Evaluation and comparison of mammalian subcellular localization prediction methods

Background: Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance. Results: In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER), peroxisome, and lysosome). The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance. Conclusion: No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE dataset and variable performance on individual subcellular localizations was observed. Proteins localized to the secretory pathway were the most difficult to predict, while nuclear and extracellular proteins were predicted with the highest sensitivity.

Addressing the project implementation challenges in the Saudi Arabian power supply industry: an investigative approach towards improving project delivery

For many decades, the Kingdom of Saudi Arabia has been widely known for being a reliable oil exporter. This fact, however, has not exempted it from facing significant domestic energy challenges. One of the most pressing of these challenges involves bridging the widening electricity supply-demand gap where, currently, the demand is growing at a very fast rate. One crucial means to address this challenge is through delivering power supply projects with maximum efficiency. Project delivery delay, however, is not uncommon in this highly capital-intensive industry, indicating electricity supplies are not coping with the demand increases. To provide a deeper insight into the challenges of project implementation and efficient practice, this research adopts a pragmatic approach by triangulating literature, questionnaires and semi-structured interviews. The research was conducted in the Saudi Arabian power supply industry – Western Operating Area. A total of 105 usable questionnaires were collected, and 28 recorded, semi-structured interviews were conducted, analysed and synthesised to produce a conceptual model of what constitutes the project implementation challenges in the investigated industry. This was achieved by conducting a comprehensive ranking analysis applied to all 58 identified and surveyed factors which, according to project practitioners in the investigated industry, contribute to project delay. 28 of these project delay factors were selected as the "most important" ones. Factor Analysis was employed to structure these 28 most important project delay factors into the following meaningful set of 7 project implementation challenges: Saudi Electricity Company's contractual commitments, Saudi Electricity Company's communication and coordination effectiveness, contractors' project planning and project control effectiveness, consultant-related aspects, manpower challenges and material uncertainties, Saudi Electricity Company's tendering system, and lack of project requirements clarity. The study has implications for industry policy in that it provides a coherent assessment of the key project stakeholders' central problems. From this analysis, pragmatic recommendations are proposed that, if enacted, will minimise the significance of the identified problems on future project outcomes, thus helping to ensure the electricity supply-demand gap is diminished.

Heat and mass transfer in membrane distillation used for desalination with slip flow

A theoretical model for the transport phenomena in an air gap membrane distillation is presented. The model is based on the conservation equations for the mass, momentum, energy and species within the feed water solution as well as on the mass and energy balances on the membrane sides. The slip flow occurs due to the hydrophobic properties of the membrane. The slip boundary condition applied on the feed saline solution-membrane interface is taken into consideration showing its effects on process parameters particularly permeate flow, heat transfer coefficient and thermal efficiency. The theoretical model was validated with available experimental data and was found to be in good agreement especially when the slip condition is introduced. Increasing slip length from zero to 200 μm was found to increase the permeate flux and the thermal efficiency by 33% and 1.7% respectively.

Analytical model for active metamaterials with quantum ingredients

We present an analytical model for describing complex dynamics of a hybrid system consisting of resonantly coupled classical resonator and quantum structures. Classical resonators in our model correspond to plasmonic metamaterials of various geometries, as well as other types of nano- and microstructure, the optical responses of which can be described classically. Quantum resonators are represented by atoms or molecules, or their aggregates (for example, quantum dots, carbon nanotubes, dye molecules, polymer or bio-molecules etc), which can be accurately modelled only with the use of the quantum mechanical approach. Our model is based on the set of equations that combines well established density matrix formalism appropriate for quantum systems, coupled with harmonic-oscillator equations ideal for modelling sub-wavelength plasmonic and optical resonators. As a particular example of application of our model, we show that the saturation nonlinearity of carbon nanotubes increases multifold in the resonantly enhanced near field of a metamaterial. In the framework of our model, we discuss the effect of inhomogeneity of the carbon-nanotube layer (bandgap value distribution) on the nonlinearity enhancement. © 2012 IOP Publishing Ltd.

Applications of Nonclassical Logic Methods for Purposes of Knowledge Discovery and Data Mining

* The work is partially supported by Grant no. NIP917 of the Ministry of Science and Education – Republic of Bulgaria.

Solving Fractional Diffusion-Wave Equations Using a New Iterative Method

Mathematics Subject Classification: 26A33, 31B10

An Analog of the Tricomi Problem for a Mixed Type Equation with a Partial Fractional Derivative

Mathematics Subject Classification 2010: 35M10, 35R11, 26A33, 33C05, 33E12, 33C20.

