Molecular microbial ecology of lignocellulose mobilisation as a carbon source in mine drainage wastewater treatment

The community structure of complex microbial consortia which develop in lignocellulose packed passive treatment systems for acid mine drainage remediation were investigated. An understanding of interactions between these populations is important in determining mechanisms by which such systems operate. A degrading packed bed reactor was packed with lignocellulositic material as a sole carbon source and fed continuously with simulated acid mine drainage. Samples were collected every two months at different depths of the reactor to isolate the total genomic DNA and PCR amplify section of 16S rDNA gene. PCR primers, GM5F and 907R incorporating GC clamp were used to amplify 586-bp region of 16S rDNA gene. Denaturing gradient gel electrophoresis (DGGE) indicated clearly a highly differentiated pattern of r-DNA – derived amplificates between different depths of the bioreactor. Predominant DGGE bands were further excised, reamplified, cloned and sequenced. Sequencing analysis revealed phylogenetic affiliation of specific bacterial populations in different depths of the bioreactor. Water SA Vol. 30 (5) 2005: pp.658-66

Technical note: Development of a gradient tube method for examining microbial population structures in floating sulphur biofilms

Floating biofilms occur in thin layers of between 50 μm and 500 μm on the surface of certain organic, sulphidic aquatic environments and, at times, may only be several cells deep. While these structures may be important in terms of energy flow pathways, and possibly also in wastewater treatment operations, little is known about their structural/functional properties. This is due, in part, to their flimsy nature but also to methodological constraints related to their sampling and manipulation. We have investigated floating sulphur biofilms that appear as white layers on the surface of anoxic sulphidic organic wastewaters and describe here the development of a novel gradient tube method for investigating these systems. This approach enables testing of the hypothesis that these floating sulphur biofilms are complex well-differentiated structures rather than disordered dispersions of microbial biomass as has been previously thought. Furthermore, if the former is correct, they would seem to resemble the structure and functionality of comparable complex bioflms that are attached to solid substrates. The gradient tube method involves the establishment of apposing gradients of sulphide and oxygen that are expanded across a tube of agarose 10 cm in length; this simulates the oxic/anoxic interface that occurs over only several micrometres in the natural biofilm system. A plug of sulphide-enriched agarose is first placed in the base of the tube. Samples of the floating sulphur biofilm are then mixed into agarose growth medium and, before it sets, this is overlaid on top of the plug. The tubes are then open capped and incubated. A variety of different microbial populations may thus become established in the separate physiological niches that are set up in this way within the gradient tube. The populations may be quite robustly sampled by extruding and then sectioning the agarose plug. This expansion of the biofilm enables more detailed molecular phylogenetic studies of the populations found in the various niches within the biofilm and also measurement of physico-chemical parameters within the system.Keywords: gradient tube method, floating biofilms, floating sulphur biofilms, microbial ecology, sulphur biotechnology, acid mine drainage wastewater

Stage at diagnosis for childhood solid cancers in Australia: A population-based study

BACKGROUND: Stage of cancer at diagnosis is one of the strongest predictors of survival and is essential for population cancer surveillance, comparison of cancer outcomes and to guide national cancer control strategies. Our aim was to describe, for the first time, the distribution of cases by stage at diagnosis and differences in stage-specific survival on a population basis for a range of childhood solid cancers in Australia. METHODS: The study cohort was drawn from the population-based Australian Childhood Cancer Registry and comprised children (<15 years) diagnosed with one of 12 solid malignancies between 2006 and 2014. Stage at diagnosis was assigned according to the Toronto Paediatric Cancer Stage Guidelines. Observed (all cause) survival was calculated using the Kaplan-Meier method, with follow-up on mortality available to 31 December 2015. RESULTS: Almost three-quarters (1256 of 1760 cases, 71%) of children in the study had localised or regional disease at diagnosis, varying from 43% for neuroblastoma to 99% for retinoblastoma. Differences in 5-year observed survival by stage were greatest for osteosarcoma (localised 85% (95% CI = 72%-93%) versus metastatic 37% (15%-59%)), neuroblastoma (localised 98% (91%-99%) versus metastatic 60% (52%-67%)), rhabdomyosarcoma (localised 85% (71%-93%) versus metastatic 53% (34%-69%)), and medulloblastoma (localised 69% (61%-75%) versus metastases to spine 42% (27%-57%)). CONCLUSION: The stage-specific information presented here provides a basis for comparison with other international population cancer registries. Understanding variations in survival by stage at diagnosis will help with the targeted formation of initiatives to improve outcomes for children with cancer

Whole breast and regional nodal irradiation in prone versus supine position in left sided breast cancer

Background: Prone whole breast irradiation (WBI) leads to reduced heart and lung doses in breast cancer patients receiving adjuvant radiotherapy. In this feasibility trial, we investigated the prone position for whole breast + lymph node irradiation (WB + LNI). Methods: A new support device was developed for optimal target coverage, on which patients are positioned in a position resembling a phase from the crawl swimming technique (prone crawl position). Five left sided breast cancer patients were included and simulated in supine and prone position. For each patient, a treatment plan was made in prone and supine position for WB + LNI to the whole axilla and the unoperated part of the axilla. Patients served as their own controls for comparing dosimetry of target volumes and organs at risk (OAR) in prone versus in supine position. Results: Target volume coverage differed only slightly between prone and supine position. Doses were significantly reduced (P < 0.05) in prone position for ipsilateral lung (Dmean, D2, V5, V10, V20, V30), contralateral lung (Dmean, D2), contralateral breast (Dmean, D2 and for total axillary WB + LNI also V5), thyroid (Dmean, D2, V5, V10, V20, V30), oesophagus (Dmean and for partial axillary WB + LNI also D2 and V5), skin (D2 and for partial axillary WB + LNI V105 and V107). There were no significant differences for heart and humeral head doses. Conclusions: Prone crawl position in WB + LNI allows for good breast and nodal target coverage with better sparing of ipsilateral lung, thyroid, contralateral breast, contralateral lung and oesophagus when compared to supine position. There is no difference in heart and humeral head doses

Non-stationary covariance function modelling in 2D least-squares collocation

Standard least-squares collocation (LSC) assumes 2D stationarity and 3D isotropy, and relies on a covariance function to account for spatial dependence in the ob-served data. However, the assumption that the spatial dependence is constant through-out the region of interest may sometimes be violated. Assuming a stationary covariance structure can result in over-smoothing of, e.g., the gravity field in mountains and under-smoothing in great plains. We introduce the kernel convolution method from spatial statistics for non-stationary covariance structures, and demonstrate its advantage fordealing with non-stationarity in geodetic data. We then compared stationary and non-stationary covariance functions in 2D LSC to the empirical example of gravity anomaly interpolation near the Darling Fault, Western Australia, where the field is anisotropic and non-stationary. The results with non-stationary covariance functions are better than standard LSC in terms of formal errors and cross-validation against data not used in the interpolation, demonstrating that the use of non-stationary covariance functions can improve upon standard (stationary) LSC

Diffractive Dijet Production at sqrt(s)=630 and 1800 GeV at the Fermilab Tevatron

We report a measurement of the diffractive structure function $F_{jj}^D$ of the antiproton obtained from a study of dijet events produced in association with a leading antiproton in $\bar pp$ collisions at $\sqrt s=630$ GeV at the Fermilab Tevatron. The ratio of $F_{jj}^D$ at $\sqrt s=630$ GeV to $F_{jj}^D$ obtained from a similar measurement at $\sqrt s=1800$ GeV is compared with expectations from QCD factorization and with theoretical predictions. We also report a measurement of the $\xi$ ($x$-Pomeron) and $\beta$ ($x$ of parton in Pomeron) dependence of $F_{jj}^D$ at $\sqrt s=1800$ GeV. In the region $0.035<\xi<0.095$, $|t|<1$ GeV$^2$ and $\beta<0.5$, $F_{jj}^D(\beta,\xi)$ is found to be of the form $\beta^{-1.0\pm 0.1} \xi^{-0.9\pm 0.1}$, which obeys $\beta$-$\xi$ factorization.Comment: LaTeX, 9 pages, Submitted to Phys. Rev. Letter

Fluorescent Transgenic Zebrafish Tg(nkx2.2a:mEGFP) Provides a Highly Sensitive Monitoring Tool for Neurotoxins

10.1371/journal.pone.0055474PLoS ONE82

Measurements of the properties of Lambda_c(2595), Lambda_c(2625), Sigma_c(2455), and Sigma_c(2520) baryons

We report measurements of the resonance properties of Lambda_c(2595)+ and Lambda_c(2625)+ baryons in their decays to Lambda_c+ pi+ pi- as well as Sigma_c(2455)++,0 and Sigma_c(2520)++,0 baryons in their decays to Lambda_c+ pi+/- final states. These measurements are performed using data corresponding to 5.2/fb of integrated luminosity from ppbar collisions at sqrt(s) = 1.96 TeV, collected with the CDF II detector at the Fermilab Tevatron. Exploiting the largest available charmed baryon sample, we measure masses and decay widths with uncertainties comparable to the world averages for Sigma_c states, and significantly smaller uncertainties than the world averages for excited Lambda_c+ states.Comment: added one reference and one table, changed order of figures, 17 pages, 15 figure

Search for a New Heavy Gauge Boson Wprime with Electron + missing ET Event Signature in ppbar collisions at sqrt(s)=1.96 TeV

We present a search for a new heavy charged vector boson $W^\prime$ decaying to an electron-neutrino pair in $p\bar{p}$ collisions at a center-of-mass energy of 1.96\unit{TeV}. The data were collected with the CDF II detector and correspond to an integrated luminosity of 5.3\unit{fb}^{-1}. No significant excess above the standard model expectation is observed and we set upper limits on $\sigma\cdot{\cal B}(W^\prime\to e\nu)$. Assuming standard model couplings to fermions and the neutrino from the $W^\prime$ boson decay to be light, we exclude a $W^\prime$ boson with mass less than 1.12\unit{TeV/}c^2 at the 95\unit{%} confidence level.Comment: 7 pages, 2 figures Submitted to PR