Development of a computer based 1D-2D dynamic flood model. Case study of the Pagsangaan river basin in Leyte, the Philippines

Floods are among the most devastating events that affect primarily tropical, archipelagic countries such as the Philippines. With the current predictions of climate change set to include rising sea levels, intensification of typhoon strength and a general increase in the mean annual precipitation throughout the Philippines, it has become paramount to prepare for the future so that the increased risk of floods on the country does not translate into more economic and human loss. Field work and data gathering was done within the framework of an internship at the former German Technical Cooperation (GTZ) in cooperation with the Local Government Unit of Ormoc City, Leyte, The Philippines, in order to develop a dynamic computer based flood model for the basin of the Pagsangaan River. To this end, different geo-spatial analysis tools such as PCRaster and ArcGIS, hydrological analysis packages and basic engineering techniques were assessed and implemented. The aim was to develop a dynamic flood model and use the development process to determine the required data, availability and impact on the results as case study for flood early warning systems in the Philippines. The hope is that such projects can help to reduce flood risk by including the results of worst case scenario analyses and current climate change predictions into city planning for municipal development, monitoring strategies and early warning systems. The project was developed using a 1D-2D coupled model in SOBEK (Deltares Hydrological modelling software package) and was also used as a case study to analyze and understand the influence of different factors such as land use, schematization, time step size and tidal variation on the flood characteristics. Several sources of relevant satellite data were compared, such as Digital Elevation Models (DEMs) from ASTER and SRTM data, as well as satellite rainfall data from the GIOVANNI server (NASA) and field gauge data. Different methods were used in the attempt to partially calibrate and validate the model to finally simulate and study two Climate Change scenarios based on scenario A1B predictions. It was observed that large areas currently considered not prone to floods will become low flood risk (0.1-1 m water depth). Furthermore, larger sections of the floodplains upstream of the Lilo- an’s Bridge will become moderate flood risk areas (1 - 2 m water depth). The flood hazard maps created for the development of the present project will be presented to the LGU and the model will be used to create a larger set of possible flood prone areas related to rainfall intensity by GTZ’s Local Disaster Risk Management Department and to study possible improvements to the current early warning system and monitoring of the basin section belonging to Ormoc City; recommendations about further enhancement of the geo-hydro-meteorological data to improve the model’s accuracy mainly on areas of interest will also be presented at the LGU.

Selective regulation of p38β protein and signaling by integrin-linked kinase mediates bladder cancer cell migration

Integrin-linked kinase (ILK) and p38MAPK are protein kinases that transduce extracellular signals regulating cell migration and actin cytoskeletal organization. ILK-dependent regulation of p38MAPK is critical for mammalian kidney development and in smooth muscle cell migration, however, specific p38 isoforms has not been previously examined in ILK-regulated responses. Signaling by ILK and p38MAPK is often dysregulated in bladder cancer, and here we report a strong positive correlation between protein levels of ILK and p38β, which is the predominant isoform found in bladder cancer cells, as well as in patient-matched normal bladder and tumor samples. Knockdown by RNA interference of either p38β or ILK disrupts serum-induced, Rac1-dependent migration and actin cytoskeletal organization in bladder cancer cells. Surprisingly, ILK knockdown causes the selective reduction in p38β cellular protein level, without inhibiting p38β messenger RNA (mRNA) expression. The loss of p38β protein in ILK-depleted cells is partially rescued by the 26S proteasomal inhibitor MG132. Using co-precipitation and bimolecular fluorescent complementation assays, we find that ILK selectively forms cytoplasmic complexes with p38β. In situ proximity ligation assays further demonstrate that serum-stimulated assembly of endogenous ILK–p38β complexes is sensitive to QLT-0267, a small molecule ILK kinase inhibitor. Finally, inhibition of ILK reduces the amplitude and period of serum-induced activation of heat shock protein 27 (Hsp27), a target of p38β implicated in actin cytoskeletal reorganization. Our work identifies Hsp27 as a novel target of ILK–p38β signaling complexes, playing a key role in bladder cancer cell migration.

Inhibition of homogenous formation of calcium carbonate by poly (acrylic acid). The effect of molar mass and end-group functionality

The ability of poly(acrylic acid) (PAA) with different end groups and molar masses prepared by Atom Transfer Radical Polymerization (ATRP) to inhibit the formation of calcium carbonate scale at low and elevated temperatures was investigated. Inhibition of CaCO3 deposition was affected by the hydrophobicity of the end groups of PAA, with the greatest inhibition seen for PAA with hydrophobic end groups of moderate size (6–10 carbons). The morphologies of CaCO3 crystals were significantly distorted in the presence of these PAAs. The smallest morphological change was in the presence of PAA with long hydrophobic end groups (16 carbons) and the relative inhibition observed for all species were in the same order at 30 °C and 100 °C. As well as distorting morphologies, the scale inhibitors appeared to stabilize the less thermodynamically favorable polymorph, vaterite, to a degree proportional to their ability to inhibit precipitation.

Spatially-explicit modelling of grassland classes - an improved method of integrating a climate-based classification model with interpolated climate surfaces

Spatially-explicit modelling of grassland classes is important to site-specific planning for improving grassland and environmental management over large areas. In this study, a climate-based grassland classification model, the Comprehensive and Sequential Classification System (CSCS) was integrated with spatially interpolated climate data to classify grassland in Gansu province, China. The study area is characterized by complex topographic features imposed by plateaus, high mountains, basins and deserts. To improve the quality of the interpolated climate data and the quality of the spatial classification over this complex topography, three linear regression methods, namely an analytic method based on multiple regression and residues (AMMRR), a modification of the AMMRR method through adding the effect of slope and aspect to the interpolation analysis (M-AMMRR) and a method which replaces the IDW approach for residue interpolation in M-AMMRR with an ordinary kriging approach (I-AMMRR), for interpolating climate variables were evaluated. The interpolation outcomes from the best interpolation method were then used in the CSCS model to classify the grassland in the study area. Climate variables interpolated included the annual cumulative temperature and annual total precipitation. The results indicated that the AMMRR and M-AMMRR methods generated acceptable climate surfaces but the best model fit and cross validation result were achieved by the I-AMMRR method. Twenty-six grassland classes were classified for the study area. The four grassland vegetation classes that covered more than half of the total study area were "cool temperate-arid temperate zonal semi-desert", "cool temperate-humid forest steppe and deciduous broad-leaved forest", "temperate-extra-arid temperate zonal desert", and "frigid per-humid rain tundra and alpine meadow". The vegetation classification map generated in this study provides spatial information on the locations and extents of the different grassland classes. This information can be used to facilitate government agencies' decision-making in land-use planning and environmental management, and for vegetation and biodiversity conservation. The information can also be used to assist land managers in the estimation of safe carrying capacities which will help to prevent overgrazing and land degradation.

Identification, functional expression and kinetic analysis of two primary amine oxidases from Rhodococcus opacus

Two native copper-containing amine oxidases (EC 1.4.3.21) have been isolated from Rhodococcus opacus and reveal phenotypic plasticity and catalytic activity with respect to structurally diverse natural and synthetic amines. Altering the amine growth substrate has enabled tailored and targeted oxidase upreg-ulation, which with subsequent treatment by precipitation, ion exchange and gel filtration, achieved a 90–150 fold purification. MALDI-TOF mass spectrometric and genomic analysis has indicated multiple gene activation with complex biodegradation pathways and regulatory mechanisms. Additional post-purification characterisation has drawn on the use of carbonyl reagent and chelating agent inhibitors. Michaelis–Menten kinetics for common aliphatic and aromatic amine substrates and several structural analogues demonstrated a broad specificity and high affinity with Michaelis constants (K M) ranging from 0.1 to 0.9 mM for C 1 –C 5 aliphatic mono-amines and <0.2 mM for a range of aromatic amines. Potential exploitation of the enzymatic versatility of the two isolated oxidases in biosensing and bioprocessing is discussed.