Accurate WKB Approximation for a 1D Problem with Low Regularity

2000 Mathematics Subject Classification: 34L40, 65L10, 65Z05, 81Q20.

Exact Solutions of Nonlocal BVPs for the Multidimensional Heat Equations

MSC 2010: 44A35, 44A45, 44A40, 35K20, 35K05

Crack tip stress study for elastic-perfectly plastic materials with some applications

The problems of plasticity and non-linear fracture mechanics have been generally recognized as the most difficult problems of solid mechanics. The present dissertation is devoted to some problems on the intersection of both plasticity and non-linear fracture mechanics. The crack tip is responsible for the crack growth and therefore is the focus of fracture science. The problem of crack has been studied by an army of outstanding scholars and engineers in this century, but has not, as yet, been solved for many important practical situations. The aim of this investigation is to provide an analytical solution to the problem of plasticity at the crack tip for elastic-perfectly plastic materials and to apply the solution to a classical problem of the mechanics of composite materials.^ In this work, the stresses inside the plastic region near the crack tip in a composite material made of two different elastic-perfectly plastic materials are studied. The problems of an interface crack, a crack impinging an interface at the right angle and at arbitrary angles are examined. The constituent materials are assumed to obey the Huber-Mises yielding condition criterion. The theory of slip lines for plane strain is utilized. For the particular homogeneous case these problems have two solutions: the continuous solution found earlier by Prandtl and modified by Hill and Sokolovsky, and the discontinuous solution found later by Cherepanov. The same type of solutions were discovered in the inhomogeneous problems of the present study. Some reasons to prefer the discontinuous solution are provided. The method is also applied to the analysis of a contact problem and a push-in/pull-out problem to determine the critical load for plasticity in these classical problems of the mechanics of composite materials.^ The results of this dissertation published in three journal articles (two of which are under revision) will also be presented in the Invited Lecture at the 7$\rm\sp{th}$ International Conference on Plasticity (Cancun, Mexico, January 1999). ^

Development of a medium-capacity guideway transit planning guide

Rapid population increase and booming economic growth have caused a significant escalation in car ownership in many cities, leading to additional or, multiple traffic problems on congested roadways. The increase of automobiles is generating a significant amount of congestion and pollution in many cities. It has become necessary to find a solution to the ever worsening traffic problems in our cities. Building more roadways is nearly impossible due to the limitations of right-of-way in cities. Studies have shown that guideway transit could provide effective transportation and could stimulate land development. The Medium-Capacity Guideway Transit (MCGT) is one of the alternatives to solve this problem. The objective of this research was to better understand the characteristics of MCGT systems, to investigate the existing MCGT systems around the world and determine the main factors behind the planning of successful systems, and to develop a MCGT planning guide. The factors utilized in this study were determined and were analyzed using Excel. A MCGT Planning Guide was developed using Microsoft Visual Basic. ^ A MCGT was defined as a transit system whose capacity can carry up to 20,000 passengers per hour per direction (pphpd). The results shown that Light Rail Transit (LRT) is favored when peak hour demand is less than 13,000 pphpd. Automated People Mover (APM) is favored when the peak hour demand is more than 18,000 pphpd. APM systems could save up to three times the waiting time cost compared to that of the LRT. If comfort and convenience are important, then using an APM does make sense. However, if cost is the critical factor, then LRT will make more sense because it is reasonable service at a reasonable price. If travel time and safety (accident/crush) costs were included in calculating life-cycle “total” costs, the capital cost advantage of LRT disappeared and APM could become very competitive. The results also included a range of cost-performance criteria for MCGT systems that help planners, engineers, and decision-makers to select the most feasible system for their respective areas. ^

The role of overseas Chinese investment in the emerging countries of Southeast and East Asia: A Confucian model of the foreign direct investment decision-making process using factors unconsidered in the West

