Order-of-magnitude speedup for steady states and traveling waves via Stokes preconditioning in Channelflow and Openpipeflow

Steady states and traveling waves play a fundamental role in understanding hydrodynamic problems. Even when unstable, these states provide the bifurcation-theoretic explanation for the origin of the observed states. In turbulent wall-bounded shear flows, these states have been hypothesized to be saddle points organizing the trajectories within a chaotic attractor. These states must be computed with Newton's method or one of its generalizations, since time-integration cannot converge to unstable equilibria. The bottleneck is the solution of linear systems involving the Jacobian of the Navier-Stokes or Boussinesq equations. Originally such computations were carried out by constructing and directly inverting the Jacobian, but this is unfeasible for the matrices arising from three-dimensional hydrodynamic configurations in large domains. A popular method is to seek states that are invariant under numerical time integration. Surprisingly, equilibria may also be found by seeking flows that are invariant under a single very large Backwards-Euler Forwards-Euler timestep. We show that this method, called Stokes preconditioning, is 10 to 50 times faster at computing steady states in plane Couette flow and traveling waves in pipe flow. Moreover, it can be carried out using Channelflow (by Gibson) and Openpipeflow (by Willis) without any changes to these popular spectral codes. We explain the convergence rate as a function of the integration period and Reynolds number by computing the full spectra of the operators corresponding to the Jacobians of both methods.Comment: in Computational Modelling of Bifurcations and Instabilities in Fluid Dynamics, ed. Alexander Gelfgat (Springer, 2018

Population genetics of seaside Sparrow (Ammodramus maritimus) subspecies along the gulf of Mexico.

Seaside Sparrows (Ammodramus maritimus) along the Gulf of Mexico are currently recognized as four subspecies, including taxa in Florida (A. m. juncicola and A. m. peninsulae) and southern Texas (Ammodramus m. sennetti), plus a widespread taxon between them (A. m. fisheri). We examined population genetic structure of this Gulf Coast clade using microsatellite and mtDNA data. Results of Bayesian analyses (Structure, GeneLand) of microsatellite data from nine locations do not entirely align with current subspecific taxonomy. Ammodramus m. sennetti from southern Texas is significantly differentiated from all other populations, but we found evidence of an admixture zone with A. m. fisheri near Corpus Christi. The two subspecies along the northern Gulf Coast of Florida are significantly differentiated from both A. m. sennetti and A. m. fisheri, but are not distinct from each other. We found a weak signal of isolation by distance within A. m. fisheri, indicating this population is not entirely panmictic throughout its range. Although continued conservation concern is warranted for all populations along the Gulf Coast, A. m. fisheri appears to be more secure than the far smaller populations in south Texas and the northern Florida Gulf Coast. In particular, the most genetically distinct populations, those in Texas south of Corpus Christi, occupy unique habitats within a very small geographic range

Localised plumes in three-dimensional compressible magnetoconvection

Within the umbrae of sunspots, convection is generally inhibited by the presence of strong vertical magnetic fields. However, convection is not completely suppressed in these regions: bright features, known as umbral dots, are probably associated with weak, isolated convective plumes. Motivated by observations of umbral dots, we carry out numerical simulations of three-dimensional, compressible magnetoconvection. By following solution branches into the subcritical parameter regime (a region of parameter space in which the static solution is linearly stable to convective perturbations), we find that it is possible to generate a solution which is characterised by a single, isolated convective plume. This solution is analogous to the steady magnetohydrodynamic convectons that have previously been found in two-dimensional calculations. These results can be related, in a qualitative sense, to observations of umbral dots.Comment: submitted to MNRA

Localized rotating convection with no-slip boundary conditions

Localized patches of stationary convection embedded in a background conduction state are called convectons. Multiple states of this type have recently been found in two-dimensional Boussinesq convection in a horizontal fluid layer with stress-free boundary conditions at top and bottom, and rotating about the vertical. The convectons differ in their lengths and in the strength of the self-generated shear within which they are embedded, and exhibit slanted snaking. We use homotopic continuation of the boundary conditions to show that similar structures exist in the presence of no-slip boundary conditions at the top and bottom of the layer and show that such structures exhibit standard snaking. The homotopic continuation allows us to study the transformation from slanted snaking characteristic of systems with a conserved quantity, here the zonal momentum, to standard snaking characteristic of systems with no conserved quantity

Preparing an unsupervised massive analysis of SPHERE high contrast data with the PACO algorithm

We aim at searching for exoplanets on the whole ESO/VLT-SPHERE archive with improved and unsupervised data analysis algorithm that could allow to detect massive giant planets at 5 au. To prepare, test and optimize our approach, we gathered a sample of twenty four solar-type stars observed with SPHERE using angular and spectral differential imaging modes. We use PACO, a new generation algorithm recently developed, that has been shown to outperform classical methods. We also improve the SPHERE pre-reduction pipeline, and optimize the outputs of PACO to enhance the detection performance. We develop custom built spectral prior libraries to optimize the detection capability of the ASDI mode for both IRDIS and IFS. Compared to previous works conducted with more classical algorithms than PACO, the contrast limits we derived are more reliable and significantly better, especially at short angular separations where a gain by a factor ten is obtained between 0.2 and 0.5 arcsec. Under good observing conditions, planets down to 5 MJup, orbiting at 5 au could be detected around stars within 60 parsec. We identified two exoplanet candidates that require follow-up to test for common proper motion. In this work, we demonstrated on a small sample the benefits of PACO in terms of achievable contrast and of control of the confidence levels. Besides, we have developed custom tools to take full benefits of this algorithm and to quantity the total error budget on the estimated astrometry and photometry. This work paves the way towards an end-to-end, homogeneous, and unsupervised massive re-reduction of archival direct imaging surveys in the quest of new exoJupiters.Comment: Accepted for publication in A&

An imaged 15Mjup companion within a hierarchical quadruple system

Since 2019, the direct imaging B-star Exoplanet Abundance Study (BEAST) at SPHERE@VLT has been scanning the surroundings of young B-type stars in order to ascertain the ultimate frontiers of giant planet formation. Recently, the $17^{+3}_{-4}$ Myr HIP 81208 was found to host a close-in (~50 au) brown dwarf and a wider (~230 au) late M star around the central 2.6Msun primary. Alongside the continuation of the survey, we are undertaking a complete reanalysis of archival data aimed at improving detection performances so as to uncover additional low-mass companions. We present here a new reduction of the observations of HIP 81208 using PACO ASDI, a recent and powerful algorithm dedicated to processing high-contrast imaging datasets, as well as more classical algorithms and a dedicated PSF-subtraction approach. The combination of different techniques allowed for a reliable extraction of astrometric and photometric parameters. A previously undetected source was recovered at a short separation from the C component of the system. Proper motion analysis provided robust evidence for the gravitational bond of the object to HIP 81208 C. Orbiting C at a distance of ~20 au, this 15Mjup brown dwarf becomes the fourth object of the hierarchical HIP 81208 system. Among the several BEAST stars which are being found to host substellar companions, HIP 81208 stands out as a particularly striking system. As the first stellar binary system with substellar companions around each component ever found by direct imaging, it yields exquisite opportunities for thorough formation and dynamical follow-up studies.Comment: 12 pages, 9 figures, 5 tables. Accepted for publication as a Letter in Astronomy and Astrophysics, section 1. Letters to the Edito

Multicentric validation of proteomic biomarkers in urine specific for diabetic nephropathy

Background: Urine proteome analysis is rapidly emerging as a tool for diagnosis and prognosis in disease states. For diagnosis of diabetic nephropathy (DN), urinary proteome analysis was successfully applied in a pilot study. The validity of the previously established proteomic biomarkers with respect to the diagnostic and prognostic potential was assessed on a separate set of patients recruited at three different European centers. In this case-control study of 148 Caucasian patients with diabetes mellitus type 2 and duration >= 5 years, cases of DN were defined as albuminuria >300 mg/d and diabetic retinopathy (n = 66). Controls were matched for gender and diabetes duration (n = 82). Methodology/Principal Findings: Proteome analysis was performed blinded using high-resolution capillary electrophoresis coupled with mass spectrometry (CE-MS). Data were evaluated employing the previously developed model for DN. Upon unblinding, the model for DN showed 93.8% sensitivity and 91.4% specificity, with an AUC of 0.948 (95% CI 0.898-0.978). Of 65 previously identified peptides, 60 were significantly different between cases and controls of this study. In <10% of cases and controls classification by proteome analysis not entirely resulted in the expected clinical outcome. Analysis of patient's subsequent clinical course revealed later progression to DN in some of the false positive classified DN control patients. Conclusions: These data provide the first independent confirmation that profiling of the urinary proteome by CE-MS can adequately identify subjects with DN, supporting the generalizability of this approach. The data further establish urinary collagen fragments as biomarkers for diabetes-induced renal damage that may serve as earlier and more specific biomarkers than the currently used urinary albumin

A Targeted Multiomics Approach to Identify Biomarkers Associated with Rapid eGFR Decline in Type 1 Diabetes

Background: Individuals with type 1 diabetes (T1D) demonstrate varied trajectories of estimated glomerular filtration rate (eGFR) decline. The molecular pathways underlying rapid eGFR decline in T1D are poorly understood, and individual-level risk of rapid eGFR decline is difficult to predict. Methods: We designed a case-control study with multiple exposure measurements nested within 4 well-characterized T1D cohorts (FinnDiane, Steno, EDC, and CACTI) to identify biomarkers associated with rapid eGFR decline. Here, we report the rationale for and design of these studies as well as results of models testing associations of clinical characteristics with rapid eGFR decline in the study population, upon which "omics" studies will be built. Cases (n = 535) and controls (n = 895) were defined as having an annual eGFR decline of >= 3 andPeer reviewe

Urinary Proteomics to Support Diagnosis of Stroke

Accurate diagnosis in suspected ischaemic stroke can be difficult. We explored the urinary proteome in patients with stroke (n = 69), compared to controls (n = 33), and developed a biomarker model for the diagnosis of stroke. We performed capillary electrophoresis online coupled to micro-time-of-flight mass spectrometry. Potentially disease-specific peptides were identified and a classifier based on these was generated using support vector machine-based software. Candidate biomarkers were sequenced by liquid chromatography-tandem mass spectrometry. We developed two biomarker-based classifiers, employing 14 biomarkers (nominal p-value <0.004) or 35 biomarkers (nominal p-value <0.01). When tested on a blinded test set of 47 independent samples, the classification factor was significantly different between groups; for the 35 biomarker model, median value of the classifier was 0.49 (−0.30 to 1.25) in cases compared to −1.04 (IQR −1.86 to −0.09) in controls, p<0.001. The 35 biomarker classifier gave sensitivity of 56%, specificity was 93% and the AUC on ROC analysis was 0.86. This study supports the potential for urinary proteomic biomarker models to assist with the diagnosis of acute stroke in those with mild symptoms. We now plan to refine further and explore the clinical utility of such a test in large prospective clinical trials