Characterisation of red mud and seawater neutralised red mud using vibrational spectroscopic techniques

Bauxite refinery residues are derived from the Bayer process by the digestion of crushed bauxite in concentrated caustic at elevated temperatures. Chemically, it comprises, in varying amounts (depending upon the composition of the starting bauxite), oxides of iron and titanium, residual alumina, sodalite, silica, and minor quantities of other metal oxides. Bauxite residues are being neutralised by seawater in recent years to reduce the alkalinity in bauxite residue, through the precipitation of hydrotalcite-like compounds and some other Mg, Ca, and Al hydroxide and carbonate minerals. A combination of X-ray diffraction (XRD) and vibrational spectroscopy techniques, including mid-infrared (IR), Raman, near-infrared (NIR), and UV-Visible, have been used to characterise bauxite residue and seawater neutralised bauxite residue. Both the ferrous (Fe2+) and ferric (Fe3+) ions within bauxite residue can be identified by their characteristic NIR bands, where ferrous ions produce a strong absorption band at around 9000 cm-1, while ferric ions produce two strong bands at 25000 and 14300 cm-1. The presence of adsorbed carbonate and hydroxide anions can be identified at around 5200 and 7000 cm-1, respectively, attributed to the 2nd overtone of the 1st fundamental overtones observed in the mid-IR spectra. The complex bands in the Raman and mid-IR spectra around 3500 cm-1 are assigned to the OH stretching vibrations of the various oxides present in bauxite residue, and water. The combination of carbonate and hydroxyl units and their fundamental overtones give rise to many of the features of the NIR spectra.

Effects of four different single exercise sessions on lipids, lipoproteins, and lipoprotein lipase

The purpose of this study was to determine the threshold of exercise energy expenditure necessary to change blood lipid and lipoprotein concentrations and lipoprotein lipase activity (LPLA) in healthy, trained men. On different days, 11 men (age, 26.7 +/- 6.1 yr; body fat, 11.0 +/- 1.5%) completed four separate, randomly assigned, submaximal treadmill sessions at 70% maximal O-2 consumption. During each session 800, 1,100, 1,300, or 1,500 kcal were expended. Compared with immediately before exercise, high-density lipoprotein cholesterol (HDL-C) concentration was significantly elevated 24 h after exercise (P < 0.05) in the 1,100-, 1,300-, and 1,500-kcal sessions. HDL-C concentration was also elevated (P < 0.05) immediately after and 48 h after exercise in the 1,500-kcal session. Compared with values 24 h before exercise, LPLA. was significantly greater (P < 0.05) 24 h after exercise in the 1,100-, 1,300-, and 1,500-kcal sessions and remained elevated 48 h after exercise in the 1,500-kcal session. These data indicate that, in healthy, trained men, 1,100 kcal of energy expenditure are necessary to elicit increased HDL-C concentrations. These HDL-C changes coincided with increased LPLA.

