Pathway Semantics: An Algebraic Data Driven Algorithm to Generate Hypotheses about Molecular Patterns Underlying Disease Progression

The overarching goal of the Pathway Semantics Algorithm (PSA) is to improve the in silico identification of clinically useful hypotheses about molecular patterns in disease progression. By framing biomedical questions within a variety of matrix representations, PSA has the flexibility to analyze combined quantitative and qualitative data over a wide range of stratifications. The resulting hypothetical answers can then move to in vitro and in vivo verification, research assay optimization, clinical validation, and commercialization. Herein PSA is shown to generate novel hypotheses about the significant biological pathways in two disease domains: shock / trauma and hemophilia A, and validated experimentally in the latter. The PSA matrix algebra approach identified differential molecular patterns in biological networks over time and outcome that would not be easily found through direct assays, literature or database searches. In this dissertation, Chapter 1 provides a broad overview of the background and motivation for the study, followed by Chapter 2 with a literature review of relevant computational methods. Chapters 3 and 4 describe PSA for node and edge analysis respectively, and apply the method to disease progression in shock / trauma. Chapter 5 demonstrates the application of PSA to hemophilia A and the validation with experimental results. The work is summarized in Chapter 6, followed by extensive references and an Appendix with additional material.

Reversible Urban Entities. Improving public-to-private continuity.

The aim of this paper is to call into question those typologies conventionally used in developing the post-industrial urban fabric (streets, cityblocks, slabs, etc.), often catering to urban designs based on speculative interests and completely overlooking community interests. By defining the concepts of ?postpublic space? and ?reversible urban entities? and illustrating them with an exemplary case of Spanish residential architecture from the 1960s, we establish one possible way of tackling contemporary urban-residential projects. This alternative approach considers the relationship between residential systems and open space systems and promotes the continuity and/or alternation of scales between house and city in an effort to improve the urban quality of life for residents and external users.

Solution of the dual reflection equation for A(n-1)((1)) solid-on-solid model

We obtain a diagonal solution of the dual reflection equation for the elliptic A(n-1)((1)) solid-on-solid model. The isomorphism between the solutions of the reflection equation and its dual is studied. (C) 2004 American Institute of Physics.

Fungible dynamics: There are only two types of entangling multiple-qubit interactions

What interactions are sufficient to simulate arbitrary quantum dynamics in a composite quantum system? It has been shown that all two-body Hamiltonian evolutions can be simulated using any fixed two-body entangling n-qubit Hamiltonian and fast local unitaries. By entangling we mean that every qubit is coupled to every other qubit, if not directly, then indirectly via intermediate qubits. We extend this study to the case where interactions may involve more than two qubits at a time. We find necessary and sufficient conditions for an arbitrary n-qubit Hamiltonian to be dynamically universal, that is, able to simulate any other Hamiltonian acting on n qubits, possibly in an inefficient manner. We prove that an entangling Hamiltonian is dynamically universal if and only if it contains at least one coupling term involving an even number of interacting qubits. For odd entangling Hamiltonians, i.e., Hamiltonians with couplings that involve only an odd number of qubits, we prove that dynamic universality is possible on an encoded set of n-1 logical qubits. We further prove that an odd entangling Hamiltonian can simulate any other odd Hamiltonian and classify the algebras that such Hamiltonians generate. Thus, our results show that up to local unitary operations, there are only two fundamentally different types of entangling Hamiltonian on n qubits. We also demonstrate that, provided the number of qubits directly coupled by the Hamiltonian is bounded above by a constant, our techniques can be made efficient.

Entanglement measure for rank-2 mixed states

We provide an easily computable formula for a bipartite mixed-state entanglement measure. Our formula can be applied to readily calculate the entanglement for any rank-2 mixed state of a bipartite system. We use this formula to provide a tight upper bound for the entanglement of formation for rank-2 states of a qubit and a qudit. We also outline situations where our formula could be applied to study the entanglement properties of complex quantum systems.

Detecting multipartite entanglement

We discuss the problem of determining whether the state of several quantum mechanical subsystems is entangled. As in previous work on two subsystems we introduce a procedure for checking separability that is based on finding state extensions with appropriate properties and may be implemented as a semidefinite program. The main result of this work is to show that there is a series of tests of this kind such that if a multiparty state is entangled this will eventually be detected by one of the tests. The procedure also provides a means of constructing entanglement witnesses that could in principle be measured in order to demonstrate that the state is entangled.

