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

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

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

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

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

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

Intercellular movement of the putative transcription factor SHR in root patterning

Positional information is pivotal for establishing developmental patterning in plants1,2,3, but little is known about the underlying signalling mechanisms. The Arabidopsis root radial pattern is generated through stereotyped division of initial cells and the subsequent acquisition of cell fate4. short-root (shr) mutants do not undergo the longitudinal cell division of the cortex/endodermis initial daughter cell, resulting in a single cell layer with only cortex attributes5,6. Thus, SHR is necessary for both cell division and endodermis specification5,6. SHR messenger RNA is found exclusively in the stele cells internal to the endodermis and cortex, indicating that it has a non-cell-autonomous mode of action6. Here we show that the SHR protein, a putative transcription factor, moves from the stele to a single layer of adjacent cells, where it enters the nucleus. Ectopic expression of SHR driven by the promoter of the downstream gene SCARECROW (SCR) results in autocatalytic reinforcement of SHR signalling, producing altered cell fates and multiplication of cell layers. These results support a model in which SHR protein acts both as a signal from the stele and as an activator of endodermal cell fate and SCR-mediated cell division

An Inverse Method to Obtain Porosity, Fibre Diameterand Density of Fibrous Sound Absorbing Materials

Characterization of sound absorbing materials is essential to predict its acoustic behaviour. The most commonly used models to do so consider the flow resistivity, porosity, and average fibre diameter as parameters to determine the acoustic impedance and sound absorbing coefficient. Besides direct experimental techniques, numerical approaches appear to be an alternative to estimate the material's parameters. In this work an inverse numerical method to obtain some parameters of a fibrous material is presented. Using measurements of the normal incidence sound absorption coefficient and then using the model proposed by Voronina, subsequent application of basic minimization techniques allows one to obtain the porosity, average fibre diameter and density of a sound absorbing material. The numerical results agree fairly well with the experimental data.This work has been supported by the Ministerio de Educacion y Ciencia-D.G. Investigacion (BIA2007-68098-C02-01 and BIA2007-68098-C02-02) and also from the Spanish Ministry of Foreign Affairs and Cooperation through the Inter-University and Scientific Research Cooperation Program (A/023748/09).Alba Fernández, J.; Rey Tormos, RMD.; Ramis Soriano, J.; Arenas, JP. (2011). An Inverse Method to Obtain Porosity, Fibre Diameterand Density of Fibrous Sound Absorbing Materials. Archives of Acoustics. 36(3):561-574. https://doi.org/10.2478/v10168-011-0040-xS561574363Allard, J., & Champoux, Y. (1992). New empirical equations for sound propagation in rigid frame fibrous materials. The Journal of the Acoustical Society of America, 91(6), 3346-3353. doi:10.1121/1.402824Attenborough, K. (1983). Acoustical characteristics of rigid fibrous absorbents and granular materials. The Journal of the Acoustical Society of America, 73(3), 785-799. doi:10.1121/1.389045Bies, D. A., & Hansen, C. H. (1980). Flow resistance information for acoustical design. Applied Acoustics, 13(5), 357-391. doi:10.1016/0003-682x(80)90002-xChampoux, Y., Stinson, M. R., & Daigle, G. A. (1991). Air‐based system for the measurement of porosity. The Journal of the Acoustical Society of America, 89(2), 910-916. doi:10.1121/1.1894653Crocker, M. J., & Arenas, J. P. (s. f.). Use of Sound-Absorbing Materials. Handbook of Noise and Vibration Control, 696-713. doi:10.1002/9780470209707.ch57Delany, M. E., & Bazley, E. N. (1970). Acoustical properties of fibrous absorbent materials. Applied Acoustics, 3(2), 105-116. doi:10.1016/0003-682x(70)90031-9Dunn, I. P., & Davern, W. A. (1986). Calculation of acoustic impedance of multi-layer absorbers. Applied Acoustics, 19(5), 321-334. doi:10.1016/0003-682x(86)90044-7Fellah, Z. E. A., Berger, S., Lauriks, W., Depollier, C., Aristégui, C., & Chapelon, J.-Y. (2003). Measuring the porosity and the tortuosity of porous materials via reflected waves at oblique incidence. The Journal of the Acoustical Society of America, 113(5), 2424-2433. doi:10.1121/1.1567275Fellah, Z. E. A., Berger, S., Lauriks, W., Depollier, C., & Fellah, M. (2003). Measuring the porosity of porous materials having a rigid frame via reflected waves: A time domain analysis with fractional derivatives. Journal of Applied Physics, 93(1), 296-303. doi:10.1063/1.1524025Fellah, Z. E. A., Berger, S., Lauriks, W., Depollier, C., Trompette, P., & Chapelon, J. Y. (2003). Ultrasonic measurement of the porosity and tortuosity of air-saturated random packings of beads. Journal of Applied Physics, 93(11), 9352-9359. doi:10.1063/1.1572191Fellah, Z. E. A., Mitri, F. G., Fellah, M., Ogam, E., & Depollier, C. (2007). Ultrasonic characterization of porous absorbing materials: Inverse problem. Journal of Sound and Vibration, 302(4-5), 746-759. doi:10.1016/j.jsv.2006.12.007Garai, M., & Pompoli, F. (2005). A simple empirical model of polyester fibre materials for acoustical applications. Applied Acoustics, 66(12), 1383-1398. doi:10.1016/j.apacoust.2005.04.008ISO (1998), 10534-2:1998. Acoustics - determination of sound absorption coefficient and impedance in impedance tubes - Part 2: transfer-function method, International Organization for Standardization, Geneva.Miki, Y. (1990). Acoustical properties of porous materials. Modifications of Delany-Bazley models. Journal of the Acoustical Society of Japan (E), 11(1), 19-24. doi:10.1250/ast.11.19Miki, Y. (1990). Acoustical properties of porous materials. Generalizations of empirical models. Journal of the Acoustical Society of Japan (E), 11(1), 25-28. doi:10.1250/ast.11.25Ramis, J., Alba, J., Del Rey, R., Escuder, E., & Sanchís, V. J. (2010). Nuevos materiales absorbentes acústicos basados en fibra de kenaf. Materiales de Construcción, 60(299), 133-143. doi:10.3989/mc.2010.50809Shoshani, Y., & Yakubov, Y. (2000). Numerical assessment of maximal absorption coefficients for nonwoven fiberwebs. 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A new empirical model for the acoustic properties of loose granular media. Applied Acoustics, 64(4), 415-432. doi:10.1016/s0003-682x(02)00105-6Wang, X., Eisenbrey, J., Zeitz, M., & Sun, J. Q. (2004). Multi-stage regression analysis of acoustical properties of polyurethane foams. Journal of Sound and Vibration, 273(4-5), 1109-1117. doi:10.1016/j.jsv.2003.09.039Wilson, D. K. (1997). Simple, relaxational models for the acoustical properties of porous media. Applied Acoustics, 50(3), 171-188. doi:10.1016/s0003-682x(96)00048-

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

MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development

The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development. We also investigated the regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield