Real-Time Gene-Expression Extraction with Fast Classification (FC) Networks

Fast Classification (FC) networks were inspired by a biologically plausible mechanism for short term memory where learning occurs instantaneously. Both weights and the topology for an FC network are mapped directly from the training samples by using a prescriptive training scheme. Only two presentations of the training data are required to train an FC network. Compared with iterative learning algorithms such as Back-propagation (which may require many hundreds of presentations of the training data), the training of FC networks is extremely fast and learning convergence is always guaranteed. Thus FC networks may be suitable for applications where real-time classification is needed. In this paper, the FC networks are applied for the real-time extraction of gene expressions for Chlamydia microarray data. Both the classification performance and learning time of the FC networks are compared with the Multi-Layer Proceptron (MLP) networks and support-vector-machines (SVM) in the same classification task. The FC networks are shown to have extremely fast learning time and comparable classification accuracy.

Optimization of pipeline transport for CO2 sequestration

Coal fired power generation will continue to provide energy to the world for the foreseeable future. However, this energy use is a significant contributor to increased atmospheric CO2 concentration and, hence, global warming. Capture and disposal Of CO2 has received increased R&D attention in the last decade as the technology promises to be the most cost effective for large scale reductions in CO2 emissions. This paper addresses CO2 transport via pipeline from capture site to disposal site, in terms of system optimization, energy efficiency and overall economics. Technically, CO2 can be transported through pipelines in the form of a gas, a supercritical. fluid or in the subcooled liquid state. Operationally, most CO2 pipelines used for enhanced oil recovery transport CO2 as a supercritical fluid. In this paper, supercritical fluid and subcooled liquid transport are examined and compared, including their impacts on energy efficiency and cost. Using a commercially available process simulator, ASPEN PLUS 10.1, the results show that subcooled liquid transport maximizes the energy efficiency and minimizes the Cost Of CO2 transport over long distances under both isothermal and adiabatic conditions. Pipeline transport of subcooled liquid CO2 can be ideally used in areas of cold climate or by burying and insulating the pipeline. In very warm climates, periodic refrigeration to cool the CO2 below its critical point of 31.1 degrees C, may prove economical. Simulations have been used to determine the maximum safe pipeline distances to subsequent booster stations as a function of inlet pressure, environmental temperature and ground level heat flux conditions. (c) 2005 Published by Elsevier Ltd.

Timing and chemistry of fluid-flow events in the Lawn Hill Platform, Northern Australia

Mudrocks and carbonates of the Isa superbasin in the Lawn Hill platform in northern Australia host major base metal sulfide mineralization, including the giant strata-bound Century Zn-Pb deposit. Mineral paragenesis, stable isotope, and K-Ar dating studies demonstrate that long-lived structures such as the Termite Range fault acted as hot fluid conduits several times during the Paleoproterozoic and Mesoproterozoic in response to major tectonic events. Illite and chlorite crystallinity studies suggest the southern part of the platform has experienced higher temperatures (up to 300 degrees C) than similar stratigraphic horizons in the north. The irregular downhole variation of illite crystallinity values provides further information oil the thermal regime in the basin and shows that clay formation was controlled not only by temperature increase with depth but also by high water/rock ratios along relatively permeable zones. K-Ar dating of illite, in combination with other data, may indicate three major thermal events in the central and northern Lawn Hill platform Lit 1500, 1440 to 1400, and 1250 to 1150 Ma. This study did not detect the earlier Century base metal mineralizing event at 1575 Ma. 1500 Ma ages are recorded only in the south and correspond to the age of the Late Isan orogeny and deposition of the Lower Roper superbasin. They may reflect exhumation of a provenance region. The 1440 to 1300 Ma ages are related to fault reactivation and a thermal pulse at similar to 1440 to 1400 Ma possibly accompanied by fluid flow, with subsequent enhanced cooling possibly due to thermal relaxation or further crustal exhumation. The youngest thermal and/or fluid-flow event at 1250 to 1150 Ma is recorded mainly to the cast of the Tern-lite Range fault and may be related to the assembly of the Rodinian supercontinent. Fluids in equilibrium with illite that formed over a range of temperatures, at different times in different parts of the platform. have relatively uniform oxygen isotope compositions and more variable hydrogen isotope compositions (delta O-18 = 3.5-9.7 parts per thousand V-SMOW; delta D = -94 to -36 parts per thousand V-SMOW). The extent of the 180 enrichment and the variably depleted hydrogen isotope compositions suggest the illite interacted with deep-basin hypersaline brines that were composed of evaporated seawater and/or highly evolved meteoric water. Siderite is the most abundant iron-rich gangue phase in the Century Zn-Pb deposit, which is surrounded by all extensive ferroan carbonate alteration halo. Modeling suggests that the ore siderite formed at temperatures of 120 degrees to 150 degrees C, whereas siderite and ankerite in the alteration halo formed at temperatures of 150 degrees to 180 degrees C. The calculated isotopic compositions of the fluids are consistent with O-18-rich basinal brines and mixed inorganic and organic carbon Sources (6180 = 3-10 parts per thousand V-SMOW, delta C-13 = -7 to -3 parts per thousand V-PDB). in the northeast Lawn Hill platform carbonate-rich rocks preserve marine to early diagenetic carbon and oxygen isotope compositions, whereas ferroan carbonate cements in siltstones and shales in the Desert Creek borehole are O-18 and C-13 depleted relative to the sedimentary carbonates. The good agreement between temperature estimates from illite crystallinity and organic reflectance (160 degrees-270 degrees C) and inverse correlation with carbonate delta O-18 values indicates that organic maturation and carbonate precipitation in the northeast Lawn Hill platform resulted from interaction with the 1250 to 1150 Ma fluids. The calculated isotopic compositions of the fluid are consistent with evolved basinal brine (delta O-18 = 5.1-9.4 parts per thousand V-SMOW; delta C-13 = -13.2 to -3.7 parts per thousand V-PDB) that contained a variable organic carbon component from the oxidation and/or hydrolysis of organic matter in the host sequence. The occurrence of extensive O-18- and C-13-depleted ankerite and siderite alteration in Desert Creek is related to the high temperature of the 1250 to 1150 Ma fluid-flow event in the northeast Lawn Hill platform, in contrast to the lower temperature fluids associated with the earlier Century Zn-Pb deposit in the central Lawn Hill platform.

Zinc deposits and related mineralization of the Burketown mineral field, including the world-class Century Deposit, Northern Australia: Fluid inclusion and stable isotope evidence for basin fluid sources

The stratiform Century Zn-Pb deposit and the discordant Zn-Pb lode deposits of the Burketown mineral field, northern Australia, host ore and gangue minerals with primary fluid inclusions that have not been affected by the Isan orogeny, thus providing a unique opportunity to investigate the nature of the ore-forming brines. All of the deposits are hosted in shales and siltstones belonging to the Isa superbasin and comprise sphalerite, pyrite, carbonate, quartz, galena, minor chalcopyrite, and minor illite. According to Pb model ages, the main ore stage of mineralization at Century formed at I575 Ma, some 20 m.y. after deposition of the host shale sequence. Microthermometry on undeformed, primary fluid inclusions hosted in porous sphalerite shows that the Zn at Century was transported to the deposit by a homogeneous, Ca2+- and Na+-bearing brine with a salinity of 21.6 wt percent NaCl equiv. delta D-fluid of the fluid inclusion water ranges from -89 to -83 per mil, consistent with a basinal brine that evolved from meteoric water. Fluid inclusion homogenization temperatures range between 74 degrees and 125 degrees C, which are lower than the 120 degrees to 160 degrees C range calculated from vitrinite reflectance and illite crystallinity data from the deposit. This discrepancy indicates that mineralization likely formed at 50 to 85 Mpa, corresponding to a depth of 1,900 to 3,100 m. Transgressive galena-sphalerite veins that cut stratiform mineralization at Century and breccia-filled quartz-dolomite-sphalerite-galena veins in the discordant Zn-Pb lodes have Pb model ages between 1575 and 1485 Ma. Raman spectroscopy and microthermometry reveal that the primary fluid inclusions in these veins contain Ca2+, Na+. but they have lower salinities between 23 and 10 wt percent NaCl equiv and higher delta D-fluid values ranging from -89 to -61 per mil than fluid inclusions in porous sphalerite from Century. Fluid inclusion water from sphalerite in one of the lode deposits has delta O-18(fluid) values of 1.6 and 2.4 per mil, indistinguishable from delta O-18(fluid) values between -0.3 to +7.4 per mil calculated from the isotopic composition of coexisting quartz, dolomite, and illite. The trend toward lower salinities and higher delta D-fluid values relative to the earlier mineralizing fluids is attributed to mixing between the fluid that formed Century and a seawater-derived fluid from a different source. Based on seismic data from the Lawn Hill platform and paragenetic and geochemical results from the Leichhardt River fault trough to the south, diagenetic aquifers in the Underlying Calvert superbasin appear to have been the most likely sources for the fluids that formed Century and the discordant lode deposits. Paragenetically late sphalerite and calcite cut sphalerite, quartz, and dolomite in the lode deposits and contain Na+-dominated fluid inclusions with much lower salinities than their older counterparts. The isotopic composition of calcite also indicates delta O-18(fluid) from 3.3 to 10.7 per mil, which is larger than the range obtained from synmineralization minerals, supporting the idea that a unique fluid source was involved. The absolute timing of this event is unclear, but a plethora of Pb model, K-Ar, and Ar-40/Ar-39 ages between 1440 and 1300 Ma indicate that a significant volume of fluid was mobilized at this time. The deposition of the Roper superbasin from ca. 1492 +/- 4 Ma suggests that these late veins formed from fluids that may have been derived from aquifers in overlying sediments of the Roper superbasin. Clear, buck, and drusy quartz in veins unrelated to any form of Pb-Zn mineralization record the last major fluid event in the Burketown mineral field and form distinct outcrops and ridges in the district. Fluid inclusions in these veins indicate formation from a low-salinity, 300 degrees +/- 80 degrees C fluid. Temperatures approaching 300 degrees C recorded in organic matter adjacent to faults and at sequence boundaries correspond to K-Ar ages spanning 1300 to 1100 Ma, which coincides with regional hydrothermal activity in the northern Lawn Hill platform and the emplacement of the Lakeview Dolerite at the time of assemblage of the Rodinia supercontinent.

