Solving Maximum Clique Problem for Protein Structure Similarity

Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK.

Manufacturing and assembly automation by integrated metrology systems for aircraft wing fabrication

Discrepancies of materials, tools, and factory environments, as well as human intervention, make variation an integral part of the manufacturing process of any component. In particular, the assembly of large volume, aerospace parts is an area where significant levels of form and dimensional variation are encountered. Corrective actions can usually be taken to reduce the defects, when the sources and levels of variation are known. For the unknown dimensional and form variations, a tolerancing strategy is typically put in place in order to minimize the effects of production inconsistencies related to geometric dimensions. This generates a challenging problem for the automation of the corresponding manufacturing and assembly processes. Metrology is becoming a major contributor to being able to predict, in real time, the automated assembly problems related to the dimensional variation of parts and assemblies. This is done by continuously measuring dimensions and coordinate points, focusing on the product's key characteristics. In this paper, a number of metrology focused activities for large-volume aerospace products, including their implementation and application in the automation of manufacturing and assembly processes, are reviewed. This is done by using a case study approach within the assembly of large-volume aircraft wing structures.

Cognitive competence and life course change in multi-problem adolescents

The dissertation reports on two studies. The purpose of Study I was to develop and evaluate a measure of cognitive competence (the Critical Problem Solving Skills Scale – Qualitative Extension) using Relational Data Analysis (RDA) with a multi-ethnic, adolescent sample. My study builds on previous work that has been conducted to provide evidence for the reliability and validity of the RDA framework in evaluating youth development programs (Kurtines et al., 2008). Inter-coder percent agreement among the TOC and TCC coders for each of the category levels was moderate to high, with a range of .76 to .94. The Fleiss' kappa across all category levels was from substantial agreement to almost perfect agreement, with a range of .72 to .91. The correlation between the TOC and the TCC demonstrated medium to high correlation, with a range of r(40)=.68, p<.001 to r(40)=.79, p<.001. Study II reports an investigation of a positive youth development program using an Outcome Mediation Cascade (OMC) evaluation model, an integrated model for evaluating the empirical intersection between intervention and developmental processes. The Changing Lives Program (CLP) is a community supported positive youth development intervention implemented in a practice setting as a selective/indicated program for multi-ethnic, multi-problem at risk youth in urban alternative high schools in the Miami Dade County Public Schools (M-DCPS). The 259 participants for this study were drawn from the CLP's archival data file. The study used a structural equation modeling approach to construct and evaluate the hypothesized model. Findings indicated that the hypothesized model fit the data (χ2 (7) = 5.651, p = .83; RMSEA = .00; CFI = 1.00; WRMR = .319). My study built on previous research using the OMC evaluation model (Eichas, 2010), and the findings are consistent with the hypothesis that in addition to having effects on targeted positive outcomes, PYD interventions are likely to have progressive cascading effects on untargeted problem outcomes that operate through effects on positive outcomes.

Subject -centered and problem -based approaches to teaching clinical competence in physical therapy

Physical therapy students must apply the relevant information learned in their academic and clinical experience to problem solve in treating patients. I compared the clinical cognitive competence in patient care of second-year masters students enrolled in two different curricular programs: modified problem-based (M P-B; n = 27) and subject-centered (S-C; n = 41). Main features of S-C learning include lecture and demonstration as the major teaching strategies and no exposure to patients or problem solving learning until the sciences (knowledge) have been taught. Comparatively, main features of M P-B learning include case study in small student groups as the main teaching strategy, early and frequent exposure to patients, and knowledge and problem solving skills learned together for each specific case. Basic and clinical orthopedic knowledge was measured with a written test with open-ended items. Problem solving skills were measured with a written case study patient problem test yielding three subscores: assessment, problem identification, and treatment planning. ^ Results indicated that among the demographic and educational characteristics analyzed, there was a significant difference between groups on ethnicity, bachelor degree type, admission GPA, and current GPA, but there was no significant difference on gender, age, possession of a physical therapy assistant license, and GRE score. In addition, the M P-B group achieved a significantly higher adjusted mean score on the orthopedic knowledge test after controlling for GRE scores. The S-C group achieved a significantly higher adjusted mean total score and treatment management subscore on the case study test after controlling for orthopedic knowledge test scores. These findings did not support their respective research hypotheses. There was no significant difference between groups on the assessment and problem identification subscores of the case study test. The integrated M P-B approach promoted superior retention of basic and clinical science knowledge. The results on problem solving skills were mixed. The S-C approach facilitated superior treatment planning skills, but equivalent patient assessment and problem identification skills by emphasizing all equally and exposing the students to more patients with a wider variety of orthopedic physical therapy needs than in the M P-B approach. ^

Presenting SAPUSS: solving aerosol problem by using synergistic strategies in Barcelona, Spain

This paper presents the summary of the key objectives, instrumentation and logistic details, goals, and initial scientific findings of the European Marie Curie Action SAPUSS project carried out in the western Mediterranean Basin (WMB) during September-October in autumn 2010. The key SAPUSS objective is to deduce aerosol source characteristics and to understand the atmospheric processes responsible for their generations and transformations - both horizontally and vertically in the Mediterranean urban environment. In order to achieve so, the unique approach of SAPUSS is the concurrent measurements of aerosols with multiple techniques occurring simultaneously in six monitoring sites around the city of Barcelona (NE Spain): a main road traffic site, two urban background sites, a regional background site and two urban tower sites (150 m and 545 m above sea level, 150 m and 80 m above ground, respectively). SAPUSS allows us to advance our knowledge sensibly of the atmospheric chemistry and physics of the urban Mediterranean environment. This is well achieved only because of both the three dimensional spatial scale and the high sampling time resolution used. During SAPUSS different meteorological regimes were encountered, including warm Saharan, cold Atlantic, wet European and stagnant regional ones. The different meteorology of such regimes is herein described. Additionally, we report the trends of the parameters regulated by air quality purposes (both gaseous and aerosol mass concentrations); and we also compare the six monitoring sites. High levels of traffic-related gaseous pollutants were measured at the urban ground level monitoring sites, whereas layers of tropospheric ozone were recorded at tower levels. Particularly, tower level night-time average ozone concentrations (80 +/- 25 mu g m(-3)) were up to double compared to ground level ones. The examination of the vertical profiles clearly shows the predominant influence of NOx on ozone concentrations, and a source of ozone aloft. Analysis of the particulate matter (PM) mass concentrations shows an enhancement of coarse particles (PM2.5-10) at the urban ground level (+64 %, average 11.7 mu g m(-3)) but of fine ones (PM1) at urban tower level (+28 %, average 14.4 mu g m(-3)). These results show complex dynamics of the size-resolved PM mass at both horizontal and vertical levels of the study area. Preliminary modelling findings reveal an underestimation of the fine accumulation aerosols. In summary, this paper lays the foundation of SAPUSS, an integrated study of relevance to many other similar urban Mediterranean coastal environment sites.

Integrated Optimal Power Flow for Distribution Networks in Local and Urban Scales

This paper develops an integrated optimal power flow (OPF) tool for distribution networks in two spatial scales. In the local scale, the distribution network, the natural gas network, and the heat system are coordinated as a microgrid. In the urban scale, the impact of natural gas network is considered as constraints for the distribution network operation. The proposed approach incorporates unbalance three-phase electrical systems, natural gas systems, and combined cooling, heating, and power systems. The interactions among the above three energy systems are described by energy hub model combined with components capacity constraints. In order to efficiently accommodate the nonlinear constraint optimization problem, particle swarm optimization algorithm is employed to set the control variables in the OPF problem. Numerical studies indicate that by using the OPF method, the distribution network can be economically operated. Also, the tie-line power can be effectively managed.

Fabrication, Optical Analysis and Photonic Applications of Certain Metallic Nanostructure-Integrated Dye Doped Polymer Optical Fibers” submitted by Ms. Suneetha Sebastian

Polymer Optical Fibers have occupied historically a place for large core flexible fibers operating in short distances. In addition to their practical passive application in short-haul communication they constitute a potential research field as active devices with organic dopants. Organic dyes are preferred as dopants over organic semiconductors due to their higher optical cross section. Thus organic dyes as gain media in a polymer fiber is used to develop efficient and narrow laser sources with a tunability throughout the visible region or optical amplifier with high gain. Dyes incorporated in fiber form has added advantage over other solid state forms such as films since the pump power required to excite the molecules in the core of the fiber is less thereby utilising the pump power effectively. In 1987, Muto et.al investigated a dye doped step index polymer fiber laser. Afterwards, numerous researches have been carried out in this area demonstrating laser emission from step index, graded index and hollow optical fibers incorporating various dyes. Among various dyes, Rhodamine6G is the most widely and commonly used laser dye for the last four decades. Rhodamine6G has many desirable optical properties which make it preferable over other organic dyes such as Coumarin, Nile Blue, Curcumin etc. The research focus on the implementation of efficient fiber lasers and amplifiers for short fiber distances. Developing efficient plastic lasers with electrical pumping can be a new proposal in this field which demands lowest possible threshold pump energy of the gain medium in the cavity as an important parameter. One way of improving the efficiency of the lasers, through low threshold pump energy, is by modifying the gain of the amplifiers in the resonator/cavity. Success in the field of Radiative Decay Engineering can pave way to this problem. Laser gain media consisting of dye-nanoparticle composites can improve the efficiency by lowering the lasing threshold and enhancing the photostability. The electric field confined near the surface of metal nanoparticles due to Localized Surface Plasmon Resonance can be very effective for the excitation of active centers to impart high optical gain for lasing. Since the Surface Plasmon Resonance of nanoparticles of gold and silver lies in the visible range, it can affect the spectral emission characteristics of organic dyes such as Rhodamine6G through plasmon field generated by the particles. The change in emission of the dye placed near metal nanoparticles depend on plasmon field strength which in turn depends on the type of metal, size of nanoparticle, surface modification of the particle and the wavelength of incident light. Progress in fabrication of different types of nanostructures lead to the advent of nanospheres, nanoalloys, core-shell and nanowires to name a few. The thesis deals with the fabrication and characterisation of polymer optical fibers with various metallic and bimetallic nanostructures incorporated in the gain media for efficient fiber lasers with low threshold and improved photostability.

Integrated Reporting in OMXS30 companies - An Analysis of Human Capital Disclosures

Background and Problem: Sustainability reporting is a growing interest in today’s organizations and it is essential to report on non-financial matters. Many of the existing frameworks have been criticized for being used only of symbolical reasons which is why the concept of integrated reporting and the <IR> framework have been developed. One of the cornerstones in the <IR> framework is human capital which is one of the most valuable assets in an organization. Traditionally, employee costs have only been treated as an expense and there have been limited disclosures in corporate reports. In the current business world it is instead seen as an investment in human resources. Since previous studies have shown an increase of human capital disclosures when corporate reports become integrated, integrated reporting might be the solution to this problem. Purpose: The purpose of this study is to examine if there are differences in human capital disclosures between integrated reports and separate annual and sustainability reports in companies listed at OMXS30. Delimitations: This study’s empirical examination is limited to include the companies listed at Stockholm OMX30. Only corporate reports issued for the year 2014 are treated. Methodology: For this study a self-constructed disclosure scoreboard with human capital- related items has been used to collect data from the companies’ corporate reports. Also additional information beyond the pre-determined items has been collected to extend the data collection. Empirical Results and Conclusion: The results show that human capital seems to be a subject that is relatively little reported about. The integrated reporting companies do not disclose more information compared to non-integrated reporting companies. However, the results show that integrated reporting companies seem to have a more future-oriented focus and that the disclosures are more dispersed throughout the reports. It can be concluded that company sector and size do not affect the amount or type of information. 

Strategic Information Disclosure through Integrated Reporting : A study on OMXS30-listed companies’ compliance with the <IR> Framework content element Strategy and Resource Allocation

Background and problem – As a result of financial crises and the realization of a broader stakeholder network, recent decades have seen an increase in stakeholder demand for non- financial information in corporate reporting. This has led to a situation of information overload where separate financial and sustainability reports have developed in length and complexity interdependent of each other. Integrated reporting has been presented as a solution to this problematic situation. The question is whether the corporate world believe this to be the solution and if the development of corporate reporting is heading in this direction. Purpose - This thesis aims to examine and assess to what extent companies listed on the OMX Stockholm 30 (OMXS30), as per 2016-02-28, comply with the Strategic content element of the <IR> Framework and how this disclosure has developed since the framework’s pilot project and official release by using a self-constructed disclosure index based on its specific items. Methodology – The purpose was fulfilled through an analysis of 104 annual reports comprising 26 companies during the period of 2011-2014. The annual reports were assessed using a self-constructed disclosure index based on the <IR> Framework content element Strategy and Resource Allocation, where one point was given for each disclosed item. Analysis and conclusions – The study found that the OMXS30-listed companies to a large extent complies with the strategic content element of the <IR> Framework and that this compliance has seen a steady growth throughout the researched time span. There is still room for improvement however with a total average framework compliance of 84% for 2014. Although many items are being reported on, there are indications that companies generally miss out on the core values of Integrated reporting. 

Security through Obscurity: Layout Obfuscation of Digital Integrated Circuits using Don't Care Conditions

Contemporary integrated circuits are designed and manufactured in a globalized environment leading to concerns of piracy, overproduction and counterfeiting. One class of techniques to combat these threats is circuit obfuscation which seeks to modify the gate-level (or structural) description of a circuit without affecting its functionality in order to increase the complexity and cost of reverse engineering. Most of the existing circuit obfuscation methods are based on the insertion of additional logic (called “key gates”) or camouflaging existing gates in order to make it difficult for a malicious user to get the complete layout information without extensive computations to determine key-gate values. However, when the netlist or the circuit layout, although camouflaged, is available to the attacker, he/she can use advanced logic analysis and circuit simulation tools and Boolean SAT solvers to reveal the unknown gate-level information without exhaustively trying all the input vectors, thus bringing down the complexity of reverse engineering. To counter this problem, some ‘provably secure’ logic encryption algorithms that emphasize methodical selection of camouflaged gates have been proposed previously in literature [1,2,3]. The contribution of this paper is the creation and simulation of a new layout obfuscation method that uses don't care conditions. We also present proof-of-concept of a new functional or logic obfuscation technique that not only conceals, but modifies the circuit functionality in addition to the gate-level description, and can be implemented automatically during the design process. Our layout obfuscation technique utilizes don’t care conditions (namely, Observability and Satisfiability Don’t Cares) inherent in the circuit to camouflage selected gates and modify sub-circuit functionality while meeting the overall circuit specification. Here, camouflaging or obfuscating a gate means replacing the candidate gate by a 4X1 Multiplexer which can be configured to perform all possible 2-input/ 1-output functions as proposed by Bao et al. [4]. It is important to emphasize that our approach not only obfuscates but alters sub-circuit level functionality in an attempt to make IP piracy difficult. The choice of gates to obfuscate determines the effort required to reverse engineer or brute force the design. As such, we propose a method of camouflaged gate selection based on the intersection of output logic cones. By choosing these candidate gates methodically, the complexity of reverse engineering can be made exponential, thus making it computationally very expensive to determine the true circuit functionality. We propose several heuristic algorithms to maximize the RE complexity based on don’t care based obfuscation and methodical gate selection. Thus, the goal of protecting the design IP from malicious end-users is achieved. It also makes it significantly harder for rogue elements in the supply chain to use, copy or replicate the same design with a different logic. We analyze the reverse engineering complexity by applying our obfuscation algorithm on ISCAS-85 benchmarks. Our experimental results indicate that significant reverse engineering complexity can be achieved at minimal design overhead (average area overhead for the proposed layout obfuscation methods is 5.51% and average delay overhead is about 7.732%). We discuss the strengths and limitations of our approach and suggest directions that may lead to improved logic encryption algorithms in the future. References: [1] R. Chakraborty and S. Bhunia, “HARPOON: An Obfuscation-Based SoC Design Methodology for Hardware Protection,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 28, no. 10, pp. 1493–1502, 2009. [2] J. A. Roy, F. Koushanfar, and I. L. Markov, “EPIC: Ending Piracy of Integrated Circuits,” in 2008 Design, Automation and Test in Europe, 2008, pp. 1069–1074. [3] J. Rajendran, M. Sam, O. Sinanoglu, and R. Karri, “Security Analysis of Integrated Circuit Camouflaging,” ACM Conference on Computer Communications and Security, 2013. [4] Bao Liu, Wang, B., "Embedded reconfigurable logic for ASIC design obfuscation against supply chain attacks,"Design, Automation and Test in Europe Conference and Exhibition (DATE), 2014 , vol., no., pp.1,6, 24-28 March 2014.

Cognitive Competence and Life Course Change in Multi-Problem Adolescents

The dissertation reports on two studies. The purpose of Study I was to develop and evaluate a measure of cognitive competence (the Critical Problem Solving Skills Scale – Qualitative Extension) using Relational Data Analysis (RDA) with a multi-ethnic, adolescent sample. My study builds on previous work that has been conducted to provide evidence for the reliability and validity of the RDA framework in evaluating youth development programs (Kurtines et al., 2008). Inter-coder percent agreement among the TOC and TCC coders for each of the category levels was moderate to high, with a range of .76 to .94. The Fleiss’ kappa across all category levels was from substantial agreement to almost perfect agreement, with a range of .72 to .91. The correlation between the TOC and the TCC demonstrated medium to high correlation, with a range of r(40)=.68, p Study II reports an investigation of a positive youth development program using an Outcome Mediation Cascade (OMC) evaluation model, an integrated model for evaluating the empirical intersection between intervention and developmental processes. The Changing Lives Program (CLP) is a community supported positive youth development intervention implemented in a practice setting as a selective/indicated program for multi-ethnic, multi-problem at risk youth in urban alternative high schools in the Miami Dade County Public Schools (M-DCPS). The 259 participants for this study were drawn from the CLP’s archival data file. The study used a structural equation modeling approach to construct and evaluate the hypothesized model. Findings indicated that the hypothesized model fit the data (χ2 (7) = 5.651, p = .83; RMSEA = .00; CFI = 1.00; WRMR = .319). My study built on previous research using the OMC evaluation model (Eichas, 2010), and the findings are consistent with the hypothesis that in addition to having effects on targeted positive outcomes, PYD interventions are likely to have progressive cascading effects on untargeted problem outcomes that operate through effects on positive outcomes.

Exact and heuristic algorithms for the integrated planning of multi-energy systems

The aim of this thesis is to present exact and heuristic algorithms for the integrated planning of multi-energy systems. The idea is to disaggregate the energy system, starting first with its core the Central Energy System, and then to proceed towards the Decentral part. Therefore, a mathematical model for the generation expansion operations to optimize the performance of a Central Energy System system is first proposed. To ensure that the proposed generation operations are compatible with the network, some extensions of the existing network are considered as well. All these decisions are evaluated both from an economic viewpoint and from an environmental perspective, as specific constraints related to greenhouse gases emissions are imposed in the formulation. Then, the thesis presents an optimization model for solar organic Rankine cycle in the context of transactive energy trading. In this study, the impact that this technology can have on the peer-to-peer trading application in renewable based community microgrids is inspected. Here the consumer becomes a prosumer and engages actively in virtual trading with other prosumers at the distribution system level. Moreover, there is an investigation of how different technological parameters of the solar Organic Rankine Cycle may affect the final solution. Finally, the thesis introduces a tactical optimization model for the maintenance operations’ scheduling phase of a Combined Heat and Power plant. Specifically, two types of cleaning operations are considered, i.e., online cleaning and offline cleaning. Furthermore, a piecewise linear representation of the electric efficiency variation curve is included. Given the challenge of solving the tactical management model, a heuristic algorithm is proposed. The heuristic works by solving the daily operational production scheduling problem, based on the final consumer’s demand and on the electricity prices. The aggregate information from the operational problem is used to derive maintenance decisions at a tactical level.

