CiteULike: Author Jiang

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

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.

Relaxation of yeast mitochondrial functions after whole-genome duplication.

Huifeng Jiang — 2008-08-07T08:27:17-00:00

Genome research (30 July 2008)

Mitochondria are essential for cellular energy production in most eukaryotic organisms. However, when glucose is abundant, yeast species that underwent whole-genome duplication (WGD) mostly conduct fermentation even under aerobic conditions, and most can survive without a functional mitochondrial genome. In this study, we show that the rate of evolution for the nuclear-encoded mitochondrial genes was greater in post-WGD species than pre-WGD species. Furthermore, codon usage bias was relaxed for these genes in post-WGD yeast species. The codon usage pattern and the distribution of a particular transcription regulatory element suggest that the change to an efficient aerobic fermentation lifestyle in this lineage might have emerged after WGD between the divergence of Kluyveromyces polysporus and Saccharomyces castellii from their common ancestor. This new energy production strategy could have led to the relaxation of mitochondrial function in the relevant yeast species.

Dimorphic effects of Notch signaling in bone homeostasis

Feyza Engin — 2008-03-07T16:12:30-00:00

Nature Medicine, Vol. 14, No. 3. (24 February 2008), pp. 299-305.

Notch signaling is a key mechanism in the control of embryogenesis. However, its in vivo function during mesenchymal cell differentiation, and, specifically, in bone homeostasis, remains largely unknown. Here, we show that osteoblast-specific gain of Notch function causes severe osteosclerosis owing to increased proliferation of immature osteoblasts. Under these pathological conditions, Notch stimulates early osteoblastic proliferation by upregulating the genes encoding cyclin D, cyclin E and Sp7 (osterix). The intracellular domain of Notch1 also regulates terminal osteoblastic differentiation by directly binding Runx2 and repressing its transactivation function. In contrast, loss of all Notch signaling in osteoblasts, generated by deletion of the genes encoding presenilin-1 and presenilin-2 in bone, is associated with late-onset, age-related osteoporosis, which in turn results from increased osteoblast-dependent osteoclastic activity due to decreased osteoprotegerin mRNA expression in these cells. Together, these findings highlight the potential dimorphic effects of Notch signaling in bone homeostasis and may provide direction for novel therapeutic applications.

Phase-contrast imaging of tissue using near-infrared diffusing light

Huabei Jiang — 2008-08-06T22:29:43-00:00

Medical Physics, Vol. 30, No. 6. (2003), pp. 1048-1051.

We describe a new model-based image reconstruction method that can extract the spatial variation of tissue refractive index with near-infrared diffusing light. The model of light propagation is a diffusion approximation to the radiative transfer equation for highly scattering media with spatially varying refractive index. The spatial map of refractive index is recovered using a finite element-based Newton-type reconstruction algorithm. The imaging method is validated using several tissue-like phantom experiments. Initial in vivo imaging of breast tissue is also presented, demonstrating the ability of this new imaging method for tumor detection. ©2003 American Association of Physicists in Medicine.

Three-dimensional optical tomographic imaging of breast in a human subject

Huabei Jiang — 2008-08-06T22:20:12-00:00

Medical Imaging, IEEE Transactions on, Vol. 20, No. 12. (2001), pp. 1334-1340.

We present for the first time a full three-dimensional (3-D) reconstruction of absorption images of breast from continuous-wave (cw) measurements performed on a premenopausal woman. Our 3-D optical images clearly reveal a large primary tumor as well as a small secondary tumor in a separate location of the breast. The multiple tumors identified by our 3-D optical imaging have been confirmed by the subsequent biopsy examination of the breast. Quantitative information of the optical images obtained is provided in terms of the location, size, and absorption coefficient of the tumors

Zinc oxide nanorod and nanowire for humidity sensor

Yongsheng Zhang — 2008-08-06T19:05:19-00:00

Applied Surface Science, Vol. 242, No. 1-2. (31 March 2005), pp. 212-217.

ZnO nanorod and nanowire films were fabricated on the Si substrates with comb type Pt electrodes by the vapor-phase transport method, and their humidity sensitive characteristics have been investigated. These nanomaterial films show high-humidity sensitivity, good long-term stability and fast response time. It was found that the resistance of the films decreases with increasing relative humidity (RH). At room temperature (RT), resistance changes of more than four and two orders of magnitude were observed when ZnO nanowire and nanorod devices were exposed, respectively, to a moisture pulse of 97% relative humidity. It appears that the ZnO nanomaterial films can be used as efficient humidity sensors.

Microcalorimetric studies on the adsorption of DNA by soil colloidal particles

Peng Cai — 2008-08-06T17:59:23-00:00

Colloids and Surfaces B: Biointerfaces, Vol. 49, No. 1. (15 April 2006), pp. 49-54.

This study applied TAM air isothermal calorimeter to measure the adsorption enthalpies of DNA on eight colloidal fractions from permanent-charge and variable-charge soils. The adsorption of DNA on soil colloids was also examined by equilibrium adsorption analysis. The data evaluated from isotherms fitted by Langmuirean model revealed that the affinity of DNA for variable-charge soil colloids was higher than that for permanent-charge soil colloids. More tightly bound DNA molecules were observed on coarse clays and inorganic clays than on fine clays and organic clays, respectively. The adsorption enthalpies of DNA on permanent-charge soil colloids were higher than those on variable-charge soil colloids. DNA adsorption on organic clays is endothermic, whereas that on inorganic clays is exothermic. Dehydration and electrostatic repulsion were considered to cause the higher adsorption enthalpies of DNA with organic clays, while hydrogen bonding, ligand exchange and electrostatic attraction result in the lower DNA adsorption enthalpies on inorganic clays. The thermodynamic parameters presented in this study have important implication for providing further insight into mechanisms of the adsorption of DNA on soil particles.

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.

De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae.

J Cai — 2008-05-27T13:07:35-00:00

Genetics, Vol. 179, No. 1. (May 2008), pp. 487-496.

Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplication, retroposition, gene fusion, and fission. However, the process of how a new gene is de novo created from noncoding sequence is largely unknown. On the basis of genome comparison among yeast species, we have identified a new de novo protein-coding gene, BSC4 in Saccharomyces cerevisiae. The BSC4 gene has an open reading frame (ORF) encoding a 132-amino-acid-long peptide, while there is no homologous ORF in all the sequenced genomes of other fungal species, including its closely related species such as S. paradoxus and S. mikatae. The functional protein-coding feature of the BSC4 gene in S. cerevisiae is supported by population genetics, expression, proteomics, and synthetic lethal data. The evidence suggests that BSC4 may be involved in the DNA repair pathway during the stationary phase of S. cerevisiae and contribute to the robustness of S. cerevisiae, when shifted to a nutrient-poor environment. Because the corresponding noncoding sequences in S. paradoxus, S. mikatae, and S. bayanus also transcribe, we propose that a new de novo protein-coding gene may have evolved from a previously expressed noncoding sequence.

Speckle variance detection of microvasculature using swept-source optical coherence tomography

Adrian Mariampillai — 2008-08-06T02:06:02-00:00

Opt. Lett., Vol. 33, No. 13. (1 July 2008), pp. 1530-1532.

We report on imaging of microcirculation by calculating the speckle variance of optical coherence tomography (OCT) structural images acquired using a Fourier domain mode-locked swept-wavelength laser. The algorithm calculates interframe speckle variance in two-dimensional and three-dimensional OCT data sets and shows little dependence to the Doppler angle ranging from 75° to 90°. We demonstrate in vivo detection of blood flow in vessels as small as 25 μm in diameter in a dorsal skinfold window chamber model with direct comparison with intravital fluorescence confocal microscopy. This technique can visualize vessel-size-dependent vascular shutdown and transient vascular occlusion during Visudyne photodynamic therapy and may provide opportunities for studying therapeutic effects of antivascular treatments without on exogenous contrast agent.

ChemmineR: A Compound Mining Framework for R.

Yiqun Cao — 2008-07-05T00:27:22-00:00

Bioinformatics (Oxford, England) (2 July 2008)

MOTIVATION: Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here we present the first open-source compound mining framework for the popular statistical programming environment R. The integration with a powerful statistical environment maximizes the flexibility, expandability and programmability of the provided analysis functions. RESULTS: We discuss the algorithms and compound mining utilities provided by the R package ChemmineR. It contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of classification algorithms and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine environment and allows bidirectional communications between the two services. AVAILABILITY: ChemmineR is freely available as an R package from the ChemMine project site: http://bioweb.ucr.edu/ChemMineV2/chemminer. CONTACT: thomas.girke@ucr.edu.

Epigenetic Natural Variation in Arabidopsis thaliana.

Matthew W Vaughn — 2007-07-12T08:02:36-00:00

PLoS Biol, Vol. 5, No. 7. (19 June 2007)

Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F2 families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.

Apolipoprotein L1, a Novel Bcl-2 Homology Domain 3-only Lipid-binding Protein, Induces Autophagic Cell Death

