Decoding Delay Minimization in Inter-Session Network Coding

Intra-session network coding has been shown to offer significant gains in terms of achievable throughput and delay in settings where one source multicasts data to several clients. In this paper, we consider a more general scenario where multiple sources transmit data to sets of clients over a wireline overlay network. We propose a novel framework for efficient rate allocation in networks where intermediate network nodes have the opportunity to combine packets from different sources using randomized network coding. We formulate the problem as the minimization of the average decoding delay in the client population and solve it with a gradient-based stochastic algorithm. Our optimized inter-session network coding solution is evaluated in different network topologies and is compared with basic intra-session network coding solutions. Our results show the benefits of proper coding decisions and effective rate allocation for lowering the decoding delay when the network is used by concurrent multicast sessions.

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.

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.

When small non-coding RNAs meet the ribosome: Tuning the translational machinery

The functions of ribosomes in translation are complex and involve different types of activities critical for decoding the genetic code, linkage of amino acids via amide bonds to form polypeptide chains, as well as the release and proper targeting of the synthesized protein. Non-protein-coding RNAs (ncRNAs) have been recognized to be crucial in establishing regulatory networks.1 However all of the recently discovered ncRNAs involved in translation regulation target the mRNA rather than the ribosome. The main goal of this project is to identify potential novel ncRNAs that directly bind and possibly regulate the ribosome during protein biosynthesis. To address this question we applied various stress conditions to the archaeal model organism Haloferax volcanii and deep-sequenced the ribosome-associated small ncRNA interactome. In total we identified 6.250 ncRNA candidates. Significantly, we observed the emersed presence of tRNA-derived fragments (tRFs). These tRFs have been identified in all domains of life and represent a growing, yet functionally poorly understood, class of ncRNAs. Here we present evidence that tRFs from H. volcanii directly bind to ribosomes. In the presented genomic screen of the ribosome-associated RNome a 26 residue long fragment originating from the 5’ part of valine tRNA was by far the most abundant tRF. The Val-tRF is processed in a stress- dependent manner and was found to primarily target the small ribosomal subunit in vitro and in vivo. As a consequence of ribosome binding, Val-tRF reduces protein synthesis by interfering with peptidyl transferase activity. Therefore this tRF functions as ribosome-bound small ncRNA capable of regulating gene expression in H. volcanii under environmental stress conditions probably by fine-tuning the rate of protein production.2 Currently we are investigating the binding site of this tRF on the 30S subunit in more detail.

In search of the internal structure of the processes underlying interval timing in the sub-second and the second range: A confirmatory factor analysis approach

One of the earliest accounts of duration perception by Karl von Vierordt implied a common process underlying the timing of intervals in the sub-second and the second range. To date, there are two major explanatory approaches for the timing of brief intervals: the Common Timing Hypothesis and the Distinct Timing Hypothesis. While the common timing hypothesis also proceeds from a unitary timing process, the distinct timing hypothesis suggests two dissociable, independent mechanisms for the timing of intervals in the sub-second and the second range, respectively. In the present paper, we introduce confirmatory factor analysis (CFA) to elucidate the internal structure of interval timing in the sub-second and the second range. Our results indicate that the assumption of two mechanisms underlying the processing of intervals in the second and the sub-second range might be more appropriate than the assumption of a unitary timing mechanism. In contrast to the basic assumption of the distinct timing hypothesis, however, these two timing mechanisms are closely associated with each other and share 77% of common variance. This finding suggests either a strong functional relationship between the two timing mechanisms or a hierarchically organized internal structure. Findings are discussed in the light of existing psychophysical and neurophysiological data.

Replication and fine-mapping of a QTL for recurrent airway obstruction in European Warmblood horses.

