Instabilities in the wake of an inclined prolate spheroid

We investigate the instabilities, bifurcations and transition in the wake behind a 45-degree inclined 6:1 prolate spheroid, through a series of direct numerical simulations (DNS) over a wide range of Reynolds numbers (Re) from 10 to 3000. We provide a detailed picture of how the originally symmetric and steady laminar wake at low Re gradually looses its symmetry and turns unsteady as Re is gradually increased. Several fascinating flow features have first been revealed and subsequently analysed, e.g. an asymmetric time-averaged flow field, a surprisingly strong side force etc. As the wake partially becomes turbulent, we investigate a dominating coherent wake structure, namely a helical vortex tube, inside of which a helical symmetry alteration scenario was recovered in the intermediate wake, together with self-similarity in the far wake.Comment: Book chapter in "Computational Modeling of Bifurcations and Instabilities in Fluid Dynamics (A. Gelfgat ed.)", Springe

Prolate spheroidal particles’ behavior in a vertical wall-bounded turbulent flow

International audienceDirect numerical simulations (DNSs) have been performed to examine the inertia, shape, and gravity field effects on the dynamics of ellipsoidal particles within a vertical turbulent channel flow. To investigate the effects induced by the particle inertia and shape, computations have been conducted for three aspect ratios and two response times. The influence of gravity has been examined through a comparison with DNS data provided in earlier studies without gravity. The originality of this study is that the prediction of the hydrodynamic force and pitching torque acting on the non-spherical particles has been carried out with recent expressions valid outside the Stokes flow regime. With the data extracted from the DNS, a statistical analysis of the particle spatial distribution, orientation, and translational and angular velocities is carried out. Results show that the presence of a significant mean relative velocity between the dispersed and continuous phases greatly modifies the dynamics of non-spherical particles. Without gravity, the dynamics of ellipsoids is close to that of spheres, whereas it becomes strongly dependent on the particle shape with gravity

The impact of convective cold pool outflows on model biases in the Sahara

Radiosonde data from Fennec supersite-1 in the remote central Sahara have been used to evaluate the impact of convectively generated cold pool outflows on model errors. Model predictions are too warm and dry, with cold pools contributing significantly to the mean bias. Although dust concentrations are high within cold pools, the sign of the errors is inconsistent with radiative impacts of dust. Cold pools cause 29% of the meridional humidity flux, but this contribution is absent in the forecast and analysis. Assimilating radiosondes reduces the errors, but significant temperature and meridional humidity flux biases remain at night. The model biases are consistent with the larger-scale heat low biases in the operational Met Office Unified Model and can be linked to known issues with convective parameterizations used in all global weather and climate models. This study suggests that the misrepresentation of moist convective processes can affect continental-scale biases, altering the West African monsoon circulation

Meteorology and dust over the central Sahara: observations from Fennec supersite-1 during the June 2011 intensive observation period

[1] We describe observations from the Fennec supersite at Bordj-Badji Mokhtar made during the June 2011 Fennec Intensive Observation Period. These are the first detailed in-situ observations of meteorology and dust from the central Sahara, close to the centre of the Saharan Heat Low and the summertime dust maximum. Historically, a shortage of such Saharan observations has created problems for evaluating processes, models and remote sensing. [2] There was a monsoon influence at BBM before the 8th and after the 12th June, with dry Harmattan winds in between. A split boundary layer, generated by ventilation from the Atlantic, persisted during the drier phase. Extensive cold-pools (haboobs) and microburst-type events were regularly observed. Moisture reached BBM at night from the monsoon and the embedded haboobs. As well as the regularly occurring nocturnal low-level jet (LLJ), a Saharan upper boundary-layer (650-hPa) jet was observed, where winds feel drag from dry convection in the afternoon. This jet is linked to the diurnal cycles of moisture and cloud. Most dust was observed in the cloudier monsoon-affected periods and co-varying dust and cloud amounts explain most of the variations in shortwave radiation that control the surface sensible flux. Dustiness is related to a standard parameterisation of uplift using 10-m winds (“uplift potential”) and this is used to estimate uplift. Around 50% of uplift is nocturnal. Around 30% is from the LLJ and 50% from haboobs, which are mainly nocturnal. This demonstrates, for the first time from observations, the key role of haboobs, which are problematic for models

Novel BRCA1 and BRCA2 Tumor Test as Basis for Treatment Decisions and Referral for Genetic Counselling of Patients with Ovarian Carcinomas

With the recent introduction of Poly(ADP‐ribose) polymerase inhibitors, a promising novel therapy has become available for ovarian carcinoma (OC) patients with inactivating BRCA1 or BRCA2 mutations in their tumor. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumor is required. For reliable evaluation of germline and somatic mutations in these genes in DNA derived from formalin‐fixed, paraffin‐embedded (FFPE) tissue, we have developed a single‐molecule molecular inversion probe (smMIP)‐based targeted next‐generation sequencing (NGS) approach. Our smMIP‐based NGS approach provides analysis of both strands of the open reading frame of BRCA1 and BRCA2, enabling the discrimination between real variants and formalin‐induced artefacts. The single molecule tag enables compilation of unique reads leading to a high analytical sensitivity and enabling assessment of the reliability of mutation‐negative results. Multiplex ligation‐dependent probe amplification (MLPA) and Methylation‐specific multiplex ligation‐dependent probe amplification (MS‐MLPA) were used to detect exon deletions of BRCA1 and methylation of the BRCA1 promoter, respectively. Here, we show that this combined approach allows the rapid and reliable detection of both germline and somatic aberrations affecting BRCA1 and BRCA2 in DNA derived from FFPE OCs, enabling improved hereditary cancer risk assessment and clinical treatment of ovarian cancer patients

BRCA Testing by Single-Molecule Molecular Inversion Probes

BACKGROUND: Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS: The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS: Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10-15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS: smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable