Diagnosing coherent structures in the convective boundary layer by optimizing their vertical turbulent scalar transfer

This is the final version. Available on open access from Springer via the DOI in this recordA new method is introduced to identify coherent structures in the convective boundary layer, based on optimizing the vertical scalar flux in a two-fluid representation of turbulent motions as simulated by a large-eddy simulation. The new approach partitions the joint frequency distribution (JFD) of the vertical velocity and a transported scalar into coherent structures (fluid 2) and their environment (fluid 1) by maximizing that part of the scalar flux resolved by the mean properties in fluid 2 and fluid 1. The proposed method does not rely on any a priori criteria for the partitioning of the flow nor any pre-assumptions about the shape of the JFD. Different flavours of the optimization approach are examined based on maximizing either the total (fluid 1 + fluid 2) or the fluid-2 resolved scalar flux, and on whether all possible partitions or only a subset are considered. These options can result in different derived area fractions for the coherent structures. The properties of coherent structures diagnosed by the optimization method are compared to the conditional sampling of a surface-emitted decaying tracer, in which coherent structures are defined as having tracer perturbation greater than some height-dependent threshold. Results show that the optimization method is able to smoothly define coherent thermal structures in both the horizontal and the vertical. Moreover, optimizing the turbulent transfer by the fluid-2 resolved flux produces very similar coherent structures to the tracer threshold method, especially in terms of their area fraction and updraft velocities. Nonetheless, further analysis of the partitioning of the JFD reveals that, even though the area fraction of coherent structures might be similar, their definition can occupy different quadrants of the JFD, implying the contribution of different physical mechanisms to the turbulent transfer in the boundary layer. Finally, the kinematic and thermodynamic characteristics of the coherent structures are examined based on their definition criteria.Natural Environment Research Council (NERC

Short-term effects of deep ploughing on soil C stocks following renewal of a dairy pasture in New Zealand

In New Zealand’s high producing permanent pastures the topsoil constitutes a large reservoir of soil organic carbon (SOC), which shows a marked stratification with depth. As consequence, sub-surface layers can contain 10 times less carbon than the surface soil. In permanent pastures with high carbon inputs, the formation and decomposition of these surface SOC stocks are often at equilibrium and C storage shows little change over time. Pastoral based dairy systems utilising ryegrass plus clover cultivars require renewal every 7-10 years to avoid reversion to less productive grasses. This may involve spring cultivation (either no-till, shallow till or full cultivation), summer forage cropping and autumn re-grassing. It has been hypothesised that SOC stocks can be increased by inverting the soil profile at pasture renewal through infrequent (once in 25-30 years) deep mouldboard ploughing (up to 30 cm depth). Increased C sequestration occurs when the new grass quickly rebuilds SOC stocks in the new topsoil (exposed low C sub-soil) at a rate faster than the decomposition of SOC in the rich former topsoil transferred to depth (now below 15 cm). However, benefits form accelerated C storage may be offset if crop and pasture production is adversely affected by the ploughing event (e.g., as result of compaction or excessive drainage). Hence, the aim of this work was to assess the short-term effects of infrequent inversion tillage of long-term New Zealand pastoral-based dairy soils under summer crop management and autumn re-grassing. An imperfectly drained Typic Fragiaqualf under dairy grazing was deep ploughed (approx. 25 cm) and re-sown with turnip in October 2016; other treatments included were shallow (< 10 cm) cultivation and no-till. The site was core sampled (0-40 cm) before cultivation and after 5 months of turnip growth to assess changes in SOC. Plant growth, herbage quality, and nutrient leaching were monitored during the 5-month period; root growth was assessed at the end of the crop rotation. Full cultivation transferred SOC below 10 cm depth, as expected. Soil bulk density decreased whereas root mass increased (10-20 cm depth; P < 0.05) under deep cultivation only. Besides, losses of mineral N were attenuated under deep tillage, resulting in a relative increase in crop yield. The potential for infrequent inversion tillage increasing soil C sequestration as a greenhouse gas (GHG) mitigation tool is currently being tested at other sites in New Zealand

