circumstances with training for HCPs delivering the intervention. Intervention delivery was considered feasible within local community stroke services. The target behaviours for the intervention were physical activity and sedentary behaviour of stroke survivors. Assessment of acceptability and usability with 11 HCPs and 21 stroke survivors/relatives identified issues around self-monitoring tools; the need for a repository of local services for physical activity; and the need for face-to-face feedback provision to HCPs following delivery of the intervention for optimisation purposes. Face-to-face training for HCPs was delivered to support faithful delivery of the intervention within community settings. A feasibility study protocol was designed to evaluate the intervention.ConclusionsA systematic development process using intervention mapping resulted in a multi-faceted evidence- and theory-informed intervention (Physical Activity Routines After Stroke - PARAS) for delivery by community stroke rehabilitation teams. Trial registration: Trial identifier: ISRCTN35516780, date of registration: 24/10/2018, URL http://www.isrctn. com/ISRCTN35516780
Method of differentiated analysis of IR thermal maps of the exposed cerebral cortex when neurosurgical operations are being performed

This paper proposes an approach to the differentiated analysis of the temperature characteristics of exposed human dura mater and cerebral cortex within the operational window when intracerebral tumors are being removed. The key features of the method are the following: Taking into account the complex shape of the regions to be analyzed, extensive automation of batch processing of the IR thermal maps, operation with sizable samples (more than forty patients), and the use of rigorous statistical estimates. The central problem of using the technique developed here is how to analyze the data on the dynamics of thermal patterns in response to a cold test.
Extended Target Tracking Algorithm Based on Random Hypersurface Model with Glint Noise

Due to the fact that the unmatching of extended targets’ measurements noise is also assumed as Gaussian distribution and conventional algorithm cannot estimate target’s extent under the circumstance of unknown measurement noise covariance, a new multiple extended target tracking algorithm based on variational bayesian random hypersurface model (VB-RHM) is proposed, which is embedded into CPHD filter frame. Measurement noise is modeled by glint noise with t-distribution, its parameters are assumed to have a Gamma prior distribution so that the predicted and updated PHDs can have mixture of Gaussians representations. A variational bayesian procedure is applied to iteratively estimate parameters of the mixture distributions through random hypersurface model CPHD prediction and update steps. The simulation results show that the proposed algorithm VB-RHM-CPHD can track multiple extended targets’ kinematic state and object extension under the condition of unknown numbers and measurement noise covariance adaptively. In addition, it has an improved precision compared with conventional RHM-GGM-CPHD algorithm.
An experimental study of the aerodynamic performance of a double annular combustor system

An experimental investigation has been carried out into the performance of an advanced twin combustor system for use in modern aircraft gas turbines. Measurements were made on a 48° sector test rig, the working section of which generically represented the geometry of a dump diffuser system. The flow entered the test rig through an inlet duct containing straight vanes and then passed immediately into the pre-diffuser. From the dump region downstream, the flow was allowed to enter the three annuli and two combustors in the correct mass flow proportions. The combustors were outwardly canted at an angle of 11.5° and although they were not engine representative in terms of dilution holes and cooling rings, the burner porosity was modelled correctly. [Continues. ]
Downstream Competition , Foreclosure , and Vertical Integration

This paper analyzes the impact of competition among downstream ̄rms on an upstream ̄rm's payo® and on its incentive to vertically integrate when ̄rms on both segments negotiate optimal contracts. We argue that the upstream ̄rm is better o® encouraging competition when the downstream ̄rms have high bargaining power. We examine the interactions between vertical integration and competition among the downstream ̄rms. The possibility of vertical integration may be a barrier to entry and may trigger strategic horizontal spin-o®s or mergers. An upstream duopoly is better o® with a competitive downstream industry, and a partially integrated structure may be anti-competitive.
Rheology signature of flocculated silica suspensions

We experimentally study the behavior of suspensions of silica particles in aqueous solution. Despite many studies on these materials, the dependence of the overall rheological properties of the suspension on particle size, solid volume fraction, ionic strength, and strain history remains debated. In this paper, we manage to manufacture materials and develop procedures that allow us (i) to approach this problem in the best possible way and (ii) to check that the results obtained with well controlled systems (monodisperse silica spherical particles) also apply to less controlled suspensions (crushed silica particles). We find that the elastic modulus-particle size and yield stress-particle size relationships follow power laws that disagree with classical models from the literature. We also show that elastic modulus versus yields stress data fall on a single master curve when rescaled by particle size, whatever are solid volume fraction, resting time, and ionic strength. This suggests that the rescaled elastic modulus can play the role of a parameter in a structural kinetics model of the behavior of thixotropic suspensions. Furthermore confocal observations of the system provided evidence that the evolution of the overall properties of the material with resting time cannot be ascribed to changes in the particle network.We experimentally study the behavior of suspensions of silica particles in aqueous solution. Despite many studies on these materials, the dependence of the overall rheological properties of the suspension on particle size, solid volume fraction, ionic strength, and strain history remains debated. In this paper, we manage to manufacture materials and develop procedures that allow us (i) to approach this problem in the best possible way and (ii) to check that the results obtained with well controlled systems (monodisperse silica spherical particles) also apply to less controlled suspensions (crushed silica particles). We find that the elastic modulus-particle size and yield stress-particle size relationships follow power laws that disagree with classical models from the literature. We also show that elastic modulus versus yields stress data fall on a single master curve when rescaled by particle size, whatever are solid volume fraction, resting time, and ionic strength. This suggests that the rescaled elast.
Orbit Spaces and Pre-Bundles of CNF-Base Hypergraphs

—In this paper an abstract discrete pre-bundle hierarchy is introduced and discussed. Numerous pre-bundles are identiﬁed for classes of CNF base hypergraphs over positive integer sets. Thereby the question whether such instances admit a given number of orbits of ﬁbre-transversals provided by the CNF complementation group is attacked. Extending a preliminary version several more pre-bundles and properties of the orbit spaces are established.
Forage fiber effects on particle size reduction, ruminal stratification, and selective retention in heifers fed highly digestible grass/clover silages.

The objective of this study was to investigate the effect of NDF content in highly digestible grass/clover silage on particle size reduction, ruminal stratification, and selective retention in dairy heifers. The reduction in particle size from feed to feces was evaluated and related to feed intake, chewing activity, and apparent digestibility. Four grass/clover harvests (Mixtures of Lolium perenne, Trifolium pratense, and Trifolium repens) were performed from early May to late August at different maturities, at different regrowth stages, and with different clover proportions, resulting in silages with NDF contents of 312, 360, 371, and 446 g/kg DM, respectively, and decreasing NDF digestibility with greater NDF content. Four rumen-fistulated dairy heifers were fed silage at 90% of ad libitum level as the only feed source in a 4 × 4 Latin square design. Silage, ingested feed boluses, medial and ventral ruminal digesta, and feces samples were washed with neutral detergent in nylon bags of 10-μm pore size, freeze dried, and divided into small (<0.212 mm), medium (0.212 to 1 mm), and large : LP; >1 mm) particles by dry-sieving. Chewing activity, rumen pool size, and apparent digestibility were measured. Intake of NDF increased linearly from 2.3 to 2.8 kg/d with greater NDF content of forages (P = 0.01), but silages were exposed to similar eating time (P = 0.55) and rumination time per kg NDF (P = 0.35). No linear effect of NDF content was found on proportion of LP in ingested feed boluses (P = 0.31), medial rumen digesta (P = 0.95), ventral rumen digesta (P = 0.84), and feces (P = 0.09). Greater proportions of DM (P < 0.001) and particulate DM (P = 0.008) were found in medial ruminal digesta compared with ventral rumen, and differences in DM proportion increased with greater NDF content (P = 0.02). Particle size distributions were similar for digesta from the medial and ventral rumen regardless of NDF content of the silages (P > 0.13). The LP proportion was >30% of particles in the ventral and medial rumen, whereas in the feces, the LP proportion was <2%. Particle size stratification of the rumen was undetectable regardless of NDF content of the silages, stressing that the retention mechanism of large undigested particles lies elsewhere than with particle entrapment in the rumen mat. In this study, forage particle breakdown, ruminal stratification, and retention of particles in the rumen were not affected by NDF content of highly digestible grass/clover silages.
Influence of a Non-uniform Longitudinal Heating on High Brightness Electron Beams for FEL

Laser-heater systems are essential tools to control and optimize high-gain free electron lasers (FELs), working in the x-ray wavelength range. Indeed, these systems induce a controllable heating of the energy spread of the electron bunch. The heating allows in turn to suppress longitudinal microbunching instabilities limiting the FEL performance. In this communication, we show that a long-wavelength energy modulation of the electron beam induced by the laser heater can persist until the beam entrance in the undulators, affecting the FEL emission process. This non-uniform longitudinal heating can be exploited to investigate the electronbeam microbunching in the linac, as well as to control the FEL spectral properties. Here, we present experimental, analytical and numerical studies carried out at FERM
Spectral Line Shape and Modulation Response of Asymmetric Non-Hermitian Photonic Meta-Molecules

A photonic dimer of two optically coupled lasers is analyzed as an optical meta-molecule for non-Hermitian photonic applications. Spectral signatures of exceptional points and Hopf bifurcations are shown for generic asymmetric configurations. A significant enhancement in the small signal modulation response under differential pumping is observed.
Functional Data Analysis

Functional data analysis (FDA) models data using functions or functional parameters. The complexity of the functions is not assumed to be known in advance, so that methods are used for approximating these with as much flexibility as the data require. Keywords: functional parameters; splines; basis functions; roughness penalty; dynamic model; registration
The effects of assembly bias on the inference of matter clustering from galaxy-galaxy lensing and galaxy clustering

The combination of galaxy-galaxy lensing (GGL) and galaxy clustering is a promising route to measuring the amplitude of matter clustering and testing modiﬁed gravity theories of cosmic acceleration. Halo occupation distribution (HOD) modeling can extend the approach down to nonlinear scales, but galaxy assembly bias could introduce systematic errors by causing the HOD to vary with large scale environment at ﬁxed halo mass. We investigate this problem using the mock galaxy catalogs created by Hearin & Watson (2013, HW13), which exhibit signiﬁcant assembly bias because galaxy luminosity is tied to halo peak circular velocity and galaxy colour is tied to halo formation time. The preferential placement of galaxies (especially red galaxies) in older halos aﬀects the cutoﬀ of the mean occupation function (cid:104) N cen ( M min ) (cid:105) for central galaxies, with halos in overdense regions more likely to host galaxies. The eﬀect of assembly bias on the satellite galaxy HOD is minimal. We introduce an extended, environment dependent HOD (EDHOD) prescription to describe these results and ﬁt galaxy correlation measurements. Crucially, we ﬁnd that the galaxy-matter cross-correlation coeﬃcient, r gm ( r ) ≡ ξ gm ( r ) · [ ξ mm ( r ) ξ gg ( r )] − 1 / 2 , is insensitive to assembly bias on scales r ∼ > 1 h − 1 Mpc, even though ξ gm ( r ) and ξ gg ( r ) are both aﬀected individ-ually. We can therefore recover the correct ξ mm ( r ) from the HW13 galaxy-galaxy and galaxy-matter correlations using either a standard HOD or EDHOD ﬁtting method. For M r ≤ − 19 or M r ≤ − 20 samples the recovery of ξ mm ( r ) is accurate to 2% or bet- ter. For a sample of red M r ≤ − 20 galaxies we achieve 2% recovery at r ∼ > 2 h − 1 Mpc with EDHOD modeling but lower accuracy at smaller scales or with a standard HOD ﬁt.
Variational calculus in several variables : a hamiltonian approach

Classical mechanics is formulated in two different ways, lagrangian mechanics and hamiltonian mechanics, and one of them is dual of the other.This paper studies the cases in which a hamiltonian formulation is possible for first order multiple integral variational calculus, that is classical field theory.In those cases we give a hamiltonian version of the theory and study the equivalence with the lagrangian formulation under suitable conditions of regularity.
Non Lyapunov stability of the constant spatially developing 1-D gas flow in presence of solutions having strictly positive exponential growth rate

Different types of stabilities (global, local) and instabilities (global absolute, local convective) of the constant spatially developing 1-D gas flow are analyzed in the phase space of continuously differentiable functions, endowed with the usual algebraic operations and the topology generated by the uniform convergence on the real axis. For this purpose the Euler equations linearized at the constant flow are used. The Lyapunov stability analysis was presented in [1] and this paper is a continuation of [1].
Statistical Issues II: Chi-Square Test Statistics

The Chi-Square statistics is the widely used non-parametric statistical test used for testing relationships between categorical variables. It describes the magnitude of discrepancy between the observed data and the data expected to be obtained with a specific hypothesis. The Chi-Square test is described with a case study, computed and interpreted using SPSS software for a 2 by 2 table. And in interpreting the chi-square statistic, the higher the chisquare value, the greater the likelihood that there is a statistically significant difference between the two groups we are comparing. As with any statistic, there are requirements for its appropriate use, which are called "assumptions” of the statistics. Additionally the X2 is a significance test, and should always be coupled with an appropriate test of strength.1
Adolescent Sexual and Reproductive Health in Uganda: Results from the 2004 National Survey of Adolescents

Addressing adolescents sexual and reproductive health needs is an important and urgent policy and programmatic concern in Uganda. To address young peoples needs effectively it is important to have a better understanding of the various aspects of adolescents sexual and reproductive health and needs. This report provides a comprehensive overview of the sexual and reproductive health of adolescents in Uganda. Specifically the report assesses the current knowledge attitudes and behaviors among adolescents and factors that put them at risk for HIV transmission and unwanted pregnancy. It examines why some adolescents are at higher risk of HIV transmission and unwanted pregnancy than others. It documents barriers that prevent adolescents from seeking sexual and reproductive health services and information and provides new information about what very young adolescents know and do with respect to sexual and reproductive health. The report is based on data from a 2004 nationally representative survey of 5112 males and females aged 12-19. (excerpt)
Rounding the Regression

Abstract Rounding is a necessary step in many mathematical processes. We are taught early in our education about significant figures and how to properly round a number. So when we are given a data set and asked to find a regression line, we are inclined to offer the line with rounded coefficients to reflect our model. However, the effects are not as insignificant as they might seem at first. In this paper, we investigate some consequences of rounding the coefficients in a least squares linear regression with respect to the calculated value of R2, and consider ways to minimize the amount of error that can arise.
Entanglement of two-mode Schrödinger cats

Quantum superpositions of coherent states are produced both in microwave and optical domains, and are considered realizations of the famous “Schroedinger cat” state. The recent progress shows an increase in the number of components and the number of modes involved. Our work gives a theoretical treatment of multicomponent two-mode Schroedinger cat states. We consider a class of single-mode states, which are superpositions of N coherent states lying on a circle in the phase space. In this class we consider an orthonormal basis created by rotationally-invariant circular states (RICS). A two-mode extension of this basis is created by splitting a single-mode RICS on a balanced beam-splitter. After performing a symmetric (Loewdin) orthogonalization of the sets of coherent states in both modes we obtain the Schmidt decomposition of the two-mode state, and therefore an analytic expression for its entanglement. We show that the states obtained by splitting a RICS are generalizations of Bell states of two qubits to the case of N -level systems encoded into superpositions of coherent states on the circle, and we propose for them the name of generalized quasi-Bell states. We show that an exact probabilistic teleportation of arbitrary superposition of coherent states on the circle is possible with such a state used as shared resource.