Streaming Support for Data Intensive Cloud-Based Sequence Analysis

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client’s site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Interactive free viewpoint video streaming using prioritized network coding

In free viewpoint applications, the images are captured by an array of cameras that acquire a scene of interest from different perspectives. Any intermediate viewpoint not included in the camera array can be virtually synthesized by the decoder, at a quality that depends on the distance between the virtual view and the camera views available at decoder. Hence, it is beneficial for any user to receive camera views that are close to each other for synthesis. This is however not always feasible in bandwidth-limited overlay networks, where every node may ask for different camera views. In this work, we propose an optimized delivery strategy for free viewpoint streaming over overlay networks. We introduce the concept of layered quality-of-experience (QoE), which describes the level of interactivity offered to clients. Based on these levels of QoE, camera views are organized into layered subsets. These subsets are then delivered to clients through a prioritized network coding streaming scheme, which accommodates for the network and clients heterogeneity and effectively exploit the resources of the overlay network. Simulation results show that, in a scenario with limited bandwidth or channel reliability, the proposed method outperforms baseline network coding approaches, where the different levels of QoE are not taken into account in the delivery strategy optimization.

Steady streaming in a two-dimensional box model of a passive cochlea

Acoustic stimulation of the cochlea leads to a travelling wave in the cochlear fluids and on the basilar membrane (BM). It has long been suspected that this travelling wave leads to a steady streaming flow in the cochlea. Theoretical investigations suggested that the steady streaming might be of physiological relevance. Here, we present a quantitative study of the steady streaming in a computational model of a passive cochlea. The structure of the streaming flow is illustrated and the sources of streaming are closely investigated. We describe a source of streaming which has not been considered in the cochlea by previous authors. This source is also related to a steady axial displacement of the BM which leads to a local stretching of this compliant structure. We present theoretical predictions for the streaming intensity which account for these new phenomena. It is shown that these predictions compare well with our numerical results and that there may be steady streaming velocities of the order of millimetres per second. Our results indicate that steady streaming should be more relevant to low-frequency hearing because the strength of the streaming flow rapidly decreases for higher frequencies.

The role of the interplay between polymer architecture and bacterial surface properties on the microbial adhesion to polyoxazoline-based ultrathin films

Surface platforms were engineered from poly(L-lysine)-graft-poly(2-methyl-2-oxazoline) (PLL-g-PMOXA) copolymers to study the mechanisms involved in the non-specific adhesion of Escherichia coli (E. coli) bacteria. Copolymers with three different grafting densities (PMOXA chains/Lysine residue of 0.09, 0.33 and 0.56) were synthesized and assembled on niobia (Nb O ) surfaces. PLL-modified and bare niobia surfaces served as controls. To evaluate the impact of fimbriae expression on the bacterial adhesion, the surfaces were exposed to genetically engineered E. coli strains either lacking, or constitutively expressing type 1 fimbriae. The bacterial adhesion was strongly influenced by the presence of bacterial fimbriae. Non-fimbriated bacteria behaved like hard, charged particles whose adhesion was dependent on surface charge and ionic strength of the media. In contrast, bacteria expressing type 1 fimbriae adhered to the substrates independent of surface charge and ionic strength, and adhesion was mediated by non-specific van der Waals and hydrophobic interactions of the proteins at the fimbrial tip. Adsorbed polymer mass, average surface density of the PMOXA chains, and thickness of the copolymer films were quantified by optical waveguide lightmode spectroscopy (OWLS) and variable-angle spectroscopic ellipsometry (VASE), whereas the lateral homogeneity was probed by time-of-flight secondary ion mass spectrometry (ToF-SIMS). Streaming current measurements provided information on the charge formation of the polymer-coated and the bare niobia surfaces. The adhesion of both bacterial strains could be efficiently inhibited by the copolymer film only with a grafting density of 0.33 characterized by the highest PMOXA chain surface density and a surface potential close to zero.

