Urban Expansion and its impact on urban agriculture - remote sensing based change analysis of Kizinga and Mzinga Valley - Dar Es Salaam, Tanzania

Urban agriculture is a phenomenon that can be observed world-wide, particularly in cities of devel- oping countries. It is contributing significantly to food security and food safety and has sustained livelihood of the urban and peri-urban low income dwe llers in developing countries for many years. Population increase due to rural-urban migration and natural - formal as well as informal - urbani- sation are competing with urban farming for available space and scarce water resources. A mul- titemporal and multisensoral urban change analysis over the period of 25 years (1982-2007) was performed in order to measure and visualise the urban expansion along the Kizinga and Mzinga valley in the south of Dar Es Salaam. Airphotos and VHR satellite data were analysed by using a combination of a composition of anisotropic textural measures and spectral information. The study revealed that unplanned built-up area is expanding continuously, and vegetation covers and agricultural lands decline at a fast rate. The validation showed that the overall classification accuracy varied depending on the database. The extracted built-up areas were used for visual in- terpretation mapping purposes and served as information source for another research project. The maps visualise an urban congestion and expansion of nearly 18% of the total analysed area that had taken place in the Kizinga valley between 1982 and 2007. The same development can be ob- served in the less developed and more remote Mzinga valley between 1981 and 2002. Both areas underwent fast changes where land prices still tend to go up and an influx of people both from rural and urban areas continuously increase the density with the consequence of increasing multiple land use interests.

Runoff Water Quality and Pollutant Mass Loads From Extensive Green Roofs

Green roof mitigation of volume and peak flow-rate of stormwater runoff has been studied extensively. However, due to the common practice of green roof fertilization, there is the potential for introduction of nutrients into local bodies of water. Therefore, this study compares green roof runoff quality with the water quality of precipitation and runoff from a bare shingle roof. The runoff from a demonstration-scale extensive green roof was analyzed during the summer of 2011 for its effect on runoff volume and analyzed during eleven storm events in the fall and winter for concentrations of copper, cadmium, zinc, lead, nitrogen species, total nitrogen, total organic carbon, sulfate, orthophosphate, and other monovalent and divalent ions. The green roof reduced the overall volume of runoff and served as a sink for NO3 - and NH4 +. However, the green roof was also a source for the pollutants PO4 3-, SO4 2-, TOC, cations, and total nitrogen. Metals such as zinc and lead showed trends of higher mass loads in the bare roof runoff than in precipitation and green roof runoff, although results were not statistically significant. The green roof also showed trends, although also not statistically significant, of retaining cadmium and copper. With the green roof serving as a source of phosphorous species and a sink for nitrogen species, and appearing to a retain metals and total volume, the life cycle impact analysis shows minimum impacts from the green roof, when compared with precipitation and bare roof runoff, in all but fresh water eutrophication. Therefore, the best environments to install a green roof may be in coastal environments.

Pseudomonas aeruginosa outbreak in a pediatric oncology care unit caused by an errant water jet into contaminated siphons

We analyzed an outbreak of invasive infections with an exotoxin U positive Pseudomonas aeruginosa strain within a pediatric oncology care unit. Environmental sampling and molecular characterization of the Pseudomonas aeruginosa strains led to identification of the outbreak source. An errant water jet into the sink within patient rooms was observed. Optimized outbreak management resulted in an abundance of further Pseudomonas aeruginosa infections within the pediatric oncology care unit.

Improved water vapour spectroscopy in the 4174-4300 cm-1 region and its impact on SCIAMACHY HDO/H2O measurements

The relative abundance of the heavy water isotopologue HDO provides a deeper insight into the atmospheric hydrological cycle. The SCanning Imaging Absorption spectroMeter for Atmospheric CartograpHY (SCIAMACHY) allows for global retrievals of the ratio HDO/H2O in the 2.3 micron wavelength range. However, the spectroscopy of water lines in this region remains a large source of uncertainty for these retrievals. We therefore evaluate and improve the water spectroscopy in the range 4174–4300 cm−1 and test if this reduces systematic uncertainties in the SCIAMACHY retrievals of HDO/H2O. We use a laboratory spectrum of water vapour to fit line intensity, air broadening and wavelength shift parameters. The improved spectroscopy is tested on a series of ground-based high resolution FTS spectra as well as on SCIAMACHY retrievals of H2O and the ratio HDO/H2O. We find that the improved spectroscopy leads to lower residuals in the FTS spectra compared to HITRAN 2008 and Jenouvrier et al. (2007) spectroscopy, and the retrievals become more robust against changes in the retrieval window. For both the FTS and SCIAMACHY measurements, the retrieved total H2O columns decrease by 2–4% and we find a negative shift of the HDO/H2O ratio, which for SCIAMACHY is partly compensated by changes in the retrieval setup and calibration software. The updated SCIAMACHY HDO/H2O product shows somewhat steeper latitudinal and temporal gradients and a steeper Rayleigh distillation curve, strengthening previous conclusions that current isotope-enabled general circulation models underestimate the variability in the near-surface HDO/H2O ratio.

