Simulation of the sedimentary fill of basins

There are many forward models that simulate sedimentary processes. The significance and utility of any particular model is a matter of need, computer hardware, and programming resources. Some forward-model simulations are one-dimensional; they are used to define third-order sea-level curves to infer the origin of peritidal cyclic carbonates, model the interdependence of sea level, depth-dependent carbonate accumulation, and the flexural response of the earths crust, and handle diagenesis of carbonate in relation to the eustatic record. Other simulations are two-dimensional and may handle clastics alone; they are used to create synthetic seismograms for sediment packages by modeling subsidence, sea level, sediment supply, and erosion, provide sedimentation rates for clastic fluvial systems using sediment compaction and tectonic movement, and simulate transport, deposition, erosion, and compaction of clastic sediments, emphasizing fluid velocity. Other simulations are two-dimensional carbonate shelf models that respond to sea-level changes and erosion, allowing redeposition of sediment with user-defined production functions; still others are two-dimensional mixed clastic and carbonate basin fill models. Both of these last kinds of models respond to sea-level changes and erosion, allowing redeposition of sediment with user-defined production functions. The program SEDPAK models some of the functions described and tests seismic interpretations based on sea-level curves. These curves are input parameters to the program. The program responds to tectonic movement, eustasy, and sedimentation, modeling sedimentary bypass and erosion. It reproduces clastic systems (including lacustrine, alluvial, and coastal plains, marine shelf, basin slope, and basin floor systems, and carbonate systems) and accounts for progradation, development of hardgrounds, downslope aprons, keep-up, catch-up, back-step, and drowned reef systems, and lagoonal and epeiric sea settings. SEDPAK simulates extensional vertical faulting of the basin, sediment compaction, and isostatic response to sediment loading. Sediment geometries can be viewed immediately on a graphics terminal as they are computed. Based on the observed geometric patterns, the user can repeatedly change the parameter and rerun the program until satisfied with the resultant geometry. This simulation is implemented in the C programming language (Kernighan and Ritchie, 1978), uses the X window system for graphical plotting functions (Scheifler and Gettys, 1986), and is operated on a Unix-based workstation, such as DEC 3 100, Sun, and Apollo. The simulation output is illustrated with examples from the Permian basin of West Texas and New Mexico, the Permian of the Sichuan basin, and the Upper Devonian of western Canada

Simulation of the sedimentary fill of basins

There are many forward models that simulate sedimentary processes. The significance and utility of any particular model is a matter of need, computer hardware, and programming resources. Some forward-model simulations are one-dimensional; they are used to define third-order sea-level curves to infer the origin of peritidal cyclic carbonates, model the interdependence of sea level, depth-dependent carbonate accumulation, and the flexural response of the earths crust, and handle diagenesis of carbonate in relation to the eustatic record. Other simulations are two-dimensional and may handle clastics alone; they are used to create synthetic seismograms for sediment packages by modeling subsidence, sea level, sediment supply, and erosion, provide sedimentation rates for clastic fluvial systems using sediment compaction and tectonic movement, and simulate transport, deposition, erosion, and compaction of clastic sediments, emphasizing fluid velocity. Other simulations are two-dimensional carbonate shelf models that respond to sea-level changes and erosion, allowing redeposition of sediment with user-defined production functions; still others are two-dimensional mixed clastic and carbonate basin fill models. Both of these last kinds of models respond to sea-level changes and erosion, allowing redeposition of sediment with user-defined production functions. The program SEDPAK models some of the functions described and tests seismic interpretations based on sea-level curves. These curves are input parameters to the program. The program responds to tectonic movement, eustasy, and sedimentation, modeling sedimentary bypass and erosion. It reproduces clastic systems (including lacustrine, alluvial, and coastal plains, marine shelf, basin slope, and basin floor systems, and carbonate systems) and accounts for progradation, development of hardgrounds, downslope aprons, keep-up, catch-up, back-step, and drowned reef systems, and lagoonal and epeiric sea settings. SEDPAK simulates extensional vertical faulting of the basin, sediment compaction, and isostatic response to sediment loading. Sediment geometries can be viewed immediately on a graphics terminal as they are computed. Based on the observed geometric patterns, the user can repeatedly change the parameter and rerun the program until satisfied with the resultant geometry. This simulation is implemented in the C programming language (Kernighan and Ritchie, 1978), uses the X window system for graphical plotting functions (Scheifler and Gettys, 1986), and is operated on a Unix-based workstation, such as DEC 3 100, Sun, and Apollo. The simulation output is illustrated with examples from the Permian basin of West Texas and New Mexico, the Permian of the Sichuan basin, and the Upper Devonian of western Canada

Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages

This study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments

Piperidinols that show anti-tubercular activity as inhibitors of arylamine N-acetyltransferase: an essential enzyme for mycobacterial survival inside macrophages

