Nutrient Pumping by Submesoscale Circulations in the Mauritanian Upwelling System

Observations made within a cold filament in the Mauritanian upwelling system demonstrate that intense submesoscale circulations at the peripheral edges of the filament are likely responsible for anomalously high levels of observed primary productivity by resupplying nutrients to the euphotic zone. Measurements made on the shelf within the recently upwelled water reveal that primary production (PP) of 8.2 gC/m−2 day−1 was supported by nitrate concentrations (NC) of 8 mmol m−3. Towards the front that defined the edge of the filament containing the upwelled water as it was transported offshore, PP dropped to 1.6 gC m−2 day−1 whilst NC dropped to 5.5 mmol m−3. Thus, whilst the observed nutrients on the shelf accounted for 90% of new production, this value dropped to ∼60% near the filament’s front after accounting for vertical turbulent fluxes and Ekman pumping. We demonstrate that the N15 was likely to have been supplied at the front by submesoscale circulations that were directly measured as intense vertical velocities ⩾100 m day−1 by a drifting acoustic Doppler current profiler that crossed a submesoscale surface temperature front. At the same time, a recently released tracer was subducted out of the mixed layer within 24 h of release, providing direct evidence that the frontal circulations were capable of accessing the reservoir of nutrients beneath the pycnocline. The susceptibility of the filament edge to submesoscale instabilities was demonstrated by O(1) Rossby numbers at horizontal scales of 1–10 km. The frontal circulations are consistent with instabilities arising from a wind-driven nonlinear Ekman buoyancy flux generated by the persistent northerly wind stress that has a down-front component at the northern edge of the inshore section of the filament. The prevalence of submesoscale instabilities and their associated vertical circulations are proposed to be a key mechanism operating at sub-grid scales and sustaining new production throughout the upwelling system

Exploiting short supports for improved encoding of arbitrary constraints into SAT

Encoding to SAT and applying a highly efficient modern SAT solver is an increasingly popular method of solving finite-domain constraint problems. In this paper we study encodings of arbitrary constraints where unit propagation on the encoding provides strong reasoning. Specifically, unit propagation on the encoding simulates generalised arc consistency on the original constraint. To create compact and efficient encodings we use the concept of short support. Short support has been successfully applied to create efficient propagation algorithms for arbitrary constraints. A short support of a constraint is similar to a satisfying tuple however a short support is not required to assign every variable in scope. Some variables are left free to take any value. In some cases a short support representation is smaller than the table of satisfying tuples by an exponential factor. We present two encodings based on short supports and evaluate them on a set of benchmark problems, demonstrating a substantial improvement over the state of the art

TGF-beta 1 induces human alveolar epithelial to mesenchymal cell transition (EMT)

Background: Fibroblastic foci are characteristic features in lung parenchyma of patients with idiopathic pulmonary fibrosis (IPF). They comprise aggregates of mesenchymal cells which underlie sites of unresolved epithelial injury and are associated with progression of fibrosis. However, the cellular origins of these mesenchymal phenotypes remain unclear. We examined whether the potent fibrogenic cytokine TGF-β1 could induce epithelial mesenchymal transition (EMT) in the human alveolar epithelial cell line, A549, and investigated the signaling pathway of TGF-β1-mediated EMT. Methods: A549 cells were examined for evidence of EMT after treatment with TGF-β1. EMT was assessed by: morphology under phase-contrast microscopy; Western analysis of cell lysates for expression of mesenchymal phenotypic markers including fibronectin EDA (Fn-EDA), and expression of epithelial phenotypic markers including E-cadherin (E-cad). Markers of fibrogenesis, including collagens and connective tissue growth factor (CTGF) were also evaluated by measuring mRNA level using RT-PCR, and protein by immunofluorescence or Western blotting. Signaling pathways for EMT were characterized by Western analysis of cell lysates using monoclonal antibodies to detect phosphorylated Erk1/2 and Smad2 after TGF-β1 treatment in the presence or absence of MEK inhibitors. The role of Smad2 in TGF-β1-mediated EMT was investigated using siRNA. Results: The data showed that TGF-β1, but not TNF-α or IL-1β, induced A549 cells with an alveolar epithelial type II cell phenotype to undergo EMT in a time-and concentration-dependent manner. The process of EMT was accompanied by morphological alteration and expression of the fibroblast phenotypic markers Fn-EDA and vimentin, concomitant with a downregulation of the epithelial phenotype marker E-cad. Furthermore, cells that had undergone EMT showed enhanced expression of markers of fibrogenesis including collagens type I and III and CTGF. MMP-2 expression was also evidenced. TGF-β1-induced EMT occurred through phosphorylation of Smad2 and was inhibited by Smad2 gene silencing; MEK inhibitors failed to attenuate either EMT-associated Smad2 phosphorylation or the observed phenotypic changes. Conclusion: Our study shows that TGF-β1 induces A549 alveolar epithelial cells to undergo EMT via Smad2 activation. Our data support the concept of EMT in lung epithelial cells, and suggest the need for further studies to investigate the phenomenon

Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline

Background: There are numerous systems and techniques to measure the growth of plant roots. However, phenotyping large numbers of plant roots for breeding and genetic analyses remains challenging. One major difficulty is to achieve high throughput and resolution at a reasonable cost per plant sample. Here we describe a cost-effective root phenotyping pipeline, on which we perform time and accuracy benchmarking to identify bottlenecks in such pipelines and strategies for their acceleration. Results: Our root phenotyping pipeline was assembled with custom software and low cost material and equipment. Results show that sample preparation and handling of samples during screening are the most time consuming task in root phenotyping. Algorithms can be used to speed up the extraction of root traits from image data, but when applied to large numbers of images, there is a trade-off between time of processing the data and errors contained in the database. Conclusions: Scaling-up root phenotyping to large numbers of genotypes will require not only automation of sample preparation and sample handling, but also efficient algorithms for error detection for more reliable replacement of manual interventions

Bayesian spatial NBDA for diffusion data with home-base coordinates

Network-based diffusion analysis (NBDA) is a statistical method that allows the researcher to identify and quantify a social influence on the spread of behaviour through a population. Hitherto, NBDA analyses have not directly modelled spatial population structure. Here we present a spatial extension of NBDA, applicable to diffusion data where the spatial locations of individuals in the population, or of their home bases or nest sites, are available. The method is based on the estimation of inter-individual associations (for association matrix construction) from the mean inter-point distances as represented on a spatial point pattern of individuals, nests or home bases. We illustrate the method using a simulated dataset, and show how environmental covariates (such as that obtained from a satellite image, or from direct observations in the study area) can also be included in the analysis. The analysis is conducted in a Bayesian framework, which has the advantage that prior knowledge of the rate at which the individuals acquire a given task can be incorporated into the analysis. This method is especially valuable for studies for which detailed spatially structured data, but no other association data, is available. Technological advances are making the collection of such data in the wild more feasible: for example, bio-logging facilitates the collection of a wide range of variables from animal populations in the wild. We provide an R package, spatialnbda, which is hosted on the Comprehensive R Archive Network (CRAN). This package facilitates the construction of association matrices with the spatial x and y coordinates as the input arguments, and spatial NBDA analyses

Cognitive vision system for control of dexterous prosthetic hands: Experimental evaluation

<p>Abstract</p> <p>Background</p> <p>Dexterous prosthetic hands that were developed recently, such as SmartHand and i-LIMB, are highly sophisticated; they have individually controllable fingers and the thumb that is able to abduct/adduct. This flexibility allows implementation of many different grasping strategies, but also requires new control algorithms that can exploit the many degrees of freedom available. The current study presents and tests the operation of a new control method for dexterous prosthetic hands.</p> <p>Methods</p> <p>The central component of the proposed method is an autonomous controller comprising a vision system with rule-based reasoning mounted on a dexterous hand (CyberHand). The controller, termed cognitive vision system (CVS), mimics biological control and generates commands for prehension. The CVS was integrated into a hierarchical control structure: 1) the user triggers the system and controls the orientation of the hand; 2) a high-level controller automatically selects the grasp type and size; and 3) an embedded hand controller implements the selected grasp using closed-loop position/force control. The operation of the control system was tested in 13 healthy subjects who used Cyberhand, attached to the forearm, to grasp and transport 18 objects placed at two different distances.</p> <p>Results</p> <p>The system correctly estimated grasp type and size (nine commands in total) in about 84% of the trials. In an additional 6% of the trials, the grasp type and/or size were different from the optimal ones, but they were still good enough for the grasp to be successful. If the control task was simplified by decreasing the number of possible commands, the classification accuracy increased (e.g., 93% for guessing the grasp type only).</p> <p>Conclusions</p> <p>The original outcome of this research is a novel controller empowered by vision and reasoning and capable of high-level analysis (i.e., determining object properties) and autonomous decision making (i.e., selecting the grasp type and size). The automatic control eases the burden from the user and, as a result, the user can concentrate on what he/she does, not on how he/she should do it. The tests showed that the performance of the controller was satisfactory and that the users were able to operate the system with minimal prior training.</p

