CiteULike: Author Liu

A two-microphone dual delay-line approach for extraction of a speech sound in the presence of multiple interferers

Chen Liu — 2008-07-24T20:27:22-00:00

The Journal of the Acoustical Society of America, Vol. 110, No. 6. (2001), pp. 3218-3231.

This paper describes algorithms for signal extraction for use as a front-end of telecommunication devices, speech recognition systems, as well as hearing aids that operate in noisy environments. The development was based on some independent, hypothesized theories of the computational mechanics of biological systems in which directional hearing is enabled mainly by binaural processing of interaural directional cues. Our system uses two microphones as input devices and a signal processing method based on the two input channels. The signal processing procedure comprises two major stages: (i) source localization, and (ii) cancellation of noise sources based on knowledge of the locations of all sound sources. The source localization, detailed in our previous paper [Liu et al., J. Acoust. Soc. Am. 108, 1888 (2000)], was based on a well-recognized biological architecture comprising a dual delay-line and a coincidence detection mechanism. This paper focuses on description of the noise cancellation stage. We designed a simple subtraction method which, when strategically employed over the dual delay-line structure in the broadband manner, can effectively cancel multiple interfering sound sources and consequently enhance the desired signal. We obtained an 8–10 dB enhancement for the desired speech in the situations of four talkers in the anechoic acoustic test (or 7–10 dB enhancement in the situations of six talkers in the computer simulation) when all the sounds were equally intense and temporally aligned. ©2001 Acoustical Society of America.

Towards Service Composition Based on Mashup

Xuanzhe Liu — 2007-10-15T23:21:14-00:00

Services, 2007 IEEE Congress on (2007), pp. 332-339.

Mashup is a hallmark of Web 2.0 and attracts both industry and academia recently. It refers to an ad hoc composition technology of Web applications that allows users to draw upon content retrieved from external data sources to create entirely new services. Compared to traditional "developer-centric" composition technologies, e.g., BPEL and WSCI, mashup provides a flexible and easy-of-use way for service composition on web. It makes the consumers free to compose services as they wish as well as simplifies the composition task. This paper makes two contributions. Firstly, we propose the mashup architecture, extend current SOA model with mashup and analyze how it facilitates service composition. Secondly, we propose a mashup component model to help developers leverage to create their own composite services. A case study is given to illustrate how to do service composition by mashup. This paper also discusses about some interesting topics about mashup.

Direct-Current Nanogenerator Driven by Ultrasonic Waves

Xudong Wang — 2007-07-25T03:43:40-00:00

Science, Vol. 316, No. 5821. (6 April 2007), pp. 102-105.

We have developed a nanowire nanogenerator that is driven by an ultrasonic wave to produce continuous direct-current output. The nanogenerator was fabricated with vertically aligned zinc oxide nanowire arrays that were placed beneath a zigzag metal electrode with a small gap. The wave drives the electrode up and down to bend and/or vibrate the nanowires. A piezoelectric-semiconducting coupling process converts mechanical energy into electricity. The zigzag electrode acts as an array of parallel integrated metal tips that simultaneously and continuously create, collect, and output electricity from all of the nanowires. The approach presents an adaptable, mobile, and cost-effective technology for harvesting energy from the environment, and it offers a potential solution for powering nanodevices and nanosystems. 10.1126/science.1139366

The marine viromes of four oceanic regions.

FE Angly — 2007-03-15T16:57:24-00:00

PLoS Biol, Vol. 4, No. 11. (November 2006)

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct "marine-ness" quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.

Short pyrosequencing reads suffice for accurate microbial community analysis

Zongzhi Liu — 2007-11-08T10:23:10-00:00

Nucl. Acids Res., Vol. 35, No. 18. (25 September 2007), e120.

Pyrosequencing technology allows us to characterize microbial communities using 16S ribosomal RNA (rRNA) sequences orders of magnitude faster and more cheaply than has previously been possible. However, results from different studies using pyrosequencing and traditional sequencing are often difficult to compare, because amplicons covering different regions of the rRNA might yield different conclusions. We used sequences from over 200 globally dispersed environments to test whether studies that used similar primers clustered together mistakenly, without regard to environment. We then tested whether primer choice affects sequence-based community analyses using UniFrac, our recently-developed method for comparing microbial communities. We performed three tests of primer effects. We tested whether different simulated amplicons generated the same UniFrac clustering results as near-full-length sequences for three recent large-scale studies of microbial communities in the mouse and human gut, and the Guerrero Negro microbial mat. We then repeated this analysis for short sequences (100-, 150-, 200- and 250-base reads) resembling those produced by pyrosequencing. The results show that sequencing effort is best focused on gathering more short sequences rather than fewer longer ones, provided that the primers are chosen wisely, and that community comparison methods such as UniFrac are surprisingly robust to variation in the region sequenced. 10.1093/nar/gkm541

Methods for peptide identification by spectral comparison

Jian Liu — 2007-01-17T23:10:13-00:00

Proteome Science, Vol. 5 (16 January 2007), 3.

Ab initio prediction of transcription factor binding sites.

LA Liu — 2007-11-12T09:14:17-00:00

Pac Symp Biocomput (2007), pp. 484-495.

Transcription factors are DNA-binding proteins that control gene transcription by binding specific short DNA sequences. Experiments that identify transcription factor binding sites are often laborious and expensive, and the binding sites of many transcription factors remain unknown. We present a computational scheme to predict the binding sites directly from transcription factor sequence using all-atom molecular simulations. This method is a computational counterpart to recent high-throughput experimental technologies that identify transcription factor binding sites (ChIP-chip and protein-dsDNA binding microarrays). The only requirement of our method is an accurate 3D structural model of a transcription factor-DNA complex. We apply free energy calculations by thermodynamic integration to compute the change in binding energy of the complex due to a single base pair mutation. By calculating the binding free energy differences for all possible single mutations, we construct a position weight matrix for the predicted binding sites that can be directly compared with experimental data. As water-bridged hydrogen bonds between the transcription factor and DNA often contribute to the binding specificity, we include explicit solvent in our simulations. We present successful predictions for the yeast MAT-alpha2 homeodomain and GCN4 bZIP proteins. Water-bridged hydrogen bonds are found to be more prevalent than direct protein-DNA hydrogen bonds at the binding interfaces, indicating why empirical potentials with implicit water may be less successful in predicting binding. Our methodology can be applied to a variety of DNA-binding proteins.

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

Jiong-Tang Li — 2008-07-24T13:22:42-00:00

Nucl. Acids Res. (24 July 2008), gkn470.

Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs in human and nine other animals, using ESTs to increase coverage significantly over previous studies. The percentage of transcriptional units (TUs) involved in trans-SAs among all TUs was as high as 4.13%. Particularly 2896 human TUs (or 2.89% of all human TUs) were involved in 3327 trans-SAs. Sequence complementarities over multiple segments with predicted RNA hybridization indicated that some trans-SAs might have sophisticated RNA-RNA pairing patterns. One-fourth of human trans-SAs involved noncoding TUs, suggesting that many noncoding RNAs may function by a trans-acting antisense mechanism. TUs in trans-SAs were statistically significantly enriched in nucleic acid binding, ion/protein binding and transport and signal transduction functions and pathways; a significant number of human trans-SAs showed concordant or reciprocal expression pattern; a significant number of human trans-SAs were conserved in mouse. This evidence suggests important regulatory functions of trans-SAs. In 30 cases, trans-SAs were related to cis-SAs through paralogues, suggesting a possible mechanism for the origin of trans-SAs. All trans-SAs are available at http://trans.cbi.pku.edu.cn/. 10.1093/nar/gkn470

A novel metamaterial-inspired electrically small antenna fed by CPW

Meng Li — 2008-07-24T12:21:02-00:00

Microwave and Millimeter Wave Technology, 2008. ICMMT 2008. International Conference on, Vol. 4 (2008), pp. 1613-1616.

This article presents the design of an inexpensive, efficient, and electrically small antenna based on metamaterial- inspired structure fed by the coplanar waveguide (CPW). The size of the proposed antenna is 12 mm x 12 mm with the resonant frequency of 1.47 GHz. Details of the proposed antenna are presented, with full-wave simulation results to support the design.

Negative and positive lateral shift of a light beam reflected from a grounded slab

Li-Gang Wang — 2008-07-24T12:15:31-00:00

Opt. Lett., Vol. 31, No. 8. (15 April 2006), pp. 1124-1126.

We consider the lateral shift (LS) of a light beam reflecting from a dielectric slab backed by a metal. It is found that the LS of the reflected beam can be negative while the intensity of reflected beam is almost equal to the incident one under a certain condition. The explanation for the negativity of the LS is given in terms of the interference of the reflected waves from the two interfaces. It is also shown that the LS can be enhanced or suppressed under some other conditions. The numerical calculation on the LS for a realistic Gaussian-shaped beam confirms our theoretical prediction.

Large positive and negative lateral optical beam shift in prism-waveguide coupling system

Xuanbin Liu — 2008-07-24T12:12:41-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 73, No. 5. (2006)

In this paper, the lateral beam shift in a prism-waveguide coupling system at wavelengths ranging from visible to near infrared is theoretically examined. A simple theoretical formula is derived to analyze the behavior of the beam shift. We demonstrate that large positive and negative lateral optical beam shifts can be obtained when guided modes are excited. It is also found that the magnitude of the beam shift is closely related to the intrinsic and radiative damping. When the intrinsic damping is larger than the radiative damping, negative lateral beam shift occurs. Numerical calculations confirm the theoretical analysis and show that a beam shift of the order of millimeters is possible.

Alignment of two-dimensional electrophoresis gels.

G Shi — 2008-07-24T09:22:16-00:00

Biochemical and biophysical research communications, Vol. 357, No. 2. (1 June 2007), pp. 427-432.

Two-dimensional electrophoresis is a major separating technique for proteins in proteomics. Alignment of gel images is critical for intra-laboratory or even more difficult inter-laboratory gel comparisons. In the paper, we propose a novel iterative closest point (ICP) method for 2D-gel electrophoresis image alignment. The paper seeks to introduce an information theoretic measure as one part of distance metric to gel image alignment. We combine intensity information of spots with geometric information of landmarks by applying information potential idea. The proposed method has been applied to both synthetic and real gel images accessible in public 2D-electrophoresis gel protein databases. The high accuracy and robustness of the algorithm indicate that it is promising for gel image alignment.

Formal and Use-Case Driven Requirement Analysis in UML

Xiaoshan Li — 2008-07-24T08:31:17-00:00

(2001), pp. 215-224.

The Genome Sequence of Drosophila melanogaster

Mark Adams — 2005-06-14T01:43:05-00:00

Science, Vol. 287, No. 5461. (24 March 2000), pp. 2185-2195.

Mitigating DoS attacks against broadcast authentication in wireless sensor networks

Peng Ning — 2008-03-06T04:26:04-00:00

ACM Trans. Sen. Netw., Vol. 4, No. 1. (January 2008), pp. 1-35.

Pharmacologic stem cell based intervention as a new approach to osteoporosis treatment in rodents.

T Yamaza — 2008-07-23T20:40:47-00:00

PLoS ONE, Vol. 3, No. 7. (2008)

BACKGROUND: Osteoporosis is the most prevalent skeletal disorder, characterized by a low bone mineral density (BMD) and bone structural deterioration, leading to bone fragility fractures. Accelerated bone resorption by osteoclasts has been established as a principal mechanism in osteoporosis. However, recent experimental evidences suggest that inappropriate apoptosis of osteoblasts/osteocytes accounts for, at least in part, the imbalance in bone remodeling as occurs in osteoporosis. The aim of this study is to examine whether aspirin, which has been reported as an effective drug improving bone mineral density in human epidemiology studies, regulates the balance between bone resorption and bone formation at stem cell levels. METHODS AND FINDINGS: We found that T cell-mediated bone marrow mesenchymal stem cell (BMMSC) impairment plays a crucial role in ovariectomized-induced osteoporosis. Ex vivo mechanistic studies revealed that T cell-mediated BMMSC impairment was mainly attributed to the apoptosis of BMMSCs via the Fas/Fas ligand pathway. To explore potential of using pharmacologic stem cell based intervention as an approach for osteoporosis treatment, we selected ovariectomy (OVX)-induced osteoporosis mouse model to examine feasibility and mechanism of aspirin-mediated therapy for osteoporosis. We found that aspirin can inhibit T cell activation and Fas ligand induced BMMSC apoptosis in vitro. Further, we revealed that aspirin increases osteogenesis of BMMSCs by aiming at telomerase activity and inhibits osteoclast activity in OVX mice, leading to ameliorating bone density. CONCLUSION: Our findings have revealed a novel osteoporosis mechanism in which activated T cells induce BMMSC apoptosis via Fas/Fas ligand pathway and suggested that pharmacologic stem cell based intervention by aspirin may be a new alternative in osteoporosis treatment including activated osteoblasts and inhibited osteoclasts.

Comparative Analysis on the Effects of Diesel Particulate Filter and Selective Catalytic Reduction Systems on a Wide Spectrum of Chemical Species Emissions

Z. Gerald Liu — 2008-07-21T19:56:26-00:00

Environ. Sci. Technol. (16 July 2008)

Abstract: Two methods, diesel particulate filter (DPF) and selective catalytic reduction (SCR) systems, for controlling diesel emissions have become widely used, either independently or together, for meeting increasingly stringent emissions regulations worldwide. Each of these systems is designed for the reduction of primary pollutant emissions including particulate matter (PM) for DPF and nitrogen oxides (NOx) for SCR. However, there have been growing concerns regarding the secondary reactions that these aftertreatment systems may promote, involving unregulated species emissions. This study was performed to gain an understanding of the effects that these aftertreatment systems may have on the emission levels of a wide spectrum of chemical species found in diesel engine exhaust. Samples were extracted using a source dilution sampling system designed to collect exhaust samples representative of real-world emissions. Testing was conducted on a heavy-duty diesel engine with no aftertreatment devices to establish a baseline measurement and also on the same engine equipped first with a DPF system and then a SCR system. Each of the samples was analyzed for a wide variety of chemical species, including elemental and organic carbon, metals, ions, n-alkanes, aldehydes, and polycyclic aromatic hydrocarbons, in addition to the primary pollutants, due to the potential risks they pose to the environment and public health. The results show that the DPF and SCR systems were capable of substantially reducing PM and NOx emissions, respectively. Further, each of the systems significantly reduced the emission levels of the unregulated chemical species, while the notable formation of new chemical species was not observed. It is expected that a combination of the two systems in some future engine applications would reduce both primary and secondary emissions significantly.

Plasmon-Induced Transparency in Metamaterials

Shuang Zhang — 2008-07-23T16:25:19-00:00

Physical Review Letters, Vol. 101, No. 4. (2008)

A plasmonic “molecule” consisting of a radiative element coupled with a subradiant (dark) element is theoretically investigated. The plasmonic molecule shows electromagnetic response that closely resembles the electromagnetically induced transparency in an atomic system. Because of its subwavelength dimension, this electromagnetically induced transparency-like molecule can be used as a building block to construct a “slow light” plasmonic metamaterial.

Timing observations of RRAT J1819-1458 at Urumqi Observatory

A Esamdin — 2008-07-23T15:15:30-00:00

(22 Jul 2008)

We report the timing-analysis results obtained for RRAT J1819-1458 from regular timing observations at 1.54 GHz using the Urumqi 25 m radio telescope between 2007 April to 2008 March. RRAT J1819-1458 is a relatively young and highly magnetized neutron star discovered by its sporadic short bursts in the Parkes Multibeam Pulsar Survey data. In 94 hrs of observation data, we detected a total of 162 dispersed bursts of RRAT J1819-1458 with the signal-to-noise ratios (S/Ns) above 5-$σ$ threshold. Among them, 5 bursts clearly show two-component structure. The S/N of the strongest burst is 13.3. The source's DM measured through our data is 196.0 $±$0.4 pc cm$^-3$. The timing position, frequency and its first derivative were determined using standard pulsar timing techniques on the arrival times of these individual bursts. The accuracy of the solved rotating parameters are improved comparing with that in previous publication. Our timing position with 2-$σ$ error is consistent with the position of its X-ray counterpart CXOU J181934.1-145804. The effect of timing noise and the phase fluctuation of the individual short bursts on the timing residuals is briefly discussed. The distribution of the timing residuals is bimodal, which cannot be explained readily by timing irregularity.

Surface Area of Reversed-Phase HPLC Columns

A Giaquinto — 2008-07-23T15:16:57-00:00

Anal. Chem. (23 July 2008)

Abstract: Six reversed-phase columns from different manufacturers were characterized in terms of adsorbent geometry (e.g., pore volume, surface area, column void volume, and interparticle volume). Measurement of the surface area of chemically modified silica-based adsorbents is discussed together with the methods for the determination of the amount of adsorbent in the column. The behavior of nearly ideal chromatographic systems was studied. Retention factors of alkylbenzenes in acetonitrile/water and methanol/water systems were compared with surface-specific retention factors. The distribution of conventional retention factor values for the same analyte among the six columns using identical chromatographic conditions exceeded 35%, while the relative standard deviation of surface-specific retention factors was on the level of 3%.

Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases.

RG Sadygov — 2007-08-30T15:28:15-00:00

Anal Chem, Vol. 76, No. 6. (15 March 2004), pp. 1664-1671.

The purpose of this work is to develop and verify statistical models for protein identification using peptide identifications derived from the results of tandem mass spectral database searches. Recently we have presented a probabilistic model for peptide identification that uses hypergeometric distribution to approximate fragment ion matches of database peptide sequences to experimental tandem mass spectra. Here we apply statistical models to the database search results to validate protein identifications. For this we formulate the protein identification problem in terms of two independent models, two-hypothesis binomial and multinomial models, which use the hypergeometric probabilities and cross-correlation scores, respectively. Each database search result is assumed to be a probabilistic event. The Bernoulli event has two outcomes: a protein is either identified or not. The probability of identifying a protein at each Bernoulli event is determined from relative length of the protein in the database (the null hypothesis) or the hypergeometric probability scores of the protein's peptides (the alternative hypothesis). We then calculate the binomial probability that the protein will be observed a certain number of times (number of database matches to its peptides) given the size of the data set (number of spectra) and the probability of protein identification at each Bernoulli event. The ratio of the probabilities from these two hypotheses (maximum likelihood ratio) is used as a test statistic to discriminate between true and false identifications. The significance and confidence levels of protein identifications are calculated from the model distributions. The multinomial model combines the database search results and generates an observed frequency distribution of cross-correlation scores (grouped into bins) between experimental spectra and identified amino acid sequences. The frequency distribution is used to generate p-value probabilities of each score bin. The probabilities are then normalized with respect to score bins to generate normalized probabilities of all score bins. A protein identification probability is the multinomial probability of observing the given set of peptide scores. To reduce the effect of random matches, we employ a marginalized multinomial model for small values of cross-correlation scores. We demonstrate that the combination of the two independent methods provides a useful tool for protein identification from results of database search using tandem mass spectra. A receiver operating characteristic curve demonstrates the sensitivity and accuracy level of the approach. The shortcomings of the models are related to the cases when protein assignment is based on unusual peptide fragmentation patterns that dominate over the model encoded in the peptide identification process. We have implemented the approach in a program called PROT_PROBE.

SOM-Based Anomaly Intrusion Detection System

Chun-Dong Wang — 2008-07-23T13:40:45-00:00

Embedded and Ubiquitous Computing (2007), pp. 356-366.

In this paper, a SOM-based anomaly intrusion detection system is proposed, which can contract high-dimension data to lower, meanwhile keeping the primary relationship between clustering and topology. During the experiment, the theory of SOM is used to train three SOMs on the layers of system, process and network. Although our experiment environment is simpler than the real one, the result shows that it has its reference value for us to build intelligent IDSs. Through the analysis of the monitoring results on the three layers from the hacking tools (NMAP, HYDRA), it is suggested that the approach of detecting and the parameters chosen be correct and effective.

Physical Modeling of Flow Field inside Urban Street Canyons

Xian-Xiang Li — 2008-07-23T11:30:19-00:00

Journal of Applied Meteorology and Climatology, Vol. 47, No. 7. (1 July 2008), pp. 2058-2067.

The flow characteristics inside urban street canyons were studied in a laboratory water channel. The approaching flow direction was horizontal and perpendicular to the street axis. The street width was adjusted to form street canyons of aspect ratios 0.5, 1.0, and 2.0. The velocity field and turbulent intensity were measured with a laser Doppler anemometer at various locations within the street canyons, which were used to elucidate the flow pattern inside the street canyons. It was found that the previous numerical modeling results are in good agreement with the current experimental results at most locations. For the street canyon of aspect ratio 0.5, which belongs to the wake interference flow regime, the mean and fluctuating velocity components were more difficult to measure as compared with the other two cases because of its more complicated flow pattern. Some guidelines for numerical modeling were developed based on the measurement results. The data presented in this paper can also be used as a comprehensive database for the validation of numerical models.

Scalable Supernode Selection in Peer-to-Peer Overlay Networks

Virginia Lo — 2008-07-23T11:23:08-00:00

We define a problem called the supernode selection problem which has emerged across a variety of peer-topeer applications. Supernode selection involves selection of a subset of the peers to serve a special role. The supernodes must be well-dispersed throughout the peerto -peer overlay network, and must fulfill additional requirements such as load balance, resource needs, adaptability to churn, and heterogeneity. While similar to dominating set and p-centers problems, the supernode selection...

Mobile ad hoc networking: imperatives and challenges

Imrich Chlamtac — 2006-05-05T12:57:37-00:00

Ad Hoc Networks, Vol. 1, No. 1. (July 2003), pp. 13-64.

Mobile ad hoc networks (MANETs) represent complex distributed systems that comprise wireless mobile nodes that can freely and dynamically self-organize into arbitrary and temporary, “ad-hoc” network topologies, allowing people and devices to seamlessly internetwork in areas with no pre-existing communication infrastructure, e.g., disaster recovery environments. Ad hoc networking concept is not a new one, having been around in various forms for over 20 years. Traditionally, tactical networks have been the only communication networking application that followed the ad hoc paradigm. Recently, the introduction of new technologies such as the Bluetooth, IEEE 802.11 and Hyperlan are helping enable eventual commercial MANET deployments outside the military domain. These recent evolutions have been generating a renewed and growing interest in the research and development of MANET. This paper attempts to provide a comprehensive overview of this dynamic field. It first explains the important role that mobile ad hoc networks play in the evolution of future wireless technologies. Then, it reviews the latest research activities in these areas, including a summary of MANET’s characteristics, capabilities, applications, and design constraints. The paper concludes by presenting a set of challenges and problems requiring further research in the future.

Bayesian biclustering of gene expression data

Jiajun Gu — 2008-05-06T21:14:20-00:00

BMC Genomics, Vol. 9, No. Suppl 1. (2008)

BACKGROUND:Biclustering of gene expression data searches for local patterns of gene expression. A bicluster (or a two-way cluster) is defined as a set of genes whose expression profiles are mutually similar within a subset of experimental conditions/samples. Although several biclustering algorithms have been studied, few are based on rigorous statistical models.RESULTS:We developed a Bayesian biclustering model (BBC), and implemented a Gibbs sampling procedure for its statistical inference. We showed that Bayesian biclustering model can correctly identify multiple clusters of gene expression data. Using simulated data both from the model and with realistic characters, we demonstrated the BBC algorithm outperforms other methods in both robustness and accuracy. We also showed that the model is stable for two normalization methods, the interquartile range normalization and the smallest quartile range normalization. Applying the BBC algorithm to the yeast expression data, we observed that majority of the biclusters we found are supported by significant biological evidences, such as enrichments of gene functions and transcription factor binding sites in the corresponding promoter sequences.CONCLUSIONS:The BBC algorithm is shown to be a robust model-based biclustering method that can discover biologically significant gene-condition clusters in microarray data. The BBC model can easily handle missing data via Monte Carlo imputation and has the potential to be extended to integrated study of gene transcription networks.

Biodiversity and ecosystem services: A multi-scale empirical study of the relationship between species richness and net primary production

Robert Costanza — 2008-07-22T21:29:22-00:00

Ecological Economics, Vol. 61, No. 2-3. (1 March 2007), pp. 478-491.

Biodiversity (BD) and Net Primary Productivity (NPP) are intricately linked in complex ecosystems such that a change in the state of one of these variables can be expected to have an impact on the other. Using multiple regression analysis at the site and ecoregion scales in North America, we estimated relationships between BD (using plant species richness as a proxy) and NPP (as a proxy for ecosystem services). At the site scale, we found that 57% of the variation in NPP was correlated with variation in BD after effects of temperature and precipitation were accounted for. At the ecoregion scale, 3 temperature ranges were found to be important. At low temperatures (- 2.1 °C average) BD was negatively correlated with NPP. At mid-temperatures (5.3 °C average) there was no correlation. At high temperatures (13 °C average) BD was positively correlated with NPP, accounting for approximately 26% of the variation in NPP after effects of temperature and precipitation were accounted for. The general conclusion of positive links between BD and ecosystem functioning from earlier experimental results in micro and mesocosms was qualified by our results, and strengthened at high temperature ranges. Our results can also be linked to estimates of the total value of ecosystem services to derive an estimate of the value of the biodiversity contribution to these services. We tentatively conclude from this that a 1% change in BD in the high temperature range (which includes most of the world's BD) corresponds to approximately a 1/2% change in the value of ecosystem services.

Anatomical methods for voxelation of the mammalian brain.

DM Sforza — 2008-07-22T17:38:51-00:00

Neurochemical research, Vol. 29, No. 6. (June 2004), pp. 1299-1306.

Voxelation allows high-throughput acquisition of three-dimensional gene expression patterns in the brain through analysis of spatially registered voxels (cubes). The method results in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging techniques. An important issue for voxelation is the development of approaches to anchor correctly harvested voxels to the underlying anatomy. Here, we describe experiments to identify fixation and cryopreservation protocols for improved registration of harvested voxels with neuroanatomical structures. Paraformaldehyde fixation greatly reduced RNA recovery as judged by ribosomal RNA abundance. However, gene expression signals from paraformaldehyde-fixed samples were not appreciably diminished as judged by average signal-noise ratios from microarrays, highlighting the difficulties of accurate quantitation of cross-linked RNA. Additional use of cryoprotection helped to improve further RNA recovery and signal from fixed tissue. It appears that the best protocol to provide the necessary resolution of neuroanatomical information in voxelation entails a controlled dose of fixation and thorough cryoprotection, complemented by histological staining.

Laboratory Evolved Biocatalysts for Stereoselective Syntheses of Substituted Benzaldehyde Cyanohydrins

Zhibin Liu — 2008-07-22T17:40:59-00:00

ChemBioChem, Vol. 9, No. 1. (2008), pp. 58-61.

No Abstract

Genome-wide association scans identified CTNNBL1 as a novel gene for obesity

Yong-Jun Liu — 2008-06-09T16:29:30-00:00

Hum. Mol. Genet., Vol. 17, No. 12. (15 June 2008), pp. 1803-1813.

Obesity is a major public health problem with strong genetic determination; however, the genetic factors underlying obesity are largely unknown. In this study, we performed a genome-wide association scan for obesity by examining approximately 500 000 single-nucleotide polymorphisms (SNPs) in a sample of 1000 unrelated US Caucasians. We identified a novel gene, CTNNBL1, which has multiple SNPs associated with body mass index (BMI) and fat mass. The most significant SNP, rs6013029, achieved experiment-wise P-values of 2.69 x 10-7 for BMI and of 4.99 x 10-8 for fat mass, respectively. The SNP rs6013029 minor allele T confers an average increase in BMI and fat mass of 2.67 kg/m2 and 5.96 kg, respectively, compared with the alternative allele G. We further genotyped the five most significant CTNNBL1 SNPs in a French case-control sample comprising 896 class III obese adults (BMI [≥] 40 kg/m2) and 2916 lean adults (BMI < 25 kg/m2). All five SNPs showed consistent associations with obesity (8.83 x 10-3 < P < 6.96 x 10-4). Those subjects who were homozygous for the rs6013029 T allele had 1.42-fold increased odds of obesity compared with those without the T allele. The protein structure of CTNNBL1 is homologous to -catenin, a family of proteins containing armadillo repeats, suggesting similar biological functions. -Catenin is involved in the Wnt/-catenin-signaling pathway which appears to contribute to maintaining the undifferentiated state of pre-adipocytes by inhibiting adipogenic gene expression. Our study hence suggests a novel mechanism for the development of obesity, where CTNNBL1 may play an important role. Our study also provided supportive evidence for previously identified associations between obesity and INSIG2 and PFKP, but not FTO. 10.1093/hmg/ddn072

Charge Displacement in Ultraintense Laser-Plasma Interaction

JF Liu — 2008-07-22T16:21:21-00:00

Physica Scripta, Vol. 72, No. 2-3. (2005), pp. 243-246.

The distribution of optical field and charge density in the interaction between ultraintense ultrashort pulse laser and plasma is studied by numerical computation. The plasma considered has an exponential density profile, which corresponds to isothermal expanding. Our calculation shows that electrons are pushed forward by the incident laser, but ions, due to their much greater inertia, remain stationary. The resulting charge displacement forms a strong electrostatic field in the plasma. After the interaction of laser pulse and plasma, electrostatic energy still exists even after the laser pulse and will be absorbed by the plasma finally. This serves as an explanation to the mechanism of laser energy deposited into plasma.

The sequence of the human genome.

JC Venter — 2005-05-11T19:14:50-00:00

Science, Vol. 291, No. 5507. (16 February 2001), pp. 1304-1351.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

NMR and X-ray Crystallography, Complementary Tools in Structural Proteomics of Small Proteins

AA Yee — 2008-06-26T16:13:18-00:00

J. Am. Chem. Soc., Vol. 127, No. 47. (30 November 2005), pp. 16512-16517.

Abstract: NMR spectroscopy and X-ray crystallography, the two primary experimental methods for protein structure determination at high resolution, have different advantages and disadvantages in terms of sample preparation and data collection and analysis. It is therefore of interest to assess their complementarity when applied to small proteins. Structural genomics/proteomics projects provide an ideal opportunity to make such comparisons as they generate data in a systematic manner for large enough numbers of proteins to allow firm conclusions to be drawn. Here we report a comparison for 263 unique proteins screened by both NMR spectroscopy and X-ray crystallography in our structural proteomics pipeline. Only 21 targets (8%) were deemed amenable to both methods based on an initial 2D 15N-HSQC NMR spectrum and optimized crystallization trials. However, the use of both methods in the pipeline increased the total number of targets amenable to structure determination to 107, with 43 amenable to NMR only and 43 amenable to X-ray crystallographic methods only. We did not observe a correlation between 15N-HSQC spectral quality and the success of the same protein in crystallization screens. Similar results were found for an independent set of 159 proteins as reported in the accompanying paper by Snyder et al.1 Thus, we conclude that both methods are highly complementary, and in order to increase the number of proteins suited for structure determination, we suggest that both methods be used in parallel in screening of all small proteins for structure determination.

Streamlining Escherichia coli S30 extract preparation for economical cell-free protein synthesis.

DV Liu — 2006-09-04T15:20:53-00:00

Biotechnol Prog, Vol. 21, No. 2. (r 2005), pp. 460-465.

Escherichia coli extracts activate cell-free protein synthesis systems by providing the catalysts for translation and other supporting reactions. Recent results suggest that high-density fermentations can be used to provide the source cells, but the subsequent cell extract preparation procedure requires multiple centrifugation and dialysis steps as well as an expensive runoff reaction. In the work reported here, the extract preparation protocol duration was reduced by nearly 50% by significantly shortening several steps. In addition, by optimizing the runoff incubation, overall reagent costs were reduced by 70%. Nonetheless, extracts produced from the shorter, less expensive procedure were equally active. Crucial steps were further examined to indicate minimal ribosome loss during the standard 30,000g centrifugations. Furthermore, sucrose density centrifugation analysis indicated that although an incubation step significantly activates the extract, ribosome/polysome dissociation is not required. These insights suggest that consistent cell extract can be produced more quickly and with considerably less expense for large-scale cell-free protein production, especially when combined with high-density fermentation protocols.

Enhanced detection of low abundant human plasma proteins using a tandem IgY12-supermix immunoaffinity separation strategy

Wei-Jun Qian — 2008-07-22T14:37:28-00:00

Mol Cell Proteomics (15 July 2008), M800008-MCP200.

The enormous dynamic range of human bodily fluid proteomes poses a significant challenge for current MS-based proteomic technologies as it makes it especially difficult to detect low abundant proteins in human biofluids such as blood plasma, an essential aspect for successful biomarker discovery efforts. Here, we present a novel tandem IgY12-SuperMix immunoaffinity separation system for enhanced detection of low abundant proteins in human plasma. The tandem IgY12-SuperMix system separates ~60 abundant proteins from the low abundant proteins in plasma, which allows for significant enrichment of low abundant plasma proteins in the SuperMix flow-through fraction. High reproducibility of the tandem separations was observed in terms of both sample processing recovery and LC-MS/MS identification results based on spectral count data. The ability to quantitatively measure differential protein abundances following application of the tandem separations was demonstrated by spiking six non-human standard proteins at three different levels into plasma. A side-by-side comparison between the SuperMix flow-through and IgY12 flow-through samples analyzed by both 1D and 2D LC-MS/MS revealed a 60-80% increase in proteome coverage as a result of the SuperMix separations, which suggests significantly enhanced detection of low abundant proteins. A total of 695 plasma proteins were confidently identified in a single analysis (with a minimum of two peptides per protein) by coupling the tandem separation strategy with 2D-LC-MS/MS, including 42 proteins with reported normal concentrations of ~100 pg/mL to 100 ng/mL. The concentrations of two selected proteins, M-CSF and MMP8, were independently validated by ELISA as 202 pg/mL and 12.4 ng/mL, respectively. Evaluation of binding efficiency revealed 45 medium-abundant proteins were efficiently captured by the SuperMix column with >90% retention. Taken together, these results illustrate the potential broad utilities of this tandem IgY12-SuperMix strategy for proteomic applications involving human biofluids, where effectively addressing the dynamic range challenge of the specimen is imperative. 10.1074/mcp.M800008-MCP200

Learning transportation mode from raw gps data for geographic applications on the web

Yu Zheng — 2008-07-22T02:46:43-00:00

(2008), pp. 247-256.

Towards identity anonymization on graphs

Kun Liu — 2008-07-22T12:47:00-00:00

(2008), pp. 93-106.

An Adaptive User Interface Based On Personalized Learning

Jiming Liu — 2007-11-26T22:39:59-00:00

IEEE Intelligent Systems, Vol. 18, No. 2. (March 2003), pp. 52-57.

In human-computer interaction, user interface events and frequencies can be recorded and organized into episodes. By computing episode frequencies and implication relations, we can automatically derive application-specific episode associations and therefore enable an application interface to adaptively provide just-in-time assistance to a user. The authors identify five issues related to designing an adaptive user interface: interaction tracking, episodes identification, user pattern recognition, user intention prediction, and user profile update. In particular, they demonstrate how to identify episodes and associate them with an interface that can act on a user's behalf to interact with an application based on certain recognized plans. To adapt to different users' needs, the interface can personalize its assistance by learning user profiles. For example, by detecting and analyzing users' behavior patterns in using Microsoft Word, the interface can automatically assist users in several Word tasks. The authors' Word interface provides episode associations at two levels: text-level (phrase association) and paragraph-level (formatting automation). They conducted two pilot experiments to evaluate the interface's performance. The suggestions it provided and its ease of use were well received by users, and the interface can to a certain extent increase the productivity of type-setting.

A peer-to-peer spatial cloaking algorithm for anonymous location-based service

Chi-Yin Chow — 2007-04-02T22:26:35-00:00

(2006), pp. 171-178.

Modeling a simplified regulatory system of blood glucose at molecular levels

Weijiu Liu — 2008-07-22T09:17:10-00:00

Journal of Theoretical Biology, Vol. 252, No. 4. (21 June 2008), pp. 608-620.

In this paper, we propose a new mathematical control system for a simplified regulatory system of blood glucose by taking into account the dynamics of glucose and glycogen in liver and the dynamics of insulin and glucagon receptors at the molecular level. Numerical simulations show that the proposed feedback control system agrees approximately with published experimental data. Sensitivity analysis predicts that feedback control gains of insulin receptors and glucagon receptors are robust. Using the model, we develop a new formula to compute the insulin sensitivity. The formula shows that the insulin sensitivity depends on various parameters that determine the insulin influence on insulin-dependent glucose utilization and reflect the efficiency of binding of insulin to its receptors. Using Lyapunov indirect method, we prove that the new control system is input-output stable. The stability result provides theoretical evidence for the phenomenon that the blood glucose fluctuates within a narrow range in response to the exogenous glucose input from food. We also show that the regulatory system is controllable and observable. These structural system properties could explain why the glucose level can be regulated.

Discovering global network communities based on local centralities

Bo Yang — 2008-07-22T08:42:10-00:00

ACM Trans. Web, Vol. 2, No. 1. (February 2008), pp. 1-32.

BrowseRank: letting web users vote for page importance

Yuting Liu — 2008-07-22T08:10:56-00:00

(2008), pp. 451-458.

Hybrid approaches to product recommendation based on customer lifetime value and purchase preferences

Duen-Ren Liu — 2008-07-22T06:57:09-00:00

Journal of Systems and Software, Vol. 77, No. 2. (August 2005), pp. 181-191.

Recommending products to attract customers and meet their needs is important in fiercely competitive environments. Recommender systems have emerged in e-commerce applications to support the recommendation of products. Recently, a weighted RFM-based method (WRFM-based method) has been proposed to provide recommendations based on customer lifetime value, including Recency, Frequency and Monetary. Preference-based collaborative filtering (CF) typically makes recommendations based on the similarities of customer preferences. This study proposes two hybrid methods that exploit the merits of the WRFM-based method and the preference-based CF method to improve the quality of recommendations. Experiments are conducted to evaluate the quality of recommendations provided by the proposed methods, using a data set concerning the hardware retail marketing. The experimental results indicate that the proposed hybrid methods outperform the WRFM-based method and the preference-based CF method.

Mutations in genes encoding inner arm dynein heavy chains in Tetrahymena thermophila lead to axonemal hypersensitivity to Ca2+.

S Liu — 2008-07-22T06:03:10-00:00

Cell motility and the cytoskeleton, Vol. 62, No. 3. (November 2005), pp. 133-140.

Calcium-dependent ciliary reversals are seen in ciliated protozoans such as Tetrahymena in response to depolarizing stimuli, but the axonemal mechanisms responsible for this response are not well understood. The model is that the outer arm dyneins (OADs) control the beating frequency while the inner arm dyneins (IADs) regulate ciliary waveform. Since ciliary reversal is a type of waveform change, the model would predict that IAD mutations could affect ciliary reversal. We have used gene disruption techniques to generate several behavioral mutants of Tetrahymena with functional disruptions of various IADs. One such mutant, called KO-6, is missing I1 (the two-headed IAD) and is unable to show ciliary reversals in response to any stimuli due to a loss of axonemal Ca2+ sensitivity [Eur J Cell Biol 80 (2001) 486-497; Cell Motil Cytoskeleton 53 (2002) 281-288.]. In contrast, disruption of 3 one-headed IADs [Liu et al., Cell Motil Cytoskeleton 59 (2004), 201-214] produced mutants, which showed over-responsiveness in bioassays measuring either their depolarization-induced avoiding reactions (AR) in Na+ and Ba2+ solutions or their duration of backward swimming (continuous ciliary reversal or CCR) in K+ solutions. Detergent-extracted and reactivated mutants also showed increased probabilities of CCR at lower Ca2+ concentrations suggesting that the behavioral over-responsiveness of these three mutants in vivo is due to increased axonemal Ca2+ sensitivity. Our data suggest the possibility that the one-headed IADs and the two-headed IAD act antagonistically in vivo and that loss of any one of the one-headed IADs leads to behavioral over-responsiveness due to less resistance to I1-induced reversals.

Chondrogenic Differentiation of Mesenchymal Stem Cells from Bone Marrow: Differentiation-Dependent Gene Expression of Matrix Components

Frank Barry — 2008-07-22T05:53:02-00:00

Experimental Cell Research, Vol. 268, No. 2. (15 August 2001), pp. 189-200.

Transforming growth factor (TGF)-[beta]-induced chondrogenesis of mesenchymal stem cells derived from bone marrow involves the rapid deposition of a cartilage-specific extracellular matrix. The sequential events in this pathway leading from the undifferentiated stem cell to a mature chondrocyte were investigated by analysis of key matrix elements. Differentiation was rapidly induced in cells cultured in the presence of TGF-[beta]3 or -[beta]2 and was accompanied by the early expression of fibromodulin and cartilage oligomeric matrix protein. An increase in aggrecan and versican core protein synthesis defined an intermediate stage, which also involved the small leucine-rich proteoglycans decorin and biglycan. This was followed by the appearance of type II collagen and chondroadherin. The pathway was also characterized by the appearance of type X collagen, usually associated with hypertrophic cartilage. There was also a change in the pattern of sulfation of chondroitin sulfate, with a progressive increase in the proportion of 6-sulfated species. The major proportion of newly synthesized glycosaminoglycan was part of an aggregating proteoglycan network. These data allow us to define the phenotype of the differentiated cell and to understand in greater detail the sequential process of matrix assembly.

Estimation of progression of multi-state chronic disease using the Markov model and prevalence pool concept

Hui-Chuan Shih — 2007-11-09T09:46:59-00:00

BMC Medical Informatics and Decision Making, Vol. 7 (09 November 2007), 34.

A random effects four-part model, with application to correlated medical costs

Lei Liu — 2008-07-22T05:13:41-00:00

Computational Statistics & Data Analysis, Vol. 52, No. 9. (15 May 2008), pp. 4458-4473.

In this paper we propose a four-part random effects model, with application to correlated medical cost data. Four joint equations are used to model respectively: (1) the probability of seeking medical treatment, (2) the probability of being hospitalized (conditional on seeking medical treatment), and the actual amount of (3) outpatient and (4) inpatient costs. Our model simultaneously takes account of the inter-temporal (or within-cluster) correlation of each patient and the cross-equation correlation of the four equations, by means of joint linear mixed models and generalized linear mixed models. The estimation is accomplished by the high-order Laplace approximation technique in Raudenbush et al. [Raudenbush, S.W., Yang, M., Yosef, M., 2000. Maximum likelihood for generalized linear models with nested random effects via high-order, multivariate Laplace approximation. Journal of Computational and Graphical Statistics 9, 141-157] and Olsen and Schafer [Olsen, M.K., Schafer, J.L., 2001. A two-part random effects model for semicontinuous longitudinal data. Journal of the American Statistical Association 96, 730-745]. Our model is used to analyze monthly medical costs of 1397 chronic heart failure patients from the clinical data repository (CDR) at the University of Virginia.

A multi-level two-part random effects model, with application to an alcohol-dependence study.

Lei Liu — 2008-04-30T09:33:54-00:00

Statistics in medicine (25 January 2008)

Two-part random effects models (J. Am. Statist. Assoc. 2001; 96:730-745; Statist. Methods Med. Res. 2002; 11:341-355) have been applied to longitudinal studies for semi-continuous outcomes, characterized by a large portion of zero values and continuous non-zero (positive) values. Examples include repeated measures of daily drinking records, monthly medical costs, and annual claims of car insurance. However, the question of how to apply such models to multi-level data settings remains. In this paper, we propose a novel multi-level two-part random effects model. Distinct random effects are used to characterize heterogeneity at different levels. Maximum likelihood estimation and inference are carried out through Gaussian quadrature technique, which can be implemented conveniently in freely available software-aML. The model is applied to the analysis of repeated measures of the daily drinking record in a randomized controlled trial of topiramate for alcohol-dependence treatment. Copyright (c) 2008 John Wiley & Sons, Ltd.

Effect of mobility on the critical transmitting range for connectivity in wireless ad hoc networks

Guanghui Zhang — 2008-07-22T04:13:28-00:00

Advanced Information Networking and Applications, 2005. AINA 2005. 19th International Conference on, Vol. 2 (2005), pp. 9-12 vol.2.

The effect of mobility on the critical transmitting range in wireless ad hoc networks is discussed in this paper. A new parameter, pause probability P/sub pause/, which is the function of the minimum velocity V/sub min/, the maximum velocity V/sub max/ and the pause time t/sub pause/ of random waypoint (RWP) mobility model, is defined. Simulation results show that the effect of RWP parameter on the critical transmitting range is determined by P/sub pause/ that is, if P/sub pause/ smaller than 0.5, the critical transmitting range of mobile network is about 10 percent larger than that of stationary one, else it equals that of stationary network approximately. If the values of t/sub pause/, V/sub min/ and V/sub max/ are given, their effect on the critical transmitting range is determined since P/sub pause/ is the function of them.

Summary of contributions to GAW15 Group 13: candidate gene association studies.

M de Andrade — 2008-07-22T00:55:06-00:00

Genetic epidemiology, Vol. 31 Suppl 1 (2007)

Here we summarize the contributions to Group 13 of the Genetic Analysis Workshop 15 held in St. Pete Beach, Florida, on November 12-14, 2006. The focus of this group was to identify candidate genes associated with rheumatoid arthritis or surrogate outcomes. The association methods proposed in this group were diverse, from better known approaches, such as logistic regression for single nucleotide polymorphism (SNP) analysis and haplotype sharing tests to methods less familiar to genetic epidemiologists, such as machine learning and visualization methods. The majority of papers analyzed Genetic Analysis Workshop 15 Problems 2 (rheumatoid arthritis data) and 3 (simulated data). The highlighted points of this group analyses were: (1) haplotype-based statistics can be more powerful than single SNP analysis for risk-locus localization; (2) considering linkage disequilibrium block structure in haplotype analysis may reduce the likelihood of false-positive results; and (3) visual representation of genetic models for continuous covariates may help identify SNPs associated with the underlying quantitative trait loci.