Design and management of a supply chain: a joint location-inventory problem under uncertainty (Part B)

In recent years, global supply chains have increasingly suffered from reliability issues due to various external and difficult to-manage events. The following paper aims to build an integrated approach for the design of a Supply Chain under the risk of disruption and demand fluctuation. The study is divided in two parts: a mathematical optimization model, to identify the optimal design and assignments customer-facility, and a discrete-events simulation of the resulting network. The first one describes a model in which plant location decisions are influenced by variables such as distance to customers, investments needed to open plants and centralization phenomena that help contain the risk of demand variability (Risk Pooling). The entire model has been built with a proactive approach to manage the risk of disruptions assigning to each customer two types of open facilities: one that will serve it under normal conditions and a back-up facility, which comes into operation when the main facility has failed. The study is conducted on a relatively small number of instances due to the computational complexity, a matheuristic approach can be found in part A of the paper to evaluate the problem with a larger set of players. Once the network is built, a discrete events Supply Chain simulation (SCS) has been implemented to analyze the stock flow within the facilities warehouses, the actual impact of disruptions and the role of the back-up facilities which suffer a great stress on their inventory due to a large increase in demand caused by the disruptions. Therefore, simulation follows a reactive approach, in which customers are redistributed among facilities according to the interruptions that may occur in the system and to the assignments deriving from the design model. Lastly, the most important results of the study will be reported, analyzing the role of lead time in a reactive approach for the occurrence of disruptions and comparing the two models in terms of costs.

Integrated Proteomics Identified Up-regulated Focal Adhesion-mediated Proteins In Human Squamous Cell Carcinoma In An Orthotopic Murine Model.

Understanding the molecular mechanisms of oral carcinogenesis will yield important advances in diagnostics, prognostics, effective treatment, and outcome of oral cancer. Hence, in this study we have investigated the proteomic and peptidomic profiles by combining an orthotopic murine model of oral squamous cell carcinoma (OSCC), mass spectrometry-based proteomics and biological network analysis. Our results indicated the up-regulation of proteins involved in actin cytoskeleton organization and cell-cell junction assembly events and their expression was validated in human OSCC tissues. In addition, the functional relevance of talin-1 in OSCC adhesion, migration and invasion was demonstrated. Taken together, this study identified specific processes deregulated in oral cancer and provided novel refined OSCC-targeting molecules.

Ihwg-μnir: A Miniaturised Near-infrared Gas Sensor Based On Substrate-integrated Hollow Waveguides Coupled To A Micro-nir-spectrophotometer.

A miniaturised gas analyser is described and evaluated based on the use of a substrate-integrated hollow waveguide (iHWG) coupled to a microsized near-infrared spectrophotometer comprising a linear variable filter and an array of InGaAs detectors. This gas sensing system was applied to analyse surrogate samples of natural fuel gas containing methane, ethane, propane and butane, quantified by using multivariate regression models based on partial least square (PLS) algorithms and Savitzky-Golay 1(st) derivative data preprocessing. The external validation of the obtained models reveals root mean square errors of prediction of 0.37, 0.36, 0.67 and 0.37% (v/v), for methane, ethane, propane and butane, respectively. The developed sensing system provides particularly rapid response times upon composition changes of the gaseous sample (approximately 2 s) due the minute volume of the iHWG-based measurement cell. The sensing system developed in this study is fully portable with a hand-held sized analyser footprint, and thus ideally suited for field analysis. Last but not least, the obtained results corroborate the potential of NIR-iHWG analysers for monitoring the quality of natural gas and petrochemical gaseous products.