Loss of PKR Activity in Chronic Lymphocytic Leukemia

There are a number of observations that suggest the dsRNA-activated protein kinase, PKR, may play an active role in formation and maintenance of leukemia, including nonrandom chromosomal deletions in acute leukemia as well as truncations and deletions of the PKR gene in some leukemia cell lines. However, there is little direct evidence from patient material that this is so. Here we show that full-length PKR is present but not active in 21 of 28 patient samples from B-cell chronic lymphocytic leukemia (B-CLL). PKR from these patients was unable to auto-activate or phosphorylate substrates but was able to bind dsRNA. Furthermore, the lack of PKR activation was not due to differing levels of the PKR activator, PACT nor of the PKR inhibitor, p58(IPK). We compared PKR status with clinical parameters and disease staging. No differences were found between the 2 groups in terms of staging (modified Rai or Binet), age, CD38 status, p53 status, 11q23 deletion status or CEP12 deletion status. However, there was a significant correlation between deletion in 13q14.3 and lack of PKR activity. We show that B-CLL cells appear to contain a soluble inhibitor of PKR, as lysates from cells lacking PKR activity were able to inhibit exogenous PKR in mixing experiments. Finally, we show suppression of PKR activity was still present following ultrafilitration through a 10,000 Da cutoff filter but was lost upon extraction with phenol/chloroform or by high salt washing. This data suggests loss of PKR activity may contribute to the formation and/or maintenance of CLL. (C) 2004 Wiley-Liss, Inc.

Hydrothermal control on organic matter alteration and illite precipitation, Mt Isa Basin, Australia

Abundant illite precipitation, in Proterozoic rocks from Northern Lawn Hill Platform, Mt Isa Basin, Australia, occurred in organic matter-rich black shales rather than in sandstones, siltstones and organic matter-poor shales. Sandstones and siltstones acted as impermeable rocks, as early diagenetic quartz and carbonate minerals reduced the porosity-permeability. Scanning and transmission electron microscopy (SEM and TEM) studies indicate a relation between creation of microporosity-permeability and organic matter alteration, suitable for subsequent mineral precipitation. K-Ar data indicate that organic matter alteration and the subsequent illite precipitation within the organic matter occurred during the regional hydrothermal event at 1172 +/- 150 (2sigma) Ma. Hot circulating fluids are considered to be responsible for organic matter alteration, migration and removal of volatile hydrocarbon, and consequently porosity-permeability creation. Those rocks lacking sufficient porosity-permeability, such as sandstones, siltstones and organic matter poor shales, may not have been affected by fluid movement. In hydrothermal systems, shales and mudstones may not be impermeable as usually assumed because of hydrocarbons being rapidly removed by fluid, even with relatively low total organic carbon.

