A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era

10.1186/1471-2164-10-S3-S36BMC Genomics10SUPPL. 3BGME

InCoB2013 introduces Systems Biology as a major conference theme

10.1186/1752-0509-7-S3-S1BMC Systems Biology7SUPPL.3

APBioNet-Transforming Bioinformatics in the Asia-Pacific Region

10.1371/journal.pcbi.1003317PLoS Computational Biology910

A steady-state Bi-substrate technique for measurement of the thermal conductivity of ceramic coatings

This paper presents a steady-state, bi-substrate technique for measurement of the through-thickness thermal conductivity of ceramic coatings, with a range of specimen thickness and porosity content. The technique is based on establishing unidirectional steady-state heat flow through the sample, sandwiched between a pair of (metallic) substrates with known thermal properties. Comparison between the heat fluxes passing through the two substrates allows a check to be made about the accuracy of the assumption of unidirectional heat flow. The interfacial conductances must be known and these can be estimated by testing samples of different thickness. Measured conductivities are likely to be more accurate if the interfacial conductance is relatively high. This is assisted by the introduction of a thin interfacial layer of a viscous, thermally conductive compound, or thermal pads of some sort, and by maintaining a suitable pressure across the setup. However, if such compounds (pastes) are used, then care must be taken to ensure that it does not enter the specimen via surface-connected pores, since this could significantly affect the measured conductivity. The reliability of the technique has been confirmed by testing fused silica samples of known thermal conductivity. It has also been applied to sprayed zirconia and plasma electrolytic oxide (PEO) alumina coatings. The values obtained were 1.05±0.10 W m?1 K?1 and 1.63±0.35 W m?1 K?1, respectively

A case for re-inventory of Australia’s plant pathogens

Australia has efficient and visible plant quarantine measures, which through various border controls and survey activities attempt to prevent the entry of unwanted pests and diseases. The ability to successfully perform this task relies heavily on determining what pathogens are present and established in Australia as well as those pathogens that are exotic and threatening. There are detailed checklists and databases of fungal plant pathogens in Australia, compiled, in part, from surveys over many years sponsored by Federal and State programmes. These checklists and databases are mostly specimen-based, which enables validation of records with reference herbarium specimens and sometimes associated cultures. Most of the identifications have been based on morphological examination. The use of molecular methods, particularly the analysis of DNA sequence data, has recently shown that several well-known and important plant pathogenic species are actually complexes of cryptic species. We provide examples of this in the important plant pathogenic genera Botryosphaeria and its anamorphs, Colletotrichum, Fusarium, Phomopsis / Diaporthe and Mycosphaerella and its anamorphs. The discovery of these cryptic species indicates that many of the fungal names in checklists need scrutiny. It is difficult, and often impossible, to extract DNA for sequence analysis from herbarium specimens in order to validate identifications that may now be considered suspect. This validation can only be done if specimens are recollected, re-isolated and subjected to DNA analysis. Where possible, herbarium specimens as well as living cultures are needed to support records. Accurate knowledge of the plant pathogens within Australia’s borders is an essential prerequisite for the effective discharge of plant quarantine activities that will prevent or delay the arrival of unwanted plant pathogens

Strong Discontinuities in the Complex Photonic Band Structure of Transmission Metallic Gratings

Complex photonic band structures (CPBS) of transmission metallic gratings with rectangular slits are shown to exhibit strong discontinuities that are not evidenced in the usual energetic band structures. These discontinuities are located on Wood's anomalies and reveal unambiguously two different types of resonances, which are identified as horizontal and vertical surface-plasmon resonances. Spectral position and width of peaks in the transmission spectrum can be directly extracted from CPBS for both kinds of resonances.Comment: 4 pages, 4 figures, REVTeX version

Cooling of a single atom in an optical trap inside a resonator

We present detailed discussions of cooling and trapping mechanisms for an atom in an optical trap inside an optical cavity, as relevant to recent experiments. The interference pattern of cavity QED and trapping fields in space makes the trapping wells distinguishable from one another. This adds considerable flexibility to creating effective trapping and cooling conditions and to detection possibilities. Friction and diffusion coefficients are calculated in and beyond the low excitation limit and full 3-D simulations of the quasiclassical motion of a Cs atom are performed.Comment: One more figure and one more autho

