Supervised Gaussian Process Latent Variable Model for Dimensionality Reduction

The Gaussian process latent variable model (GP-LVM) has been identified to be an effective probabilistic approach for dimensionality reduction because it can obtain a low-dimensional manifold of a data set in an unsupervised fashion. Consequently, the GP-LVM is insufficient for supervised learning tasks (e. g., classification and regression) because it ignores the class label information for dimensionality reduction. In this paper, a supervised GP-LVM is developed for supervised learning tasks, and the maximum a posteriori algorithm is introduced to estimate positions of all samples in the latent variable space. We present experimental evidences suggesting that the supervised GP-LVM is able to use the class label information effectively, and thus, it outperforms the GP-LVM and the discriminative extension of the GP-LVM consistently. The comparison with some supervised classification methods, such as Gaussian process classification and support vector machines, is also given to illustrate the advantage of the proposed method.

Simulating a typhoon storm surge in the East Sea of China using a coupled model

A coupled numerical model with a 2' x 2' resolution grid has been developed and used to simulate five typical typhoon storm surges (5612, 7413, 7910, 8114, and 9711) in the East Sea of China. Three main driving forces have been considered in this coupled model: wave radiation stress, combined wave-current bottom shear stress and wave-state-dependent surface wind stress. This model has then been compared with in situ measurements of the storm set-up. The effect of different driving force components on the total storm surge has also been investigated. This study has found that the coupled model with high resolution is capable of simulating the five typical typhoons better than the uncoupled models, and that the wave-dependent surface wind stress plays an important role in typhoon storm surge-wave coupling in this area and can increase the storm set-up by 1 m. The study of the five typhoon cases has shown that the general coupling effects could increase storm set-up by 20-32%. Thus, it is suggested that to predict typhoon storm surges in the East Sea of China, a storm surge-wave coupled model be adopted. (C) 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

An extended variable-grid global ocean circulation model and its preliminary results of the equatorial Pacific circulation

To investigate the interaction between the tropical Pacific and China seas a variable-grid global ocean circulation model with fine grid[(1/6)degrees] covering the area from 20degreesS to 50degreesN and from 99degrees to 150degreesE is developed. Numerical computation of the annually cyclic circulation fields is performed. The results of the annual mean zonal currents and deep to abyssal western boundary currents in the equatorial Pacific Ocean are reported. The North Equatorial Current,the North Equatorial Countercurrent, the South Equatorial Current and the Equatorial Undercurrent are fairly well simulated. The model well reproduces the northward flowing abyssal western boundary current. From the model results a lower deep western boundary current east of the Bismarck-Solomon-New Hebrides Island chain at depths around 2 000 in has been found. The model results also show that the currents in the equatorial Pacific Ocean have multi-layer structures both in zonal currents and western boundary currents, indicating that the global ocean overturning thermohaline circulation appears of multi-layer pattern.

Mud mass transport due to waves based on an empirical rheology model featured by hysteresis loop

A vertical 2-D water-mud numerical model is developed for estimating the rate of mud mass transport under wave action. A nonlinear semi-empirical rheology model featured by remarkable hysteresis loops in the relationships of the shear stress versus both the shear strain and the rate of shear strain of mud is applied to this water mud model. A logarithmic grid in the vertical direction is employed for numerical treatment, which increases the resolution of the flow in the neighborhood of both sides of the interface. Model verifications are given through comparisons between the calculated and the measured mud mass transport velocities as well as wave height changes. (C) 2006 Elsevier Ltd. All rights reserved.

Seasonal and interannual variability of primary and export production in the South China Sea: a three-dimensional physical-biogeochemical model study

To investigate the seasonal and interannual variations in biological productivity in the South China Sea (SCS), a Pacific basin-wide physical - biogeochemical model has been developed and used to estimate the biological productivity and export flux in the SCS. The Pacific circulation model, based on the Regional Ocean Model Systems (ROMS), is forced with daily air-sea fluxes derived from the NCEP (National Centers for Environmental Prediction) reanalysis between 1990 and 2004. The biogeochemical processes are simulated with a carbon, Si(OH)(4), and nitrogen ecosystem (CoSiNE) model consisting of silicate, nitrate, ammonium, two phytoplankton groups (small phytoplankton and large phytoplankton), two zooplankton grazers (small micrograzers and large mesozooplankton), and two detritus pools. The ROMS-CoSiNE model favourably reproduces many of the observed features, such as ChI a, nutrients, and primary production (PP) in the SCS. The modelled depth-integrated PP over the euphotic zone (0-125 m) varies seasonally, with the highest value of 386 mg C m (-2) d (-1) during winter and the lowest value of 156 mg C m (-2) d (-1) during early summer. The annual mean value is 196 mg C m (-2) d (-1). The model-integrated annual mean new production (uptake of nitrate), in carbon units, is 64.4 mg C m (-2) d (-1) which yields an f-ratio of 0.33 for the entire SCS. The modelled export ratio (e-ratio: the ratio of export to PP) is 0.24 for the basin-wide SCS. The year-to-year variation of biological productivity in the SCS is weaker than the seasonal variation. The large phytoplankton group tends to dominate over the smaller phytoplankton group, and likely plays an important role in determining the interannual variability of primary and new production.

