Spatio-temporal bivariate statistical models for atmospheric trace-gas inversion

Atmospheric trace-gas inversion refers to any technique used to predict spatial and temporal fluxes using mole-fraction measurements and atmospheric simulations obtained from computer models. Studies to date are most often of a data-assimilation flavour, which implicitly consider univariate statistical models with the flux as the variate of interest. This univariate approach typically assumes that the flux field is either a spatially correlated Gaussian process or a spatially uncorrelated non-Gaussian process with prior expectation fixed using flux inventories (e.g., NAEI or EDGAR in Europe). Here, we extend this approach in three ways. First, we develop a bivariate model for the mole-fraction field and the flux field. The bivariate approach allows optimal prediction of both the flux field and the mole-fraction field, and it leads to significant computational savings over the univariate approach. Second, we employ a lognormal spatial process for the flux field that captures both the lognormal characteristics of the flux field (when appropriate) and its spatial dependence. Third, we propose a new, geostatistical approach to incorporate the flux inventories in our updates, such that the posterior spatial distribution of the flux field is predominantly data-driven. The approach is illustrated on a case study of methane (CH$_4$) emissions in the United Kingdom and Ireland.Comment: 39 pages, 8 figure

Exposing knowledge: providing a real-time view of the domain under study for students

With the amount of information that exists online, it is impossible for a student to find relevant information or stay focused on the domain under study. Research showed that search engines have deficiencies that might prevent students from finding relevant information. To this end, this research proposes a technical solution that takes the personal search history of a student into consideration and provides a holistic view of the domain under study. Based on algorithmic approaches to assert semantic similarity, the proposed framework makes use of a user interface to dynamically assist students through aggregated results and wordcloud visualizations. The effectiveness of our approach is finally evaluated through the use of commonly used datasets and compared in line with existing research

Reducing the dependency of having prior domain knowledge for effective online information retrieval

Sometimes Internet users struggle to find what they are looking for on the Internet due to information overload. Search engines intend to identify documents related to a given keyphrase on the Internet and provide suggestions. Having some background knowledge about a topic or a domain will help in building effective search keyphrases that will lead to accurate results in information retrieval. This is further pronounced among students that rely on the internet to learn about a new topic. Students might not have the required background knowledge to build effective keyphrases and find what they are looking for. In this research, we are addressing this problem, and aim to help students find relevant information online. This research furthers existing literature by enhancing information retrieval frameworks through keyphrase assignment, aiming to expose students to new terminologies, therefore reducing the dependency of having background knowledge about the domain under study. We evaluated this framework and identified how it can be enhanced to suggest more effective search keyphrases. Our proposed suggestion is to introduce a keyphrase Ranking Mechanism that will improve the keyphrase assignment part of the framework by taking into consideration the part-of-speech of the generated keyphrases. To evaluate the proposed approach, various data sets were downloaded and processed. The results obtained showed that our proposed approach produces more effective keyphrases than the existing framework

In vivo monitoring of glycerolipid metabolism in animal nutrition biomodel-fed smart-farm eggs

Although many studies have examined the biochemical metabolic pathways by which an egg (egg yolk) lowers blood lipid levels, data on the molecular biological mechanisms that regulate and induce the partitioning of hepatic glycerolipids are missing. The aim of this study was to investigate in vivo monitoring in four study groups using an animal nutrition biomodel fitted with a jugular-vein cannula after egg yolk intake: CON (control group, oral administration of 1.0 g of saline), T1 (oral administration of 1.0 g of pork belly fat), T2 (oral administration of 1.0 g of smart-farm egg yolk), and T3 (oral administration of T1 and T2 alternately every week). The eggs induced significant and reciprocal changes in incorporating 14C lipids into the total glycerolipids and releasing 14CO2, thereby regulating esterification and accelerating oxidation in vivo. The eggs increased phospholipid secretion from the liver into the blood and decreased triacylglycerol secretion by regulating the multiple cleavage of fatty acyl-CoA moieties’ fluxes. In conclusion, the results of the current study reveal the novel fact that eggs can lower blood lipids by lowering triacylglycerol secretion in the biochemical metabolic pathway of hepatic glycerolipid partitioning while simultaneously increasing phospholipid secretion and 14CO2 emission

Effect of digital livestock system on animal behavior and welfare, and fatty acid profiles of egg in laying hens

Digital livestock system through convergence of livestock production and information and communication technology (ICT) is being applied to livestock farms to improve animal behavior and welfare, production, and quality of animal food. In previously study, we noted that the egg production were greatly enhanced in laying hens using digital livestock system. The present study investigated effects of a digital livestock system on fatty acid profiles and cholesterol of eggs, animal behavior, and welfare of laying hens. A total of 300 laying hens (Hy-Line Brown) at 48 weeks old were divided into two treatment groups: conventional livestock system (CON) and digital livestock system (DLS) in a randomized complete block design for 10 weeks. Drinking, feather squatting, eating, moving, preening, and resting scores as behavior indicators of laying hens were significantly improved in the DLS group than in the CON group (all P < 0.05). Animal welfare scores such as appearance, feather condition, body condition, and health of laying hens were significantly higher in the DLS group than in the CON group (P < 0.05). Contents of oleic acid and unsaturated fatty acid of eggs were significantly increased in the DLS group compared to the CON group (P < 0.05). However, content of saturated fatty acid and n-6/n-3 fatty acid ratio of eggs of the DLS group were significantly lower than those in the CON group (P < 0.05). These results indicate that the digital livestock system can be used as a future livestock farming algorithm to significantly improve egg fatty acid profile, animal behavior, and welfare in laying hens