Non-additivity of attractive potentials in modeling of N-2 and Ar adsorption isotherms on graphitized carbon black and porous carbon by means of density functional theory

We present a new approach accounting for the nonadditivity of attractive parts of solid-fluid and fluidfluid potentials to improve the quality of the description of nitrogen and argon adsorption isotherms on graphitized carbon black in the framework of non-local density functional theory. We show that the strong solid-fluid interaction in the first monolayer decreases the fluid-fluid interaction, which prevents the twodimensional phase transition to occur. This results in smoother isotherm, which agrees much better with experimental data. In the region of multi-layer coverage the conventional non-local density functional theory and grand canonical Monte Carlo simulations are known to over-predict the amount adsorbed against experimental isotherms. Accounting for the non-additivity factor decreases the solid-fluid interaction with the increase of intermolecular interactions in the dense adsorbed fluid, preventing the over-prediction of loading in the region of multi-layer adsorption. Such an improvement of the non-local density functional theory allows us to describe experimental nitrogen and argon isotherms on carbon black quite accurately with mean error of 2.5 to 5.8% instead of 17 to 26% in the conventional technique. With this approach, the local isotherms of model pores can be derived, and consequently a more reliab * le pore size distribution can be obtained. We illustrate this by applying our theory against nitrogen and argon isotherms on a number of activated carbons. The fitting between our model and the data is much better than the conventional NLDFT, suggesting the more reliable PSD obtained with our approach.

An experimental and finite element poroelastic creep response analysis of an intervertebral hydrogel disc model in axial compression

A hydrogel intervertebral disc (lVD) model consisting of an inner nucleus core and an outer anulus ring was manufactured from 30 and 35% by weight Poly(vinyl alcohol) hydrogel (PVA-H) concentrations and subjected to axial compression in between saturated porous endplates at 200 N for 11 h, 30 min. Repeat experiments (n = 4) on different samples (N = 2) show good reproducibility of fluid loss and axial deformation. An axisymmetric nonlinear poroelastic finite element model with variable permeability was developed using commercial finite element software to compare axial deformation and predicted fluid loss with experimental data. The FE predictions indicate differential fluid loss similar to that of biological IVDs, with the nucleus losing more water than the anulus, and there is overall good agreement between experimental and finite element predicted fluid loss. The stress distribution pattern indicates important similarities with the biological lVD that includes stress transference from the nucleus to the anulus upon sustained loading and renders it suitable as a model that can be used in future studies to better understand the role of fluid and stress in biological IVDs. (C) 2005 Springer Science + Business Media, Inc.

Bajo de la Alumbrera copper-gold deposit: Stable isotope evidence for a porphyry-related hydrothermal system dominated by magmatic aqueous fluids

Alteration zones at the gold-rich Bajo de la Alumbrera porphyry copper deposit in northwestern Argentina are centered on several porphyritic intrusions. They are zoned from a central copper-iron sulfide and gold-mineralized potassic (biotite-K-feldspar +/- quartz) core outward to propylitic (chlorite-illite-epidote-calcite) assemblages. A mineralized intermediate argillic alteration assemblage (chlorite-illite +/- pyrite) has overprinted the potassic alteration zone across the top and sides of the deposit and is itself zoned outward into phyllic (quartzinuscovite-illite +/- pyrite) alteration. This study contributes new data to previously reported delta(18)O and delta D compositions of fluids responsible for the alteration at Bajo de la Alumbrera, and the data are used to infer likely ore-forming processes. Measured and calculated delta(18)O and delta D values of fluids (+8.3 to +10.2 and -33 to -81 parts per thousand, respectively) confirm a primary magmatic origin for the earliest potassic alteration phase. Lower temperature potassic alteration formed from magmatic fluids with lower delta D values (down to -123 parts per thousand). These depleted compositions are distinct from meteoric water and consistent with degassing and volatile exsolution of magmatic fluids derived from an underlying magma. Variability in the calculated composition of fluid associated with potassic alteration is explained in terms of phase separation (or boiling). if copper-iron sulfide deposition occurred during cooling (as proposed elsewhere), this cooling was largely a result of phase separation. Magmatic water was directly involved in the formation of overprinting intermediate argillic alteration assemblages at Bajo de la Alumbrera. Calculated delta(18)O and delta D values of fluids associated with this alteration range from +4.8 to +8.1 and -31 to -71 per mil, respectively Compositions determined for fluids associated with phyllic alteration (-0.8 to +10.2 and -31 to -119 parts per thousand) overlap with the values determined for the intermediate argillic alteration. We infer that phyllic alteration assemblages developed during two stages; the first was a high-temperature (400 degrees-300 degrees C) stage with D-depleted water (delta D = -66 to -119 parts per thousand). This compositional range may have resulted from magma degassing and/or the injection of new magmatic water into a compositionally evolved hydrothermal system. The isotopic variations also can be explained by increased fluid-rock interaction. The second stage of phyllic alteration occurred at a lower temperature (similar to 200 degrees C), and variations in the modeled isotopic compositions imply mixing of magmatic and meteoric waters. Ore deposition that occurred late in the evolution of the hydrothermal system was probably associated with further cooling of the magmatic fluid, in part caused by fluid-rock interaction and phase separation. Changing pH and/or oxygen fuoracity may have caused additional ore deposition. The ingress of meteoric water appears to postdate the bulk of mineralization and occurred as the system at Bajo de la Alumbrera waned.

