Postglacial migration supplements climate in determining plant species ranges in Europe

The influence of dispersal limitation on species ranges remains controversial. Considering the dramatic impacts of the last glaciation in Europe, species might not have tracked climate changes through time and, as a consequence, their present-day ranges might be in disequilibrium with current climate. For 1016 European plant species, we assessed the relative importance of current climate and limited postglacial migration in determining species ranges using regression modelling and explanatory variables representing climate, and a novel species-specific hind-casting-based measure of accessibility to postglacial colonization. Climate was important for all species, while postglacial colonization also constrained the ranges of more than 50 per cent of the species. On average, climate explained five times more variation in species ranges than accessibility, but accessibility was the strongest determinant for one-sixth of the species. Accessibility was particularly important for species with limited long-distance dispersal ability, with southern glacial ranges, seed plants compared with ferns, and small-range species in southern Europe. In addition, accessibility explained one-third of the variation in species' disequilibrium with climate as measured by the realized/potential range size ratio computed with niche modelling. In conclusion, we show that although climate is the dominant broad-scale determinant of European plant species ranges, constrained dispersal plays an important supplementary role

A meta-analysis of fMRI studies of semantic cognition in children

Our capacity to derive meaning from things that we see and words that we hear is unparalleled in other animal species and current AI systems. Despite a wealth of functional magnetic resonance imaging (fMRI) studies on where different semantic features are processed in the adult brain, the development of these systems in children is poorly understood. Here we conducted an extensive database search and identified 50 fMRI experiments investigating semantic world knowledge, semantic relatedness judgments, and the differentiation of visual semantic object categories in children (total N = 1,018, mean age = 10.1 years, range 4–15 years). Synthesizing the results of these experiments, we found consistent activation in the bilateral inferior frontal gyri (IFG), fusiform gyri (FG), and supplementary motor areas (SMA), as well as in the left middle and superior temporal gyri (MTG/STG). Within this system, we found little evidence for age-related changes across childhood and high overlap with the adult semantic system. In sum, the identification of these cortical areas provides the starting point for further research on the mechanisms by which the developing brain learns to make sense of its environment

Nonlinear Propagation in Multimode and Multicore Fibers: Generalization of the Manakov Equations

This paper starts by an investigation of nonlinear transmission in space-division multiplexed (SDM) systems using multimode fibers exhibiting a rapidly varying birefringence. A primary objective is to generalize the Manakov equations, well known in the case of single-mode fibers. We first investigate a reference case where linear coupling among the spatial modes of the fiber is weak and after averaging over birefringence fluctuations, we obtain new Manakov equations for multimode fibers. Such an averaging reduces the number of intermodal nonlinear terms drastically since all four-wave-mixing terms average out. Cross-phase modulation terms still affect multimode transmission but their effectiveness is reduced. We then verify the accuracy of our new Manakov equations by transmitting multiple PDM-QPSK signals over different modes of a multimode fiber and comparing the numerical results with those obtained by solving the full stochastic equation. The agreement is excellent in all cases studied. A great benefit of the new equations is to reduce the computation time by a factor of 10 or more. Another important feature observed is that birefringence fluctuations improve system performance by reducing the impact of fiber nonlinearities. Finally multimode fibers with strong random coupling among all spatial modes are considered. Linear coupling is modeled using the random matrix theory approach. We derive new Manakov equations for multimode fibers in that regime and show that such fibers can perform better than single-modes fiber for large number of propagating spatial modes.Comment: Submitted to journal of lightwave technology on the 17-Jul-2012. Ref number: JLT-14391-201

Traceability of Requirements and Software Architecture for Change Management

At the present day, software systems get more and more complex. The requirements of software systems change continuously and new requirements emerge frequently. New and/or modified requirements are integrated with the existing ones, and adaptations to the architecture and source code of the system are made. The process of integration of the new/modified requirements and adaptations to the software system is called change management. The size and complexity of software systems make change management costly and time consuming. To reduce the cost of changes, it is important to apply change management as early as possible in the software development cycle. Requirements traceability is considered crucial in change management for establishing and maintaining consistency between software development artifacts. It is the ability to link requirements back to stakeholders’ rationales and forward to corresponding design artifacts, code, and test cases. When changes for the requirements of the software system are proposed, the impact of these changes on other requirements, design elements and source code should be traced in order to determine parts of the software system to be changed. Determining the impact of changes on the parts of development artifacts is called change impact analysis. Change impact analysis is applicable to many development artifacts like requirements documents, detailed design, source code and test cases. Our focus is change impact analysis in requirements and software architecture. The need for change impact analysis is observed in both requirements and software architecture. When a change is introduced to a requirement, the requirements engineer needs to find out if any other requirement related to the changed requirement is impacted. After determining the impacted requirements, the software architect needs to identify the impacted architectural elements by tracing the changed requirements to software architecture. It is hard, expensive and error prone to manually trace impacted requirements and architectural elements from the changed requirements. There are tools and approaches that automate change impact analysis like IBM Rational RequisitePro and DOORS. In most of these tools, traces are just simple relations and their semantics is not considered. Due to the lack of semantics of traces in these tools, all requirements and architectural elements directly or indirectly traced from the changed requirement are candidate impacted. The requirements engineer has to inspect all these candidate impacted requirements and architectural elements to identify changes if there are any. In this thesis we address the following problems which arise in performing change impact analysis for requirements and software architecture. Explosion of impacts in requirements after a change in requirements. In practice, requirements documents are often textual artifacts with implicit structure. Most of the relations among requirements are not given explicitly. There is a lack of precise definition of relations among requirements in most tools and approaches. Due to the lack of semantics of requirements relations, change impact analysis may produce high number of false positive and false negative impacted requirements. A requirements engineer may have to analyze all requirements in the requirements document for a single change. This may result in neglecting the actual impact of a change. Manual, expensive and error prone trace establishment. Considerable research has been devoted to relating requirements and design artifacts with source code. Less attention has been paid to relating Requirements (R) with Architecture (A) by using well-defined semantics of traces. Designing architecture based on requirements is a problem solving process that relies on human experience and creativity, and is mainly manual. The software architect may need to manually assign traces between R&A. Manual trace assignment is time-consuming, expensive and error prone. The assigned traces might be incomplete and invalid. Explosion of impacts in software architecture after a change in requirements. Due to the lack of semantics of traces between R&A, change impact analysis may produce high number of false positive and false negative impacted architectural elements. A software architect may have to analyze all architectural elements in the architecture for a single requirements change. In this thesis we propose an approach that reduces the explosion of impacts in R&A. The approach employs semantic information of traces and is supported by tools. We consider that every relation between software development artifacts or between elements in these artifacts can play the role of a trace for a certain traceability purpose like change impact analysis. We choose Model Driven Engineering (MDE) as a solution platform for our approach. MDE provides a uniform treatment of software artifacts (e.g. requirements documents, software design and test documents) as models. It also enables using different formalisms to reason about development artifacts described as models. To give an explicit structure to requirements documents and treat requirements, architecture and traces in a uniform way, we use metamodels and models with formally defined semantics. The thesis provides the following contributions: A modeling language for definition of requirements models with formal semantics. The language is defined according to the MDE principles by defining a metamodel. It is based on a survey about the most commonly found requirements types and relation types. With this language, the requirements engineer can explicitly specify the requirements and the relations among them. The semantics of these entities is given in First Order Logic (FOL) and allows two activities. First, new relations among requirements can be inferred from the initial set of relations. Second, requirements models can be automatically checked for consistency of the relations. Tool for Requirements Inferencing and Consistency Checking (TRIC) is developed to support both activities. The defined semantics is used in a technique for change impact analysis in requirements models. A change impact analysis technique for requirements using semantics of requirements relations and requirements change types. The technique aims at solving the problem of explosion of impacts in requirements when semantics of requirements relations is missing. The technique uses formal semantics of requirements relations and requirements change types. A classification of requirements changes based on the structure of a textual requirement is given and formalized. The semantics of requirements change types is based on FOL. We support three activities for impact analysis. First, the requirements engineer proposes changes according to the change classification before implementing the actual changes. Second, the requirements engineer indentifies the propagation of the changes to related requirements. The change alternatives in the propagation are determined based on the semantics of change types and requirements relations. Third, possible contradicting changes are identified. We extend TRIC with a support for these activities. The tool automatically determines the change propagation paths, checks the consistency of the changes, and suggests alternatives for implementing the change. A technique that provides trace establishment between R&A by using architecture verification and semantics of traces. It is hard, expensive and error prone to manually establish traces between R&A. We present an approach that provides trace establishment by using architecture verification together with semantics of requirements relations and traces. We use a trace metamodel with commonly used trace types. The semantics of traces is formalized in FOL. Software architectures are expressed in the Architecture Analysis and Design Language (AADL). AADL is provided with a formal semantics expressed in Maude. The Maude tool set allows simulation and verification of architectures. The first way to establish traces is to use architecture verification techniques. A given requirement is reformulated as a property in terms of the architecture. The architecture is executed and a state space is produced. This execution simulates the behavior of the system on the architectural level. The property derived from the requirement is checked by the Maude model checker. Traces are generated between the requirement and the architectural components used in the verification of the property. The second way to establish traces is to use the requirements relations together with the semantics of traces. Requirements relations are reflected in the connections among the traced architectural elements based on the semantics of traces. Therefore, new traces are inferred from existing traces by using requirements relations. We use semantics of requirements relations and traces to both generate/validate traces and generate/validate requirements relations. There is a tool support for our approach. The tool provides the following: (1) generation/validation of traces by using requirements relations and/or verification of architecture, (2) generation/validation of requirements relations by using traces. A change impact analysis technique for software architecture using architecture verification and semantics of traces between R&A. The software architect needs to identify the impacted architectural elements after requirements change. We present a change impact analysis technique for software architecture using architecture verification and semantics of traces. The technique is semi-automatic and requires participation of the software architect. Our technique has two parts. The first part is to identify the architectural elements that implement the system properties to which proposed requirements changes are introduced. By having the formal semantics of requirements relations and traces, we identify which parts of software architecture are impacted by a proposed change in requirements. We have extended TRIC for determining candidate impacted architectural elements. The second part of our technique is to propose possible changes for software architecture when the software architecture does not satisfy the new and/or changed requirements. The technique is based on architecture verification. The output of verification is a counter example if the requirements are not satisfied. The counter example is used with a classification of architectural changes in order to propose changes in the software architecture. These changes produce a new version of the architecture that possibly satisfies the new or the changed requirements

