A computer-aided diagnostic system to characterize CT focal liver lesions: design and optimization of a neural network classifier

In this paper, a computer-aided diagnostic (CAD) system for the classification of hepatic lesions from computed tomography (CT) images is presented. Regions of interest (ROIs) taken from nonenhanced CT images of normal liver, hepatic cysts, hemangiomas, and hepatocellular carcinomas have been used as input to the system. The proposed system consists of two modules: the feature extraction and the classification modules. The feature extraction module calculates the average gray level and 48 texture characteristics, which are derived from the spatial gray-level co-occurrence matrices, obtained from the ROIs. The classifier module consists of three sequentially placed feed-forward neural networks (NNs). The first NN classifies into normal or pathological liver regions. The pathological liver regions are characterized by the second NN as cyst or "other disease." The third NN classifies "other disease" into hemangioma or hepatocellular carcinoma. Three feature selection techniques have been applied to each individual NN: the sequential forward selection, the sequential floating forward selection, and a genetic algorithm for feature selection. The comparative study of the above dimensionality reduction methods shows that genetic algorithms result in lower dimension feature vectors and improved classification performance.

Creatine supports propagation and promotes neuronal differentiation of inner ear progenitor cells

Long-term propagation of inner ear-derived progenitor/stem cells beyond the third generation and differentiation into inner ear cell types has been shown to be feasible, but challenging. We investigated whether the known neuroprotective guanidine compound creatine (Cr) promotes propagation of inner ear progenitor/stem cells as mitogen-expanded neurosphere cultures judged from the formation of spheres over passages. In addition, we studied whether Cr alone or in combination with brain-derived neurotrophic factor (BDNF) promotes neuronal differentiation of inner ear progenitors. For this purpose, early postnatal rat spiral ganglia, utricle, and organ of Corti-derived progenitors were grown as floating spheres in the absence (controls) or presence of Cr (5 mM) from passage 3 onward. Similarly, dissociated sphere-derived cultures were differentiated for 14 days in the presence or absence of Cr (5 mM) and spiral ganglia sphere-derived cultures in a combination of Cr with the neurotrophin BDNF (50 ng/ml). We found that the cumulative total number of spheres over all passages was significantly higher after Cr supplementation as compared with controls in all the three inner ear cultures. In contrast, sphere sizes were not affected by the administration of Cr. Administration of Cr during differentiation of spiral ganglia cells resulted in a significantly higher density of β-III-tubulin-positive cells compared with controls, whereas densities of myosin VIIa-positive cells in cultures of utricle and organ of Corti were not affected by the treatment. Importantly, a combination of Cr with the neurotrophin BDNF resulted in further significantly increased densities of β-III-tubulin-positive cells in cultures of spiral ganglia cells as compared with single treatments. In sum, Cr promoted continuing propagation of rat inner ear-derived progenitor cells and supported specifically in combination with BDNF the differentiation of neuronal cell types from spiral ganglion-derived spheres.

Methane emissions from floodplains in the Amazon Basin: challenges in developing a process-based model for global applications