Plasma lipid and lipoprotein responses during exercise

The purpose of this study was to examine the effect of prolonged exercise oil plasma lipid and lipoprotein concentrations and to identify caloric time-points where changes occurred. Eleven active male Subjects ran oil a treadmill at 70%,, of maximal fitness (VO2max) and expended 6 278.7 kilojoules (Kj) energy (1500 kcal). Blood samples were obtained at the 4185.8 Kj (1000 kcal) time-point during exercise and at each additional 418.6 Kj (100 kcal) expenditure until 6278.7 Kj was expended. After correcting for plasma volume changes, decreases in low-density lipoprotein cholesterol (LDL-C) were observed during exercise at time-points corresponding to 4604.4 and 5441.5 Kj (1100 and 1300 kcal) of energy expenditure, and immediately after exercise. Total cholesterol concentrations decreased significantly at exercise kilojoule expenditures of 4604.4, 5441.5 and 5860.1 (1100, 1300 and 1400 kcal). There were also exercise induced increases in high-density lipoprotein cholesterol (HDL-C) and HDL2-C concentrations immediately after exercise. Although acute lipid and lipoprotein changes are typically reported in the days following exercise, the Current data indicate that some lipoprotein concentrations change during acute exercise. Our data suggest that a threshold of exercise may be necessary to change lipoproteins during exercise. Future work Should identify potential mechanisms (lipoprotein lipase, cholesterol ester transport protein, LDL uptake) that alter lipoprotein concentrations during prolonged exercise.

Formation and electron field emission of graphene films grown by hot filament chemical vapor deposition

Graphene films with different structures were catalytically grown on the silicon substrate pre-deposited with a gold film by hot filament chemical vapor deposition under different conditions, where methane, hydrogen and nitrogen were used as the reactive gases. The morphological and compositional properties of graphene films were studied using advanced instruments including field emission scanning electron microscopy, micro-Raman spectroscopy and X-ray photoelectron spectroscopy. The results indicate that the structure and composition of graphene films are changed with the variation of the growth conditions. According to the theory related to thermodynamics, the formation of graphene films was theoretically analyzed and the results indicate that the formation of graphene films is related to the fast incorporation and precipitation of carbon. The electron field emission (EFE) properties of graphene films were studied in a high vacuum system of ∼10-6 Pa and the EFE results show that the turn-on field is in a range of 5.2-5.64 V μm-1 and the maximum current density is about 63 μ A cm-2 at the field of 7.7 V μm-1. These results are important to control the structure of graphene films and have the potential applications of graphene in various nanodevices.

Carbon nanorods and graphene-like nanosheets by hot filament CVD : growth mechanisms and electron field emission

Carbon nanorods and graphene-like nanosheets are catalytically synthesized in a hot filament chemical vapor deposition system with and without plasma enhancement, with gold used as a catalyst. The morphological and structural properties of the carbon nanorods and nanosheets are investigated by field-emission scanning electron microscopy, transmission electron microscopy and micro-Raman spectroscopy. It is found that carbon nanorods are formed when a CH4 + H2 + N2 plasma is present while carbon nanosheets are formed in a methane environment without a plasma. The formation of carbon nanorods and carbon nanosheets are analyzed. The results suggest that the formation of carbon nanorods is primarily a precipitation process while the formation of carbon nanosheets is a complex process involving surface-catalysis, surface diffusion and precipitation influenced by the Gibbs–Thomson effect. The electron field emission properties of the carbon nanorods and graphene-like nanosheets are measured under high-vacuum; it is found that the carbon nanosheets have a lower field emission turn-on than the carbon nanorods. These results are important to improve the understanding of formation mechanisms of carbon nanomaterials and contribute to eventual applications of these structures in nanodevices.

Single-step, catalyst-free plasma-assisted synthesis and growth mechanism of single-crystalline aluminum nitride nanorods

Synthesis of one-dimensional AlN nanostructures commonly requires high process temperatures (>900 °C), metal catalyst, and hazardous gas/powder precursors. We report on a simple, single-step, catalyst-free, plasma-assisted growth of dense patterns of size-uniform single-crystalline AlN nanorods at a low substrate temperature (∼650 °C) without any catalyst or hazardous precursors. This unusual growth mechanism is based on highly effective plasma dissociation of N2 molecules, localized species precipitation on AlN islands, and reduced diffusion on the nitrogen-rich surface. This approach can also be used to produce other high-aspect-ratio oxide and nitride nanostructures for applications in energy conversion, sensing, and optoelectronics. © 2010 American Institute of Physics.