Postnatal developmental expression of the PDZ scaffolds Na+-H+ exchanger regulatory factors 1 and 2 in the rat cochlea

Sensory transduction in the mammalian cochlea requires the maintenance of specialized fluid compartments with distinct ionic compositions. This is achieved by the concerted action of diverse ion channels and transporters, some of which can interact with the PDZ scaffolds, Na+-H+ exchanger regulatory factors 1 and 2 (NHERF-1, NHERF-2). Here, we report that NHERF-1 and NHERF-2 are widely expressed in the rat cochlea, and that their expression is developmentally regulated. Reverse transcription/polymerase chain reaction (RT-PCR) and Western blotting initially confirmed the RNA and protein expression of NHERFs. We then performed immunohistochemistry on cochlea during various stages of postnatal development. Prior to the onset of hearing (P8), NHERF-1 immunolabeling was prominently polarized to the apical membrane of cells lining the endolymphatic compartment, including the stereocilia and cuticular plates of the inner and outer hair cells, marginal cells of the stria vascularis, Reissner's epithelia, and tectorial membrane. With maturation (P21, P70), NHERF-1 immunolabeling was reduced in the above structures, whereas labeling increased in the apical membrane of the interdental cells of the spiral limbus and the inner and outer sulcus cells, Hensen's cells, the inner and outer pillar cells, Deiters cells, the inner border cells, spiral ligament fibrocytes, and spiral ganglion neurons (particularly type II). NHERF-1 expression in strial basal and intermediate cells was persistent. NHERF-2 immunolabeling was similar to that for NHERF-1 during postnatal development, with the exception of expression in the synaptic regions beneath the outer hair cells. NHERF-1 and NHERF-2 co-localized with glial fibrillary acidic protein and vimentin in glia. The cochlear localization of NHERF scaffolds suggests that they play important roles in the developmental regulation of ion transport, homeostasis, and auditory neurotransmission.

Technical and economic factors in applying the enhanced coalbed methane recovery process

Geological sequestration of CO2 is a technically feasible and potentially economic option for significantly and safely reducing greenhouse gas emissions, with CO2 injection already practiced in Canada and the USA to enhance crude oil production. The Enhanced Coalbed Methane (ECBM) process is seen as the next most economical sequestration options. The authors estimate an incremental methane recovery factor from 20% to 50%, depending on coal rank and seam depth. Others have estimated the potential to increase worldwide CBM production, utilising ECBM, by 18 Trillion cubic meters, while simultaneously sequestering 345 Giga tonnes of CO2. This paper presents technical and economic factors to consider for developing a commercial ECBM project. Technical factors include: geostructural and hydrogeological issues, geochemical reactions, stressed and competitive sorption, counter-diffusion, effective and relative 4-D coal permeability and methane recovery levels. Key economic factors are injectant acquisition price, sale price of methane and the level of carbon credits.

Simulation of binary mixture adsorption of methane and CO2 at supercritical conditions in carbons

Knowledge of the adsorption behavior of coal-bed gases, mainly under supercritical high-pressure conditions, is important for optimum design of production processes to recover coal-bed methane and to sequester CO2 in coal-beds. Here, we compare the two most rigorous adsorption methods based on the statistical mechanics approach, which are Density Functional Theory (DFT) and Grand Canonical Monte Carlo (GCMC) simulation, for single and binary mixtures of methane and carbon dioxide in slit-shaped pores ranging from around 0.75 to 7.5 nm in width, for pressure up to 300 bar, and temperature range of 308-348 K, as a preliminary study for the CO2 sequestration problem. For single component adsorption, the isotherms generated by DFT, especially for CO2, do not match well with GCMC calculation, and simulation is subsequently pursued here to investigate the binary mixture adsorption. For binary adsorption, upon increase of pressure, the selectivity of carbon dioxide relative to methane in a binary mixture initially increases to a maximum value, and subsequently drops before attaining a constant value at pressures higher than 300 bar. While the selectivity increases with temperature in the initial pressure-sensitive region, the constant high-pressure value is also temperature independent. Optimum selectivity at any temperature is attained at a pressure of 90-100 bar at low bulk mole fraction of CO2, decreasing to approximately 35 bar at high bulk mole fractions. (c) 2005 American Institute of Chemical Engineers.