Understanding Subsystems in Biology through Dimensionality Reduction, Graph Partitioning and Analytical Modeling

Biological systems exhibit rich and complex behavior through the orchestrated interplay of a large array of components. It is hypothesized that separable subsystems with some degree of functional autonomy exist; deciphering their independent behavior and functionality would greatly facilitate understanding the system as a whole. Discovering and analyzing such subsystems are hence pivotal problems in the quest to gain a quantitative understanding of complex biological systems. In this work, using approaches from machine learning, physics and graph theory, methods for the identification and analysis of such subsystems were developed. A novel methodology, based on a recent machine learning algorithm known as non-negative matrix factorization (NMF), was developed to discover such subsystems in a set of large-scale gene expression data. This set of subsystems was then used to predict functional relationships between genes, and this approach was shown to score significantly higher than conventional methods when benchmarking them against existing databases. Moreover, a mathematical treatment was developed to treat simple network subsystems based only on their topology (independent of particular parameter values). Application to a problem of experimental interest demonstrated the need for extentions to the conventional model to fully explain the experimental data. Finally, the notion of a subsystem was evaluated from a topological perspective. A number of different protein networks were examined to analyze their topological properties with respect to separability, seeking to find separable subsystems. These networks were shown to exhibit separability in a nonintuitive fashion, while the separable subsystems were of strong biological significance. It was demonstrated that the separability property found was not due to incomplete or biased data, but is likely to reflect biological structure.

An Interpolative Analytical Cache Model with Application to Performance-Power Design Space Exploration

Caches are known to consume up to half of all system power in embedded processors. Co-optimizing performance and power of the cache subsystems is therefore an important step in the design of embedded systems, especially those employing application specific instruction processors. In this project, we propose an analytical cache model that succinctly captures the miss performance of an application over the entire cache parameter space. Unlike exhaustive trace driven simulation, our model requires that the program be simulated once so that a few key characteristics can be obtained. Using these application-dependent characteristics, the model can span the entire cache parameter space consisting of cache sizes, associativity and cache block sizes. In our unified model, we are able to cater for direct-mapped, set and fully associative instruction, data and unified caches. Validation against full trace-driven simulations shows that our model has a high degree of fidelity. Finally, we show how the model can be coupled with a power model for caches such that one can very quickly decide on pareto-optimal performance-power design points for rapid design space exploration.

Markov Process Modeling of A System Under WIPLOAD Control

This paper analyzes a proposed release controlmethodology, WIPLOAD Control (WIPLCtrl), using a transfer line case modeled by Markov process modeling methodology. The performance of WIPLCtrl is compared with that of CONWIP under 13 system configurations in terms of throughput, average inventory level, as well as average cycle time. As a supplement to the analytical model, a simulation model of the transfer line is used to observe the performance of the release control methodologies on the standard deviation of cycle time. From the analysis, we identify the system configurations in which the advantages of WIPLCtrl could be observed.

Forms of participatory democracy: an analytical framework based on the experiences of Bolivia, brazil and Colombia

Based on the experiences of Colombia, Brazil and Bolivia, the paper proposes a general analytical framework for participatory mechanisms. The analysis is oriented to detect the incentives in each system and theethics and behavior sustaining them. It investigates about the sustainability of participatory democracy, in the face of tensions with representative democracy. The article presents a theoretical framework built from theseexperiences of institutional design and political practice, and confronts it against the theoretical conceptualizationsof participatory democracy in Bobbio, Sartori, Elster and Nino, among others. In this context, different waysin which those schemes can be inserted in the political systems become apparent, along with the variables thatresult from combining elements of direct, representative and participatory democracy”

The 'direct costs' of livestock disease: The development of a system of models for the analysis of 30 endemic livestock diseases in Great Britain

The 'direct costs' attributable to 30 different endemic diseases of farm animals in Great Britain are estimated using a standardised method to construct a simple model for each disease that includes consideration of disease prevention and treatment costs. The models so far developed provide a basis for further analyses including cost-benefit analyses for the economic assessment of disease control options. The approach used reflects the inherent livestock disease information constraints, which limit the application of other economic analytical methods. It is a practical and transparent approach that is relatively easily communicated to veterinary scientists and policy makers. The next step is to develop the approach by incorporating wider economic considerations into the analyses in a way that will demonstrate to policy makers and others the importance of an economic perspective to livestock disease issues.

EnvironalPlanning: an analytical network process model for environmentally conscious construction planning

Although the construction pollution index has been put forward and proved to be an efficient approach to reducing or mitigating pollution level during the construction planning stage, the problem of how to select the best construction plan based on distinguishing the degree of its potential adverse environmental impacts is still a research task. This paper first reviews environmental issues and their characteristics in construction, which are critical factors in evaluating potential adverse impacts of a construction plan. These environmental characteristics are then used to structure two decision models for environmental-conscious construction planning by using an analytic network process (ANP), including a complicated model and a simplified model. The two ANP models are combined and called the EnvironalPlanning system, which is applied to evaluate potential adverse environmental impacts of alternative construction plans.

Decision making for HVAC&R system selection for a typical office building in the UK

Demands for thermal comfort, better indoor air quality together with lower environmental impacts have had ascending trends in the last decade. In many circumstances, these demands could not be fully covered through the soft approach of bioclimatic design like optimisation of the building orientation and internal layout. This is mostly because of the dense urban environment and building internal energy loads. In such cases, heating, ventilation, air-conditioning and refrigeration (HVAC&R) systems make a key role to fulfill the requirements of indoor environment. Therefore, it is required to select the most proper HVAC&R system. In this study, a robust decision making approach for HVAC&R system selection is proposed. Technical performance, economic aspect and environmental impacts of 36 permutations of primary and secondary systems are taken into account to choose the most proper HVAC&R system for a case study office building. The building is a representative for the dominant form of office buildings in the UK. Dynamic performance evaluation of HVAC&R alternatives using TRNSYS package together with life cycle energy cost analysis provides a reliable basis for decision making. Six scenarios broadly cover the decision makers' attitudes on HVAC&R system selection which are analysed through Analytical Hierarchy Process (AHP). One of the significant outcomes reveals that, despite both the higher energy demand and more investment requirements associated with compound heating, cooling and power system (CCHP); this system is one of the top ranked alternatives due to the lower energy cost and C02 emissions. The sensitivity analysis reveals that in all six scenarios, the first five top ranked alternatives are not changed. Finally, the proposed approach and the results could be used by researchers and designers especially in the early stages of a design process in which all involved bodies face the lack of time, information and tools for evaluation of a variety of systems.

A multi-level analytical approach for detection and visualization of intracellular NO production and nitrosation events using diaminofluoresceins

Diaminofluoresceins are widely used probes for detection and intracellular localization of NO formation in cultured/isolated cells and intact tissues. The fluorinated derivative, 4-amino-5-methylamino-2′,7′-difluorofluorescein (DAF-FM), has gained increasing popularity in recent years due to its improved NO-sensitivity, pH-stability, and resistance to photo-bleaching compared to the first-generation compound, DAF-2. Detection of NO production by either reagent relies on conversion of the parent compound into a fluorescent triazole, DAF-FM-T and DAF-2-T, respectively. While this reaction is specific for NO and/or reactive nitrosating species, it is also affected by the presence of oxidants/antioxidants. Moreover, the reaction with other molecules can lead to the formation of fluorescent products other than the expected triazole. Thus additional controls and structural confirmation of the reaction products are essential. Using human red blood cells as an exemplary cellular system we here describe robust protocols for the analysis of intracellular DAF-FM-T formation using an array of fluorescence-based methods (laser-scanning fluorescence microscopy, flow cytometry and fluorimetry) and analytical separation techniques (reversed-phase HPLC and LC-MS/MS). When used in combination, these assays afford unequivocal identification of the fluorescent signal as being derived from NO and are applicable to most other cellular systems without or with only minor modifications.

