CiteULike: Author He

Self-directed self-assembly of nanoparticle/copolymer mixtures

Yao Lin — 2005-03-02T19:56:44-00:00

Nature, Vol. 434, No. 7029. (03 March 2005), pp. 55-59.

Oocyte CD9 is enriched on the microvillar membrane and required for normal microvillar shape and distribution.

KE Runge — 2008-08-07T00:16:43-00:00

Developmental biology, Vol. 304, No. 1. (1 April 2007), pp. 317-325.

Microvilli are found on the surface of many cell types, including the mammalian oocyte, where they are thought to act in initial contact of sperm and oocyte plasma membranes. CD9 is currently the only oocyte protein known to be required for sperm-oocyte fusion. We found CD9 is localized to the oocyte microvillar membrane using transmission electron microscopy (TEM). Scanning electron microscopy (SEM) showed that CD9 null oocytes, which are unable to fuse with sperm, have an altered length, thickness and density of their microvilli. One aspect of this change in morphology was quantified using TEM by measuring the radius of curvature at the microvillar tips. A small radius of curvature is thought to promote fusibility and the radius of curvature of microvillar tips on CD9 wild-type oocytes was found to be half that of the CD9 null oocytes. We found that oocyte CD9 co-immunoprecipitates with two Ig superfamily cis partners, EWI-2 and EWI-F, which could have a role in linking CD9 to the oocyte microvillar actin core. We also examined latrunculin B-treated oocytes, which are known to have reduced fusion ability, and found altered microvillar morphology by SEM and TEM. Our data suggest that microvilli may participate in sperm-oocyte fusion. Microvilli could act as a platform to concentrate adhesion/fusion proteins and/or provide a membrane protrusion with a low radius of curvature. They may also have a dynamic interaction with the sperm that serves to capture the sperm cell and bring it into close contact with the oocyte plasma membrane.

Range-free localization schemes for large scale sensor networks

Tian He — 2007-08-28T03:22:53-00:00

(2003), pp. 81-95.

Parcellation-dependent small-world brain functional networks: A resting-state fMRI study.

Jinhui Wang — 2008-07-25T06:36:17-00:00

Human brain mapping (22 July 2008)

Recent studies have demonstrated small-world properties in both functional and structural brain networks that are constructed based on different parcellation approaches. However, one fundamental but vital issue of the impact of different brain parcellation schemes on the network topological architecture remains unclear. Here, we used resting-state functional MRI (fMRI) to investigate the influences of different brain parcellation atlases on the topological organization of brain functional networks. Whole-brain fMRI data were divided into ninety and seventy regions of interest according to two predefined anatomical atlases, respectively. Brain functional networks were constructed by thresholding the correlation matrices among the parcellated regions and further analyzed using graph theoretical approaches. Both atlas-based brain functional networks were found to show robust small-world properties and truncated power-law connectivity degree distributions, which are consistent with previous brain functional and structural networks studies. However, more importantly, we found that there were significant differences in multiple topological parameters (e.g., small-worldness and degree distribution) between the two groups of brain functional networks derived from the two atlases. This study provides quantitative evidence on how the topological organization of brain networks is affected by the different parcellation strategies applied. Hum Brain Mapp 2008. (c) 2008 Wiley-Liss, Inc.

Dynamics in the plasma membrane: how to combine fluidity and order.

D Marguet — 2008-08-06T10:49:25-00:00

The EMBO journal, Vol. 25, No. 15. (9 August 2006), pp. 3446-3457.

Cell membranes are fascinating supramolecular aggregates that not only form a barrier between compartments but also harbor many chemical reactions essential to the existence and functioning of a cell. Here, it is proposed to review the molecular dynamics and mosaic organization of the plasma membrane, which are thought to have important functional implications. We will first summarize the basic concepts of Brownian diffusion and lipid domain formation in model membranes and then track the development of ideas and tools in this field, outlining key results obtained on the dynamic processes at work in membrane structure and assembly. We will focus in particular on findings made using fluorescent labeling and imaging procedures to record these dynamic processes. We will also discuss a few examples showing the impact of lateral diffusion on cell signal transduction, and outline some future methodological challenges which must be met before we can answer some of the questions arising in this field of research.

Fat redistribution and adipocyte transformation in uninephrectomized rats

Hai-Lu Zhao — 2008-08-06T08:55:23-00:00

Kidney Int, Vol. 74, No. 4. (21 May 2008), pp. 467-477.

Systematic identification of mammalian regulatory motifs' target genes and functions

Jason Warner — 2008-03-28T16:35:46-00:00

Nature Methods, Vol. 5, No. 4. (02 March 2008), pp. 347-353.

Gene complexity and gene duplicability.

X He — 2005-10-05T17:30:20-00:00

Curr Biol, Vol. 15, No. 11. (7 June 2005), pp. 1016-1021.

Eukaryotic genes are on average more complex than prokaryotic genes in terms of expression regulation, protein length, and protein-domain structure [1-5]. Eukaryotes are also known to have a higher rate of gene duplication than prokaryotes do [6, 7]. Because gene duplication is the primary source of new genes [], the average gene complexity in a genome may have been increased by gene duplication if complex genes are preferentially duplicated. Here, we test this "gene complexity and gene duplicability" hypothesis with yeast genomic data. We show that, on average, duplicate genes from either whole-genome or individual-gene duplication have longer protein sequences, more functional domains, and more cis-regulatory motifs than singleton genes. This phenomenon is not a by-product of previously known mechanisms, such as protein function [10-13], evolutionary rate [14, 15], dosage [11], and dosage balance [16], that influence gene duplicability. Rather, it appears to have resulted from the sub-neo-functionalization process in duplicate-gene evolution [11]. Under this process, complex genes are more likely to be retained after duplication because they are prone to subfunctionalization, and gene complexity is regained via subsequent neofunctionalization. Thus, gene duplication increases both gene number and gene complexity, two important factors in the origin of genomic and organismal complexity.

MicroRNA-encoding long non-coding RNAs

Shunmin He — 2008-05-22T03:59:10-00:00

BMC Genomics, Vol. 9 (21 May 2008), 236.

Missing value imputation for microarray gene expression data using histone acetylation information

Qian Xiang — 2008-05-29T17:55:02-00:00

BMC Bioinformatics, Vol. 9 (29 May 2008), 252.

Phospholipid-Stabilized Au-Nanoparticles

P He — 2008-08-05T10:43:23-00:00

Biomacromolecules, Vol. 6, No. 3. (9 May 2005), pp. 1224-1225.

Abstract: This communication outlines a simple two-step approach of modification of 1 nm diameter Au nanoparticles using an aqueous solution of (1,2-dipalmitoyl-sn-glycero-3-phosphothio-ethanol) phospholipid (PL). Transmission electron microscopy as well as particle size analysis show that, as a result of PL reactions with Au particles, the initial Au nanoparticle size increases to 5 nm. Considering the size of the PL and their ability to form liposomes, 5 nm diameter spheres indicate that the PL bilayer was attached to the surface of Au particles and the PL-Au interactions are facilitated by the presence of thiol functionality. The change of surface electronic properties of PL-stabilized Au particles is manifested by the disappearance of the 217 and 290 nm absorbances due to 5d-6sp transitions in Au, which is likely attributed to the presence of S-H functionalities which increase the free electron density of the particle. As a consequence, two surface plasmons resulting from a collective oscillation of electrons in response to UV excitation disappear.

A bacterial metapopulation adapts locally to phage predation despite global dispersal

Victor Kunin — 2008-04-12T02:43:33-00:00

Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 293-297.

Using a combination of bacterial and phage-targeted metagenomics, we analyzed two geographically remote sludge bioreactors enriched in a single bacterial species Candidatus Accumulibacter phosphatis (CAP). We inferred unrestricted global movement of this species and identified aquatic ecosystems as the primary environmental reservoirs facilitating dispersal. Highly related and geographically remote CAP strains differed principally in genomic regions encoding phage defense mechanisms. We found that CAP populations were high density, clonal, and nonrecombining, providing natural targets for "kill-the-winner" phage predation. Community expression analysis demonstrated that phages were consistently active in the bioreactor community. Genomic signatures linking CAP to past phage exposures were observed mostly between local phage and host. We conclude that CAP strains disperse globally but must adapt to phage predation pressure locally. 10.1101/gr.6835308

Experimental evaluation of using dynamic slices for fault location

Xiangyu Zhang — 2008-08-02T00:40:21-00:00

(2005), pp. 33-42.

Dynamic slicing algorithms have been considered to aid in debugging for many years. However, as far as we know, no detailed studies on evaluating the benefits of using dynamic slicing for detecting faulty statements in programs have been carried out. We have developed a dynamic slicing framework that uses dynamic instrumentation to efficiently collect dynamic slices and reduced ordered Binary Decision Diagrams (roBDDs) to compactly store them. We have used the above framework to implement three variants of dynamic slicing algorithms including: data slicing, full slicing, and relevant slicing algorithms. We have carried out detailed experiments to evaluate these algorithms. Our results show that full slices and relevant slices can considerably reduce the subset of program statements that need to be examined to locate faulty statements. We expect that the observations presented here will enable development of new slicing based algorithms for automated debugging.

Mapping Anatomical Connectivity Patterns of Human Cerebral Cortex Using In Vivo Diffusion Tensor Imaging Tractography

Gaolang Gong — 2008-07-10T18:36:53-00:00

Cereb. Cortex (20 June 2008), bhn102.

The characterization of the topological architecture of complex networks underlying the structural and functional organization of the brain is a basic challenge in neuroscience. However, direct evidence for anatomical connectivity networks in the human brain remains scarce. Here, we utilized diffusion tensor imaging deterministic tractography to construct a macroscale anatomical network capturing the underlying common connectivity pattern of human cerebral cortex in a large sample of subjects (80 young adults) and further quantitatively analyzed its topological properties with graph theoretical approaches. The cerebral cortex was divided into 78 cortical regions, each representing a network node, and 2 cortical regions were considered connected if the probability of fiber connections exceeded a statistical criterion. The topological parameters of the established cortical network (binarized) resemble that of a "small-world" architecture characterized by an exponentially truncated power-law distribution. These characteristics imply high resilience to localized damage. Furthermore, this cortical network was characterized by major hub regions in association cortices that were connected by bridge connections following long-range white matter pathways. Our results are compatible with previous structural and functional brain networks studies and provide insight into the organizational principles of human brain anatomical networks that underlie functional states. 10.1093/cercor/bhn102

MethyCancer: the database of human DNA methylation and cancer.

X He — 2008-03-07T07:52:35-00:00

Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)

Cancer is ranked as one of the top killers in all human diseases and continues to have a devastating effect on the population around the globe. Current research efforts are aiming to accelerate our understanding of the molecular basis of cancer and develop effective means for cancer diagnostics, treatment and prognosis. An altered pattern of epigenetic modifications, most importantly DNA methylation events, plays a critical role in tumorigenesis through regulating oncogene activation, tumor suppressor gene silencing and chromosomal instability. To study interplay of DNA methylation, gene expression and cancer, we developed a publicly accessible database for human DNA Methylation and Cancer (MethyCancer, http://methycancer.genomics.org.cn). MethyCancer hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Furthermore, a powerful search tool is developed to provide user-friendly access to all the data and data connections. A graphical MethyView shows DNA methylation in context of genomics and genetics data facilitating the research in cancer to understand genetic and epigenetic mechanisms that make dramatic changes in gene expression of tumor cells.

Renalase gene is a novel susceptibility gene for essential hypertension: a two-stage association study in northern Han Chinese population

Zhao — 2007-09-08T00:08:42-00:00

Journal of Molecular Medicine, Vol. 85, No. 8. (August 2007), pp. 877-885.

BrowseRank: letting web users vote for page importance

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

(2008), pp. 451-458.

How many human genes can be defined as housekeeping with current expression data?

Jiang Zhu — 2008-04-16T11:53:22-00:00

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

BACKGROUND:Housekeeping (HK) genes are ubiquitously expressed in all tissue/cell types and constitute a basal transcriptome for the maintenance of basic cellular functions. Partitioning transcriptomes into HK and tissue-specific (TS) genes relatively is fundamental for studying gene expression and cellular differentiation. Although many studies have aimed at large-scale and thorough categorization of human HK genes, a meaningful consensus has yet to be reached.RESULTS:We collected two latest gene expression datasets (both EST and microarray data) from public databases and analyzed the gene expression profiles in 18 human tissues that have been well-documented by both two data types. Benchmarked by a manually-curated HK gene collection (HK408), we demonstrated that present data from EST sampling was far from saturated, and the inadequacy has limited the gene detectability and our understanding of TS expressions. Due to a likely over-stringent threshold, microarray data showed higher false negative rate compared with EST data, leading to a significant underestimation of HK genes. Based on EST data, we found that 40.0% of the currently annotated human genes were universally expressed in at least 16 of 18 tissues, as compared to only 5.1% specifically expressed in a single tissue. Our current EST-based estimate on human HK genes ranged from 3,140 to 6,909 in number, a ten-fold increase in comparison with previous microarray-based estimates.CONCLUSIONS:We concluded that a significant fraction of human genes, at least in the currently annotated data depositories, was broadly expressed. Our understanding of tissue-specific expression was still preliminary and required much more large-scale and high-quality transcriptomic data in future studies. The new HK gene list categorized in this study will be useful for genome-wide analyses on structural and functional features of HK genes.

Mapping the connectivity with structural equation modeling in an fMRI study of shape-from-motion task

Jiancheng Zhuang — 2008-07-31T16:29:52-00:00

NeuroImage, Vol. 42, No. 2. (15 August 2008), pp. 799-806.

In this fMRI study, we explore the connectivity among brain regions in a shape-from-motion task using the causal mapping analysis of structural equation modeling (SEM). An important distinction of our approach is that we have adapted SEM from its traditional role in confirmatory analysis to provide utility as an exploratory mapping technique. Our current approaches include (I) detecting brain regions that fit well in a hypothesized neural network model, and (II) identifying the best connectivity model at each brain region. We demonstrate that SEM effectively detects the dorsal and ventral visual pathways from the covariance structure in fMRI data, confirming previous neuroscience results. Further, our SEM mapping methodology found that the two pathways interact through specific cortical areas such as the superior lateral occipital cortex in the perception of shape from motion.

Resonant acceleration of electrons by intense circularly polarized Gaussian laser pulses

HY Niu — 2008-07-31T13:39:48-00:00

Laser and Particle Beams, Vol. 26, No. 01. (2008), pp. 51-60.

Resonant acceleration of plasma electrons in combined circularly polarized Gaussian laser fields and self-generated quasistatic fields has been investigated theoretically and numerically. The latter includes the radial quasistatic electric field, the azimuthal quasistatic magnetic field and the axial one. The resonant condition is theoretically given and numerically testified. The results show some of the resonant electrons are accelerated to velocities larger than the laser group velocity and thus gain high energy. For peak laser intensity I0 = 1 × 1020 W cm−2 and plasma density n0 = 0.1ncr, the relativistic electron beam with energies increased from 207 MeV to 262 MeV with a relative energy width around 24% and extreme low beam divergence less than 1° has been obtained. The effect of laser intensity and plasma density on the final energy gain of resonant electrons is also investigated.

Personalized web exploration with task models

Jae-Wook Ahn — 2008-07-31T11:19:56-00:00

(2008), pp. 1-10.

Combining Particle Filter and Active Shape Models for Lip Tracking

Min Jiang — 2008-07-31T05:15:55-00:00

Intelligent Control and Automation, 2006. WCICA 2006. The Sixth World Congress on, Vol. 2 (2006), pp. 9897-9901.

In this paper, a new algorithm for lip tracking is proposed, fusing the strength of stochastic tracker and deterministic tracker. Particle filter and Active Shape Models (ASM) are used as deterministic tracker and stochastic tracker respectively. In order not to build complex dynamic model, we use deterministic tracker instead of stochastic tracker to estimate the local deformation part parameters of shape. Furthermore, to generate the initial optimal parameter sets of deterministic search, Resource Limited Artificial Immune System Clustering (RLAIS) is used, which avoids deterministic tracker searching for each sample. Our method improves experimental results considerably compared to particle filter, ASM or earlier hybrid methods.

High-performance photorefractive polymer composite with 2-dicyanomethylen-3-cyano-2,5-dihydrofuran chromophore

Daniel Wright — 2008-07-30T23:21:51-00:00

Applied Physics Letters, Vol. 79, No. 26. (2001), pp. 4274-4276.

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Recent Advances in Understanding and Development of Photorefractive Polymers and Glasses

O Ostroverkhova — 2008-07-30T23:21:32-00:00

Advanced Functional Materials, Vol. 12, No. 9. (2002), pp. 621-629.

The photoconductive, orientational, and photorefractive properties of monolithic glasses based on new nonlinear optical chromophores containing a 2-dicyanomethylene-3-cyano-2,5-dihydrofuran (DCDHF) acceptor group are presented. Large net gain coefficients are observed in both red and infrared wavelength regions. The physical and optical properties of glasses based on various DCDHF-containing derivatives are compared and analyzed, and the factors limiting steady-state and dynamical photorefractive performance are discussed.

Regional homogeneity, functional connectivity and imaging markers of Alzheimer's disease: A review of resting-state fMRI studies

Y Liu — 2008-07-30T15:01:34-00:00

Neuropsychologia, Vol. 46, No. 6. (2008), pp. 1648-1656.

Resting-state functional magnetic resonance imaging (fMRI), a promising technique for measuring brain activities during rest, has attracted much attention in the past few years. In this paper, we review recent progress on the study of Alzheimer's disease (AD) based on resting-state fMRI. First, we briefly introduce some AD-related studies from other groups. Then we describe our AD-related work in detail from three aspects: (1) alterations in regional homogeneity (ReHo) of the fMRI signal in the resting state, (2) altered patterns of functional connectivity from regions of interest and whole brain analyses, and (3) discriminative analyses based on classification features from resting-state fMRI data for differentiating AD patients from healthy elders. Finally, we summarize the main results and some prospects for future work. © 2008.

CDD: a curated Entrez database of conserved domain alignments.

A Marchler-Bauer — 2006-03-19T17:04:56-00:00

Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 383-387.

The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein-protein queries submitted to BLAST(R) at http://www.ncbi.nlm.nih.gov/BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.

Removal of Cu2+ from aqueous solution by adsorption onto a novel activated nylon-based membrane

Zhi-Yan He — 2008-07-30T04:44:46-00:00

Bioresource Technology, Vol. 99, No. 17. (November 2008), pp. 7954-7958.

A novel activated nylon-based membrane was prepared and applied as an adsorbent for the removal of Cu2+ from aqueous solutions. It involved three stages: (i) deposition of a chitosan layer that functionalized the nylon membrane, (ii) cross-linking with epichlorohydrin to stabilize the polymer layer and enabling grafting, and (iii) iminodiacetic acid grafting. SEM and EDX techniques were used to characterize the composition of the membranes. Dynamic adsorption experiments on membranes were carried out at various pH values, contact times, adsorption dosages and initial metal concentrations to determine optimum membrane adsorption properties. The adsorption isotherm relating to Cu2+ fitted the Langmuir equation and an adsorption equilibrium constant and adsorption capacity of 2.345 נ10-3 mg/ml and 10.794 mg/g were determined, respectively. The experimental data was analyzed using two adsorption kinetic models, pseudo-first-order and pseudo-second-order with the latter system providing the best fit. Finally complete regeneration of the activated nylon membrane was possible using 100 mmol/l Na2EDTA.

Cloning, expression and chromosome locations of the human DNMT3 gene family

Shaoping Xie — 2008-07-30T02:45:08-00:00

Gene, Vol. 236, No. 1. (5 August 1999), pp. 87-95.

DNA methylation plays an important role in animal development and gene regulation. In mammals, several genes encoding DNA cytosine methyltransferases have been identified. DNMT1 is constitutively expressed and is required for the maintenance of global methylation after DNA replication. In contrast, the murine Dnmt3 family genes appear to be developmentally regulated and behave like de novo DNA methyltransferases in vitro. In this study, we have cloned human DNMT3A and DNMT3B that encode full-length DNMT3A and DNMT3B proteins with 98% and 94% amino acid sequence identity to their murine homologues. The DNMT3A and DNMT3B show high homology in the carboxy terminal catalytic domain and contain a conserved cysteine-rich region, which shares homology with the X-linked ATRX gene of the SNF2/SWI family. We have mapped human DNMT3A and DNMT3B to chromosomes 2p23 and 20q11.2 respectively, and determined the DNMT3B genomic structure. We further show that DNMT3A expression is ubiquitous and can be readily detected in most adult tissues, whereas DNMT3B is expressed at very low levels in most tissues except testis, thyroid and bone marrow. Significantly, both DNMT3A and DNMT3B expression is elevated in several tumor cell lines to levels comparable to DNMT1. The cloning of the human DNMT3 genes will facilitate further biochemical and genetic studies of their functions in establishment of DNA methylation patterns, regulation of gene expression and tumorigenesis.

Rethinking internet traffic management: from multiple decompositions to a practical protocol

Jiayue He — 2008-07-30T00:44:31-00:00

(2007), pp. 1-12.

Towards Robust Multi-Layer Traffic Engineering: Optimization of Congestion Control and Routing

J He — 2008-07-30T00:33:34-00:00

Selected Areas in Communications, IEEE Journal on, Vol. 25, No. 5. (2007), pp. 868-880.

In the Internet today, traffic engineering is performed assuming that the offered traffic is inelastic. In reality, end hosts adapt their sending rates to network congestion, and network operators adapt the routing to the measured traffic. This raises the question of whether the joint system of congestion control (transport layer) and routing (network layer) is stable and optimal. Using the established optimization models for TCP and traffic engineering as a basis, we find the joint system can be stabilized and often maximizes aggregate user utility. We prove that both stability and optimality of the joint system can be guaranteed for sufficiently elastic traffic simply by tuning the cost function used for traffic engineering. Then, we present a new algorithm that adapts on a smaller timescale to changes in traffic distribution and is more robust to large traffic bursts. Uniting the network and transport layers in a multi-layer approach, this algorithm, distributed adaptive traffic engineering (DATE), jointly optimizes the goals of end users and network operators and reacts quickly to avoid bottlenecks. Simulations demonstrate that DATE converges quickly

Critical role of TRAF3 in the Toll-like receptor-dependent and -independent antiviral response

Gagik Oganesyan — 2005-11-23T18:52:34-00:00

Nature (23 November 2005)

Type I interferon (IFN) production is a critical component of the innate defence against viral infections1. Viral products induce strong type I IFN responses through the activation of Toll-like receptors (TLRs) and intracellular cytoplasmic receptors such as protein kinase R (PKR)2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12. Here we demonstrate that cells lacking TRAF3, a member of the TNF receptor-associated factor family, are defective in type I IFN responses activated by several different TLRs. Furthermore, we show that TRAF3 associates with the TLR adaptors TRIF and IRAK1, as well as downstream IRF3/7 kinases TBK1 and IKK-, suggesting that TRAF3 serves as a critical link between TLR adaptors and downstream regulatory kinases important for IRF activation. In addition to TLR stimulation, we also show that TRAF3-deficient fibroblasts are defective in their type I IFN response to direct infection with vesicular stomatitis virus, indicating that TRAF3 is also an important component of TLR-independent viral recognition pathways. Our data demonstrate that TRAF3 is a major regulator of type I IFN production and the innate antiviral response.

An aggregation index (AI) to quantify spatial patterns of landscapes

Hong He — 2008-07-29T22:27:58-00:00

Landscape Ecology, Vol. 15, No. 7. (1 October 2000), pp. 591-601.

There is often need to measure aggregation levels of spatial patterns within a single map class in landscape ecological studies. The contagion index (CI), shape index (SI), and probability of adjacency of the same class (Qi), all have certain limits when measuring aggregation of spatial patterns. We have developed an aggregation index (AI) that is class specific and independent of landscape composition. AI assumes that a class with the highest level of aggregation (AI =1) is comprised of pixels sharing the most possible edges. A class whose pixels share no edges (completely disaggregated) has the lowest level of aggregation (AI =0). AI is similar to SI and Qi, but it calculates aggregation more precisely than the latter two. We have evaluated the performance of AI under varied levels of (1) aggregation, (2) number of patches, (3) spatial resolutions, and (4) real species distribution maps at various spatial scales. AI was able to produce reasonable results under all these circumstances. Since it is class specific, it is more precise than CI, which measures overall landscape aggregation. Thus, AI provides a quantitative basis to correlate the spatial pattern of a class with a specific process. Since AI is a ratio variable, map units do not affect the calculation. It can be compared between classes from the same or different landscapes, or even the same classes from the same landscape under different resolutions.

Counterion-dependent microrheological properties of F-actin solutions across the isotropic-nematic phase transition

Jun He — 2008-07-29T18:55:43-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 78, No. 1. (2008)

We studied microrheological properties of F-actin across the isotropic-nematic phase transition region by video particle tracking (VPT) and by laser deflection particle tracking (LDPT). Both methods track the motion of thermally driven micron-sized beads, and convert the temporal mean square displacement (MSD) to shear moduli. The two methods give consistent results for the elastic modulus G and less so for the loss modulus G. As the nematic order parameter increases with actin concentration, G||[prime]" align="middle"> (measured parallel to the nematic director) and G[perpendicular][prime]" align="middle"> (perpendicular to the director) grow apart, with G[perpendicular][prime]" align="middle"> larger than G||[prime]" align="middle">. The moduli scale with actin concentration as G||[prime]" align="middle">~c0.54±0.13 and G[perpendicular][prime]" align="middle">~c1.38±0.15. Furthermore, G and G dependence on [Mg2+] were measured and compared for 1 mg/ml isotropic and 4 mg/ml nematic F-actin solutions, respectively. In the isotropic phase, G increases with [Mg2+] up to 6 mM and then plateaus. In the nematic phase, G[perpendicular][prime]" align="middle"> is larger than G||[prime]" align="middle">, and both G[perpendicular][prime]" align="middle"> and G||[prime]" align="middle"> increase with [Mg2+] progressively up to 16 mM, above which F-actin form large bundles. In both isotropic and nematic phases, G only weakly depends on [Mg2+]. In conclusion, particle tracking microrheology reveals rich rheological features of F-actin affected by the isotropic-nematic phase transition and by tuning weak electrostatic interactions among the protein filaments.

MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control

Yi Zhao — 2008-06-04T14:14:19-00:00

Trends in Genetics, Vol. In Press, Corrected Proof

Metazoan microRNAs (miRNAs) are commonly encoded by primary mRNA-like characteristics (mlRNAs). To investigate whether mlRNAs are subject to miRNA control, we compared the expression of mlRNAs to that of tissue-specific miRNAs. We show that, like mRNAs, the expression levels of predicted mlRNA targets are significantly reduced in tissues where a targeting miRNA is expressed. On the basis of these results, we describe a potential network for posttranscriptional miRNA-miRNA control.

c-myc in the hematopoietic lineage is crucial for its angiogenic function in the mouse embryo.

Chen He — 2008-06-17T07:16:06-00:00

Development (Cambridge, England) (11 June 2008)

The c-myc proto-oncogene, which is crucial for the progression of many human cancers, has been implicated in key cellular processes in diverse cell types, including endothelial cells that line the blood vessels and are critical for angiogenesis. The de novo differentiation of endothelial cells is known as vasculogenesis, whereas the growth of new blood vessels from pre-existing vessels is known as angiogenesis. To ascertain the function of c-myc in vascular development, we deleted c-myc in selected cell lineages. Embryos lacking c-myc in endothelial and hematopoietic lineages phenocopied those lacking c-myc in the entire embryo proper. At embryonic day (E) 10.5, both mutant embryos were grossly normal, had initiated primitive hematopoiesis, and both survived until E11.5-12.5, longer than the complete null. However, they progressively developed defective hematopoiesis and angiogenesis. The majority of embryos lacking c-myc specifically in hematopoietic cells phenocopied those lacking c-myc in endothelial and hematopoietic lineages, with impaired definitive hematopoiesis as well as angiogenic remodeling. c-myc is required for embryonic hematopoietic stem cell differentiation, through a cell-autonomous mechanism. Surprisingly, c-myc is not required for vasculogenesis in the embryo. c-myc deletion in endothelial cells does not abrogate endothelial proliferation, survival, migration or capillary formation. Embryos lacking c-myc in a majority of endothelial cells can survive beyond E12.5. Our findings reveal that hematopoiesis is a major function of c-myc in embryos and support the notion that c-myc functions in selected cell lineages rather than in a ubiquitous manner in mammalian development.

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Gordon Robertson — 2007-07-13T14:43:43-00:00

Nat Methods (11 June 2007)

We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIPseq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes. By ChIP-seq, using 15.1 and 12.9 million uniquely mapped sequence reads, and an estimated false discovery rate of less than 0.001, we identified 41,582 and 11,004 putative STAT1-binding regions in stimulated and unstimulated cells, respectively. Of the 34 loci known to contain STAT1 interferon-responsive binding sites, ChIP-seq found 24 (71%). ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%.

Absence of CD9 enhances adhesion-dependent morphologic differentiation, survival, and matrix metalloproteinase-2 production in small cell lung cancer cells.

Y Saito — 2008-07-28T14:03:37-00:00

Cancer research, Vol. 66, No. 19. (1 October 2006), pp. 9557-9565.

While adhering to extracellular matrix proteins in vitro and in vivo, small cell lung cancer (SCLC) cells frequently show morphologic differentiation and are protected from apoptosis. Integrin beta(1)-mediated protein phosphorylation is suggested to be an essential signaling event in these processes. CD9 is an almost ubiquitously expressed tetraspanin protein that suppresses tumor progression by regulating cell motility and signaling through complex formation with beta(1) integrins. We reported previously that, among tetraspanins, CD9 is selectively absent in most SCLC cells and that ectopic expression of CD9 suppresses their motility. Here, we show that the ectopic expression of CD9 suppressed neurite-like process outgrowth and promoted apoptotic death of SCLC cells that were adherent to fibronectin in serum-starved conditions. This correlated with attenuation of adhesion-dependent phosphorylation of Akt but not that of focal adhesion kinase or c-Jun NH(2)-terminal kinase. Treatment of CD9(-) parent cells with a phosphatidylinositol 3-kinase (PI3K) inhibitor, LY294002, inhibited process outgrowth and survival, suggesting that PI3K/Akt signaling is required for the morphologic change and cell survival. Production of matrix metalloproteinase (MMP)-2 was likewise suppressed in the CD9 transfectants and in LY294002-treated parent cells. These results suggest that the absence of CD9 in SCLC cells may contribute to postadhesive morphologic differentiation, survival, and MMP-2 production via PI3K/Akt pathway.

Reproducibility Probability Score—incorporating measurement variability across laboratories for gene selection

Guixian Lin — 2006-12-12T03:05:10-00:00

Nature Biotechnology, Vol. 24, No. 12., pp. 1476-1477.

Ecological footprint and biological capacity time series assessment for a forest region in northeastern China

Liu — 2007-10-01T18:11:00-00:00

The International Journal of Sustainable Development and World Ecology, Vol. 14, No. 5. (October 2007), pp. 493-502.

A GIS-based moving window analysis of landscape pattern in the Beijing metropolitan area, China

Wu — 2006-12-24T14:52:25-00:00

The International Journal of Sustainable Development and World Ecology, Vol. 13, No. 5. (October 2006), pp. 419-434.

Genome sequencing in microfabricated high-density picolitre reactors

Marcel Margulies — 2005-07-31T21:14:04-00:00

Nature (31 July 2005)

Ontology-based Semantic Integration Scheme for Medical Image Grid

Hai Jin — 2008-07-25T17:57:07-00:00

(2007), pp. 127-134.

Giant negative Goos-Hänchen shifts for a photonic crystal with a negative effective index

Jinlong He — 2008-07-25T08:00:30-00:00

Opt. Express, Vol. 14, No. 7. (3 April 2006), pp. 3024-3029.

The Goos-Hänchen effects are investigated for a monochromatic Gaussian beam totally reflected by a photonic crystal with a negative effective index. By choosing an appropriate thickness for the homogeneous cladding layer, a giant negative GH lateral shift can be obtained and the totally reflected beam retains a single beam of good profile even for a very narrow incident beam. The GH lateral shift can be very sensitive to the change of the refractive index of the cladding layer, and this property can be utilized for e.g. the switching applications.

Linking UML models of design and requirement

Jing Liu — 2006-10-09T18:28:22-00:00

Software Engineering Conference, 2004. Proceedings. 2004 Australian (2004), pp. 329-338.

Both a UML model of requirement and a UML model of a design are defined as a pair of class diagram and a family of sequence diagrams. We then give an unified semantics for models of requirements and designs. We define the consistency between a design class diagram and the interaction diagrams and show how the removal of inconsistency can be treated as a model refinement. We then formally define the correctness of UML model of design with respect to the model of requirement.

Increased Retention of Early Computer Science and Software Engineering Students Using Pair Programming

Carver — 2008-07-24T18:47:53-00:00

cseet, Vol. 00 (2007), pp. 115-122.

An important problem faced by many Computer Science and Software Engineering programs is declining enrollment. In an effort to reverse that trend at Mississippi State University, we have instituted pair programming for the laboratory exercises in the introductory programming course. This paper describes a study performed to analyze whether using pair programming would increase retention. An important goal of this study was not only to measure increased retention, but to provide insight into why retention increased or decreased. The results of the study showed that retention significantly increased for those students already majoring in Computer Science, Software Engineering, or Computer Engineering. In addition, survey results indicated that the students viewed many aspects of pair programming to be very beneficial to their learning experience.

A graph-based approach to developing adaptive representations of complex reaction mechanisms

Kaiyuan He — 2008-07-24T17:49:24-00:00

Combustion and Flame, Vol. In Press, Corrected Proof

An effective adaptive mechanism reduction approach based on flux graph clustering is proposed in this paper. The instantaneous element flux is quantified and considered as a proxy for describing the reactive propensities of the system. Our underlying hypothesis is that even though particular conditions may be characterized by a multitude of combinations of species mass fraction, T, and P, the essential chemistry, and hence the reaction propensity of the mixture that is active under this family of conditions, is the same. Therefore, we opt to use the instantaneous fluxes through the active reactions as an intrinsic property of the system. Flux graphs are first constructed for the chemical reaction system under numerous conditions aiming at capturing the attainable region. Similarity between flux graphs is quantified through the distances between corresponding vectors, using the cosine coefficient and a novel graph-distance metric taking into account the magnitude of each flux and the activity distribution of different fluxes. A hierarchical clustering algorithm is implemented to group similar instantaneous flux graphs into clusters, and consequently a reduced mechanism is generated for each cluster. A search algorithm is defined afterward to assign a new query point to a particular flux graph cluster, and subsequently the reduced mechanism associated with this cluster is used to describe the system at this time point. Finally, the methodology is demonstrated using n-pentane combustion in an adiabatic plug flow reactor model and a pairwise mixing stirred reactor model.

Formal and Use-Case Driven Requirement Analysis in UML

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

(2001), pp. 215-224.

The role of extraesophageal reflux in otitis media in infants and children.

RC O'Reilly — 2008-07-24T04:00:19-00:00

The Laryngoscope, Vol. 118, No. 7 Part 2 Suppl 116. (July 2008), pp. 1-9.

OBJECTIVES/HYPOTHESIS: Gastroesophageal reflux disease (GERD) is common in children, and extraesophageal reflux disease (EORD) has been implicated in the pathophysiology of otitis media (OM). We sought to 1) determine the incidence of pepsin/pepsinogen presence in the middle ear cleft of a large sample of pediatric patients undergoing myringotomy with tube placement for OM; 2) compare this with a control population of pediatric patients undergoing middle ear surgery (cochlear implantation) with no documented history of OM; 3) analyze potential risk factors for OM in children with EORD demonstrated by the presence of pepsin in the middle ear cleft; and 4) determine if pepsin positivity at the time of myringotomy with tube placement predisposes to posttympanostomy tube otorrhea. STUDY DESIGN AND METHODS: Study Group: prospective samples of 509 pediatric patients (n = 893 ear samples) undergoing myringotomy with tube placement for recurrent acute OM and/or otitis media with effusion in a tertiary care pediatric hospital with longitudinal follow-up of posttympanostomy tube otorrhea. Control Group: prospective samples of 64 pediatric patients (n = 74 ears) with negative history of OM undergoing cochlear implantation at one of the three tertiary care pediatric hospitals. A previously validated, highly sensitive and specific modified enzymatic assay was used to detect the presence of pepsin in the middle ear aspirates of study and control patients. Risk factors for OM and potentially associated conditions, including GERD, allergy, and asthma were analyzed for the study group through review of the electronic medical record and correlated topresence of pepsin in the middle ear space. Study patients were followed longitudinally postoperatively to determine the incidence of posttympanostomy tube otorrhea. RESULTS: The incidence of pepsin in the middle ear cleft of the study group was 20% of patients and 14% of ears, which is significantly higher than 1.4% of control patients and 1.5% of control ears (P < .05). Study patients younger than 1 year had a higher rate of purulent effusions and pepsin in the middle ear cleft (P < .05). Patients with pepsin in the middle ear cleft were more likely to have an effusion at the time of surgery than patients without pepsin in the middle ear cleft (P < .05). There was no statistical association found between the presence of pepsin and clinical history of GERD, allergy, asthma, or posttympanostomy tube otorrhea. CONCLUSIONS: Pepsin is detectable in the middle ear cleft of 20% of pediatric patients with OM undergoing tympanostomy tube placement, compared with 1.4% of controls; recovery of pepsin in the middle ear space of pediatric patients with OM is an independent risk factor for OM. Patients under 1 year of age have a higher incidence of purulent effusions and pepsin-positive effusions. Clinical history of GERD, allergy, and asthma do not seem to correlate with evidence of EORD reaching the middle ear cleft. The presence of pepsin in the middle ear space at the time of tube placement does not seem to predispose to posttympanostomy tube otorrhea.

Range-free localization and its impact on large scale sensor networks

Tian He — 2006-11-02T22:55:16-00:00

Trans. on Embedded Computing Sys., Vol. 4, No. 4. (November 2005), pp. 877-906.

Influential publications in ecological economics: a citation analysis

Robert Costanza — 2008-07-22T21:30:56-00:00

Ecological Economics, Vol. 50, No. 3-4. (1 October 2004), pp. 261-292.

We assessed the degree of influence of selected papers and books in ecological economics using citation analysis. We looked at both the internal influence of publications on the field of ecological economics and the external influence of those same publications on the broader academic community. We used four lists of papers and books for the analysis: (1) 92 papers nominated by the Ecological Economics (EE) Editorial Board; (2) 71 papers that were published in EE and that received 15 or more citations in all journals included in the Institute for Scientific Information (ISI) Citation Index; (3) 57 papers that had been cited in EE 15 or more times; and (4) 77 monographs and edited books that had been cited in EE 15 or more times. In all, we analyzed 251 unique publications. For each publication, we counted the total number of ISI citations as well as the total number of citations in EE. We calculated the average number of citations per year to each paper since its publication in both the ISI database and in EE, along with the percentage of the total ISI citations that were in EE. Ranking the degree of influence of the publications can be done in several ways, including using the number of ISI citations, the number of EE citations or both. We discuss both the internal and external influence of publications and show how these influences might be considered jointly. We display and analyze the results in several ways. By plotting the ISI citations against the EE citations, we can identify those papers that are mainly influential in EE with some broader influence, those that are mainly influential in the broader literature but have also had influence on EE and other patterns of influence. There are both overlaps and interesting lacunae among the four lists that give us a better picture of the real influence of publications in ecological economics vs. perceptions of those publications' importance. By plotting the number of citations vs. dates of publication, we can identify those publications that are projected to be most influential. Plots of the time series of citations over the 1990-2003 period show a generally increasing trend (contrary to what one would expect for an "average" paper) for the top papers. We suggest that this pattern of increasing citations (and thus influence) over time is one hallmark of a "foundational" paper. Data used in the analysis is available for download from the International Society for Ecological Economics (ISEE) web site to allow further analysis by interested readers.