Rainbow smelt population responses to species invasions and change in environmental condition

Invasive species can cause major disruptions in native food webs, yet the impact of species introductions and whether they will become invasive appears to be context-dependent. Rainbow smelt and alewife co-exist as invasive species in the Laurentian Great Lakes and as native species on the Atlantic coast of North America, but in Lake Champlain rainbow smelt is the dominant native forage fish and alewife are invasive. Alewife became abundant by 2007, providing an opportunity to explore the dynamics of these two species in a system where only one is invasive. We used data from a 28-year forage fish survey to compare demographics of rainbow smelt populations in three basins of Lake Champlain with different volumes, nutrient levels, and predator abundances. Rainbow smelt catch-per-unit-effort (CPUE) remained constant in the large, deep Main Lake before and after alewife invaded, but decreased in the two smaller basins. Declines were primarily a result of increased age-0 and age-1 mortality. Predation by top piscivores, system productivity, and competition for resources alone could not explain the patterns in CPUE across the basins. The mechanisms that allow alewife and rainbow smelt to co-exist could be related to system volume and oxythermal habitat availability, and may explain why the two species do not negatively affect each other in the Great Lakes. Summer hypoxia in the smaller basins could force individuals into smaller habitat volumes with higher densities of competitors and cannibalistic adult rainbow smelt. Habitat availability may mediate the impact of invasive alewife on native rainbow smelt.     

A neuron membrane mesh representation for visualization of electrophysiological simulations

We present a process to automatically generate three-dimensional mesh representations of the complex, arborized cell membrane surface of cortical neurons (the principal information processing cells of the brain) from nonuniform morphological measurements. Starting from manually sampled morphological points (3D points and diameters) from neurons in a brain slice preparation, we construct a polygonal mesh representation that realistically represents the continuous membrane surface, closely matching the original experimental data. A mapping between the original morphological points and the newly generated mesh enables simulations of electrophysiolgical activity to be visualized on this new membrane representation. We compare the new mesh representation with the state of the art and present a series of use cases and applications of this technique to visualize simulations of single neurons and networks of multiple neurons.     

Designing content distribution networks for optimal cost and performance

One strategy for alleviating excess latency (delay) in the Internet is the caching of web content at multiple locations. This reduces the number of hops necessary to reach the desired content. This strategy is used for web content such as html pages, images, streaming video, and Internet radio. The network of servers which store this content, and the collections of objects stored on each server, is called a content distribution network (CDN). In order to optimally design a CDN, given a network topology with available server storage capacity at various points in the network, one must decide which object collections to place on each server in order to achieve performance or cost objectives. The placements must be within the storage limits of the servers and must reflect the request patterns for each collection of objects to be cached. Researchers have suggested formulations for the CDN problem which address performance by minimizing latency (the average number of hops is a commonly accepted measure of latency) from client to content, or formulations that focus on minimizing cost of storage and/or bandwidth. In this research, we develop a model which allows for the simultaneous treatment of performance and cost, present examples to illustrate the application of the model and perform a detailed designed experiment to gain insights into cost/hops tradeoff for a variety of network parameters.     

Register allocation for write activity minimization on non-volatile main memory for embedded systems

Non-volatile memories are good candidates for DRAM replacement as main memory in embedded systems and they have many desirable characteristics. Nevertheless, the disadvantages of non-volatile memory co-exist with its advantages. First, the lifetime of some of the non-volatile memories is limited by the number of erase operations. Second, read and write operations have asymmetric speed or power consumption in non-volatile memory. This paper focuses on the embedded systems using non-volatile memory as main memory. We propose register allocation technique with re-computation to reduce the number of store instructions. When non-volatile memory is applied as the main memory, reducing store instructions will reduce write activities on non-volatile memory. To re-compute the spills effectively during register allocation, a novel potential spill selection strategy is proposed. During this process, live range splitting is utilized to split certain long live ranges such that they are more likely to be assigned into registers. In addition, techniques for re-computation overhead reduction is proposed on systems with multiple functional units. With the proposed approach, the lifetime of non-volatile memory is extended accordingly. The experimental results demonstrate that the proposed technique can efficiently reduce the number of store instructions on systems with non-volatile memory by 33% on average.     

Ensuring reliability in B2B services: Fault tolerant inter-organizational workflows

In the age of Business-to-Business (B2B) collaboration, ensuring reliability of workflows underlying inter-organizational business processes is of significant importance. There are, however, quite a few challenges towards achieving seamless operation. Such challenges arise from heterogeneity in infrastructure and coordination mechanism at participant organizations, as well as time and cost associated with recovery from failure. Our research presents foundations for a reliable scheme for recovery from failure of workflow processes spanning through multiple business entities. First, a system model is adapted from the mobile computing literature that serves to establish the requirements to be enforced by each participating organization. In our model, we adopt the Maximal Sequence Path (MSP) approach from Yoo et al. (Lecture Notes in Artificial Intelligence 2132:222–236, 2001), as a means of decomposing workflows into mobile agent-driven processes that communicate via web services at each organization. This decomposition ensures defining logical points within the dynamics of a workflow instance for locating accurate and consistent states of the system for recovery in case of a failure. Then, a set of algorithms for various business scenarios are developed and presented as practical solutions. These algorithms are shown to create checkpoints such that the system is always in a globally consistent state. As such, these algorithms constitute a set of standards that can be incorporated in business process management suites that support reliable inter-organizational collaboration.     