Trapping and cooling single atoms with far-off resonance intracavity doughnut modes

We investigate cooling and trapping of single atoms inside an optical cavity using a quasi-resonant field and a far-off resonant mode of the Laguerre-Gauss type. The far-off resonant doughnut mode provides an efficient trapping in the case when it shifts the atomic internal ground and excited state in the same way, which is particularly useful for quantum information applications of cavity quantum electrodynamics (QED) systems. Long trapping times can be achieved, as shown by full 3-D simulations of the quasi-classical motion inside the resonator.Comment: 18 pages, 18 figures, RevTe

Trapping of Single Atoms with Single Photons in Cavity QED

Two recent experiments have reported the trapping of individual atoms inside optical resonators by the mechanical forces associated with single photons [Hood et al., Science 287, 1447 (2000) and Pinkse et al., Nature 404, 365 (2000)]. Here we analyze the trapping dynamics in these settings, focusing on two points of interest. Firstly, we investigate the extent to which light-induced forces in these experiments are distinct from their free-space counterparts. Secondly, we explore the quantitative features of the resulting atomic motion and how these dynamics are mapped onto variations of the intracavity field. Not surprisingly, qualitatively distinct atomic dynamics arise as the coupling and dissipative rates are varied. For the experiment of Hood et al., we show that atomic motion is largely conservative and is predominantly in radial orbits transverse to the cavity axis. A comparison with the free-space theory demonstrates that the fluctuations of the dipole force are suppressed by an order of magnitude. This effect is based upon the Jaynes-Cummings eigenstates of the atom-cavity system and represents qualitatively new physics for optical forces at the single-photon level. By contrast, even in a regime of strong coupling in the experiment of Pinkse et al., there are only small quantitative distinctions between the free-space theory and the quantum theory, so it is not clear that description of this experiment as a novel single-quantum trapping effect is necessary. The atomic motion is strongly diffusive, leading to an average localization time comparable to the time for an atom to transit freely through the cavity and to a reduction in the ability to infer aspects of the atomic motion from the intracavity photon number.Comment: 19 pages, 22 figure files, REVTEX, corrected spelling, LaTeX now produces postscript which includes figures, minor changes to figures. Final version to be published in Physical Review A, expanded summary of results in introduction, minor changes to figures and tex

Long-term neurodevelopmental outcome in children after antenatal intravenous immune globulin treatment in fetal and neonatal alloimmune thrombocytopenia

BACKGROUND: Children with fetal and neonatal alloimmune throm-bocytopenia face increased risk of intracranial hemorrhage potentially leading to developmental impairment. To prevent intracranial hemorrhage, pregnant women with alloantibodies against fetal platelets are often treated with intravenous immunoglobulin. Intravenous immunoglobulin seems effective in vastly reducing the risk of fetal or neonatal bleeding complications. However, information on long-term neurodevelopment of these children is lacking. OBJECTIVE: This study aimed to evaluate long-term neurodevelopmental outcome in children with fetal and neonatal alloimmune thrombocytopenia who were treated with intravenous immunoglobulin antenatally. STUDY DESIGN: An observational cohort study was performed, including children of mothers treated with intravenous immunoglobulin during pregnancy because a previous child was diagnosed with fetal and neonatal alloimmune thrombocytopenia. Children were invited for a follow-up assessment including standardized cognitive and neurologic tests. The parents were asked to complete a behavioral questionnaire and school performance reports. The primary outcome was severe neurodevelopmental impairment, defined as severe cognitive impairment (intelligence quotient = 3, bilateral blindness, and/or bilateral deafness (requiring amplification). The secondary outcome was mild to moderate neurodevelopmental impairment, defined as either mild to moderate cognitive impairment (intelligence quotient Immunobiology of allogeneic stem cell transplantation and immunotherapy of hematological disease