Photosynthesis-irradiance response at physiological level: A mechanistic model

A mechanistic model is developed to present the photosynthetic response of phytoplankton to irradiance at the physiological level. The model is operated on photosynthetic units (PSU), and each PSU is assumed to have two states: reactive and activated. Light absorption that drives a reactive PSU into the activated state results from the effective absorption of the PSU. Transitions between the two states are asymmetrical in rate. A PSU in the reactive state becomes activated much faster than it recovers from the activated state to the reactive one. The turnover time for an activated PSU to transit into the reactive one is defined by the turnover time of the electron transport chain. The present model yields a photosynthesis-irradiance curve (PE-curve) in a hyperbola, which is described by three physiological parameters: effective cross-section (sigma (PSII)), turnover time of electron transport chain (tau) and number of PSUs (N). The PE-curve has an initial slope of sigma (PSII) x N, a half-saturated irradiance of 1/(sigma (PSII)), and a maximal photosynthetic rate of Nlc at the saturated irradiance. The PE-curve from the present model is comparable to the empirical function based on the target theory described by the Poisson distribution. (C) 2001 Academic Press.

A collision model for DNA separation by capillary electrophoresis in dilute polymer solution

A theoretical description. based on chemical kinetics and electrochemistry, is given of DNA separation in dilute polymer solution by capillary electrophoresis. A self-consistent model was developed leading to predictions of the DNA electrophoretic velocity as a function of the experimental conditions - polymer concentration, temperature, and electric field strength. The effect of selected experimental variables is discussed. The phenomena discussed are illustrated for the example of 100 bp DNA ladder separation in dilute HPMC solution by capillary electrophoresis. This model is the first single model that can fully explain the dependence of DNA electrophoretic velocity on electrophoretic conditions.

Development of an in vitro multicellular tumor spheroid model using microencapsulation and its application in anticancer drug screening and testing

In this study, an in vitro multicellular tumor spheroid model was developed using microencapsulation, and the feasibility of using the microencapsulated. multicellular tumor spheroid (MMTS) to test the effect of chemotherapeutic drugs was investigated. Human MCF-7 breast cancer cells were encapsulated in alginate-poly-L-lysine-alginate (APA) microcapsules, and a single multicellular spheroid 150 mu m in diameter was formed in the microcapsule after 5 days of cultivation. The cell morphology, proliferation, and viability of the MMTS were characterized using phase contrast microscopy, BrdU-Iabeling, MTT stain, calcein AM/ED-2 stain, and H&E stain. It demonstrated that the MMTS was viable and that the proliferating cells were mainly localized to the periphery of the cell spheroid and the apoptotic cells were in the core. The MCF-7 MMTS was treated with mitomycin C (MC) at a concentration of 0.1, 1, or 10 times that of peak plasma concentration (ppc) for up to 72 h. The cytotoxicity was demonstrated. clearly by the reduction in cell spheroid size and the decrease in cell viability. The MMTS was further used to screen the anticancer effect of chemotherapeutic drugs, treated with MC, adriamycin (ADM) and 5-fluorouracil (5-FU) at concentrations of 0.1, 1, and 10 ppc for 24, 48, and 72 h. MCF-7 monolayer culture was used as control. Similar to monolayer culture, the cell viability of MMTS was reduced after treatment with anticancer drugs. However, the inhibition rate of cell viability in MMTS was much lower than that in monolayer culture. The MMTS was more resistant to anticancer drugs than monolayer culture. The inhibition rates of cell viability were 68.1%, 45.1%, and 46.8% in MMTS and 95.1%, 86.8%, and 91.6% in monolayer culture treated with MC, ADM, and 5-FU at 10 ppc for 72 h, respectively. MC showed the strongest cytotoxicity in both MMTS and monolayer, followed by 5-FU and ADM. It demonstrated that the MMTS has the potential to be a rapid and valid in vitro model to screen chemotherapeutic drugs with a feature to mimic in vivo three-dimensional (3-D) cell growth pattern.