An analytical method for capacity dimensioning of WCDMA with high speed wireless link

Capacity dimensioning is one of the key problems in wireless network planning. Analytical and simulation methods are usually used to pursue the accurate capacity dimensioning of wireless network. In this paper, an analytical capacity dimensioning method for WCDMA with high speed wireless link is proposed based on the analysis on relations among system performance and high speed wireless transmission technologies, such as H-ARQ, AMC and fast scheduling. It evaluates system capacity in closed-form expressions from link level and system level. Numerical results show that the proposed method can calculate link level and system level capacity for WCDMA system with HSDPA and HSUPA.

Analytical and numerical solutions describing the inward solidification of a binary melt

We present a mathematical model describing the inward solidification of a slab, a circular cylinder and a sphere of binary melt kept below its equilibrium freezing temperature. The thermal and physical properties of the melt and solid are assumed to be identical. An asymptotic method, valid in the limit of large Stefan number is used to decompose the moving boundary problem for a pure substance into a hierarchy of fixed-domain diffusion problems. Approximate, analytical solutions are derived for the inward solidification of a slab and a sphere of a binary melt which are compared with numerical solutions of the unapproximated system. The solutions are found to agree within the appropriate asymptotic regime of large Stefan number and small time. Numerical solutions are used to demonstrate the dependence of the solidification process upon the level of impurity and other parameters. We conclude with a discussion of the solutions obtained, their stability and possible extensions and refinements of our study.

Proposal of a floating mechanism based on magnetic levitation method toward EEG-driven robotic system

We discussed a floating mechanism based on quasi-magnetic levitation method that can be attached at the endpoint of a robot arm in order to construct a novel redundant robot arm for producing compliant motions. The floating mechanism can be composed of magnets and a constraint mechanism such that the repelling force of the magnets floats the endpoint part of the mechanism stable for the guided motions. The analytical and experimental results show that the proposed floating mechanism can produce stable floating motions with small inertia and viscosity. The results also show that the proposed mechanism can detect small force applied to the endpoint part because the friction force of the mechanism is very small.

Versatile microanalytical system with porous polypropylene capillary membrane for calibration gas generation and trace gaseous pollutants sampling applied to the analysis of formaldehyde, formic acid, acetic acid and ammonia in outdoor air

The analytical determination of atmospheric pollutants still presents challenges due to the low-level concentrations (frequently in the mu g m(-3) range) and their variations with sampling site and time In this work a capillary membrane diffusion scrubber (CMDS) was scaled down to match with capillary electrophoresis (CE) a quick separation technique that requires nothing more than some nanoliters of sample and when combined with capacitively coupled contactless conductometric detection (C(4)D) is particularly favorable for ionic species that do not absorb in the UV-vis region like the target analytes formaldehyde formic acid acetic acid and ammonium The CMDS was coaxially assembled inside a PTFE tube and fed with acceptor phase (deionized water for species with a high Henry s constant such as formaldehyde and carboxylic acids or acidic solution for ammonia sampling with equilibrium displacement to the non-volatile ammonium ion) at a low flow rate (8 3 nLs(-1)) while the sample was aspirated through the annular gap of the concentric tubes at 25 mLs(-1) A second unit in all similar to the CMDS was operated as a capillary membrane diffusion emitter (CMDE) generating a gas flow with know concentrations of ammonia for the evaluation of the CMDS The fluids of the system were driven with inexpensive aquarium air pumps and the collected samples were stored in vials cooled by a Peltier element Complete protocols were developed for the analysis in air of NH(3) CH(3)COOH HCOOH and with a derivatization setup CH(2)O by associating the CMDS collection with the determination by CE-C(4)D The ammonia concentrations obtained by electrophoresis were checked against the reference spectrophotometric method based on Berthelot s reaction Sensitivity enhancements of this reference method were achieved by using a modified Berthelot reaction solenoid micro-pumps for liquid propulsion and a long optical path cell based on a liquid core waveguide (LCW) All techniques and methods of this work are in line with the green analytical chemistry trends (C) 2010 Elsevier B V All rights reserved