The purpose of this study was to gain a better understanding of the foreign direct investment location decision making process through the examination of non-Western investors and their investment strategies in non-traditional markets. This was accomplished through in-depth personal interviews with 50 Overseas Chinese business owners and executives in several different industries from Hong Kong, Singapore, Taiwan, Malaysia, and Thailand about 97 separate investment projects in Southeast and East Asia, including The Philippines, Malaysia, Hong Kong, Singapore, Vietnam, India, Pakistan, South Korea, Australia, Indonesia, Cambodia, Thailand, Burma, Taiwan, and Mainland China.^ Traditional factors utilized in Western models of the foreign direct investment decision making process are reviewed, as well as literature on Asian management systems and the current state of business practices in emerging countries of Southeast and East Asia. Because of the lack of institutionalization in these markets and the strong influences of Confucian and patriarchal value systems on the Overseas Chinese, it was suspected that while some aspects of Western rational economic models of foreign direct investment are utilized, these models are insufficient in this context, and thus are not fully generalizable to the unique conditions of the Overseas Chinese business network in the region without further modification.^ Thus, other factors based on a Confucian value system need to be integrated into these models. Results from the analysis of structured interviews suggest Overseas Chinese businesses rely more heavily on their network and traditional Confucian values than rational economic factors when making their foreign direct investment location decisions in emerging countries in Asia. This effect is moderated by the firm's industry and the age of the firm's owners. ^

Learning Data-Driven Models of Non-Verbal Behaviors for Building Rapport Using an Intelligent Virtual Agent

There is a growing societal need to address the increasing prevalence of behavioral health issues, such as obesity, alcohol or drug use, and general lack of treatment adherence for a variety of health problems. The statistics, worldwide and in the USA, are daunting. Excessive alcohol use is the third leading preventable cause of death in the United States (with 79,000 deaths annually), and is responsible for a wide range of health and social problems. On the positive side though, these behavioral health issues (and associated possible diseases) can often be prevented with relatively simple lifestyle changes, such as losing weight with a diet and/or physical exercise, or learning how to reduce alcohol consumption. Medicine has therefore started to move toward finding ways of preventively promoting wellness, rather than solely treating already established illness. Evidence-based patient-centered Brief Motivational Interviewing (BMI) interven- tions have been found particularly effective in helping people find intrinsic motivation to change problem behaviors after short counseling sessions, and to maintain healthy lifestyles over the long-term. Lack of locally available personnel well-trained in BMI, however, often limits access to successful interventions for people in need. To fill this accessibility gap, Computer-Based Interventions (CBIs) have started to emerge. Success of the CBIs, however, critically relies on insuring engagement and retention of CBI users so that they remain motivated to use these systems and come back to use them over the long term as necessary. Because of their text-only interfaces, current CBIs can therefore only express limited empathy and rapport, which are the most important factors of health interventions. Fortunately, in the last decade, computer science research has progressed in the design of simulated human characters with anthropomorphic communicative abilities. Virtual characters interact using humans’ innate communication modalities, such as facial expressions, body language, speech, and natural language understanding. By advancing research in Artificial Intelligence (AI), we can improve the ability of artificial agents to help us solve CBI problems. To facilitate successful communication and social interaction between artificial agents and human partners, it is essential that aspects of human social behavior, especially empathy and rapport, be considered when designing human-computer interfaces. Hence, the goal of the present dissertation is to provide a computational model of rapport to enhance an artificial agent’s social behavior, and to provide an experimental tool for the psychological theories shaping the model. Parts of this thesis were already published in [LYL+12, AYL12, AL13, ALYR13, LAYR13, YALR13, ALY14].

A teoria de Callista Roy, a nanda-i e o cuidado ao paciente prostatectomizado

Trata-se de um estudo descritivo de caso clínico, com abordagem qualitativa, o qual possui como objetivo estabelecer relações entre os diagnósticos de enfermagem da NANDA-I e os problemas de adaptação segundo o Modelo Teórico de Roy em um paciente prostatectomizado. A coleta de dados ocorreu em um hospital universitário localizado na cidade de Natal-RN, no mês de janeiro de 2011, por meio de um roteiro de entrevista e exame físico. Os diagnósticos que apresentaram relações entre a NANDA-I e o Modelo de Roy foram: dor, ansiedade, constipação, sono, atividade, volume de líquido e infecção. Conclui-se que grande parte dos problemas adaptativos segundo o Modelo de Roy, manifestados pelos pacientes no pós-operatório de prostatectomia, possuem semelhança com os diagnósticos da NANDA-I

Properties of a composite material with mixed imperfect contact conditions

We present an analytical solution of a mixed boundary value problem for an unbounded 2D doubly periodic domain which is a model of a composite material with mixed imperfect interface conditions. We find the effective conductivity of the composite material with mixed imperfect interface conditions, and also give numerical analysis of several of their properties such as temperature and flux.