Study for the Revision of the plaice box - Draft Final Report

This project has attempted to evaluate the effectiveness of the fisheries management measure known as the “Plaice Box” (PB) for the conservation of plaice and other species of marine organisms in the south-eastern North Sea. The study provides an inventory of existing information and collects new material on the effects of the PB on the conservation of plaice and the impact of the PB on various components of the commercial fishing fleets. Based on an analysis of key processes that affect the impact of the PB, modifications will be explored to improve the positive effect on the conservation of plaice and other species of marine organisms, including catches and bycatches of other marketable fish. An economic assessment of the consequences of those modifications, in terms of their cost-effectiveness, and implications for profitability of the activity is presented. Finally, the data requirements for future evaluations of the effects of the PB on conservation is discussed

Regional variability in the trophic requirements of shelf sea fisheries in the Northeast Atlantic, 1973-2000

Hydrographic, plankton, benthos, fisheries landings, and fish diet data from shelf sea areas in the Northeast Atlantic have been combined into an analysis of the foodweb structure and secondary production requirements of regional fisheries. Fish landings from the Baltic and North Sea are shown to be taken from a lower trophic level and are shown to be overall more planktivorous than those from shelf edge regions. The secondary production required per unit of landed fish from the North Sea was approximately half that for landings from the southwest approaches to the UK, referred to as the Celtic Seas, where zooplankton production accounted for only a small fraction of the secondary production demands of the fisheries. In the North Sea, variability in zooplankton production seems to have exerted a bottom-up effect on fish production, which in turn has exerted a top-down effect on the benthos. Conversely, Celtic Seas benthos production has been a bottom-up driver of fish production, which seems to have been independent of variability in plankton production.Thus, climate and fishing pressures can be expected to influence these regional fisheries in very different ways. Overall, the results indicate very strong spatial patterns in the fish foodweb structure and function, which will be important considerations in the establishment of regional management plans for fisheries

Variation in chronic nicotinamide treatment after traumatic brain injury can alter components of functional recovery independent of histological damage

Previously, we have shown that the window of opportunity for nicotinamide (NAM) therapy (50 mg/kg) following cortical contusion injuries (CCI) extended to 4–8 hrs post-CCI when administered over a six day post-CCI interval. The purpose of the present study was to determine if a more chronic NAM treatment protocol administered following CCI would extend the current window of opportunity for effective treatment onset. Groups of rats received either unilateral CCI's or sham procedures. Initiation of NAM therapy (50 mg/kg, ip) began at either 15-min, 4-hrs, 8-hrs or 24-hrs post-injury. All groups received daily systemic treatments for 12 days post-CCI at 24 hr intervals. Behavioral assessments were conducted for 28 days post injury and included: vibrissae forelimb placing, bilateral tactile adhesive removal, forelimb asymmetry task and locomotor placing testing. Behavioral analysis on both the tactile removal and locomotor placing tests showed that all NAM-treated groups facilitated recovery of function compared to saline treatment. However, on the vibrissae-forelimb placing and forelimb asymmetry tests only the 4-hr and 8-hr NAM-treated groups were significantly different from the saline-treated group. The lesion analysis showed that treatment with NAM out to 8 hrs post-CCI significantly reduced the size of the injury cavity. The window of opportunity for NAM treatment is task-dependent and in some situations can extend to 24 hrs post-CCI. These results suggest that a long term treatment regimen of 50 mg/kg of NAM starting at the clinically relevant time points may prove efficacious in human TBI

Platelet-Induced Clumping of Plasmodium falciparum–Infected Erythrocytes from Malawian Patients with Cerebral Malaria—Possible Modulation In Vivo by Thrombocytopenia

Platelets may play a role in the pathogenesis of human cerebral malaria (CM), and they have been shown to induce clumping of Plasmodium falciparum–parasitized red blood cells (PRBCs) in vitro. Both thrombocytopenia and platelet-inducedPRBCclumping are associated with severe malaria and, especially, withCM.In the present study, we investigated the occurrence of the clumping phenomenon in patients with CM by isolating and coincubating their plasma and PRBCs ex vivo. Malawian children with CM all had low platelet counts, with the degree of thrombocytopenia directly proportional to the density of parasitemia. Plasma samples obtained from these patients subsequently induced weak PRBC clumping. When the assays were repeated, with the plasma platelet concentrations adjusted to within the physiological range considered to be normal, massive clumping occurred. The results of this study suggest that thrombocytopenia may, through reduction of platelet-mediated clumping of PRBCs, provide a protective mechanism for the host during CM

Identification of Individual Glandular Regions Using LCWT and Machine Learning Techniques

