DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family
DetectIng Variability in Evolutionary Rates among GEnes (DIVERGE) is a software system to study functional divergence of a protein family by detecting site-specific change in evolutionary rate using a multiple alignment of amino acid sequences for a given phylogenetic tree. The program first conducts a statistical test for site-specific rate shifts along the tree, and predicting candidate amino acid residues responsible for functional divergence based on posterior analysis. These results can then be mapped on the 3D protein structure if available.


AVAILABILITY
DIVERGE is available free of charge from http://xgu1.zool.iastate.edu/. Distribution packages for both Linux and Microsoft Windows operating systems are available, including manual and example files.

title: A Greedy Algorithm for Optimal Recombination
abstract: Let Σ be an alphabet and Σn denote the collection of all sequences of length n over Σ. For any s1 = ajaj+1 . . . an+s2 = b1b2 . . . bj bj+1 . . . bn ∈ Σn, a recombination of s1 and s2 at position j is defined as an operation that crosses s1 and s2 at position j and generates t1 = a1a2 . . .  . bn and t2 = b1b2 . . .  Denote A and S two collections of sequences. In this paper, we discuss generating A from S by a series of recombinations in minimum number of steps. We present a greedy algorithm for finding the optimal recombination evolutionary history from S to any tree A of sequences when |S| = 2.

title: Functional Divergence in TGF-b Signaling Pathway

title: Evolutionary analysis of functional divergence in TGF- signaling pathway
abstract: TGF-β cytokines and their interacting receptors form an intricate signaling network and play important roles in cell differentiation and development. Members in gene families involved in this complicated pathway are usually conserved in sequence but distinct in temporal and tissue-specific expression. Starting from an evolutionary perspective, we have statistically tested the functional divergence in major pathway components, targeted the critical amino acid residues responsible for functional divergence. Our results show that altered functional constraints is a common pattern in the evolution of TGF-β pathway. Moreover, we have found the correlation between structural divergence and functional divergence in the extracellular ligand-binding domain of Type II receptors. This study helps understand the complex intrinsic mechanisms of signaling.

title: Silhouette clipping
abstract: Approximating detailed with coarse, texture-mapped meshes results in polygonal silhouettes. To eliminate this artifact, we introduce silhouette clipping, a framework for efficiently clipping the rendering of coarse geometry to the exact silhouette of the original model. The coarse mesh is obtained using progressive hulls, a novel representation with the nesting property required for proper clipping. We describe an improved technique for constructing texture and normal maps over this coarse mesh. Given a perspective view, silhouettes are efficiently extracted from the original mesh using a precomputed search tree. Within the tree, hierarchical culling is achieved using pairs of anchored cones. The extracted silhouette edges are used to set the hardware stencil buffer and alpha buffer, which in turn clip and antialias the rendered coarse geometry. Results demonstrate that silhouette clipping can produce renderings of similar quality to high-resolution meshes in less rendering time.

title: Performance evaluation of DCCP: A focus on smoothness and TCP-friendliness
abstract: Recent years have seen dramatic increases of the use of multimedia applications on the Internet, which typically either lack congestion control or use proprietary congestion control mechanisms. This can easily cause congestion collapse or compatibility problems. Datagram Congestion Control Protocol (Dccp) fills the gap betweenUdp andTcp, featuring congestion control rather than reliability for packet-switched rich content delivery with high degree of flexibility. We present aDccp model designed and implemented withOpnet Modeler, and the experiments and evaluation focused on largely the smoothness of the data rates, and the fairness between concurrentDccp flows andTcp flows. We foundDccp-ccid3 demonstrates stable data rates under different scenarios, and the fairness betweenDccp andTcp is only achieved under certain conditions. We also validated that the throughput ofDccp-Ccid3 is proportional to the average packet size, and relatively fixed packet size is critical for the optimal operation ofDccp. Problems in the slow start phase and insufficient receiver buffer size were identified and we hereby proposed solutions on this.RésuméLe nombre d’applications multimédias sur l’internet a considérablement augmenté ces dernières années. Ces applications généralement ne gèrent pas les congestions ou bien utilisent des mécanismes de contrôle propriétaires. Il peut en résulter facilement des congestions graves ou des problèmes d’incompatibilité. Le protocoleDccp (Datagram Congestion Control Protocol) se positionne entreUdp etTcp puisqu ’il fournit, pour des paquets multimédias, un contrôle de congestion hautement flexible mais sans la fiabilité de délivrance. Cet article présente un modèleDccp conçu et implémenté avec le simulateurOpnet. Les expérimentations et les analyses portent principalement sur le lissage des débits et l’équité entre des fluxDccp etTcp concurrents. On montre queDccp-Ccid3 affiche des débits stables sous divers scénarios et que l’équité entreDccp etTcp n’est atteinte que sous certaines conditions. On valide également que le débit deDccp-Ccid3 est proportionnel à la taille moyenne des paquets et que le fait d’avoir des paquets de taille relativement constante est un facteur essentiel pour un fonctionnement optimal deDccp. Les problèmes pendant la phase de démarrage lent et ceux dus à une mémoire tampon insuffisante côté récepteur sont également analysés et résolus.

title: A programming framework for quality-aware ubiquitous multimedia applications
abstract: Ubiquitous computing promises a computing environment that seamlessly and pervasively delivers applications to the user, despite changes of resources, devices, and locations. However, few ubiquitous multimedia applications (UMAs) exist up-to-date. One of the main reasons lies in the fact that it is difficult and error-prone to build a UMA which is mobile and deployable in different ubiquitous environments, and still provides acceptable application-specific Quality-of-Service (QoS) guarantees. In this paper, we present the design and implementation of a novel programming framework, called 'QCompiler" to address the challenges. The framework includes (1) a high-level application specification for the application developer to easily write a UMA with specific quality, mobility, and ubiquity supports, (2) a meta-data compilation, which provides automated consistency checks, translations, and substitutions, to relieve the application developer from dealing with complex programming related to quality, mobility, and ubiquity, (3) a binding, which prepares a quality-aware specification to be executable, in a specific deployment environment, and (4)a run-time meta-data execution, utilizing the meta-data compilation's results, to manage and control a quality-aware multimedia application. As a case study, we apply the programming framework to build a mobile Video-on-Demand (VoD) application. The experimental results show tradeoffs between easiness and flexibility to develop and deploy UMA, and overheads during UMA instantiation and adaptation.

title: Visual QoS programming environment for ubiquitous multimedia services
abstract: The provision of distributed multimedia services is becoming mobile and ubiquitous. Different multimedia services require application-specific Quality of Service (QoS). In this paper, we present QoSTalk, a unified component-based programming environment that allows application developers to specify different application-specific QoS requirements easily. In QoSTalk, we adopt a hierarchical approach to model application configuration graphs for different distributed multimedia services. We design and implement the XML-based Hierarchical QoS Markup Language, called HQML, to describe the hierarchical configuration graph as well as other application-specific QoS requirements and policies. QoSTalk promotes the separation of concerns in developing QoS-aware ubiquitous multimedia applications and thus enables easy programming of QoS-aware applications, running on top of a unified QoS-aware middleware framework. We have prototyped the QoSTalk in Java and CORBA. Our case studies with several multimedia applications show that QoSTalk effectively fills the gap for application developers between the very general facilities provided by the QoS-aware middleware and different kinds of distributed multimedia applications.