Monte Carlo simulation of a dynamic MLC based on a multiple source model

Detailed knowledge of the characteristics of the radiation field shaped by a multileaf collimator (MLC) is essential in intensity modulated radiotherapy (IMRT). A previously developed multiple source model (MSM) for a 6 MV beam was extended to a 15 MV beam and supplemented with an accurate model of an 80-leaf dynamic MLC. Using the supplemented MSM and the MC code GEANT, lateral dose distributions were calculated in a water phantom and a portal water phantom. A field which is normally used for the validation of the step and shoot technique and a field from a realistic IMRT treatment plan delivered with dynamic MLC are investigated. To assess possible spectral changes caused by the modulation of beam intensity by an MLC, the energy spectra in five portal planes were calculated for moving slits of different widths. The extension of the MSM to 15 MV was validated by analysing energy fluences, depth doses and dose profiles. In addition, the MC-calculated primary energy spectrum was verified with an energy spectrum which was reconstructed from transmission measurements. MC-calculated dose profiles using the MSM for the step and shoot case and for the dynamic MLC case are in very good agreement with the measured data from film dosimetry. The investigation of a 13 cm wide field shows an increase in mean photon energy of up to 16% for the 0.25 cm slit compared to the open beam for 6 MV and of up to 6% for 15 MV, respectively. In conclusion, the MSM supplemented with the dynamic MLC has proven to be a powerful tool for investigational and benchmarking purposes or even for dose calculations in IMRT.

A multiple source model for 6 MV photon beam dose calculations using Monte Carlo

A multiple source model (MSM) for the 6 MV beam of a Varian Clinac 2300 C/D was developed by simulating radiation transport through the accelerator head for a set of square fields using the GEANT Monte Carlo (MC) code. The corresponding phase space (PS) data enabled the characterization of 12 sources representing the main components of the beam defining system. By parametrizing the source characteristics and by evaluating the dependence of the parameters on field size, it was possible to extend the validity of the model to arbitrary rectangular fields which include the central 3 x 3 cm2 field without additional precalculated PS data. Finally, a sampling procedure was developed in order to reproduce the PS data. To validate the MSM, the fluence, energy fluence and mean energy distributions determined from the original and the reproduced PS data were compared and showed very good agreement. In addition, the MC calculated primary energy spectrum was verified by an energy spectrum derived from transmission measurements. Comparisons of MC calculated depth dose curves and profiles, using original and PS data reproduced by the MSM, agree within 1% and 1 mm. Deviations from measured dose distributions are within 1.5% and 1 mm. However, the real beam leads to some larger deviations outside the geometrical beam area for large fields. Calculated output factors in 10 cm water depth agree within 1.5% with experimentally determined data. In conclusion, the MSM produces accurate PS data for MC photon dose calculations for the rectangular fields specified.

Preference polymorphism for coloration but no speciation in a population of Lake Victoria cichlids

Female mating preference based on male nuptial coloration has been suggested to be an important source of diversifying selection in the radiation of Lake Victoria cichlid fish. Initial variation in female preference is a prerequisite for diversifying selection; however, it is rarely studied in natural populations. In clear water areas of Lake Victoria, the sibling species Pundamilia pundamilia with blue males and Pundamilia nyererei with red males coexist, intermediate phenotypes are rare, and most females have species-assortative mating preferences. Here, we study a population of Pundamilia that inhabits turbid water where male coloration is variable from reddish to blue with most males intermediate. We investigated male phenotype distribution and female mating preferences. Male phenotype was unimodally distributed with a mode on intermediate color in 1 year and more blue-shifted in 2 other years. In mate choice experiments with females of the turbid water population and males from a clearer water population, we found females with a significant and consistent preference for P. pundamilia (blue) males, females with such preferences for P. nyererei (red) males, and many females without a preference. Hence, female mating preferences in this population could cause disruptive selection on male coloration that is probably constrained by the low signal transduction of the turbid water environment. We suggest that if environmental signal transduction was improved and the preference/color polymorphism was stabilized by negative frequency-dependent selection, divergent sexual selection might separate the 2 morphs into reproductively isolated species resembling the clear water species P. pundamilia and P. nyererei.

Gene expression variation between distinct areas of breast cancer measured from paraffin-embedded tissue cores

BACKGROUND: Diagnosis and prognosis in breast cancer are mainly based on histology and immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE) material. Recently, gene expression analysis was shown to elucidate the biological variance between tumors and molecular markers were identified that led to new classification systems that provided better prognostic and predictive parameters. Archived FFPE samples represent an ideal source of tissue for translational research, as millions of tissue blocks exist from routine diagnostics and from clinical studies. These should be exploited to provide clinicians with more accurate prognostic and predictive information. Unfortunately, RNA derived from FFPE material is partially degraded and chemically modified and reliable gene expression measurement has only become successful after implementing novel and optimized procedures for RNA isolation, demodification and detection. METHODS: In this study we used tissue cylinders as known from the construction of tissue microarrays. RNA was isolated with a robust protocol recently developed for RNA derived from FFPE material. Gene expression was measured by quantitative reverse transcription PCR. RESULTS: Sixteen tissue blocks from 7 patients diagnosed with multiple histological subtypes of breast cancer were available for this study. After verification of appropriate localization, sufficient RNA yield and quality, 30 tissue cores were available for gene expression measurement on TaqMan(R) Low Density Arrays (16 invasive ductal carcinoma (IDC), 8 ductal carcinoma in situ (DCIS) and 6 normal tissue), and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO), the estrogen receptor status and the HER2 status. The PRO scores measured from entire sections were similar to PRO scores determined from IDC tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores than cores derived from IDC or DCIS of the same block or from different blocks of the same patient. CONCLUSION: We have developed optimized protocols for RNA isolation from histologically distinct areas. RNA prepared from FFPE tissue cores is suitable for gene expression measurement by quantitative PCR. Distinct molecular scores could be determined from different cores of the same tumor specimen.