Loss of allele diversity in introduced populations of the hermaphroditic bay scallop Argopecten irradians

The bay scallop Argopecten irradians is a hermaphroditic bivalve native to the Atlantic coast of the United States that was introduced to China for aquaculture production in 1982. It now supports a major aquaculture industry in China. Introduced species often start with limited genetic variability, which is problematic for the further selective breeding. Bay scallop aquaculture is exclusively hatchery based and as the initial introduction consisted of only 26 scallops, there have been concerns about inbreeding and inbreeding depression in cultured populations in China. In this study, eleven simple sequence repeat (SSR) markers were used to compare genetic variation in cultured populations from China with that in a natural population from the east coast of America. Although the difference in heterozygosity was small, the Chinese populations lost 9 of the 45 alleles (20%) found in the wild population. The reduced allele diversity suggests that the Chinese bay scallop populations experienced a bottleneck in genetic diversity that remains significant despite several recent introductions of new stocks aimed at expanding the gene pool. The loss of allele diversity may affect future efforts in selective breeding and domestication, and results of this study highlight the need for additional introductions, advanced breeding programs that minimize inbreeding and continued genetic monitoring. (c) 2007 Elsevier B.V. All rights reserved.

Determination of fractional energy loss of waves in nearshore waters using an improved high-order Boussinesq-type model

Fractional energy losses of waves due to wave breaking when passing over a submerged bar are studied systematically using a modified numerical code that is based on the high-order Boussinesq-type equations. The model is first tested by the additional experimental data, and the model's capability of simulating the wave transformation over both gentle slope and steep slope is demonstrated. Then, the model's breaking index is replaced and tested. The new breaking index, which is optimized from the several breaking indices, is not sensitive to the spatial grid length and includes the bottom slopes. Numerical tests show that the modified model with the new breaking index is more stable and efficient for the shallow-water wave breaking. Finally, the modified model is used to study the fractional energy losses for the regular waves propagating and breaking over a submerged bar. Our results have revealed that how the nonlinearity and the dispersion of the incident waves as well as the dimensionless bar height (normalized by water depth) dominate the fractional energy losses. It is also found that the bar slope (limited to gentle slopes that less than 1:10) and the dimensionless bar length (normalized by incident wave length) have negligible effects on the fractional energy losses.

Tandem duplication-random loss is not a real feature of oyster mitochondrial genomes

Duplications and rearrangements of coding genes are major themes in the evolution of mitochondrial genomes, bearing important consequences in the function of mitochondria and the fitness of organisms. Yu et al. (BMC Genomics 2008, 9: 477) reported the complete mt genome sequence of the oyster Crassostrea hongkongensis (16,475 bp) and found that a DNA segment containing four tRNA genes (trnK(1), trnC, trnQ(1) and trnN), a duplicated (rrnS) and a split rRNA gene (rrnL5') was absent compared with that of two other Crassostrea species. It was suggested that the absence was a novel case of "tandem duplication-random loss" with evolutionary significance. We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence. Further, we designed primers, verified sequences and demonstrated that the sequence loss in Yu et al.'s study was an artifact caused by placing primers in a duplicated region. The duplication and split of ribosomal RNA genes are unique for Crassostrea oysters and not lost in C. hongkongensis. Our study highlights the need for caution when amplifying and sequencing through duplicated regions of the genome.

Pure mechanical wear loss measurement in corrosive wear

The method for the measurement of the pure mechanical wear loss for 321 stainless steel, 1045 steel and pure iron in the study of the synergy between corrosion and wear was studied, The methods studied included the measurement in distilled water, by cathodic protection and by adding inhibitor KI, and all were compared with the wear loss in air. The experiment showed that the pure mechanical wear losses and friction coefficients obtained by the three methods were close to each other and can be used to calculate the various wear components in the study of the interaction of corrosion and wear, but the measurements in distilled water for pure iron and 1045 steel are not recommended due to their corrosion.

Experimental warming causes large and rapid species loss, dampened by simulated grazing, on the Tibetan Plateau

We investigated the independent and combined effects of experimental warming and grazing on plant species diversity on the north-eastern Tibetan Plateau, a region highly vulnerable to ongoing climate and land use changes. Experimental warming caused a 26-36% decrease in species richness, a response that was generally dampened by experimental grazing. Higher species losses occurred at the drier sites where N was less available. Moreover, we observed an indirect effect of climate change on species richness as mediated by plant-plant interactions. Heat stress and warming-induced litter accumulation are potential explanations for the species' responses to experimental warming. This is the first reported experimental evidence that climate warming could cause dramatic declines in plant species diversity in high elevation ecosystems over short time frames and supports model predictions of species losses with anthropogenic climate change.