Peat as a natural solid-phase for copper preconcentration and determination in a multicommuted flow system coupled to flame atomic absorption spectrometry

The physical and chemical characteristics of peat were assessed through measurement of pH, percentage of organic matter, cationic exchange capacity (CEC), elemental analysis, infrared spectroscopy and quantitative analysis of metals by ICP OES. Despite the material showed to be very acid in view of the percentage of organic matter, its CEC was significant, showing potential for retention of metal ions. This characteristic was exploited by coupling a peat mini-column to a flow system based on the multicommutation approach for the in-line copper concentration prior to flame atomic absorption spectrometric determination. Cu(II) ions were adsorbed at pH 4.5 and eluted with 0.50 mol L(-1) HNO(3). The influence of chemical and hydrodynamic parameters, such as sample pH, buffer concentration, eluent type and concentration, sample flow-rate and preconcentration time were investigated. Under the optimized conditions, a linear response was observed between 16 and 100 mu g L(-1), with a detection limit estimated as 3 mu g L(-1) at the 99.7% confidence level and an enrichment factor of 16. The relative standard deviation was estimated as 3.3% (n = 20). The mini-column was used for at least 100 sampling cycles without significant variation in the analytical response. Recoveries from copper spiked to lake water or groundwater as well as concentrates used in hemodialysis were in the 97.3-111 % range. The results obtained for copper determination in these samples agreed with those achieved by graphite furnace atomic absorption spectrometry (GFAAS) at the 95% confidence level. (C) 2009 Elsevier B.V. All rights reserved.

A multicommuted flow-system for spectrophotometric determination of tannin exploiting the Cu(I)/BCA complex formation

A flow system exploiting the multicommutation approach is proposed for spectrophotometric determination of tannin in beverages. The procedure is based on the reduction of Cu(II) in the presence of 4,4`-dicarboxy-2,2`-biquinoline, yielding a complex with maximum absorption at 558 nm. Calibration graph was linear (r=0.999) for tannic acid concentrations up to 5.00 mu mol L-1. The detection limit and coefficient of variation were estimated as 10 nmol L-1 (99.7% confidence level) and 1% (1.78 mu mol L-1 tannic acid, n=10), respectively. The sampling rate was 50 determinations per hour. The proposed procedure is more sensitive and selective than the official Folin-Denis method, also minimizing drastically waste generation. Recoveries within 91.8 and 115% were estimated for total tannin determination in tea and wine samples. (C) 2007 Elsevier B.V. All rights reserved.

Automated two-dimensional separation flow system with electrochemical preconcentration, stripping, capillary electrophoresis and contactless conductivity detection for trace metal ion analysis

This paper describes the automation of a fully electrochemical system for preconcentration, cleanup, separation and detection, comprising the hyphenation of a thin layer electrochemical flow cell with CE coupled with contactless conductivity detection (CE-C(4)D). Traces of heavy metal ions were extracted from the pulsed-flowing sample and accumulated on a glassy carbon working electrode by electroreduction for some minutes. Anodic stripping of the accumulated metals was synchronized with hydrodynamic injection into the capillary. The effect of the angle of the slant polished tip of the CE capillary and its orientation against the working electrode in the electrochemical preconcentration (EPC) flow cell and of the accumulation time were studied, aiming at maximum CE-C(4)D signal enhancement. After 6 min of EPC, enhancement factors close to 50 times were obtained for thallium, lead, cadmium and copper ions, and about 16 for zinc ions. Limits of detection below 25 nmol/L were estimated for all target analytes but zinc. A second separation dimension was added to the CE separation capabilities by staircase scanning of the potentiostatic deposition and/or stripping potentials of metal ions, as implemented with the EPC-CE-C(4)D flow system. A matrix exchange between the deposition and stripping steps, highly valuable for sample cleanup, can be straightforwardly programmed with the multi-pumping flow management system. The automated simultaneous determination of the traces of five accumulable heavy metals together with four non-accumulated alkaline and alkaline earth metals in a single run was demonstrated, to highlight the potentiality of the system.