ANALYSIS OF LOW-COST UAV PHOTOGRAMMETRY SOLUTIONS FOR BEACH MODELLING AND MONITORING USING THE OPENSOURCE QUANTUM GIS

Coastlines are fundamentally unique features. Their behavioural patterns are predominantly subjects of numerous environmental and engineering studies. With the magnitude of the effects of coastal flooding and erosion, there is a need for accurate techniques for data capture and data processing. With an emphasis on the zero-cost open source GIS software, there is no existing evaluative procedure for demonstrating the analytical capabilities of large-scale UAV-based outputs for microscale analysis for small changes on the beach such as sediment movement, erosion/accretion of individual features. There were four different drone surveys in the study area to determine microscale change over time. A three-stage analysis procedure helps in determining the overview of the coastline and highlights the region(s) of optimum change requiring further spatial analysis with micro-scale change detection. Results obtained show the analytical capabilities of large-scale UAV-based outputs for relatively small but detailed analysis using the open-source QGIS. Results obtained show that spatial analyses of the zoomed areas at different viewpoints and scales improve the confidence level of the hillshading and contour of that particular section on the coastline. The UAV photogrammetry and the three-stage analysis procedure can detect a 1cm change on the beach using the free and open-source QGIS software. It shows the profile modelling of the coastal inundations for both pre and post-flooding events at sub-centimetre intervals can be obtained from QGIS modelling, data computation, analysis, and visualization

Measurement of geo-neutrinos from 1353 days of Borexino

We present a measurement of the geo--neutrino signal obtained from 1353 days of data with the Borexino detector at Laboratori Nazionali del Gran Sasso in Italy. With a fiducial exposure of (3.69 $\pm$ 0.16) $\times$ $10^{31}$ proton $\times$ year after all selection cuts and background subtraction, we detected (14.3 $\pm$ 4.4) geo-neutrino events assuming a fixed chondritic mass Th/U ratio of 3.9. This corresponds to a geo-neutrino signal $S_{geo}$ = (38.8 $\pm$ 12.0) TNU with just a 6 $\times$ $10^{-6}$ probability for a null geo-neutrino measurement. With U and Th left as free parameters in the fit, the relative signals are $S_{\mathrm{Th}}$ = (10.6 $\pm$ 12.7) TNU and $S_\mathrm{U}$ = (26.5 $\pm$ 19.5) TNU. Borexino data alone are compatible with a mantle geo--neutrino signal of (15.4 $\pm$ 12.3) TNU, while a combined analysis with the KamLAND data allows to extract a mantle signal of (14.1 $\pm$ 8.1) TNU. Our measurement of a reactor anti--neutrino signal $S_{react}$ = 84.5$^{+19.3}_{-18.9}$ TNU is in agreement with expectations in the presence of neutrino oscillations.Comment: 9 pages, 6 figure

Borexino calibrations: Hardware, Methods, and Results

Borexino was the first experiment to detect solar neutrinos in real-time in the sub-MeV region. In order to achieve high precision in the determination of neutrino rates, the detector design includes an internal and an external calibration system. This paper describes both calibration systems and the calibration campaigns that were carried out in the period between 2008 and 2011. We discuss some of the results and show that the calibration procedures preserved the radiopurity of the scintillator. The calibrations provided a detailed understanding of the detector response and led to a significant reduction of the systematic uncertainties in the Borexino measurements

Twisting the arm: structural constraints in bicyclic expanded-ring N-heterocyclic carbenes

A series of diaryl, mono-aryl/alkyl and dialkyl mono- and bicyclic expanded-ring N-heterocyclic carbenes (ER-NHCs) have been prepared and their complexation to Au(I) investigated through the structural analysis of fifteen Au(NHC)X and/or [Au(NHC)2]X complexes. The substituted diaryl 7-NHCs are the most sterically encumbered with large buried volume (%VB) values of 40–50% with the less flexible six-membered analogues having %VB values at least 5% smaller. Although the bicyclic systems containing fused 6- and 7-membered rings (6,7-NHCs) are constrained with relatively acute NCN bond angles, they have the largest %VB values of the dialkyl derivatives reported here, a feature related to the fixed conformation of the heterocyclic rings and the compressional effect of a pre-set methyl substituent

The Borexino detector at the Laboratori Nazionali del Gran Sasso

Borexino, a large volume detector for low energy neutrino spectroscopy, is currently running underground at the Laboratori Nazionali del Gran Sasso, Italy. The main goal of the experiment is the real-time measurement of sub MeV solar neutrinos, and particularly of the mono energetic (862 keV) Be7 electron capture neutrinos, via neutrino-electron scattering in an ultra-pure liquid scintillator. This paper is mostly devoted to the description of the detector structure, the photomultipliers, the electronics, and the trigger and calibration systems. The real performance of the detector, which always meets, and sometimes exceeds, design expectations, is also shown. Some important aspects of the Borexino project, i.e. the fluid handling plants, the purification techniques and the filling procedures, are not covered in this paper and are, or will be, published elsewhere (see Introduction and Bibliography).Comment: 37 pages, 43 figures, to be submitted to NI

Microdissection of Shoot Meristem Functional Domains

The shoot apical meristem (SAM) maintains a pool of indeterminate cells within the SAM proper, while lateral organs are initiated from the SAM periphery. Laser microdissection–microarray technology was used to compare transcriptional profiles within these SAM domains to identify novel maize genes that function during leaf development. Nine hundred and sixty-two differentially expressed maize genes were detected; control genes known to be upregulated in the initiating leaf (P0/P1) or in the SAM proper verified the precision of the microdissections. Genes involved in cell division/growth, cell wall biosynthesis, chromatin remodeling, RNA binding, and translation are especially upregulated in initiating leaves, whereas genes functioning during protein fate and DNA repair are more abundant in the SAM proper. In situ hybridization analyses confirmed the expression patterns of six previously uncharacterized maize genes upregulated in the P0/P1. P0/P1-upregulated genes that were also shown to be downregulated in leaf-arrested shoots treated with an auxin transport inhibitor are especially implicated to function during early events in maize leaf initiation. Reverse genetic analyses of asceapen1 (asc1), a maize D4-cyclin gene upregulated in the P0/P1, revealed novel leaf phenotypes, less genetic redundancy, and expanded D4-CYCLIN function during maize shoot development as compared to Arabidopsis. These analyses generated a unique SAM domain-specific database that provides new insight into SAM function and a useful platform for reverse genetic analyses of shoot development in maize

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

MicroRNAs (miRNAs) posttranscriptionally regulate targeted messenger RNAs (mRNAs) by inducing cleavage or otherwise repressing their translation. We address the problem of detecting m/miRNA targeting relationships in homo sapiens from microarray data by developing statistical models that are motivated by the biological mechanisms used by miRNAs. The focus of our modeling is the construction, activity, and mediation of RNA-induced silencing complexes (RISCs) competent for targeted mRNA cleavage. We demonstrate that regression models accommodating RISC abundance and controlling for other mediating factors fit the expression profiles of known target pairs substantially better than models based on m/miRNA expressions alone, and lead to verifications of computational target pair predictions that are more sensitive than those based on marginal expression levels. Because our models are fully independent of exogenous results from sequence-based computational methods, they are appropriate for use as either a primary or secondary source of information regarding m/miRNA target pair relationships, especially in conjunction with high-throughput expression studies

The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway

In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway, also suppress the phenotypes associated with HWS loss of function, corroborating epistatic relations between the miRNA pathway genes and HWS. In agreement with these data, accumulation of miRNA is modified in HWS loss or gain of function mutants. Our data propose HWS as a new player in the miRNA pathway, important for plant growth

Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis

Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA cleavage site. Antisense smRNAs were also found associated with MIRNA genes. This suggests that miRNA-associated “transitivity” (production of small interfering RNAs through antisense transcription) is more common than previously reported. High-resolution (3 nt) custom tiling microarray transcriptome analysis was performed with probes 400 bp 5′ upstream and 3′ downstream of the miRNA cleavage sites (direction relative to the mRNA) for 22 select miRNA target genes. We hybridized RNAs labeled from the smRNA pathway mutants, including hen1-1, dcl1-7, hyl1-2, rdr6-15, and sgs3-14. Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants. This was corroborated by semi-quantitative reverse transcription PCR; however, a direct correlation of antisense transcript abundance in MIR164 gene knockouts was not observed. Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation. HEN1 and SGS3 may be links for miRNA target entry into different RNA processing pathways