Object mobility in large scale systems

Standards such as CORBA are spreading in the development of large scale projects. However, CORBA lacks a mobility mechanism which is an interesting feature to deal with system dynamics. In this paper, we propose a generic solution for object mobility in CORBA in the framework of its lifecycle service. Implementation at the object level handles the migration process using intermediary objects. A group mechanism is used to manage the object creation infrastructure so as to allow scalability. We have chosen a multi-agent auto-organizational group mechanism to reduce the administrative task for a large system. Performance tests show that reasonable performance can be achieved using a high level generic and portable implementation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Industrial Ecology Education at Tsinghua University

As a leading university in engineering education in China, Tsinghua University implemented industrial ecology (IE) education in the 1990s. This article describes the evolution of IE education at Tsinghua. Tsinghua mainstreams IE education into green education and engineering education not only by establishing independent courses of IE for both undergraduate and graduate students, but also by incorporating IE principles and knowledge modules into an increasing number of courses. During 2002–2015, a total of 1,023 undergraduates from 33 schools and departments participated in an IE course. To cope with the diversity of participants, four knowledge modules were customized for an undergraduate course: concepts and history; methods and tools; topics and applications; and policy and perspectives. Meanwhile, an interdisciplinary teaching method was adopted by inviting experts from diverse disciplines and organizing group discussions. Though the course has received strong positive feedback, four challenges still remain in IE education: defining the knowledge boundary, presenting an integrated view, utilizing an interdisciplinary methodology, and cultivating a class culture.     

The Effect of Age and Sex on Object Exploration and Manipulative Behavior in a Neotropical Raptor,the Chimango Caracara,Milvago chimango

We studied object exploration and manipulative behavior in wild‐caught Chimango Caracaras (Milvago chimango), an opportunistic and generalist raptor species, in relation to age and sex differences. Each bird was presented with six objects. We then recorded the latencies to approach and first contact with the objects, the number of objects explored, and the number of exploration events performed on each object. Age influenced the tendency to explore in M. chimango. Compared with adults, juveniles were more likely to explore the objects, approaching and contacting them more quickly. The number of objects explored was also higher in young than adult birds. Both age classes used a variety of manipulative behaviors to explore the objects, some of which have been described as play in others studies. Sex did not affect an individual's likelihood to explore or the number and frequency of manipulative behaviors used during object exploration. The tendency for both young and adult birds to explore and manipulate objects that not resemble prey is likely to be a distinct advantage for a generalist species like M. chimango which must cope with a high diversity of modified environments.     

wFleaBase: the <Emphasis Type="Italic">Daphnia</Emphasis> genome database

Background  

wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Commonly known as the water-flea, Daphnia's ecological merit is unequaled among metazoans, largely because of its sentinel role within freshwater ecosystems and over 200 years of biological investigations. By consequence, the Daphnia Genomics Consortium (DGC) has launched an interdisciplinary research program to create the resources needed to study genes that affect ecological and evolutionary success in natural environments.     

Image analysis as a tool for quantitative phycology: a computational approach to cyanobacterial taxa identification

In the following work we discuss the application of image processing and pattern recognition to the field of quantitative phycology. We overview the area of image processing and review previously published literature pertaining to the image analysis of phycological images and, in particular, cyanobacterial image processing. We then discuss the main operations used to process images and quantify data contained within them. To demonstrate the utility of image processing to cyanobacteria classification, we present details of an image analysis system for automatically detecting and classifying several cyanobacterial taxa of Lake Biwa, Japan. Specifically, we initially target the genus Microcystis for detection and classification from among several species of Anabaena. We subsequently extend the system to classify a total of six cyanobacteria species. High-resolution microscope images containing a mix of the above species and other nontargeted objects are analyzed, and any detected objects are removed from the image for further analysis. Following image enhancement, we measure object properties and compare them to a previously compiled database of species characteristics. Classification of an object as belonging to a particular class membership (e.g., “Microcystis,”“A. smithii,”“Other,” etc.) is performed using parametric statistical methods. Leave-one-out classification results suggest a system error rate of approximately 3%. Received: September 6, 1999 / Accepted: February 6, 2000     

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

We propose definitions and procedures for comparing nucleosome maps and discuss current agreement and disagreement on the effect of histone sequence preferences on nucleosome organization in vivo.     

