bluuebunny/crossref_metadata_2025 huggingface dataset:
Phonon polariton generation and detection using near-field heterodyne transient grating method
Authors: Katayama Kenji , Shen Qing , Toyoda Taro , Nelson Keith A.
Published: April 2007

A technique for the generation and detection of phonon polariton was developed based on the near-field heterodyne transient grating method. It features a compact and simple optical setup and easy wavelength tuning ability of the phonon polariton. The wavelength was tuned by changing the grating spacing of a transmission grating positioned in front of a sample, and this was performed by sliding a glass plate with transmission gratings with many different grating spacings along the glass plate surface.
Low threshold current single-cell hexapole mode photonic crystal laser
Authors: Seo Min-Kyo , Jeong Kwang-Yong , Yang Jin-Kyu , Lee Yong-Hee , Park Hong-Gyu , Kim Sung-Bock
Published: April 2007

The authors report an electrically driven, hexapole mode, single-cell photonic crystal laser operating at 1537.8nm. Electrical current is supplied through a submicrometer-sized current post beneath the cavity center. This wavelength-scale single-cell photonic crystal laser operates in a single mode with threshold current of ∼100μA at room temperature. Operation in the hexapole mode is confirmed by the near-field profile, far-field polarization, and the finite-difference time-domain computation based on the fabricated cavity structure.
Special strain hardening mechanism and nanocrack generation in nanocrystalline materials
Authors: Ovid’ko I. A. , Sheinerman A. G.
Published: April 2007

A special mechanism of strain hardening in deformed nanocrystalline materials (NCMs) is suggested and theoretically described. The mechanism represents generation of disclination dipoles at grain boundaries (GBs) due to GB sliding. It is shown that special strain hardening can effectively suppress plastic flow instability in metallic and ceramic NCMs and thus enhance their ductility. At the same time, the disclination dipoles formed due to GB sliding serve as dangerous stress sources that can induce nucleation of nanocracks, decreasing ductility of NCMs.
Fast switchable electrochromic properties of tungsten oxide nanowire bundles
Authors: Yoo Sung Jong , Lim Ju Wan , Sung Yung-Eun , Jung Young Hwa , Choi Hong Goo , Kim Do Kyung
Published: April 2007

The authors prepared uniformly shaped WO2.72 nanowire bundles using the solvothermal synthesis method. They investigated the potential of the WO2.72 nanowire bundles to be used as a cathode electrode for electrochromic devices and the effect of the Li+ insertion (or extraction) kinetics and diffusion of Li+. An electrode consisting of arrays of WO2.72 nanowire bundles was formed and used in an experiment using the Langmuir-Blodgett technique. The one-dimensional nanostructure of WO2.72 has a high Li-ion diffusion coefficient (∼5.2×10−11cm2∕s) and low charge transfer resistance (∼28.6Ω), which result in its having a fast electrochromic response time (coloring time <3.5s, bleaching time <1.1s), and outstanding high coloration efficiency (>55cm2∕C).
Ga
Sb
∕
Ga
As
type II quantum dot solar cells for enhanced infrared spectral response
Authors: Laghumavarapu R. B. , Moscho A. , Khoshakhlagh A. , El-Emawy M. , Lester L. F. , Huffaker D. L.
Published: April 2007

The authors report an enhanced infrared spectral response of GaAs-based solar cells that incorporate type II GaSb quantum dots (QDs) formed using interfacial misfit array growth mode. The material and devices, grown by molecular beam epitaxy, are characterized by current-voltage and spectral response characteristics. From 0.9to1.36μm, these solar cells show significantly more infrared response compared to reference GaAs cells and previously reported InAs QD solar cells. The short circuit current density and open circuit voltages of solar cells with and without dots measured under identical conditions are 1.29mA∕cm2, 0.37V and 1.17mA∕cm2, 0.6V, respectively.
Heat flow in AlGaInP∕GaAs light-emitting diodes
Authors: Chen N. C. , Yang Y. K. , Wang Y. N. , Huang Y. C.
Published: April 2007

The differential equations of heat flow with boundary conditions suited to light-emitting diodes (LEDs) were analytically solved. An AlGaInP∕GaAs LED is considered as an example. The agreement between the theoretical and experimental evolutions of the junction temperature demonstrates the accuracy of this analytical solution. Additionally, since the increase of the junction temperature depends on the thermal properties of the substrate, the measured junction temperature together with the analytical solution yield the thermal properties of the substrate.
Role of the Si excess on the excitation of Er doped SiOx
Authors: Franzò Giorgia , Pecora Emanuele , Priolo Francesco , Iacona Fabio
Published: April 2007

The authors have investigated the role of the Si excess on the photoluminescence properties of Er doped substoichiometric SiOx layers. They demonstrate that the Si excess has two competing roles: when agglomerated to form Si nanoclusters (Si-nc’s) it enhances the Er excitation efficiency but it also introduces new nonradiative decay channels. When Er is excited through an energy transfer from Si-nc's, the beneficial effect on the enhanced excitation efficiency prevails and the Er emission increases with increasing Si content. However, when pumped resonantly, the Er luminescence intensity always decreases with increasing Si content. These data are presented and their implications are discussed.
Manipulation of the vortex motion in nanostructured ferromagnetic/superconductor hybrids
Authors: Silhanek A. V. , Gillijns W. , Moshchalkov V. V. , Metlushko V. , Gozzini F. , Ilic B. , Uhlig W. C. , Unguris J.
Published: April 2007

The authors investigate the rectified motion of vortices in superconducting films deposited on top of a close-packed array of open in-plane magnetized triangular micromagnets. The dc voltage induced by the vortex drift under an ac excitation is recorded for three different magnetic configurations of the triangles. When the magnetic elements are in the as-grown state a rectification signal which reverses sign when the field changes polarity is observed. In contrast to that, when the array of triangles is magnetized the observed rectification effect is independent of the field polarity and can be reverted by reorienting the magnetization of the micromagnets.
A Simple Method to Stand outside Oneself
Authors: Altschuler Eric Lewin , Ramachandran Vilayanur S
Published: April 2007

Here we outline a simple method of using two mirrors which allows one to stand out-side oneself. This method demonstrates that registration of vision with touch and proprioception is crucial for the perception of the corporeal self. Our method may also allow the disassociation of taste from touch, proprioception, and movement.
Haptic Roughness Perception of Linear Gratings via Bare Finger or Rigid Probe
Authors: Lawrence Michael A , Kitada Ryo , Klatzky Roberta L , Lederman Susan J
Published: April 2007

The magnitude of perceived roughness was haptically estimated as subjects freely explored linear gratings with either the bare finger or a rigid stylus-shaped probe. A considerably expanded range of ridge and groove width was investigated, relative to the extant literature. The four experiments collectively indicate that, for both finger and probe-end effectors, the variance in the estimates of perceived roughness was predominantly predicted by a single parameter: groove width. The functions relating perceived roughness to groove width increased over a narrow band relative to the full range of values, then flattened. These data have archival values for models of roughness perception involving both direct and indirect touch.
Separate oscillating cell groups in mouse suprachiasmatic nucleus couple photoperiodically to the onset and end of daily activity
Authors: Inagaki Natsuko , Honma Sato , Ono Daisuke , Tanahashi Yusuke , Honma Ken-ichi
Published: April 2007

