Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding order in the design landscape of simple optical systems

Contrary to the frequent tacit assumption that the local minima of a merit function are points scattered more or less randomly over the design landscape, we have found that, at least for simple imaging systems (doublets with three and triplets with five variables) all design shapes we have observed thus far form a strictly ordered set of points, the "fundamental network". The design shapes obtained for practical specifications with global optimization algorithms are a subset of the set of local minima in the fundamental network and are organized in a way that can be understood on the basis of the fundamental network.
Drop Size Distributions Measured by a 2D Video Disdrometer: Comparison with Dual-Polarization Radar Data

Abstract An analysis of drop size distributions (DSDs) measured in four very different precipitation regimes is presented and is compared with polarimetric radar measurements. The DSDs are measured by a 2D video disdrometer, which is designed to measure drop size, shape, and fall speed with unprecedented accuracy. The observations indicate that significant DSD variability exists not only from one event to the next, but also within each system. Also, despite having vastly different storm structures and maximum rain rates, large raindrops with diameters greater than 5 mm occurred with each system. By comparing the occurrence of large drops with rainfall intensity, the authors find that the largest median diameters are not always associated with the heaviest rainfall, but are sometimes located either in advance of convective cores or, occasionally, in stratiform regions where rainfall rates are relatively low. Disdrometer and polarimetric radar measurements of radar reflectivity Z, differential reflectivity .
Pangolin Genomes Offer Key Insights and Resources for the World’s Most Trafficked Wild Mammals

Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and medicinal properties. Despite their great conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3 238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera of pangolins, and highlighted the existence of an undescribed species closely related to South-East Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of South-East Asian pangolins, provides new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental vs. island populations and species lineages, suggesting that conservation planning should consider intra-specific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet been realized in pangolins, we recommend that populations are genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors required for conserving pangolins, including tracing their illegal trade. These include the completion of whole-genomes for pangolins through the first reference genome with long reads for the giant pangolin (Smutsia gigantea) and new draft genomes (~43x–77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.
Biomimetic multi-channel microstimulation of somatosensory cortex conveys high resolution force feedback for bionic hands

Manual interactions with objects are supported by tactile signals from the hand. This tactile feedback can be restored in brain-controlled bionic hands via intracortical microstimulation (ICMS) of somatosensory cortex (S1). In ICMS-based tactile feedback, contact force can be signaled by modulating the stimulation intensity based on the output of force sensors on the bionic hand, which in turn modulates the perceived magnitude of the sensation. In the present study, we gauged the dynamic range and precision of ICMS-based force feedback in three human participants implanted with arrays of microelectrodes in S1. To this end, we measured the increases in sensation magnitude resulting from increases in ICMS amplitude and participant’s ability to distinguish between different intensity levels. We then assessed whether we could improve the fidelity of this feedback by implementing “biomimetic” ICMS-trains, designed to evoke patterns of neuronal activity that more closely mimic those in natural touch, and by delivering ICMS through multiple channels at once. We found that multi-channel biomimetic ICMS gives rise to stronger and more distinguishable sensations than does its single-channel counterpart. Finally, we implemented biomimetic multi-channel feedback in a bionic hand and had the participant perform a compliance discrimination task. We found that biomimetic multi-channel tactile feedback yielded improved discrimination over its single-channel linear counterpart. We conclude that multi-channel biomimetic ICMS conveys finely graded force feedback that more closely approximates the sensitivity conferred by natural touch.
The oncogenic role of Streptococcus gallolyticus subsp. gallolyticus is linked to activation of multiple cancer-related signaling pathways