Natural Language Syntax and First Order Preference

We have argued elsewhere that first order inference can be made more efficient by using non-standard syntax for first order logic. In this paper we show how a fragment of English syntax under Montague semantics provides the foundation of a new inference procedure. This procedure seems more effective than corresponding procedures based on either classical syntax of our previously proposed taxonomic syntax. This observation may provide a functional explanation for some of the syntactic structure of English.

Computational Consequences of Agreement and Ambiguity in Natural Language

The computer science technique of computational complexity analysis can provide powerful insights into the algorithm-neutral analysis of information processing tasks. Here we show that a simple, theory-neutral linguistic model of syntactic agreement and ambiguity demonstrates that natural language parsing may be computationally intractable. Significantly, we show that it may be syntactic features rather than rules that can cause this difficulty. Informally, human languages and the computationally intractable Satisfiability (SAT) problem share two costly computional mechanisms: both enforce agreement among symbols across unbounded distances (Subject-Verb agreement) and both allow ambiguity (is a word a Noun or a Verb?).

The Behavior Language; User's Guide

The Behavior Language is a rule-based real-time parallel robot programming language originally based on ideas from [Brooks 86], [Connell 89], and [Maes 89]. It compiles into a modified and extended version of the subsumption architecture [Brooks 86] and thus has backends for a number of processors including the Motorola 68000 and 68HCll, the Hitachi 6301, and Common Lisp. Behaviors are groups of rules which are activatable by a number of different schemes. There are no shared data structures across behaviors, but instead all communication is by explicit message passing. All rules are assumed to run in parallel and asynchronously. It includes the earlier notions of inhibition and suppression, along with a number of mechanisms for spreading of activation.

Advanced Programming Language Features for Executable Design Patterns "Better Patterns Through Reflection

The Design Patterns book [GOF95] presents 24 time-tested patterns that consistently appear in well-designed software systems. Each pattern is presented with a description of the design problem the pattern addresses, as well as sample implementation code and design considerations. This paper explores how the patterns from the "Gang of Four'', or "GOF'' book, as it is often called, appear when similar problems are addressed using a dynamic, higher-order, object-oriented programming language. Some of the patterns disappear -- that is, they are supported directly by language features, some patterns are simpler or have a different focus, and some are essentially unchanged.

Revised Report on the Algorithmic Language Scheme

Data and procedures and the values they amass, Higher-order functions to combine and mix and match, Objects with their local state, the message they pass, A property, a package, the control of point for a catch- In the Lambda Order they are all first-class. One thing to name them all, one things to define them, one thing to place them in environments and bind them, in the Lambda Order they are all first-class. Keywords: Scheme, Lisp, functional programming, computer languages.

Leveraging Learning and Language Via Communication Bootstrapping

In a Communication Bootstrapping system, peer components with different perceptual worlds invent symbols and syntax based on correlations between their percepts. I propose that Communication Bootstrapping can also be used to acquire functional definitions of words and causal reasoning knowledge. I illustrate this point with several examples, then sketch the architecture of a system in progress which attempts to execute this task.

Naive Physics, Event Perception, Lexical Semantics, and Language Acquisition

This thesis proposes a computational model of how children may come to learn the meanings of words in their native language. The proposed model is divided into two separate components. One component produces semantic descriptions of visually observed events while the other correlates those descriptions with co-occurring descriptions of those events in natural language. The first part of this thesis describes three implementations of the correlation process whereby representations of the meanings of whole utterances can be decomposed into fragments assigned as representations of the meanings of individual words. The second part of this thesis describes an implemented computer program that recognizes the occurrence of simple spatial motion events in simulated video input.

ARLO: Another Representation Language Offer

This paper describes ARLO, a representation language loosely modelled after Greiner and Lenant's RLL-1. ARLO is a structure-based representation language for describing structure-based representation languages, including itself. A given representation language is specified in ARLO by a collection of structures describing how its descriptions are interpreted, defaulted, and verified. This high level description is compiles into lisp code and ARLO structures whose interpretation fulfills the specified semantics of the representation. In addition, ARLO itself- as a representation language for expressing and compiling partial and complete language specifications- is described and interpreted in the same manner as the language it describes and implements. This self-description can be extended of modified to expand or alter the expressive power of ARLO's initial configuration. Languages which describe themselves like ARLO- provide powerful mediums for systems which perform automatic self-modification, optimization, debugging, or documentation. AI systems implemented in such a self-descriptive language can reflect on their own capabilities and limitations, applying general learning and problem solving strategies to enlarge or alleviate them.