Cognitive binding in schizophrenia: weakened integration of temporal intersensory information

Cognitive functioning is based on binding processes, by which different features and elements of neurocognition are integrated and coordinated. Binding is an essential ingredient of, for instance, Gestalt perception. We have implemented a paradigm of causality perception based on the work of Albert Michotte, in which 2 identical discs move from opposite sides of a monitor, steadily toward, and then past one another. Their coincidence generates an ambiguous percept of either "streaming" or "bouncing," which the subjects (34 schizophrenia spectrum patients and 34 controls with mean age 27.9 y) were instructed to report. The latter perception is a marker of the binding processes underlying perceived causality (type I binding). In addition to this visual task, acoustic stimuli were presented at different times during the task (150 ms before and after visual coincidence), which can modulate perceived causality. This modulation by intersensory and temporally delayed stimuli is viewed as a different type of binding (type II). We show here, using a mixed-effects hierarchical analysis, that type II binding distinguishes schizophrenia spectrum patients from healthy controls, whereas type I binding does not. Type I binding may even be excessive in some patients, especially those with positive symptoms; Type II binding, however, was generally attenuated in patients. The present findings point to ways in which the disconnection (or Gestalt) hypothesis of schizophrenia can be refined, suggesting more specific markers of neurocognitive functioning and potential targets of treatment.

Enhancing IEEE 802.11 Energy Efficiency for Continuous Media Applications

This paper proposes the Optimized Power save Algorithm for continuous Media Applications (OPAMA) to improve end-user device energy efficiency. OPAMA enhances the standard legacy Power Save Mode (PSM) of IEEE 802.11 by taking into consideration application specific requirements combined with data aggregation techniques. By establishing a balanced cost/benefit tradeoff between performance and energy consumption, OPAMA is able to improve energy efficiency, while keeping the end-user experience at a desired level. OPAMA was assessed in the OMNeT++ simulator using real traces of variable bitrate video streaming applications. The results showed the capability to enhance energy efficiency, achieving savings up to 44% when compared with the IEEE 802.11 legacy PSM.

The free escape continuum of diffuse ions upstream of the Earth's quasi-parallel bow shock

The Earth's bow shock is very efficient in accelerating ions out of the incident solar wind distribution to high energies (≈ 200 keV/e). Fluxes of energetic ions accelerated at the quasi-parallel bow shock, also known as diffuse ions, are best represented by exponential spectra in energy/charge, which require additional assumptions to be incorporated into these model spectra. One of these assumptions is a so-called "free escape boundary" along the interplanetary magnetic field into the upstream direction. Locations along the IBEX orbit are ideally suited for in situ measurements to investigate the existence of an upstream free escape boundary for bow shock accelerated ions. In this study we use 2 years of ion measurements from the background monitor on the IBEX spacecraft, supported by ACE solar wind observations. The IBEX Background Monitor is sensitive to protons > 14 keV, which includes the energy of the maximum flux for diffuse ions. With increasing distance from the bow shock along the interplanetary magnetic field, the count rates for diffuse ions stay constant for ions streaming away from the bow shock, while count rates for diffuse ions streaming toward the shock gradually decrease from a maximum value to ~1/e at distances of about 10 RE to 14 RE. These observations of a gradual decrease support the transition to a free escape continuum for ions of energy >14 keV at distances from 10 RE to 14 RE from the bow shock.

A real-time video quality estimator for emerging wireless multimedia systems

Wireless Mesh Networks (WMNs) are increasingly deployed to enable thousands of users to share, create, and access live video streaming with different characteristics and content, such as video surveillance and football matches. In this context, there is a need for new mechanisms for assessing the quality level of videos because operators are seeking to control their delivery process and optimize their network resources, while increasing the user’s satisfaction. However, the development of in-service and non-intrusive Quality of Experience assessment schemes for real-time Internet videos with different complexity and motion levels, Group of Picture lengths, and characteristics, remains a significant challenge. To address this issue, this article proposes a non-intrusive parametric real-time video quality estimator, called MultiQoE that correlates wireless networks’ impairments, videos’ characteristics, and users’ perception into a predicted Mean Opinion Score. An instance of MultiQoE was implemented in WMNs and performance evaluation results demonstrate the efficiency and accuracy of MultiQoE in predicting the user’s perception of live video streaming services when compared to subjective, objective, and well-known parametric solutions.

Informative State-Based Video Communication

We study state-based video communication where a client simultaneously informs the server about the presence status of various packets in its buffer. In sender-driven transmission, the client periodically sends to the server a single acknowledgement packet that provides information about all packets that have arrived at the client by the time the acknowledgment is sent. In receiver-driven streaming, the client periodically sends to the server a single request packet that comprises a transmission schedule for sending missing data to the client over a horizon of time. We develop a comprehensive optimization framework that enables computing packet transmission decisions that maximize the end-to-end video quality for the given bandwidth resources, in both prospective scenarios. The core step of the optimization comprises computing the probability that a single packet will be communicated in error as a function of the expected transmission redundancy (or cost) used to communicate the packet. Through comprehensive simulation experiments, we carefully examine the performance advances that our framework enables relative to state-of-the-art scheduling systems that employ regular acknowledgement or request packets. Consistent gains in video quality of up to 2B are demonstrated across a variety of content types. We show that there is a direct analogy between the error-cost efficiency of streaming a single packet and the overall rate-distortion performance of streaming the whole content. In the case of sender-driven transmission, we develop an effective modeling approach that accurately characterizes the end-to-end performance as a function of the packet loss rate on the backward channel and the source encoding characteristics.

An IEEE 802.11 energy efficient mechanism for continuous media applications

The widespread deployment of wireless mobile communications enables an almost permanent usage of portable devices, which imposes high demands on the battery of these devices. Indeed, battery lifetime is becoming one the most critical factors on the end-users satisfaction when using wireless communications. In this work, the optimized power save algorithm for continuous media applications (OPAMA) is proposed, aiming at enhancing the energy efficiency on end-users devices. By combining the application specific requirements with data aggregation techniques, {OPAMA} improves the standard {IEEE} 802.11 legacy Power Save Mode (PSM) performance. The algorithm uses the feedback on the end-user expected quality to establish a proper tradeoff between energy consumption and application performance. {OPAMA} was assessed in the OMNeT++ simulator, using real traces of variable bitrate video streaming applications, and in a real testbed employing a novel methodology intended to perform an accurate evaluation concerning video Quality of Experience (QoE) perceived by the end-users. The results revealed the {OPAMA} capability to enhance energy efficiency without degrading the end-user observed QoE, achieving savings up to 44 when compared with the {IEEE} 802.11 legacy PSM.

Distributed Rate Allocation in Inter-Session Network Coding

In this work, we propose a distributed rate allocation algorithm that minimizes the average decoding delay for multimedia clients in inter-session network coding systems. We consider a scenario where the users are organized in a mesh network and each user requests the content of one of the available sources. We propose a novel distributed algorithm where network users determine the coding operations and the packet rates to be requested from the parent nodes, such that the decoding delay is minimized for all clients. A rate allocation problem is solved by every user, which seeks the rates that minimize the average decoding delay for its children and for itself. Since this optimization problem is a priori non-convex, we introduce the concept of equivalent packet flows, which permits to estimate the expected number of packets that every user needs to collect for decoding. We then decompose our original rate allocation problem into a set of convex subproblems, which are eventually combined to obtain an effective approximate solution to the delay minimization problem. The results demonstrate that the proposed scheme eliminates the bottlenecks and reduces the decoding delay experienced by users with limited bandwidth resources. We validate the performance of our distributed rate allocation algorithm in different video streaming scenarios using the NS-3 network simulator. We show that our system is able to take benefit of inter-session network coding for simultaneous delivery of video sessions in networks with path diversity.

Fluid-structure interaction of an elastic pipe immersed inside a coaxial rigid pipe: a model for the Tullio phenomenon

An axisymmetric, elastic pipe is filled with an incompressible fluid and is immersed in a second, coaxial rigid pipe which contains the same fluid. A pressure pulse in the outer fluid annulus deforms the elastic pipe which invokes a fluid motion in the fluid core. It is the aim of this study to investigate streaming phenomena in the core which may originate from such a fluid-structure interaction. This work presents a numerical solver for such a configuration. It was developed in the OpenFOAM software environment and is based on the Arbitrary Lagrangian Eulerian (ALE) approach for moving meshes. The solver features a monolithic integration of the one-dimensional, coupled system between the elastic structure and the outer fluid annulus into a dynamic boundary condition for the moving surface of the fluid core. Results indicate that our configuration may serve as a mechanical model of the Tullio Phenomenon (sound-induced vertigo).