Streptococcus gallolyticus subsp. gallolyticus (SGG), an opportunistic gram-positive pathogen responsible for septicemia and endocarditis in the elderly, is often associated with colon cancer (CRC). In this work, we investigated the oncogenic role of SGG strain UCN34 using the azoxymethane (AOM)-induced CRC model in vivo, organoid formation ex vivo and proteomic and phosphoproteomic analyses from murine colons. We showed that SGG UCN34 accelerates colon tumor development in the murine CRC model. Full proteome and phosphoproteome analysis of murine colons chronically colonized by SGG UCN34 or the closely related non-pathogenic S. gallolyticus subsp. macedonicus (SGM) revealed that 164 proteins and 725 phosphorylation sites were differentially regulated following colonization by SGG UCN34. Ingenuity Pathway Analysis (IPA) indicates a pro-tumoral shift specifically induced following colonization by SGG UCN34, as most proteins and phosphoproteins identified were associated with digestive cancer. Comprehensive analysis of the altered phosphoproteins using ROMA software revealed significantly elevated activities in several cancer hallmark pathways affecting tumoral cells and their microenvironment, i.e. MAPK (ERK, JNK and p38), mTOR and integrin/ILK/actin signaling, in SGG UCN34 colonized colon. Importantly, analysis of protein arrays of human colon tumors colonized with SGG showed up-regulation of PI3K/Akt/mTOR and MAPK pathways, providing clinical relevance to our findings. To test SGG’s capacity to induce pre-cancerous transformation of the murine colonic epithelium, we grew ex vivo organoids which revealed unusual structures with compact morphology following exposure to SGG. Taken together, our results reveal that the oncogenic role of SGG UCN34 is associated with activation of multiple cancer-related signaling pathways. Author Summary Colorectal cancer is the third most common cause of cancer mortality worldwide. The colon is a very singular organ, colonized by a vast and complex community of microorganisms, known as the gut microbiota. Strong evidence supports a role of the microbiota in colon cancer development. Streptococcus gallolyticus subsp. gallolyticus (SGG), a gut commensal, was one of the first bacteria to be associated with colorectal cancer. A better understanding of the role of SGG in colon cancer development is critical to developing novel strategies to improve clinical diagnosis and treatment of this disease. Here, using a global proteomic analysis of mouse colonic tissue colonized by SGG, we show that over 90% of the proteins with altered levels are involved in cancer. SGG colonization promotes autocrine and paracrine pro-tumor signals contributing to transformation of the colonic epithelium but also modifying the stromal microenvironment, which in turn sustains tumor development. Importantly, two tumor hallmark pathways (PI3K/Akt/mTOR and MAPK) identified in our mouse model were also found in human colon tumor biopsies colonized by SGG, strengthening the clinical relevance to our study.
Vimentin supports cell polarization by enhancing centrosome function and microtubule acetylation

Cell polarity is important for controlling cell shape, motility, and cell division processes. Vimentin intermediate filaments are necessary for proper polarization of migrating fibroblasts and assembly of vimentin and microtubule networks is dynamically coordinated, but the precise details of how vimentin mediates cell polarity remain unclear. Here, we characterize the effects of vimentin on the structure and function of the centrosome and the stability of microtubule filaments in wild-type and vimentin-null mouse embryonic fibroblasts (mEFs). We find that vimentin mediates the structure of the pericentrosomal material, promotes centrosome-mediated microtubule regrowth, and increases the level of stable acetylated microtubules in the cell. Loss of vimentin also impairs centrosome repositioning during cell polarization and migration processes that occur during wound closure. Our results suggest that vimentin modulates centrosome structure and function as well as microtubule network stability, which has important implications for how cells establish proper cell polarization and persistent migration.
Extension of some numerical schemes to the analysis of gas and particle mixtures

In this paper, several numerical schemes are extended to obtain approximate solutions to the system of equations encountered in the analysis of multiphase mixtures of gas and particles. Both dense and dilute mixtures are studied, the gas is modelled as a perfect gas and the solid is considered incompressible. Although the tests employed throughout this work for studying the behaviour of the schemes are essentially one dimensional, the finite volume method developed permits its application to multidimensional problems in unstructured grids. Copyright © 2007 John Wiley & Sons, Ltd.
Generalization Ability of Wide Neural Networks on ℝ

We perform a study on the generalization ability of the wide two-layer ReLU neural network on $\mathbb{R}$. We first establish some spectral properties of the neural tangent kernel (NTK): $a)$ $K_{d}$, the NTK defined on $\mathbb{R}^{d}$, is positive definite; $b)$ $\lambda_{i}(K_{1})$, the $i$-th largest eigenvalue of $K_{1}$, is proportional to $i^{-2}$. We then show that: $i)$ when the width $m\rightarrow\infty$, the neural network kernel (NNK) uniformly converges to the NTK; $ii)$ the minimax rate of regression over the RKHS associated to $K_{1}$ is $n^{-2/3}$; $iii)$ if one adopts the early stopping strategy in training a wide neural network, the resulting neural network achieves the minimax rate; $iv)$ if one trains the neural network till it overfits the data, the resulting neural network can not generalize well. Finally, we provide an explanation to reconcile our theory and the widely observed ``benign overfitting phenomenon''.
Supergranules over the solar cycle

Context. The origin of supergranulation has not been understood yet. Contradictory results have been obtained in the past concerning the relation between supergranule properties (mostly cell size) and the solar cycle. Aims. We propose to study the variation in supergranule cell sizes and velocity fields over the solar cycle, as well as the intensity variation inside supergranules. Methods. We define supergranule cells from maps of horizontal velocity field divergences. The flow fields are derived from MDI/SOHO intensity maps. The intensity variation in supergranules are compared to the variation inside granules resulting from a numerical simulation. The variation in these profiles with the cell size and over the solar cycle is also analysed. Results. We find that cell sizes are smaller on average at cycle maximum. We also find that the slope between Log (Vrms )a nd Log (R) is weakly correlated with the spot number (i.e. the global activity level) but anti-correlated with the local magnetic field. We also confirm the decrease in the intensity variation from cell centre to the boundary, which puts a lower limit on the temperature variation of 0.57 ± 0.06 K. This temperature difference is of 1.03 ± 0.05 K when considering the areas of strongest divergence and strongest convergence. We observe a strong similarity in the intensity variation inside supergranules and granules. A significant variation with the cell size is observed, also similar to that in granules, but the variation over the solar cycle is not significant. Conclusions. The sign of the variation in supergranule cell sizes over the solar cycle is in agreement with what can be expected from the influence of the magnetic field. The observed intensity variations show that a common process could be the origin of both granules and supergranules.
Flow separation at the upstream edge of a square-edged broad-crested weir