The pattern of circadian behavioral rhythms is photoperiod-dependent, highlighted by the conservation of a phase relation between the behavioral rhythm and photoperiod. A model of two separate, but mutually coupled, circadian oscillators has been proposed to explain photoperiodic responses of behavioral rhythm in nocturnal rodents: an evening oscillator, which drives the activity onset and entrains to dusk, and a morning oscillator, which drives the end of activity and entrains to dawn. Continuous measurement of circadian rhythms in clock gene
Per1
expression by a bioluminescence reporter enabled us to identify the separate oscillating cell groups in the mouse suprachiasmatic nucleus (SCN), which composed circadian oscillations of different phases and responded to photoperiods differentially. The circadian oscillation in the posterior SCN was phase-locked to the end of activity under three photoperiods examined. On the other hand, the oscillation in the anterior SCN was phase-locked to the onset of activity but showed a bimodal pattern under a long photoperiod [light–dark cycle (LD)18:6]. The bimodality in the anterior SCN reflected two circadian oscillatory cell groups of early and late phases. The anterior oscillation was unimodal under intermediate (LD12:12) and short (LD6:18) photoperiods, which was always phase-lagged behind the posterior oscillation when the late phase in LD18:6 was taken. The phase difference was largest in LD18:6 and smallest in LD6:18. These findings indicate that three oscillating cell groups in the SCN constitute regionally specific circadian oscillations, and at least two of them are involved in photoperiodic response of behavioral rhythm.
Selective chemical probe inhibitor of Stat3, identified through structure-based virtual screening, induces antitumor activity
Authors: Siddiquee Khandaker , Zhang Shumin , Guida Wayne C. , Blaskovich Michelle A. , Greedy Benjamin , Lawrence Harshani R. , Yip M. L. Richard , Jove Richard , McLaughlin Mark M. , Lawrence Nicholas J. , Sebti Said M. , Turkson James
Published: April 2007

S3I-201 (NSC 74859) is a chemical probe inhibitor of Stat3 activity, which was identified from the National Cancer Institute chemical libraries by using structure-based virtual screening with a computer model of the Stat3 SH2 domain bound to its Stat3 phosphotyrosine peptide derived from the x-ray crystal structure of the Stat3β homodimer. S3I-201 inhibits Stat3·Stat3 complex formation and Stat3 DNA-binding and transcriptional activities. Furthermore, S3I-201 inhibits growth and induces apoptosis preferentially in tumor cells that contain persistently activated Stat3. Constitutively dimerized and active Stat3C and Stat3 SH2 domain rescue tumor cells from S3I-201-induced apoptosis. Finally, S3I-201 inhibits the expression of the Stat3-regulated genes encoding cyclin D1, Bcl-xL, and survivin and inhibits the growth of human breast tumorsin vivo. These findings strongly suggest that the antitumor activity of S3I-201 is mediated in part through inhibition of aberrant Stat3 activation and provide the proof-of-concept for the potential clinical use of Stat3 inhibitors such as S3I-201 in tumors harboring aberrant Stat3.
Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes
Authors: Huang Yi , Greene Eriko , Murray Stewart Tracy , Goodwin Andrew C. , Baylin Stephen B. , Woster Patrick M. , Casero Robert A.
Published: April 2007

Epigenetic chromatin modification is a major regulator of eukaryotic gene expression, and aberrant epigenetic silencing of gene expression contributes to tumorigenesis. Histone modifications include acetylation, phosphorylation, and methylation, resulting in a combination of histone marks known collectively as the histone code. The chromatin marks at a given promoter determine, in part, whether specific promoters are in an open/active conformation or closed/repressed conformation. Dimethyl-lysine 4 histone H3 (H3K4me2) is a transcription-activating chromatin mark at gene promoters, and demethylation of this mark by the lysine-specific demethylase 1 (LSD1), a homologue of polyamine oxidases, may broadly repress gene expression. We now report that novel biguanide and bisguanidine polyamine analogues are potent inhibitors of LSD1. These analogues inhibit LSD1 in human colon carcinoma cells and affect a reexpression of multiple, aberrantly silenced genes important in the development of colon cancer, including members of the secreted frizzle-related proteins (
SFRPs
) and the
GATA
family of transcription factors. Furthermore, we demonstrate by chromatin immunoprecipitation analysis that the reexpression is concurrent with increased H3K4me2 and acetyl-H3K9 marks, decreased H3K9me1 and H3K9me2 repressive marks. We thus define important new agents for reversing aberrant repression of gene transcription.
NKG2D recognition mediates Toll-like receptor 3 signaling-induced breakdown of epithelial homeostasis in the small intestines of mice
Authors: Zhou Rongbin , Wei Haiming , Sun Rui , Zhang Jian , Tian Zhigang
Published: April 2007

