Experimental dataset on water levels, sediment depths and wave front celerity values in the study of multiphase shock wave for different initial up- and down-stream conditions

This data article presents a rich original experimental video sources and wide collections of laboratory data on water levels, sediment depths and wave front celerity values arose from different multiphase dam-break scenarios. The required data of dam-break shock waves in highly silted-up reservoirs with various initial up- and down-stream hydraulic conditions is obtained directly from high-quality videos. The multi-layer shock waves were recorded by three professional cameras mounted along the laboratory channel. The extracted video images were rigorously scrutinized, and the datasets were obtained through the images via image processing method. Different sediment depths in the upstream reservoir and dry- or wet-bed downstream conditions were considered as initial conditions, compromising a total of 32 different scenarios. A total of 198 original experimental videos are made available online in the public repository "Mendeley Data" in 8 groups based on 8 different initial upstream sediment depths [1], [2], [3], [4], [5], [6], [7], [8]. 20 locations along the flume and 15 time snaps after the dam breaks were considered for data collecting. Consequently, a total of 18,000 water level and sediment depth data points were collected to prepare four datasets, which are uploaded in the public repository "Mendeley Data". A total of 9600 water level data points could be accessed in [9], [10], while 8400 sediment depth data points are available online in [11], [12] and could be utilized for validation and practical purposes by other researchers. This data article is related to another research article entitled "Experimental study and numerical verification of silted-up dam-break" [13]

Involvement of RDR6 in short-range intercellular RNA silencing in Nicotiana benthamiana

In plants, non-cell autonomous RNA silencing spreads between cells and over long distances. Recent work has revealed insight on the genetic and molecular components essential for cell-to-cell movement of RNA silencing in Arabidopsis. Using a local RNA silencing assay, we report on a distinct mechanism that may govern the short-range (6–10 cell) trafficking of virus-induced RNA silencing from epidermal to neighbouring palisade and spongy parenchyma cells in Nicotiana benthamiana. This process involves a previously unrecognised function of the RNA-dependent RNA polymerase 6 (RDR6) gene. Our data suggest that plants may have evolved distinct genetic controls in intercellular RNA silencing among different types of cells

Comparative Analysis of Gene Regulation by the Transcription Factor PPARα between Mouse and Human

Studies in mice have shown that PPARalpha is an important regulator of hepatic lipid metabolism and the acute phase response. However, little information is available on the role of PPARalpha in human liver. Here we set out to compare the function of PPARalpha in mouse and human hepatocytes via analysis of target gene regulation

Elevated Fibroblast growth factor 21 (FGF21) in obese, insulin resistant states is normalised by the synthetic retinoid Fenretinide in mice

The authors would like to thank undergraduate student Aleksandra Kowalczuk (University of Aberdeen) for assisting in experiments and Dr. Emma K. Lees (School of Health Sciences, Liverpool Hope University, Liverpool, UK) for invaluable discussions concerning the regulation of FGF21. We thank Dr. Calum Sutherland and Dr. Amy Cameron (both Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Scotland, UK) for technical support and expertise in performing hepatocyte studies. Fenretinide was a generous gift of T. Martin (Johnson & Johnson, New Brunswick, NJ) and U. Thumeer (Cilag AG, Schaffhausen, Switzerland), for use completely without restriction or obligation. Quantitative-PCR was carried out using the qPCR Core Facility (Institute of Medical Sciences, University of Aberdeen). RNA-sequencing was carried out at the University of Aberdeen Centre for Genome Enabled Biology and Medicine. Pancreas histology was performed by Dr Linda Davidson (Department of Histology, Aberdeen Royal Infirmary, NHS Grampian, Foresterhill Health Campus, Aberdeen, UK). This study was supported by the British Heart Foundation Intermediate Basic Research Fellowship FS/09/026 to N. Mody, RCUK fellowship to MD, EFSD/Lilly Programme Grant to MD and N. Mody, Tenovus Scotland grants G10/04 and G14/14 to N. Mody, University of Aberdeen Centre for Genome Enabled Biology and Medicine (CGEBM) PhD studentship to N. Morrice and Biotechnology and Biological Sciences Research Council studentship to GDM.Peer reviewedPublisher PD

Influence of Neonatal Hypothyroidism on Hepatic Gene Expression and Lipid Metabolism in Adulthood

Thyroid hormones are required for normal growth and development in mammals. Congenital-neonatal hypothyroidism (CH) has a profound impact on physiology, but its specific influence in liver is less understood. Here, we studied how CH influences the liver gene expression program in adulthood. Pregnant rats were given the antithyroid drug methimazole (MMI) from GD12 until PND30 to induce CH in male offspring. Growth defects due to CH were evident as reductions in body weight and tail length from the second week of life. Once the MMI treatment was discontinued, the feed efficiency increased in CH, and this was accompanied by significant catch-up growth. On PND80, significant reductions in body mass, tail length, and circulating IGF-I levels remained in CH rats. Conversely, the mRNA levels of known GH target genes were significantly upregulated. The serum levels of thyroid hormones, cholesterol, and triglycerides showed no significant differences. In contrast, CH rats showed significant changes in the expression of hepatic genes involved in lipid metabolism, including an increased transcription of PPARα and a reduced expression of genes involved in fatty acid and cholesterol uptake, cellular sterol efflux, triglyceride assembly, bile acid synthesis, and lipogenesis. These changes were associated with a decrease of intrahepatic lipids. Finally, CH rats responded to the onset of hypothyroidism in adulthood with a reduction of serum fatty acids and hepatic cholesteryl esters and to T3 replacement with an enhanced activation of malic enzyme. In summary, we provide in vivo evidence that neonatal hypothyroidism influences the hepatic transcriptional program and tissue sensitivity to hormone treatment in adulthood. This highlights the critical role that a euthyroid state during development plays on normal liver physiology in adulthood

Prevalence and phylogenetic analysis of Fig mosaic virus and Fig badnavirus-1 in Iran

Fig mosaic virus (FMV) and Fig badnavirus-1 (FBV-1) are two of the most important fig infecting viruses. The incidence and distribution of FBV-1 and FMV were determined by testing in PCR 138 asymptomatic and symptomatic samples. These samples were collected from 60 fig gardens and agricultural fields in three provinces of Iran. The fig infecting viruses FBV-1 and FMV, respectively, were detected in 92 (66.6%) and 34 (24.6%) samples collected from all the surveyed fields. Overall, 24 out of 138 (17.3%) samples showed mixed infections. The sequence analysis of a genomic fragment of 922 nt, comprising the entire ORF-2 and part of the 5’ termini of the ORF-3 of 10 selected FBV-1 Iranian isolates from different provinces, and of the type member from GenBank (Acc. No: JF411989), showed a variation ranging from 1 to 3% at nucleotide level and 1% at the amino acid level. The phylogenetic analysis grouped the FBV-1 isolates into two groups, with the Iranian isolates clustered in two distinct subgroups of group I, according to their geographical origin. In our research, the prevalence and sequence analysis of FBV-1 as the only identified DNA virus infecting fig trees, was studied for the first time in Iran

Occurrence and distribution of nematodes in rice fields in Guilan province, Iran and the first record of Mylonchulus polonicus (Stefanski, 1915) Cobb, 1917 (Nematoda: Mononchina)

The distribution of nematodes was studied in rice fields in Guilan province, Iran, from 2014 to 2016. Nematode biodiversity of 250 soil and root samples was examined. Thirty nematode species were identified morphologically, including plant parasites, microbivores and mycetophagous and predator species. Molecular techniques were also used for further identification of three plant parasitic species. Indicators of population were also estimated. Spiral nematodes (Helicotylenchus crenacauda Sher, 1966 and H. digitiformis Ivanova, 1967) and stunt nematode (Tylenchorhynchus agri) were the predominant parasitic species identified. Among other species, three mononchid species were identified namely Mononchus aquaticus, Mylonchulus sigmaturus and M. polonicus. The species M. polonicus was found and reported in Iran for the first time. The two plant parasitic species T. agri and Xiphinema index were reported in association with rice in Iran for the first time. To evaluate the distribution and incidence of Aphelenchoides besseyi (rice white-tip nematode) in different regions of Guilan province, a total of 255 fresh seed samples were collected/inspected, of which, about 40% of them were infested with A. besseyi. Of the 16 studied counties, the highest percentage of infected seeds came from fields around the city of Astara (69.2%) and the second highest infection was observed near the city of Anzali (60%)

Application of RBF-DQ Method to Time-Dependent Analysis of Unsaturated Seepage

Richards’ equation is a nonlinear partial differential equation governing unsteady seepage flow through unsaturated porous media. This paper investigates applicability of radial basis function-based differential quadrature (RBF-DQ), as a meshless method, to simulate one-dimensional flow processes in the unsaturated zone under different initial and boundary conditions. Fourth-order Runge–Kutta scheme has been adopted for time integration. Results of solving three numerical examples using RBF-DQ are compared with those of analytical, numerical, and experimental solutions presented in the literature. The comparison indicates that RBF-DQ can provide more accurate results comparing with traditional FDM or FEM without the need to discretize the computational domain. Moreover, the merit of mesh-free characteristic in RBF-DQ makes it suitable not only for solving nonlinear problems but also for dealing with multidimensional problems since meshless methods are not restricted to dimensional limitations. A key parameter in utilizing multiquadratic approximation in RBF-DQ method is the user-defined shape parameter C, which may significantly affect solution accuracy. Thus, a sensitivity analysis has been conducted to study possible effects of shape parameter on achieved results