Recurrent airway obstruction (RAO), or 'heaves', is a common performance-limiting allergic respiratory disease of mature horses. It is related to sensitization and exposure to mouldy hay and has a familial basis with a complex mode of inheritance. In a previous study, we detected a QTL for RAO on ECA 13 in a half-sib family of European Warmblood horses. In this study, we genotyped additional markers in the family and narrowed the QTL down to about 1.5 Mb (23.7-25.2 Mb). We detected the strongest association with SNP BIEC2-224511 (24,309,405 bp). We also obtained SNP genotypes in an independent cohort of 646 unrelated Warmblood horses. There was no genome-wide significant association with RAO in these unrelated horses. However, we performed a genotypic association study of the SNPs on ECA 13 in these unrelated horses, and the SNP BIEC2-224511 also showed the strongest association with RAO in the unrelated horses (p(raw) = 0.00037). The T allele at this SNP was associated with RAO both in the family and the unrelated horses. Thus, the association study in the unrelated animals provides independent support for the previously detected QTL. The association study allows further narrowing of the QTL interval to about 0.5 Mb (24.0-24.5 Mb). We sequenced the coding regions of the genes in the critical region but did not find any associated coding variants. Therefore, the causative variant underlying this QTL is likely to be a regulatory mutation.

The effects of type of interval, sensory modality, base duration, and psychophysical task on the discrimination of brief time intervals

The present study was designed to investigate the influences of type of psychophysical task (two-alternative forced-choice [2AFC] and reminder tasks), type of interval (filled vs. empty), sensory modality (auditory vs. visual), and base duration (ranging from 100 through 1,000 ms) on performance on duration discrimination. All of these factors were systematically varied in an experiment comprising 192 participants. This approach allowed for obtaining information not only on the general (main) effect of each factor alone, but also on the functional interplay and mutual interactions of some or all of these factors combined. Temporal sensitivity was markedly higher for auditory than for visual intervals, as well as for the reminder relative to the 2AFC task. With regard to base duration, discrimination performance deteriorated with decreasing base durations for intervals below 400 ms, whereas longer intervals were not affected. No indication emerged that overall performance on duration discrimination was influenced by the type of interval, and only two significant interactions were apparent: Base Duration × Type of Interval and Base Duration × Sensory Modality. With filled intervals, the deteriorating effect of base duration was limited to very brief base durations, not exceeding 100 ms, whereas with empty intervals, temporal discriminability was also affected for the 200-ms base duration. Similarly, the performance decrement observed with visual relative to auditory intervals increased with decreasing base durations. These findings suggest that type of task, sensory modality, and base duration represent largely independent sources of variance for performance on duration discrimination that can be accounted for by distinct nontemporal mechanisms.

A mutation in hairless dogs implicates FOXI3 in ectodermal development

Mexican and Peruvian hairless dogs and Chinese crested dogs are characterized by missing hair and teeth, a phenotype termed canine ectodermal dysplasia (CED). CED is inherited as a monogenic autosomal semidominant trait. With genomewide association analysis we mapped the CED mutation to a 102-kilo-base pair interval on chromosome 17. The associated interval contains a previously uncharacterized member of the forkhead box transcription factor family (FOXI3), which is specifically expressed in developing hair and teeth. Mutation analysis revealed a frameshift mutation within the FOXI3 coding sequence in hairless dogs. Thus, we have identified FOXI3 as a regulator of ectodermal development.

Content-Aware Delivery of Scalable Video in Network Coding Enabled Named Data Networks

In this work, we propose a novel network coding enabled NDN architecture for the delivery of scalable video. Our scheme utilizes network coding in order to address the problem that arises in the original NDN protocol, where optimal use of the bandwidth and caching resources necessitates the coordination of the forwarding decisions. To optimize the performance of the proposed network coding based NDN protocol and render it appropriate for transmission of scalable video, we devise a novel rate allocation algorithm that decides on the optimal rates of Interest messages sent by clients and intermediate nodes. This algorithm guarantees that the achieved flow of Data objects will maximize the average quality of the video delivered to the client population. To support the handling of Interest messages and Data objects when intermediate nodes perform network coding, we modify the standard NDN protocol and introduce the use of Bloom filters, which store efficiently additional information about the Interest messages and Data objects. The proposed architecture is evaluated for transmission of scalable video over PlanetLab topologies. The evaluation shows that the proposed scheme performs very close to the optimal performance

Temporal trends in the systemic inflammatory response syndrome, sepsis, and medical coding of sepsis.

BACKGROUND Recent reports using administrative claims data suggest the incidence of community- and hospital-onset sepsis is increasing. Whether this reflects changing epidemiology, more effective diagnostic methods, or changes in physician documentation and medical coding practices is unclear. METHODS We performed a temporal-trend study from 2008 to 2012 using administrative claims data and patient-level clinical data of adult patients admitted to Barnes-Jewish Hospital in St. Louis, Missouri. Temporal-trend and annual percent change were estimated using regression models with autoregressive integrated moving average errors. RESULTS We analyzed 62,261 inpatient admissions during the 5-year study period. 'Any SIRS' (i.e., SIRS on a single calendar day during the hospitalization) and 'multi-day SIRS' (i.e., SIRS on 3 or more calendar days), which both use patient-level data, and medical coding for sepsis (i.e., ICD-9-CM discharge diagnosis codes 995.91, 995.92, or 785.52) were present in 35.3 %, 17.3 %, and 3.3 % of admissions, respectively. The incidence of admissions coded for sepsis increased 9.7 % (95 % CI: 6.1, 13.4) per year, while the patient data-defined events of 'any SIRS' decreased by 1.8 % (95 % CI: -3.2, -0.5) and 'multi-day SIRS' did not change significantly over the study period. Clinically-defined sepsis (defined as SIRS plus bacteremia) and severe sepsis (defined as SIRS plus hypotension and bacteremia) decreased at statistically significant rates of 5.7 % (95 % CI: -9.0, -2.4) and 8.6 % (95 % CI: -4.4, -12.6) annually. All-cause mortality, SIRS mortality, and SIRS and clinically-defined sepsis case fatality did not change significantly during the study period. Sepsis mortality, based on ICD-9-CM codes, however, increased by 8.8 % (95 % CI: 1.9, 16.2) annually. CONCLUSIONS The incidence of sepsis, defined by ICD-9-CM codes, and sepsis mortality increased steadily without a concomitant increase in SIRS or clinically-defined sepsis. Our results highlight the need to develop strategies to integrate clinical patient-level data with administrative data to draw more accurate conclusions about the epidemiology of sepsis.

NetCodCCN: a Network Coding approach for Content-Centric Networks

Content-Centric Networking (CCN) naturally supports multi-path communication, as it allows the simultaneous use of multiple interfaces (e.g. LTE and WiFi). When multiple sources and multiple clients are considered, the optimal set of distribution trees should be determined in order to optimally use all the available interfaces. This is not a trivial task, as it is a computationally intense procedure that should be done centrally. The need for central coordination can be removed by employing network coding, which also offers improved resiliency to errors and large throughput gains. In this paper, we propose NetCodCCN, a protocol for integrating network coding in CCN. In comparison to previous works proposing to enable network coding in CCN, NetCodCCN permit Interest aggregation and Interest pipelining, which reduce the data retrieval times. The experimental evaluation shows that the proposed protocol leads to significant improvements in terms of content retrieval delay compared to the original CCN. Our results demonstrate that the use of network coding adds robustness to losses and permits to exploit more efficiently the available network resources. The performance gains are verified for content retrieval in various network scenarios.

An intergenic non-coding RNA targets and regulates the ribosome in H. volcanii

As translation is the final step in gene expression it is particularly important to understand the processes involved in translation regulation. It was shown in the last years that a class of RNA, the non-protein-coding RNAs (ncRNAs), is involved in regulation of gene expression via various mechanisms (e.g. gene silencing by microRNAs). Almost all of these ncRNA discovered so far target the mRNA in order to modulate protein biosynthesis, this is rather unexpected considering the crucial role of the ribosome during gene expression. However, recent data from our laboratory showed that there is a new class of ncRNAs, which target the ribosome itself [Gebetsberger et al., 2012/ Pircher et al, 2014]. These so called ribosome-associated ncRNAs (rancRNAs) have an impact on translation regulation, mainly by interfering / modulating the rate of protein biosynthesis. The main goal of this project is to identify and describe novel potential regulatory rancRNAs in H. volcanii with the focus on intergenic candidates. Northern blot analyses already revealed interactions with the ribosome and showed differential expression of rancRNAs during different growth phases or under specific stress conditions. To investigate the biological relevance of these rancRNAs, knock-outs were generated in H. volcanii which were used for phenotypic characterization studies. The rancRNA s194 showed association with the 50S ribosomal subunit in vitro and in vivo and was capable of inhibiting peptide bond formation and seems to inhibit translation in vitro. These preliminary data for the rancRNA s194 make it an interesting candidate for further functional studies to identify the molecular mechanisms by which rancRNAs can modulate protein biosynthesis. Characterization of further rancRNA candidates are also underway.