A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

Long-term monitoring of habitats and reef fish found inside and outside the U.S. Virgin Islands Coral Reef National Monument: a comparative assessment

The primary objective of this study was to assess the efficacy of the Virgin Islands Coral Reef National Monument (VICR), a marine protected area in St John, US Virgin Islands. Surveys of habitat and fishes inside and outside of VICR were conducted in 2003-2008. Areas outside the VICR had significantly more scleractinian corals, greater habitat complexity, and greater species richness and density of reef fishes than areas inside., Areas inside and outside the VICR exhibited significant decreases in percent scleractinian coral coverage over the study period. A contrasting trend of increasing macroalgal cover was also observed. No clear effect of the severe 2005 coral bleaching event was observed suggesting other causal factors. No obvious trends in the fish community were observed across the study period. The significant decline in habitat condition, coupled with the initial incorporation of some of the more degraded reefs into the marine protected area may result in a longer time period necessary to detect positive changes in the St. John coral reef ecosystem and associated reef fish abundance and community structure.

Radiocarbon record of solar variability and Holocene climatic change in coastal southern California

EXTRACT (SEE PDF FOR FULL ABSTRACT): Pollen analysis and 5 radiocarbon dates for a 687-cm core provide a detailed chronology of environmental change for San Joaquin Marsh at the head of Newport Bay, Orange County, California. Sediment deposition kept pace with sea level rise during the mid-Holocene, but after 4500 years BP, sea water regularly reached the coring site, and salt marsh was the local vegetation. Brief periods of dominance by fresh-water vegetation 3800, 2800, 2300 and after 560 years BP correlate global cooling events and (except the 3800-year BP event) with carbon-14 production anomalies. The coincidence of climate change and carbon-14 anomalies support a causal connection with solar variability, but regardless of the causal mechanism(s) the delta-carbon-14 curves provide a chronology for global, high-frequency climatic change comparable to that of Milankovitch cyclicity for longer time scales.

Near and distant connection of atmospheric systems to ocean temperature change in the coastal California Current region

In studying hydrosphere, atmosphere, and biosphere interactions, it is useful to focus on specific subsystem processes and energy exchanges (forcing). Since subsystem scales range over ten orders of magnitude, it may be difficult to focus research on scales that will yield useful results in terms of establishing causal and predictive connections between more easily and less easily observed subsystems. In an effort to find pertinent scales, we have begun empirical investigations into relationships between atmospheric, oceanic, and biological systems having spatial scales exceeding 10^3 kilometers and temporal scales of six months or more.

Manipulation of chromosomes in fish: review of various techniques and their implications in aquaculture

Human ingenuity has made it possible to advent the chromosome manipulation techniques to produce individuals with differing genomic status in a number of fish using various causal agents such as physical shocks (temperature or hydrostatic pressure), chemical (endomitotics) and anesthetic treatments either to suppress the second meiotic division shortly after fertilization of eggs or to prevent the first mitotic division shortly prior to mitotic cleavage formation. This results in the induction of polyploidy (triploidy and tetraploidy), gynogenesis (both meiotic and mitotic leading to clonal lines) and androgenesis in fish population. The rationale for the induction of such ploidy in fish has been its potential for generating sterile individuals, rapidly inbred lines and masculinized fish, which could be of benefit to fish farming and aquaculture. In this paper, these are critically reviewed and the implication of recently developed chromosome manipulation techniques to various fin fishes is discussed.

Network structure preserving model reduction with weak a priori structural information

This paper extends a state projection method for structure preserving model reduction to situations where only a weaker notion of system structure is available. This weaker notion of structure, identifying the causal relationship between manifest variables of the system, is especially relevant is settings such as systems biology, where a clear partition of state variables into distinct subsystems may be unknown, or not even exist. The resulting technique, like similar approaches, does not provide theoretical performance guarantees, so an extensive computational study is conducted, and it is observed to work fairly well in practice. Moreover, conditions characterizing structurally minimal realizations and sufficient conditions characterizing edge loss resulting from the reduction process, are presented. ©2009 IEEE.

Integrated online speaker clustering and adaptation

For many applications, it is necessary to produce speech transcriptions in a causal fashion. To produce high quality transcripts, speaker adaptation is often used. This requires online speaker clustering and incremental adaptation techniques to be developed. This paper presents an integrated approach to online speaker clustering and adaptation which allows efficient clustering of speakers using the same accumulated statistics that are normally used for adaptation. Using a consistent criterion for both clustering and adaptation should yield gains for both stages. The proposed approach is evaluated on a meetings transcription task using audio from multiple distant microphones. Consistent gains over standard clustering and adaptation were obtained. Copyright © 2011 ISCA.