Guanghua Wan — 2008-08-05T00:46:43-00:00

J. Biol. Chem., Vol. 283, No. 31. (1 August 2008), pp. 21540-21549.

The Bcl-2 family proteins are important regulators of type I programmed cell death apoptosis; however, their role in autophagic cell death (AuCD) or type II programmed cell death is still largely unknown. Here we report the cloning and characterization of a novel Bcl-2 homology domain 3 (BH3)-only protein, apolipoprotein L1 (apoL1), that, when overexpressed and accumulated intracellularly, induces AuCD in cells as characterized by the increasing formation of autophagic vacuoles and activating the translocation of LC3-II from the cytosol to the autophagic vacuoles. Wortmannin and 3-methyladenine, inhibitors of class III phosphatidylinostol 3-kinase and, subsequently, autophagy, blocked apoL1-induced AuCD. In addition, apoL1 failed to induce AuCD in autophagy-deficient ATG5-/- and ATG7-/- mouse embryonic fibroblast cells, suggesting that apoL1-induced cell death is indeed autophagy-dependent. Furthermore, a BH3 domain deletion construct of apoL1 failed to induce AuCD, demonstrating that apoL1 is a bona fide BH3-only pro-death protein. Moreover, we showed that apoL1 is inducible by p53 in p53-induced cell death and is a lipid-binding protein with high affinity for phosphatidic acid (PA) and cardiolipin (CL). Previously, it has been shown that PA directly interacted with mammalian target of rapamycin and positively regulated the ability of mammalian target of rapamycin to activate downstream effectors. In addition, CL has been shown to activate mitochondria-mediated apoptosis. Sequestering of PA and CL with apoL1 may alter the homeostasis between survival and death leading to AuCD. To our knowledge, this is the first BH3-only protein with lipid binding activity that, when overproduced intracellularly, induces AuCD. 10.1074/jbc.M800214200

Automated breast cancer classification using near-infrared optical tomographic images

James Wang — 2008-08-01T20:43:08-00:00

Journal of Biomedical Optics, Vol. 13, No. 4. (2008)

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

Zhao — 2007-09-08T00:08:42-00:00

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

Nucleosome organization in the Drosophila genome.

Travis N Mavrich — 2008-04-16T22:48:07-00:00

Nature (13 April 2008)

Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines.

Combining Particle Filter and Active Shape Models for Lip Tracking

Min Jiang — 2008-07-31T05:15:55-00:00

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

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

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

Y Liu — 2008-07-30T15:01:34-00:00

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

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

Default mode network as revealed with multiple methods for resting-state functional MRI analysis.

XY Long — 2008-05-26T10:37:35-00:00

Journal of neuroscience methods, Vol. 171, No. 2. (30 June 2008), pp. 349-355.

Recently, human brain activity during a resting-state has attracted increasing attention. Several studies have found that there are two networks: the default mode network and its anti-correlation network. Some studies have subsequently showed that the functions of brain areas within the default mode network are crucial in human mental activity. To further discern the brain default mode network as well as its anti-correlation network during resting-state, we used three methods to analyze resting-state functional magnetic resonance imaging (fMRI) data; regional homogeneity analysis, linear correlation and independent component analysis, on four groups of dataset. Our results showed the existence of these two networks prominently and consistently during a resting- and conscious-state across the three methods. This consistency was exhibited in four independent groups of normal adults. Moreover, the current results provided evidences that the brain areas within the two anti-correlated networks are highly integrated at both the intra- and inter-regional level.

Microstructure control of ZnO thin films prepared by single source chemical vapor deposition

H Deng — 2008-07-30T03:06:42-00:00

Thin Solid Films, Vol. 458, No. 1-2. (30 June 2004), pp. 43-46.

The columnar structure of ZnO thin films with respect to the incident angle prepared by single source chemical vapor deposition (SS CVD) on Si (1 0 0) substrate was examined. Growth was performed using a volatile precursor Zn4O(CO2NEt2)6. It was found by scanning electron microscopy that the columnar structure depended on the incident angle between substrates and vapor sources. However, the X-ray diffraction spectra indicate that the [0 0 2] crystallographic orientations of ZnO thin films were perpendicular to the substrate planes, irrespective of the incident angle, and were not aligned with the columnar growth orientations as may be expected. The c-axis orientation of SS CVD ZnO thin films is easily aligned with the (0 0 2) plane surface of the substrate because of its surface anisotropy and the optimal growth is on the face with the highest density and the lowest surface-free energy.

An elt-3/elt-5/elt-6 GATA Transcription Circuit Guides Aging in C. elegans

Yelena Budovskaya — 2008-07-29T19:08:43-00:00

Cell, Vol. 134, No. 2. (25 July 2008), pp. 291-303.

Summary To define the C. elegans aging process at the molecular level, we used DNA microarray experiments to identify a set of 1294 age-regulated genes and found that the GATA transcription factors ELT-3, ELT-5, and ELT-6 are responsible for age regulation of a large fraction of these genes. Expression of elt-5 and elt-6 increases during normal aging, and both of these GATA factors repress expression of elt-3, which shows a corresponding decrease in expression in old worms. elt-3 regulates a large number of downstream genes that change expression in old age, including ugt-9, col-144, and sod-3. elt-5(RNAi) and elt-6(RNAi) worms have extended longevity, indicating that elt-3, elt-5, and elt-6 play an important functional role in the aging process. These results identify a transcriptional circuit that guides the rapid aging process in C. elegans and indicate that this circuit is driven by drift of developmental pathways rather than accumulation of damage.

Band structure asymmetry of bilayer graphene revealed by infrared spectroscopy

ZQ Li — 2008-07-25T00:25:52-00:00

(24 Jul 2008)

We report on infrared spectroscopy of bilayer graphene integrated in gated structures. We observed a significant asymmetry in the optical conductivity upon electrostatic doping of electrons and holes. We show that this finding arises from a marked asymmetry between the valence and conduction bands, which is mainly due to the inequivalence of the two sublattices within the graphene layer. From the conductivity data, the energy difference of the two sublattices is determined.

Measurement of piezoelectric coefficient of gallium nitride using metal-insulator-semiconductor capacitors

Vinayak Tilak — 2008-07-29T17:11:44-00:00

Applied Physics Letters, Vol. 90, No. 4. (2007)

View this record in Web of Science

Statistical properties of world investment networks

Dong-Ming Song — 2008-07-29T09:48:13-00:00

(26 Jul 2008)

We have performed a detailed investigation on the world investment networks constructed from the Coordinated Portfolio Investment Survey (CPIS) data of the International Monetary Fund, ranging from 2001 to 2006. The distributions of degrees and node strengthes are scale-free. The weight distributions can be well modeled by the Weibull distribution. The maximum flow spanning trees of the world investment networks possess two universal allometric scaling relations, independent of time and the investment type. The topological scaling exponent is $1.17±0.02$ and the flow scaling exponent is $1.03±0.01$.

Fiber tract-based atlas of human white matter anatomy.

S Wakana — 2006-04-20T01:50:07-00:00

Radiology, Vol. 230, No. 1. (January 2004), pp. 77-87.

Two- and three-dimensional (3D) white matter atlases were created on the basis of high-spatial-resolution diffusion tensor magnetic resonance (MR) imaging and 3D tract reconstruction. The 3D trajectories of 17 prominent white matter tracts could be reconstructed and depicted. Tracts were superimposed on coregistered anatomic MR images to parcel the white matter. These parcellation maps were then compared with coregistered diffusion tensor imaging color maps to assign visible structures. The results showed (a). which anatomic structures can be identified on diffusion tensor images and (b). where these anatomic units are located at each section level and orientation. The atlas may prove useful for educational and clinical purposes.

Risk evaluation using evidence reasoning theory

Yan-Qiong Liu — 2008-07-29T08:51:35-00:00

Machine Learning and Cybernetics, 2005. Proceedings of 2005 International Conference on, Vol. 5 (2005), pp. 2855-2860 Vol. 5.

The evidence reasoning theory can generally represent uncertainty associated with propositions and datum and clearly distinguishes probability uncertainty caused by information deficiency from unknown caused by zero information. This paper proposed the conception of the risk basic strength assignment and built the general method and model of risk evaluation based on the evidence reasoning theory. This method permits experts to evaluate the risk event completely on their own professional experiences and knowledge independently. The new risk integrated basic strength assignment and the new risk factors integrated basic belief assignment generated by the Dempster-Shafer rule of combination both synthesize several experts' free judgments and reserve experts' characteristic cognition at the same time. Thus, experts are released from the traditional evaluation method which restricts them to assign probability to certain risk factors under certain risk occurring model. By this method we can get the integrated representation of the experts' knowledge and extract the experts' knowledge accurately.

CD14 is required for MyD88-independent LPS signaling

Zhengfan Jiang — 2005-05-19T18:58:09-00:00

Nature Immunology, Vol. 6, No. 6. (15 May 2005), pp. 565-570.

The recessive mutation 'Heedless' (hdl) was detected in third-generation N-ethyl-N-nitrosourea-mutated mice that showed defective responses to microbial inducers. Macrophages from Heedless homozygotes signaled by the MyD88-dependent pathway in response to rough lipopolysaccharide (LPS) and lipid A, but not in response to smooth LPS. In addition, the Heedless mutation prevented TRAM-TRIF-dependent signaling in response to all LPS chemotypes. Heedless also abolished macrophage responses to vesicular stomatitis virus and substantially inhibited responses to specific ligands for the Toll-like receptor 2 (TLR2)-TLR6 heterodimer. The Heedless phenotype was positionally ascribed to a premature stop codon in Cd14. Our data suggest that the TLR4-MD-2 complex distinguishes LPS chemotypes, but CD14 nullifies this distinction. Thus, the TLR4-MD-2 complex receptor can function in two separate modes: one in which full signaling occurs and one limited to MyD88-dependent signaling.

Plasticity of the corticospinal tract in early blindness revealed by quantitative analysis of fractional anisotropy based on diffusion tensor tractography.

C Yu — 2008-07-28T13:32:35-00:00

NeuroImage, Vol. 36, No. 2. (June 2007), pp. 411-417.

Early visual deprivation may induce plastic changes, not only in the visual system, but also in the remaining sensory systems, secondary to altered experience in these spared modalities. Most of previous studies were focused on the plasticity of cortical areas of sensory modalities, but little attention was paid to the plasticity of motor system and white matter fiber tracts. Our purpose is to investigate the plasticity of the corticospinal tract (CST) in early blindness by tract-based quantitative analysis of fractional anisotropy (FA). Diffusion tensor imaging was performed in 17 early blind and 17 gender- and age-matched sighted subjects. The entire CST of each subject was reconstructed and the average FA of the tract was analyzed. To validate the results derived from the entire CST, we further analyzed a segment of the CST between the lowest slice of the cerebral peduncle and the uppermost slice of the lateral ventricle, in which the fibers are coherently arranged and the anatomical correspondence of the CST across subjects is established. On comparison with matched sighted participants, the average FA of the CST was significantly increased in the early blind men, but not in the early blind women. In conclusion, the plasticity of the CST is present in the early blind men, which might be related to the changes of motor experience during critical developmental period of the CST. This study also supports the perspective that experience-dependent plasticity occurs not only in the cortical areas but also in the white matter fiber tracts.

Capital Punishment Views in China and the United States: A Preliminary Study Among College Students

Shanhe Jiang — 2008-07-28T03:04:52-00:00

Int J Offender Ther Comp Criminol, Vol. 51, No. 1. (1 February 2007), pp. 84-97.

There is a lack of research on attitudes toward capital punishment in China, and there is even less research on cross-national comparisons of capital punishment views. Using data recently collected from college students in the United States and China, this study finds that U.S. and Chinese students have differences in their views on the death penalty and its functions of deterrence, rehabilitation, and incapacitation. This study also reveals that the respondents' perspectives of deterrence, rehabilitation, retribution, and incapacitation all affect their attitudes toward the death penalty in the United States, whereas only the first three views affect attitudes toward capital punishment in China. Furthermore, retribution is the strongest predictor in the United States, whereas deterrence is the strongest predictor in China. 10.1177/0306624X06294138

Process consistency for AdaBoost

W Jiang — 2008-07-27T19:07:21-00:00

(2000)

Introduction. Some recent experimental results [e.g., Friedman, Hastie and Tibshirani (1999); Grove and Schuurmans (1998); Mason et al. (1998)] and theoretical examples [Jiang (1999)] suggest that the AdaBoost algorithm [e.g., Schapire (1999); Freund and Schapire (1997)] can overfit in the limit of (very) large time (or the number of rounds of AdaBoost), despite the observation that the algorithm is often found to be resistant to overfitting after running hundreds of rounds. Jiang (1999)...

Loss of bone mass after Colles' fracture: a follow-up study.

LY Dai — 2008-07-26T14:52:06-00:00

Chinese medical journal, Vol. 117, No. 3. (March 2004), pp. 327-330.

BACKGROUND: Colles' fracture usually associated with osteoporosis is regarded as the predictor of subsequent osteoporotic fracture. However, it is not clear how the local changes of bone mass take place during the course of treatment and whether the changes are related to clinical practice. The objective of the current study was to investigate the local changes of bone mass in patients with Colles' fracture and their possible clinical relevance in a follow-up study. METHODS: The radiograms of the second metacarpal in 64 patients with Colles' fracture were assessed for bone density immediately after fracture, 6 weeks, 6 months and 1 year after fracture, respectively. Functional results were evaluated at one year. RESULTS: Bone mass six weeks after Colles' fracture was significantly decreased without returning to normal at one year though increased bone mass had been identified 6 months after fracture (P < 0.05), (P < 0.01). At one year significant (P < 0.05) or highly significant (P < 0.01) correlations were observed between bone mass indices of metacarpal and functional results, indicating that poor function is associated with lower bone density. Significant differences (P < 0.05) between fracture patterns also suggested that patients with more severe fractures have a more pronounced bone loss. CONCLUSIONS: Bone loss during the course of treatment will have a direct effect upon the prognosis, so different treatment should be proposed for different patterns of fractures. Active exercise should be made to improve the recovery of bone mass.

Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA

Takeshi Saito — 2008-06-12T04:36:13-00:00

Nature (11 June 2008)

Effects of bismuth on wide-depletion-width GaInNAs solar cells

AJ Ptak — 2008-07-25T14:40:24-00:00

25th North American Molecular Beam Epitaxy Conference (NAMBE), Vol. 26, No. 3. (2008), pp. 1053-1057.

GaInNAs solar cells could be useful in next-generation multijunction solar cells if issues surrounding low photocurrents and photovoltages are surmounted. Wide-depletion-width devices generate significant photocurrent using a p-i-n structure grown by molecular beam epitaxy, but these depletion widths are only realized in a region of parameter space that leads to rough surface morphologies. Here, bismuth is explored as a surfactant for the growth of GaInNAs solar cells. Very low fluxes of Bi are effective at maintaining smooth surfaces, even at high growth temperatures and In contents. However, Bi also increases the net donor concentration in these materials, manifested in our n-on-p device structures as a pn-junction that moves deeper into the base layer with increasing Bi fluxes. Quantum efficiency modeling and scanning kelvin probe microscopy measurements confirm the type conversion of the base layer from p type to n type. Bi incorporation in GaAsBi samples shows signs of surface segregation, leading to a finite buildup time, and this effect may lead to slow changes in the electrical properties of the GaInNAs(Bi) devices. Bi also appears to create a defect level, although this defect level is not deleterious enough to increase the dark current in the devices. ©2008 American Vacuum Society

A prevalence-based association test for case-control studies.

Kelli K Ryckman — 2008-07-25T05:26:03-00:00

Genetic epidemiology (12 May 2008)

Genetic association is often determined in case-control studies by the differential distribution of alleles or genotypes. Recent work has demonstrated that association can also be assessed by deviations from the expected distributions of alleles or genotypes. Specifically, multiple methods motivated by the principles of Hardy-Weinberg equilibrium (HWE) have been developed. However, these methods do not take into account many of the assumptions of HWE. Therefore, we have developed a prevalence-based association test (PRAT) as an alternative method for detecting association in case-control studies. This method, also motivated by the principles of HWE, uses an estimated population allele frequency to generate expected genotype frequencies instead of using the case and control frequencies separately. Our method often has greater power, under a wide variety of genetic models, to detect association than genotypic, allelic or Cochran-Armitage trend association tests. Therefore, we propose PRAT as a powerful alternative method of testing for association. Genet. Epidemiol. 2008. (c) 2008 Wiley-Liss, Inc.

GeneTrack--a genomic data processing and visualization framework

Istvan Albert — 2008-05-07T11:06:27-00:00

Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1305-1306.

Motivation: High-throughput ChIP-chip' and ChIP-seq' methodologies generate sufficiently large data sets that analysis poses significant informatics challenges, particularly for research groups with modest computational support. To address this challenge, we devised a software platform for storing, analyzing and visualizing high resolution genome-wide binding data. GeneTrack automates several steps of a typical data processing pipeline, including smoothing and peak detection, and facilitates dissemination of the results via the web. Our software is freely available via the Google Project Hosting environment at http://genetrack.googlecode.com Contact: iual@psu.edu 10.1093/bioinformatics/btn119

Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy

JJ Jiang — 2006-11-07T14:53:47-00:00

(September 1997), 9008.

This paper presents a new approach for measuring semantic similarity/distance between words and concepts. It combines a lexical taxonomy structure with corpus statistical information so that the semantic distance between nodes in the semantic space constructed by the taxonomy can be better quantified with the computational evidence derived from a distributional analysis of corpus data. Specifically, the proposed measure is a combined approach that inherits the edge-based approach of the edge counting scheme, which is then enhanced by the node-based approach of the information content calculation. When tested on a common data set of word pair similarity ratings, the proposed approach outperforms other computational models. It gives the highest correlation value (r = 0.828) with a benchmark based on human similarity judgements, whereas an upper bound (r = 0.885) is observed when human subjects replicate the same task.

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

Xi Chen — 2008-06-13T18:29:13-00:00

Cell, Vol. 133, No. 6. (13 June 2008), pp. 1106-1117.

Summary Transcription factors (TFs) and their specific interactions with targets are crucial for specifying gene-expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem (ES) cells, we use chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of 13 sequence-specific TFs (Nanog, Oct4, STAT3, Smad1, Sox2, Zfx, c-Myc, n-Myc, Klf4, Esrrb, Tcfcp2l1, E2f1, and CTCF) and 2 transcription regulators (p300 and Suz12). These factors are known to play different roles in ES-cell biology as components of the LIF and BMP signaling pathways, self-renewal regulators, and key reprogramming factors. Our study provides insights into the integration of the signaling pathways into the ES-cell-specific transcription circuitries. Intriguingly, we find specific genomic regions extensively targeted by different TFs. Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity.

Alignment of two-dimensional electrophoresis gels.

G Shi — 2008-07-24T09:22:16-00:00

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

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

Effects of High Temperature on Key Enzymes Involved in Starch and Protein Formation in Grains of Two Wheat Cultivars

Zhao — 2008-02-06T12:59:27-00:00

Journal of Agronomy and Crop Science, Vol. 194, No. 1. (February 2008), pp. 47-54.

Energy expended playing video console games: an opportunity to increase children's physical activity?

R Maddison — 2007-12-10T05:53:28-00:00

Pediatr Exerc Sci, Vol. 19, No. 3. (August 2007), pp. 334-343.

This study sought to quantify the energy expenditure and physical activity associated with playing the "new generation" active and nonactive console-based video games in 21 children ages 10-14 years. Energy expenditure (kcal) derived from oxygen consumption (VO2) was continuously assessed while children played nonactive and active console video games. Physical activity was assessed continuously using the Actigraph accelerometer. Significant (p < .001) increases from baseline were found for energy expenditure (129-400%), heart rate (43-84%), and activity counts (122-1288 versus 0-23) when playing the active console video games. Playing active console video games over short periods of time is similar in intensity to light to moderate traditional physical activities such as walking, skipping, and jogging.

Couch potatoes to jumping beans: a pilot study of the effect of active video games on physical activity in children

Cliona Mhurchu — 2008-02-08T00:55:10-00:00

International Journal of Behavioral Nutrition and Physical Activity, Vol. 5 (07 February 2008), 8.

Macroscopic graphene membranes and their extraordinary stiffness

TJ Booth — 2008-07-23T21:05:14-00:00

(18 Jun 2008)

The properties of suspended graphene are currently attracting enormous interest, but the small size of available samples and the difficulties in making them severely restrict the number of experimental techniques that can be used to study the optical, mechanical, electronic, thermal and other characteristics of this one-atom-thick material. Here we describe a new and highly-reliable approach for making graphene membranes of a macroscopic size (currently up to 100 microns in diameter) and their characterization by transmission electron microscopy. In particular, we have found that long graphene beams supported by one side only do not scroll or fold, in striking contrast to the current perception of graphene as a supple thin fabric, but demonstrate sufficient stiffness to support extremely large loads, millions of times exceeding their own weight, in agreement with the presented theory. Our work opens many avenues for studying suspended graphene and using it in various micromechanical systems and electron microscopy.

A general framework for biclustering gene expression data.

H Li — 2008-01-20T03:08:44-00:00

J Bioinform Comput Biol, Vol. 4, No. 4. (August 2006), pp. 911-933.

A large number of biclustering methods have been proposed to detect patterns in gene expression data. All these methods try to find some type of biclusters but no one can discover all the types of patterns in the data. Furthermore, researchers have to design new algorithms in order to find new types of biclusters/patterns that interest biologists. In this paper, we propose a novel approach for biclustering that, in general, can be used to discover all computable patterns in gene expression data. The method is based on the theory of Kolmogorov complexity. More precisely, we use Kolmogorov complexity to measure the randomness of submatrices as the merit of biclusters because randomness naturally consists in a lack of regularity, which is a common property of all types of patterns. On the basis of algorithmic probability measure, we develop a Markov Chain Monte Carlo algorithm to search for biclusters. Our method can also be easily extended to solve the problems of conventional clustering and checkerboard type biclustering. The preliminary experiments on simulated as well as real data show that our approach is very versatile and promising.

Overexpression of GSTA2 protects against cell cycle arrest and apoptosis induced by the DNA inter-strand crosslinking nitrogen mustard, mechlorethamine.

J Xie — 2008-07-22T20:12:32-00:00

Journal of cellular biochemistry, Vol. 95, No. 2. (15 May 2005), pp. 339-351.

The effectiveness of bifunctional alkylating nitrogen mustard compounds in chemotherapy is related to their ability to form DNA inter-strand crosslinks. Patients exposed to DNA inter-strand crosslinking (ICL) agents subsequently experience an elevated incidence of myelodysplastic syndromes (MDS) and MDS related acute myeloid leukemia. Fanconi's anemia (FA) patients are deficient in the repair of crosslink DNA damage and they experience a high incidence of MDS. These observations indicate that hematopoietic cells are specific target for the transforming effects of DNA crosslinking damage. Changes in transcript levels were characterized in human hematopoietic cells occurring in response to the nitrogen mustard, mechlorethamine (HN2), but not in response to monofunctional analogs. Only modest changes in a few gene transcripts were detected in HL60 cells exposed to levels of HN2 tittered to maximal dose that caused growth suppression with minimal cell death and allowed eventual resumption of normal cell growth. Under conditions of transient growth suppression, a subset of glutathione-S-transferase (GST) isoenzyme genes was consistently upregulated three to fourfold by HN2, but not by monofunctional analogs. Subsequent efforts to confirm the changes detected by microarray analyses revealed an unexpected dependence on treatment conditions. The GST alpha class A2 subfamily member transcripts were upregulated 24 h after a 1 h exposure to HN2 that caused an extensive, but transient block in late S/G2 cell cycle phase, but were minimally altered with continuous exposure. The 1-h exposure to HN2 caused a transient late S/G2 cell cycle arrest in both the HL-60 cell line and the Colo 320HSR human colon cancer cell line. Overexpression of GSTA2 by transient transfection protected Colo 320HSR cells against both cycle arrest and apoptosis following exposure to HN2. Overexpression of GSTA2 in Colo 320HSR cells induced after exposure to HN2 did not alter cycle arrest or apoptosis. The results indicate that human GSTA2 facilitates the protection of cells from HN2 damage and not repair. Our results are consistent with the possibility that GSTA2 polymorphisms, variable isoenzyme expression, and variable induced expression may be factors in the pathogenesis of MDS.

