Mass spectra alignments and their significance

Mass Spectrometry has become one of the most popular analysis techniques in Genomics and Systems Biology. We investigate a general framework that allows the alignment (or matching) of any two mass spectra. In particular, we examine the alignment of a reference mass spectrum generated in silico from a database, with a measured sample mass spectrum. In this context, we assess the significance of alignment scores for character-specific cleavage experiments, such as tryptic digestion of amino acids. We present an efficient approach to estimate this significance, with runtime linear in the number of detected peaks. In this context, we investigate the probability that a random string over a weighted alphabet contains a substring of some given weight.     

On Multi-threaded Metrical Task Systems

Traditionally, on-line problems have been studied under the assumption that there is a unique sequence of requests that must be served. This approach is common to most general models of on-line computation, such as Metrical Task Systems. However, there exist on-line problems in which the requests are organized in more than one independent thread. In this more general framework, at every moment the first unserved request of each thread is available. Therefore, apart from deciding how to serve a request, at each stage it is necessary to decide which request to serve among several possibilities.In this paper we introduce Multi-threaded Metrical Task Systems, that is, the generalization of Metrical Task Systems to the case in which there are many threads of tasks. We study the problem from a competitive analysis point of view, proving lower and upper bounds on the competitiveness of on-line algorithms. We consider finite and infinite sequences of tasks, as well as deterministic and randomized algorithms. In this work we present the first steps towards a more general framework for on-line problems which is not restricted to a sequential flow of information.     

Hybrid Dynamics of Stochastic π-Calculus

In this paper we describe a method to map stochastic π-calculus processes in chemical ground form into hybrid automata. Hybrid automata are tools widely employed to model systems characterized by both discrete and continuous evolution and their use in the context of Systems Biology allows us to address rather fundamental issues. Specifically, the key ingredient we use in this work is the possibility granted by hybrid automata to implement a separation of control and molecular terms in biochemical systems. The computational counterpart of our analysis turns out to be related to the determination of conservation properties of the system.      

Analysis,modeling, emergence & integration in complex systems: A modeling and integration framework & system biology

Analysis and Modeling is the first “phase” of understanding or developing a system. It is also, maybe more importantly, the foundation of understanding a natural science or system. It's abstract and conceptually difficult but, being foundational, contributes the most to the quality of understanding of (designed or natural) systems. Complex Systems have a natural hierarchy of levels and multiple subsystems. The character and functionality of each level or subsystem “emerges” across its boundaries. Both sides of these boundaries must be understood within that side's natural thought patterns. Integrated interdisciplinary collaboration is essential for making sense of complex systems; but collaboration among disciplines is difficult, because of their different ways of thinking. This creates a dilemma, “understanding complex systems” is one horn; “integrated interdisciplinary collaboration” is the other. This dilemma in complex system analysis/modeling and interdiscipline collaboration, is currently addressed by “grabbing the bull by the horns.” This takes on this doubly complex problem, by painstakingly building up abstract “bull wrestling” skills in and across domains and disciplines. There's another wrinkle; complexity requires interdisciplinary collaboration at deeper, more dissimilar, levels. The usual approach, finding a way to “pass between the horns of the dilemma” will not work here, due to this cross coupling. Rather than trying to pass between the horns, by abstracting away the coupling, we overtly organizing this coupling. We weave a semantic unification space of conceptual connections linking each side of a boundary to its appropriate way of thinking. This allows us to abstracting away the dilemma and iron out the wrinkle. The threads of common image schemas, cognitive metaphors and conceptual interfaces, weave a bridge between the semantics foundations and organizations of each problem. These allow addressing the problems synergistically. This paper presents and explores a naturally valid way for discipline specific and discipline integrating addressing complex systems. We start with the methodological insights from analysis and modeling from the perspective of object orientation, with its ontologies, organizing lexical semantics. We advance from there by integrating in imagistic, imaginative semantics and affordance based interaction methodology, as the keys to addressing complex systems analysis, modeling and integration. © 2007 Wiley Periodicals, Inc. Complexity, 2007     

Statistics and game theory: Estimating coalitional values in R software

In this paper we illustrate the usage of R software in cooperative game theory. In particular, we address the problems that arise in exactly calculating the coalitional values for general TU-games in which a large amount of players is involved. In these settings, their approximation may be useful in practice. We analyse these sampling methods from a statistical point of view, from a theoretical and an empirical approach.     

