Shared Tree Research Articles

Heterogeneous Mediation Analysis for Cox Proportional Hazards Model With Multiple Mediators.

This study proposes a heterogeneous mediation analysis for survival data that accommodates multiple mediators and sparsity of the predictors. We introduce a joint modeling approach that links the mediation regression and proportional hazards models through Bayesian additive regression trees with shared typologies. The shared tree component is motivated by the fact that confounders and effect modifiers on the causal pathways linked by different mediators often overlap. A sparsity-inducing prior is incorporated to capture the most relevant confounders and effect modifiers on different causal pathways. The individual-specific interventional direct and indirect effects are derived on the scale of the logarithm of hazards and survival function. A Bayesian approach with an efficient Markov chain Monte Carlo algorithm is developed to estimate the conditional interventional effects through the Monte Carlo implementation of the mediation formula. Simulation studies are conducted to verify the empirical performance of the proposed method. An application to the ACTG175 study further demonstrates the method's utility in causal discovery and heterogeneity quantification.

Out-of-sync evolutionary patterns and mutual interplay of major and minor capsid proteins in norovirus GII.2.

Human noroviruses are the most common cause of viral gastroenteritis, resulting annually in 219 000 deaths and a societal cost of $60 billion, and no antivirals or vaccines are available. The minor capsid protein may play a significant role in the evolution of norovirus. GII.4 is the predominant genotype of norovirus, and its VP2 undergoes epochal co-evolution with the major capsid protein VP1. Since the sudden emergence of norovirus GII.2[P16] in 2016, it has consistently remained a significant epidemic strain in recent years. In the construction of phylogenetic trees, the phylogenetic trees of VP2 closely parallel those of VP1 due to the shared tree topology of both proteins. To investigate the interaction patterns between the major and minor capsid proteins of norovirus GII.2, we chose five representative strains of GII.2 norovirus and investigated their evolutionary patterns using a yeast two-hybrid experiment. Our study shows VP1-VP2 interaction in GII.2, with critical interaction sites at 167-178 and 184-186 in the highly variable region. In the intra-within GII.2, we observed no temporal co-evolution between VP1 and VP2 of GII.2. Notable distinctions were observed in the interaction intensity of VP2 among inter-genotype (P<0.05), highlighting the divergent evolutionary patterns of VP2 within different norovirus genotypes. In summary, the interactions between VP2 and VP1 of GII.2 norovirus exhibit out-of-sync evolutionary patterns. This study offered valuable insights for further understanding and completing the evolutionary mechanism of norovirus.

Multi-core shared tree based MP2MP RWA algorithms in large scale and multi-domain optical networks

The increasing demands of bandwidth-intensive parallel computing and collaborative applications, efficient service provisioning to support multipoint to multipoint (MP2MP) communications have attracted increasing attention. However, with the development of larger-scale and multi-domain optical networks, MP2MP RWA are introduced optimal domain sequence selection and core nodes belong to which domains problems which cannot be tackled by the conventional algorithms proposed aim at a signal domain. In this paper, we proposed a multi-core node shared multicast tree heuristic algorithm (MCSMT) which calculation could be parallelized, delay and minimal cost constrained for multi-domain optical networks. It could realize the accurate calculation of minimum number of cores and the hosted domains of the cores. The source and destination nodes were added in different shared trees respectively with delay constrained algorithms according to specific QoS selection strategy. At the same time, according to more complicated MP2MP algorithms we propose a PCE-cloud based control architecture for optical networks by applying the cloud computing technology (e.g. virtualization and parallel computing) to reform the control plane for improving system reliability, intelligence and maximizing resource utilization. The performances of the proposed heuristic with regard to the number of multi-core nodes, wavelength channel occupied and MP2MP setup latency are compared. In addition, the performance about path computing latency for PCE-cloud control architecture is compared with conversional control architecture.

Wild Floral Visitors Are More Important Than Honeybees as Pollinators of Avocado Crops

Wild insects provide pollination services in agroecosystems. Avocado is an economically important crop grown in the Chilean Mediterranean climate region and exported worldwide. Avocado pollination is managed using honeybee hives, while the role of wild insects as pollinators remains poorly known. We quantified the relative contributions of wild floral visitors and honeybees to the fruit set of avocados in two contrasting seasons (2015 and 2016) in Central Chile. Observations were made in 60 trees grown nearby (~300 m) to remnant patches of native sclerophyll vegetation. We found that honeybees and wild insects accounted for 48.6% and 51.4% of total floral visitation, respectively, with a 68% taxonomic similarity of floral visitors between seasons. The presence of honeybees significantly modulated the floral visitor composition and modified plant-pollination network parameters, which resulted in the biotic homogenization of the interaction network, through the increase of shared tree–floral visitor interactions, to the detriment of exclusive interactions. Finally, wild insects were more effective than honeybees in pollinating avocado trees and their contribution was greatest during the dry year. Thus, honeybees alone cannot be relied upon to deliver maximum pollination. We highlight ecological intensification practices to encourage wild insect visits and avoid native vegetation replacement with orchards. Therefore, we emphasize that future ecological intensification research should address agricultural practices to promote wild insects and evaluate the role of native vegetation as wild pollinator habitat in agricultural landscapes.

QoS-VNS-CS: QoS constraints Core Selection Algorithm based on Variable Neighborhood Search Algorithm

Within the development of network multimedia technology, more and more real-time multimedia applications arrive with the need to transmit information using multicast communication. Multicast IP routing is an important topic, covering both theoretical and practical interest in different networks layers. In network layer, there are several multicast routing protocols using multicast routing trees different in the literature. However PIM-SM and CBT protocols remains the most used multicast routing protocols; they propose using a shared Core-based Tree CBT. This kind of tree provides efficient management of multicast path in changing group memberships, scalability and performance. The prime problem concerning construction of a shared tree is to determine the best position of the core. QoS-CS’s problem (QoS constraints core Selection) consists in choosing an optimal multicast router in the network as core of the Shared multicast Tree (CBT) within specified QoS constraints associated. The choice of this specific router, called RP in PIM-SM protocol and core in CBT protocol, affects the structure of multicast routing tree, and therefore influences performances of both multicast session and routing scheme. QoS-CS is an NP complete problem need to be solved through a heuristic algorithm, in this paper, we propose a new core Selection algorithm based on Variable Neighborhood Search algorithm and new CMP fitness function. Simulation results show that good performance is achieved in multicast cost, end-to-end delay, tree construction delay and others metrics.

Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms

Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth’s woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.

A Two-Layered Shared Tree Multicast Routing Algorithm for Software Defined Hybrid Satellite-Terrestrial Communication Networks

Dynamic routing and congestion control are two major problems in software-defined hybrid satellite-terrestrial multicast networks research. Due to terrestrial users being allowed to join or leave the multicast group at any time and the differences between the satellite and the terrestrial networks, many multicast routing algorithms reroute rapidly and thus increase the rerouting overheads. Meanwhile, the congestion ratio is increased by some hot nodes of satellite-terrestrial link transmission paths. This paper focuses on rerouting overheads and congestion problems in satellite-terrestrial multicast networks. We present a satellite-terrestrial network architecture with the Software-Defined Networking (SDN) features to offer dynamic multicast services for terrestrial users. A Two-Layered Shared Tree Multicast (TSTM) routing algorithm is proposed to achieve efficient dynamic multicast group management, address the trade-off between bandwidth consumption and rerouting overheads. The algorithm also implements congestion control by using a load factor to reflect on the global network bandwidth usage in routing calculations. This algorithm balances the rerouting frequencies of satellite and terrestrial networks to decrease the rerouting overheads and also reduces the network congestion ratio. The simulation shows TSTM decreases rerouting cost, user time delay, and node congestion ratio compared with the locality-aware multicast approach (LAMA).

WITHDRAWN: A QoS Multicast Protocol Optimization for MANET in Wireless Communications

The principle objective of QoS multicast routing is to build a multicast communication in form of shared tree, gathering multiple QoS constraints and Mobile Ad Hoc Networks (MANETs) are an up-and-coming kind of wireless communication networks, in which mobile nodes link on an ad hoc basis. MANETs can change their areas without anyone else too having capacity to design all alone, encouraging friend level communications among mobile nodes independent of fixed infrastructure. Multicast routing problem with numerous QoS limitations, which may cope the deferral, postpone jitter, transmission capacity, and parcel misfortune measurements. additionally, depicts an association model for investigating directing issue, in this paper we presenting IP-EMRP convention which centers around upgrade of demonstration of MANET with assistance of an energy effective steering convention for usage of Quality of service (QoS) and it requires data transfer capacity reservation by assessing the presentation of the organization regarding throughput, time delay and steering overheads for various number of hubs.

An Identifier and Locator Decoupled Multicast Approach (ILDM) Based on ICN

Many bandwidth-intensive applications (such as online live, online games, etc.) are more suitable for using multicast to transmit information. Due to the advantages in scalability, Shared Tree (ST) is more suitable for large-scale deployment than Source-Based Tree (SBT). However, in ST-based multicast, all multicast sources need to send multicast data to a center node called a core, which will lead to core overload and traffic concentration. Besides, most existing multicast protocols use the shortest path between the source or the core and each receiver to construct the multicast tree, which will result in traffic overload on some links. In this paper, we propose an Identifier and Locator Decoupled Multicast approach (ILDM) based on Information-Centric Networking (ICN). ILDM uses globally unique names to identify multicast services. For each multicast service, the mapping between the multicast service name and the addresses of multicast tree nodes is stored in the Name Resolution System (NRS). To avoid core overload and traffic aggregation, we presented a dynamic core management and selection mechanism, which can dynamically select a low-load core for each multicast service. Furthermore, we designed a path state-aware multicast tree node selection mechanism to achieve traffic load balancing by using low-load links more effectively. Experimental results showed that our proposed multicast approach outperformed some other multicast methods in terms of core load, number of join requests, link load, traffic concentration, and routing state.

Network Traffic Sampling System Based on Storage Compression for Application Classification Detection

With the development of the Internet, numerous new applications have emerged, the features of which are constantly changing. It is necessary to perform application classification detection on the network traffic to monitor the changes in the applications. Using RelSamp to sample traffic can provide the sampled traffic with sufficient application features to support application classification. RelSamp separately assigns counters for each flow to record the statistical features and introduces a collision chain into the hash flow table to resolve hash conflicts in the table entries. However, in high-speed networks, owing to the number of concurrent flows and heavy-tailed nature of the traffic, the storage allocation method of RelSamp results in a significant waste of storage on the traffic sampling device. Moreover, the hash conflict resolution of RelSamp causes the collision chains of several hash table entries to be excessively deep, thereby reducing the search efficiency of the flow nodes. To overcome the shortcomings of RelSamp, this study presents a sampling model known as MiniSamp. Based on the RelSamp sampling mechanism, MiniSamp introduces shared counter trees to compress the storage space of the counters during the sampling process and integrates an efficient search tree into the hash table. The search tree structure is adjusted according to the network environment to improve the search efficiency of the flow nodes. The experimental results demonstrate that MiniSamp can effectively aid network operators to classify traffic in the high-speed network.

Fitness Consequences of Interspecific Nesting Associations among Cavity-Nesting Birds.

Interspecific aggregations of prey may provide benefits by mitigating predation risk, but they can also create costs if they increase competition for resources or are more easily detectable by predators. Variation in predation risk and resource availability may influence the occurrence and fitness effects of aggregating in nature. Yet tests of such possibilities are lacking. Cavity-nesting birds provide an interesting test case. They compete aggressively for resources and experience low nest predation rates, which might predict dispersion, but across 19 years of study we found that they commonly aggregate by sharing nest trees. Tree sharing was more common when aspen were more abundant and was somewhat more common in years with higher nest predation risk. Nest success was higher in shared trees when nest predation risk was higher than average. Ultimately, the costs and benefits of aggregating (nest tree sharing) varied across years, and we outline hypotheses for future studies.

Multipoint to multipoint routing and wavelength assignment in multi-domain optical networks

In multi-point to multi-point (MP2MP) routing and wavelength assignment (RWA) problems, researchers usually assume the optical networks to be a single domain. However, the optical networks develop toward to multi-domain and larger scale in practice. In this context, multi-core shared tree (MST)-based MP2MP RWA are introduced problems including optimal multicast domain sequence selection, core nodes belonging in which domains and so on. In this letter, we focus on MST-based MP2MP RWA problems in multi-domain optical networks, mixed integer linear programming (MILP) formulations to optimally construct MP2MP multicast trees is presented. A heuristic algorithm base on network virtualization and weighted clustering algorithm (NV-WCA) is proposed. Simulation results show that, under different traffic patterns, the proposed algorithm achieves significant improvement on network resources occupation and multicast trees setup latency in contrast with the conventional algorithms which were proposed base on a single domain network environment.

A green intelligent routing algorithm supporting flexible QoS for many-to-many multicast

The tremendous energy consumption attributed to the Information and Communication Technology (ICT) field has become a persistent concern during the last few years, attracting significant academic and industrial efforts. Networks have begun to be improved towards being “green”. Considering Quality of Service (QoS) and power consumption for green Internet, a Green Intelligent flexible QoS many-to-many Multicast routing algorithm (GIQM) is presented in this paper. In the proposed algorithm, a Rendezvous Point Confirming Stage (RPCS) is first carried out to obtain a rendezvous point and the candidate Many-to-many Multicast Sharing Tree (M2ST); then an Optimal Solution Identifying Stage (OSIS) is performed to generate a modified M2ST rooted at the rendezvous point, and an optimal M2ST is obtained by comparing the original M2ST and the modified M2ST. The network topology of Cernet2, GéANT and Internet2 were considered for the simulation of GIQM. The results from a series of experiments demonstrate the good performance and outstanding power-saving potential of the proposed GIQM with QoS satisfied.

Scalable multicasting with multiple shared trees in software defined networking

With Software Defined Networking (SDN), IP multicast becomes promising again. For IPTV applications over SDN, existing works would not scale well since they are based on per-source trees. As control-plane in SDN is logically centralized, constructing multiple shared trees is more feasible than that in traditional IP networks. Thus, in this work, we present a locality-aware multicast approach (LAMA) to construct multi-group shared trees in SDN, where each shared tree covers multiple multicast groups. In LAMA, the controller first clusters the multicast sources located in the vicinity into the same multicast cluster. For each multicast cluster, the controller selects the center switch which has the minimum distance to all multicast sources as its rendezvous point (RP) and then constructs a shortest-path multicast tree from the RP to its hosts. Finally, based on the multi-group shared trees, the controller can establish coarse-grained flow entries into on-tree switches to reduce the number of installed flow entries. Emulations on the Ryu controller and the Mininet emulator show that only 2–5 shared trees would suffice. The computation time in the controller using LAMA is around 70ms, much less than hundreds ms required for per-source trees. Moreover, LAMA only establishes 2300 flow entries, 4% of that with per-source trees in a large topology.

Scalable and efficient file sharing in information-centric networking

Internet usage has been increasingly shifting toward massive content retrieval and distribution. To satisfy the demand, information-centric networking (ICN) approaches have emerged. These approaches have common features such as in-network caching and the decoupling of content and location to enable efficient content delivery. In this paper, we investigate the performance issue of file sharing in ICN. Compared to web and user generated content (UGC), file sharing entails relatively low request rates, but much larger content. These characteristics make it difficult for file sharing traffic to take advantage of in-network caching while competing with web and UGC traffic. For scalable and efficient file sharing, we design a peer-aware routing (PAR) protocol to utilize peers׳ storage in ICN. PAR uses a name-based shared tree without additional name resolution service. The shared tree is built at a network layer to connect peers for the same purpose, allowing a peer to discover the nearest peer holding the requested content in the tree. To evaluate the proposed PAR protocol, we conducted a large-scale simulation with a BitTorrent trace over the Internet-scale topology. We show that our protocol can substantially reduce inter-domain traffic, while keeping network overhead low.

A Multi-core Shared Tree Algorithm Based on Network Coding for Multi-point Optical Multicast

AbstractWith the growth of multi-point to multi-point multicast applications, the optical network bandwidth resource consumption is increasing rapidly. It attracted more and more researchers to improve the limited wavelength bandwidth utilization for multicast applications in wavelength division multiplexing (WDM) networks. In the paper, a multi-core shared multicast tree algorithm based on network coding is proposed to minimize the fiber link stress. The proposed algorithm includes three processes: searching the core node candidate set excluding core node loop path, selecting the core nodes from the convergence matrix based on heuristic algorithm, and constructing the multi-core nodes shared trees. The convergence matrix based on the heuristic method is constructed for selecting the core nodes from candidate core node set. To improve the limited wavelength utilization, we introduce network coding into the shared tree to compress the transmitting information. The simulation results show that the proposed algorithm’s performance is better than the existing algorithms’ performance in terms of link stress and balance degree.

多域光网络基于多核点共享树的多点对多点组播

多域光网络基于多核点共享树的多点对多点组播

CompPhy: a web-based collaborative platform for comparing phylogenies.

BackgroundCollaborative tools are of great help in conducting projects involving distant workers. Recent web technologies have helped to build such tools for jointly editing office documents and scientific data, yet none are available for handling phylogenies. Though a large number of studies and projects in evolutionary biology and systematics involve collaborations between scientists of different institutes, current tree comparison visualization software and websites are directed toward single-user access. Moreover, tree comparison functionalities are dispersed between different software that mainly focus on high level single tree visualization but to the detriment of basic tree comparison features.ResultsThe web platform presented here, named CompPhy, intends to fill this gap by allowing collaborative work on phylogenies and by gathering simple advanced tools dedicated to tree comparison. It offers functionalities for tree edition, tree comparison, supertree inference and data management in a collaborative environment. The latter aspect is a specific feature of the platform, allowing people located in different places to work together at the same time on a common project. CompPhy thus proposes shared tree visualization, both synchronous and asynchronous tree manipulation, data exchange/storage, as well as facilities to keep track of the progress of analyses in working sessions. Specific advanced comparison tools are also available, such as consensus and supertree inference, or automated branch swaps of compared trees. As projects can be readily created and shared, CompPhy is also a tool that can be used easily to interact with students in a educational setting, either in the classroom or for assignments.ConclusionsCompPhy is the first web platform devoted to the comparison of phylogenetic trees allowing real-time distant collaboration on a phylogenetic/phylogenomic project. This application can be accessed freely with a recent browser at the following page of the ATGC bioinformatics platform: http://www.atgc-montpellier.fr/compphy/.

QoS-Based Parallel GRASP Algorithm for RP Selection in PIM-SM Multicast Routing and Mobile IPv6

On account the progress of network multimedia technology, more and more real-time multimedia applications arrive with the need to transmit information using multicast IP communication. These applications are more important with arrival of mobile IPv6 protocol with mobile members and require a multicast routing protocol which has packets arriving to members within a specified QoS guaranteed and a quick recovery mechanism. Multicast IP is a bandwidth-conserving technology that reduces traffic by simultaneously delivering a single stream of information to a group members. Internet research community has proposed many multicast routing protocols to support efficient multimedia application, expect that they were developed for multicast parties whose members are topologically stationary. The mobility of multicast receivers or senders may lead to serious problems, when a receiver or sender moves, the quality of full multicast tree may degrade hens multicast datagrams cannot be forwarded efficiently.D2V-RPM (delay and delay variation RP Manager) problem consist of choosing an optimal multicast router in the network as the root of the Shared RP Tree within a specified delay and delay variation bound, and recovering this RP if it’s off optimal. This NP hard problem needs to be solved through a heuristic algorithm. In this paper we propose a new RP Management algorithm based on PGRAS Procedure. 2DV-PGRASP-RPM selects and recovers the RP by considering cost, delay and delay variation functions and can be easily integrated to bootstrap RP protocol used by PIM-SM protocol. Simulation results show that good performance is achieved in multicast cost.

Nested Hierarchical Dirichlet Processes.

We develop a nested hierarchical Dirichlet process (nHDP) for hierarchical topic modeling. The nHDP generalizes the nested Chinese restaurant process (nCRP) to allow each word to follow its own path to a topic node according to a per-document distribution over the paths on a shared tree. This alleviates the rigid, single-path formulation assumed by the nCRP, allowing documents to easily express complex thematic borrowings. We derive a stochastic variational inference algorithm for the model, which enables efficient inference for massive collections of text documents. We demonstrate our algorithm on 1.8 million documents from The New York Times and 2.7 million documents from Wikipedia.