Jet substructure at the Large Hadron Collider

Jet substructure has emerged to play a central role at the Large Hadron Collider, where it has provided numerous innovative ways to search for new physics and to probe the standard model, particularly in extreme regions of phase space. This review focuses on the development and use of state-of-the-art jet substructure techniques by the ATLAS and CMS experiments

Definition of a Type System for Generic and Reflective Graph Transformations

This thesis presents the extension of the graph transformation language SDM (Story Driven Modeling) with generic and reflective features as well as the definition of type checking rules for this language. The generic and reflective features aim at improving the reusability and expressiveness of SDM, whereas the type checking rules will ensure the type-safety of graph transformations. This thesis starts with an explanation of the relevant concepts as well as a description of the context in order to provide the reader with a better understanding of our approach. The model driven development of software, today considered as the standard paradigm, is generally based on the use of domain-specific languages such as MATLAB Simulink and Stateflow. To increase the quality, the reliability,and the efficiency of models and the generated code, checking and elimination of detected guideline violations defined in huge catalogues has become an essential, but error-prone and time-consuming task in the development process. The MATE/MAJA projects, which are based on the use of the SDM language, aim at an automation of this task for MATLAB Simulink/Stateflow models. Modeling guidelines can be specified on a very high level of abstraction by means of graph transformations. Moreover, these specifications allow for the generation of guideline checking tools. Unfortunately, most graph transformation languages do not offer appropriate concepts for reuse of specification fragments - a MUST, when we deal with hundreds of guidelines. As a consequence we present an extension of the SDM language which supports the definition of generic rewrite rules and combines them with the reflective programming mechanisms of Java and the model repository interface standard JMI. Reusability and expressiveness are not the only aspects we want to improve. Another fundamental aspect of graph transformations must be ensured: their correctness in order to prevent type errors while executing the transformations. Checking and testing the graph transformations manually would ruin the benefit obtained by the automation of the guideline checking and by the generic and reflective features. Therefore, we propose in this work a type-checking method for graph transformations. We introduce a new notation for rules of inference and define a type system for SDM. We also proposed an algorithm to apply this type system. We illustrate and evaluate both contributions of our work by applying them on running examples. Proposals for other additional SDM features as well as for possible improvements of our type checking open new perspectives and future research to pursue our work

Acrocephalus orinus: A Case of Mistaken Identity

Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered