CiteULike: Author Ren

Expression, Purification, and Characterization of Human Cytosolic Serine Hydroxymethyltransferase

H Kruschwitz — 2008-08-06T22:13:47-00:00

Protein Expression and Purification, Vol. 6, No. 4. (August 1995), pp. 411-416.

A cDNA which codes for human cytosolic serine hydroxymethyltransferase (Garrow et al., 1993, J. Biol. Chem. 268, 11910-11916) has been cloned into a pT7-7 vector as a NdeI-EcoRI insert, HMS174 (de3) cells were transformed with this plasmid and, after induction with isopropyl thiogalactoside, expressed a catalytically active serine hydroxymethyltransferase. The enzyme was purified and shown to be the expressed human enzyme by N-terminal amino acid sequencing. About 225 mg of pure enzyme can be obtained from a 20-liter culture. Spectral characteristics of the bound pyridoxal phosphate were essentially identical to the spectral properties of rabbit cytosolic serine hydroxymethyltransferase. Kinetic constants for the natural substrates L-serine and tetrahydrofolate were also similar to the values obtained previously for the rabbit cytosolic enzyme.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Ray Ming — 2008-04-23T19:37:29-00:00

Nature, Vol. 452, No. 7190. (24 April 2008), pp. 991-996.

Finding failure-inducing changes in java programs using change classification

Maximilian Stoerzer — 2008-08-02T01:02:27-00:00

(2006), pp. 57-68.

Testing and code editing are interleaved activities during program development. When tests fail unexpectedly, the changes that caused the failure(s) are not always easy to find. We explore how change classification can focus programmer attention on failure-inducing changes by automatically labeling changes Red, Yellow, or Green, indicating the likelihood that they have contributed to a test failure. We implemented our change classification tool JUnit/CIA as an ex-tension to the JUnit component within Eclipse, and evaluated its effectiveness in two case studies. Our results indicate that change classification is an effective technique for finding failure-inducing changes.

beta-Arrestin 1 and Galphaq/11 coordinately activate RhoA and stress fiber formation following receptor stimulation.

WG Barnes — 2008-07-31T11:59:12-00:00

The Journal of biological chemistry, Vol. 280, No. 9. (4 March 2005), pp. 8041-8050.

beta-Arrestins were initially shown, in conjunction with G protein-coupled receptor kinases, to be involved in the desensitization and internalization of activated seven-transmembrane receptors. Recently, beta-arrestin 2 has been shown to act as a signal mediator in mitogen-activated protein kinase cascades and to play a positive regulatory role in chemotaxis. We now show that beta-arrestin 1 is required to activate the small GTPase RhoA leading to the re-organization of stress fibers following the activation of the angiotensin II type 1A receptor. This angiotensin II type 1A receptor-directed RhoA activation and stress fiber formation also require the activation of the heterotrimeric G protein G(alphaq/11). Whereas neither beta-arrestin 1 nor G(alphaq/11) activation alone is sufficient to robustly activate RhoA, the concurrent recruitment of beta-arrestin 1 and activation of G(alphaq/11) leads to full activation of RhoA and to the subsequent formation of stress fibers.

Valence bond glass -- A unified theory of electronic disorder and pseudogap phenomena in high temperature superconductors

Liang Ren — 2008-07-30T17:50:37-00:00

(29 Jul 2008)

We show that the low-energy fluctuations of the valence bond in underdoped high-T_c cuprates, originating from quantum fluctuations of the superexchange interaction, are pinned by the electronic disorder due to off-stoichiometric dopants, leading to a valence bond glass (VBG) pseudogap phase. The antinodal Fermi surface sections are gapped out, giving rise to a normal state Fermi arc whose length shrinks with underdoping below a temperature T* determined by thermal filling. Below T_c, the superexchange interaction induces a d-wave superconducting gap that coexists with the VBG pseudogap. The evolution of the local and momentum-space spectroscopy with doping and temperature captures the salient properties of the pseudogap phenomena and the electronic disorder revealed by recent ARPES and STM experiments. Our unified theory elucidates the interplay between strong correlation and the intrinsic electronic disorder in doped transition metal oxides.

Transcriptional regulatory networks in Saccharomyces cerevisiae

TI Lee — 2004-12-06T15:36:56-00:00

Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804.

We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators.

Molecular diversity and phylogeny of Hantaan virus in Guizhou, China: evidence for Guizhou as a radiation center of the present Hantaan virus.

Y Zou — 2008-07-30T10:47:10-00:00

The Journal of general virology, Vol. 89, No. Pt 8. (August 2008), pp. 1987-1997.

To gain further insight into the molecular epidemiology of Hantaan virus (HTNV) in Guizhou, China, rodents were captured in this region in 2004 and 2005. In addition, serum samples were collected from four patients. Ten hantaviruses were isolated successfully in cell culture from four humans, two Apodemus agrarius, three Rattus norvegicus and one Rattus nitidus. The nucleotide sequences for their small (S), medium (M) and partial large (L) segments were determined. Phylogenetic analysis of the S and M segment sequences revealed that all of these isolates belong to the species HTNV, suggesting a spillover of HTNV from A. agrarius to Rattus rats. All available isolates from Guizhou were divided into four distinct groups either in the S segment tree or in the M segment tree. The clustering pattern of these isolates in the S segment tree was not in agreement with that in the M or L segment tree, showing that genetic reassortment between HTNV had occurred naturally. Analysis of the S segment sequences from available HTNV strains indicated that they formed three clades. The first clade, which comprised only viruses from Guizhou, was the outgroup of clades II and III. The viruses in the second clade were found in Guizhou and mainly in the far-east Asian region, including China. However, the viruses in the third clade were found in most areas of China, including Guizhou, in which haemorrhagic fever with renal syndrome (HFRS) is endemic. Our results reveal that the highest genetic diversity of HTNV is in a limited geographical region of Guizhou, and suggest that Guizhou might be a radiation centre of the present form of HTNV.

Genome-Wide Location and Function of DNA Binding Proteins

Bing Ren — 2006-06-28T21:52:27-00:00

Science, Vol. 290, No. 5500. (22 December 2000), pp. 2306-2309.

10.1126/science.290.5500.2306

Discretely guided electromagnetic effective medium

K Kempa — 2008-07-28T11:43:25-00:00

(22 Oct 2007)

A material comprised of an array of subwavelength coaxial waveguides decomposes incident electromagnetic waves into spatially discrete wave components, propagates these components without frequency cut-off, and reassembles them on the far side of the material. The propagation of these wave components is fully controlled by the physical properties of the waveguides and their geometrical distribution in the array. This allows for an exceptional degree of control over the electromagnetic response of this effective medium, with numerous potential applications. With the development of nanoscale subwavelength coaxial waveguides, these applications (including metamaterial functionality) can be enabled in the visible frequency range.

Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice.

DE Fouts — 2008-07-28T10:15:58-00:00

PLoS genetics, Vol. 4, No. 7. (July 2008)

We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. Genomic analysis examined K. pneumoniae 342 for the presence of previously identified genes from other bacteria involved in colonization of, or growth in, plants. From this set, approximately one-third were identified in K. pneumoniae 342, suggesting additional factors most likely contribute to its endophytic lifestyle. Comparative genome analyses were used to provide new insights into this question. Results included the identification of metabolic pathways and other features devoted to processing plant-derived cellulosic and aromatic compounds, and a robust complement of transport genes (15.4%), one of the highest percentages in bacterial genomes sequenced. Although virulence and antibiotic resistance genes were predicted, experiments conducted using mouse models showed pathogenicity to be attenuated in this strain. Comparative genomic analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed that MGH78578 apparently cannot fix nitrogen, and the distribution of genes essential to surface attachment, secretion, transport, and regulation and signaling varied between each genome, which may indicate critical divergences between the strains that influence their preferred host ranges and lifestyles (endophytic plant associations for K. pneumoniae 342 and presumably human pathogenesis for MGH78578). Little genome information is available concerning endophytic bacteria. The K. pneumoniae 342 genome will drive new research into this less-understood, but important category of bacterial-plant host relationships, which could ultimately enhance growth and nutrition of important agricultural crops and development of plant-derived products and biofuels.

The branch processes of vortex filaments and Hopf Invariant Constraint on Scroll Wave

Tao Zhu — 2008-07-25T14:44:08-00:00

(24 Jul 2008)

In this paper, by making use of Duan's topological current theory, the evolution of the vortex filaments in excitable media is discussed in detail. The vortex filaments are found generating or annihilating at the limit points and encountering, splitting, or merging at the bifurcation points of a complex function $Z(ecx,t)$. It is also shown that the Hopf invariant of knotted scroll wave filaments is preserved in the branch processes (splitting, merging, or encountering) during the evolution of these knotted scroll wave filaments. Furthermore, it also revealed that the "exclusion principle" in some chemical media is just the special case of the Hopf invariant constraint, and during the branch processes the "exclusion principle" is also protected by topology.

Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation.

X Ren — 2008-07-24T14:54:01-00:00

Molecular and cellular biology, Vol. 28, No. 9. (May 2008), pp. 2884-2895.

Polycomb group (PcG) transcription regulatory proteins maintain cell identity by sustained repression of numerous genes. The differentiation of embryonic stem (ES) cells induces a genome-wide shift in PcG target gene expression. We investigated the effects of differentiation and protein interactions on CBX family PcG protein localization and dynamics by using fluorescence imaging. In mouse ES cells, different CBX proteins exhibited distinct distributions and mobilities. Most CBX proteins were enriched in foci known as Polycomb bodies. Focus formation did not affect CBX protein mobilities, and the foci dispersed during ES cell differentiation. The mobilities of CBX proteins increased upon the induction of differentiation and decreased as differentiation progressed. The deletion of the chromobox, which mediates interactions with RING1B, prevented the immobilization of CBX proteins. In contrast, the deletion of the chromodomain, which can bind trimethylated lysine 27 of histone H3, had little effect on CBX protein dynamics. The distributions and mobilities of most CBX proteins corresponded to those of CBX-RING1B complexes detected by using bimolecular fluorescence complementation analysis. Epigenetic reprogramming during ES cell differentiation is therefore associated with global changes in the subnuclear distributions and dynamics of CBX protein complexes.