Toll-like receptors (TLRs) and NK receptors are the two most important receptor families in innate immunity. Although it has been observed that TLR signaling can induce or up-regulate the expression of the ligands for stimulatory NK receptors on monocytes or muscle cells, there is not yet a report indicating whether TLR signaling can break down self-tolerance through NK receptors. The present work reports that TLR3 signaling by polyinosinic–polycytidylic acid stimulation induces intestinal epithelial cells (IECs) to express retinoic acid early inducible-1 (a ligand for NKG2D) and to induce NKG2D expression on CD8αα intestinal intraepithelial lymphocytes by IL-15 derived from TLR3-activated IECs. The blockade of interaction between NKG2D and Rae1 inhibits the cytotoxicity of intraepithelial lymphocytes against IECs in a cell–cell contact-dependent manner and therefore alleviates polyinosinic–polycytidylic acid-induced epithelial destruction and acute mucosal injury of small intestine. These results demonstrate that TLR signaling induces tissue injury through the NKG2D pathway, suggesting that TLR signaling may break down self-tolerance through induction of abnormal expression of ligands for stimulatory NK receptors.
Cyclophilin D inactivation protects axons in experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis
Authors: Forte Michael , Gold Bruce G. , Marracci Gail , Chaudhary Priya , Basso Emy , Johnsen Dustin , Yu Xiaolin , Fowlkes Jonathan , Rahder Micha , Stem Katie , Bernardi Paolo , Bourdette Dennis
Published: April 2007

Multiple sclerosis (MS) is the leading cause of neurological disability in young adults, affecting some two million people worldwide. Traditionally, MS has been considered a chronic, inflammatory disorder of the central white matter in which ensuing demyelination results in physical disability [Frohman EM, Racke MK, Raine CS (2006)
N Engl J Med
354:942–955]. More recently, MS has become increasingly viewed as a neurodegenerative disorder in which neuronal loss, axonal injury, and atrophy of the CNS lead to permanent neurological and clinical disability. Although axonal pathology and loss in MS has been recognized for >100 years, very little is known about the underlying molecular mechanisms. Progressive axonal loss in MS may stem from a cascade of ionic imbalances initiated by inflammation, leading to mitochondrial dysfunction and energetic deficits that result in mitochondrial and cellular Ca
2+
overload. In a murine disease model, experimental autoimmune encephalomyelitis (EAE) mice lacking cyclophilin D (CyPD), a key regulator of the mitochondrial permeability transition pore (PTP), developed EAE, but unlike WT mice, they partially recovered. Examination of the spinal cords of CyPD-knockout mice revealed a striking preservation of axons, despite a similar extent of inflammation. Furthermore, neurons prepared from CyPD-knockout animals were resistant to reactive oxygen and nitrogen species thought to mediate axonal damage in EAE and MS, and brain mitochondria lacking CyPD sequestered substantially higher levels of Ca
2+
. Our results directly implicate pathological activation of the mitochondrial PTP in the axonal damage occurring during MS and identify CyPD, as well as the PTP, as a potential target for MS neuroprotective therapies.
Utilizing genetic resources to enhance productivity of salt-prone land.
Authors: Munns R.
Published: April 2007

Unexplored biodiversity exists within crop species and their close relatives, which could be used to improve germplasm for salt-affected land. However, screening large germplasm collections for salt tolerance is difficult, and more specific and feasible selection techniques are required. Knowledge of the target environment and understanding of the genetic basis for salt tolerance of plants will help to choose the most appropriate screening method. Towards this end, the different types of salinity and the physiological and molecular mechanisms for salt tolerance are summarized in this review. There is great scope for improving the tolerance of important food and feed crops. Wheat, rice and alfalfa (lucerne), the most widely grown food and forage species, are used as examples of this approach.
Practicalities of developing and registering microbial biologicalcontrol agents.
Authors: Kiewnick S.
Published: April 2007

There is considerable interest in the exploitation of microbial biological control agents (MBCAs) for the control of crop pests, weeds and diseases. MBCAs can be used where chemical pesticides are banned or being phased out or where pests have developed resistance to standard chemicals. The use of MBCAs can play an important role in crop protection, as a key element in integrated pest management (IPM) programmes. However, despite considerable research efforts on the development of new biological control agents the number of such products on the market in the European Union (EU) is still extremely low compared with the USA or Canada. In areas that previously constrained the commercialization of MBCAs, discovery, fermentation, formulation and application, significant progress has been made. The low number of products is mainly due to the slow registration process. In the EU, MBCAs are regulated by and follow Directive 91/414/EEC for placing plant protection products in the market. Once an active ingredient is listed in Annex I, national registrations for the formulated product have to follow. This time consuming and expensive process has forced most companies to suspend their efforts in research and development. Initiatives by stakeholders from industry, science, regulatory authorities, policy and environment are underway to accelerate market introduction of MBCAs.
Transplanting large trees.
Authors: Harris J. R.
Published: April 2007

Rapid urbanization has resulted in an increased need for installed landscapes. Transplanting large trees (over 2m tall) into these urban and residential landscapes has become an essential practice because smaller trees do not have significant impact when first planted. In addition, poor site conditions and vandalism severely limit the chances that a newly planted small tree will eventually grow large enough to provide such intended services as cooling shade, air pollution and stormwater abatement, and psychological well-being. Transplanting large trees poses a different set of challenges to those normally encountered for transplanting small trees or annual agricultural crops. In addition to requiring longer attention to production details, large trees take much longer to fully establish after transplanting than small trees planted for reforestation purposes, and compared with annual agricultural crops, the long-term expectations for the transplanted large tree increase the importance of good transplanting techniques. This paper is a review of the biological underpinnings of the challenges encountered when transplanting large trees and how these challenges have been identified and addressed.
Libaffy: software for processing Affymetrix(R) GeneChip(R) data
Authors: Eschrich Steven A. , Hoerter Andrew M.
Published: April 2007

Summary: Affymetrix(R) GeneChip(R) microarrays are increasingly used in gene expression studies and in greater number. A software library was developed that supports Affymetrix file formats and implements two popular summary algorithms (MAS5.0 and RMA). The library is modular in design for integration into larger systems and processing pipelines. Additionally, a graphical interface (GENE) was developed to allow end-user access to the functionality within the library.

Availability: libaffy is free to use under the GNU GPL license. The source code and Windows binaries can be freely accessed from the website http://src.moffitt.usf.edu/libaffy. Additional API documentation and user manual are available.

Contact:  Steven.Eschrich@moffitt.org
Human recombination rates are increased around accelerated conserved regions—evidence for continued selection?
Authors: Freudenberg Jan , Fu Ying-Hui , Ptáček Louis J.
Published: April 2007

Motivation: We hypothesized that recombination rates might be increased at genetic loci that are subject to more intense selection. Here, we test this hypothesis by using a recently published set of accelerated conserved regions and fine-scale recombination rate estimates provided by the HapMap project.

Results: We observed that fine-scale recombination rates are increased around conserved noncoding regions that show accelerated evolution in human or chimp, as compared to noncoding regions showing accelerated evolution in mouse and those being conserved between human and fugu. Recombination rates around hominid accelerated conserved regions (ACRs) are furthermore increased as compared to exonic regions. On the other hand, GC-content is reduced around ACRs, excluding a major confounding influence of GC-content on the observed variation in recombination rate.

Conclusion: Our observations indicate that selection intensity could be an important determinant of local recombination rate variation and that continued positive selection might act at many ACR loci. Alternatively, a confounding factor needs to be found that causes a congruent signal in recombination rate estimates based on human polymorphism data and in the comparative genomic data. Researchers who consider the explanation involving selection as more likely may expect more common functional sequence variants at ACRs in genetic association studies.

Contact:  jan.freudenberg@ucsf.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Two-stage designs applying methods differing in costs
Authors: Goll Alexandra , Bauer Peter
Published: April 2007

Motivation: Two-stage pilot and integrated designs are powerful tools for investigating large numbers of hypotheses. Asymptotically, optimal two-stage designs controlling the familywise error or false discovery rate are considered when costs and effect sizes per measurement differ between stages and total costs are constrained.

Results: Depending on the cost and effect size ratios between the measurements, it is generally more powerful to apply two-stage procedures using one measurement method at both stages. For the practically relevant case that the same method is applied at both stages but designing the second-stage measurements raises extra costs, two-stage designs are more powerful than the single-stage design even for large costs ratios. The power of the optimal pilot and integrated two-stage designs generally are similar, however, the integrated approach is less sensitive even to severe design misspecifications in the planning phase.

Availability: R-programs (R, 2005) to calculate asymptotically optimal designs are available on: http://statistics.msi.meduniwien.ac.at/index.php?page=ao2stage

Contact:  alexandra.goll@meduniwien.ac.at
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks
Authors: Ching Wai-Ki , Zhang Shuqin , Ng Michael K. , Akutsu Tatsuya
Published: April 2007

Motivation: Probabilistic Boolean networks (PBNs) have been proposed to model genetic regulatory interactions. The steady-state probability distribution of a PBN gives important information about the captured genetic network. The computation of the steady-state probability distribution usually includes construction of the transition probability matrix and computation of the steady-state probability distribution. The size of the transition probability matrix is 2n-by-2n where n is the number of genes in the genetic network. Therefore, the computational costs of these two steps are very expensive and it is essential to develop a fast approximation method.

Results: In this article, we propose an approximation method for computing the steady-state probability distribution of a PBN based on neglecting some Boolean networks (BNs) with very small probabilities during the construction of the transition probability matrix. An error analysis of this approximation method is given and theoretical result on the distribution of BNs in a PBN with at most two Boolean functions for one gene is also presented. These give a foundation and support for the approximation method. Numerical experiments based on a genetic network are given to demonstrate the efficiency of the proposed method.

Contact:  sqzhang@hkusua.hku.hk

Supplementary information: Supplementary data are available at Bioinformatics online.
iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences
Authors: Gaëta Bruno A. , Malming Harald R. , Jackson Katherine J.L. , Bain Michael E. , Wilson Patrick , Collins Andrew M.
Published: April 2007

Motivation: Immunoglobulin heavy chain (IGH) genes in mature B lymphocytes are the result of recombination of IGHV, IGHD and IGHJ germline genes, followed by somatic mutation. The correct identification of the germline genes that make up a variable VH domain is essential to our understanding of the process of antibody diversity generation as well as to clinical investigations of some leukaemias and lymphomas.

Results: We have developed iHMMune-align, an alignment program that uses a hidden Markov model (HMM) to model the processes involved in human IGH gene rearrangement and maturation. The performance of iHMMune-align was compared to that of other immunoglobulin gene alignment utilities using both clonally related and randomly selected IGH sequences. This evaluation suggests that iHMMune-align provides a more accurate identification of component germline genes than other currently available IGH gene characterization programs.

Availability: iHMMune-align cross-platform Java executable and web interface are freely available to academic users and can be accessed at http://www.emi.unsw.edu.au/~ihmmune/

Contact: bgaeta@cse.unsw.edu.au
Meta-analysis of gene expression data: a predictor-based approach
Authors: Fishel Irit , Kaufman Alon , Ruppin Eytan
Published: April 2007

Motivation: With the increasing availability of cancer microarray data sets there is a growing need for integrative computational methods that evaluate multiple independent microarray data sets investigating a common theme or disorder. Meta-analysis techniques are designed to overcome the low sample size typical to microarray experiments and yield more valid and informative results than each experiment separately.