A Group I Intron in the Nuclear Small Subunit rRNA Gene of Cryptendoxyla hypophloia, an Ascomycetous Fungus: Evidence for a New Major Class of Group I Introns

The ascomycetous fungus Cryptendoxyla hypophloia contains an insertion of 433 base pairs in the genes encoding nuclear small subunit ribosomal RNA. Secondary structure analyses of the insert reveal characteristics indicative of a Group I intron, including elements P, Q, R, and S; however, the sequences of these conserved regions deviate significantly from recognized consensus sequences for Group I introns. Principal-components analysis, based on 79 nucleotide positions from the conserved core sequences of 93 Group I introns, identified 17 introns similar to that of C. hypophloia. This grouping, which includes inserts from phylogenetically diverse organisms, cannot readily be classified in any previously recognized major group of Group I introns. We propose the creation of a new group, IE, to accommodate these sequences, and discuss the evolutionary relationships between group IE and other major groups of Group I introns. Received: 11 January 1998 / Accepted: 12 October 1998     

Proposed definitions related to induced disease resistance

A clear definition of induced disease resistance is lacking, even though the area has been extensively researched and described. The lack of a precise definition leads to potential confusion on whether an underlying mechanism for biological control is induced resistance. We propose definitions, which were developed at a NATO Advanced Research Workshop on biological control, for induced disease resistance and related terms. These definitions are intended to invoke debate and increase effective communication among investigators of induced resistance.     

Everything you wanted to ask about EEG but were afraid to get the right answer

We answer several important questions concerning EEG. We also shortly discuss importance of nonlinear methods of contemporary physics in EEG analysis. Basic definitions and explanation of fundamental concepts may be found in my previous publications in NBP.     

A formalization of consensus index methods

A consensus in dex method comprises a consensus method and a consensus index that are defined on a common set of objects (e.g. classifications). For each profile of objects, the consensus method returns a consensus object representing information or structure shared among profile objects, while the consensus index returns a quantitative measure of agreement among profile objects. Since the relationship between consensus method and consensus index is poorly understood, we propose simple axioms prescribing it in the most general terms. Many taxonomic consensus index methods violate these axioms because their consensus indices measure consensus object invariants rather than profile agreement. We propose paradigms to obtain consensus index methods that measure agreement and satisfy the axioms. These paradigms salvage concepts underlying consensus index methods violating the axioms. This work was supported in part by the Faculty of Science at Memorial University of Newfoundland, and by the Natural Sciences and Engineering Research Council of Canada Under Grant A-4142.     

Coregulation mapping based on individual phenotypic variation in response to virus infection

Background

Biology is moving fast toward the virtuous circle of other disciplines: from data to quantitative modeling and back to data. Models are usually developed by mathematicians, physicists, and computer scientists to translate qualitative or semi-quantitative biological knowledge into a quantitative approach. To eliminate semantic confusion between biology and other disciplines, it is necessary to have a list of the most important and frequently used concepts coherently defined.

Results

We propose a novel paradigm for generating new concepts for an ontology, starting from model rather than developing a database. We apply that approach to generate concepts for cell and molecule interaction starting from an agent based model. This effort provides a solid infrastructure that is useful to overcome the semantic ambiguities that arise between biologists and mathematicians, physicists, and computer scientists, when they interact in a multidisciplinary field.

Conclusions

This effort represents the first attempt at linking molecule ontology with cell ontology, in IMGT-ONTOLOGY, the well established ontology in immunogenetics and immunoinformatics, and a paradigm for life science biology. With the increasing use of models in biology and medicine, the need to link different levels, from molecules to cells to tissues and organs, is increasingly important.     

