Sources, fate, and pathways of Leeuwin Current water in the Indian Ocean and Great Australian Bight: A Lagrangian study in an eddy-resolving ocean model

The Leeuwin Current is the dominant circulation feature in the eastern Indian Ocean, transporting tropical and subtropical water southward. While it is known that the Leeuwin Current draws its water from a multitude of sources, existing Indian Ocean circulation schematics have never quantified the fluxes of tropical and subtropical source water flowing into the Leeuwin Current. This paper uses virtual Lagrangian particles to quantify the transport of these sources along the Leeuwin Current's mean pathway. Here the pathways and exchange of Leeuwin Current source waters across six coastally bound sectors on the south-west Australian coast are analyzed. This constitutes the first quantitative assessment of Leeuwin Current pathways within an offline, 50 year integration time, eddy-resolving global ocean model simulation. Along the Leeuwin Current's pathway, we find a mean poleward transport of 3.7 Sv in which the tropical sources account for 60-78% of the transport. While the net transport is small, we see large transports flowing in and out of all the offshore boundaries of the Leeuwin Current sectors. Along the Leeuwin Current's pathway, we find that water from the Indonesian Throughflow contributes 50-66% of the seasonal signal. By applying conditions on the routes particles take entering the Leeuwin Current, we find particles are more likely to travel offshore north of 30°S, while south of 30°S, particles are more likely to continue downstream. We find a 0.2 Sv pathway of water from the Leeuwin Current's source regions, flowing through the entire Leeuwin Current pathway into the Great Australian Bight

Opportunities and Challenges of Magnetic Seeded Filtration in Multidimensional Fractionation

This study examines the general applicability of magnetic seeded filtration (MFS) for the fractionation of complex particulate systems by multiple particle features. Experimental studies on a laboratory scale showed that especially the electrostatic interactions govern the separation process. Furthermore, a clear size dependency could be shown, as the separation efficiency decreases with increasing size of target particles. Since MSF is both surface‐ and size‐dependent, it is generally applicable in a multidimensional fractionation. Finally, the challenges to be overcome are addressed as well

Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process

Background: Causal networks based on the vector autoregressive (VAR) process are a promising statistical tool for modeling regulatory interactions in a cell. However, learning these networks is challenging due to the low sample size and high dimensionality of genomic data. Results: We present a novel and highly efficient approach to estimate a VAR network. This proceeds in two steps: (i) improved estimation of VAR regression coefficients using an analytic shrinkage approach, and (ii) subsequent model selection by testing the associated partial correlations. In simulations this approach outperformed for small sample size all other considered approaches in terms of true discovery rate (number of correctly identified edges relative to the significant edges). Moreover, the analysis of expression time series data from Arabidopsis thaliana resulted in a biologically sensible network. Conclusion: Statistical learning of large-scale VAR causal models can be done efficiently by the proposed procedure, even in the difficult data situations prevalent in genomics and proteomics. Availability: The method is implemented in R code that is available from the authors on request

The present and future system for measuring the Atlantic meridional overturning circulation and heat transport

of the global combined atmosphere-ocean heat flux and so is important for the mean climate of the Atlantic sector of the Northern Hemisphere. This meridional heat flux is accomplished by both the Atlantic Meridional Overturning Circulation (AMOC) and by basin-wide horizontal gyre circulations. In the North Atlantic subtropical latitudes the AMOC dominates the meridional heat flux, while in subpolar latitudes and in the subtropical South Atlantic the gyre circulations are also important. Climate models suggest the AMOC will slow over the coming decades as the earth warms, causing widespread cooling in the Northern hemisphere and additional sea-level rise. Monitoring systems for selected components of the AMOC have been in place in some areas for decades, nevertheless the present observational network provides only a partial view of the AMOC, and does not unambiguously resolve the full variability of the circulation. Additional observations, building on existing measurements, are required to more completely quantify the Atlantic meridional heat transport. A basin-wide monitoring array along 26.5°N has been continuously measuring the strength and vertical structure of the AMOC and meridional heat transport since March 31, 2004. The array has demonstrated its ability to observe the AMOC variability at that latitude and also a variety of surprising variability that will require substantially longer time series to understand fully. Here we propose monitoring the Atlantic meridional heat transport throughout the Atlantic at selected critical latitudes that have already been identified as regions of interest for the study of deep water formation and the strength of the subpolar gyre, transport variability of the Deep Western Boundary Current (DWBC) as well as the upper limb of the AMOC, and inter-ocean and intrabasin exchanges with the ultimate goal of determining regional and global controls for the AMOC in the North and South Atlantic Oceans. These new arrays will continuously measure the full depth, basin-wide or choke-point circulation and heat transport at a number of latitudes, to establish the dynamics and variability at each latitude and then their meridional connectivity. Modeling studies indicate that adaptations of the 26.5°N type of array may provide successful AMOC monitoring at other latitudes. However, further analysis and the development of new technologies will be needed to optimize cost effective systems for providing long term monitoring and data recovery at climate time scales. These arrays will provide benchmark observations of the AMOC that are fundamental for assimilation, initialization, and the verification of coupled hindcast/forecast climate models

Exome sequencing helped the fine diagnosis of two siblings afflicted with atypical Timothy syndrome (TS2)

BACKGROUND: Long-QT syndrome (LQTS) causes a prolongation of the QT-interval in the ECG leading to life threatening tachyarrhythmia and ventricular fibrillation. One atypical form of LQTS, Timothy syndrome (TS), is associated with syndactyly, immune deficiency, cognitive and neurological abnormalities as well as distinct cranio-facial abnormalities. CASE PRESENTATION: On a family with both children diagnosed with clinical LQTS, we performed whole exome sequencing to comprehensively screen for causative mutations after a targeted candidate gene panel screen for Long-QT syndrome target genes failed to identify any underlying genetic defect. Using exome sequencing, we identified in both affected children, a p.402G > S mutation in exon 8 of the CACNA1C gene, a voltage-dependent Ca2+ channel. The mutation was inherited from their father, a mosaic mutation carrier. Based on this molecular finding and further more careful clinical examination, we refined the diagnosis to be Timothy syndrome (TS2) and thereby were able to present new therapeutic approaches. CONCLUSIONS: Our study highlights the difficulties in accurate diagnosis of patients with rare diseases, especially those with atypical clinical manifestation. Such challenge could be addressed with the help of comprehensive and unbiased mutation screening, such as exome sequencing

Gene network reconstruction from microarray data

<p>Abstract</p> <p>Background</p> <p>Often, software available for biological pathways reconstruction rely on literature search to find links between genes. The aim of this study is to reconstruct gene networks from microarray data, using Graphical Gaussian models.</p> <p>Results</p> <p>The <it>GeneNet </it>R package was applied to the Eadgene chicken infection data set. No significant edges were found for the list of differentially expressed genes between conditions MM8 and MA8. On the other hand, a large number of significant edges were found among 85 differentially expressed genes between conditions MM8 and MM24.</p> <p>Conclusion</p> <p>Many edges were inferred from the microarray data. Most of them could, however, not be validated using other pathway reconstruction software. This was partly due to the fact that a quite large proportion of the differentially expressed genes were not annotated. Further biological validation is therefore needed for these networks, using for example in vitro invalidation of genes.</p

Randomized trial of neoadjuvant chemotherapy in oropharyngeal carcinoma

The objective of the study was to evaluate the effect of neoadjuvant chemotherapy on the survival of patients with oropharyngeal cancer. Patients with a squamous cell carcinoma of the oropharynx for whom curative radiotherapy or surgery was considered feasible were entered in a multicentric randomized trial comparing neoadjuvant chemotherapy followed by loco-regional treatment to the same loco-regional treatment without chemotherapy. The loco-regional treatment consisted either of surgery plus radiotherapy or of radiotherapy alone. Three cycles of chemotherapy consisting of Cisplatin (100 mg/m2) on day 1 followed by a 24-hour i.v. infusion of fluorouracil (1000 mg/m2/day) for 5 days were delivered every 21 days. 2–3 weeks after the end of chemotherapy, local treatment was performed. The trial was conducted by the Groupe d'Etude des Tumeurs de la Tête Et du Cou (GETTEC). A total of 318 patients were enrolled in the study between 1986 and 1992. Overall survival was significantly better (P = 0.03) in the neoadjuvant chemotherapy group than in the control group, with a median survival of 5.1 years versus 3.3 years in the no chemotherapy group. The effect of neoadjuvant chemotherapy on event-free survival was smaller and of borderline significance (P = 0.11). Stratification of the results on the type of local treatment, surgery plus radiotherapy or radiotherapy alone, did not reveal any heterogeneity in the effect of chemotherapy. © 2000 Cancer Research Campaign http://www.bjcancer.co