Basal lamina remodeling at the skeletal muscle stem cell niche mediates stem cell self-renewal

A central question in stem cell biology is the relationship between stem cells and their niche. Although previous reports have uncovered how signaling molecules released by niche cells support stem cell function, the role of the extra-cellular matrix (ECM) within the niche is unclear. Here, we show that upon activation, skeletal muscle stem cells (satellite cells) induce local remodeling of the ECM and the deposition of laminin-α1 and laminin-α5 into the basal lamina of the satellite cell niche. Genetic ablation of laminin-α1, disruption of integrin-α6 signaling or blocking matrix metalloproteinase activity impairs satellite cell expansion and self-renewal. Collectively, our findings establish that remodeling of the ECM is an integral process of stem cell activity to support propagation and self-renewal, and may explain the effect laminin-α1-containing supports have on embryonic and adult stem cells, as well as the regenerative activity of exogenous laminin-111 therapy

Three-Dimensional Human iPSC-Derived Artificial Skeletal Muscles Model Muscular Dystrophies and Enable Multilineage Tissue Engineering

Summary: Generating human skeletal muscle models is instrumental for investigating muscle pathology and therapy. Here, we report the generation of three-dimensional (3D) artificial skeletal muscle tissue from human pluripotent stem cells, including induced pluripotent stem cells (iPSCs) from patients with Duchenne, limb-girdle, and congenital muscular dystrophies. 3D skeletal myogenic differentiation of pluripotent cells was induced within hydrogels under tension to provide myofiber alignment. Artificial muscles recapitulated characteristics of human skeletal muscle tissue and could be implanted into immunodeficient mice. Pathological cellular hallmarks of incurable forms of severe muscular dystrophy could be modeled with high fidelity using this 3D platform. Finally, we show generation of fully human iPSC-derived, complex, multilineage muscle models containing key isogenic cellular constituents of skeletal muscle, including vascular endothelial cells, pericytes, and motor neurons. These results lay the foundation for a human skeletal muscle organoid-like platform for disease modeling, regenerative medicine, and therapy development. : Maffioletti et al. generate human 3D artificial skeletal muscles from healthy donors and patient-specific pluripotent stem cells. These human artificial muscles accurately model severe genetic muscle diseases. They can be engineered to include other cell types present in skeletal muscle, such as vascular cells and motor neurons. Keywords: skeletal muscle, pluripotent stem cells, iPS cells, myogenic differentiation, tissue engineering, disease modeling, muscular dystrophy, organoid

Integrated Functions of Pax3 and Pax7 in the Regulation of Proliferation, Cell Size and Myogenic Differentiation

Pax3 and Pax7 are paired-box transcription factors with roles in developmental and adult regenerative myogenesis. Pax3 and Pax7 are expressed by postnatal satellite cells or their progeny but are down regulated during myogenic differentiation. We now show that constitutive expression of Pax3 or Pax7 in either satellite cells or C2C12 myoblasts results in an increased proliferative rate and decreased cell size. Conversely, expression of dominant-negative constructs leads to slowing of cell division, a dramatic increase in cell size and altered morphology. Similarly to the effects of Pax7, retroviral expression of Pax3 increases levels of Myf5 mRNA and MyoD protein, but does not result in sustained inhibition of myogenic differentiation. However, expression of Pax3 or Pax7 dominant-negative constructs inhibits expression of Myf5, MyoD and myogenin, and prevents differentiation from proceeding. In fibroblasts, expression of Pax3 or Pax7, or dominant-negative inhibition of these factors, reproduce the effects on cell size, morphology and proliferation seen in myoblasts. Our results show that in muscle progenitor cells, Pax3 and Pax7 function to maintain expression of myogenic regulatory factors, and promote population expansion, but are also required for myogenic differentiation to proceed

OptiJ: Open-source optical projection tomography of large organ samples

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples

WebGIS implementation for dynamic mapping and visualization of coastal geospatial data: A case study of BESS project

Within an E.U.-funded project, BESS (Pocket Beach Management and Remote Surveillance System), the notion of a geographic information system is an indispensable tool for managing the dynamics of georeferenced data and information for any form of territorial planning. This notion was further explored with the creation of a WebGIS portal that will allow local and regional stake-holders/authorities obtain an easy remote access tool to monitor the status of pocket beaches (PB) in the Maltese Archipelago and Sicily. In this paper, we provide a methodological approach for the implementation of a WebGIS necessary for very detailed dynamic mapping and visualization of geospatial coastal data; the description of the dataset necessary for the monitoring of coastal areas, especially the PBs; and a demonstration of a case study for the PBs of Sicily and Malta by using the methodology and the dataset used during the BESS project. Detailed steps involved in the creation of the WebGIS are presented. These include data preparation, data storage, and data publication and transformation into geo-services. With the help of different Open Geospatial Consortium pro-tocols, the WebGIS displays different layers of information for 134 PBs including orthophotos, sed-imentological/geomorphological beach characteristics, shoreline evolution, geometric and morphological parameters, shallow water bathymetry, and photographs of pocket beaches. The WebGIS allows not only for identifying, evaluating, and directing potential solutions to present and arising issues, but also enables public access and involvement. It reflects a platform for future local and regional coastal zone monitoring and management, by promoting public/private involvement in addressing coastal issues and providing local public administrations with an improved technology to monitor coastal changes and help better plan suitable interventions