基于分级诊疗体系的转诊与政府投资决策研究

针对我国分级诊疗实施过程中,由于基层医疗机构服务能力不足所造成的“上转容易下转难”的困境,研究了政府部门对社区医院服务能力进行投资以促进病人下转的问题.通过构建四阶段的博弈模型,探讨了为实现医疗系统总病人效用最大化的政府资金均衡投入策略,为实现三甲医院期望效益最大化的病人下转策略,病人效用最大化下的社区医院服务能力规划以及基于期望效益最大化下的病人选择.研究发现：1)三甲医院的期望效益受到政府投资金额的影响,当政府投资金额不足时,三甲医院的期望效益仅能达到次优;2)三甲医院病人的均衡转诊率受到三甲医院的治疗价格和政府的资金投入量的影响;3)在实现整个医疗系统总病人效用最大化上,虽然总病人效用随政府投入金额的增加而增加,但从政府角度来讲,政府投资金额不宜过大.     

Growing between barriers

Growth in living materials is the result of the changes in volume and mass during their development. If volume expansion occurs in a constrained case, some living materials change its growth behaviour. For example, when growth takes place in an environment with restrictions of volume, living materials will stop their volume expansion under compression due to the high amount of water that makes these bodies nearly incompressible. In case boundary conditions limit the growth of the body, the growth direction changes and gives the body another shape as expected. We present a modelling approach that takes volume and shape restrictions during growth into account. (© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Purposeful Control

At present both management and biological sciences are faced with a common problem in methodology—how to model systems of organized complexity. In their approach to this problem the management sciences have adopted several concepts from the biological sciences, such as adaptation, goal-seeking, purposefulness, and so on, but have as yet donated little in return.This paper offers a contribution towards redressing the balance. A simple mathematical model of purposeful control is presented, and quantitative examples are then given to illustrate the application of the model to both living and practical systems.     

Complex impure systems: Sheaves,freeways, and chains

Fundamental to the approach of Complex Impure Systems is the definition of the concept of an s‐impure set as a set of perceptual beliefs or denotative significances (relative beings) of material and/or energetic real objects (absolute beings). But any Subject not only the subject S perceives objects O as significances, and he perceives the existing relations between these significances or, alternatively, he infers them. The study of these relations, conceived not as a singular relation between singular objects, but as sheaves of relations in both directions and forming relational freeways, will be studied here. In this work, we approach the structure of the system, from a synchronous point of view, as a first approach to this class of systems. © 2016 Wiley Periodicals, Inc. Complexity 21: 387–400, 2016     

Very Large-Scale Neighborhood Search for the K-Constraint Multiple Knapsack Problem

The K-Constraint Multiple Knapsack Problem (K-MKP) is a generalization of the multiple knapsack problem, which is one of the representative combinatorial optimization problems known to be NP-hard. In K-MKP, each item has K types of weights and each knapsack has K types of capacity. In this paper, we propose several very large-scale neighborhood search (VLSN) algorithms to solve K-MKP. One of the VLSN algorithms incorporates a novel approach that consists of randomly perturbing the current solution in order to efficiently produce a set of simultaneous non-profitable moves. These moves would allow several items to be transferred from their current knapsacks and assigned to new knapsacks, which makes room for new items to be inserted through multi-exchange movements and allows for improved solutions. Computational results presented show that the method is effective, and provides better solutions compared to exact algorithms run for the same amount of time. This paper was written during Dr. Cunha's sabbatical at the Industrial and Systems Engineering Department at the University of Florida, Gainesville as a visiting faculty     

'Model your genes the mathematical way'--a mathematical biology workshop for secondary school teachers

This article describes a mathematical biology workshop givento secondary school teachers of the Danville area in Virginia,USA. The goal of the workshop was to enable teams of teacherswith biology and mathematics expertise to incorporate lessonplans in mathematical modelling into the curriculum. The biologicalfocus of the activities is the lactose operon in Escherichiacoli, one of the first known intracellular regulatory networks.The modelling approach utilizes Boolean networks and tools fromdiscrete mathematics for model simulation and analysis. Theworkshop structure simulated the team science approach commonin today's practice in computational molecular biology and thusrepresents a social case study in collaborative research. Theworkshop provided all the necessary background in molecularbiology and discrete mathematics required to complete the project.The activities developed in the workshop show students the valueof mathematical modelling in understanding biochemical networkmechanisms and dynamics. The use of Boolean networks, ratherthan the more common systems of differential equations, makesthe material accessible to students with a minimal mathematicalbackground. High school students can be exposed to the excitement of mathematicalbiology from both the biological and mathematical point of view.Through the development of instructional modules, high schoolbiology and mathematics courses can be joined without havingto restructure the curriculum for either subject. The relevanceof an early introduction to mathematical biology allows studentsnot only to learn curriculum material in a innovative setting,but also creates an awareness of new educational and careeropportunities that are arising from the interconnections betweenbiological and mathematical sciences. The materials used in this workshop are available at a websitecreated by the directors: http://polymath.vbi.vt.edu/mathbio2006/.     

