CiteULike: Author Wiegand

How individual species structure diversity in tropical forests.

T Wiegand — 2008-07-30T22:10:07-00:00

Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 48. (27 November 2007), pp. 19029-19033.

A persistent challenge in ecology is to explain the high diversity of tree species in tropical forests. Although the role of species characteristics in maintaining tree diversity in tropical forests has been the subject of theory and debate for decades, spatial patterns in local diversity have not been analyzed from the viewpoint of individual species. To measure scale-dependent local diversity structures around individual species, we propose individual species-area relationships (ISAR), a spatial statistic that marries common species-area relationships with Ripley's K to measure the expected alpha diversity in circular neighborhoods with variable radius around an arbitrary individual of a target species. We use ISAR to investigate if and at which spatial scales individual species increase in tropical forests' local diversity (accumulators), decrease local diversity (repellers), or behave neutrally. Our analyses of data from Barro Colorado Island (Panama) and Sinharaja (Sri Lanka) reveal that individual species leave identifiable signatures on spatial diversity, but only on small spatial scales. Most species showed neutral behavior outside neighborhoods of 20 m. At short scales (<20 m), we observed, depending on the forest type, two strongly different roles of species: diversity repellers dominated at Barro Colorado Island and accumulators at Sinharaja. Nevertheless, we find that the two tropical forests lacked any key species structuring species diversity at larger scales, suggesting that "balanced" species-species interactions may be a characteristic of these species-rich forests. We anticipate our analysis method will be a starting point for more powerful investigations of spatial structures in diversity to promote a better understanding of biodiversity in tropical forests.

Overview of the H.264/AVC video coding standard

T Wiegand — 2007-05-01T05:30:12-00:00

Circuits and Systems for Video Technology, IEEE Transactions on, Vol. 13, No. 7. (2003), pp. 560-576.

H.264/AVC is newest video coding standard of the ITU-T Video Coding Experts Group and the ISO/IEC Moving Picture Experts Group. The main goals of the H.264/AVC standardization effort have been enhanced compression performance and provision of a "network-friendly" video representation addressing "conversational" (video telephony) and "nonconversational" (storage, broadcast, or streaming) applications. H.264/AVC has achieved a significant improvement in rate-distortion efficiency relative to existing standards. This article provides an overview of the technical features of H.264/AVC, describes profiles and applications for the standard, and outlines the history of the standardization process.

Context-based adaptive binary arithmetic coding in the H.264/AVC video compression standard

D Marpe — 2008-07-09T10:34:31-00:00

Circuits and Systems for Video Technology, IEEE Transactions on, Vol. 13, No. 7. (2003), pp. 620-636.

Context-based adaptive binary arithmetic coding (CABAC) as a normative part of the new ITU-T/ISO/IEC standard H.264/AVC for video compression is presented. By combining an adaptive binary arithmetic coding technique with context modeling, a high degree of adaptation and redundancy reduction is achieved. The CABAC framework also includes a novel low-complexity method for binary arithmetic coding and probability estimation that is well suited for efficient hardware and software implementations. CABAC significantly outperforms the baseline entropy coding method of H.264/AVC for the typical area of envisaged target applications. For a set of test sequences representing typical material used in broadcast applications and for a range of acceptable video quality of about 30 to 38 dB, average bit-rate savings of 9%-14% are achieved.

Overview of the Scalable Video Coding Extension of the H.264/AVC Standard

H Schwarz — 2008-05-25T21:05:24-00:00

Circuits and Systems for Video Technology, IEEE Transactions on, Vol. 17, No. 9. (2007), pp. 1103-1120.

With the introduction of the H.264/AVC video coding standard, significant improvements have recently been demonstrated in video compression capability. The Joint Video Team of the ITU-T VCEG and the ISO/IEC MPEG has now also standardized a Scalable Video Coding (SVC) extension of the H.264/AVC standard. SVC enables the transmission and decoding of partial bit streams to provide video services with lower temporal or spatial resolutions or reduced fidelity while retaining a reconstruction quality that is high relative to the rate of the partial bit streams. Hence, SVC provides functionalities such as graceful degradation in lossy transmission environments as well as bit rate, format, and power adaptation. These functionalities provide enhancements to transmission and storage applications. SVC has achieved significant improvements in coding efficiency with an increased degree of supported scalability relative to the scalable profiles of prior video coding standards. This paper provides an overview of the basic concepts for extending H.264/AVC towards SVC. Moreover, the basic tools for providing temporal, spatial, and quality scalability are described in detail and experimentally analyzed regarding their efficiency and complexity.

Pattern-Oriented Modeling of Agent-Based Complex Systems: Lessons from Ecology

Volker Grimm — 2006-01-09T22:34:10-00:00

Science, Vol. 310, No. 5750. (11 November 2005), pp. 987-991.

Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern-oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity.

Texture Synthesis Method for Generic Video Sequences

P Ndjiki-Nya — 2008-06-19T18:50:50-00:00

Image Processing, 2007. ICIP 2007. IEEE International Conference on, Vol. 3 (2007), pp. III - 397-III - 400.

An effective texture synthesis method is presented that is inspired by the work of Kwatra et al. [1]. Their algorithm is non-parametric and patch-based. Blending between overlapping patches is optimized using graph cut techniques. We generalize the initial approach [ 1 ] to achieve a new synthesis algorithm that yields improved results for a much larger class of natural video sequences. For that, two major extensions have been provided: (1) the ability to handle constrained texture synthesis applications and (2) robustness against global camera motion. Constrained synthesis thereby refers to integrating synthetic textures into natural video sequences, as opposed to unconstrained texture synthesis, where (infinite) spatio-temporal extensions of single textures are generated. Camera motion compensation enables applicability of the synthesis algorithm to video sequences with a moving camera. The results presented in this paper show that the proposed improvements yield significant subjective gains compared to the initial algorithm.