Deconvolution of overlapped peaks based on the exponentially modified Gaussian model in comprehensive two-dimensional gas chromatography

Comprehensive two-dimensional gas chromatography (GC x GC) has attracted much attention for the analys is of complex samples. Even with a large peak capacity in GC x GC, peak overlapping is often met. In this paper, a new method was developed to resolve overlapped peaks based on the mass conservation and the exponentially modified Gaussian (EMG) model. Linear relationships between the calculated sigma, tau of primary peaks with the corresponding retention time (t(R)) were obtained, and the correlation coefficients were over 0.99. Based on such relationships, the elution profile of each compound in overlapped peaks could be simulated, even for the peak never separated on the second-dimension. The proposed method has proven to offer more accurate peak area than the general data processing method. (c) 2005 Elsevier B.V. All rights reserved.

Supporting the case for “progressive universalism” in health visiting: Scottish mothers and health visitors’ perspectives on targeting and rationing health visiting services, with a focus on the Lothian Child Concern Model.

Aims. To explore parents and professionals’ experience of family assessment in health visiting (public health nursing), with a focus on the Lothian Child Concern Model (LCCM). Background. Health visitors (HVs) currently assess families as requiring core, additional or intensive support, and offer support at a corresponding level. The majority of families are assessed as core and receive no pro-active support beyond the early days. Previous assessment tools, consisting of checklists, have been criticised as being ineffective in identifying a range of health needs and unacceptable to parents and HVs. The LCCM model was developed and introduced in the study area to promote a partnership approach with parents and assess strengths as well as difficulties in parents’ capacity to care for their child. Methods. Qualitative methods were used. Ten mothers and twelve HVs took part in individual semi-structured interviews. Results. Most mothers were aware of the assessment process but some felt that they were not involved in the decision making process. Explaining the assessment process to parents is problematic and not all HVs do so. The assessment process was stressful for some mothers. HVs find the model useful for structuring and documenting the assessment process. Many believe that most families benefit from some support, using public health approaches. Families are often assessed as core because there are insufficient resources to support all those who meet the criteria of the additional category, and managers assess caseloads in terms of families with child protection concerns. Conclusions. The study findings support the concept of “progressive universalism” which provides a continuum of intensity of support to families, depending on need. Mothers would like better partnership working with HVs. Relevance to clinical practice. The study endorses proposed policy changes to re-establish the public health role of HVs and to lower the threshold for families to qualify for support.

The development of entrepreneurial culture in a transition economy: an empirical model discussion.

This conceptual paper will focus on the presentation of the model developed from empirical, qualitative research covering 20 years of analysis on the relationship between culture and entrepreneurship in Poland. It is aimed at proposing a comprehensive framework that describes the development of entrepreneurial culture. In this empirical model culture is understood as a set of values and beliefs held by a social group that endorse and are conducive to entrepreneurial behaviour; while entrepreneurial behaviour is treated as an expected outcome and narrowed down to opening the company. The model proves that the differentiation between entrepreneurship (behaviour) and entrepreneurs (who demonstrate this behaviour) needs to be recognised in future research. The case of Poland offers a historical example, which can shed more light on the process of cultural change and the role of entrepreneurship and entrepreneurs in the development of entrepreneurial culture. In the case presented, the behaviour of entrepreneurs has been identified as the key factor leading to further development.

Model-Based Reasoning: A Principled Approach for Software Engineering

Lee M.H., Model-Based Reasoning: A Principled Approach for Software Engineering, Software - Concepts and Tools,19(4), pp179-189, 2000.

Knowledge representation for fuzzy model composition

X. Fu and Q. Shen. 'Knowledge representation for fuzzy model composition', in Proceedings of the 21st International Workshop on Qualitative Reasoning, 2007, pp. 47-54. Sponsorship: EPSRC

Model-based detection of spiculated lesions in mammograms

R. Zwiggelaar, T.C. Parr, J.E. Schumm. I.W. Hutt, S.M. Astley, C.J. Taylor and C.R.M. Boggis, 'Model-based detection of spiculated lesions in mammograms', Medical Image Analysis 3 (1), 39-62 (1999)

Brachypodium distachyon. A new model system for functional genomics in grasses

John Draper, Luis A.J. Mur, Glyn Jenkins, Gadab C. Ghosh-Biswas, Pauline Bablak, Robert Hasterok,and Andrew P.M. Routledge (2001). Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiology, 127 (4), 1539-1555. Sponsorship: BBSRC / Gatsby Foundation RAE2008