Tropical wetlands are estimated to represent about 50% of the natural wetland methane (CH4) emissions and explain a large fraction of the observed CH4 variability on timescales ranging from glacial–interglacial cycles to the currently observed year-to-year variability. Despite their importance, however, tropical wetlands are poorly represented in global models aiming to predict global CH4 emissions. This publication documents a first step in the development of a process-based model of CH4 emissions from tropical floodplains for global applications. For this purpose, the LPX-Bern Dynamic Global Vegetation Model (LPX hereafter) was slightly modified to represent floodplain hydrology, vegetation and associated CH4 emissions. The extent of tropical floodplains was prescribed using output from the spatially explicit hydrology model PCR-GLOBWB. We introduced new plant functional types (PFTs) that explicitly represent floodplain vegetation. The PFT parameterizations were evaluated against available remote-sensing data sets (GLC2000 land cover and MODIS Net Primary Productivity). Simulated CH4 flux densities were evaluated against field observations and regional flux inventories. Simulated CH4 emissions at Amazon Basin scale were compared to model simulations performed in the WETCHIMP intercomparison project. We found that LPX reproduces the average magnitude of observed net CH4 flux densities for the Amazon Basin. However, the model does not reproduce the variability between sites or between years within a site. Unfortunately, site information is too limited to attest or disprove some model features. At the Amazon Basin scale, our results underline the large uncertainty in the magnitude of wetland CH4 emissions. Sensitivity analyses gave insights into the main drivers of floodplain CH4 emission and their associated uncertainties. In particular, uncertainties in floodplain extent (i.e., difference between GLC2000 and PCR-GLOBWB output) modulate the simulated emissions by a factor of about 2. Our best estimates, using PCR-GLOBWB in combination with GLC2000, lead to simulated Amazon-integrated emissions of 44.4 ± 4.8 Tg yr−1. Additionally, the LPX emissions are highly sensitive to vegetation distribution. Two simulations with the same mean PFT cover, but different spatial distributions of grasslands within the basin, modulated emissions by about 20%. Correcting the LPX-simulated NPP using MODIS reduces the Amazon emissions by 11.3%. Finally, due to an intrinsic limitation of LPX to account for seasonality in floodplain extent, the model failed to reproduce the full dynamics in CH4 emissions but we proposed solutions to this issue. The interannual variability (IAV) of the emissions increases by 90% if the IAV in floodplain extent is accounted for, but still remains lower than in most of the WETCHIMP models. While our model includes more mechanisms specific to tropical floodplains, we were unable to reduce the uncertainty in the magnitude of wetland CH4 emissions of the Amazon Basin. Our results helped identify and prioritize directions towards more accurate estimates of tropical CH4 emissions, and they stress the need for more research to constrain floodplain CH4 emissions and their temporal variability, even before including other fundamental mechanisms such as floating macrophytes or lateral water fluxes.

Patient classification system: An integrated method for measuring nursing intensity and optimizing resource allocation

A patient classification system was developed integrating a patient acuity instrument with a computerized nursing distribution method based on a linear programming model. The system was designed for real-time measurement of patient acuity (workload) and allocation of nursing personnel to optimize the utilization of resources.^ The acuity instrument was a prototype tool with eight categories of patients defined by patient severity and nursing intensity parameters. From this tool, the demand for nursing care was defined in patient points with one point equal to one hour of RN time. Validity and reliability of the instrument was determined as follows: (1) Content validity by a panel of expert nurses; (2) predictive validity through a paired t-test analysis of preshift and postshift categorization of patients; (3) initial reliability by a one month pilot of the instrument in a practice setting; and (4) interrater reliability by the Kappa statistic.^ The nursing distribution system was a linear programming model using a branch and bound technique for obtaining integer solutions. The objective function was to minimize the total number of nursing personnel used by optimally assigning the staff to meet the acuity needs of the units. A penalty weight was used as a coefficient of the objective function variables to define priorities for allocation of staff.^ The demand constraints were requirements to meet the total acuity points needed for each unit and to have a minimum number of RNs on each unit. Supply constraints were: (1) total availability of each type of staff and the value of that staff member (value was determined relative to that type of staff's ability to perform the job function of an RN (i.e., value for eight hours RN = 8 points, LVN = 6 points); (2) number of personnel available for floating between units.^ The capability of the model to assign staff quantitatively and qualitatively equal to the manual method was established by a thirty day comparison. Sensitivity testing demonstrated appropriate adjustment of the optimal solution to changes in penalty coefficients in the objective function and to acuity totals in the demand constraints.^ Further investigation of the model documented: correct adjustment of assignments in response to staff value changes; and cost minimization by an addition of a dollar coefficient to the objective function. ^

Involvement of heparin-like glycosaminoglycans and expression of a novel heparan sulfate binding protein (p24) during human placentation and in a model for human implantation

Previous studies in our laboratory have indicated that heparan sulfate proteoglycans (HSPGs) play an important role in murine embryo implantation. To investigate the potential function of HSPGs in human implantation, two human cell lines (RL95 and JAR) were selected to model uterine epithelium and embryonal trophectoderm, respectively. A heterologous cell-cell adhesion assay showed that initial binding between JAR and RL95 cells is mediated by cell surface glycosaminoglycans (GAG) with heparin-like properties, i.e., heparan sulfate and dermatan sulfate. Furthermore, a single class of highly specific, protease-sensitive heparin/heparan sulfate binding sites exist on the surface of RL95 cells. Three heparin binding, tryptic peptide fragments were isolated from RL95 cell surfaces and their amino termini partially sequenced. Reverse transcription-polymerase chain reaction (RT-PCR) generated 1 to 4 PCR products per tryptic peptide. Northern blot analysis of RNA from RL95 cells using one of these RT-PCR products identified a 1.2 Kb mRNA species (p24). The amino acid sequence predicted from the cDNA sequence contains a putative heparin-binding domain. A synthetic peptide representing this putative heparin binding domain was used to generate a rabbit polyclonal antibody (anti-p24). Indirect immunofluorescence studies on RL95 and JAR cells as well as binding studies of anti-p24 to intact RL95 cells demonstrate that p24 is distributed on the cell surface. Western blots of RL95 membrane preparations identify a 24 kDa protein (p24) highly enriched in the 100,000 g pellet plasma membrane-enriched fraction. p24 eluted from membranes with 0.8 M NaCl, but not 0.6 M NaCl, suggesting that it is a peripheral membrane component. Solubilized p24 binds heparin by heparin affinity chromatography and $\sp{125}$I-heparin binding assays. Furthermore, indirect immunofluorescence studies indicate that cytotrophoblast of floating and attached villi of the human fetal-maternal interface are recognized by anti-p24. The study also indicates that the HSPG, perlecan, accumulates where chorionic villi are attached to uterine stroma and where p24-expressing cytotrophoblast penetrate the stroma. Collectively, these data indicate that p24 is a cell surface membrane-associated heparin/heparan sulfate binding protein found in cytotrophoblast, but not many other cell types of the fetal-maternal interface. Furthermore, p24 colocalizes with HSPGs in regions of cytotrophoblast invasion. These observations are consistent with a role for HSPGs and HSPG binding proteins in human trophoblast-uterine cell interactions. ^

Paracrine or virus-mediated induction of decorin expression by endothelial cells contributes to tube formation and prevention of apoptosis in collagen lattices

Resting endothelial cells express the small proteoglycan biglycan, whereas sprouting endothelial cells also synthesize decorin, a related proteoglycan. Here we show that decorin is expressed in endothelial cells in human granulomatous tissue. For in vitro investigations, the human endothelium-derived cell line, EA.hy 926, was cultured for 6 or more days in the presence of 1% fetal calf serum on top of or within floating collagen lattices which were also populated by a small number of rat fibroblasts. Endothelial cells aligned in cord-like structures and developed cavities that were surrounded by human decorin. About 14% and 20% of endothelial cells became apoptotic after 6 and 12 days of co-culture, respectively. In the absence of fibroblasts, however, the extent of apoptosis was about 60% after 12 days, and cord-like structures were not formed nor could decorin production be induced. This was also the case when lattices populated by EA.hy 926 cells were maintained under one of the following conditions: 1) 10% fetal calf serum; 2) fibroblast-conditioned media; 3) exogenous decorin; or 4) treatment with individual growth factors known to be involved in angiogenesis. The mechanism(s) by which fibroblasts induce an angiogenic phenotype in EA.hy 926 cells is (are) not known, but a causal relationship between decorin expression and endothelial cell phenotype was suggested by transducing human decorin cDNA into EA.hy 926 cells using a replication-deficient adenovirus. When the transduced cells were cultured in collagen lattices, there was no requirement of fibroblasts for the formation of capillary-like structures and apoptosis was reduced. Thus, decorin expression seems to be of special importance for the survival of EA.hy 926 cells as well as for cord and tube formation in this angiogenesis model.

West Antarctic Ice Streams

Solar heat is the acknowledged driving force for climatic change. However, ice sheets are also capable of causing climatic change. This property of ice sheets derives from the facts that ice and rock are crystalline whereas the oceans and atmosphere are fluids and that ice sheets are massive enough to depress the earth's crust well below sea level. These features allow time constants for glacial flow and isostatic compensation to be much larger than those for ocean and atmospheric circulation and therefore somewhat independent of the solar variations that control this circulation. This review examines the nature of dynamic processes in ice streams that give ice sheets their degree of independent behavior and emphasizes the consequences of viscoplastic instability inherent in anisotropic polycrystalline solids such as glacial ice. Viscoplastic instability and subglacial topography are responsible for the formation of ice streams near ice sheet margins grounded below sea level. As a result the West Antarctic marine ice sheet is inherently unstable and can be rapidly carved away by calving bays which migrate up surging ice streams. Analyses of tidal flexure along floating ice stream margins, stress and velocity fields in ice streams, and ice stream boundary conditions are presented and used to interpret ERTS 1 photomosaics for West Antarctica in terms of characteristic ice sheet crevasse patterns that can be used to monitor ice stream surges and to study calving bay dynamics.

Correction to Variations of Ice Bed Coupling Beneath and Beyond Ice Streams: The Force Balance

A geometrical force balance that links stresses to ice bed coupling along a flow band of an ice sheet was developed in 1988 for longitudinal tension in ice streams and published 4 years later. It remains a work in progress. Now gravitational forces balanced by forces producing tensile, compressive, basal shear, and side shear stresses are all linked to ice bed coupling by the floating fraction phi of ice that produces the concave surface of ice streams. These lead inexorably to a simple formula showing how phi varies along these flow bands where surface and bed topography are known: phi = h(O)/h(I) with h(O) being ice thickness h(I) at x = 0 for x horizontal and positive upslope from grounded ice margins. This captures the basic fact in glaciology: the height of ice depends on how strongly ice couples to the bed. It shows how far a high convex ice sheet (phi = 0) has gone in collapsing into a low flat ice shelf (phi = 1). Here phi captures ice bed coupling under an ice stream and h(O) captures ice bed coupling beyond ice streams.

On the Pulling Power of Ice Streams

Gravity wants to pull an ice sheet to the center of the Earth, but cannot because the Earth's crust is in the way, so ice is pushed out sideways instead. Or is it? The ice sheet "sees" nothing preventing it from spreading out except air, which is much less massive than ice. Therefore, does not ice rush forward to fill this relative vacuum; does not the relative vacuum suck ice into it, because Nature abhors a vacuum? If so, the ice sheet is not only pulled downward by gravity, it is also pulled outward by the relative vacuum. This pulling outward will be most rapid where the ice sheet encounters least resistance. The least resistance exists along the bed of ice streams, where ice-bed coupling is reduced by a basal water layer, especially if the ice stream becomes afloat and the floating part is relatively unconfined around its perimeter and unpinned to the sea floor. Ice streams are therefore fast currents of ice that develop near the margins of an ice sheet where these conditions exist. Because of these conditions, ice streams pull ice out of ice sheets and have pulling power equal to the longitudinal gravitational pulling force multiplied by the ice-stream velocity. These boundary conditions beneath and beyond ice streams can be quantified by a basal buoyancy factor that provides a life-cycle classification of ice streams into inception, growth, mature, declining and terminal stages, during which ice streams disintegrate the ice sheet. Surface profiles of ice streams are diagnostic of the stage in a life cycle and, hence, of the vitality of the ice sheet.

Variations of Ice Bed Coupling Beneath and Beyond Ice Streams: The Force Balance

A geometrical force balance that links stresses to ice bed coupling along a flow band of an ice sheet was developed in 1988 for longitudinal tension in ice streams and published 4 years later. It remains a work in progress. Now gravitational forces balanced by forces producing tensile, compressive, basal shear, and side shear stresses are all linked to ice bed coupling by the floating fraction phi of ice that produces the concave surface of ice streams. These lead inexorably to a simple formula showing how phi varies along these flow bands where surface and bed topography are known: phi = h(O)/h(I) with h(O) being ice thickness h(I) at x = 0 for x horizontal and positive upslope from grounded ice margins. This captures the basic fact in glaciology: the height of ice depends on how strongly ice couples to the bed. It shows how far a high convex ice sheet (phi = 0) has gone in collapsing into a low flat ice shelf (phi = 1). Here phi captures ice bed coupling under an ice stream and h(O) captures ice bed coupling beyond ice streams.