Miracle-dz/UniFAR-FTUs huggingface dataset:
European Autism GEnomics Registry (EAGER): Protocol for a multicentre cohort study and registry

Introduction: Autism is a common neurodevelopmental condition with a complex genetic aetiology that includes contributions from monogenic and polygenic factors. Many autistic people have unmet healthcare needs that could be served by genomics-informed research and clinical trials. The primary aim of the European Autism GEnomics Registry (EAGER) is to establish a registry of participants with a diagnosis of autism or an associated rare genetic condition who have undergone whole-genome sequencing. The registry can facilitate recruitment for future clinical trials and research studies, based on genetic, clinical, and phenotypic profiles, as well as participant preferences. The secondary aim of EAGER is to investigate the association between mental and physical health characteristics and genetic profiles. Methods and analysis: EAGER is a European multisite cohort study and registry and is part of the AIMS-2-TRIALS consortium. EAGER was developed with input from the AIMS-2-TRIALS Autism Representatives and representatives from the rare genetic conditions community. 1,500 participants with a diagnosis of autism or an associated rare genetic condition will be recruited at 13 sites across 8 countries. Participants will give a blood or saliva sample for whole-genome sequencing and answer a series of online questionnaires. Participants may also consent for the study to access pre-existing clinical data. Participants will be added to the EAGER registry. Data will be shared via the Autism Sharing Initiative, a new international collaboration aiming to create a federated system for autism data sharing. Ethics and dissemination: EAGER has received full ethical approval from ethics committees in the UK (REC 23/SC/0022), Germany (S-375/2023), Portugal (CE-085/2023) and Spain (HCB/2023/0038, PIC-164-22). Approvals are in the process of being obtained from committees in Italy, Sweden, Ireland, and France. Findings will be disseminated via scientific publications and conferences, but also beyond to participants and the wider community (e.g., the AIMS-2-TRIALS website, stakeholder meetings, newsletters).
Microbiome-based risk prediction in incident heart failure: a community challenge

Heart failure (HF) is a major public health problem. Early identification of at-risk individuals could allow for interventions that reduce morbidity or mortality. The community-based FINRISK Microbiome DREAM challenge (synapse.org/finrisk) evaluated the use of machine learning approaches on shotgun metagenomics data obtained from fecal samples to predict incident HF risk over 15 years in a population cohort of 7231 Finnish adults (FINRISK 2002, n=559 incident HF cases). Challenge participants used synthetic data for model training and testing. Final models submitted by seven teams were evaluated in the real data. The two highest-scoring models were both based on Cox regression but used different feature selection approaches. We aggregated their predictions to create an ensemble model. Additionally, we refined the models after the DREAM challenge by eliminating phylum information. Models were also evaluated at intermediate timepoints and they predicted 10-year incident HF more accurately than models for 5- or 15-year incidence. We found that bacterial species, especially those linked to inflammation, are predictive of incident HF. This highlights the role of the gut microbiome as a potential driver of inflammation in HF pathophysiology. Our results provide insights into potential modeling strategies of microbiome data in prospective cohort studies. Overall, this study provides evidence that incorporating microbiome information into incident risk models can provide important biological insights into the pathogenesis of HF.
Time-of-flight polarization contrast neutron imaging for enhanced characterization of ferritic phase fractions in Fe-Mn-Si shape memory alloys

The determination of the amount and distribution of different phase fractions in additively manufactured shape memory alloys processed with laser powder bed fusion is crucial for understanding the correlation between processing parameters, microstructure, and mechanical properties. Neutron imaging techniques, such as Bragg edge imaging and polarization contrast neutron imaging (PNI), have been introduced to complement and overcome the limitations of traditional characterization methods, which are often destructive and limited to surface analyses and small-sized specimens. Bragg edge imaging can distinguish and quantify crystallographic phase fractions with spatial resolutions of a few tens of micrometers, while PNI is highly sensitive to crystallographic phases and is particularly suited for sub-percent phase fractions and in-situ, time-resolved, and tomographic analyses. In this work, we present a time-of-flight PNI method that enables simultaneous measurements of phase fractions.
Hysteretic nonlinear elasticity of Berea sandstone at low‐vibrational strain revealed by dynamic acousto‐elastic testing

Through changes in wave speed of ultrasonic pulses traversing the sample, we measure variations in the elasticity of dry Berea sandstone as a function of the applied low‐frequency (LF) axial strain (varied from 10−7 to 10−5). The approach, termed dynamic acousto‐elasticity, is the dynamic analog of static acousto‐elasticity where the wave speed is measured as a function of the applied static load. Dynamic acousto‐elasticity uses low‐frequency vibrational loading of smaller strain amplitude, typically below 10−4, and it includes inertial effects. At strain amplitudes around 10−6, compression and tension produce a material softening of the material. In contrast, a quasi‐static compression inducing a strain between 10−4 and 10−3 leads to a material stiffening. At 10−5 strain amplitude, elaborate hysteretic signatures of modulus strain are observed. The measurements provide the first direct experimental evidence of hysteretic nonlinear (wave amplitude dependent) elasticity in a sandstone at low dynamic strains.
ADVANCED METHOD FOR SELF‐ADAPTIVE ESTIMATION OF RESIDUAL STATIC CORRECTIONS*

The estimation of residual static corrections is investigated as a linear system. For 1200% coverage shot one way offset weighting functions—or in other words, estimation error operators—are computed. Assuming zero time shift determination errors and zero RNMO it is seen that large residual corrections will distort the effectivity of the estimation. With an iterative procedure which includes the repeated averaging according to depth point, shot point, and geophone point the effectivity of the method becomes more favourable. This can be learnt from the evaluation of estimation error operators computed by recursive formulae. In practice, due to the time shift determination errors, the routine does not give improved results in the desired level. Errors can be reduced with a more reliable time shift determination routine. For detecting and suppressing the unfavourable effect of time shift errors still remaining in the data a self-adaptive method was developed. In this non linear routine the data are evaluated at all three averaging processes according to limit values and weighting factors computed from the data itself. Field examples processed in different ways are presented.
A Reexamination of the Relationship between Organizational Forms and Distribution Channels in the U.S. Property Liability Insurance Industry

How do property liability insurance companies choose their organizational forms and distribution channels? Prior studies have not yet provided a consistent conclusion. In this paper, we propose a reduced form approach to reexamine the relationship between organizational forms and distribution channels in the insurance industry, using cross-sectional data pertaining to U.S. property liability insurance companies in 2004. We adopt a conditional dependence test, which can overcome the sensitivity problem of the structural form setting. The results show that after we control for all explanatory variables, the relationship between organizational forms and distribution channels is conditionally uncorrelated. The result is consistent with Regan and Tzeng (1999), but contradicts the findings of Baranoff and Sager (2003) and Kim et al. (1996).
Temperature-dependent propagation of P- and S-waves in Cold Lake oil sands: Comparison of theory and experiment

The measured dependence of ultrasonic velocity in Cold Lake oil sands on temperature is compared to theoretical model predictions for seismic wave propagation in porous media. The experiments indicated that change in fluid properties with temperature most greatly affect observed velocities. The theoretical model was constructed to account for temperature dependent fluid properties using correlations independent of the ultrasonic experiments. Theoretical and experimental P‐wave velocities agree within 5 percent for temperatures between 22°C to 125°C and effective stresses of 1 MPa and 8 MPa. The modeling indicates that the change in fluid bulk modulus with temperature dominates the observed 15 percent P‐wave velocity decrease between 22°C to 125°C. Over the same temperature range the model predicts the S‐wave velocity remains almost constant (<1 percent increase).
Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data

In recent work, several authors have introduced methods for sparse canonical correlation analysis (sparse CCA). Suppose that two sets of measurements are available on the same set of observations. Sparse CCA is a method for identifying sparse linear combinations of the two sets of variables that are highly correlated with each other. It has been shown to be useful in the analysis of high-dimensional genomic data, when two sets of assays are available on the same set of samples. In this paper, we propose two extensions to the sparse CCA methodology. (1) Sparse CCA is an unsupervised method; that is, it does not make use of outcome measurements that may be available for each observation (e.g., survival time or cancer subtype). We propose an extension to sparse CCA, which we call sparse supervised CCA, which results in the identification of linear combinations of the two sets of variables that are correlated with each other and associated with the outcome. (2) It is becoming increasingly common for researchers to collect data on more than two assays on the same set of samples; for instance, SNP, gene expression, and DNA copy number measurements may all be available. We develop sparse multiple CCA in order to extend the sparse CCA methodology to the case of more than two data sets. We demonstrate these new methods on simulated data and on a recently published and publicly available diffuse large B-cell lymphoma data set.
Multi-scale three-dimensional characterization of iron particles in dusty olivine: Implications for paleomagnetism of chondritic meteorites

Abstract Dusty olivine (olivine containing multiple sub-micrometer inclusions of metallic iron) in chondritic meteorites is considered an ideal carrier of paleomagnetic remanence, capable of maintaining a faithful record of pre-accretionary magnetization acquired during chondrule formation. Here we show how the magnetic architecture of a single dusty olivine grain from the Semarkona LL3.0 ordinary chondrite meteorite can be fully characterized in three dimensions, using a combination of focused ion beam nanotomography (FIB-nT), electron tomography, and finite-element micromagnetic modeling. We present a three-dimensional (3D) volume reconstruction of a dusty olivine grain, obtained by selective milling through a region of interest in a series of sequential 20 nm slices, which are then imaged using scanning electron microscopy. The data provide a quantitative description of the iron particle ensemble, including the distribution of particle sizes, shapes, interparticle spacings and orientations. Iron particles are predominantly oblate ellipsoids with average radii 242 ± 94 × 199 ± 80 × 123 ± 58 nm. Using analytical TEM we observe that the particles nucleate on sub-grain boundaries and are loosely arranged in a series of sheets parallel to (001) of the olivine host. This is in agreement with the orientation data collected using the FIB-nT and highlights how the underlying texture of the dusty olivine is crystallographically constrained by the olivine host. The shortest dimension of the particles is oriented normal to the sheets and their longest dimension is preferentially aligned within the sheets. Individual particle geometries are converted to a finite-element mesh and used to perform micromagnetic simulations. The majority of particles adopt a single vortex state, with “bulk” spins that rotate around a central vortex core. We observed no particles that are in a true single domain state. The results of the micromagnetic simulations challenge some preconceived ideas about the remanence-carrying properties of vortex states. There is often not a simple predictive relationship between the major, intermediate, and minor axes of the particles and the remanence vector imparted in different fields. Although the orientation of the vortex core is determined largely by the ellipsoidal geometry (i.e., parallel to the major axis for prolate ellipsoids and parallel to the minor axis for oblate ellipsoids), the core and remanence vectors can sometimes lie at very large (tens of degrees) angles to the principal axes. The subtle details of the morphology can control the overall remanence state, leading in some cases to a dominant contribution from the bulk spins to the net remanence, with profound implications for predicting the anisotropy of the sample. The particles have very high switching fields (several hundred millitesla), demonstrating their high stability and suitability for paleointensity studies.
An observation of the horizontal and vertical diffusion of a passive tracer in the deep ocean

An experiment to measure the dispersion of a passive tracer injected at 300 and 1000 m depth in the Pacific 600 miles southwest of San Diego is described. Rhodamine dye was released as a (very nearly). point source, and the subsequent growth of the patch was mapped at various times, up to 66.2 hours after release, using a self-propelled underwater research vehicle (SPURV), which carried temperature, conductivity, pressure, and dye sensors on a depth cycling trajectory through the patch. The analysis shows that the horizontal diffusion rates decrease with depth, that it is difficult to resolve the mixing in terms of a constant diffusion parameter based on any one of a number of models, that the 300 m results agree with those obtained by Schuert (1970), and that the patch growth began to develop eddy behavior at 66.2 hours when the rms second moment of the dye distribution was (r2)l/2 = 210 m. For the purpose of predicting horizontal mixing, the results indicate that eddy diffusivities of 1150 and 360 cm2/s at 300 and 1000 m, respectively, are the best fit values for spatial scales <200 m horizontally. Although we have focused on horizontal (isopycnal) diffusion, a few aspects of the vertical (diapycnal) characteristics of the patch are also discussed.
The effect of varying the source spectrum of a gravity wave parameterization in a middle atmosphere general circulation model

Climate simulations of the middle atmosphere circulation with general circulation models are now starting to include parameterizations of the momentum flux deposition due to unresolved gravity wave spectra. A current uncertainty in the application of such parameterizations is the specification of the imposed gravity wave spectrum. The aim of this work is to quantify the effect of varying within a realistic range the source spectrum of a gravity wave parameterization in a general circulation model. Results from two simulations with the gravity wave spectrum launched at two different heights, the surface and the 110-hPa pressure level, respectively, are compared. Noteworthy differences found in the simulated middle atmosphere response include the following (1) The average temperature in the southern winter upper stratosphere is about 40 K warmer in the experiment with the surface as the launching height, virtually eliminating the typical cold polar bias that affects many general circulation models. (2) Stronger easterlies in the subtropical summer mesosphere, again in the experiment with the surface as the launching height. Diagnostics of the parameterized gravity waves indicate that in the experiment with the surface as the launching height, the net zonal momentum flux transported by the gravity waves is negative just above the troposphere at middle latitudes. This negative net momentum flux facilitates the deceleration of the mesospheric winter westerlies. The meridional circulation induced by such deceleration is thereafter responsible for the substantial polar winter warming. In contrast, in summer the negative net momentum flux limits the upper mesospheric deceleration of the easterlies. In the experiment with launching height at 110-hPa, the gravity wave net momentum flux is instead zero by construction at the launching height.
Development of a Forest Health Index Using Multispectral Airborne Digital Camera Imagery

RÉSUMÉ Des recherches sont en cours sur un site de mine abandonnée générateur d'acide minier près de Timmins, en Ontario, pour évaluer les relations entre les symptômes des dommages structuraux de la forêt et les valeurs fractionnaires de l'information spectrale, texturale et radiométrique dans les images à haute résolution acquises par caméra numérique aéroportée. Les mesures réalisées sur les images telles que la luminance moyenne de la bande spectrale, la texture de co-occurrence, la variation de texture, l'amplitude de la semivariance et la proportion des fractions de surface d'ombre multispectral ont été démontrées comme significativement reliées aux mesures individuelles de la structure de la forêt telles que l'indice foliaire effectif (LAI), la fermeture de la canopée et la surface terrière du peuplement. Les objectifs de cette étude sont: 1. d'effectuer une analyse multivariée des relations entre des ensembles de données sur les sols, la structure de la forêt, la structure de la forêt par rapport au volume vivant sur pied et les variables des images multispectrales acquises à l'aide d'une caméra numérique et, 2. à l'aide des relations les plus significatives entre les variables des images de la forêt, de développer un indice intégré de l'état de santé de la forêt basé sur les images. Pour étudier les relations entre n'importe lesquels de deux des quatre ensembles de données, chacun étant constitué d'une multitude de variables, une analyse de corrélation canonique a été réalisée utilisant les composantes principales de chaque ensemble de données. Les résultats montrent que certaines des variables structurelles de la forêt sont fortement reliées aux propriétés du sol. Par exemple, les zones plus importantes de chablis sont associées aux sols plus sablonneux et à une présence plus faible de matière organique. À partir des relations entre l'image et les variables relatives de la structure de la forêt, il a été démontré qu'une diminution de la surface foliaire, de la fermeture de la canopée et de la dimension des tiges, qu'un accroissement de la surface terrière des zones de morbidité ou de chablis, et qu'un accroissement dans le nombre de tiges mortes et de tiges affectées par le chablis sont associées à une augmentation de la texture dans l'image, de la variation de la texture et la proportion d'ombre pale, et à une diminution dans l'éclairement moyen de la sous-scène et la proportion d'ombre profond. À partir de ces résultats, un indice de l'état de santé de la forêt basé sur les images a été développé permettant de combiner l'information spectrale et spatiale tout en demeurant sensible à une grande diversité de conditions de santé de la forêt sur le site.
Fault‐bend folding as an end‐member solution of (double‐edge) fault‐propagation folding

Fault‐bend folding is the most commonly used kinematic mechanism to interpret the architecture and evolution of thrust‐related anticlines in thrust wedges. However, its basic requirement of an instantaneous propagation of the entire fault before hangingwall deformation, limits its kinematic effectiveness. To overcome this limitation, we used the interdependence between fold shape and fault slip vs. propagation rate (S/P ratio) implemented in double‐edge fault‐propagation folding. We show that very small S/P values produce fault‐propagation anticlines that, when transported forelandward along an upper décollement layer, closely resemble fault‐bend anticlines. Accordingly, if small geometric discrepancies between the two solutions are accepted, transported double‐edge fault‐propagation provides an effective kinematic alternative to fault‐bend folding. Even at very low S/P values, it in fact predicts a fast but finite propagation rate of the fault. We thus propose that double‐edge fault‐propagation folding provides a broadly applicable model of fault‐related folding that includes fault‐bend folding as an end‐member kinematic solution.
Hyporheic flow and transport processes: Mechanisms, models, and biogeochemical implications

Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface‐subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed.