CiteULike: Author Li

Security-constrained unit commitment for simultaneous clearing of energy and ancillary services markets

Zuyi Li — 2006-08-07T13:17:59-00:00

Power Systems, IEEE Transactions on, Vol. 20, No. 2. (2005), pp. 1079-1088.

This paper introduces a security-constrained unit commitment (SCUC) model with emphases on the simultaneous optimization of energy and ancillary services markets. Benders decomposition is used to decouple the SCUC into a unit commitment (UC) master problem and hourly network security checking subproblems. Lagrangian relaxation is used to decouple the UC problem into individual single-unit commitment problems. Dynamic programming is used to find the optimal commitment decision. A simultaneous marginal curve algorithm is proposed to find the optimal values of energy and ancillary services. A six-bus system with three units and the IEEE 118-bus system with 54 units are analyzed to illustrate the proposed model.

The environmental light influences the circulatory levels of retinoic acid and associates with hepatic lipid metabolism

Wenqiang Pang — 2008-08-07T18:37:11-00:00

Endocrinology (31 July 2008), en.2008-0562.

Environmental light is involved in the regulation of photochemical reaction in mouse retina. It remains unclear whether light-mediated increase in all-trans retinoic acid (ATRA) synthesis in retina will result in altering the circulatory levels of ATRA and regulating downstream gene expression and physiological function. Here we showed circulatory levels of ATRA decreased in mice under constant darkness and elevated by light exposure. Fat gene pancreatic lipase-related protein 2 (mPlrp2) and its partner procolipase (mClps), but not hepatic lipase (mHl), activated in livers for responding to lack of light illuminating. Light-triggered alterations in circulatory ATRA levels regulated ecto-5'-nucleotidase (Cd73) gene expression by retinoic acid receptor RARalpha and modulated 5'-adenosine monophosphate (5'-AMP) levels in blood and were associated with mPlrp2 and mClps expression in the livers. Mice deficient in adenosine receptors displayed mPlrp2 and mClps expression in livers under 12h/12h light/dark cycles. Caffeine blocked adenosine receptors and induced hepatic mPlrp2 and mClps expression in wild type mice. Mice activated in hepatic mPlrp2 and mClps expression lowered hepatic and serum lipid levels and markedly elevated circulatory levels of all-trans retinol (ATR). Our results suggest environmental light influence hepatic lipid homeostasis by light-modulated retinoic acid signaling associated with mPlrp2 and mClps gene expression in livers. 10.1210/en.2008-0562

Potential of Mean Force and pKa Profile Calculation for a Lipid Membrane-Exposed Arginine Side Chain

Libo Li — 2008-07-20T01:17:15-00:00

J. Phys. Chem. B (18 July 2008)

Abstract: The issue of ionizable protein side chains interacting with lipid membranes has been the focus of much attention since the proposal of the paddle model of voltage-gated ion channels, which suggested multiple arginine (Arg) side chains may move through the hydrocarbon core of a lipid membrane. Recent cell biology experiments have also been interpreted to suggest that these side chains would face only small free energy penalties to cross membranes, challenging a long-standing view in membrane biophysics. Here, we employ side chain analog and transmembrane helix models to determine the free energy of an Arg side chain, as a function of protonation state, across a membrane. We observe high free energy barriers for both the charged and neutral states that would prohibit lipid-exposed movement. The mechanisms for charged and neutral Arg transport are, however, very different, with the neutral state experiencing simple dehydration, whereas the charged state experiences a complex mechanism involving connections to the bilayer interfaces that deform the local membrane structure. We employ special methods to ensure sampling of these interfacial connections and decompose the free energy to shed light on the mechanisms. These deformations are found to preferentially stabilize the protonated form, such that the Arg side chain remains almost exclusively charged inside the membrane, with a pKa shift of d4.5 units. In contrast, the analog models are found to exaggerate the variations in energetics across the membrane and have larger pKa shifts. These results have implications for models of voltage gated ion channels, suggesting that although Arg side chains are ideally suited for carrying charge, the thermodynamics dictate that they must remain sequestered from the lipid bilayer environment.

Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane

Igor Vorobyov — 2008-07-23T15:53:08-00:00

J. Phys. Chem. B (18 July 2008)

Abstract: Ionizable amino acid side chains play important roles in membrane protein structure and function, including the activation of voltage-gated ion channels, where it has been previously suggested that charged side chains may move through the hydrocarbon core of the membrane. However, all-atom molecular dynamics simulations have demonstrated large free energy barriers for such lipid-exposed motions. These simulations have also revealed that the membrane will deform due to the presence of a charged side chain, leading to a complex solvation microenvironment for which empirical force fields were not specifically parametrized. We have tested the ability of the all-atom CHARMM, Drude polarizable CHARMM, and a recent implementation of a coarse-grained force field to measure the thermodynamics of argininemembrane interactions as a function of protonation state. We have employed model systems to attempt to match experimental bulk partitioning and quantum mechanical interactions within the membrane and found that free energy profiles from nonpolarizable and polarizable CHARMM simulations are accurate to within 12 kcal/mol. In contrast, the coarse-grained simulations failed to reproduce the same membrane deformations, exhibit interactions that are an order of magnitude too small, and thus, have incorrect free energy profiles. These results illustrate the need for careful parametrization of coarse-grained force fields and demonstrate the utility of atomistic molecular dynamics for providing quantitative thermodynamic and mechanistic analysis of proteinlipid interactions.

