Dynamic Quality of Service Model for Improving Performance of Multimedia Real-Time Transmission in Industrial Networks

Nowadays, quality of service (QoS) is very popular in various research areas like distributed systems, multimedia real-time applications and networking. The requirements of these systems are to satisfy reliability, uptime, security constraints and throughput as well as application specific requirements. The real-time multimedia applications are commonly distributed over the network and meet various time constraints across networks without creating any intervention over control flows. In particular, video compressors make variable bit-rate streams that mismatch the constant-bit-rate channels typically provided by classical real-time protocols, severely reducing the efficiency of network utilization. Thus, it is necessary to enlarge the communication bandwidth to transfer the compressed multimedia streams using Flexible Time Triggered- Enhanced Switched Ethernet (FTT-ESE) protocol. FTT-ESE provides automation to calculate the compression level and change the bandwidth of the stream. This paper focuses on low-latency multimedia transmission over Ethernet with dynamic quality-of-service (QoS) management. This proposed framework deals with a dynamic QoS for multimedia transmission over Ethernet with FTT-ESE protocol. This paper also presents distinct QoS metrics based both on the image quality and network features. Some experiments with recorded and live video streams show the advantages of the proposed framework. To validate the solution we have designed and implemented a simulator based on the Matlab/Simulink, which is a tool to evaluate different network architecture using Simulink blocks.     

A cost-efficient scheduling algorithm for streaming processing applications on cloud

Cluster Computing - Stream processing is a new memory computing paradigm that deals with dynamic data streams efficiently. Storm is one of the stream processing frameworks, but the default stream...     

Supporting high‐performance I/O in QoS‐enabled ORB middleware

To be an effective platform for high‐performance distributed applications, off-the-shelf Object Request Broker (ORB) middleware, such as CORBA, must preserve communication-layer quality of service (QoS) properties both vertically (i.e., network interface ↔ application layer) and horizontally (i.e., end-to-end). However, conventional network interfaces, I/O subsystems, and middleware interoperability protocols are not well-suited for applications that possess stringent throughput, latency, and jitter requirements. It is essential, therefore, to develop vertically and horizontally integrated ORB endsystems that can be (1) configured flexibly to support high-performance network interfaces and I/O subsystems and (2) used transparently by performance-sensitive applications. This paper provides three contributions to research on high-performance I/O support for QoS-enabled ORB middleware. First, we outline the key research challenges faced by high-performance ORB endsystem developers. Second, we describe how our real-time I/O (RIO) subsystem and pluggable protocol framework enables ORB endsystems to preserve high-performance network interface QoS up to applications running on off-the-shelf hardware and software. Third, we illustrate empirically how highly optimized ORB middleware can be integrated with real-time I/O subsystem to reduce latency bounds on communication between high-priority clients without unduly penalizing low-priority and best-effort clients. Our results demonstrate how it is possible to develop ORB endsystems that are both highly flexible and highly efficient. This revised version was published online in July 2006 with corrections to the Cover Date.     

An exploration of factors influencing lotic insect species richness

An understanding of factors that influence species richness of lotic insects is generally lacking. We present comparative data on aquatic insect species richness from several North American and other streams. Factors such as large sample numbers and drainage area (species area relationships) are not significant predictors of species richness across the streams we examined. We explore several hypotheses regarding the origins and maintenance of species richness using Upper Three Runs Creek (UTR), South Carolina, USA, as a reference stream. UTR has the highest species richness of any stream in the Western Hemisphere. Hypotheses examined included historical, regional and local processes such as: (1) Evolutionary time, (2) disturbance regime/environmental variability, (3) temperature/evolutionary-speed, (4) productivity, and (5) habitat heterogeneity. Of these hypotheses, we suggest that productivity and habitat heterogeneity appear to contribute most to the high species richness found in UTR. We believe that multidisciplinary analysis of other streams is necessary because without this crucial information our knowledge of, and desire to protect biodiversity in streams will be wanting.     

Posterior Parietal Cortex Drives Inferotemporal Activations During Three-Dimensional Object Vision

The primate visual system consists of a ventral stream, specialized for object recognition, and a dorsal visual stream, which is crucial for spatial vision and actions. However, little is known about the interactions and information flow between these two streams. We investigated these interactions within the network processing three-dimensional (3D) object information, comprising both the dorsal and ventral stream. Reversible inactivation of the macaque caudal intraparietal area (CIP) during functional magnetic resonance imaging (fMRI) reduced fMRI activations in posterior parietal cortex in the dorsal stream and, surprisingly, also in the inferotemporal cortex (ITC) in the ventral visual stream. Moreover, CIP inactivation caused a perceptual deficit in a depth-structure categorization task. CIP-microstimulation during fMRI further suggests that CIP projects via posterior parietal areas to the ITC in the ventral stream. To our knowledge, these results provide the first causal evidence for the flow of visual 3D information from the dorsal stream to the ventral stream, and identify CIP as a key area for depth-structure processing. Thus, combining reversible inactivation and electrical microstimulation during fMRI provides a detailed view of the functional interactions between the two visual processing streams.     

The architecture of a middleware layer for controlling the quality of multimedia sessions

Collaborative multimedia systems demand overall session quality control beyond the level of Quality of Service (QoS) as pertaining to individual streams in isolation of others. To this end, we have recently introduced the concept of Quality of Session (QoSess) control. At every instant in time, the quality of the session depends on the actual QoS offered by the system to each of the application streams, as well as on the relative priorities of these streams according to the application semantics. In this paper, we present the architecture of a middleware layer for controlling the quality of a session. In addition, we describe the inter-stream bandwidth adaptation mechanisms, which are used by the QoSess layer to dynamically control the bandwidth shares of the streams belonging to a session. This revised version was published online in July 2006 with corrections to the Cover Date.     

The role of predictive models in the formation of auditory streams.

Sounds provide us with useful information about our environment which complements that provided by other senses, but also poses specific processing problems. How does the auditory system distentangle sounds from different sound sources? And what is it that allows intermittent sound events from the same source to be associated with each other? Here we review findings from a wide range of studies using the auditory streaming paradigm in order to formulate a unified account of the processes underlying auditory perceptual organization. We present new computational modelling results which replicate responses in primary auditory cortex [Fishman, Y.I., Arezzo, J.C., Steinschneider, M., 2004. Auditory stream segregation in monkey auditory cortex: effects of frequency separation, presentation rate, and tone duration. J. Acoust. Soc. Am. 116, 1656-1670; Fishman, Y. I., Reser, D. H., Arezzo, J.C., Steinschneider, M., 2001. Neural correlates of auditory stream segregation in primary auditory cortex of the awake monkey. Hear. Res. 151, 167-187] to tone sequences. We also present the results of a perceptual experiment which confirm the bi-stable nature of auditory streaming, and the proposal that the gradual build-up of streaming may be an artefact of averaging across many subjects [Pressnitzer, D., Hupé, J. M., 2006. Temporal dynamics of auditory and visual bi-stability reveal common principles of perceptual organization. Curr. Biol. 16(13), 1351-1357.]. Finally we argue that in order to account for all of the experimental findings, computational models of auditory stream segregation require four basic processing elements; segregation, predictive modelling, competition and adaptation, and that it is the formation of effective predictive models which allows the system to keep track of different sound sources in a complex auditory environment.     

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow

Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of data. Complex bioinformatics analyses are required to turn these data into scientific findings. In order to run these analyses fast, automated workflows implemented on high performance computers are state of the art. While providing sufficient compute power and storage to meet the NGS data challenge, high performance computing (HPC) systems require special care when utilized for high throughput processing. This is especially true if the HPC system is shared by different users. Here, stability, robustness and maintainability are as important for automated workflows as speed and throughput. To achieve all of these aims, dedicated solutions have to be developed. In this paper, we present the tricks and twists that we utilized in the implementation of our exome data processing workflow. It may serve as a guideline for other high throughput data analysis projects using a similar infrastructure. The code implementing our solutions is provided in the supporting information files.     

Effects of atmospheric N deposition on coarse organic matter in a headwater stream

Input, storage, export potential, and system-level processing of coarse organic matter were investigated in the intermittent streams that drain the Bear Brook Watershed in Maine (BBWM). BBWM is a paired catchment study investigating ecosystem effects of atmospheric N and S deposition. We predicted that the increased N loading to the treatment catchment would elevate input of organic matter, result in higher levels of coarse organic matter biomass, and increase litter processing rates in the treatment stream relative to the reference stream. We found that the streams draining BBWM did not have statistically different coarse organic matter input, biomass, or processing rates and we found only modest differences in export potential. System-level processing rates for maple (Acer spp.) litter were similar to rates previously quantified using litterbag methods. However, system-level processing rates for American beech (Fagus grandifolia) litter were an order of magnitude faster than rates measured with litterbags. This difference was likely due to movements of these leaves from riffle/runs and pools into debris dams, rather than differences in measurements of leaf tissue processing rates between methods. Organic matter dynamics of the intermittent streams at BBWM were similar to other forested, headwater streams. Our results indicate that the long-term N manipulation experiment at BBWM has not altered input, storage or processing of coarse organic matter in the treatment stream. Physical characteristics of these stream ecosystems appear to regulate organic matter dynamics rather than differences in nutrient chemistry.     

Colonization and processing of leaf litter by macroinvertebrate shredders in streams of contrasting pH

• 1 Leaf litter processing rates and macroinvertebrate shredder assemblages in leaf packs were compared in four streams on the Allegheny plateau in the central Appalachian Mountains, U.S.A.; these streams were characterized by different bedrock geology and streamwater pH.
• 2 Leaf litter processing rates were fastest in the neutral streams, slowest in the acidic stream, and intermediate in the most alkaline stream.
• 3 Slower processing rates in the acidic stream were associated with lower total shredder biomass, made up predominantly by small leuctrid and nemourid stoneflies.
• 4 The differences in processing rates between the more alkaline stream and the neutral streams were not associated with differences in shredder biomass, but appeared to be related to taxonomic differences in the shredder assembiages. Insects were dominant in the neutral streams, and amphipods were dominant in the more alkaline stream.

     

Assessing channel-forming characteristics of an impacted headwater stream in Ohio, USA

Since the start of European settlement in Ohio the landscape has been greatly modified to accommodate anthropogenic land uses. This, in turn, has altered the hydrologic characteristics of many streams from those that are stable channel systems in dynamic equilibrium to those of modified incised channels that are more characteristic of anthropogenic influences. As stream restoration practices gain importance and prevalence there is a need to prioritize project funds based on the restoration potential of a stream. Regional curves that relate channel-forming geometry to drainage area, and applications of channel-forming discharge concepts, are tools that are used in making restoration and management decisions. Regional curves are usually developed for unmodified natural streams and/or gaged river systems and not for small, ungaged modified channels that are common throughout agricultural areas or mixed use watersheds. This study focuses on the development and potential usefulness of regional curves and channel-forming discharge concepts for Mac-o-chee Creek, a small, ungaged headwater stream system in Ohio. Results show that these approaches and a weight of evidence analysis could be useful in providing information for management and restoration decisions on these small stream systems as well as aiding in the assessment and modeling of trends within these streams with dynamic hydrologic conditions due to changes in land use/land cover.     

Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System

In this review we describe the principles, protocols, and applications of two commercially available SNP genotyping platforms, the TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. Combined, these two technologies meet the requirements of multiple SNP applications in genetics research and pharmacogenetics. We also describe a set of SNP selection tools and validated assay resources which we developed to accelerate the cycle of experimentation on these platforms. Criteria for selecting the more appropriate of these two genotyping technologies are presented: the genetic architecture of the trait of interest, the throughput required, and the number of SNPs and samples needed for a successful study. Overall, the TaqMan assay format is suitable for low- to mid-throughput applications in which a high assay conversion rate, simple assay workflow, and low cost of automation are desirable. The SNPlex Genotyping System, on the other hand, is well suited for SNP applications in which throughput and cost-efficiency are essential, e.g., applications requiring either the testing of large numbers of SNPs and samples, or the flexibility to select various SNP subsets.     

Riparian land use and the relationship between the benthos and litter decomposition in tropical montane streams

1. Although stream–catchment interactions have been analysed in some detail in temperate environments, little is known about the effects of land‐use changes in the tropics. Here, we analyse differences in benthic communities (macroinvertebrates and fungi) under two contrasting land uses (mature secondary forest and pasture) in montane streams in north‐western Ecuador and their influence on the rates of litter processing. 2. Between 2005 and 2006, we used a combination of coarse and fine mesh bags to study the relative contribution of macroinvertebrates and fungi to processing of two types of litter, Alnus acuminata and Inga spectabilis, in three‐first‐order streams running through mature secondary montane forests and adjacent downstream reaches running through pastures. At the same time, we characterised the assemblages of shreddering macroinvertebrates and fungi communities and the litter processing rates in stream reaches under both vegetation types. 3. Litter processing rates attributable to invertebrate feeding (coarse mesh bags) were significantly slower in streams running through pastures. Nevertheless, shredder diversity and richness were similar between pasture and forest sections, while shredder abundance was significantly higher in forest streams (mainly Phylloicus sp. :Trichoptera). Fungal reproductive activity and litter processing rates were low (fine mesh bags) and did not differ significantly between pasture and forest stream reaches. 4. Phylloicus sp. abundance was the best predictor of the percentage of litter remaining in coarse mesh bags across pasture and forest sites. Neither shredder diversity nor their species richness was a significant predictor of mass loss, as most of the decomposition was performed by a single keystone species. Although litter decomposition by microbial decomposers was low, fungal biomass (but not diversity) was the best variable explaining the percentage of litter remaining in fine mesh bags. 5. Our data suggest that, in these Neotropical montane streams, land use can have a significant impact on the rates of critical ecosystem processes, such as litter decomposition. In this study, this effect was not mediated by a major shift in the structure of the benthos, but by a decrease in the abundance and relative representation of a single species whose life history makes it critical to litter processing. 6. This study highlights the significant role that macroinvertebrate fauna can have in the processing of litter in Neotropical streams and the predominant role that single species can have in terms of controlling stream ecosystem‐level processes. Understanding the extent to which these patterns affect the long‐term and large‐scale functioning of stream ecosystems still needs further research and will become increasingly important in terms of managing lotic ecosystems in the context of rapid land‐use change.     

淡黄绒泡菌和全白绒泡菌原生质流向的观察

显型原质团是绒泡菌目黏菌的营养生长阶段,其最明显的现象是往返原生质流,但一直并不清楚原生质流反向流动的原因。观察研究了淡黄绒泡菌和全白绒泡菌原质团中的原生质流,结果表明：由于菌脉中堵塞或是在原质团前缘尚未分化通道引起反向原生质流,从而引起原质团多方向生长使原质团前缘呈现扇面状。原生质流总的方向是扇面端,并完成原质团运动。     

The Role of Parieto-Occipital Junction in the Interaction between Dorsal and Ventral Streams in Disparity-Defined Near and Far Space Processing

Neuropsychological and functional MRI data suggest that two functionally and anatomically dissociable streams of visual processing exist: a ventral perception-related stream and a dorsal action-related stream. However, relatively little is known about how the two streams interact in the intact brain during the production of adaptive behavior. Using functional MRI and a virtual three-dimensional paradigm, we aimed at examining whether the parieto-occipital junction (POJ) acts as an interface for the integration and processing of information between the dorsal and ventral streams in the near and far space processing. Virtual reality three-dimensional near and far space was defined by manipulating binocular disparity, with -68.76 arcmin crossed disparity for near space and +68.76 arcmin uncrossed disparity for near space. Our results showed that the POJ and bilateral superior occipital gyrus (SOG) showed relative increased activity when responded to targets presented in the near space than in the far space, which was independent of the retinotopic and perceived sizes of target. Furthermore, the POJ showed the enhanced functional connectivity with both the dorsal and ventral streams during the far space processing irrespective of target sizes, supporting that the POJ acts as an interface between the dorsal and ventral streams in disparity-defined near and far space processing. In contrast, the bilateral SOG showed the enhanced functional connectivity only with the ventral stream if retinotopic sizes of targets in the near and far spaces were matched, which suggested there was a functional dissociation between the POJ and bilateral SOG.     

Detrital processing in streams exposed to acidic precipitation in the Central Appalachian Mountains

Continuing high rates of acidic deposition in the eastern United States may lead to long-term effects on stream communities, because sensitive catchments are continuing to lose anions and cations. We conducted a two-year study of the effects of pH and associated water chemistry variables on detrital processing in three streams with different bedrock geology in the Monongahela National Forest, West Virginia. We compared leaf pack processing rates and macroinvertebrate colonization and microbial biomass (ATP concentration) on the packs in the three streams. Breakdown rates of red maple and white oak leaf packs were significantly lower in the most acidic stream. The acidic stream also had significantly lower microbial and shredder biomass than two more circumneutral streams. Shredder composition differed among streams; large-particle detritivores dominated the shredder assemblages of the two circumneutral streams, and smaller shredders dominated in the acidic stream. Within streams, processing rates for three leaf species were not significantly different between the two years of the study even though invertebrate and microbial communities were different in the two years. Thus, macroinvertebrate and microbial communities differed both among streams that differed in their capacity to buffer the effects of acidic precipitation and among years in the same stream; these differences in biotic communities were not large enough to affect rates of leaf processing between the two years of the study, but they did significantly affect processing rates between acidic and circumneutral streams.The Unit is jointly sponsored by the National Biological Service, the West Virginian Division of Natural Resources, West Virginia University, and the Wildlife Management Institute.The Unit is jointly sponsored by the National Biological Service, the West Virginian Division of Natural Resources, West Virginia University, and the Wildlife Management Institute.     

Direct and indirect food web regulation of microbial decomposers in headwater streams

The direct and indirect regulation of primary productivity has been well established in autotrophic‐based ecosystems; however, less is known about the processes affecting decomposers in detrital‐based ecosystems. Because, small headwater, woodland streams are a dominate feature in most ecosystems and are tightly linked to terrestrial detritus, understanding decomposer‐mediated functions in these systems is critical for understanding carbon processes across the landscape. In this light, we conducted a microcosm and mesocosm experiment to test the direct and indirect food web effects on decomposers in small stream ecosystems. The results from the microcosm experiment supported an existing literature, demonstrating that nutrients directly stimulate decomposers and that microbivores directly reduce decomposers. Based on well‐founded food web theory in autotrophic systems, we predicted that fishes from different trophic‐functional guilds would indirectly stimulate decomposers by enhancing dissolved nutrients and by reducing microbivore densities. Our mesocosm experiment partially supported these predictions. Specifically, we found that fishes that consumed mostly terrestrial foods increased decomposers from the bottom–up by enhancing allochthonous nutrient loading into the stream ecosystems. Contrary to our predictions, however, predatory fishes that consume microbivores did not increase decomposers from the top–down. Rather, in streams with the predatory fish species, microbivores increased (rather than decreased) on leaf litter. This may have resulted from an experimental artifact associated with refuge provided by leaf packs. In conclusion, our data demonstrate that decomposers are regulated by similar direct and indirect processes important in autotrophic‐based ecosystems. This provides further evidence that food web processes can regulate leaf decomposition and flux of detrital carbon through ecosystems.     

Macroinvertebrate diversity in headwater streams: a review

1. Headwater streams are ubiquitous in the landscape and are important sources of water, sediments and biota for downstream reaches. They are critical sites for organic matter processing and nutrient cycling, and may be vital for maintaining the 'health' of whole river networks.
2. Macroinvertebrates are an important component of biodiversity in stream ecosystems and studies of macroinvertebrate diversity in headwater streams have mostly viewed stream systems as linear reaches rather than as networks, although the latter may be more appropriate to the study of diversity patterns in headwater systems.
3. Studies of macroinvertebrate diversity in headwater streams from around the world illustrated that taxonomic richness is highly variable among continents and regions, and studies addressing longitudinal changes in taxonomic richness of macroinvertebrates generally found highest richness in mid-order streams.
4. When stream systems are viewed as networks at the landscape-scale, α-diversity may be low in individual headwater streams but high β-diversity among headwater streams within catchments and among catchments may generate high γ-diversity.
5. Differing ability and opportunity for dispersal of macroinvertebrates, great physical habitat heterogeneity in headwater streams, and a wide range in local environmental conditions may all contribute to high β-diversity among headwater streams both within and among catchments.
6. Moving beyond linear conceptual models of stream ecosystems to consider the role that spatial structure of river networks might play in determining diversity patterns at the landscape scale is a promising avenue for future research.     

Genome-wide high throughput analysis of DNA methylation in eukaryotes

Cytosine methylation is the quintessential epigenetic mark. Two well-established methods, bisulfite sequencing and methyl-DNA immunoprecipitation (MeDIP) lend themselves to the genome-wide analysis of DNA methylation by high throughput sequencing. Here we provide an overview and brief review of these methods. We summarize our experience with MeDIP followed by high throughput Illumina/Solexa sequencing, exemplified by the analysis of the methylated fraction of the Neurospora crassa genome ("methylome"). We provide detailed methods for DNA isolation, processing and the generation of in vitro libraries for Illumina/Solexa sequencing. We discuss potential problems in the generation of sequencing libraries. Finally, we provide an overview of software that is appropriate for the analysis of high throughput sequencing data generated by Illumina/Solexa-type sequencing by synthesis, with a special emphasis on approaches and applications that can generate more accurate depictions of sequence reads that fall in repeated regions of a chosen reference genome.