A secure cookie scheme

Cookies are the primary means for web applications to authenticate HTTP requests and to maintain client states. Many web applications (such as those for electronic commerce) demand a secure cookie scheme. Such a scheme needs to provide the following four services: authentication, confidentiality, integrity, and anti-replay. Several secure cookie schemes have been proposed in previous literature; however, none of them are completely satisfactory. In this paper, we propose a secure cookie scheme that is effective, efficient, and easy to deploy. In terms of effectiveness, our scheme provides all of the above four security services. In terms of efficiency, our scheme does not involve any database lookup or public key cryptography. In terms of deployability, our scheme can be easily deployed on existing web services, and it does not require any change to the Internet cookie specification. We implemented our secure cookie scheme using PHP and conducted experiments. The experimental results show that our scheme is very efficient on both the client side and the server side.A notable adoption of our scheme in industry is that our cookie scheme has been used by Wordpress since version 2.4. Wordpress is a widely used open source content management system.     

Diffusive gradients in thin films predicts crop response better than calcium-acetate-lactate extraction

Nutrient Cycling in Agroecosystems - Soil P testing has been widely used to predict crop yields, P uptake, and fertilizer demands in agriculture. Diffusive gradients in thin films (DGT) provides a...     

An Engineered sgsh Mutant Zebrafish Recapitulates Molecular and Behavioural Pathobiology of Sanfilippo Syndrome A/MPS IIIA

Mucopolysaccharidosis IIIA (MPS IIIA, Sanfilippo syndrome type A), a paediatric neurological lysosomal storage disease, is caused by impaired function of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH) resulting in impaired catabolism of heparan sulfate glycosaminoglycan (HS GAG) and its accumulation in tissues. MPS IIIA represents a significant proportion of childhood dementias. This condition generally leads to patient death in the teenage years, yet no effective therapy exists for MPS IIIA and a complete understanding of the mechanisms of MPS IIIA pathogenesis is lacking. Here, we employ targeted CRISPR/Cas9 mutagenesis to generate a model of MPS IIIA in the zebrafish, a model organism with strong genetic tractability and amenity for high-throughput screening. The sgsh^Δex5−6 zebrafish mutant exhibits a complete absence of Sgsh enzymatic activity, leading to progressive accumulation of HS degradation products with age. sgsh^Δex5−6 zebrafish faithfully recapitulate diverse CNS-specific features of MPS IIIA, including neuronal lysosomal overabundance, complex behavioural phenotypes, and profound, lifelong neuroinflammation. We further demonstrate that neuroinflammation in sgsh^Δex5−6 zebrafish is largely dependent on interleukin-1β and can be attenuated via the pharmacological inhibition of Caspase-1, which partially rescues behavioural abnormalities in sgsh^Δex5−6 mutant larvae in a context-dependent manner. We expect the sgsh^Δex5−6 zebrafish mutant to be a valuable resource in gaining a better understanding of MPS IIIA pathobiology towards the development of timely and effective therapeutic interventions.     

Ergovaline and peramine production in endophyte-infected tall fescue: Independent regulation and effects of plant and endophyte genotype

Peramine and ergovaline have ecological and economical significance because they possess insect and/or mammalian toxicity properties. The relationship between these endophytically derived alkaloids in tall fescue (Festuca arundinacea Schreb.) is unknown. Seasonal and plant tissue effects on the concentration of peramine and ergovaline was investigated in field and greenhouse experiments. The relationship between the alkaloids and the regulatory effects of endophyte and plant on their content were investigated among progeny of reciprocal crosses between high- and low-ergovaline and peramine plant-endophyte combinations. Variation in peramine concentration ranged from 750 to 1742 µg/kg in greenhouse-grown plants, and there was no seasonal trend in peramine content. There was a correlation (r=0.69) between peramine and ergovaline content among leaf tissues of field-grown plants, but there was no correlation between the alkaloids in the culm (r=0.20) or panicle (r=0.17) tissues. Mean leaf ergovaline concentration of progeny derived from the low-ergovaline parent (163 µg/kg) was less than the midparent value (228 µg/kg), but mean of progeny from the high-ergovaline parent was not different from the mid-parent value. Ranges within each progeny set were approximately double their mean. Mean leaf peramine concentrations of the progeny sets were similar to the mid-parent value (3354 µg/kg) but ranges were from 1716 to 8753 µg/kg. There was no correlation between leaf peramine and ergovaline (r=0.01). These data suggest that endophytically produced alkaloids are independently regulated and are controlled by both plant and endophyte genotype.     

Decentralized observers with consensus filters for distributed discrete-time linear systems

This paper presents a decentralized observer with a consensus filter for the state observation of discrete-time linear distributed systems. Each agent in the distributed system has an observer with a model of the plant that utilizes the set of locally available measurements, which may not make the full plant state detectable. This lack of detectability is overcome by utilizing a consensus filter that blends the state estimate of each agent with its neighbors’ estimates. It is proven that the state estimates of the proposed observer exponentially converge to the actual plant states under arbitrarily changing, but connected, communication and pseudo-connected sensing graph topologies. Except these connectivity properties, full knowledge of the sensing and communication graphs is not needed at the design time. As a byproduct, we obtained a result on the location of eigenvalues, i.e., the spectrum, of the Laplacian for a family of graphs with self-loops.