Providing perioperative care for patients with hip fractures

Providing perioperative care for patients with hip fractures can present major challenges for the anaesthesiologist. These patients often have multiple comorbidities, the deterioration of any one of which may have precipitated the fall. A careful balance has to be achieved between minimising the time before operation and spending time to optimise their medical status. This review will present insights into preoperative patient assessment and optimization in this group of patients from the anaesthesiologists’ perspective. In particular, it will highlight important medical issues of concern that may alter anaesthetic risks and management. With a greater understanding of what these issues are, potentially a more prompt and integrated approach to managing these patients may be made. Hopefully, this would result in minimising last minute cancellations due to medical reasons for these patients

Interaction of microtubules and actin during the post-fusion phase of exocytosis

Exocytosis is the intracellular trafficking step where a secretory vesicle fuses with the plasma membrane to release vesicle content. Actin and microtubules both play a role in exocytosis; however, their interplay is not understood. Here we study the interaction of actin and microtubules during exocytosis in lung alveolar type II (ATII) cells that secrete surfactant from large secretory vesicles. Surfactant extrusion is facilitated by an actin coat that forms on the vesicle shortly after fusion pore opening. Actin coat compression allows hydrophobic surfactant to be released from the vesicle. We show that microtubules are localized close to actin coats and stay close to the coats during their compression. Inhibition of microtubule polymerization by colchicine and nocodazole affected the kinetics of actin coat formation and the extent of actin polymerisation on fused vesicles. In addition, microtubule and actin cross-linking protein IQGAP1 localized to fused secretory vesicles and IQGAP1 silencing influenced actin polymerisation after vesicle fusion. This study demonstrates that microtubules can influence actin coat formation and actin polymerization on secretory vesicles during exocytosis

Principal components analysis based control of a multi-dof underactuated prosthetic hand

<p>Abstract</p> <p>Background</p> <p>Functionality, controllability and cosmetics are the key issues to be addressed in order to accomplish a successful functional substitution of the human hand by means of a prosthesis. Not only the prosthesis should duplicate the human hand in shape, functionality, sensorization, perception and sense of body-belonging, but it should also be controlled as the natural one, in the most intuitive and undemanding way. At present, prosthetic hands are controlled by means of non-invasive interfaces based on electromyography (EMG). Driving a multi degrees of freedom (DoF) hand for achieving hand dexterity implies to selectively modulate many different EMG signals in order to make each joint move independently, and this could require significant cognitive effort to the user.</p> <p>Methods</p> <p>A Principal Components Analysis (PCA) based algorithm is used to drive a 16 DoFs underactuated prosthetic hand prototype (called CyberHand) with a two dimensional control input, in order to perform the three prehensile forms mostly used in Activities of Daily Living (ADLs). Such Principal Components set has been derived directly from the artificial hand by collecting its sensory data while performing 50 different grasps, and subsequently used for control.</p> <p>Results</p> <p>Trials have shown that two independent input signals can be successfully used to control the posture of a real robotic hand and that correct grasps (in terms of involved fingers, stability and posture) may be achieved.</p> <p>Conclusions</p> <p>This work demonstrates the effectiveness of a bio-inspired system successfully conjugating the advantages of an underactuated, anthropomorphic hand with a PCA-based control strategy, and opens up promising possibilities for the development of an intuitively controllable hand prosthesis.</p