Genome-wide mapping of allele-specific protein-DNA interactions in human cells

Nathaniel Maynard — 2008-03-28T16:35:47-00:00

Nature Methods, Vol. 5, No. 4. (16 March 2008), pp. 307-309.

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs

Leah Barrera — 2007-11-30T07:05:35-00:00

Genome Res. (27 November 2007), gr.6654808.

By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic stem cells (mES) as well as adult brain, heart, kidney, and liver. We identified [~]24,000 promoters across these samples, including 16,976 annotated mRNA 5' ends and 5153 additional sites validating cap-analysis of gene expression (CAGE) 5' end data. We showed that promoters with CpG islands are typically non-tissue specific, with the majority associated with Polr2a and the active chromatin modifications in nearly all the tissues examined. By contrast, the promoters without CpG islands are generally associated with Polr2a and the active chromatin marks in a tissue-dependent way. We defined 4396 tissue-specific promoters by adapting a quantitative index of tissue-specificity based on Polr2a occupancy. While there is a general correspondence between Polr2a occupancy and active chromatin modifications at the tissue-specific promoters, a subset of them appear to be persistently marked by active chromatin modifications in the absence of detectable Polr2a binding, highlighting the complexity of the functional relationship between chromatin modification and gene expression. Our results provide a resource for exploring promoter Polr2a binding and epigenetic states across pluripotent and differentiated cell types in mammals. 10.1101/gr.6654808

Talk amongst yourselves: inviting users to participate in online conversations

Maxwell Harper — 2007-02-03T17:47:50-00:00

(2007), pp. 62-71.

Association between microsatellites within the human MHC and nasopharyngeal carcinoma.

EE Ooi — 2008-07-16T07:29:00-00:00

International journal of cancer. Journal international du cancer, Vol. 74, No. 2. (22 April 1997), pp. 229-232.

Nasopharyngeal carcinoma (NPC) has been known to be associated with specific HLA haplotypes, in particular HLA A2, B46 and A33, B58 haplotypes. A linkage study based on this observation suggested that HLA antigens are not the cause of NPC but that there exists a gene that lies close to if not within the major histocompatibility complex locus and confers a greatly increased relative risk of NPC. Since then, no further work has elucidated the presence of this gene. One of the difficulties faced by researchers has been the size of the region of chromosome implicated. The MHC locus alone is almost 4 Mb in length, and the number of genes encoded within it is numerous. The purpose of our study was thus to reduce the region of DNA in which the NPC susceptibility gene is likely to be. We report that the NPC susceptibility gene may be within the centromeric end of the class-1 and the telomeric end of the class-III regions of the MHC, near the D6S1624 microsatellite locus, where the presence of allele 4 of the microsatellite conferred a 3 1/2-fold increase in the risk of NPC, the highest reported for a single locus, and the presence of allele 1 of the same microsatellite conferred a highly significant protective effect against NPC.

Targeted oligonucleotide-mediated microsatellite identification (TOMMI) from large-insert library clones.

K Chen — 2008-07-22T15:00:38-00:00

BMC genetics, Vol. 6 (2005)

BACKGROUND: In the last few years, microsatellites have become the most popular molecular marker system and have intensively been applied in genome mapping, biodiversity and phylogeny studies of livestock. Compared to single nucleotide polymorphism (SNP) as another popular marker system, microsatellites reveal obvious advantages. They are multi-allelic, possibly more polymorphic and cheaper to genotype. Calculations showed that a multi-allelic marker system always has more power to detect Linkage Disequilibrium (LD) than does a di-allelic marker system. Traditional isolation methods using partial genomic libraries are time-consuming and cost-intensive. In order to directly generate microsatellites from large-insert libraries a sequencing approach with repeat-containing oligonucleotides is introduced. RESULTS: Seventeen porcine microsatellite markers were isolated from eleven PAC clones by targeted oligonucleotide-mediated microsatellite identification (TOMMI), an improved efficient and rapid flanking sequence-based approach for the isolation of STS-markers. With the application of TOMMI, an average of 1.55 (CA/GT) microsatellites per PAC clone was identified. The number of alleles, allele size distribution, polymorphism information content (PIC), average heterozygosity (HT), and effective allele number (NE) for the STS-markers were calculated using a sampling of 336 unrelated animals representing fifteen pig breeds (nine European and six Chinese breeds). Sixteen of the microsatellite markers proved to be polymorphic (2 to 22 alleles) in this heterogeneous sampling. Most of the publicly available (porcine) microsatellite amplicons range from approximately 80 bp to 200 bp. Here, we attempted to utilize as much sequence information as possible to develop STS-markers with larger amplicons. Indeed, fourteen of the seventeen STS-marker amplicons have minimal allele sizes of at least 200 bp. Thus, most of the generated STS-markers can easily be integrated into multilocus assays covering a broader separation spectrum. Linkage mapping results of the markers indicate their potential immediate use in QTL studies to further dissect trait associated chromosomal regions. CONCLUSION: The sequencing strategy described in this study provides a targeted, inexpensive and fast method to develop microsatellites from large-insert libraries. It is well suited to generate polymorphic markers for selected chromosomal regions, contigs of overlapping clones and yields sufficient high quality sequence data to develop amplicons greater than 250 bases.

E2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpoints

Bing Ren — 2006-02-07T20:42:19-00:00

Genes Dev., Vol. 16, No. 2. (15 January 2002), pp. 245-256.

The E2F transcription factor family is known to play a key role in the timely expression of genes required for cell cycle progression and proliferation, but only a few E2F target genes have been identified. We explored the possibility that E2F regulators play a broader role by identifying additional genes bound by E2F in living human cells. A protocol was developed to identify genomic binding sites for DNA-binding factors in mammalian cells that combines immunoprecipitation of cross-linked protein-DNA complexes with DNA microarray analysis. Among ~1200 genes expressed during cell cycle entry, we found that the promoters of 127 were bound by the E2F4 transcription factor in primary fibroblasts. A subset of these targets was also bound by E2F1. Most previously identified target genes known to have roles in DNA replication and cell cycle control and represented on the microarray were confirmed by this analysis. We also identified a remarkable cadre of genes with no previous connection to E2F regulation, including genes that encode components of the DNA damage checkpoint and repair pathways, as well as factors involved in chromatin assembly/condensation, chromosome segregation, and the mitotic spindle checkpoint. Our data indicate that E2F directly links cell cycle progression with the coordinate regulation of genes essential for both the synthesis of DNA as well as its surveillance.

Second-order splitting schemes for a class of reactive systems

Zhuyin Ren — 2008-07-21T16:41:32-00:00

Journal of Computational Physics, Vol. 227, No. 17. (1 September 2008), pp. 8165-8176.

We consider the numerical time integration of a class of reaction-transport systems that are described by a set of ordinary differential equations for primary variables. In the governing equations, the terms involved may require the knowledge of secondary variables, which are functions of the primary variables. Specifically, we consider the case where, given the primary variables, the evaluation of the secondary variables is computationally expensive. To solve this class of reaction-transport equations, we develop and demonstrate several computationally efficient splitting schemes, wherein the portions of the governing equations containing chemical reaction terms are separated from those parts containing the transport terms. A computationally efficient solution to the transport sub-step is achieved through the use of linearization or predictor-corrector methods. The splitting schemes are applied to the reactive flow in a continuously stirred tank reactor (CSTR) with the Davis-Skodjie reaction model, to the CO+H2 oxidation in a CSTR with detailed chemical kinetics, and to a reaction-diffusion system with an extension of the Oregonator model of the Belousov-Zhabotinsky reaction. As demonstrated in the test problems, the proposed splitting schemes, which yield efficient solutions to the transport sub-step, achieve second-order accuracy in time.

Recovering human body configurations: combining segmentation and recognition

G Mori — 2008-07-21T08:22:52-00:00

Computer Vision and Pattern Recognition, 2004. CVPR 2004. Proceedings of the 2004 IEEE Computer Society Conference on, Vol. 2 (2004), pp. II-326-II-333 Vol.2.

The goal of this work is to detect a human figure image and localize his joints and limbs along with their associated pixel masks. In this work we attempt to tackle this problem in a general setting. The dataset we use is a collection of sports news photographs of baseball players, varying dramatically in pose and clothing. The approach that we take is to use segmentation to guide our recognition algorithm to salient bits of the image. We use this segmentation approach to build limb and torso detectors, the outputs of which are assembled into human figures. We present quantitative results on torso localization, in addition to shortlisted full body configurations.

Learning a Classification Model for Segmentation

Xiaofeng Ren — 2008-07-21T08:10:49-00:00

(2003)

Consensus seeking in multiagent systems under dynamically changing interaction topologies

Wei Ren — 2008-07-18T02:24:21-00:00

Automatic Control, IEEE Transactions on, Vol. 50, No. 5. (2005), pp. 655-661.

This note considers the problem of information consensus among multiple agents in the presence of limited and unreliable information exchange with dynamically changing interaction topologies. Both discrete and continuous update schemes are proposed for information consensus. This note shows that information consensus under dynamically changing interaction topologies can be achieved asymptotically if the union of the directed interaction graphs have a spanning tree frequently enough as the system evolves.

A survey of consensus problems in multi-agent coordination

Wei Ren — 2008-07-16T21:07:35-00:00

American Control Conference, 2005. Proceedings of the 2005 (2005), pp. 1859-1864 vol. 3.

As a distributed solution to multi-agent coordination, consensus or agreement problems have been studied extensively in the literature. This paper provides a survey of consensus problems in multi-agent cooperative control with the goal of promoting research in this area. Theoretical results regarding consensus seeking under both time-invariant and dynamically changing information exchange topologies are summarized. Applications of consensus protocols to multiagent coordination are investigated. Future research directions and open problems are also proposed.

Gramene: a bird's eye view of cereal genomes.

P Jaiswal — 2008-07-16T12:08:18-00:00

Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006)

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication.

Gramene: a growing plant comparative genomics resource

Chengzhi Liang — 2007-11-28T10:54:50-00:00

Nucl. Acids Res. (4 November 2007), gkm968.

Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions. 10.1093/nar/gkm968

Strain Effect on Energy Gaps of Armchair Graphene Nanoribbons

Lian Sun — 2008-07-16T09:01:59-00:00

(30 Mar 2007)

We report a first-principles study on electronic structures of the deformed armchair graphene nanoribbons (AGNRs). The variation of the energy gap of AGNRs as a function of uniaxial strain displays a zigzag pattern, which indicates that the energy gaps of AGNRs can be effectively tuned. The spatial distributions of two occupied and two empty subbands close to the Fermi level are swapped under different strains. The tunable width of energy gaps becomes narrower as increasing the width of AGNRs. Our simulations with tight binding approximation, including the nearest neighbor hopping integrals between $π$- orbitals of carbon atoms, reproduce these results by first-principles calculations. One simple empirical formula is obtained to describe the scaling behavior of the maximal value of energy gap as a function of the width of AGNRs.

Tuning the electronic structures of armchair graphene nanoribbons through chemical edge modification: A theoretical study

ZF Wang — 2008-07-16T08:54:37-00:00

(30 Mar 2007)

We report combined first-principle and tight-binding (TB) calculations to simulate the effects of chemical edge modifications on structural and electronic properties. The C-C bond lengths and bond angles near the GNR edge have considerable changes when edge carbon atoms are bounded to different atoms. By introducing a phenomenological hopping parameter $t_1$ for nearest-neighboring hopping to represent various chemical edge modifications, we investigated the electronic structural changes of nanoribbons with different widths based on the tight-binding scheme. Theoretical results show that addends can change the band structures of armchair GNRs and even result in observable metal-to-insulator transition.

PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites

Florian Gnad — 2007-11-26T23:36:31-00:00

Genome Biology, Vol. 8, No. 11. (2007)

PHOSIDA http://www.phosida.com, a phosphorylation site database, integrates thousands of high-confidence in-vivo phosphosites identified by mass spectrometry-based proteomics in various species. For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites.

Angular dependence of resistivity in the superconducting state of NdFeAsO$_0.82$F$_0.18$ single crystals

Ying Jia — 2008-07-10T01:51:47-00:00

(9 Jul 2008)

We report the results of angle dependent resistivity of NdFeAsO$_0.82$F$_0.18$ single crystals in the superconducting state. By doing the scaling of resistivity within the frame of the anisotropic Ginzburg-Landau theory, it is found that the angle dependent resistivity measured under different magnetic fields at a certain temperature can be collapsed onto one curve. As a scaling parameter, the anisotropy $Γ$ can be determined for different temperatures. It is found that $Γ(T)$ increases slowly with decreasing temperature, varying from $Γ ∼eq$ 5.48 at T=50 K to $Γ ∼eq$ 6.24 at T=44 K. This temperature dependence can be understood within the picture of multi-band superconductivity.

Electromagnetic Fluctuations during Fast Reconnection in a Laboratory Plasma

Hantao Ji — 2008-07-08T15:53:47-00:00

Physical Review Letters, Vol. 92, No. 11. (18 March 2004), 115001.

Ischemic preconditioning suppresses apoptosis of rabbit spinal neurocytes by inhibiting ASK1-14-3-3 dissociation.

Chengwei Yang — 2008-07-08T13:17:32-00:00

Neuroscience letters (18 June 2008)

The mechanism by which a brief episode of sublethal ischemia followed by reperfusion (ischemic preconditioning, IPC) prevents the lethal effects of subsequent periods of prolonged ischemia, are poorly understood. A completely randomized, controlled study was designed to study the effect of IPC using a rabbit model of ischemic spinal cord injury. Twenty-four white adult New England rabbits were randomly assigned to one of 3 groups (n=8 per group); the groups were assigned as follows: Group I: sham-operation group, Group II: ischemic reperfusion (I/R) group, and Group III: ischemic preconditioning group. Spinal cord ischemia was induced by introducing an infra renal aortic cross-clamp for 30min. Following injury, rabbits were subjected to 30min, 2h, or 8h of reperfusion in Group II. In Group III, subjects underwent three cycles, 5min each, of ischemia followed by 5min of reperfusion, before receiving 30min of ischemia. We previously reported that the association between ASK1 (apoptosis signal-regulating kinase 1) and 14-3-3 played an important role in regulating ischemia/reperfusion spinal cord injuries. To evaluate the effect of ischemic preconditioning in injured spinal cords, we examined alterations in spinal tissue morphology, activation of key members of the ASK1-mediated signaling pathway, and the association between ASK1 and 14-3-3. Changes in spinal cord morphology were observed with hematoxylin and eosin (H&E) staining and electron microscopy. The phosphorylation levels of ASK1, JNK, and p38 were assessed by immunoblot analysis. The association between ASK1 and 14-3-3 was analyzed by co-immunoprecipitation experiments. We observed that swelling of the neurocyte bodies and hemorrhage of the spinal cord were dramatically decreased in Group III compared to Group II. In addition, the degree of apoptosis among neurocytes was reduced in Group III compared to Group II. Finally, the phosphorylation of ASK1, JNK, p38 and the dissociation of ASK1 from 14-3-3 were dramatically decreased in Group III compared with Group II. These results indicate that ischemic preconditioning may have a protective affect against ASK1/14-3-3 dissociation-induced spinal cord injuries.

Calculation of protein-ligand binding free energy by using a polarizable potential

Dian Jiao — 2008-04-29T17:41:01-00:00

Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295.