A new approach for the segmentation of gland units in histological images is proposed with the aim of contributing to the improvement of the prostate cancer diagnosis. Clustering methods on several colour spaces are applied to each sample in order to generate a binary mask of the different tissue components. From the mask of lumen candidates, the Locally Constrained Watershed Transform (LCWT) is applied as a novel gland segmentation technique never before used in this type of images. 500 random gland candidates, both benign and pathological, are selected to evaluate the LCWT technique providing results of Dice coefficient of 0.85. Several shape and textural descriptors in combination with contextual features and a fractal analysis are applied, in a novel way, on different colour spaces achieving a total of 297 features to discern between artefacts and true glands. The most relevant features are then selected by an exhaustive statistical analysis in terms of independence between variables and dependence with the class. 3.200 artefacts, 3.195 benign glands and 3.000 pathological glands are obtained, from a data set of 1468 images at 10x magnification. A careful strategy of data partition is implemented to robustly address the classification problem between artefacts and glands. Both linear and non-linear approaches are considered using machine learning techniques based on Support Vector Machines (SVM) and feedforward neural networks achieving values of sensitivity, specificity and accuracy of 0.92, 0.97 and 0.95, respectivelyThis work has been funded by the Ministry of Economy, Industry and Competitiveness under the SICAP project (DPI2016-77869-C2-1-R). The work of Adri´an Colomer has been supported by the Spanish FPI Grant BES-2014-067889. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan Xp GPU used for this researchGarcía-Pardo, JG.; Colomer, A.; Naranjo Ornedo, V.; Peñaranda, F.; Sales, MÁ. (2018). Identification of Individual Glandular Regions Using LCWT and Machine Learning Techniques. En Intelligent Data Engineering and Automated Learning – IDEAL 2018. Springer. 642-650. https://doi.org/10.1007/978-3-030-03493-1_67S642650Gleason, D.F.: Histologic grading and clinical staging of prostatic carcinoma. In: Urologic Pathology (1977)Naik, S., Doyle, S., Feldman, M., Tomaszewski, J., Madabhushi, A.: Gland segmentation and computerized gleason grading of prostate histology by integrating low-, high-level and domain specific information. In: MIAAB Workshop, pp. 1–8 (2007)Nguyen, K., Sabata, B., Jain, A.K.: Prostate cancer grading: gland segmentation and structural features. Pattern Recogn. Lett. 33(7), 951–961 (2012)Kwak, J.T., Hewitt, S.M.: Multiview boosting digital pathology analysis of prostate cancer. Comput. Methods Programs Biomed. 142, 91–99 (2017)Ren, J., Sadimin, E., Foran, D.J., Qi, X.: Computer aided analysis of prostate histopathology images to support a refined gleason grading system. In: SPIE Medical Imaging, International Society for Optics and Photonics, p. 101331V (2017)Soille, P.: Morphological Image Analysis: Principles and Applications. Springer, Berlin (2013)Nguyen, K., Sarkar, A., Jain, A.K.: Structure and context in prostatic gland segmentation and classification. In: Ayache, N., Delingette, H., Golland, P., Mori, K. (eds.) MICCAI 2012. LNCS, vol. 7510, pp. 115–123. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-33415-3_15Beare, R.: A locally constrained watershed transform. IEEE Trans. Pattern Anal. Mach. Intell. 28(7), 1063–1074 (2006)Gertych, A., et al.: Machine learning approaches to analyze histological images of tissues from radical prostatectomies. Comput. Med. Imaging Graph. 46, 197–208 (2015)Ojala, T., Pietikainen, M., Maenpaa, T.: Multiresolution gray-scale and rotation invariant texture classification with local binary patterns. IEEE Trans. Pattern Anal. Mach. Intell. 24(7), 971–987 (2002)Guo, Z., Zhang, L., Zhang, D.: A completed modeling of local binary pattern operator for texture classification. IEEE Trans. Image Process. 19(6), 1657–1663 (2010)Huang, P., Lee, C.: Automatic classification for pathological prostate images based on fractal analysis. IEEE Trans. Med. Imaging 28(7), 1037–1050 (2009)Ruifrok, A.C., Johnston, D.A., et al.: Quantification of histochemical staining by color deconvolution. Anal. Quant. Cytol. Histol. 23(4), 291–299 (2001