Entanglement and boundary critical phenomena

We investigate boundary critical phenomena from a quantum-information perspective. Bipartite entanglement in the ground state of one-dimensional quantum systems is quantified using the Renyi entropy S-alpha, which includes the von Neumann entropy (alpha -> 1) and the single-copy entanglement (alpha ->infinity) as special cases. We identify the contribution of the boundaries to the Renyi entropy, and show that there is an entanglement loss along boundary renormalization group (RG) flows. This property, which is intimately related to the Affleck-Ludwig g theorem, is a consequence of majorization relations between the spectra of the reduced density matrix along the boundary RG flows. We also point out that the bulk contribution to the single-copy entanglement is half of that to the von Neumann entropy, whereas the boundary contribution is the same.

The future of manufacturing

Anyone who looks at the title of this special issue will agree that the intent behind the preparation of this volume was ambitious: to predict and discuss “The Future of Manufacturing”. Will manufacturing be important in the future? Even though some sceptics might say not, and put on the table some old familiar arguments, we would strongly disagree. To bring subsidies for the argument we issued the call-for-papers for this special issue of Journal of Manufacturing Technology Management, fully aware of the size of the challenge in our hands. But we strongly believed that the enterprise would be worthwhile. The point of departure is the ongoing debate concerning the meaning and content of manufacturing. The easily visualised internal activity of using tangible resources to make physical products in factories is no longer a viable way to characterise manufacturing. It is now a more loosely defined concept concerning the organisation and management of open, interdependent, systems for delivering goods and services, tangible and intangible, to diverse types of markets. Interestingly, Wickham Skinner is the most cited author in this special issue of JMTM. He provides the departure point of several articles because his vision and insights have guided and inspired researchers in production and operations management from the late 1960s until today. However, the picture that we draw after looking at the contributions in this special issue is intrinsically distinct, much more dynamic, and complex. Seven articles address the following research themes: 1.new patterns of organisation, where the boundaries of firms become blurred and the role of the firm in the production system as well as that of manufacturing within the firm become contingent; 2.new approaches to strategic decision-making in markets characterised by turbulence and weak signals at the customer interface; 3.new challenges in strategic and operational decisions due to changes in the profile of the workforce; 4.new global players, especially China, modifying the manufacturing landscape; and 5.new techniques, methods and tools that are being made feasible through progress in new technological domains. Of course, many other important dimensions could be studied, but these themes are representative of current changes and future challenges. Three articles look at the first theme: organisational evolution of production and operations in firms and networks. Karlsson's and Skold's article represent one further step in their efforts to characterise “the extraprise”. In the article, they advance the construction of a new framework, based on “the network perspective” by defining the formal elements which compose it and exploring the meaning of different types of relationships. The way in which “actors, resources and activities” are conceptualised extends the existing boundaries of analytical thinking in operations management and open new avenues for research, teaching and practice. The higher level of abstraction, an intrinsic feature of the framework, is associated to the increasing degree of complexity that characterises decisions related to strategy and implementation in the manufacturing and operations area, a feature that is expected to become more and more pervasive as time proceeds. Riis, Johansen, Englyst and Sorensen have also based their article on their previous work, which in this case is on “the interactive firm”. They advance new propositions on strategic roles of manufacturing and discuss why the configuration of strategic manufacturing roles, at the level of the network, will become a key issue and how the indirect strategic roles of manufacturing will become increasingly important. Additionally, by considering that value chains will become value webs, they predict that shifts in strategic manufacturing roles will look like a sequence of moves similar to a game of chess. Then, lastly under the first theme, Fleury and Fleury develop a conceptual framework for the study of production systems in general derived from field research in the telecommunications industry, here considered a prototype of the coming information society and knowledge economy. They propose a new typology of firms which, on certain dimensions, complements the propositions found in the other two articles. Their telecoms-based framework (TbF) comprises six types of companies characterised by distinct profiles of organisational competences, which interact according to specific patterns of relationships, thus creating distinct configurations of production networks. The second theme is addressed by Kyläheiko and SandstroÍm in their article “Strategic options based framework for management of dynamic capabilities in manufacturing firms”. They propose a new approach to strategic decision-making in markets characterised by turbulence and weak signals at the customer interface. Their framework for a manufacturing firm in the digital age leads to active asset selection (strategic investments in both tangible and intangible assets) and efficient orchestrating of the global value net in “thin” intangible asset markets. The framework consists of five steps based on Porter's five-forces model, the resources-based view, complemented by means of the concepts of strategic options and related flexibility issues. Thun, GroÍssler and Miczka's contribution to the third theme brings the human dimension to the debate regarding the future of manufacturing. Their article focuses on the challenges brought to management by the ageing of workers in Germany but, in the arguments that are raised, the future challenges associated to workers and work organisation in every production system become visible and relevant. An interesting point in the approach adopted by the authors is that not only the factual problems and solutions are taken into account but the perception of the managers is brought into the picture. China cannot be absent in the discussion of the future of manufacturing. Therefore, within the fourth theme, Vaidya, Bennett and Liu provide the evidence of the gradual improvement of Chinese companies in the medium and high-tech sectors, by using the revealed comparative advantage (RCA) analysis. The Chinese evolution is shown to be based on capabilities developed through combining international technology transfer and indigenous learning. The main implication for the Western companies is the need to take account of the accelerated rhythm of capability development in China. For other developing countries China's case provides lessons of great importance. Finally, under the fifth theme, Kuehnle's article: “Post mass production paradigm (PMPP) trajectories” provides a futuristic scenario of what is already around us and might become prevalent in the future. It takes a very intensive look at a whole set of dimensions that are affecting manufacturing now, and will influence manufacturing in the future, ranging from the application of ICT to the need for social transparency. In summary, this special issue of JMTM presents a brief, but undisputable, demonstration of the possible richness of manufacturing in the future. Indeed, we could even say that manufacturing has no future if we only stick to the past perspectives. Embracing the new is not easy. The new configurations of production systems, the distributed and complementary roles to be performed by distinct types of companies in diversified networked structures, leveraged by the new emergent technologies and associated the new challenges for managing people, are all themes that are carriers of the future. The Guest Editors of this special issue on the future of manufacturing are strongly convinced that their undertaking has been worthwhile.

Screening of pharmaceuticals and other pollutants of concern by a combination of chemical and biological methods

This study examined the occurrence of pharmaceuticals and personal care products (PPCP's) in surface waters of Florida and their potential to be use as indicators of wastewater contamination. Previous studies have shown that elimination of pharmaceuticals in municipal sewage treatment plants is often incomplete. Aquatic ecosystems are under increased stress from human activities, particularly in heavily populated areas. The purpose of this study was to find an ideal indicator for wastewater. The applied methods, GC/MS and LC/MS, were suitable for the determination of pharmaceuticals and personal care products in aqueous environmental samples to the lower parts-per-trillion (ng/L) level. As a result of this study a snapshot view of the occurrence of pharmaceuticals and personal care products in south Florida was produced. PPCP's were commonly detected in coastal environments of South Florida at relatively low concentrations. In general, PPCP's were higher inside the canals and contained bodies of water than in open water systems. Caffeine was successfully used to describe impacted versus pristine locations. However, no particular correlation was observed among caffeine and other traditional water quality parameters.

Temperature measurement of cold atoms using transient absorption of a resonant probe through an optical nanofibre

Optical nanofibres are ultrathin optical fibres with a waist diameter typically less than the wavelength of light being guided through them. Cold atoms can couple to the evanescent field of the nanofibre-guided modes and such systems are emerging as promising technologies for the development of atom-photon hybrid quantum devices. Atoms within the evanescent field region of an optical nanofibre can be probed by sending near or on-resonant light through the fibre; however, the probe light can detrimentally affect the properties of the atoms. In this paper, we report on the modification of the local temperature of laser-cooled 87Rb atoms in a magneto-optical trap centred around an optical nanofibre when near-resonant probe light propagates through it. A transient absorption technique has been used to measure the temperature of the affected atoms and temperature variations from 160 μk to 850 μk, for a probe power ranging from 0 to 50 nW, have been observed. This effect could have implications in relation to using optical nanofibres for probing and manipulating cold or ultracold atoms.

Work Extraction and Energy Storage in the Dicke Model

We study work extraction from the Dicke model achieved using simple unitary cyclic transformations keeping into account both a non optimal unitary protocol, and the energetic cost of creating the initial state. By analyzing the role of entanglement, we find that highly entangled states can be inefficient for energy storage when considering the energetic cost of creating the state. Such surprising result holds notwithstanding the fact that the criticality of the model at hand can sensibly improve the extraction of work. While showing the advantages of using a many-body system for work extraction, our results demonstrate that entanglement is not necessarily advantageous for energy storage purposes, when non optimal processes are considered. Our work shows the importance of better understanding the complex interconnections between non-equilibrium thermodynamics of quantum systems and correlations among their subparts.

Between Memory and History : The Nineteenth Century in Jewelle Gomez’s Vampire Novel The Gilda Stories and the TV Series True Blood

This article examines two American vampire narratives that depict the perspective and memories of a main character who is turned into a vampire in the US in the nineteenth century: Jewelle Gomez’s novel The Gilda Stories (1991), and the first season of Alan Ball’s popular TV series True Blood (2008). In both narratives, the relationship between the past and the present, embodied by the main vampire character, is of utmost importance, but the two narratives use vampire conventions as well as representations of and references to the nineteenth century in different ways that comment on, revise, or reinscribe generic and socio-historical assumptions about race, gender, class, and sexuality.

Towards balanced exploitation and management of the fishery resources of Uganda

A casual study of the hydrological map of Uganda would convince every serious fisherman and fisheater that he is most favoured to be in Uganda. The extent and distribution of the country's aquatic system plus the rich variety of fish species there is promises a fishery potential of considerable magnitude: The open waterways comprised by the Uganda portions of Lakes Victoria, Albert and Edward; and Lakes Kyoga, George plus minor lakes Wamala, Kijanebarora, mutanda, etc. occupy about 15% of the total surface area (91,000 m2; Depart. Land Survey, 1962). Most of the nation's fish supplies are currontly from this source. 1.2. A rich network of permanent and seasonal rivers and streams filling and/or emptying various water systems covers most of Uganda. This aquatic network is associated with a fish fauna whose immense significance as a source of protein is perhaps better appreciated by the local subsistance fisherman and consumer than by the fisheries scientist and manager in this country. Many species of this fish fauna have strong affinities with the open water systems while some are typically riverine. 1.3. Then there are wetlands composed mainly of expanses of swamp, but including some areas of bog. These cover about 2% of the country. While the variety of fish fauna found here is limited by the rather hostile nature of the environment (comparatively de-oxygenated under a canopy of dense stands of emergont vegetation) several specialised fishes e.g. Clarias spp. and Protpterus aethiopicus (Kamongo) occur here. Availability of permanent and seasonal sources of water, well distributed throughout most areas of Uganda, opens up immense potential for a variety of aquaculture practices. However, while active exploitation of much of these fishery resources is currently underway, important questions regarding the magnitudes of the various resource potentials and dynamics, and about suitable levels and modes of exploitation, are yet unanswered. These gaps in knowledge go about the fishery resources of Uganda would hinder formulation of adequate development and management schemes. This short paper examines some of the above problems and suggests some approaches towards balanced oxploitation and management of the fisheries of Uganda.

Specification of a smart meter/actuator description mechanism & development of a mobile application

Home Automation holds the potential of realizing cost savings for end users while reducing the carbon footprint of domestic energy consumption. Yet, adoption is still very low. High cost of vendor-supplied home automation systems is a major prohibiting factor. Open source systems such as FHEM, Domoticz, OpenHAB etc. are a cheaper alternative and can drive the adoption of home automation. Moreover, they have the advantage of not being limited to a single vendor or communication technology which gives end users flexibility in the choice of devices to include in their installation. However, interaction with devices having diverse communication technologies can be inconvenient for users thus limiting the utility they derive from it. For application developers, creating applications which interact with the several technologies in the home automation systems is not a consistent process. Hence, there is the need for a common description mechanism that makes interaction smooth for end users and which enables application developers to make home automation applications in a consistent and uniform way. This thesis proposes such a description mechanism within the context of an open source home automation system – FHEM, together with a system concept for its application. A mobile application was developed as a proof of concept of the proposed description mechanism and the results of the implementation are reflected upon.

An hr-adaptive discontinuous Galerkin method for advection-diffusion problems

We propose an adaptive mesh refinement strategy based on exploiting a combination of a pre-processing mesh re-distribution algorithm employing a harmonic mapping technique, and standard (isotropic) mesh subdivision for discontinuous Galerkin approximations of advection-diffusion problems. Numerical experiments indicate that the resulting adaptive strategy can efficiently reduce the computed discretization error by clustering the nodes in the computational mesh where the analytical solution undergoes rapid variation.