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.

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data

Peter Li — 2008-08-07T16:34:39-00:00

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

BACKGROUND:There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools.RESULTS:Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench.CONCLUSIONS:Taverna can be used by data analysis experts as a generic tool for composing ad hoc analyses of quantitative data by combining the use of scripts written in the R programming language with tools exposed as services in workflows. When these workflows are shared with colleagues and the wider scientific community, they provide an approach for other scientists wanting to use tools such as R without having to learn the corresponding programming language to analyse their own data.

BLogo: A tool for visualization of bias in biological sequences

Wencheng Li — 2008-08-07T16:33:03-00:00

Bioinformatics (4 August 2008), btn407.

Summary: Blogo is a web-based tool that detects and displays statistically significant position-specific sequence bias with reduced background noise. The over-represented and under-represented symbols in a particular position are shown above and below the zero line. When the sequences are in open reading frames, the background frequency of nucleotides could be calculated separately for the three positions of a codon, thus greatly reducing the background noise. Thechi 2 test or fisher's exact test is used to evaluate the statistical significance of every symbol in every position and only those that are significant are highlighted in the resulting logo. The perl source code of the program is freely available and can be run locally. Availability: http://acephpx.cropdb.org/blogo/, http://www.bioinformatics.org/blogo/ Contact: lwcbio@yahoo.com.cn, xnwang@21cn.net 10.1093/bioinformatics/btn407

PDTD: a web-accessible protein database for drug target identification

Zhenting Gao — 2008-02-20T02:00:30-00:00

BMC Bioinformatics, Vol. 9 (19 February 2008), 104.

Sequences downstream of the start codon and their relations to G + C content and optimal growth temperature in prokaryotic genomes

Wencheng Li — 2008-08-07T15:58:45-00:00

Antonie van Leeuwenhoek, Vol. 92, No. 4. (26 November 2007), pp. 417-427.

Abstract The mechanism of translation initiation is responsible for shaping the mRNA sequences downstream of the start codon. However, this region has not been systematically analyzed in prokaryotes. We used sequence logos and statistic methods to analyze the patterns of overrepresented sequences in this region for 125 species of bacteria and 23 species of archaea. The specific positions are compared to the first 33 amino acids in the proteins. At the 2nd amino acid position, Lys, Ser or Thr is highly overrepresented for 68% to 84% of the genomes examined and Ala is highly overrepresented for 57% of the genomes. Overrepresentation of Lys2 is negatively correlated with the G + C content and overrepresentation of Ser2 or Thr2 is positively correlated with the G + C content of genomes. Ile at the 4th to the 8th positions were found to be overrepresented for 91% of the genomes analyzed and this seemed to be conserved for both bacteria and archaea. Organisms growing at high temperatures have relatively low extent of nucleotides bias at 5′ termini of open reading frames (ORFs). The extent of overrepresenting A and underrepresenting G at ORF 5′ termini is reduced in thermophiles and hyperthermophiles for both archaea and bacteria.

Divergent resistance at the Dirac point in graphene: evidence for a transition in high magnetic field

Joseph Checkelsky — 2008-08-07T15:42:36-00:00

(6 Aug 2008)

We have greatly extended measurements of the Dirac-point resistance $R_0$ in graphene, using an ultralow-dissipation ($<$3 fW) technique that avoids self-heating problems. At 0.3 K, $R_0(H)$ is observed to increase a 1000-fold to 40 M$Ω$ in a relatively narrow span of field $B$. The abruptness of the increase implies that a transition occurs to an insulating, ordered state at large $B$. Remarkably, $R_0$ accurately fits a Kosterlitz-Thouless-type correlation length over 3 decades. The results imply a field-induced phase transition to a high-field ordered state that is insulating. The effect of tuning the chemical potential away from the Dirac point is also investigated.

Improving the Download Time of BitTorrent-Like Systems

Chi-Jen Wu — 2008-08-07T12:37:57-00:00

Communications, 2007. ICC '07. IEEE International Conference on (2007), pp. 1125-1129.

The content distribution techniques have recently started embracing peer-to-peer system as an alternative to the client-server architecture, such as BitTorrent system. BitTorrent system offers a scale mechanism for distributing a large volume of data to a set of peers over the Internet, but it is not designed for minimizing the time taken for all peers to receive the file. As a result, the peers of BitTorrent system may suffer a long download time, specifically the narrow-band peers. In this paper, in order to reduce the download time of BitTorrent, we propose a weighty piece selection strategy instead of the local rarest first strategy in BitTorrent. The proposed strategy is based on the greedy concept that a peer assigns each missing piece a weight according to total number of neighbor's downloaded pieces. The peer selects the missing piece with the highest priority for next download. This strategy can speed up the cooperation between heterogeneous peers while making the BitTorrent more efficient in terms of the average download time and the total elapsed time. The simulation results show that weighty piece selection strategy can improve more than 15% average download time and reduce in average 60% total elapsed time than the BitTorrent system.

The limits of localization using signal strength: a comparative study

E Elnahrawy — 2006-03-19T11:57:34-00:00

Sensor and Ad Hoc Communications and Networks, 2004. IEEE SECON 2004. 2004 First Annual IEEE Communications Society Conference on (2004), pp. 406-414.

We characterize the fundamental limits of localization using signal strength in indoor environments. Signal strength approaches are attractive because they are widely applicable to wireless sensor networks and do not require additional localization hardware. We show that although a broad spectrum of algorithms can trade accuracy for precision, none has a significant advantage in localization performance. We found that using commodity 802.11 technology over a range of algorithms, approaches and environments, one can expect a median localization error of 10 ft and 97th percentile of 30 ft. We present strong evidence that these limitations are fundamental and that they are unlikely to transcend without a fundamentally more complex environmental models or additional localization infrastructure.

Spatial motion constraints: theory and demonstrations for robot guidance using virtual fixtures

P Marayong — 2008-08-07T11:50:24-00:00

Robotics and Automation, 2003. Proceedings. ICRA '03. IEEE International Conference on, Vol. 2 (2003), pp. 1954-1959 vol.2.

In this article, we describe and demonstrate control algorithms for general motion constraints. These constraints are designed to enhance the accuracy and speed of a user manipulating in an environment with the assistance of a cooperative or telerobotic system. Our method uses a basis of preferred directions, created off-line or in real-time using sensor data, to generate virtual fixtures that may constrain the user to a curve, surface, orientation, etc. in space. Open loop virtual fixtures seek only to maintain user motion along preferred directions, whereas closed loop fixtures additionally guide the user toward a point, line, or surface. This article demonstrates and compares the effects of open and closed loop fixtures in both autonomous and human-machine cases.

A Synthetical Approach for Blog Recommendation: Combining Trust, Social Relation, and Semantic Analysis

Yung-Ming Li — 2008-08-07T11:36:39-00:00

Expert Systems with Applications, Vol. In Press, Accepted Manuscript

Picomolar Inhibitors as Transition-State Probes of 5′-Methylthioadenosine Nucleosidases

Jemy Gutierrez — 2008-08-07T10:58:25-00:00

ACS Chem. Biol., Vol. 2, No. 11. (20 November 2007), pp. 725-734.

Transition states can be predicted from an enzymes affinity to related transition-state analogues. 52-Methylthioadenosine nucleosidases (MTANs) are involved in bacterial quorum sensing pathways and thus are targets for antibacterial drug design. The transition-state characteristics of six MTANs are compared by analyzing dissociation constants (Kd) with a small array of representative transition-state analogues. These inhibitors mimic early or late dissociative transition states with Kd values in the picomolar range. Our results indicate that the Kd ratio for mimics of early and late transition states are useful in distinguishing between these states. By this criterion, the transition states of Neisseria meningitides and Helicobacter pylori MTANs are early dissociative, whereas Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, and Klebsiella pneumoniae MTANs have late dissociative characters. This conclusion is confirmed independently by the characteristic [12-3H] and [12-14C] kinetic isotope effects (KIEs) of these enzymes. Large [12-3H] and unity [12-14C] KIEs are observed for late dissociative transition states, whereas early dissociative states showed close-to-unity [12-3H] and significant [12-14C] KIEs. Kd values of various MTANs for individual transition-state analogues provide tentative information about transition-state structures due to varying catalytic efficiencies of enzymes. Comparing Kd ratios for mimics of early and late transition states removes limitations inherent to the enzyme and provides a better predictive tool in discriminating between possible transition-state structures.

Peripheral blood pressure changes induced by dobutamine do not alter BOLD signals in the human brain.

H Liu — 2006-06-29T17:15:42-00:00

Neuroimage, Vol. 30, No. 3. (15 April 2006), pp. 745-752.

In extending the use of functional MRI to neuropharmacology, a primary area of concern is that peripheral blood pressure changes induced by pharmacological agents could independently produce a change in the blood oxygenation level-dependent (BOLD) signal, resulting in difficulties distinguishing or interpreting drug-induced neural activations. In the present study, we utilized intravenous dobutamine, a beta-adrenergic receptor agonist, to increase the mean arterial blood pressure (MABP), while examining the effects of MABP changes on the BOLD signal in cocaine-dependent participants. Dobutamine infusion significantly increased the MABP from 93 +/- 8 mm Hg to 106 +/- 12 mm Hg (P < 0.0005), but did not produce a significant global BOLD signal. Yet, a few voxels in the anterior cingulate showed BOLD signal changes that paralleled the changes in blood pressure (BP). Our observations support the conclusion that following the infusion of psychoactive agents, brain BOLD signals accurately reflect neuronal activity, even in the face of relatively large peripheral cardiovascular effects that transiently increase systemic BP.

Comprehensive Association Study of Type 2 Diabetes and Related Quantitative Traits with 222 Candidate Genes.

Kyle J Gaulton — 2008-08-07T09:12:43-00:00

Diabetes (4 August 2008)

Objective: Type 2 diabetes (T2D) is a common complex disorder with environmental and genetic components. We used a candidate gene-based approach to identify single nucleotide polymorphism (SNP) variants in 222 candidate genes that influence susceptibility to T2D. Research Design and Method: In a case-control study of 1,161 T2D and 1,174 normal glucose tolerant (NGT) control Finns, we genotyped 3,531 tagSNPs and annotation-based SNPs and imputed an additional 7,498 SNPs, providing 99.9% coverage of common HapMap variants in the 222 candidate genes. Selected SNPs were genotyped in an additional 1,211 T2D cases and 1,259 NGT controls, also from Finland. Results: Using SNP and gene-based analysis methods, we replicated previously reported SNP- T2D associations in PPARG, KCNJ11, and SLC2A2, identified significant SNPs in genes with previously reported associations, ENPP1 (rs2021966, p=.00026) and NRF1 (rs1882095, p=.00096), and implicated novel genes in T2D susceptibility including RAPGEF1 (rs4740283, p=.00013) and TP53 (rs1042522; Arg72Pro, p=.00086). Conclusion: Our study provides an effective gene-based approach to association study design and analysis. One or more of the newly implicated genes may contribute to T2D pathogenesis; analysis of additional samples will be necessary to determine their effect on susceptibility.

Negative Lateral Shift of a Light Beam Transmitted through a Dielectric Slab and Interaction of Boundary Effects

Chun-Fang Li — 2008-08-07T08:38:46-00:00

Physical Review Letters, Vol. 91, No. 13. (2003), 133903.

It is found that when a light beam travels through a slab of optically denser dielectric medium in air, the lateral shift of the transmitted beam can be negative. This is a novel phenomenon that is reversed in comparison with the geometrical optic prediction according to Snell’s law of refraction. A Gaussian-shaped beam is analyzed in the paraxial approximation, and a comparison with numerical simulations is made. Finally, an explanation for the negativity of the lateral shift is suggested, in terms of the interaction of boundary effects of the slab’s two interfaces with air.

Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes.

YS Lin — 2007-10-17T10:21:03-00:00

Proc Natl Acad Sci U S A, Vol. 103, No. 39. (26 September 2006), pp. 14412-14416.

Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-genome duplication (WGD) unexpectedly show a small synonymous divergence (K(S)), a higher sequence similarity to each other than to orthologues in Saccharomyces bayanus, or slow evolution compared with the orthologue in Kluyveromyces waltii, a non-WGD species. This decelerated evolution was attributed to gene conversion between duplicates. Using approximately 300 WGD gene pairs in four species and their orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are two important causes for decelerated evolution of duplicate genes, whereas gene conversion is effective only in the presence of strong codon-usage bias or protein-sequence conservation. Furthermore, we find that change in mutation pattern or in tDNA copy number changed codon-usage bias and increased the K(S) distance between K. waltii and S. cerevisiae. Intriguingly, some proteins showed fast evolution before the radiation of WGD species but little or no sequence divergence between orthologues and paralogues thereafter, indicating that functional conservation after the radiation may also be responsible for decelerated evolution in duplicates.

The sequence of the human genome.

JC Venter — 2005-05-11T19:14:50-00:00

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

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

Desmosome assembly and disassembly are regulated by reversible protein phosphorylation in cultured epithelial cells.

M Pasdar — 2008-08-07T03:48:22-00:00

Cell motility and the cytoskeleton, Vol. 30, No. 2. (1995), pp. 108-121.

Desmosomes are one component of the intercellular junctional complex in epithelia. In cultures of epithelial cells, desmosome assembly can be regulated by modulating the calcium concentrations of the growth media. At present, very little is known about the intracellular signal transduction mechanisms that regulate desmosome assembly and disassembly in response to changing extracellular calcium concentrations. We have used inhibitors of protein kinases and phosphatases in a combined biochemical and morphological approach to analyze the role of protein phosphorylation in the assembly and disassembly of desmosomes in Madin-Darby canine kidney epithelial cells. Our results suggest that desmosomal proteins (desmoplakins I/II and desmoglein 1) are primarily phosphorylated on serine residues. Electron microscopic analyses of desmosome assembly upon induction of cell-cell contact, in the presence of protein kinase inhibitor, H-7, revealed an apparently normal assembly of desmosomes. However, complete disassembly of desmosomes was inhibited by H-7 upon removal of extracellular calcium. Under these conditions, although desmosomes split, desmosomal plaques and their associated cytokeratin filaments can not be internalized. In contrast, treatment of the cultures with okadaic acid (OA), an inhibitor of protein phosphatases, inhibited desmosome assembly but had no effect on disassembly. In addition, the inhibitory effect of okadaic acid on desmosome assembly was specific to this junction since we observed apparently normal tight junction and adherens junction in okadaic acid-treated cultures. These results suggest that assembly and disassembly of desmosomes may be regulated by extracellular Ca2+ via reversible protein phosphorylation involving both protein kinase and protein phosphatases.

Tetraspanin CD9 regulates invasion during mouse embryo implantation.

WM Liu — 2008-08-07T00:26:33-00:00

Journal of molecular endocrinology, Vol. 36, No. 1. (February 2006), pp. 121-130.

The expression of tetraspanin CD9 was found on blastocysts in mice and endometrium epithelial cells in human and bovine. However, it remains unknown how CD9 is involved in the precise dialogue between embryo and uterus during early pregnancy. This study was designed to investigate the functional roles of CD9 in the embryo implantation with monoclonal antibody against CD9 protein (anti-CD9 mAb) and antisense oligonucleotide against CD9 gene (AS-CD9). Our results showed that intrauterine injection of anti-CD9 mAb on day 4 of pregnancy significantly increased the number of embryos implanted (7.24+/-0.39 versus 4.04+/-0.38). In vitro, anti-CD9 mAb or AS-CD9 significantly enhanced embryo-outgrowth ability on the monolayer of uterus epithelial cells in a dose-dependent manner. However, the attachment of blastocysts to epithelial cells was unaffected. Furthermore, we found that anti-CD9 mAb or AS-CD9 stimulated matrix metalloproteinase 2 (MMP-2) production of blastocysts on Fibronectin. LY294002, a specific inhibitor of phosphoinositide 3-kinase, was able to counteract the effect of anti-CD9 mAb and AS-CD9 on outgrowth ability and production of MMP-2. Our results indicated that CD9 played a role of inhibiting embryo implantation. CD9 was able to impair embryo invasion and the production of MMP-2 through the phosphoinositide 3-kinase signaling pathway.

The mechanical and metabolic basis of myocardial blood flow heterogeneity

James Bassingthwaighte — 2008-08-06T22:27:39-00:00

Basic Research in Cardiology, Vol. 96, No. 6. (24 December 2001), pp. 582-594.

Abstract Precise measurements of regional myocardial blood flow heterogeneity had to be developed before one could seek causation for the heterogeneity. Deposition techniques (particles or molecular microspheres) are the most precise, but imaging techniques have begun to provide high enough resolution to allow in vivo studies. Assigning causation has been difficult. There is no apparent association with the regional concentrations of energy-related enzymes or substrates, but these are measures of status, not of metabolism. There is statistical correlation between flow and regional substrate uptake and utilization. Attribution of regional flow variation to vascular anatomy or to vasomotor control appears not to be causative on a long-term basis. The closest relationships appear to be with mechanical function, but one cannot say for sure whether this is related to ATP hydrolysis at the crossbridge or associated metabolic reactions such as calcium uptake by the sarcoplasmic reticulum.

Intracellular Delivery of Quantum Dots Tagged Antisense Oligodeoxynucleotides by Functionalized Multiwalled Carbon Nanotubes

N Jia — 2008-08-06T21:39:56-00:00

Nano Lett., Vol. 7, No. 10. (10 October 2007), pp. 2976-2980.

Abstract: With the goal of identifying an improved delivery scheme for intracellular tracking and anticancer therapy, we explored a novel double functionalization of a carbon nanotube delivery system containing antisense oligodeoxynucleotides (ASODNs) as a therapeutic gene and CdTe quantum dots as fluorescent labeling probes via electrostatically layer-by-layer assembling. This is the first time that we used mercaptoacetic acid-capped CdTe quantum dots as fluorescent labeling probes for clearly tracking the intracellular transport and evaluating delivery efficiency of ASODNs by functionalized multiwalled carbon nanotubes (MWNTs).

Hints on writing technical papers and making presentations

VOK Li — 2006-11-30T10:10:30-00:00

Education, IEEE Transactions on, Vol. 42, No. 2. (1999), pp. 134-137.

This paper is an attempt to give some guidelines on how to write a good technical paper and to make good presentations, important skills for a successful career in research and teaching

Classification of Text Documents

YH Li — 2008-08-06T20:11:22-00:00

The Computer Journal, Vol. 41, No. 8. (1 August 1998), pp. 537-546.

The exponential growth of the internet has led to a great deal of interest in developing useful and efficient tools and software to assist users in searching the Web. Document retrieval, categorization, routing and filtering can all be formulated as classification problems. However, the complexity of natural languages and the extremely high dimensionality of the feature space of documents have made this classification problem very difficult. We investigate four different methods for document classification: the naive Bayes classifier, the nearest neighbour classifier, decision trees and a subspace method. These were applied to seven-class Yahoo news groups (business, entertainment, health, international, politics, sports and technology) individually and in combination. We studied three classifier combination approaches: simple voting, dynamic classifier selection and adaptive classifier combination. Our experimental results indicate that the naive Bayes classifier and the subspace method outperform the other two classifiers on our data sets. Combinations of multiple classifiers did not always improve the classification accuracy compared to the best individual classifier. Among the three different combination approaches, our adaptive classifier combination method introduced here performed the best. The best classification accuracy that we are able to achieve on this seven-class problem is approximately 83%, which is comparable to the performance of other similar studies. However, the classification problem considered here is more difficult because the pattern classes used in our experiments have a large overlap of words in their corresponding documents. 10.1093/comjnl/41.8.537

Fibroblast growth factor (FGF) signaling through PI 3-kinase and Akt/PKB is required for embryoid body differentiation.

Y Chen — 2008-08-06T18:31:29-00:00

Oncogene, Vol. 19, No. 33. (3 August 2000), pp. 3750-3756.

The role of FGF signaling in early epithelial differentiation was investigated in ES (embryonic stem) cell derived embryoid bodies. A dominant negative fibroblast growth factor receptor (FGFR) mutation was created by stably introducing into ES cells an Fgfr2 cDNA, truncated in its enzymatic domains. These cells failed to differentiate into cystic embryoid bodies. No epithelial differentiation and cavitation morphogenesis could be observed, in the mutant, although its rate of cell proliferation remained unchanged. This phenotype was associated with a significant decrease in the activation of Akt/PKB and PLCgamma-1, as compared to the wild type, while the activation of MAPK/Erk was less affected. Requirement for PI 3-kinase signaling in embryoid body differentiation was demonstrated by specific inhibitors. Akt/PKB activation was abrogated by wortmannin in short-term experiments. In long-term cultures Ly294002 inhibited the differentiation of ES cells into embryoid bodies. Our data demonstrate that for early epithelial differentiation FGF signaling is required through the PI 3-kinase-Akt/ PKB pathway.

Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice.

L Huang — 2008-08-06T17:02:21-00:00

Plant physiology, Vol. 144, No. 3. (July 2007), pp. 1508-1519.

The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD(+)-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions. In this work, we investigated the role of OsSRT1, one of the two SIR2-related genes found in rice (Oryza sativa). We show that OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues. OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H(2)O(2) production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1. Our data together suggest that the rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth, but likely implicates different molecular mechanisms than yeast and animal homologs.

Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

Guangan Hu — 2007-09-20T20:06:43-00:00

BMC Bioinformatics, Vol. 8 (19 September 2007), 350.

Evolution of Eukaryotic Transcription Circuits

Brian Tuch — 2008-03-28T16:40:57-00:00

Science, Vol. 319, No. 5871. (28 March 2008), pp. 1797-1799.

The gradual modification of transcription circuits over evolutionary time scales is an important source of the diversity of life. Over the past decade, studies in animals have shown how seemingly small molecular changes in gene regulation can have large effects on morphology and physiology and how selective pressures can act on these changes. More recently, genome-wide studies, particularly those in single-cell yeasts, have uncovered evidence of extensive transcriptional rewiring, indicating that even closely related organisms regulate their genes using markedly different circuitries. 10.1126/science.1152398

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.

5nm-gate nanowire FinFET

Fu-Liang Yang — 2008-08-06T14:32:26-00:00

VLSI Technology, 2004. Digest of Technical Papers. 2004 Symposium on (2004), pp. 196-197.

A new nanowire FinFET structure is developed for CMOS device scaling into the sub-10 nm regime. Accumulation mode P-FET and inversion mode N-FET with 5 nm and 10 nm physical gate length, respectively, are fabricated. N-FET gate delay (CV/I) of 0.22 ps and P-FET gate delay of 0.48 ps with excellent subthreshold characteristics are achieved, both with very low off leakage cur-rent less than 10 nA/ /spl mu/m. Nanowire FinFET device operation is also explored using 3-D full quantum mechanical simulation.

River stage prediction based on a distributed support vector regression

CL Wu — 2008-08-06T12:22:13-00:00

Journal of Hydrology, Vol. 358, No. 1-2. (30 August 2008), pp. 96-111.

Summary An accurate and timely prediction of river flow flooding can provide time for the authorities to take pertinent flood protection measures such as evacuation. Various data-derived models including LR (linear regression), NNM (the nearest-neighbor method) ANN (artificial neural network) and SVR (support vector regression), have been successfully applied to water level prediction. Of them, SVR is particularly highly valued, because it has the advantage over many data-derived models in overcoming overfitting of training data. However, SVR is computationally time-consuming when used to solve large-size problems. In the context of river flow prediction, equipped with LR model as a benchmark and genetic algorithm-based ANN (ANN-GA) and NNM as counterparts, a novel distributed SVR (D-SVR) model is proposed in this study. It implements a local approximation to training data because partitioned original training data are independently fitted by each local SVR model. ANN-GA and LR models are also used to help determine input variables. A two-step GA algorithm is employed to find the optimal triplets (C, [epsilon], [sigma]) for D-SVR model. The validation results reveal that the proposed D-SVR model can carry out the river flow prediction better in comparison with others, and dramatically reduce the training time compared with the conventional SVR model. The pivotal factor contributing to the performance of D-SVR may be that it implements a local approximation method and the principle of structural risk minimization.

Millimeter-wave spectroscopy of cold Rb Rydberg atoms in a magneto-optical trap: Quantum defects of the ns, np, and nd series

Wenhui Li — 2008-08-06T11:37:23-00:00

Physical Review A, Vol. 67, No. 5. (13 May 2003), 052502.

Conductance of a quantum dot with a Hubbard interaction in the presence of a boson field

Xi Li — 2008-08-06T05:47:38-00:00

Physical Review B, Vol. 52, No. 16. (15 October 1995), 12202.

Comparison of Two-Dimensional Fractionation Techniques for Shotgun Proteomics

James Dowell — 2008-08-06T03:59:48-00:00

Anal. Chem. (5 August 2008)

Abstract: Two-dimensional (2D) fractionation is a commonly used tool to increase dynamic range and proteome coverage for bottom-up, shotgun proteomics. However, there are few reports comparing the relative separation efficiencies of 2D methodologies using low-microgram sample quantities. In order to systematically evaluate 2D separation techniques, we fractionated microgram quantities of E. coli protein extract by seven different methods. The first dimension of separation was performed with either reversed-phase high-pressure liquid chromatography (RP-HPLC), gel electrophoresis (SDS-PAGE), or strong cation exchange (SCX-HPLC). The second dimension consisted of a standard reversed-phase capillary HPLC coupled to an electrospray ionization quadrupole time-of-flight mass spectrometer for tandem mass spectrometric analysis. The overall performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The protein-level RP-HPLC and the high-pH RP-HPLC peptide-level separations performed the best, identifying 281 and 266 proteins, respectively. The online pH variance SCX and the SDS-PAGE returned modest performances with 178 and 139 proteins identified, respectively. The offline SCX had the worst performance with 81 proteins identified. We also examined various chromatographic factors that contribute to separation efficiency, including resolving power, orthogonality, and sample loss.

New Insights into Mechanisms of Spontaneous Liver Transplant Tolerance: The Role of Foxp3-Expressing CD25CD4 Regulatory T Cells

Li — 2008-07-25T19:18:01-00:00

American Journal of Transplantation, Vol. 8, No. 8. (August 2008), pp. 1639-1651.

Bioconductor: open software development for computational biology and bioinformatics.

RC Gentleman — 2005-04-21T13:38:17-00:00

Genome Biol, Vol. 5, No. 10. (2004)

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

An Effective Implementation of a Direct Spanning Tree Representation in GAs

Yu Li — 2008-08-05T22:49:55-00:00

Applications of Evolutionary Computing (2001), pp. 11-19.

This paper presents an effective implementation based on predecessor vectors of a genetic algorithm using a direct tree representation. The main operations associated with crossovers and mutations can be achieved in O(d) time, where d is the length of a path. Our approach can avoid usual drawbacks of the fixed linear representations, and provide a framework facilitating the incorporation of problem-specific knowledge into initialization and operators for constrained minimum spanning tree problems.

Electronic transport in PANI-CSA/PANI-DBSA polyblends

Yunze Long — 2008-08-05T21:23:48-00:00

Physica B: Condensed Matter, Vol. 344, No. 1-4. (15 February 2004), pp. 82-87.

New polyaniline (PANI) blends, PANI-camphor sulfonic acid (PANI-CSA) and PANI-dodecylbenzene sulfonic acid (PANI-DBSA) composite films with high room-temperature conductivity (~200 S/cm) were prepared. The experimental data show a transition from negative temperature coefficient of resistivity (TCR) to positive TCR at around 210 K. An equation [rho](T)=a·[rho]m exp(-Tm/T)+b·[rho]0 exp(T0/T)1/4 combining 3D variable-range hopping in disordered regions with quasi-one-dimensional metallic conduction in ordered regions has been used, which are consistent well with the resistivity data even from 1.8 up to 370 K. It is found that the PANI blends show positive magnetoresistance (MR) from 240 K down to 1.8 K and show negative MR from 240 K up to 350 K, which can be attributed to different dominant conduction mechanisms in different temperature ranges.

A study of AdaBoost with SVM based weak learners

Xuchun Li — 2008-08-05T20:22:56-00:00

Neural Networks, 2005. IJCNN '05. Proceedings. 2005 IEEE International Joint Conference on, Vol. 1 (2005), pp. 196-201 vol. 1.

In this article, we focus on designing an algorithm, named AdaBoostSVM, using SVM as weak learners for AdaBoost. To obtain a set of effective SVM weak learners, this algorithm adaptively adjusts the kernel parameter in SVM instead of using a fixed one. Compared with the existing AdaBoost methods, the AdaBoostSVM has advantages of easier model selection and better generalization performance. It also provides a possible way to handle the over-fitting problem in AdaBoost. An improved version called Diverse AdaBoostSVM is further developed to deal with the accuracy/diversity dilemma in Boosting methods. By implementing some parameter adjusting strategies, the distributions of accuracy and diversity over these SVM weak learners are tuned to achieve a good balance. To the best of our knowledge, such a mechanism that can conveniently and explicitly balances this dilemma has not been seen in the literature. Experimental results demonstrated that both proposed algorithms achieve better generalization performance than AdaBoost using other kinds of weak learners. Benefiting from the balance between accuracy and diversity, the Diverse AdaBoostSVM achieves the best performance. In addition, the experiments on unbalanced data sets showed that the AdaBoostSVM performed much better than SVM.

Processable aqueous dispersions of graphene nanosheets

Dan Li — 2008-08-05T20:08:30-00:00

Nat Nano, Vol. 3, No. 2. (February 2008), pp. 101-105.

Optimal Dialog in Consumer-Rating Systems using POMDP Framework

Zhifei Li — 2008-08-05T20:04:46-00:00

(June 2008), pp. 104-111.

Organismal complexity, protein complexity, and gene duplicability.

J Yang — 2008-08-05T15:57:49-00:00

Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 26. (23 December 2003), pp. 15661-15665.

Although the evolutionary significance of gene duplication has long been recognized, it remains unclear what determines gene duplicability. We find protein complexity to be an important determinant because the proportion of unduplicated genes (P) increases with the number of subunits in a protein. However, P is high (>or=65%) for both monomers and multimers in yeast, but <or=30% in human except for subunits of large multimers, implying that organismal complexity is a stronger determinant of gene duplicability than protein complexity. The same conclusion is reached from a comparison of family sizes in yeast and human.

Protein complexity, gene duplicability and gene dispensability in the yeast genome.

YS Lin — 2008-08-05T15:57:38-00:00

Gene, Vol. 387, No. 1-2. (31 January 2007), pp. 109-117.

Using functional genomic and protein structural data we studied the effects of protein complexity (here defined as the number of subunit types in a protein) on gene dispensability and gene duplicability. We found that in terms of gene duplicability the major distinction in protein complexity is between hetero-complexes, each of which includes at least two different types of subunits (polypeptides), and homo-complexes, which include monomers and complexes that consist of only subunits of one polypeptide type. However, gene dispensability decreases only gradually as the number of subunit types in a protein complex increases. These observations suggest that the dosage balance hypothesis can explain well gene duplicability of complex proteins, but cannot completely explain the difference in dispensabilities between hetero-complex subunits. It is likely that knocking out a gene coding for a hetero-complex subunit would disrupt the function of the whole complex, so that the deletion effect on fitness would increase with protein complexity. We also found that multi-domain polypeptide genes are less dispensable but more duplicable than single-domain polypeptide genes. Duplicate genes derived from the whole genome duplication event in yeast are more dispensable (except for ribosomal protein genes) than other duplicate genes. Further, we found that subunits of the same protein complex tend to have similar expression levels and similar effects of gene deletion on fitness. Finally, we estimated that in yeast the contribution of duplicate genes to genetic robustness against null mutation is approximately 9%, smaller than previously estimated. In yeast, protein complexity may serve as a better indicator of gene dispensability than do duplicate genes.

Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability

Han Liang — 2008-02-04T14:37:12-00:00

PLoS Genetics, Vol. 4, No. 1. (1 January 2008), e11.

A fundamental issue in molecular evolution is how to identify the evolutionary forces that determine the fate of duplicated genes. The dosage balance hypothesis has been invoked to explain gene duplication patterns at the genomic level under the premise that a dosage imbalance among protein-complex subunits or interacting partners is often deleterious. Here we examine this hypothesis by investigating the molecular basis of dosage sensitivity. We focus on the extent of protein wrapping, which indicates how strongly the structural integrity of a protein relies on its interactive context. From this perspective, we predict that the duplicates of a highly under-wrapped protein or protein subunit should (1) be more sensitive to dosage imbalance and be less likely to be retained and (2) be more likely to survive from a whole-genome duplication (WGD) than from a non-WGD because a WGD causes little or no dosage imbalance. Our under-wrapping analysis of more than 12,000 protein structures strongly supports these predictions and further reveals that the effect of dosage sensitivity on gene duplicability decreases with increasing organismal complexity.

Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila

Shuang Yang — 2008-02-04T14:39:04-00:00

PLoS Genetics, Vol. 4, No. 1. (1 January 2008), e3.

Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use ∼7,000 cDNA probes (∼112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.

Newer pathologic assessment techniques for colorectal carcinoma.

RR Turner — 2008-08-05T15:54:51-00:00

Clinical cancer research : an official journal of the American Association for Cancer Research, Vol. 13, No. 22 Pt 2. (15 November 2007)

The pathogenesis of colorectal carcinoma is characterized by progressive genetic abnormalities, which lead to proteomic and cellular changes that determine the cancer malignant phenotype. Phenotypic characteristics seen on histopathologic examination (e.g., tumor stage, histologic grade, and vasoinvasiveness) are essential to planning patient management and should continue to be the major focus of pathologists' efforts. Nonetheless, additional markers that improve the prognostic and predictive power of the pathologic analysis of the primary tumor have been the focus of intense research in recent years. Improved prognostic power may derive from advancements in histopathologic evaluation, more sensitive lymph node staging techniques, and specific molecular analysis methods, such as genetic tests or immunophenotypic profiles. Histopathologic improvements are needed to better standardize histologic grade determination and recognize tumor budding at the invasive front as a marker of aggressive biological behavior and an adverse parameter. Ultrastaging of mesenteric lymph nodes remains a controversial area. Genotypic studies are well developed in the areas of microsatellite instability and chromosome 18q deletion/loss of heterozygosity. Immunophenotypic studies are available in a range of areas including tumor suppressor gene/oncogene expression, proliferation/apoptosis, angiogenesis, and cell adhesion and signaling. Gene expression profiles identified by microarray techniques may help to subtype the large category of microsatellite-stable colorectal carcinoma and define immunophenotypic panels to subclassify tumors into prognostic and therapeutic groups. This brief review discusses the most promising of these approaches and evidence supporting their potential clinical utility.