Uniform fractional factorial designs

The minimum aberration criterion has been frequently used in the selection of fractional factorial designs with nominal factors. For designs with quantitative factors, however, level permutation of factors could alter their geometrical structures and statistical properties. In this paper uniformity is used to further distinguish fractional factorial designs, besides the minimum aberration criterion. We show that minimum aberration designs have low discrepancies on average. An efficient method for constructing uniform minimum aberration designs is proposed and optimal designs with 27 and 81 runs are obtained for practical use. These designs have good uniformity and are effective for studying quantitative factors.Comment: Published in at http://dx.doi.org/10.1214/12-AOS987 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

MLGO: phylogeny reconstruction and ancestral inference from gene-order data

Background The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements. Results MLGOMLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGOMLGO is based on likelihood computation and shows advantages over existing methods in terms of accuracy, scalability and flexibility. Conclusions To the best of our knowledge, it is the first web tool for analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions and duplications. The web tool is available from http://www.geneorder.org/server.php

Continuous volumetric imaging via an optical phase-locked ultrasound lens

In vivo imaging at high spatiotemporal resolution is key to the understanding of complex biological systems. We integrated an optical phase-locked ultrasound lens into a two-photon fluorescence microscope and achieved microsecond-scale axial scanning, thus enabling volumetric imaging at tens of hertz. We applied this system to multicolor volumetric imaging of processes sensitive to motion artifacts, including calcium dynamics in behaving mouse brain and transient morphology changes and trafficking of immune cells

Investigation of in situ soil nitrogen mineralization in a Picea-Abies forest in Tibet Plateau: effects of increased nitrogen input

The main objective of this study was to quantify the dynamics of ammonium (NH4+) and nitrate (NO3-) in the humus (0-7cm) and the uppermost mineral layer (0-15cm) of a forest soil. The soil was treated annually from 2012 to 2013 with one single dose of nitrogen (0, 15, 30kg N ha-1yr-1 applied as (NH4)2SO4, NH4Cl, KNO3). Net N mineralization, including net ammonification and net nitrification was determined in four in situ incubation periods over 2 years in a Picea-Abies forest stand at the Qinghai-Tibet Plateau, Southwest China. Measurements were done using soil cores (7cm or 15cm deep) with a resin bag filled with combined anion and cation exchange resins placed at the base to collect the N leaching from the soil. The accumulation rate of N was corrected for both deposition and fertilizer N inputs. In all treatments, both the content and accumulation of the mineral N were dominated by NH4+ which accounts for about 76-89% of the net mineralization. The accumulation rate of N decreased to 64-83% in KNO3 treatments. The net N mineralization rate increased with nitrogen input, especially in NH4+-N treatments (p<0.05). However, this promoting role decreased over time. At the highest (NH4)2SO4 additions, the net ammonification and net mineralization rate increased notably in the humus (0-7cm) rather than in the uppermost mineral layer (0-15 cm). Previous studies that reported on soil net mineralization from forests under different environmental conditions were compiled and assessed for the effects of atmospheric N deposition and environmental factors, annual precipitation, and annual temperature on annual fluxes of net nitrogen mineralization in forest soils, worldwide. The results show that an increase in atmospheric N deposition significantly enhances the soil net nitrogen mineralization rate. Variation in atmospheric N deposition accounts for 48% of the variation in the rate of soil net nitrogen mineralization across the forests.</p