pinecone/core-2020-05-10-deduplication huggingface dataset:
Cytoskeleton and Cell Motility

The present article is an invited contribution to the Encyclopedia of
Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009).
It is a review of the biophysical mechanisms that underly cell motility. It
mainly focuses on the eukaryotic cytoskeleton and cell-motility mechanisms.
Bacterial motility as well as the composition of the prokaryotic cytoskeleton
is only briefly mentioned. The article is organized as follows. In Section III,
I first present an overview of the diversity of cellular motility mechanisms,
which might at first glance be categorized into two different types of
behaviors, namely "swimming" and "crawling". Intracellular transport, mitosis -
or cell division - as well as other extensions of cell motility that rely on
the same essential machinery are briefly sketched. In Section IV, I introduce
the molecular machinery that underlies cell motility - the cytoskeleton - as
well as its interactions with the external environment of the cell and its main
regulatory pathways. Sections IV D to IV F are more detailed in their
biochemical presentations; readers primarily interested in the theoretical
modeling of cell motility might want to skip these sections in a first reading.
I then describe the motility mechanisms that rely essentially on
polymerization-depolymerization dynamics of cytoskeleton filaments in Section
V, and the ones that rely essentially on the activity of motor proteins in
Section VI. Finally, Section VII is devoted to the description of the
integrated approaches that have been developed recently to try to understand
the cooperative phenomena that underly self-organization of the cell
cytoskeleton as a whole.Comment: 31 pages, 16 figures, 295 reference
Field-theoretic methods

Many complex systems are characterized by intriguing spatio-temporal
structures. Their mathematical description relies on the analysis of
appropriate correlation functions. Functional integral techniques provide a
unifying formalism that facilitates the computation of such correlation
functions and moments, and furthermore allows a systematic development of
perturbation expansions and other useful approximative schemes. It is explained
how nonlinear stochastic processes may be mapped onto exponential probability
distributions, whose weights are determined by continuum field theory actions.
Such mappings are madeexplicit for (1) stochastic interacting particle systems
whose kinetics is defined through a microscopic master equation; and (2)
nonlinear Langevin stochastic differential equations which provide a mesoscopic
description wherein a separation of time scales between the relevant degrees of
freedom and background statistical noise is assumed. Several well-studied
examples are introduced to illustrate the general methodology.Comment: Article for the Encyclopedia of Complexity and System Science, B.
  Meyers (Ed.), Springer-Verlag Berlin, 200
Market games and clubs

The equivalence of markets and games concerns the relationship between two sorts of structures that appear fundamentally different -- markets and games. Shapley and Shubik (1969) demonstrates that: (1) games derived from markets with concave utility functions generate totally balanced games where the players in the game are the participants in the economy and (2) every totally balanced game generates a market with concave utility functions. A particular form of such a market is one where the commodities are the participants themselves, a labor market for example.
    But markets are very special structures, more so when it is required that utility functions be concave. Participants may also get utility from belonging to groups, such as marriages, or clubs, or productive coalitions. It may be that participants in an economy even derive utility (or disutility) from engaging in processes that lead to the eventual exchange of commodities. The question is when are such economic structures equivalent to markets with concave utility functions.
    This paper summarizes research showing that a broad class of large economies generate balanced market games. The economies include, for example, economies with clubs where individuals may have memberships in multiple clubs, with indivisibile commodities, with nonconvexities and with non-monotonicities. The main assumption are: (1) that an option open to any group of players is to break into smaller groups and realize the sum of the worths of these groups, that is, essential superadditivity is satisfied and :(2) relatively small groups of participants can realize almost all gains to coalition formation.
    The equivalence of games with many players and markets with many participants indicates that relationships obtained for markets with concave utility functions and many participants will also hold for diverse social and economic situations with many players. These relationships include: (a) equivalence of the core and the set of competitive outcomes; (b) the Shapley value is contained in the core or approximate cores; (c) the equal treatment property holds -- that is, both market equilibrium and the core treat similar players similarly. These results can be applied to diverse economic models to obtain the equivalence of cooperative outcomes and competitive, price taking outcomes in economies with many participants and indicate that such results hold in yet more generality.
Odors treatment : biological technologies

Physical-chemical waste gas cleaning techniques have proven their effi ciency and reliability and will continue to occupy their niche, but several disadvantages remain. Among them are high investment and operation costs and the possible generation of secondary waste streams. With biological waste treatment techniques, reactor engineering is often less complicated  and consequently costs are less. In addition, usually no secondary wastes are produced. Biological methods are nonhazardous and benign for the environment. Possible drawbacks are restricted knowledge about the biodegradation processes, limited process control, and relatively slow reaction kinetics. Anyway, the biological methods for the removal of odors and volatile organic compounds (VOCs) from waste gases are cost-effective technologies, when low concentrations (below 1-10 g/m -3 ) are to be dealt with (Kosteltz et al., 1996). Therefore, decision making can be based merely on economical analysis. Like the treatment of liquid effl uents, gaseous streams will be more often considered for biological treatment. For organic compounds, the biological reaction can be described as: CHO + O 2  + nutrients C 5  H 7  O  2  N (cell dry weight) + CO 2  + H 2 O + heat When heteroatoms are present (e.g., chlorine, sulfur), end-products like HCl or H 2 SO 4  can be formed. For effi cient pollutant removal, target pollutants have to be suffi ciently biodegradable and bioavailable. A major advantage in the case of odor treatment is that biocatalysts have high affi nity for the substrates, which allows effi cient treatment of low infl uent concentrations. Biocatalysts also operate at room temperature and they have innocuous fi nal products (e.g., carbon dioxide and water). Provided that you have the right inocula, microorganisms can metabolize almost every compound there is. In general, odors consist of a very complex mixture of volatile organic as well as inorganic compounds. The most relevant compounds regarding odors in the food industry are nitrogencontaining compo
Remote lab experiments: opening possibilities for distance learning in engineering fields

Remote experimentation laboratories are systems based on real equipment, allowing students to perform practical work through a computer connected to the internet. In engineering fields lab activities play a fundamental role. Distance learning has not demonstrated good results in engineering fields because traditional lab activities cannot be covered by this paradigm. These activities can be set for one or for a group of students who work from different locations. All these configurations lead to considering a flexible model that covers all possibilities (for an individual or a group). An inter-continental network of remote laboratories supported by both European and Latin American institutions of higher education has been formed. In this network context, a learning collaborative model for students working from different locations has been defined. The first considerations are presented
SOFHIA: a CAD environment to design digital control systems

"Series Title: IFIP - The International Federation for Information Processing, ISSN 1868-4238"Petri Nets (PNs) prove to be an e cient methodology to model discrete-event
systems with parallel activities. The main advantages lie on the graphical
interface and on the availability of a set of techniques for formal analysis,
including the validation and the test of the modelled system. A proposal to
modify the normal PN behaviour is presented, which aims a fast speci cation
of synchronous parallel digital systems, including both the data path and
the control unit. A CAD environment, SOFHIA, was developed to model
digital systems, to validate their properties and to simulate their behaviour.
The environment includes the automatic generation of VHDL code to allow
simulation and synthesis on existing CAD tools
Proving the correctness of the interlock mechanism in processor design.

In this paper, Interval Temporal Logic (ITL) us used to specify and verify the event processor EP/3, which is a multi-threaded pipeline processor capable of executing parallel programs. We first give the high level specification of the EP/3 with emphasis on the interlock mechanism. The interlock mechanism is used in processor design especially for dealing with pipeline conflict problems. We prove that the specification satisfies certain safety and liveness properties. An advantage of ITL is that it has an executable part, i.e., we can simulate a specification before proving properties about it. This will help us to get the right specification.Nick Coleman - full name J. Nick Colema
An architecture for reliable distributed computer-controlled systems

In Distributed Computer-Controlled Systems (DCCS), both real-time and reliability
requirements are of major concern. Architectures for DCCS must be designed
considering the integration of processing nodes and the underlying communication
infrastructure. Such integration must be provided by appropriate software support
services.
In this paper, an architecture for DCCS is presented, its structure is outlined, and
the services provided by the support software are presented. These are considered in
order to guarantee the real-time and reliability requirements placed by current and
future systems
Components as processes: an exercise in coalgebraic modeling

IFIP TC6/WG6.1. Fourth International Conference on Formal Methods for Open Object-Based Distributed Systems (FMOODS 2000) September 6–8, 2000, Stanford, California, USASoftware components, arising, typically, in systems ’ analysis and design, are characterized by a public interface and a private encapsulated state. They persist (and evolve) in time, according to some behavioural patterns. This paper is an exercise in modeling such components as coalgebras for some kinds of endofunctors on , capturing both (interface) types and behavioural aspects. The construction of component categories, cofibred over the interface space, emerges by generalizing the usual notion of a coalgebra morphism. A collection of composition operators as well as a generic notion of bisimilarity, are discussed
Conceptual frames of reference and their influence on e-commerce system development

[Abstract]: The complexity and uncertainty that is inherent in the E-Commerce environment poses a number of challenges to the development of E-commerce applications. Key stakeholders consistently use heuristics to make sense of the challenges they face. The most pervasive of these heuristics is framing, whereby people rely on a conceptual set to organise their perceptions. This process has some benefits but it can also lead to a narrow approach, ignorance concerning important elements of the decision environment and an absolute reliance on a specialist area of knowledge. This has significant implications for coherence of effort and vision, elements crucial to the success of e-Commerce projects. This paper uses a case study, qualitative approach in order to establish whether there is evidence for the operation of the framing heuristic, particularly within the context of risk perception, within a variety of E-Commerce system development environments
A holonic approach to dynamic manufacturing scheduling

Indexado ISIManufacturing scheduling is a complex combinatorial problem, particularly in distributed and dynamic environments. This paper presents a holonic approach to manufacturing scheduling, which in opposite to traditional approaches, distributes the scheduling functions over several entities, combining their calculation power and local optimization. In this scheduling and control approach, the scheduling mechanism evolves dynamically to combine optimized scheduling, achieved by central entities, and distributed scheduling, improving its responsiveness and robustness
Ontological evaluation of business models: comparing traditional and component-based paradigms in information systems re-engineering

The majority of current information systems were implemented using traditional paradigms which include business modeling techniques applied during the analysis phase such as Data Flow Diagrams and Entity-Relationship Diagrams. These legacy systems are now struggling to cope with recent developments, particularly trends towards e-Commerce applications, platform independence, reusability of pre-built components, capacity for reconfiguration and higher reliability.  Many organizations now realize they need to re-engineer their systems using new component-based systems. Although the traditional and component-based approaches have different grammars for representing business models, these business models can be compared, based on their ontological grammars. This paper illustrates how an ontological evaluation of business models by using the Bunge-Wand-Weber model can be used to compare them for equivalency of representation of business requirements, when re-engineering legacy systems into component-based information systems
Iterative refinement approach for QOS-Aware service configuration

In heterogeneous environments, diversity of resources among the devices
may affect their ability to perform services with specific QoS constraints,
and drive peers to group themselves in a coalition for cooperative service
execution. The dynamic selection of peers should be influenced
by user’s QoS requirements as well as local computation availability,
tailoring provided service to user’s specific needs. However, complex
dynamic real-time scenarios may prevent the possibility of computing
optimal service configurations before execution. An iterative refinement
approach with the ability to trade off deliberation time for the quality
of the solution is proposed. We state the importance of quickly finding
a good initial solution and propose heuristic evaluation functions that
optimise the rate at which the quality of the current solution improves
as the algorithms have more time to run
A demonstration case on the transformation of software architectures for service specification

This paper presents a demonstration case on the successive application of a model-based technique to assist on the refinement of software logical architectures. The technique is essentially based on the transformation of use cases into object diagrams. The applicability of the technique is illustrated by presenting some results from a mobile application. For mobile software, the definition of the underlying service-oriented architecture must consider as user requirements the services themselves, the mobile operators entry points and the final clients interfaces, and use them to characterize the platform. Within the presented demonstration case, the specification of one service of the mobile application was obtained by successively applying the technique.Research funded by FCT and FEDER under project STACOS (POSI/CHS/48875/2002)
Pharmacokinetics and pharmacodynamics of curcumin

This is the authors' final draft of the paper published as Advances in Experimental Medicine and Biology, 2007, 595, pp.453-470 (Volume title: Molecular targets and therapeutic uses of curcumin in health and disease).  The final published version is available via www.springerlink.com, DOI: 10.1007/978-0-387-46401-5_20Curcuma spp. contain turmerin, essential oils, and curcuminoids,\ud
including curcumin. Curcumin [1,7-bis-(4-hydroxy-3-methoxyphenyl)-1,6-\ud
heptadiene-3,5-dione] is regarded as the most biologically active constituent of the\ud
spice turmeric and it comprises 2–8% of most turmeric preparations. Preclinical\ud
data from animal models and phase I clinical studies performed with human volunteers\ud
and patients with cancer have demonstrated low systemic bioavailability\ud
following oral dosing. Efficient first-pass metabolism and some degree of intestinal\ud
metabolism, particularly glucuronidation and sulfation of curcumin, might\ud
explain its poor systemic availability when administered via the oral route. A\ud
daily oral dose of 3.6 g of curcumin is compatible with detectable levels of the\ud
parent compound in colorectal tissue from patients with cancer. The levels demonstrated\ud
might be sufficient to exert pharmacological activity. There appears to be\ud
negligible distribution of the parent drug to hepatic tissue or other tissues beyond\ud
the gastrointestinal tract. Curcumin possesses wide-ranging anti-inflammatory and\ud
anticancer properties. Many of these biological activities can be attributed to its\ud
potent antioxidant capacity at neutral and acidic pH, its inhibition of cell signaling\ud
pathways at multiple levels, its diverse effects on cellular enzymes, and its effects\ud
on cell adhesion and angiogenesis. In particular, curcumin’s ability to alter gene\ud
transcription and induce apoptosis in preclinical models advocates its potential\ud
utility in cancer chemoprevention and chemotherapy.With regard to considerable\ud
public and scientific interest in the use of phytochemicals derived from dietary\ud
components to combat or prevent human diseases, curcumin is currently a leading\ud
agent
Feature Selection and Dimensionality Reduction in Genomics and Proteomics

International audienceFinding reliable, meaningful patterns in data with high numbers of attributes can be extremely difficult. Feature selection helps us to decide what attributes or combination of attributes are most important for finding these patterns. In this chapter, we study feature selection methods for building classification models from high-throughput genomic (microarray) and proteomic (mass spectrometry) data sets. Thousands of feature candidates must be analyzed, compared and combined in such data sets. We describe the basics of four different approaches used for feature selection and illustrate their effects on an MS cancer proteomic data set. The closing discussion provides assistance in performing an analysis in high-dimensional genomic and proteomic data
An abstract schema modeling adaptivity management

International audienceNowadays, component application adaptivity in Grid environments has been afforded in different ways, such those provided by the Dynaco/AFPAC framework and by the ASSIST environment. We propose an abstract schema that catches all the designing aspects a model for parallel component applications on Grid should define in order to uniformly handle the dynamic behavior of computing resources within complex parallel applications. The abstraction is validated by demonstrating how two different approaches to adaptivity, ASSIST and Dynaco/AFPAC, easily map to such schema
Implementing digital enterprise technologies for agile design in the virtual enterprise.

Digital Enterprise Technology (DET) is defined as a synthesis of digital and physical systems across the product lifecycle which can be exploited for two main benefits: risk mitigation through consistent and seamless data standards; and reduction in product development times through improved access to the most accurate project data at any time, from anywhere, by anyone. Agility is defined as responsiveness to unpredictability, particularly unpredictable events in the environment external to a process. The general need for agile response in turbulent environments is well documented and has been analyzed at the manufacture phase. \ud
This paper introduces a framework for an agile response to these turbulent environments during the design stages of product development. The Agile Design Framework is based on the founding principles described as DET, with the added benefit of reduced reaction time and therefore greater agility in the face of unpredicted external events. A 4 level classification scheme for event impact is discussed and a common toolbox of Digital Enterprise Technologies (Core Tools) for agile design is introduced. The paper proposes the implementation of the DET-based Core Tools during a meta-design stage, for maximum benefit from the synergies of the many systems
History of clinical transplantation

How transplantation came to be a clinical discipline can be pieced together by perusing two volumes of reminiscences collected by Paul I. Terasaki in 1991-1992 from many of the persons who were directly involved. One volume was devoted to the discovery of the major histocompatibility complex (MHC), with particular reference to the human leukocyte antigens (HLAs) that are widely used today for tissue matching.1 The other focused on milestones in the development of clinical transplantation.2 All the contributions described in both volumes can be traced back in one way or other to the demonstration in the mid-1940s by Peter Brian Medawar that the rejection of allografts is an immunological phenomenon.3,4 © 2008 Springer New York
Addition theorems in acyclic semigroups

6 páginas.-- 2000 Mathematics Subject Classification. 11P70.-- En: David Chudnovsky, Gregory Chudnovsky (eds.).We give a necessary and sufficient condition on a given family A of finite\ud
subsets of integers for the Cauchy-Davenport inequality\ud
|A + B|<=  |A| + |B| − 1,\ud
to hold for any family B of finite subsets of integers. We also describe the extremal families\ud
for this inequality. We prove this result in the general context of acyclic semigroups,\ud
which contain also the semigroup of sequences of elements in an ordered group.Peer reviewe
Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing
knowledge-based potential functions essential for protein structure prediction,
protein-protein interaction, and protein sequence design. We discuss in some
details about the Miyazawa-Jernigan contact statistical potential,
distance-dependent statistical potentials, as well as geometric statistical
potentials. We also describe a geometric model for developing both linear and
non-linear potential functions by optimization. Applications of knowledge-based
potential functions in protein-decoy discrimination, in protein-protein
interactions, and in protein design are then described. Several issues of
knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe