Heat shock and structural proteins associated with meat tenderness in Nellore beef cattle,a Bos indicus breed

Nellore beef cattle, a Bos indicus (Zebu) breed, is well adapted to tropical conditions and has allowed Brazil to become one of the largest producers of red meat. Nevertheless, B. indicus breeds are reported to have less tender meat than Bos taurus. This study was designed to identify genes associated with meat tenderness and thus provides important information for breeding programs. A group of 138 animals was evaluated for longissimus thoracis muscle shear force (SF). Animals with the highest and lowest SF values (six animals each) were then selected for protein abundance studies. Samples were subjected to two-dimensional gel electrophoresis (2-DE) followed by peptide sequencing through mass spectrometry (MS) to identify differentially expressed proteins associated with SF values. Seventeen differentially expressed spots were observed (p < 0.05) between the two groups. The 13 proteins identified included structural proteins (alpha actin-1, MLC1, MLC3, MLC2F and tropomyosin), related to cell organization (HSPB1 and HSP70), metabolism (beta-LG, ACBD6 and Complex III subunit I) and some uncharacterized proteins. Results confirm the existence of differentially expressed proteins associated with SF, which can lead to a better understanding of mechanisms involved in meat tenderness.     

RE-tree: an efficient index structure for regular expressions

Due to their expressive power, regular expressions (REs) are quickly becoming an integral part of language specifications for several important application scenarios. Many of these applications have to manage huge databases of RE specifications and need to provide an effective matching mechanism that, given an input string, quickly identifies the REs in the database that match it. In this paper, we propose the RE-tree, a novel index structure for large databases of RE specifications. Given an input query string, the RE-tree speeds up the retrieval of matching REs by focusing the search and comparing the input string with only a small fraction of REs in the database. Even though the RE-tree is similar in spirit to other tree-based structures that have been proposed for indexing multidimensional data, RE indexing is significantly more challenging since REs typically represent infinite sets of strings with no well-defined notion of spatial locality. To address these new challenges, our RE-tree index structure relies on novel measures for comparing the relative sizes of infinite regular languages. We also propose innovative solutions for the various RE-tree operations including the effective splitting of RE-tree nodes and computing a "tight" bounding RE for a collection of REs. Finally, we demonstrate how sampling-based approximation algorithms can be used to significantly speed up the performance of RE-tree operations. Preliminary experimental results with moderately large synthetic data sets indicate that the RE-tree is effective in pruning the search space and easily outperforms naive sequential search approaches.Received: 16 September 2002, Published online: 8 July 2003Edited by R. Ramakrishnan     

Tracking set-expression cardinalities over continuous update streams

There is growing interest in algorithms for processing and querying continuous data streams (i.e., data seen only once in a fixed order) with limited memory resources. In its most general form, a data stream is actually an update stream, i.e., comprising data-item deletions as well as insertions. Such massive update streams arise naturally in several application domains (e.g., monitoring of large IP network installations or processing of retail-chain transactions). Estimating the cardinality of set expressions defined over several (possibly distributed) update streams is perhaps one of the most fundamental query classes of interest; as an example, such a query may ask what is the number of distinct IP source addresses seen in passing packets from both router R ₁ and R ₂ but not router R ₃?. Earlier work only addressed very restricted forms of this problem, focusing solely on the special case of insert-only streams and specific operators (e.g., union). In this paper, we propose the first space-efficient algorithmic solution for estimating the cardinality of full-fledged set expressions over general update streams. Our estimation algorithms are probabilistic in nature and rely on a novel, hash-based synopsis data structure, termed 2-level hash sketch. We demonstrate how our 2-level hash sketch synopses can be used to provide low-error, high-confidence estimates for the cardinality of set expressions (including operators such as set union, intersection, and difference) over continuous update streams, using only space that is significantly sublinear in the sizes of the streaming input (multi-)sets. Furthermore, our estimators never require rescanning or resampling of past stream items, regardless of the number of deletions in the stream. We also present lower bounds for the problem, demonstrating that the space usage of our estimation algorithms is within small factors of the optimal. Finally, we propose an optimized, time-efficient stream synopsis (based on 2-level hash sketches) that provides similar, strong accuracy-space guarantees while requiring only guaranteed logarithmic maintenance time per update, thus making our methods applicable for truly rapid-rate data streams. Our results from an empirical study of our synopsis and estimation techniques verify the effectiveness of our approach.Received: 20 October 2003, Accepted: 16 April 2004, Published online: 14 September 2004Edited by: J. Gehrke and J. Hellerstein.Sumit Ganguly: sganguly@cse.iitk.ac.in Current affiliation: Department of Computer Science and Engineering, Indian Institute of Technology, Kanpur, India     

On periodic resource scheduling for continuous-media databases

The Enhanced Pay-Per-View (EPPV) model for providing continuous-media services associates with each continuous-media clip a display frequency that depends on the clip's popularity. The aim is to increase the number of clients that can be serviced concurrently beyond the capacity limitations of available resources, while guaranteeing a constraint on the response time. This is achieved by sharing periodic continuous-media streams among multiple clients. The EPPV model offers a number of advantages over other data-sharing schemes (e.g., batching), which make it more attractive to large-scale service providers. In this paper, we provide a comprehensive study of the resource-scheduling problems associated with supporting EPPV for continuous-media clips with (possibly) different display rates, frequencies, and lengths. Our main objective is to maximize the amount of disk bandwidth that is effectively scheduled under the given data layout and storage constraints. Our formulation gives rise to -hard combinatorial optimization problems that fall within the realm of hard real-time scheduling theory. Given the intractability of the problems, we propose novel heuristic solutions with polynomial-time complexity. We also present preliminary experimental results for the average case behavior of the proposed scheduling schemes and examine how they compare to each other under different workloads. A major contribution of our work is the introduction of a robust scheduling framework that, we believe, can provide solutions for a variety of realistic EPPV resource-scheduling scenarios, as well as any scheduling problem involving regular, periodic use of a shared resource. Based on this framework, we propose various interesting research directions for extending the results presented in this paper. Received June 9, 1998 / Accepted October 13, 1998     

Development of an innovative information system: a fish identification e-key with update capabilities

A dichotomous identification key organizes fishes based on their similarities and differences, and is an essential tool in which ichthyologists, biologists, fishery biologists and others can use for accurate identification of specimens or finding information on correct names, biology and distribution of species. This research work focuses on the development and implementation of a totally new information system that is able to identify correctly fish species names. The developed system is a fully interactive fish identification e-key, which can be used in both forms; locally and remotely via the World Wide Web. This new dichotomous classification e-key provides the capability to identify any species in a compact and easy to use environment, which gives the user excellent operation capabilities and complete information about all included fish species. Moreover, the application provides the capability to search for a random fish species and to show a list which includes all the fish species that currently exist in the application's database. There is an extra attribute that makes the new system novel, and this is its expandability: the information system is fully dynamic having the capability to be extended every time a new species is identified. This attribute is innovative because, until now, there is not any fish identification e-key that gives the user the capability to insert new fish species into the application's database.     

Noncontact optical imaging in mice with full angular coverage and automatic surface extraction

During the past decade, optical imaging combined with tomographic approaches has proved its potential in offering quantitative three-dimensional spatial maps of chromophore or fluorophore concentration in vivo. Due to its direct application in biology and biomedicine, diffuse optical tomography (DOT) and its fluorescence counterpart, fluorescence molecular tomography (FMT), have benefited from an increase in devoted research and new experimental and theoretical developments, giving rise to a new imaging modality. The most recent advances in FMT and DOT are based on the capability of collecting large data sets by using CCDs as detectors, and on the ability to include multiple projections through recently developed noncontact approaches. For these to be implemented, we have developed an imaging setup that enables three-dimensional imaging of arbitrary shapes in fluorescence or absorption mode that is appropriate for small animal imaging. This is achieved by implementing a noncontact approach both for sources and detectors and coregistering surface geometry measurements using the same CCD camera. A thresholded shadowgrammetry approach is applied to the geometry measurements to retrieve the surface mesh. We present the evaluation of the system and method in recovering three-dimensional surfaces from phantom data and live mice. The approach is used to map the measured in vivo fluorescence data onto the tissue surface by making use of the free-space propagation equations, as well as to reconstruct fluorescence concentrations inside highly scattering tissuelike phantom samples. Finally, the potential use of this setup for in vivo small animal imaging and its impact on biomedical research is discussed.     

Optimal configuration of OSPF aggregates

Open Shortest Path First (OSPF) is a popular protocol for routing within an autonomous system (AS) domain. In order to scale for large networks containing hundreds and thousands of subnets, OSPF supports a two-level hierarchical routing scheme through the use of OSPF areas. Subnet addresses within an area are aggregated, and this aggregation is a crucial requirement for scaling OSPF to large AS domains, as it results in significant reductions in routing table sizes, smaller link-state databases, and less network traffic to synchronize the router link-state databases. On the other hand, address aggregation also implies loss of information about the length of the shortest path to each subnet, which in turn, can lead to suboptimal routing. We address the important practical problem of configuring OSPF aggregates to minimize the error in OSPF shortest-path computations due to subnet aggregation. We first develop an optimal dynamic programming algorithm that, given an upper bound k on the number of aggregates to be advertised and a weight assignment function for the aggregates, computes the k aggregates that result in the minimum cumulative error in the shortest-path computations for all source-destination subnet pairs. Subsequently, we tackle the problem of assigning weights to OSPF aggregates such that the cumulative error in the computed shortest paths is minimized. We demonstrate that, while for certain special cases (e.g., unweighted cumulative error) efficient optimal algorithms for the weight assignment problem can be devised, the general problem itself is NP-hard. Consequently, we have to rely on search heuristics to solve the weight assignment problem. To the best of our knowledge, our work is the first to address the algorithmic issues underlying the configuration of OSPF aggregates and to propose efficient configuration algorithms that are provably optimal for many practical scenarios.     

Performance estimation of banyan semi layer networks with drop resolution mechanism

Multistage interconnection networks (MINs) are a basic class of switch-based network architectures, which are used for constructing scalable parallel computers or for connecting networks. Semi-layer MINs are a special case of MINs. A performance evaluation of semi-layer MINs (using simulation models) is presented in this paper. The configurations of the under study networks apply a conflict drop resolution mechanism. The proposed architecture's performance is studied under uniform traffic conditions and various offered loads, buffer-lengths and MIN sizes. In this paper, the improvements on semi-layer MIN performance, in terms of throughput and latency, are demonstrated quantitatively. These performance measures can be valuable tools for designers of parallel multiprocessor systems and networks, in order to minimize the overall deployment costs and help deliver efficient systems.