A structured modelling approach to simulating dynamic behaviours in complex organisations

This article reports a case study application of a systematic approach to modelling complex organisations, centred on simulation modelling (SM). The approach leads to populated instances of complementary model types, in ways that systematically capture, validate and facilitate various uses of organisational understandings, knowledge and data normally distributed amongst multiple knowledge holders. The model-driven approach to decision making enables improved manufacturing responsiveness. Literature on modelling technologies relevant to manufacturing systems organisation design and change is presented, as is literature on production planning and control. This provides a rationale for the development of a new modelling methodology which combines the use of enterprise, causal loop and SM. Subsequently, this article describes how in the case of a specific manufacturing enterprise the combined modelling techniques have informed the choice of alternative production planning and control policies. An example enterprise model of a capacitor manufacturing company is illustrated as derivative causal-loop models that structure and enable the design and use of a general purpose simulation model.

Unified modelling in support of organization design and change

The aim of this research is to provide a unified modelling-based method to help with the evaluation of organization design and change decisions. Relevant literature regarding model-driven organization design and change is described. This helps identify the requirements for a new modelling methodology. Such a methodology is developed and described. The three phases of the developed method include the following. First, the use of CIMOSA-based multi-perspective enterprise modelling to understand and capture the most enduring characteristics of process-oriented organizations and externalize various types of requirement knowledge about any target organization. Second, the use of causal loop diagrams to identify dynamic causal impacts and effects related to the issues and constraints on the organization under study. Third, the use of simulation modelling to quantify the effects of each issue in terms of organizational performance. The design and case study application of a unified modelling method based on CIMOSA (computer integrated manufacturing open systems architecture) enterprise modelling, causal loop diagrams, and simulation modelling, is explored to illustrate its potential to support systematic organization design and change. Further application of the proposed methodology in various company and industry sectors, especially in manufacturing sectors, would be helpful to illustrate complementary uses and relative benefits and drawbacks of the methodology in different types of organization. The proposed unified modelling-based method provides a systematic way of enabling key aspects of organization design and change. The case company, its relevant data, and developed models help to explore and validate the proposed method. The application of CIMOSA-based unified modelling method and integrated application of these three modelling techniques within a single solution space constitutes an advance on previous best practice. Also, the purpose and application domain of the proposed method offers an addition to knowledge. © IMechE 2009.

Dynamical structure function identifiability conditions enabling signal structure reconstruction

Networks of controlled dynamical systems exhibit a variety of interconnection patterns that could be interpreted as the structure of the system. One such interpretation of system structure is a system's signal structure, characterized as the open-loop causal dependencies among manifest variables and represented by its dynamical structure function. Although this notion of structure is among the weakest available, previous work has shown that if no a priori structural information is known about the system, not even the Boolean structure of the dynamical structure function is identifiable. Consequently, one method previously suggested for obtaining the necessary a priori structural information is to leverage knowledge about target specificity of the controlled inputs. This work extends these results to demonstrate precisely the a priori structural information that is both necessary and sufficient to reconstruct the network from input-output data. This extension is important because it significantly broadens the applicability of the identifiability conditions, enabling the design of network reconstruction experiments that were previously impossible due to practical constraints on the types of actuation mechanisms available to the engineer or scientist. The work is motivated by the proteomics problem of reconstructing the Per-Arnt-Sim Kinase pathway used in the metabolism of sugars. © 2012 IEEE.

Integrating design attributes, knowledge and uncertainty in aerospace sector

The delivery of integrated product and service solutions is growing in the aerospace industry, driven by the potential of increasing profits. Such solutions require a life cycle view at the design phase in order to support the delivery of the equipment. The influence of uncertainty associated with design for services is increasingly a challenge due to information and knowledge constraints. There is a lack of frameworks that aim to define and quantify relationship between information and knowledge with uncertainty. Driven by this gap, the paper presents a framework to illustrate the link between uncertainty and knowledge within the design context for services in the aerospace industry. The paper combines industrial interaction and literature review to initially define the design attributes, the associated knowledge requirements and the uncertainties experienced. The framework is then applied in three cases through development of causal loop models (CLMs), which are validated by industrial and academic experts. The concepts and inter-linkages are developed with the intention of developing a software prototype. Future recommendations are also included. © 2014 CIRP.

Unified expressions of all integral variational principles

In terms of the quantitative causal principle, this paper obtains a general variational principle, gives unified expressions of the general, Hamilton, Voss, Holder, Maupertuis-Lagrange variational principles of integral style, the invariant quantities of the general, Voss, Holder, Maupertuis-Lagrange variational principles are given, finally the Noether conservation charges of the general, Voss, Holder, Maupertuis-Lagrange variational principles axe deduced, and the intrinsic relations among the invariant quantities and the Noether conservation charges of all the integral variational principles axe achieved.