A Content-Based Video Coding Approach for Rigid and Non-Rigid Textures

P Ndjiki-Nya — 2008-06-19T18:45:56-00:00

Image Processing, 2006 IEEE International Conference on (2006), pp. 3169-3172.

A generic, content-based video coding framework is described. The approach is based on H.264/MPEG4-AVC that is extended by a closed-loop texture analysis/synthesis algorithm. The texture analysis yields regions that can be reproduced with reduced accuracy at the decoder without noticeable quality degradations. These textures are synthesized at the decoder given side information generated through analysis. The remainder regions are coded using H.264/MPEG4-AVC that serves as fallback option in our framework. Texture synthesis is constrained in the proposed system as the area to synthesize is typically surrounded by one or more textures. In this paper, it is shown that constrained synthesis can be done successfully for a large class of textures including non-rigid textures such as water. Experimental results verify improvements of the proposed system compared to H.264/MPEG4-AVC without our approach

A Task-Based Ontology Approach to Automate Geospatial Data Retrieval

Nancy Wiegand — 2007-06-14T09:22:19-00:00

Transactions in GIS, Vol. 11, No. 3. (2007), pp. 355-376.

Abstract This paper presents a task-based and Semantic Web approach to find geospatial data. The purpose of the project is to improve data discovery and facilitate automatic retrieval of data sources. The work presented here helps create the beginnings of a Geospatial Semantic Web. The intent is to create a system that provides appropriate results to application users who search for data when facing tasks such as emergency response or planning activities. In our task-based system, we formalize the relationships between types of tasks, including emergency response, and types of data sources needed for those tasks. Domain knowledge, including criteria describing data sources, is recorded in an ontology language. With the ontology, reasoning can be done to infer various types of information including which data sources meet specific criteria for use in particular tasks. The vision presented here is that in an emergency, for example, a user accesses a Web-based application and selects the type of emergency and the geographic area. The application then returns the types and locations (URLs) of the specific geospatial data needed. We explore the abilities and limitations of the OWL Web Ontology Language along with other Semantic Web technologies for this purpose.

A genome-wide map of diversity in Plasmodium falciparum.

Sarah K Volkman — 2006-12-15T10:45:43-00:00

Nat Genet (10 December 2006)

Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality. Here we describe an initial survey of genetic variation across the P. falciparum genome. We performed extensive sequencing of 16 geographically diverse parasites and identified 46,937 SNPs, demonstrating rich diversity among P. falciparum parasites (pi = 1.16 x 10(-3)) and strong correlation with gene function. We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites. We further characterized 54 worldwide isolates by genotyping SNPs across 20 genomic regions. These data begin to define population structure among African, Asian and American groups and illustrate the degree of linkage disequilibrium, which extends over relatively short distances in African parasites but over longer distances in Asian parasites. We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite.

Performance comparison of video coding standards using Lagrangian coder control

A Joch — 2008-05-22T04:30:29-00:00

Image Processing. 2002. Proceedings. 2002 International Conference on, Vol. 2 (2002), pp. II-501-II-504 vol.2.

A unified approach to the coder control of video coding standards such as MPEG-2, H.263, MPEG-4, and the draft video coding standard JVT/H.26L/AVC is presented. Using this unified framework, the performance of the various standards is compared by means of PSNR and subjective testing results. The results indicate that JVT/H.26L/AVC compliant encoding can typically achieve essentially the same objective PSNR reproduction quality as encoders that are compliant with previous standards while requiring as little as 60% or less of the bit rate of the next best standard, particularly for higher-latency applications and particularly for more difficult source material. Subjective testing shows that the bit savings produced by this draft standard are even larger than the PSNR results indicate.

De Novo Synthesis of N and P Proteins as a Key Step in Sendai Virus Gene Expression

Marian Wiegand — 2008-05-11T22:18:05-00:00

J. Virol., Vol. 81, No. 24. (15 December 2007), pp. 13835-13844.

Among the members of the paramyxovirus family, the transcription process and the components involved have been studied under in vitro conditions thus far. Here, we reexamined the function of the viral RNA-dependent RNA polymerase through infection studies with Sendai virus (SeV) N and P deletion (Delta) mutants. To elucidate solely transcription-specific processes, all virus mutants also were rendered deficient in genome replication. Using mutant SeV DeltaP, the earlier suspected supplemental role of P protein was clearly demonstrated to be essential during viral gene expression. Moreover, when SeV DeltaN or DeltaN PDelta2-77 (with the 5' end of the P gene deleted) mutant was used for infections, a completely unexpected new and essential role for N protein was discovered for viral gene expression. In the early phases of an infection and in the absence of de novo viral protein synthesis, primary transcription occurs at hardly detectable levels. In contrast, if newly synthesized N protein is present, primary viral transcription reaches normal levels. From our data, we conclude that de novo synthesis of SeV N and P proteins is a key step for viral gene expression that facilitates the transition from preliminary to normal primary transcriptional activity. 10.1128/JVI.00914-07

Low-delay peer-to-peer streaming using scalable video coding

Pierpaolo Baccichet — 2008-05-09T20:50:52-00:00

Packet Video 2007 (2007), pp. 173-181.