Latent M. tuberculosis infection presents one of the major obstacles in the global eradication of tuberculosis (TB). Cholesterol plays a critical role in the persistence of M. tuberculosis within the macrophage during latent infection. Catabolism of cholesterol contributes to the pool of propionyl-CoA, a precursor that is incorporated into cell-wall lipids. Arylamine N-acetyltransferase (NAT) is encoded within a gene cluster that is involved in the cholesterol sterol-ring degradation and is essential for intracellular survival. The ability of the NAT from M. tuberculosis (TBNAT) to utilise propionyl-CoA links it to the cholesterol-catabolism pathway. Deleting the nat gene or inhibiting the NAT enzyme prevents intracellular survival and results in depletion of cell-wall lipids. TBNAT has been investigated as a potential target for TB therapies. From a previous high-throughput screen, 3-benzoyl-4-phenyl-1-methylpiperidinol was identified as a selective inhibitor of prokaryotic NAT that exhibited antimycobacterial activity. The compound resulted in time-dependent irreversible inhibition of the NAT activity when tested against NAT from M. marinum (MMNAT). To further evaluate the antimycobacterial activity and the NAT inhibition of this compound, four piperidinol analogues were tested. All five compounds exert potent antimycobacterial activity against M. tuberculosis with MIC values of 2.3-16.9 µM. Treatment of the MMNAT enzyme with this set of inhibitors resulted in an irreversible time-dependent inhibition of NAT activity. Here we investigate the mechanism of NAT inhibition by studying protein-ligand interactions using mass spectrometry in combination with enzyme analysis and structure determination. We propose a covalent mechanism of NAT inhibition that involves the formation of a reactive intermediate and selective cysteine residue modification. These piperidinols present a unique class of antimycobacterial compounds that have a novel mode of action different from known anti-tubercular drugs

High resolution seismic stratigraphic analysis: An integrated approach to the subsurface geology of the SE Persian Gulf

Papers included in this dissertation: Paper 1: Farzadi, P. 2006a. The development of Middle Cretaceous carbonate platforms, Persian Gulf, Iran: Constraints from seismic stratigraphy, well and biostratigraphy. Petroleum Geoscience, 12, 59-68. Paper 2: Farzadi, P. 2006b. Seismic facies analysis based on 3D multi-attribute volume classification, Dariyan Formation, SE Persian Gulf. Journal of Petroleum Geology,29/2, 159-174. Paper 3: Farzadi, P. & Hesthammer, J. (Submitted 2006). Diagnosis of the Upper Cretaceous paleokarst and turbidite systems from the Iranian Persian Gulf using volume-based multiple seismic attribute analysis and pattern recognition. N.B.: Originally accepted for publication in the AAPG Bulletin, later rejected because the US government prohibits the publication of papers using Iranian government datasets. The manuscript has been re-submitted to Petroleum Geoscience. Paper 4: Farzadi, P. & Alaei, B. (Submitted 2006). Stratigraphic architecture of the Zagros Basin: towards an objective comparison of the Fold-Thrust Belt and Foreland provinces. Submitted to the Journal of Petroleum Geology; under consideration for a thematic issue. Presentation (at international meeting and on web): Farzadi, P. 2005. Stratal geometries of the Cretaceous carbonate systems: application of multiple volumes attributes analysis to 3-D seismic data from the Persian Gulf. At: Middle to Far East Carbonate Reservoirs: Exploration, Development and Exploitation. PESGB Carbonate conference, 15th & 16th Nov. 2005 London

Motor control or graded activity exercises for chronic low back pain? A randomised controlled trial

Background: Chronic low back pain remains a major health problem in Australia and around the world. Unfortunately the majority of treatments for this condition produce small effects because not all patients respond to each treatment. It appears that only 25-50% of patients respond to exercise. The two most popular types of exercise for low back pain are graded activity and motor control exercises. At present however, there are no guidelines to help clinicians select the best treatment for a patient. As a result, time and money are wasted on treatments which ultimately fail to help the patient

Conservation of Forest Birds: Evidence of a Shifting Baseline in Community Structure

Quantifying changes in forest bird diversity is an essential task for developing effective conservation actions. When subtle changes in diversity accumulate over time, annual comparisons may offer an incomplete perspective of changes in diversity. In this case, progressive change, the comparison of changes in diversity from a baseline condition, may offer greater insight because changes in diversity are assessed over longer periods of times. Our objectives were to determine how forest bird diversity has changed over time and whether those changes were associated with forest disturbance.We used North American Breeding Bird Survey data, a time series of Landsat images classified with respect to land cover change, and mixed-effects models to associate changes in forest bird community structure with forest disturbance, latitude, and longitude in the conterminous United States for the years 1985 to 2006. We document a significant divergence from the baseline structure for all birds of similar migratory habit and nest location, and all forest birds as a group from 1985 to 2006. Unexpectedly, decreases in progressive similarity resulted from small changes in richness (<1 species per route for the 22-year study period) and modest losses in abundance (-28.7 - -10.2 individuals per route) that varied by migratory habit and nest location. Forest disturbance increased progressive similarity for Neotropical migrants, permanent residents, ground nesting, and cavity nesting species. We also documented highest progressive similarity in the eastern United States.Contemporary forest bird community structure is changing rapidly over a relatively short period of time (e.g., approximately 22 years). Forest disturbance and forest regeneration are primary factors associated with contemporary forest bird community structure, longitude and latitude are secondary factors, and forest loss is a tertiary factor. Importantly, these findings suggest some regions of the United States may already fall below the habitat amount threshold where fragmentation effects become important predictors of forest bird community structure