多表征模型组合仿真的形式描述与因果序研究

多表征模型组合仿真是可组合仿真、遗留系统集成的重要研究领域，也是多表征建模与仿真的一项关键技术，无论在理论研究还是实际应用上都有重要意义。本文针对多表征模型组合仿真问题在以下几个方面展开了较深入的研究：（1）并发控制机制；（2）多表征模型组合的形式描述；（3）因果序保持；（4）所有权管理服务。 在分析并发表示法特点的基础上，针对并发表示法中对于交互控制过于集中的问题，将集中式的并发控制机制改为分布式的并发控制机制，改进了整个并发控制的体系结构模型；对于多表征实体中的集中式并发控制处理中容易造成服务瓶颈的问题，利用多表征仿真的分层交互规则，将原有的单个交互消解器和一致性执行器改成分布式的控制方式，以有效缓解单个交互消解器的负担。 在改进的采用分布式并发控制机制的体系结构基础上，对多表征模型组合的机制及过程进行了分析，然后使用并行离散事件规范PDEVS对多表征原子模型与耦合模型进行了形式化定义，证明了多表征耦合模型具有耦合封闭性，这使得可以将多表征耦合模型与其它的多表征原子模型或多表征耦合模型一起不断地组合成更大的系统，即多表征模型可以以构件耦合的方式层次式地组成整个仿真系统。并提出了一个多表征模型组合框架。通过多表征模型组合框架清晰地描述了多表征模型组合的过程以及与HLA/RTI协调的机制。 针对HLA时间管理服务中没有提供因果排序机制，而多表征模型组合仿真需要保证以因果序提交模型交互的问题，我们通过引入向量时间，设计了一个符合因果序提交的通信协议，并对其相关的正确性问题进行了证明。 分析了HLA所有权协议应用于多表征模型组合仿真时存在的不足，并以HLA协商型推模式所有权服务为例进行了改进，使得所有权协议可以支持指定某个成员为对象属性所有权的接收者、解决了RTI不存储释放了所有权的属性的更新值，以及HLA属性所有权服务本身不包含时间管理机制等问题。

甘肃西峰黄土剖面500 ka以来的蜗牛化石记录及其古气候、古环境变化研究

The loess-paleosol sequences in China are among the best continental records of paleoclimate changes. Although numerous sedimentological and geochemical studies have contributed greatly to the understanding of past climate changes during this period, it is still necessary to decipher more details through investigating these sequences using various approaches including biological analyses. In this study, we analyze the mollusk fossil assemblages preserved in the upper part of the Xifeng section, from the fifth loess layer (L5) to the Holocene soil (S0), with the sampling interval of 10 cm. The main results and conclusions obtained are as follows: 1. A continuous terrestrial mollusk fossil record, covering the past 500 ka, has been obtained from the Xifeng loess-paleosol sequence, which provides important biological data for the study of paleoenvironmental changes in the Loess Plateau and its comparison with marine record during this period. A total of 475 mollusk assemblages were studied, and twenty-one species have been identified among the 210,000 mollusk individuals counted. Among these species, most have modern representatives and are found in previous terrestrial mollusk studies of Chinese loess-paleosol sequences. Thus, they can be grouped into cold-aridiphilous, thermo-humidiphilous, oriental, and cool-humidiphilous ecological groups, as defined by previous studies. 2. Comparison of mollusk assemblages between the last five glacials and four interglacials and Holocene shows very different climate conditions. The warmest period occurred at MIS 11, MIS 5e, and Holocene, respectively. The coldest period is the Last Glacial Maximam, rather than the MIS 12. 3. Our mollusk record provides insight into the climate conditions in the Loess Plateau during the MIS 11, interpreted as the closest analog to the present interglacial. S4 paleosol, equivalent of MIS 11, developed under two major different climate regimes: ranging from the very warm–humid early phase to the mild-cool late interval. Furthermore, a cooling spell has been documented at the interglacial optimum, reflecting unstable climate conditions. The early warm–humid conditions lasted over 30 ka, supporting that MIS 11 is a unique long interglacial in the Quaternary climate history. 4. Comparison of MIS 11 and Holocene climates based on the mollusk species compositions indicates major differences. The climate at the early part of MIS 11 was warmer and more humid than during the Holocene optimum period, but the conditions during the late part of MIS 11 were similar to or cooler than late Holocene. Our study indicates that the extent of warming during the Holocene might be significantly less than the conditions that prevailed during the early part of MIS 11 interglacial period. 5. Two strong summer monsoon events were observed during the MIS 12 and MIS 10. They correspond to the maximam values of insolation gradient between low and high latitudes, suggesting a causal linkage. 6. Our study, combined with the previously investigated Luochuan land snail record, reveals that the climate in the Loess Plateau during MIS 3 experienced three stages: relatively warm, humid climate prevailed during MIS 3c, relatively cold, dry climate during MIS 3b, and relatively warm-humid period during MIS 3a. Climate at this time fluctuated frequently in Luochuan, and changed from warm-cool to cold-dry in Xifeng. Our results reveal that the relatively warm-humid climate during MIS 3c may be resulted from an increasing insolation gradient controlled by obliquity. Our result also reveals that obvious regional difference existed in the Loess Plateau during MIS 3. A greater climate gradient occurred during this time compared with today’s climate pattern in the Loess Plateau.