Peer-to-peer (P2P) networks represent a valuable architecture for streaming video over the Internet. In these systems, users contribute their resources to relay the media to others and no dedicated infrastructure is required. In order to ensure a low end-to-end delay, P2P overlay networks are often organized as a set of complementary multicast trees. The source of the stream multiplexes the data on top of these trees and the routing of packets is statically defined. In this scenario, the reliability of the overlay links is critical for the performance of the system since temporary link failure or network congestion can cause a significant disruption of the end-user quality. The novel Scalable Video Coding (SVC) standard enables efficient usage of the network capacity by allowing intermediate high capacity nodes in the overlay network to dynamically extract layers from the scalable bit stream to serve less capable peers. On the other hand, SVC incurs a certain loss in terms of coding efficiency with respect to H.264/AVC single-layer coding. We propose a simple model that allows to evaluate the trade-off of using a scalable codec with respect to single-layer coding, given the distribution of the receivers’ capacities in an error-free network. We also report experimental results obtained by using SVC on top of a real-time implementation of the Stanford Peer-to-Peer Multicast (SPPM) protocol that clearly show the benefits of a prioritization mechanism to react to network congestion.

Spatial ecology of a root parasite from pattern to process

David Watson — 2007-05-11T16:49:28-00:00

Austral Ecology, Vol. 32, No. 4. (June 2007), pp. 359-369.

Robustness in cooperative coevolution

Paul Wiegand — 2008-02-26T00:25:18-00:00

(2006), pp. 369-376.

Infusion of brain-derived neurotrophic factor into the lateral ventricle of the adult rat leads to new neurons in the parenchyma of the striatum, septum, thalamus, and hypothalamus.

V Pencea — 2005-12-01T18:10:44-00:00

J Neurosci, Vol. 21, No. 17. (1 September 2001), pp. 6706-6717.

The findings that brain-derived neurotrophic factor (BDNF) promotes in vitro the survival and/or differentiation of postnatal subventricular zone (SVZ) progenitor cells and increases in vivo the number of the newly generated neurons in the adult rostral migratory stream and olfactory bulb prompted us to investigate whether the infusion of BDNF influences the proliferation and/or differentiation of cells in other regions of the adult forebrain. We examined the distribution and phenotype of newly generated cells in the adult rat forebrain 16 d after intraventricular administration of BDNF in conjunction with the cell proliferation marker bromodeoxyuridine (BrdU) for 12 d. BDNF infusion resulted in numerous BrdU(+) cells, not only in the SVZ lining the infused lateral ventricle, but moreover, in specific parenchymal structures lining the lateral and third ventricles, including the striatum and septum, as well as the thalamus and hypothalamus, in which neurogenesis had never been demonstrated previously during adulthood. In each region, newly generated cells expressed the neuronal marker microtubule-associated protein-2, or neuron-specific tubulin, identified by the antibody TuJ1. The percentage of the newly generated cells expressing TuJ1 ranged from 27 to 42%, suggesting that the adult forebrain has a more profound capacity to produce neurons than recognized previously. The extent of cell proliferation after BDNF infusion was correlated with the level of expression of full-length TrkB, the high-affinity receptor for BDNF, despite the fact that the BrdU(+) cells were not themselves TrkB(+). Collectively, our results demonstrate that the adult brain parenchyma may recruit and/or generate new neurons, which could replace those lost as a result of injury or disease.

Cellular inhibitors of long interspersed element 1 and Alu retrotransposition

Hal Bogerd — 2006-10-10T13:59:31-00:00

PNAS, Vol. 103, No. 23. (6 June 2006), pp. 8780-8785.

Long interspersed element (LINE) 1 retrotransposons are major genomic parasites that represent approx17% of the human genome. The LINE-1 ORF2 protein is also responsible for the mobility of Alu elements, which constitute a further approx11% of genomic DNA. Representative members of each element class remain mobile, and deleterious retrotransposition events can induce spontaneous genetic diseases. Here, we demonstrate that APOBEC3A and APOBEC3B, two members of the APOBEC3 family of human innate antiretroviral resistance factors, can enter the nucleus, where LINE-1 and Alu reverse transcription occurs, and specifically inhibit both LINE-1 and Alu retrotransposition. These data suggest that the APOBEC3 protein family may have evolved, at least in part, to defend the integrity of the human genome against endogenous retrotransposons. 10.1073/pnas.0603313103

Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.

M Wu — 2005-09-05T09:00:46-00:00

PLoS Biol, Vol. 2, No. 3. (March 2004)

The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.

Misfolded plant virus proteins: elicitors and targets of ubiquitylation

Harald Jockusch — 2008-02-28T14:18:22-00:00

FEBS Letters, Vol. 545, No. 2-3. (19 June 2003), pp. 229-232.

Mutant tobacco mosaic virus (TMV) coat proteins (CPs) with known amino acid replacements provide well defined examples of destabilized tertiary structures. Here we show that misfolded TMV CPs, but not functional wild-type CPs, induce massive ubiquitylation in tobacco cells and that denatured, insoluble CP subunits are the main substrates of ubiquitin conjugation. As TMV CPs can be easily manipulated they are unique tools to study the molecular basis of the plant cell's response to aberrant protein structures and the associated intracellular stress reactions.

H.264/AVC in wireless environments

T Stockhammer — 2005-09-02T04:10:06-00:00

Circuits and Systems for Video Technology, IEEE Transactions on, Vol. 13, No. 7. (2003), pp. 657-673.

Video transmission in wireless environments is a challenging task calling for high-compression efficiency as well as a network friendly design. Both have been major goals of the H.264/AVC standardization effort addressing "conversational" (i.e., video telephony) and "nonconversational" (i.e., storage, broadcast, or streaming) applications. The video compression performance of the H.264/AVC video coding layer typically provides a significant improvement. The network-friendly design goal of H.264/AVC is addressed via the network abstraction layer that has been developed to transport the coded video data over any existing and future networks including wireless systems. The main objective of this paper is to provide an overview over the tools which are likely to be used in wireless environments and discusses the most challenging application, wireless conversational services in greater detail. Appropriate justifications for the application of different tools based on experimental results are presented.

Biasing Coevolutionary Search for Optimal Multiagent Behaviors

L Panait — 2008-02-19T01:16:48-00:00

Evolutionary Computation, IEEE Transactions on, Vol. 10, No. 6. (2006), pp. 629-645.

Cooperative coevolutionary algorithms (CEAs) offer great potential for concurrent multiagent learning domains and are of special utility to domains involving teams of multiple agents. Unfortunately, they also exhibit pathologies resulting from their game-theoretic nature, and these pathologies interfere with finding solutions that correspond to optimal collaborations of interacting agents. We address this problem by biasing a cooperative CEA in such a way that the fitness of an individual is based partly on the result of interactions with other individuals (as is usual), and partly on an estimate of the best possible reward for that individual if partnered with its optimal collaborator. We justify this idea using existing theoretical models of a relevant subclass of CEAs, demonstrate how to apply biasing in a way that is robust with respect to parameterization, and provide some experimental evidence to validate the biasing approach. We show that it is possible to bias coevolutionary methods to better search for optimal multiagent behaviors

Video Compression - from concepts to the H.264/AVC standard

GJ Sullivan — 2007-04-27T09:13:34-00:00

Proceedings of the IEEE, Vol. 93, No. 1. (2005), pp. 18-31.

Over the last one and a half decades, digital video compression technologies have become an integral part of the way we create, communicate, and consume visual information. In this paper, techniques for video compression are reviewed, starting from basic concepts. The rate-distortion performance of modern video compression schemes is the result of an interaction between motion representation techniques, intra-picture prediction techniques, waveform coding of differences, and waveform coding of various refreshed regions. The paper starts with an explanation of the basic concepts of video codec design and then explains how these various features have been integrated into international standards, up to and including the most recent such standard, known as H.264/AVC.

Exon junction complexes mediate the enhancing effect of splicing on mRNA expression.

HL Wiegand — 2008-02-03T07:34:46-00:00

Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11327-11332.

Intron-containing genes are generally expressed more effectively in human cells than are intronless versions of the same gene. We have asked whether this effect is due directly to splicing or instead reflects the action of components of the exon junction complex (EJC) that is assembled at splice junctions after splicing is completed. Here, we show that intron removal does not enhance gene expression if EJC formation is blocked. Conversely, RNA tethering of the EJC components SRm160 or RNPS1 boosts the expression of intronless mRNAs but not of spliced mRNAs. Splicing and RNPS1 tethering are shown to enhance the same steps in mRNA biogenesis and function, including mRNA 3' end processing and translation. Together, these data argue that the EJC is primarily responsible for the positive effect of splicing on gene expression.

Patterns for parameters in simulation models

Stephanie Kramer-Schadt — 2007-04-30T01:59:48-00:00

Ecological Modelling, Vol. 204, No. 3-4. (16 June 2007), pp. 553-556.

Population simulation models are often used in conservation biology to assess human impact on species survival, but have been under heavy critique due to parameterization problems. The general notion is that only models for which parameters were directly assessed from field data can show that a certain process is working, in contrast to using field data to fit models. We would like to provide an update regarding the relationship between simulation model parameterization and the use of field data as `pattern' for revealing `structurally realistic' parameters and processes. `Pattern-oriented modelling' is an inverse modelling technique in ecology that considers the use of multiple field data pattern simultaneously to filter the parameterizations which were successfully tested against all available data on system dynamics. We highlight this technique with an example of our own research and conclude that this approach is especially suitable for models in conservation of rare and elusive species, where data are generally scarce.

Step proof mass dynamics

M Wiegand — 2004-12-28T18:41:32-00:00

Acta Astronautica, Vol. 54, No. 9. (May 2004), pp. 631-638.

Representation, coding, and rendering of 3D video objects with MPEG-4 and H.264/AVC

A Smolic — 2007-12-05T05:30:14-00:00

Multimedia Signal Processing, 2004 IEEE 6th Workshop on (2004), pp. 379-382.

3D video objects provide the same functionalities as virtual computer graphics objects but depict the motion and appearance of real world moving objects. They can be viewed interactively from any direction and integrated in complete 3D scenes with other virtual and real world elements. So far, related work only considered extraction, representation, and rendering methods. Compression and transmission has not yet been studied in detail and combined with the other components into one complete system. In this paper, we present such a complete system for efficient 3D video object extraction, representation, coding, and interactive rendering. Data representation is based on 3D mesh models and view-dependent texture mapping using video textures. The geometry extraction is based on a shape-from-silhouette algorithm. The resulting voxel models are converted into 3D meshes that are coded using MPEG-4 SNHC tools. The corresponding video textures are preprocessed taking the object's shape into account and coded using an H.264/AVC codec. The presented results illustrate that based on the proposed methods a complete transmission system for 3D video objects can be built.

When coevolutionary algorithms exhibit evolutionary dynamics

S Luke — 2007-11-29T09:18:54-00:00

(2002)

The task of understanding the dynamics of coevolutionary algorithms or comparing performance between such algorithms is complicated by the fact the internal fitness measures are subjective.

Introductory tutorial on coevolution

Edwin de Jong — 2007-11-28T10:50:44-00:00

(2007), pp. 3133-3157.

Inhibition of Alpharetrovirus Replication by a Range of Human APOBEC3 Proteins

Heather Wiegand — 2007-11-24T22:29:56-00:00

J. Virol., Vol. 81, No. 24. (15 December 2007), pp. 13694-13699.

The mammalian APOBEC3 family of cytidine deaminases includes members that can act as potent inhibitors of retroviral infectivity and retrotransposon mobility. Here, we have examined whether the alpharetrovirus Rous sarcoma virus (RSV) is susceptible to inhibition by a range of human APOBEC3 proteins. We report that RSV is highly susceptible to inhibition by human APOBEC3G, APOBEC3F, and APOBEC3B and moderately susceptible to inhibition by human APOBEC3C and APOBEC3A. For all five proteins, inhibition of RSV infectivity was associated with selective virion incorporation and with C-to-T editing of the proviral DNA minus strand. In the case of APOBEC3G, editing appeared to be critical for effective inhibition. These data represent the first report of inhibition of retroviral infectivity and induction of proviral DNA editing by human APOBEC3A and reveal that alpharetroviruses, which do not normally encounter APOBEC3 proteins in their avian hosts, are susceptible to inhibition by all human APOBEC3 proteins tested. These data further suggest that the resistance of mammalian retroviruses to inhibition by the APOBEC3 proteins expressed in their normal host species is likely to have evolved subsequent to the appearance of this family of mammalian antiretroviral proteins some 35 million years ago; i.e., the base state of a naive retrovirus is susceptibility to inhibition. 10.1128/JVI.01646-07

Using viral species specificity to define a critical protein/RNA interaction surface

Glen Coburn — 2007-10-12T07:52:34-00:00

Genes Dev., Vol. 15, No. 10. (15 May 2001), pp. 1194-1205.

The Tap protein mediates the sequence-specific nuclear export of mRNAs bearing the retroviral constitutive transport element (CTE) and also plays a critical role in the sequence nonspecific export of cellular mRNAs. Previously, we have demonstrated that CTE function displays species specificity, that is, the CTE functions in human but not quail cells. Here, we demonstrate that quail Tap fails to support CTE function because it cannot bind the CTE. However, changing a single residue in quail Tap, glutamine 246, to arginine, the residue found in human Tap, rescues both CTE function and CTE binding. This residue, which is located on the exterior of a recently reported molecular structure of Tap, defines a surface on Tap that is critical for CTE binding. These data emphasize the potential importance of cross-species genetic complementation in the identification and characterization of cellular factors that are critical for different aspects of viral replication. 10.1101/gad.888201

Topiramate for treating alcohol dependence: a randomized controlled trial.

BA Johnson — 2007-10-11T17:47:53-00:00

JAMA, Vol. 298, No. 14. (10 October 2007), pp. 1641-1651.

CONTEXT: Hypothetically, topiramate can improve drinking outcomes among alcohol-dependent individuals by reducing alcohol's reinforcing effects through facilitation of gamma-aminobutyric acid function and inhibition of glutaminergic pathways in the corticomesolimbic system. OBJECTIVE: To determine if topiramate is a safe and efficacious treatment for alcohol dependence. DESIGN, SETTING, AND PARTICIPANTS: Double-blind, randomized, placebo-controlled, 14-week trial of 371 men and women aged 18 to 65 years diagnosed with alcohol dependence, conducted between January 27, 2004, and August 4, 2006, at 17 US sites. INTERVENTIONS: Up to 300 mg/d of topiramate (n = 183) or placebo (n = 188), along with a weekly compliance enhancement intervention. MAIN OUTCOME MEASURES: Primary efficacy variable was self-reported percentage of heavy drinking days. Secondary outcomes included other self-reported drinking measures (percentage of days abstinent and drinks per drinking day) along with the laboratory measure of alcohol consumption (plasma gamma-glutamyltransferase). RESULTS: Treating all dropouts as relapse to baseline, topiramate was more efficacious than placebo at reducing the percentage of heavy drinking days from baseline to week 14 (mean difference, 8.44%; 95% confidence interval, 3.07%-13.80%; P = .002). Prespecified mixed-model analysis also showed that topiramate compared with placebo decreased the percentage of heavy drinking days (mean difference, 16.19%; 95% confidence interval, 10.79%-21.60%; P < .001) and all other drinking outcomes (P < .001 for all comparisons). Adverse events that were more common with topiramate vs placebo, respectively, included paresthesia (50.8% vs 10.6%), taste perversion (23.0% vs 4.8%), anorexia (19.7% vs 6.9%), and difficulty with concentration (14.8% vs 3.2%). CONCLUSION: Topiramate is a promising treatment for alcohol dependence. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT00210925.

Evolution of sensory complexity recorded in a myxobacterial genome

BS Goldman — 2006-12-12T13:51:28-00:00

PNAS, Vol. 103, No. 41. (10 October 2006), pp. 15200-15205.

Myxobacteria are single-celled, but social, eubacterial predators. Upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. Development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. The growth and development of Myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiological signals from within. A collection of M. xanthus cells behaves, in many respects, like a multicellular organism. For these reasons M. xanthus offers unparalleled access to a regulatory network that controls development and that organizes cell movement on surfaces. The genome of M. xanthus is large (9.14 Mb), considerably larger than the other sequenced delta-proteobacteria. We suggest that gene duplication and divergence were major contributors to genomic expansion from its progenitor. More than 1,500 duplications specific to the myxobacterial lineage were identified, representing >15% of the total genes. Genes were not duplicated at random; rather, genes for cell-cell signaling, small molecule sensing, and integrative transcription control were amplified selectively. Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation. 10.1073/pnas.0607335103

Review on fluoride-releasing restorative materials--fluoride release and uptake characteristics, antibacterial activity and influence on caries formation.

A Wiegand — 2007-10-05T23:21:05-00:00

Dent Mater, Vol. 23, No. 3. (March 2007), pp. 343-362.

OBJECTIVES: The purpose of this article was to review the fluoride release and recharge capabilities, and antibacterial properties, of fluoride-releasing dental restoratives, and discuss the current status concerning the prevention or inhibition of caries development and progression. METHODS: Information from original scientific full papers or reviews listed in PubMed (search term: fluoride release AND (restorative OR glass-ionomer OR compomer OR polyacid-modified composite resin OR composite OR amalgam)), published from 1980 to 2004, was included in the review. Papers dealing with endodontic or orthodontic topics were not taken into consideration. Clinical studies concerning secondary caries development were only included when performed in split-mouth design with an observation period of at least three years. RESULTS: Fluoride-containing dental materials show clear differences in the fluoride release and uptake characteristics. Short- and long-term fluoride releases from restoratives are related to their matrices, setting mechanisms and fluoride content and depend on several environmental conditions. Fluoride-releasing materials may act as a fluoride reservoir and may increase the fluoride level in saliva, plaque and dental hard tissues. However, clinical studies exhibited conflicting data as to whether or not these materials significantly prevent or inhibit secondary caries and affect the growth of caries-associated bacteria compared to non-fluoridated restoratives. SIGNIFICANCE: Fluoride release and uptake characteristics depend on the matrices, fillers and fluoride content as well as on the setting mechanisms and environmental conditions of the restoratives. Fluoride-releasing materials, predominantly glass-ionomers and compomers, did show cariostatic properties and may affect bacterial metabolism under simulated cariogenic conditions in vitro. However, it is not proven by prospective clinical studies whether the incidence of secondary caries can be significantly reduced by the fluoride release of restorative materials.

Mechanisms of gene regulation in Plasmodium.

K Deitsch — 2007-09-26T16:20:46-00:00

Am J Trop Med Hyg, Vol. 77, No. 2. (August 2007), pp. 201-208.

The H.264/AVC Video Coding Standard Standards in a nutshell

T Wiegand — 2007-03-13T11:00:17-00:00

Signal Processing Magazine, IEEE, Vol. 24, No. 2. (2007), pp. 148-153.

Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci

Mark Mort — 2007-03-05T10:35:44-00:00

Am. J. Bot., Vol. 94, No. 2. (1 February 2007), pp. 173-183.

Plant molecular systematic studies of closely related taxa have relied heavily on sequence data from nuclear ITS and cpDNA. Positive attributes of using ITS sequence data include the rapid rate of evolution compared to most plastid loci and availability of universal primers for amplification and sequencing. On the other hand, ITS sequence data may not adequately track organismal phylogeny if concerted evolution and high rDNA array copy number do not permit identification of orthologous copies. Shaw et al. (American Journal of Botany 92: 142-166) recently identified nine plastid regions that appear to provide more potentially informative characters than many other plastid loci. In the present study, sequences of these loci and ITS were obtained for six taxonomic groups in which phylogenetic relationships have been difficult to establish using other data. The relative utility of these regions was compared by assessing the number of parsimony informative characters, character congruence, resolution of inferred trees, clade support, and accuracy. No single locus emerged as the best in all lineages for any of these measures of utility. Results further indicated that in preliminary studies, sampling strategy should include at least four exemplar taxa. The importance of sampling data from independent distributions is also discussed.

Analysis with respect to instrumental variables for the exploration of microarray data structures

Florent Baty — 2006-09-29T15:01:10-00:00

BMC Bioinformatics, Vol. 7 (29 September 2006), 422.

Rate-constrained coder control and comparison of video coding standards

T Wiegand — 2006-11-23T10:19:54-00:00

Circuits and Systems for Video Technology, IEEE Transactions on, Vol. 13, No. 7. (2003), pp. 688-703.

A unified approach to the coder control of video coding standards such as MPEG-2, H.263, MPEG-4, and the draft video coding standard H.264/AVC (advanced video coding) is presented. The performance of the various standards is compared by means of PSNR and subjective testing results. The results indicate that H.264/AVC compliant encoders typically achieve essentially the same reproduction quality as encoders that are compliant with the previous standards while typically requiring 60% or less of the bit rate.

The Design, Synthesis, and Evaluation of Organ-Specific Iron Chelators

RJ Bergeron — 2006-11-09T06:58:15-00:00

J. Med. Chem. (7 November 2006)

Combined scalability support for the scalable extension of H.264/AVC

H Schwarz — 2006-10-01T14:10:27-00:00

Multimedia and Expo, 2005. ICME 2005. IEEE International Conference on (2005), 4 pp..

The scalability extension of H.264/AVC (H. Schwarz, et al., 2004) uses a layered approach for providing spatial, temporal, and SNR scalability. Due to this concept, only a restricted set of spatio-temporal-SNR points can be extracted and decoded from a global scalable bit-stream, and this set of points is defined by the chosen encoder configuration. In this paper, we present a new approach for providing flexible combined spatial, temporal, and SNR scalability. The increased flexibility is achieved by introducing NAL units that represent a refinement signal for a picture in a coarse-to-fine-description and can be truncated at any arbitrary point. The simulation results show that this approach is capable of providing flexible combined scalability while the coding efficiency is only slightly worse than that of the layered approach.

Carbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics.

M Machius — 2006-09-28T01:19:19-00:00

J Mol Biol, Vol. 260, No. 3. (19 July 1996), pp. 409-421.

The crystal structures of porcine pancreatic alpha-amylase isozyme II (PPA II) in its free form and complexed with the trestatin A derived pseudo-octasaccharide V-1532 have been determined using Patterson search techniques at resolutions of 2.3 and 2.2 angstroms, respectively. Seven rings of the competitive inhibitor V-1532 could be detected in the active site region as well as two maltose units in secondary binding sites on the surface. V-1532 occupies the five central sugar binding subsites similar to the PPA/acarbose structure. A sixth ring exists at the reducing end, connecting two symmetry related PPA molecules. The seventh moiety, a 6-hydroxymethylconduritol ring, is located at the non-reducing end. The electron density for this ring is relatively weak, indicating considerable disorder. This study shows that PPA is able to accommodate more than five rings in the active site region, but that additional rings would increase the binding affinity only slightly, which is in accordance with kinetic experiments. A comparison of the structures of free PPA, PPA/V-1532 and PPA/Tendamistat shows the characteristic conformational changes that accompany inhibitor binding and distinguish pseudo-oligosaccharide inhibitors from proteinaceous inhibitors. Although both classes of inhibitors block the sugar binding subsites in the active site region, the extreme specificity and binding affinity of the proteinaceous inhibitors is probably due to an intricate interaction pattern involving areas further away from the catalytic center.

Standards report - The H.264/MPEG4 advanced video coding standard and its applications

D Marpe — 2006-08-22T22:18:27-00:00

Communications Magazine, IEEE, Vol. 44, No. 8. (2006), pp. 134-143.

Extending point pattern analysis for objects of finite size and irregular shape

Thorsten Wiegand — 2006-06-02T12:04:19-00:00

Journal of Ecology, Vol. 94, No. 4. (July 2006), pp. 825-837.

Qualitative and quantitative observations on the flea population dynamics of dogs and cats in several areas of Germany

W Beck — 2006-05-11T08:40:43-00:00

Veterinary Parasitology, Vol. 137, No. 1-2. (15 April 2006), pp. 130-136.

From an ongoing country-wide study on the spectrum, the epidemiology and the population dynamics of flea infestations in dogs and cats, important preliminary results from the three areas of Karlsruhe, Nuernberg and Leipzig are presented. A total of 1922 dogs and 1838 cats from 12 different veterinary practices or clinics in three areas of Germany were systematically examined between July 2003 and June 2004. All dogs and cats appearing for a clinical veterinary consultation on one regular working day per month, per practice, were clinically examined. Dogs and cats were examined irrespective of any kind of prior therapeutic or prophylactic insecticidal treatment. The results show that a total of 99 dogs (5.13%) and 263 cats (14.33%) were infested. Cats were more often flea-infested than dogs (p ) were detected between July and October, and for cats () between July and September, the lowest infestation rates for dogs () were observed between November and May, and for cats () between November and April (p Ctenocephalides felis, Ctenocephalides canis, Archaeopsylla erinacei, Pulex irritans, Ceratophyllus gallinae, etc. The overall frequencies reveal that C. felis was the most prominent species (81.5%), followed by C. canis (12.5%), A. erinacei (2.7%) and P. irritans (1.7%).

Cardiac troponin T for prediction of short- and long-term morbidity and mortality after elective open heart surgery.

S Lehrke — 2006-04-04T03:46:47-00:00

Clin Chem, Vol. 50, No. 9. (September 2004), pp. 1560-1567.

BACKGROUND: Increased cardiac troponins in blood are observed after virtually every open heart surgery, indicating perioperative myocardial cell injury. We sought to determine the optimum time point for blood sampling and the respective cutoff value of cardiac troponin T (cTnT) for risk assessment in patients undergoing cardiac surgery. METHODS: In a series of 204 patients undergoing scheduled open heart surgery, mainly for coronary artery bypass grafting (n = 132) or valve repair (n = 27), cTnT concentrations were measured before and 4 and 8 h after cross-clamping and then daily for 7 days. Individual risk was assessed by use of the Cleveland Clinic Foundation Risk score and intraoperative risk indicators such as duration of cardiopulmonary bypass, cross-clamping, and perioperative release of cardiac markers. Patients were followed for 28 months. RESULTS: Cardiac mortality, all-cause mortality rates, and rates of nonfatal acute myocardial infarction (AMI) at 28 months were 6.9%, 8.8%, and 6.8%, respectively. cTnT was higher in patients with Q-wave AMI or postoperative heart failure requiring inotropic support, and in nonsurvivors. The ROC curve revealed a cTnT > or = 0.46 microg/L at 48 h as the optimum discriminator for long-term cardiac mortality. Stepwise logistic regression identified higher Cleveland Clinic Risk Score [odds ratio (OR) = 2.6 per point], cross-clamp time >65 min (OR = 6.6), and cTnT (OR = 4.9) as significant and independent predictors of long-term cardiac mortality. CONCLUSIONS: A single postoperative cTnT measurement can be used to estimate myocardial cell injury that impacts long-term survival after open heart surgery. It adds independently to established risk indicators.

Expression, localization and hormonal control of angiopoietin-1 in the rhesus macaque endometrium: potential role in spiral artery growth

Nihar Nayak — 2006-02-06T03:58:52-00:00

Mol. Hum. Reprod., Vol. 11, No. 11. (1 November 2005), pp. 791-799.

Angiopoietin-1 (Ang-1) is an important angiogenic factor that has not been thoroughly studied in the primate endometrium. We evaluated the endometrial expression of Ang-1 and its receptor, Tie2, during induced menstrual cycles in rhesus macaques. Tie2 expression was confined to the vascular endothelium without marked change during the cycle. However, Ang-1 expression varied considerably during the cycle. In the proliferative phase, Ang-1 was only expressed in the basal zone glands, and this expression was estradiol (E2) dependent. In the early- to mid-secretory phase, Ang-1 expression spread to the upper glands, luminal epithelium and the vascular smooth muscle cells (VSMC) of spiral arteries. In the late secretory phase, the signal disappeared from the glands but remained elevated in the VSMC of spiral arteries. Notably, there was a significant correlation between VSMC proliferation and Ang-1 expression in the VSMC of the spiral arteries. Progesterone (P) withdrawal in the early secretory phase induced a decline in Ang-1 expression in the glands and VSMC of spiral arteries along with a complete suppression of VSMC proliferation. These data suggest, for the first time, that Ang-1 may play a key role in the P-dependent growth of the unique spiral arteries in the primate endometrium.

Crystallographic refinement and atomic models of two different forms of citrate synthase at 2[middle dot]7 and 1[middle dot]7 A resolution

Stephen Remington — 2005-11-29T01:11:39-00:00

Journal of Molecular Biology, Vol. 158, No. 1. (15 June 1982), pp. 111-152.

The structures of pig heart and chicken heart citrate synthase have been determined by multiple isomorphous replacement and restrained crystallographic refinement for two crystal forms, a tetragonal form at 2[middle dot]7 A and a monoclinic form at 1[middle dot]7 A resolution, with crystallographic R-values of 0[middle dot]199 and 0[middle dot]192, respectively. The structure determination involved a novel application of restrained crystallographic refinement, in that the refinement of incomplete models was necessary in order to completely determine the course of the polypeptide chain. The recently determined amino acid sequence (Bloxham et al., 1981) has been fitted to the models. The molecule has substantially different conformations in the two crystal forms, and there is evidence that a conformational change is required for enzymatic activity.The molecule is a dimer of identical subunits with 437 amino acid residues each. The conformation is all [alpha]-helix, with 40 helices per dimer packing tightly to form a globular molecule. Many of the helices are kinked in various ways or bent smoothly over a large angle. Several of the helices show an unusual antiparallel packing.Each subunit is clearly divided into a large and a small domain. The two crystal forms differ by the relative arrangement of the two domains. The tetragonal form represents an open configuration with a deep cleft between the two domains, the monoclinic form is closed. The structural change from the open to the closed form can be described by an 18 [deg] rotation of the small domain relative to the large domain.Crystallographic analyses were performed with the product citrate bound in both crystal forms, with coenzyme A (CoA) and a citryl-CoA analogue bound to the monoclinic form. These studies establish the CoA and the citrate binding sites, and the conformations of the two product molecules in atomic detail. The subunits are extensively interdigitated, with one subunit making significant contributions to both the citrate and the CoA binding sites of the other subunit. The adenine moiety of CoA is bound to the small domain, and the pantothenic arm is bound to the large domain. The citrate molecule is bound in a cleft between the large domain. The citrate molecule is bound in a cleft between the large and small domain, with the si carboxymethylene group facing the SH arm of coenzyme A. In the monoclinic form, the cysteamine part of CoA shields the bound citrate completely from the solution. Partial reaction of CoA-SH and aspartate 375 to form aspartyl-CoA, and citrate to form citryl-CoA may occur in the crystals. The conformation of CoA is compact, characterized by an internal hydrogen bond O-52 ... N-7 and a tightlybound water molecule O-51 ... HOH ... O-20.

Structural analysis at 2.2 A of orthorhombic crystals presents the asymmetry of the allophycocyanin-linker complex, AP.LC7.8, from phycobilisomes of Mastigocladus laminosus.

W Reuter — 2005-11-23T12:32:15-00:00

Proc Natl Acad Sci U S A, Vol. 96, No. 4. (16 February 1999), pp. 1363-1368.

An electrophoretically purified allophycocyanin-linker complex, AP. LC7.8, from phycobilisomes of Mastigocladus laminosus has been crystallized in the orthorhombic space group P212121. Cryocrystallographic x-ray measurements enabled the structural analysis of the complex at a resolution of 2.2 A. The asymmetric unit contains two side-to-side associated "trimeric" (alphabeta)3 allophycocyanin complexes comprising the linker polypeptide in a defined orientation inside the trimer. The linker representing a protein fold related to the prosegment of procarboxypeptidase A is in contact with only two of the three beta-subunits and directly interacts with the corresponding chromophores of these proteins. In addition to a modulation of the chromophores' spectral properties, the linker polypeptide attracts the alphabeta-subcomplexes, thereby bringing the beta-chromophores closer together. These results will enable interpretations of energy-transfer mechanisms within phycobiliproteins.

Depletion of latent HIV-1 infection in vivo: a proof-of-concept study.

G Lehrman — 2005-08-24T14:42:39-00:00

Lancet, Vol. 366, No. 9485. (9 2005), pp. 549-555.

BACKGROUND: Persistent infection in resting CD4+ T cells prevents eradication of HIV-1. Since the chromatin remodeling enzyme histone deacetylase 1 (HDAC1) maintains latency of integrated HIV, we tested the ability of the HDAC inhibitor valproic acid to deplete persistent, latent infection in resting CD4+ T cells. PROCEDURES: We did a proof-of-concept study in four volunteers infected with HIV and on highly-active antiretroviral therapy (HAART). After intensifying the effect of HAART with subcutaneous enfuvirtide 90 mug twice daily for 4-6 weeks to prevent the spread of HIV, we added oral valproic acid 500-750 mg twice daily to their treatment regimen for 3 months. We quantified latent infection of resting CD4+ T cells before and after augmented treatment by limiting-dilution culture of resting CD4+ T cells after ex-vivo activation. FINDINGS: The frequency of resting cell infection was stable before addition of enfuvirtide and valproic acid, but declined thereafter. This decline was significant in three of four patients (mean reduction 75%, range 68% to >84%). Patients had slight reactions to enfuvirtide at the injection site, but otherwise tolerated treatment well. INTERPRETATION: Combination therapy with an HDAC inhibitor and intensified HAART safely accelerates clearance of HIV from resting CD4+ T cells in vivo, suggesting a new and practical approach to eliminate HIV infection in this persistent reservoir. This finding, though not definitive, suggests that new approaches will allow the cure of HIV in the future.