Understanding how the Australian climate can affect pipe failure

This paper details a statistical analysis of historical failure data, which focuses on determining the manner in which local climate affects pipe failure rates. It was found that seasonality exists in the data, indicating an affect of local climate on failure rate. Significant variation in failure rates was seen between the months of December and May, especially in February/March, whilst limited variations were seen in other months of the year. Further analysis found that failure rates were strongly correlated with minimum antecedent precipitation index and net evaporation and that climate affected failure rate by influencing soil moisture content. Interaction affects between static attributes of the pipe-environment system and local climate were also investigated.

High-yeld RNA-extraction method for saliva

BACKGROUND: The use of salivary diagnostics is increasing because of its noninvasiveness, ease of sampling, and the relatively low risk of contracting infectious organisms. Saliva has been used as a biological fluid to identify and validate RNA targets in head and neck cancer patients. The goal of this study was to develop a robust, easy, and cost-effective method for isolating high yields of total RNA from saliva for downstream expression studies. METHODS: Oral whole saliva (200 mu L) was collected from healthy controls (n = 6) and from patients with head and neck cancer (n = 8). The method developed in-house used QIAzol lysis reagent (Qiagen) to extract RNA from saliva (both cell-free supernatants and cell pellets), followed by isopropyl alcohol precipitation, cDNA synthesis, and real-time PCR analyses for the genes encoding beta-actin ("housekeeping" gene) and histatin (a salivary gland-specific gene). RESULTS: The in-house QIAzol lysis reagent produced a high yield of total RNA (0.89 -7.1 mu g) from saliva (cell-free saliva and cell pellet) after DNase treatment. The ratio of the absorbance measured at 260 nm to that at 280 nm ranged from 1.6 to 1.9. The commercial kit produced a 10-fold lower RNA yield. Using our method with the QIAzol lysis reagent, we were also able to isolate RNA from archived saliva samples that had been stored without RNase inhibitors at -80 degrees C for >2 years. CONCLUSIONS: Our in-house QIAzol method is robust, is simple, provides RNA at high yields, and can be implemented to allow saliva transcriptomic studies to be translated into a clinical setting.

Geochemistry-based coral palaeoclimate studies and the potential of ‘non-traditional’ (non-massive Porites) corals : recent developments and future progression

Understanding the natural variability of the Earth's climate system and accurately identifying potential anthropogenic influences requires long term, geographically distributed records of key climate indicators, such as temperature and precipitation that extend prior to the last 400. years of the Holocene. Reef corals provide an excellent source of high resolution climate records, and importantly represent the tropical marine environment where palaeoclimate data are urgently required. Recent decades have seen significant improvement in our understanding of coral biomineralisation, the associated uptake of geochemical proxies and methods of identifying and understanding the effects of both early and late, post depositional diagenetic alteration. These processes all have significant implications for interpreting geochemical proxies relevant to palaeoclimatic reconstructions. This paper reviews the current 'state of the art' in terms of coral based palaeoclimate reconstructions and highlights a key remaining problem. The majority of coral based palaeoclimate research has been derived from massive colonies of Porites. However, massive Porites are not globally abundant and may not provide material of a particular age of interest in those regions where they are present. Therefore, there is great potential for alternate coral genera to act as complimentary climate archives. While it remains critical to consider five key factors - vital effects, differential growth morphologies, geochemical heterogeneity in the skeletal ultrastructure, transfer equation selection and diagenetic screening of skeletal material - in order to allow the highest level of accuracy in coral palaeoclimate reconstructions, it is also important to develop alternate taxa for palaeoclimate studies in regions where Porites colonies are absent or rare. Currently as many as nine genera other than Porites have proven at least limited utility in palaeothermometry, most of which are found in the Atlantic/Caribbean region where massive Porites do not exist. Even branching taxa such as Acropora have significant potential to preserve environmental archives. Increasing this capability will greatly expand the number of potential geochemical archives available for longer term temporal records of palaeoclimate.