DOES SIZE MATTER MOST? THE EFFECT OF GROWTH HISTORY ON PROBABILISTIC REACTION NORM FOR SALMON MATURATION

Body size is widely believed to affect the occurrence of sexual maturation. Recent studies have used changes in the age-specific body size at which the probability of maturing is 50%, a feature of probabilistic reaction norms, to quantify purported evolution of life histories. However, body size results from a combination of growth rates during successive developmental stages. Therefore, to understand the evolution of the maturation schedule, it is necessary to comprehend the relationships among body size, growth history, and maturation schedule. We examined the relationships among body size, previous growth history, and maturation probability in chum salmon (Oncorhynchus keta). In this study, previous growth history was estimated from yearly specific growth increments that provide information describing body size. Previous growth history was found to be more closely linked to maturation probability than body size. The most recent growth condition was the most important factor affecting whether a fish matured during the subsequent breeding season. Because individuals of similar body size and same age can have different growth histories, the relationship between body size and maturation probability could be plastically modified by growth history. This may violate an assumption required to infer evolution, namely that size-related maturation trends in probabilistic reaction norms are immune to growth history.     

Design of multispecific protein sequences using probabilistic graphical modeling

In nature, proteins partake in numerous protein– protein interactions that mediate their functions. Moreover, proteins have been shown to be physically stable in multiple structures, induced by cellular conditions, small ligands, or covalent modifications. Understanding how protein sequences achieve this structural promiscuity at the atomic level is a fundamental step in the drug design pipeline and a critical question in protein physics. One way to investigate this subject is to computationally predict protein sequences that are compatible with multiple states, i.e., multiple target structures or binding to distinct partners. The goal of engineering such proteins has been termed multispecific protein design. We develop a novel computational framework to efficiently and accurately perform multispecific protein design. This framework utilizes recent advances in probabilistic graphical modeling to predict sequences with low energies in multiple target states. Furthermore, it is also geared to specifically yield positional amino acid probability profiles compatible with these target states. Such profiles can be used as input to randomly bias high‐throughput experimental sequence screening techniques, such as phage display, thus providing an alternative avenue for elucidating the multispecificity of natural proteins and the synthesis of novel proteins with specific functionalities. We prove the utility of such multispecific design techniques in better recovering amino acid sequence diversities similar to those resulting from millions of years of evolution. We then compare the approaches of prediction of low energy ensembles and of amino acid profiles and demonstrate their complementarity in providing more robust predictions for protein design. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

GEMS: Gossip-Enabled Monitoring Service for Scalable Heterogeneous Distributed Systems

Gossip protocols have proven to be effective means by which failures can be detected in large, distributed systems in an asynchronous manner without the limitations associated with reliable multicasting for group communications. In this paper, we discuss the development and features of a Gossip-Enabled Monitoring Service (GEMS), a highly responsive and scalable resource monitoring service, to monitor health and performance information in heterogeneous distributed systems. GEMS has many novel and essential features such as detection of network partitions and dynamic insertion of new nodes into the service. Easily extensible, GEMS also incorporates facilities for distributing arbitrary system and application-specific data. We present experiments and analytical projections demonstrating scalability, fast response times and low resource utilization requirements, making GEMS a potent solution for resource monitoring in distributed computing.     

Propagating uncertainty in microarray data analysis

Microarray technology is associated with many sources of experimentaluncertainty. In this review we discuss a number of approachesfor dealing with this uncertainty in the processing of datafrom microarray experiments. We focus here on the analysis ofhigh-density oligonucleotide arrays, such as the popular AffymetrixGeneChip® array, which contain multiple probes for eachtarget. This set of probes can be used to determine an estimatefor the target concentration and can also be used to determinethe experimental uncertainty associated with this measurement.This measurement uncertainty can then be propagated throughthe downstream analysis using probabilistic methods. We giveexamples showing how these credibility intervals can be usedto help identify differential expression, to combine informationfrom replicated experiments and to improve the performance ofprincipal component analysis.      

Delineation of spatial boundaries in a wetland habitat

A probabilistic similarity technique was used to locate spatial and temporal biotic boundaries in two west-central Florida marshes. By investigating spatial and temporal boundaries simultaneously, insights into community dynamics that were not apparent from examination of either kind of boundary in isolation were obtained. Recurring spatial boundaries in both marshes were found at the edges of deeper basins or near the edges of the marshes. Spatial boundaries shifted more frequently in Big Marsh, a large, well-drained marsh with extensive transition zones, than in Little Marsh, a poorly drained marsh with a relatively stable water level. Temporal boundaries occurred most frequently in autumn in both marshes. Temporal boundaries were associatd frequently with changes in spatial boundaries in Big Marsh, but only infrequently in Little Marsh. Simultaneous investigation of spatial and temporal boundary dynamics can be used to identify transition zones within marshes and can be used to determine from one year seasonal sampling surveys whether wetland boundaries will remain stable over more than one year.     

An Ecological Risk Assessment of Inorganic Chloramines in Surface Water

Inorganic chloramines are formed when chlorine and ammonia are combined in water. These substances are frequently used as a secondary disinfectant for drinking water and are by-products of processes involving the disinfection of wastewaters and the control of biological fouling in cooling water systems. For chloraminate drinking water, the total residual chlorine (TRC) concentration may be almost completely due to monochloramine. Based on 1995 and 1996 survey data, the most significant and prevalent TRC loading to the Canadian environment is from municipal wastewater releases. Drinking water releases are the next most important source of chloramine entry into the Canadian environment, while TRC releases from other sources, such as cooling water, zebra mussel control practices and industrial wastewater, are much less important. A probabilistic water quality model was used to model two wastewater discharges and a cooling water discharge to different freshwater systems. The resulting exposure distributions were then compared with three incipient lethality endpoints, i.e., 50% mortality to the invertebrate Ceriodaphnia dubia and 50% and 20% mortality to juvenile chinook salmon (Oncorhynchus tshawytscha). For each discharge scenario studied, there were moderate to high probabilities of significant adverse effects on aquatic life up to 1.9?km from the effluent sources.     

Consequences of chemosensory phenomena for leukocyte chemotactic orientation

The stochastic nature of cell surface receptor-ligand binding is known to limit the accuracy of detection of chemoattractant gradients by leukocytes (11, 12), thus limiting the orientation ability that is crucial to the chemotactic response in host defense. The probabilistic cell orientation model of Lauffenburger (11) is extended here to assess the consequences of recently discovered receptor phenomena: “down-regulation” of total surface receptor number, spatial asymmetry of surface receptors, and existence of a higher-affinity receptor subpopulation. In general, a reduction in orientation accuracy is predicted by inclusion of these phenomena. An orientation signal based on a simple model of chemosensory adaptation (i.e., a spatial difference inrelative receptor occupancy) is found to be functionally different from the signal suggested by an experimental correlation (i.e., a spatial difference inabsolute receptor occupancy). However, in the context of receptor “signal noise,” the signal based on adaptation yields predictions in better qualitative agreement with the experimental orientation data of Zigmond (10). From this cell orientation model we can estimate the effective timeaveraging period required for noise diminution to a level allowing orientation predictions to match observed levels. This time-averaging period presumably reflects the time constant for receptor signal transduction and locomotory response.     

基于贝叶斯网络的生态系统服务权衡协同关系及其驱动因子分析——以陕北黄土高原为例

了解生态系统服务的权衡协同关系及其驱动因子效应是实现生态系统有效管理和改善人类福祉的基础。以陕北黄土高原为例，定量评估其2018年土壤保持、产水服务、粮食供给和固碳服务，在构建贝叶斯网络生态系统服务模型的基础上，通过节点的重要性分析识别影响生态系统服务的关键节点，利用联合概率分布、概率推理和情景模拟探讨生态系统服务权衡协同关系及其驱动因子效应。结果表明：（1）陕北黄土高原各类生态系统服务空间异质性较强。其中，土壤保持、产水服务和固碳服务的空间分布情况较为一致，高值区集中在东南部，低值区在西北部，呈"南高北低"的分布特征；粮食供给呈"中部高、南北低"的分布特征。（2）土壤保持、产水服务和固碳服务之间互为协同关系，粮食供给分别与土壤保持、产水服务、固碳服务为权衡关系。其中，产水服务与固碳服务的协同关系、产水服务与粮食供给的权衡关系较强。（3）土地利用、降水和NPP （Net primary production）是影响生态系统服务权衡协同关系的主要驱动因子，其中土地利用主要影响生态系统服务的协同关系，而降水和NPP在影响协同关系的同时对权衡关系也有一定的制约作用。研究发现：不同驱动因子在不同状态下产生相同的协同（或权衡）方式，相同驱动因子在不同状态则会造成协同（或权衡）方式的差异。研究对于认识多种生态系统服务间的复杂关系及其驱动因子差异，为后续提出改善生态系统管理和提高人类福祉的对策与措施，具有重要的理论和实践价值。     

The Correlated Bivariate Inverted Beta Distribution

The correlated bivariate inverted beta distribution is constructed from the bivariate mixture of two independent gamma random variables whose scale parameters follow Kibble's correlated gamma distribution. Explicit expressions have been derived for the form of the joint probability density function, the joint cumulative distributive function and other statistical properties of interest. These results confirm and extend some of the conjectures of HUTCHINSON in connection with generalizations of probabilistic models of severity distribution arising from injuries sustained in two-vehicle head on collison.