The binding of charged ligands benzamidine and diazamidine to trypsin was investigated by using a polarizable potential energy function and explicit-water molecular dynamics simulations. The binding free energies were computed from the difference between the free energies of decoupling the ligand from water and protein environments. Both the absolute and the relative free energies from the perturbation simulations agree with experimental measurements to within 0.5 kcalmiddle dotmol-1. Comparison of free-energy components sampled from different thermodynamic paths indicates that electrostatics is the main driving force behind benzamidine recognition of trypsin. The contribution of electronic polarization to binding appears to be crucial. By computing the free-energy contribution caused by the polarization between the ligand and its surroundings, we found that polarization has the opposite effect in dissimilar environments. Although polarization favors ligand solvation in water, it weakens the protein-ligand attraction by screening the electrostatic interaction between trypsin and benzamidine. We also examined the relative binding free energies of a benzamidine analog diazamidine to trypsin. The changes in free energy on benzamidine-diazamidine substitution were tens of kilocalories in both water and trypsin environments; however, the change in the total binding free energy is <2 kcalmiddle dotmol-1 because of cancellation, consistent with the experimental results. Overall, our results suggest that the use of a polarizable force field, given adequate sampling, is capable of achieving chemical accuracy in molecular simulations of protein-ligand recognition. 10.1073/pnas.0711686105

The research of the distributed stripped storage spatial model

Qingsong Wei — 2008-07-05T08:40:03-00:00

SIGOPS Oper. Syst. Rev., Vol. 38, No. 1. (January 2004), pp. 90-96.

Constructing an Ontology for a Research Program from a Knowledge Science Perspective

Jing Tian — 2007-11-15T21:33:11-00:00

Knowledge Science, Engineering and Management (2007), pp. 372-383.

Although ontologies as an important component are widely used for different purpose in different communities and a number of approaches have been reported for developing ontologies, few works have been done to clarify the concept of knowledge science as far as we know. This paper presents a novel attempt to create an ontology characterizing a research program “Technology Creation Based on Knowledge Science” from a Knowledge Science perspective. We address a combination of bottom-up and top-down approaches to ontology creation, which is a first time to put forward a perspective of combining explicit knowledge with tacit, intuitive and experiential knowledge for constructing an ontology. An example of application of this ontology, related to a software tool named adaptive hermeneutic agent (AHA), is also given in the paper.

Specialized Inhibitory Synaptic Actions Between Nearby Neocortical Pyramidal Neurons

Ming Ren — 2007-05-05T06:14:40-00:00

Science, Vol. 316, No. 5825. (4 May 2007), pp. 758-761.

We found that, in the mouse visual cortex, action potentials generated in a single layer-2/3 pyramidal (excitatory) neuron can reliably evoke large, constant-latency inhibitory postsynaptic currents in other nearby pyramidal cells. This effect is mediated by axo-axonic ionotropic glutamate receptor-mediated excitation of the nerve terminals of inhibitory interneurons, which connect to the target pyramidal cells. Therefore, individual cortical excitatory neurons can generate inhibition independently from the somatic firing of inhibitory interneurons. 10.1126/science.1135468

Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain.

E Spiteri — 2008-07-02T14:45:29-00:00

American journal of human genetics, Vol. 81, No. 6. (December 2007), pp. 1144-1157.

Mutations in FOXP2, a member of the forkhead family of transcription factor genes, are the only known cause of developmental speech and language disorders in humans. To date, there are no known targets of human FOXP2 in the nervous system. The identification of FOXP2 targets in the developing human brain, therefore, provides a unique tool with which to explore the development of human language and speech. Here, we define FOXP2 targets in human basal ganglia (BG) and inferior frontal cortex (IFC) by use of chromatin immunoprecipitation followed by microarray analysis (ChIP-chip) and validate the functional regulation of targets in vitro. ChIP-chip identified 285 FOXP2 targets in fetal human brain; statistically significant overlap of targets in BG and IFC indicates a core set of 34 transcriptional targets of FOXP2. We identified targets specific to IFC or BG that were not observed in lung, suggesting important regional and tissue differences in FOXP2 activity. Many target genes are known to play critical roles in specific aspects of central nervous system patterning or development, such as neurite outgrowth, as well as plasticity. Subsets of the FOXP2 transcriptional targets are either under positive selection in humans or differentially expressed between human and chimpanzee brain. This is the first ChIP-chip study to use human brain tissue, making the FOXP2-target genes identified in these studies important to understanding the pathways regulating speech and language in the developing human brain. These data provide the first insight into the functional network of genes directly regulated by FOXP2 in human brain and by evolutionary comparisons, highlighting genes likely to be involved in the development of human higher-order cognitive processes.

The reporting quality of meta-analyses improves: a random sampling study

Jin Wen — 2008-06-30T17:44:35-00:00

Journal of Clinical Epidemiology, Vol. 61, No. 8. (August 2008), pp. 770-775.