On a class of pseudodifferential operators on the product of compact Lie groups

In this paper, a bisingular pseudodifferential calculus, along the lines of the one introduced by L. Rodino in his paper of 1975, is developed in the global setting of a product of compact Lie groups. The approach follows that introduced by M. Ruzhansky and V. Turunen in their book of 2010 (see also V. Fischer's paper of 2015), in that it exploits the harmonic analysis of the groups involved.     

A review of the recent contribution of systems thinking to operational research and management science

The systems approach, or systems thinking, has been intimately connected with the development of OR and management science initially through the work of founders such as Churchman and Ackoff and latterly through innovations such as soft systems. In this paper we have undertaken a review of the contribution that systems thinking has been making more recently, especially to the practice of OR. Systems thinking is a discipline in its own right, with many theoretical and methodological developments, but it is also applicable to almost any problem area because of its generality, and so such a review must always be selective. We have looked at the literature from both a theoretical and an applications orientation. In the first part we consider the main systems theories and methodologies in terms of their recent developments and also their applications. This covers: the systems approach, complexity theory, cybernetics, system dynamics, soft OR and PSMs, critical systems and multimethodology. In the second part we review the main domains of application: strategy, information systems, organisations, production and operations, ecology and agriculture, and medicine and health. Our overall conclusion is that while systems may not be well established institutionally, in terms of academic departments, it is incredibly healthy in terms of the quantity and variety of its applications.     

Teaching spline approximation techniques using maple

Using Computer Algebra Systems (CAS)-such as MAPLE-in teaching and learning mathematical concepts is a great challenge both from a didactical and a scientific point of view. We have to rewrite our traditional paper based teaching materials for interactive and living electronic worksheets, Only few statements and principles have to be acquired by the learner and the teacher from the CAS and after they can visualise, make animations modify quickly the program data, perform symbolic and numeric calculations step by step and in the whole, and verify deductions on their own. The author prepared Maple worksheets for teaching different types of function approximating techniques, such as interpolation-, least square-, spline and uniform approximation methods for post-graduate mechanical engineering students. In this paper we want to demonstrate how can we keep and improve the famous problem solving principles and rules given by G. Pólya and R. Descartes (Pólya 1962), when we use the capabilities of CAS. The education principles active learning, motivations and the successive phases are getting new meaning in the CAS. Our examples are always concerning with spline functions. Handling the formulas, calculating values and giving proofs are always in the form of Maple statements.     

The role of software Modellus in a teaching approach based on model analysis

We discuss some results of a study carried out over the past 4 years to investigate the role of Modellus, a software package, in the development of an approach to teaching calculus for Biology majors. The central idea of the teaching approach is to propose the analysis of a mathematical model for a biological phenomenon at the very beginning of the course, in a way that this analysis is interrelated with some of the mathematical concepts listed in the syllabus. In this paper, we focus on the role of the software during the development of one of the activities proposed to the students, the purpose of which was to discuss the relation between secant lines and the instantaneous rate of change. It was found that this software played two roles in the development of this activity: providing information about the phenomenon and the model; and acting as a trigger, making evident to the student an important aspect that contributed to his understanding. Based on our theoretical perspective of digital technology, we believe that students’ interaction with the software played a fundamental role in the thinking collective composed of humans and media involved in mathematical learning.     

Argue to agree: A case-based argumentation approach

The capability of reaching agreements is a necessary feature that large computer systems where agents interoperate must include. In these systems, agents represent self-motivated entities that have a social context, including dependency relations among them, and different preferences and beliefs. Without agreement there is no cooperation and thus, complex tasks which require the interaction of agents with different points of view cannot be performed. In this work, we propose a case-based argumentation approach for Multi-Agent Systems where agents reach agreements by arguing and improve their argumentation skills from experience. A set of knowledge resources and a reasoning process that agents can use to manage their positions and arguments are presented. These elements are implemented and validated in a customer support application.     

分子系统生物学的数学建模与分析

本质上,分子系统生物学就是要研究分子水平上的各种层次网络,并整合这些网络信息为系统信息。广泛使用的化学主方程为研究生物分子网络提供了一个建模框架,但应用起来具有局限性;传统的矩封闭方法可以简化生物分子网络的研究,但并没有解决反应物种的联合概率分布的重构问题。本文简单介绍了生物分子网络的数学建模与分析,特别地,对生化反应系统提出二项矩的分析方法,它与传统方法相比具有许多优势,如能够降低计算复杂度、方便联合概率分布的重构,甚至可用于非线性行为的线性逼近等。