A mobile agent model for fault-tolerant manipulation on distributed objects

In this paper, we discuss how to realize fault-tolerant applications on distributed objects. Servers supporting objects can be fault-tolerant by taking advantage of replication and checkpointing technologies. However, there is no discussion on how application programs being performed on clients are tolerant of clients faults. For example, servers might block in the two-phase commitment protocol due to the client fault. We newly discuss how to make application programs fault-tolerant by taking advantage of mobile agent technologies where a program can move from a computer to another computer in networks. An application program to be performed on a faulty computer can be performed on another operational computer by moving the program in the mobile agent model. In this paper, we discuss a transactional agent model where a reliable and efficient application for manipulating objects in multiple computers is realized in the mobile agent model. In the transactional agent model, only a small part of the application program named routing subagent moves around computers. A routing subagent autonomously finds a computer which to visit next. We discuss a hierarchical navigation map which computer should be visited price to another computer in a transactional agent. A routing subagent makes a decision on which computer visit for the hierarchical navigation map. Programs manipulating objects in a computer are loaded to the computer on arrival of the routing subagent in order to reduce the communication overhead. This part of the transactional agent is a manipulating subagent. The manipulation subagent still exists on the computer even after the routing subagent leaves the computer in order to hold objects until the commitment. We assume every computer may stop by fault while networks are reliable. There are kinds of faulty computers for a transactional agent; current, destination, and sibling computers where a transactional agent now exists, will move, and has visited, respectively. The types of faults are detected by neighbouring manipulation subagents by communicating with each other. If some of the manipulation subagents are faulty, the routing subagent has to be aborted. However, the routing subagent is still moving. We discuss how to efficiently deliver the abort message to the moving routing subagent. We evaluate the transactional agent model in terms of how long it takes to abort the routing subagent if some computer is faulty.

An Efficient Alternative to Average Ranks for Testing with Incomplete Ranking Data

In this paper we consider the setting where a group of n judges are to independently rank a series of k objects, but the intended complete rankings are not realized and we are faced with analyzing randomly incomplete ranking vectors. In this paper we propose a new testing procedure for dealing with such data realizations. We concentrate on the problem of testing for no differences in the objects being ranked (i.e., they are indistinguishable) against general alternatives, but our approach could easily be extended to restricted (e.g., ordered or umbrella) alternatives. Using an improvement of a preliminary screening approach previously proposed by the authors, we present an algorithm for computation of the relevant Friedman‐type statistic in the general alternatives setting and present the results of an extensive simulation study comparing the new procedure with the standard approach of imputing average within‐judge ranks to the unranked objects.     

Classifying tissue samples from measurements on cells with within-class tissue sample heterogeneity

We consider here the problem of classifying a macro-level object based on measurements of embedded (micro-level) observations within each object, for example, classifying a patient based on measurements on a collection of a random number of their cells. Classification problems with this hierarchical, nested structure have not received the same statistical understanding as the general classification problem. Some heuristic approaches have been developed and a few authors have proposed formal statistical models. We focus on the problem where heterogeneity exists between the macro-level objects within a class. We propose a model-based statistical methodology that models the log-odds of the macro-level object belonging to a class using a latent-class variable model to account for this heterogeneity. The latent classes are estimated by clustering the macro-level object density estimates. We apply this method to the detection of patients with cervical neoplasia based on quantitative cytology measurements on cells in a Papanicolaou smear. Quantitative cytology is much cheaper and potentially can take less time than the current standard of care. The results show that the automated quantitative cytology using the proposed method is roughly equivalent to clinical cytopathology and shows significant improvement over a statistical model that does not account for the heterogeneity of the data.     

Controlled rotation of biological microscopic objects using optical line tweezers

Controlled, continuous rotation of cells or intracellular objects was achieved using optical tweezers with an elliptic beam profile (line tweezers), which was generated by placing a cylindrical lens in the path of the trapping beam. By rotating the cylindrical lens, rotation of the elliptic trapping beam and hence of the object trapped therein was achieved. Compared to previously reported techniques for rotation of microscopic objects, this approach is much simpler, gives better utilization of available laser power and also allows much easier control of the trap beam profile. We have used this approach for rotation of biological objects varying in size from 2 to 40 m. At 25 mW trapping beam power at the object plane E. coli bacteria could be rotated at speeds approaching 10 Hz and an intracellular object (presumably a calcium oxalate crystal) trapped inside Elodea densa plant cell could be rotated with speeds of up to 4 Hz. To our knowledge, this is the first report for rotation of an intracellular object.     

Tests of aggregative preferences of wandering salamanders (Aneides vagrans)

Plethodontid salamanders usually exhibit territorial spacing patterns and behaviors. Previous works suggest that plethodontids from Vancouver Island, Canada lack strong territoriality. In one Vancouver Island species, Aneides vagrans, salamanders may even be found in the field in small aggregations. We investigated preferences of A. vagrans for occupied vs unoccupied cover objects and for cover objects occupied by conspecifics of different age/size classes. We also tested A. vagrans preferences for conspecific vs heterospecific salamanders in an attempt to determine if the lack of territoriality by A. vagrans is species-specific and perhaps related to habitat segregation. A. vagrans did not avoid occupied cover objects or exhibit a preference for occupied vs unoccupied sites. Age class did not affect cover object choice. A. vagrans did not avoid heterospecifics that exhibit the highest degree of resource overlap (Plethodon vehiculum), which we believe might be attributable to a benign and resource-rich habitat, although alternative explanations exist. A. vagrans did avoid syntopic newts (Taricha granulosa), though this is probably due to toxic newt skin secretions.     

Nullius in Verba1: Advancing Data Transparency in Industrial Ecology

With the growth of the field of industrial ecology (IE), research and results have increased significantly leading to a desire for better utilization of the accumulated data in more sophisticated analyses. This implies the need for greater transparency, accessibility, and reusability of IE data, paralleling the considerable momentum throughout the sciences. The Data Transparency Task Force (DTTF) was convened by the governing council of the International Society for Industrial Ecology in late 2016 to propose best‐practice guidelines and incentives for sharing data. In this article, the members of the DTTF present an overview of developments toward transparent and accessible data within the IE community and more broadly. We argue that increased transparency, accessibility, and reusability of IE data will enhance IE research by enabling more detailed and reproducible research, and also facilitate meta‐analyses. These benefits will make the results of IE work more timely. They will enable independent verification of results, thus increasing their credibility and quality. They will also make the uptake of IE research results easier within IE and in other fields as well as by decision makers and sustainability practitioners, thus increasing the overall relevance and impact of the field. Here, we present two initial actions intended to advance these goals: (1) a minimum publication requirement for IE research to be adopted by the Journal of Industrial Ecology; and (2) a system of optional data openness badges rewarding journal articles that contain transparent and accessible data. These actions will help the IE community to move toward data transparency and accessibility. We close with a discussion of potential future initiatives that could build on the minimum requirements and the data openness badge system.     

Poisons,toxungens, and venoms: redefining and classifying toxic biological secretions and the organisms that employ them

Despite extensive study of poisonous and venomous organisms and the toxins they produce, a review of the literature reveals inconsistency and ambiguity in the definitions of ‘poison’ and ‘venom’. These two terms are frequently conflated with one another, and with the more general term, ‘toxin.’ We therefore clarify distinctions among three major classes of toxins (biological, environmental, and anthropogenic or man‐made), evaluate prior definitions of venom which differentiate it from poison, and propose more rigorous definitions for poison and venom based on differences in mechanism of delivery. We also introduce a new term, ‘toxungen’, thereby partitioning toxic biological secretions into three categories: poisons lacking a delivery mechanism, i.e. ingested, inhaled, or absorbed across the body surface; toxungens delivered to the body surface without an accompanying wound; and venoms, delivered to internal tissues via creation of a wound. We further propose a system to classify toxic organisms with respect to delivery mechanism (absent versus present), source (autogenous versus heterogenous), and storage of toxins (aglandular versus glandular). As examples, a frog that acquires toxins from its diet, stores the secretion within cutaneous glands, and transfers the secretion upon contact or ingestion would be heteroglandular–poisonous; an ant that produces its own toxins, stores the secretion in a gland, and sprays it for defence would be autoglandular–toxungenous; and an anemone that produces its own toxins within specialized cells that deliver the secretion via a penetrating wound would be autoaglandular–venomous. Adoption of our scheme should benefit our understanding of both proximate and ultimate causes in the evolution of these toxins.     

Nearnest behavior of a solitary muddaubing wasp,Sceliphron caementarium (Hymenoptera: Sphecidae)

Mud dauber wasps (Sceliphronspp.)construct nests by sequential flights to gather mud and return it to their aerial nests. Individual S. caementariumdiffer in the mean time spent in four states of construction: approach, daubing, inspection, and departure. Placing a novel object near nests or replacing a white object by a black one resulted in an increase in individuals' approach times but no change in departure times. Removal of objects or replacing a black object by a white one had no effect. A change in the color of objects near nests elicited increased approach times but did not affect departure. S. caementariumappears to memorize three-dimensional objects in the nearnest environment, and changes in the nearnest environment are learned during the approach flight to the nest. The frequency of significant responses to all manipulations decreased with successive visits by the wasps, suggesting habituation to nearnest changes.