Objectives To determine the overall quality of reporting of meta-analyses (QUOROMs) of randomized controlled trials (RCTs) based on the QUOROM statement, to compare the reporting quality of paper-based articles and Cochrane reviews, and to determine whether compliance with the statement improves over time.Study Design and Setting A random sample of systematic reviews or meta-analyses of RCTs was selected from Medline (2000-2005).Results A total of 161 articles were included. The mean QUOROM score was 12.3 (95% confidence interval [CI]: 12.0, 12.6), which rose from 10.5 (95% CI: 8.8, 12.1) in 2000 to 13.0 (95% CI: 12.2, 13.8) in 2005. The mean QUOROM scores of Cochrane reviews and paper-based articles were 14.2 (95% CI: 13.9, 14.5) and 11.7 (95% CI: 11.3, 12.1), respectively. Compared with the paper-based articles, the Cochrane reviews had better reporting quality in the abstract section, while the quality of their trial flows was poor. The fulfillment of most QUOROM items improved with time. A linear relation of the QUOROM score with time was revealed.Conclusions The reporting quality of meta-analyses improves with time. The reporting quality of Cochrane reviews is better compared with paper-based articles. Room still exists for improvements in the reporting quality of both Cochrane and paper-based articles.

Up-regulated HIF-1alpha is involved in the hypoxic tolerance induced by hyperbaric oxygen preconditioning.

Z Peng — 2008-06-29T22:48:36-00:00

Brain research, Vol. 1212 (30 May 2008), pp. 71-78.

Hyperbaric oxygen preconditioning (HBO-PC) has been shown to be effective in preventing hypoxic injuries in many animal models. The aim of the present study was to examine the hypoxic tolerance induced by HBO-PC and to explore the role of hypoxia-inducible factor-1alpha (HIF-1alpha) in a global hypoxia model. Male mice received HBO-PC before hypoxia exposure and swimming. HBO-PC significantly prolonged the survival time and the tolerance time of swimming under normobaric hypoxia. HBO-PC increased the protein content of HIF-1alpha and erythropoietin (EPO) in the cerebral cortex and hippocampus and prevented the changes of blood brain barrier (BBB) permeability and brain edema caused by hypoxia exposure. The results suggested that HBO-PC induced hypoxic tolerance in mice via up-regulation of HIF-1alpha and its downstream genes.

Comparative genomics of emerging human ehrlichiosis agents.

JC Hotopp — 2008-06-26T22:19:23-00:00

PLoS genetics, Vol. 2, No. 2. (February 2006)

Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens.

Temperature-stress phase diagram of strain glass Ti48.5Ni51.5

Y Wang — 2008-06-24T12:25:31-00:00

Acta Materialia, Vol. 56, No. 12. (July 2008), pp. 2885-2896.

The temperature and stress dependence of the properties of a recently discovered strain glass Ti48.5Ni51.5, which is a glass of frozen local lattice strains, was investigated systematically. It was found that the ideal freezing temperature (T0) of the strain glass decreases with increasing stress. When the stress exceeds a critical value [sigma]c(T), the pseudo-B2 strain glass transforms into B19' martensite. However, the stress-strain behavior associated with such a stress-induced transition showed a crossover at a crossover temperature TCR, which is ~20 K below T0. Above TCR, the sample showed superelastic behavior; however, below TCR, the sample demonstrated plastic behavior. More interestingly, the [sigma]c vs. temperature relation for unfrozen strain glass obeys the Clausius-Clapyeron relationship, whereas that for frozen strain glass disobeys this universal thermodynamic law. A phenomenological explanation is provided for all the phenomena observed, and it is shown that all the anomalous effects come from the broken ergodicity of the glass system and a temperature-dependent relative stability of the martensitic phase. Based on experimental observations, a temperature-stress phase diagram is constructed for this strain glass, which may serve as a guide map for understanding and predicting the properties of strain glass.

Combined Lithium And Valproate Treatment Delays Disease Onset, Reduces Neurological Deficits And Prolongs Survival In An Als Mouse Model

HL Feng — 2008-06-23T10:32:45-00:00

Neuroscience, Vol. In Press, Accepted Manuscript

Using semantic caching to manage location dependent data in mobile computing

Qun Ren — 2008-06-20T06:02:32-00:00

(2000), pp. 210-221.

AMP kinase is required for mitochondrial biogenesis in skeletal muscle in response to chronic energy deprivation.

H Zong — 2008-06-20T00:18:06-00:00

Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 25. (10 December 2002), pp. 15983-15987.

Mitochondrial biogenesis is a critical adaptation to chronic energy deprivation, yet the signaling mechanisms responsible for this response are poorly understood. To examine the role of AMP-activated protein kinase (AMPK), an evolutionarily conserved fuel sensor, in mitochondrial biogenesis we studied transgenic mice expressing a dominant-negative mutant of AMPK in muscle (DN-AMPK). Both DN-AMPK and WT mice were treated with beta-guanidinopropionic acid (GPA), a creatine analog, which led to similar reductions in the intramuscular ATPAMP ratio and phosphocreatine concentrations. In WT mice, GPA treatment resulted in activation of muscle AMPK and mitochondrial biogenesis. However, the same GPA treatment in DN-AMPK mice had no effect on AMPK activity or mitochondrial content. Furthermore, AMPK inactivation abrogated GPA-induced increases in the expression of peroxisome proliferator-activated receptor gamma coactivator 1alpha and calciumcalmodulin-dependent protein kinase IV (both master regulators of mitochondrial biogenesis). These data demonstrate that by sensing the energy status of the muscle cell, AMPK is a critical regulator involved in initiating mitochondrial biogenesis.

PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.

W Gong — 2008-06-19T19:31:58-00:00

Nucleic acids research, Vol. 36, No. Database issue. (January 2008)

Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P approximately PEP is a newly constructed database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions. Our motivation is to provide the research community with a rich information source emphasizing the reported, experimentally validated data for specific PPBD-PPEP interactions. This information is not only useful for designing, comparing and validating the relevant experiments, but it also serves as a knowledge-base for computationally constructing systems signaling pathways and networks. PepCyber:P approximately PEP is accessible through the URL, http://www.pepcyber.org/PPEP/. The current release of the database contains 7044 PPBD-mediated interactions involving 337 PPBD-containing proteins and 1123 substrate proteins.

Chaperone-dependent amyloid assembly protects cells from prion toxicity

Peter Douglas — 2008-05-21T12:07:12-00:00

Proceedings of the National Academy of Sciences, Vol. 105, No. 20. (20 May 2008), pp. 7206-7211.

Protein conformational diseases are associated with the aberrant accumulation of amyloid protein aggregates, but whether amyloid formation is cytotoxic or protective is unclear. To address this issue, we investigated a normally benign amyloid formed by the yeast prion [RNQ+]. Surprisingly, modest overexpression of Rnq1 protein was deadly, but only when preexisting Rnq1 was in the [RNQ+] prion conformation. Molecular chaperones protect against protein aggregation diseases and are generally believed to do so by solubilizing their substrates. The Hsp40 chaperone, Sis1, suppressed Rnq1 proteotoxicity, but instead of blocking Rnq1 protein aggregation, it stimulated conversion of soluble Rnq1 to [RNQ+] amyloid. Furthermore, interference with Sis1-mediated [RNQ+] amyloid formation exacerbated Rnq1 toxicity. These and other data establish that even subtle changes in the folding homeostasis of an amyloidogenic protein can create a severe proteotoxic gain-of-function phenotype and that chaperone-mediated amyloid assembly can be cytoprotective. The possible relevance of these findings to other phenomena, including prion-driven neurodegenerative diseases and heterokaryon incompatibility in fungi, is discussed. 10.1073/pnas.0802593105

Broadband ZnO Single-Nanowire Light-Emitting Diode

J Bao — 2008-06-18T08:47:16-00:00

Nano Lett., Vol. 6, No. 8. (9 August 2006), pp. 1719-1722.

Abstract: We present a novel technique for reliable electrical injection into single semiconductor nanowires for light-emitting diodes and lasers. The method makes use of a high-resolution negative electron-beam resist and direct electron-beam patterning for the precise fabrication of a metallic top contact along the length of the nanowire, while a planar substrate is used as a bottom contact. It can be applied to any nanowire structure with an arbitrary cross section. We demonstrate this technique by constructing the first zinc oxide single-nanowire light-emitting diode. The device exhibits broad sub-bandgap emission at room temperature.

Low Temperature Processable Ultra-Low Dielectric Porous Polyimide for High Frequency Applications

Yuxing Ren — 2008-06-18T08:04:48-00:00

Electronic Materials and Packaging, 2006. EMAP 2006. International Conference on (2006), pp. 1-5.

Ultra-low dielectric porous polymer coatings reduce electrical losses of high speed and high frequency circuitries. In this investigation, a room temperature process to produce ultra-low dielectric polyimide films was developed. The films have low elastic properties which reduce thermal stresses and package warpage. The dielectric properties of the porous polyimide were characterized at 100 KHz as well as between 8.2 and 18 GHz. Results showed that the dielectric constant reached as low as 1.67 in high porosity films. The results indicate that the high frequency dielectric properties are stable and the films are suited for use in wide band applications. On the basis of the improved properties, the usages of low temperature processable ultra-low-k polyimide in advanced applications are discussed.

WLC17-6: An Enhanced Energy Saving Mechanism in IEEE 802.16e

Junfeng Xiao — 2008-06-16T22:16:57-00:00

Global Telecommunications Conference, 2006. GLOBECOM '06. IEEE (2006), pp. 1-5.

Discrimination between serous low malignant potential and invasive epithelial ovarian tumors using molecular profiling

Véronique Ouellet — 2005-06-06T20:24:52-00:00

Oncogene, Vol. aop, No. current.

Characterizations of elastic behaviors of silicon nitride thin films with varying thicknesses

Yuxing Ren — 2008-06-11T07:35:03-00:00

Materials Science and Engineering: A, Vol. 467, No. 1-2. (15 October 2007), pp. 93-96.

The microstructure and composition of submicron silicon nitride films directly affect the mechanical behaviors of beams with different thicknesses. LPCVD silicon nitride beams were fabricated and bending tests were conducted to examine the size dependence. Bending results showed that the elastic moduli of the beams varied with thickness. X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) analyses revealed that crystalline phase fractions varied with thicknesses. The beams were annealed and bending tests were conducted to investigate the effect of crystalline phase fractions. XRD results showed that crystalline phase fractions increased for all thicknesses after annealing, but the elastic modulus fluctuations did not change significantly before and after annealing. The differences in crystallinity are insufficient to induce significant effect in elastic properties. Size dependence of the elastic modulus of LPCVD silicon nitride is insignificant in the submicron scale.