Parallel methods for short read assembly

This work is on the parallel de novo assembly of genomic sequences from short sequence reads. With short reads eliminating the reliability of read overlaps in predicting genomic co-location, a revival of graph-based methods has underpinned the development of short-read assemblers. While these methods predate short read technology, their reach has not extended significantly beyond bacterial genomes due to the memory resources required in their use. These memory limitations are exacerbated by the high coverage needed to compensate for shorter read lengths. As a result, prior to our work, short-read de novo assembly had been demonstrated on relatively small genome sizes with a few million bases. In our work, we advance the field of short sequence assembly in a number of ways. First, we extend models and ideas proposed and tested with small genomes on serial machines to large-scale distributed memory parallel machines. Second, we present ideas for assembly that are especially suited to the reconstruction of very large genomes on these machines. Additionally, we present the first assembler that specifically takes advantage a variable number of fragment sizes or insert lengths concurrently when making assembly decisions, while still working well for data with one insertion length

Microwave Properties of Ice-Phase Hydrometeors for Radar and Radiometers: Sensitivity to Model Assumptions

A simplied framework is presented for assessing the qualitative sensitivities of computed microwave properties, satellite brightness temperatures, and radar reflectivities to assumptions concerning the physical properties of ice-phase hydrometeors. Properties considered included the shape parameter of a gamma size distribution andthe melted-equivalent mass median diameter D0, the particle density, dielectric mixing formula, and the choice of complex index of refraction for ice. We examine these properties at selected radiometer frequencies of 18.7, 36.5, 89.0, and 150.0 GHz; and radar frequencies at 2.8, 13.4, 35.6, and 94.0 GHz consistent with existing and planned remote sensing instruments. Passive and active microwave observables of ice particles arefound to be extremely sensitive to the melted-equivalent mass median diameter D0 ofthe size distribution. Similar large sensitivities are found for variations in the ice vol-ume fraction whenever the geometric mass median diameter exceeds approximately 1/8th of the wavelength. At 94 GHz the two-way path integrated attenuation is potentially large for dense compact particles. The distribution parameter mu has a relatively weak effect on any observable: less than 1-2 K in brightness temperature and up to 2.7 dB difference in the effective radar reflectivity. Reversal of the roles of ice and air in the MaxwellGarnett dielectric mixing formula leads to a signicant change in both microwave brightness temperature (10 K) and radar reflectivity (2 dB). The choice of Warren (1984) or Warren and Brandt (2008) for the complex index of refraction of ice can produce a 3%-4% change in the brightness temperature depression

Multisensor Observation and Simulation of Snowfall During the 2003 Wakasa Bay Field Experiment

This research seeks to assess and improve the accuracy of microphysical assumptions used in satellite passive microwave radiative transfer models and retrieval algorithms by exploiting complementary observations from satellite radiometers, such as TRMM/AMSR-E/GPM, and coincident aircraft instruments, such as the next generation precipitation radar (PR-2). We focus in particular on aircraft data obtained during the Wakasa Bay field experiment, Japan 2003, pertaining to surface snowfall events. The observations of vertical profiles of reflectivity and Doppler-derived fall speeds are used in conjunction with the radiometric measurements to identify 1-D profiles of precipitation particle types, sizes, and concentrations that are consistent with the observations

Application of Conservation and Veterinary Tools in the Management of Stray Wildlife in Zambia

In recent years, Zambia has seen an increase in the incidences of conflicts involving stray wild animals with humans. Notable among these animals include the African elephants, buffalo and lion. Consequently, this triggers a response from law enforcement units of both government and the department of national parks to control the animals. Regrettably, most of their responses have involved the shooting down of these animals, rather than taking advantage of conservation and veterinary tools to relocate the animals back into protected areas, and this raises concerns about the welfare of these animals. Therefore, this chapter will bring to light some of the locally available tools that could be used to control stray wildlife in order to contribute towards both conservation and reducing human-wildlife conflicts in Zambia

Aberrant Cell Cycle and Apoptotic Changes Characterise Severe Influenza A Infection – A Meta-Analysis of Genomic Signatures in Circulating Leukocytes

Influenza A infection is a global disease that has been responsible for four pandemics over the last one hundred years. However, it remains poorly understood as to why some infected individuals succumb to life threatening complications whilst others recover and are relatively unaffected. Using gene-expression analysis of circulating leukocytes, here we show that the progression towards severe influenza A infection is characterised by an abnormal transcriptional reprogramming of cell cycle and apoptosis pathways. In severely infected humans, leukocyte gene-expression profiles display opposing cell cycle activities; an increased aberrant DNA replication in the G1/S phase yet delayed progression in the G2/M phase. In mild infection, cell cycle perturbations are fewer and are integrated with an efficient apoptotic program. Importantly, the loss of integration between cell cycle perturbations and apoptosis marks the transition from a mild viral illness to a severe, life threatening infection. Our findings suggest that circulating immune cells may play a significant role in the evolution of the host response. Further study may reveal alternative host response factors previously unrecognized in the current disease model of influenza

Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

This corrects the article DOI: 10.1038/sdata.2017.179

Human Resources and the Resource Based View of the Firm

The resource-based view (RBV) of the firm has influenced the field of strategic human resource management (SHRM) in a number of ways. This paper explores the impact of the RBV on the theoretical and empirical development of SHRM. It explores how the fields of strategy and SHRM are beginning to converge around a number of issues, and proposes a number of implications of this convergence

Observing the Evolution of the Universe

How did the universe evolve? The fine angular scale (l>1000) temperature and polarization anisotropies in the CMB are a Rosetta stone for understanding the evolution of the universe. Through detailed measurements one may address everything from the physics of the birth of the universe to the history of star formation and the process by which galaxies formed. One may in addition track the evolution of the dark energy and discover the net neutrino mass. We are at the dawn of a new era in which hundreds of square degrees of sky can be mapped with arcminute resolution and sensitivities measured in microKelvin. Acquiring these data requires the use of special purpose telescopes such as the Atacama Cosmology Telescope (ACT), located in Chile, and the South Pole Telescope (SPT). These new telescopes are outfitted with a new generation of custom mm-wave kilo-pixel arrays. Additional instruments are in the planning stages.Comment: Science White Paper submitted to the US Astro2010 Decadal Survey. Full list of 177 author available at http://cmbpol.uchicago.ed