A simple model is suggested to explain the flow mechanism at the upstream edge of a square-edged broad-crested weir. The separation bubble that may be seen to occur at this point is treated as an area of constant static head, while the main flow outside the bubble is deemed to be irrotational and divided from the bubble by a free streamline. If this model is accepted, the flow pattern will be such that energy requirements will be met along the free surface and the streamline bounding the bubble while, within these boundaries, the Laplace equation will be satisfied at every point. Accordingly, a solution satisfying these conditions is established by the use of a relaxation technique. In practice, it is likely that the cavity flow within the bubble will be bounded not by a single streamline but by a turbulent mixing zone and that there will be some increase in pressure near the point of re-attachment. Nevertheless, the surface profile and flow pattern observed in experiments show fair agreement with those predicted using the simple model. Whilst acknowledging, then, that the bubble and the zone bounding it are in fact of a more complex character, we may say that this simplified treatment affords a sound model of the main flow and so permits a better understanding of the action of the square-edged broad-crested weir.
Turbulent diffusion near a free surface

We study numerically and analytically the turbulent diffusion characteristics in a low-Froude-number turbulent shear flow beneath a free surface. In the numerical study, the Navier–Stokes equations are solved directly subject to viscous boundary conditions at the free surface. From an ensemble of such simulations, we find that a boundary layer develops at the free surface characterized by a fast reduction in the value of the eddy viscosity. As the free surface is approached, the magnitude of the mean shear initially increases over the boundary (outer) layer, reaches a maximum and then drops to zero inside a much thinner inner layer. To understand and model this behaviour, we derive an analytical similarity solution for the mean flow. This solution predicts well the shape and the time-scaling behaviour of the mean flow obtained in the direct simulations. The theoretical solution is then used to derive scaling relations for the thickness of the inner and outer layers. Based on this similarity solution, we propose a free-surface function model for large-eddy simulations of free-surface turbulence. This new model correctly accounts for the variations of the Smagorinsky coefficient over the free-surface boundary layer and is validated in both a priori and a posteriori tests.
Experimental validation of a sediment transport two-dimensional depth-averaged numerical model using PIV and 3D Scanning technologies

This paper presents the experimental validation of a two–dimensional depth–averaged numerical model with uncoupled flow and sediment transport using the finite volume method. Tests were conducted at the Civil Engineering School of the University ofA Coruña (Spain), using laser technologies such as particle image velocimetry and a three–dimensional scanner (3D–Scanner). This device measures bed elevations through calculations that take refraction into account. The numerical model presented here solves shallow water equations in the hydraulic field and calculates, through wellknown empirical formulas, bedload transport of uniform granular sediments. A comparison between the numerical and experimental results in the longitudinal and transversal direction, as well as in the evolution of the fundamental variables lead to the validation of the numerical model. Moreover, the application of laser technologies in fluvial hydraulics, especially with promising tools such as the 3D–scanner, here presented, is another key point of this work.
Direct simulation of a turbulent boundary layer up to Rθ = 1410

The turbulent boundary layer on a flat plate, with zero pressure gradient, is simulated numerically at four stations between Rθ = 225 and Rθ = 1410. The three-dimensional time-dependent Navier-Stokes equations are solved using a spectral method with up to about 107 grid points. Periodic spanwise and streamwise conditions are applied, and a multiple-scale procedure is applied to approximate the slow streamwise growth of the boundary layer. The flow is studied, primarily, from a statistical point of view. The solutions are compared with experimental results. The scaling of the mean and turbulent quantities with Reynolds number is compared with accepted laws, and the significant deviations are documented. The turbulence at the highest Reynolds number is studied in detail. The spectra are compared with various theoretical models. Reynolds-stress budget data are provided for turbulence-model testing.
A Running Average Method for Predicting the Size and Length of a Solar Cycle

The running correlation coefficient between the solar cycle amplitudes and the max-max cycle lengths at a given cycle lag is found to vary roughly in a cyclical wave with the cycle number, based on the smoothed monthly mean Group sunspot numbers available since 1610. A running average method is proposed to predict the size and length of a solar cycle by the use of the varying trend of the coefficients. It is found that, when a condition (that the correlation becomes stronger) is satisfied, the mean prediction error (16.1) is much smaller than when the condition is not satisfied (38.7). This result can be explained by the fact that the prediction must fall on the regression line and increase the strength of the correlation. The method itself can also indicate whether the prediction is reasonable or not. To obtain a reasonable prediction, it is more important to search for a running correlation coefficient whose varying trend satisfies the proposed condition, and the result does not depend so much on the size of the correlation coefficient. As an application, the peak sunspot number of cycle 24 is estimated as 140.4±15.7, and the peak as May 2012±11 months.
On the optimal control of discrete-time linear systems with random parameters

This work is concerned with the optimal control of a discrete-time linear system with random parameters. It is assumed that the parameters of the system vary randomly during the process, namely, the parameters constitute sequences of random variables. These random variables are not necessarily independent. An important particular case occurs where there are unknown constant parameters in the system. The measurements of the state of the system contain additive noise. A quadratic function of the state and controller, with appropriate weighting, serves as the criterion function. The solutions for the open-loop controller and the open-loop feedback controller are presented. The method of solution is based on the dynamic programming approach which leads to functional recurrence equations.
Automatic approach for classifying sympathetic quasiperiodic, n:m periodic and aperiodic dynamics produced by lung inflation in rats

A method for classifying non linear interactions between two event series, a forcing input and a forced output, is proposed. The approach allows to classify: 1) independent dynamics; 2) quasiperiodic dynamics; 3) n:m periodic synchronized dynamics in which n events of the forced signal occur every m cycles of the driving signal; 4) aperiodic dynamic. The method is automatic and fully independent of the researcher's judgment. In addition, it calculates the ratio and the strength of the coupling in the case of synchronized dynamics. The method is applied to verify whether sympathetic oscillators underlying the discharges of single postganglionic sympathetic neurons innervating the ventral caudal artery of the rat tail could be synchronized by the lung inflation cycle. The application confirms the capability of the method in classifying the dynamics and the synchronizing action of the lung inflation cycle over the single sympathetic neuron discharges.
Testing Isotropy in Spatial Econometric Models

Abstract Stationarity in space presents two aspects: homogeneity and isotropy. They correspond respectively to stationarity under translations and stationarity under rotations. Testing the hypothesis of isotropy is a common practice in many fields of application of spatial statistics where directional biases are of paramount importance like, for instance, in meteorology, geology or medicine to name only a few. In spatial econometrics, however, isotropy has been systematically neglected and just assumed away with no formal testing. This lack is somehow surprising, because anisotropies are more the rule rather than the exception when observing most economic phenomena. In this paper we introduce a testing procedure for spatial econometric models based on regional data that derives from Besag's idea of the unilateral approximations (Besag, 1974). The power of the test is assessed by means of a Monte Carlo experiment. Finally, we perform an empirical data analysis to test isotropy when analysing the regional convergence in Italy in the years 2000–2008. RÉSUMÉ la stationnarité dans l'espace implique à la fois l'homogénéité et l'isotropie. Les tests d'isotropie sont une pratique courante dans un grand nombre de domaines d'application, mais, dans celui de l’économétrie spatiale, ils ont été tout simplement présumés sans procéder au moindre essai officiel. Dans la présente communication, nous présentons une procédure pour tester l'isotropie dans des modèles d’économétrie spatiale, basés sur des données régionales dérivés du concept des approximations unilatérales. Nous évaluons la puissance de ce test à l'aide d'une expérience de Monte Carlo. Enfin, nous effectuons une analyse de données empiriques pour tester l'isotropie, dans le cadre de l'analyse de la convergence régionale en Italie dans les années 2000–2008. EXTRACTO La estacionariedad en el espacio denota homogeneidad e isotropía. La comprobación de la isotropía es una práctica común en muchos campos de aplicación, pero en la econometría espacial se ha descartado sin una comprobación formal. En este estudio introducimos un procedimiento para comprobar la isotropía en modelos econométricos espaciales basados en datos regionales que derivan del concepto de las aproximaciones unilaterales. El poder de la prueba se evalúa mediante un experimento de Monte Carlo. Finalmente, realizamos un análisis de datos empíricos para comprobar la isotropía al analizar la convergencia regional en Italia en los años 2000 al 2008. 摘要 : 太空中的定态表示了均匀性和各向同性。 检验各向同性是许多应用领域的常见做法, 但在空间计量经济学领域, 人们一直认为并没有正式的检验方法。 本文中, 我们引入了一个适用于各向同性的空间经济计量模型的检验程序, 模型基于从单方面近似概念推导出的区域数据。 采用蒙特卡罗实验方法来对检定力进行评估。 最后, 我们要在分析2000–2008年间意大利区域趋同的时候进行实证数据分析, 以检验各向同性。