S100P is selectively upregulated in tumor cell lines challenged with DNA cross-linking agents.

F Jiang — 2008-07-22T20:02:10-00:00

Leukemia research, Vol. 29, No. 10. (October 2005), pp. 1181-1190.

Bifunctional alkylating agents that cross-link DNA are implicated in the pathogenesis of therapy related myelodysplastic syndromes (MDS) and MDS related acute myeloid leukemia (MDR-AML). We exposed HL60 cells to the highest level of bifunctional alkylating nitrogen mustard mechlorethamine (HN2) that was consistent with recovery following suppressed growth. Microarray analyses showed minor changes in transcripts in HN2 treated cells. A moderate up-regulation of S100P mRNA was consistently observed after 1 day of exposure to bifunctional alkylating agents and expression was not induced with monofunctional agents. Elevated S100P protein/antigen was not detected until days later in a subset of non-mitotic G2 cells. Elevated S100P protein persisted over the course of a delayed recovery phase. The results confirm recent reports indicating that S100P is a survival factor. In addition, our results indicate that S100P has a specific role in G2 cell function associated with a prolonged phase of recovery after exposure to bifunctional alkylating agents.

Vertebrate heart growth is regulated by functional antagonism between Gridlock and Gata5.

H Jia — 2008-07-22T17:32:54-00:00

Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 35. (28 August 2007), pp. 14008-14013.

Embryonic organs attain their final dimensions through the generation of proper cell number and size, but the control mechanisms remain obscure. Here, we establish Gridlock (Grl), a Hairy-related basic helix-loop-helix (bHLH) transcription factor, as a negative regulator of cardiomyocyte proliferative growth in zebrafish embryos. Mutations in grl cause an increase in expression of a group of immediate-early growth genes, myocardial genes, and development of hyperplastic hearts. Conversely, cardiomyocytes with augmented Grl activity have diminished cell volume and fail to divide, resulting in a marked reduction in heart size. Both bHLH domain and carboxyl region are required for Grl negative control of myocardial proliferative growth. These Grl-induced cardiac effects are counterbalanced by the transcriptional activator Gata5 but not Gata4, which promotes cardiomyocyte expansion in the embryo. Biochemical analyses show that Grl forms a complex with Gata5 through the carboxyl region and can repress Gata5-mediated transcription via the bHLH domain. Hence, our studies suggest that Grl regulates embryonic heart growth via opposing Gata5, at least in part through their protein interactions in modulating gene expression.

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

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

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

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

Effects of geometrical characteristics of surface roughness on droplet wetting

Yu Sheng — 2008-07-22T05:23:50-00:00

J. Chem. Phys., Vol. 127, No. 23. (2007), 234704.

View this record in Web of Science

Activation of platelet-activating factor receptor and pleiotropic effects on tyrosine phospho-EGFR/Src/FAK/paxillin in ovarian cancer.

M Aponte — 2008-07-22T03:23:37-00:00

Cancer research, Vol. 68, No. 14. (15 July 2008), pp. 5839-5848.

Among the proinflammatory mediators, platelet-activating factor (PAF, 1-O-alkyl-2-acetyl-sn-glycero-3-phosphorylcholine) is a major primary and secondary messenger involved in intracellular and extracellular communication. Evidence suggests that PAF plays a significant role in oncogenic transformation, tumor growth, angiogenesis, and metastasis. However, PAF, with its receptor (PAFR) and their downstream signaling targets, has not been thoroughly studied in cancer. Here, we characterized the PAFR expression pattern in 4 normal human ovarian surface epithelial (HOSE) cell lines, 13 ovarian cancer cell lines, paraffin blocks (n = 84), and tissue microarrays (n = 230) from patients with ovarian cancer. Overexpression of PAFR was found in most nonmucinous types of ovarian cancer but not in HOSE and mucinous cancer cells. Correspondingly, PAF significantly induced cell proliferation and invasion only in PAFR-positive cells (i.e., OVCA429 and OVCA432), but not in PAFR-negative ovarian cells (HOSE and mucinous RMUG-L). The dependency of cell proliferation and invasion on PAFR was further confirmed using PAFR-specific small interfering RNA gene silencing probes, antibodies against PAFR and PAFR antagonist, ginkgolide B. Using quantitative multiplex phospho-antibody array technology, we found that tyrosine phosphorylation of EGFR/Src/FAK/paxillin was coordinately activated by PAF treatment, which was correlated with the activation of phosphatidylinositol 3-kinase and cyclin D1 as markers for cell proliferation, as well as matrix metalloproteinase 2 and 9 for invasion. Specific tyrosine Src inhibitor (PP2) reversibly blocked PAF-activated cancer cell proliferation and invasion. We suggest that PAFR is an essential upstream target of Src and other signal pathways to control the PAF-mediated cancer progression.