Results: We propose a new meta-analysis technique that aims at finding a set of classifying genes, whose expression level may be used to answering the classification question in hand. Specifically, we apply our method to two independent lung cancer microarray data sets and identify a joint core subset of genes which putatively play an important role in tumor genesis of the lung. The robustness of the identified joint core set is demonstrated on a third unseen lung cancer data set, where it leads to successful classification using very few top-ranked genes. Identifying such a set of genes is of significant importance when searching for biologically meaningful biomarkers.

Contact: ruppin@post.tau.ac.il

Supplementary information: Supplementary data are available at Bioinformatics online.
A network-based method for target selection in metabolic networks
Authors: Guimerà R. , Sales-Pardo M. , Amaral L.A.N.
Published: April 2007

Motivation: The lack of new antimicrobials, combined with increasing microbial resistance to old ones, poses a serious threat to public health. With hundreds of genomes sequenced, systems biology promises to help in solving this problem by uncovering new drug targets.

Results: Here, we propose an approach that is based on the mapping of the interactions between biochemical agents, such as proteins and metabolites, onto complex networks. We report that nodes and links in complex biochemical networks can be grouped into a small number of classes, based on their role in connecting different functional modules. Specifically, for metabolic networks, in which nodes represent metabolites and links represent enzymes, we demonstrate that some enzyme classes are more likely to be essential, some are more likely to be species-specific and some are likely to be both essential and specific. Our network-based enzyme classification scheme is thus a promising tool for the identification of drug targets.

Contact: rguimera@northwestern.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method
Authors: Fujita A. , Sato J.R. , Garay-Malpartida H.M. , Morettin P.A. , Sogayar M.C. , Ferreira C.E.
Published: April 2007

Motivation: A variety of biological cellular processes are achieved through a variety of extracellular regulators, signal transduction, protein–protein interactions and differential gene expression. Understanding of the mechanisms underlying these processes requires detailed molecular description of the protein and gene networks involved. To better understand these molecular networks, we propose a statistical method to estimate time-varying gene regulatory networks from time series microarray data. One well known problem when inferring connectivity in gene regulatory networks is the fact that the relationships found constitute correlations that do not allow inferring causation, for which, a priori biological knowledge is required. Moreover, it is also necessary to know the time period at which this causation occurs. Here, we present the Dynamic Vector Autoregressive model as a solution to these problems.

Results: We have applied the Dynamic Vector Autoregressive model to estimate time-varying gene regulatory networks based on gene expression profiles obtained from microarray experiments. The network is determined entirely based on gene expression profiles data, without any prior biological knowledge. Through construction of three gene regulatory networks (of p53, NF-κB and c-myc) for HeLa cells, we were able to predict the connectivity, Granger-causality and dynamics of the information flow in these networks.

Contact: cef@ime.usp.br

Supplementary information: Additional figures may be found at http://mariwork.iq.usp.br/dvar/
OSLay: optimal syntenic layout of unfinished assemblies
Authors: Richter Daniel C. , Schuster Stephan C. , Huson Daniel H.
Published: April 2007

Summary: The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure.

Motivation: To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly.

Availability: OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay

Contact: drichter@informatik.uni-tuebingen.de
SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates
Authors: Hayes Ben J. , Nilsen Kjetil , Berg Paul R. , Grindflek Eli , Lien Sigbjørn
Published: April 2007

Motivation: Single nucleotide polymorphism (SNP) detection exploiting redundancy in expressed sequence tag (EST) collections that arises from the presence of transcripts of the same gene from different individuals has been used to generate large collections of SNPs for many species. A second source of redundancy, namely that EST collections can contain multiple transcripts of the same gene from the same individual, can be exploited to distinguish true SNPs from sequencing error. In this article, we demonstrate with Atlantic salmon and pig EST collections that splitting the EST collection in two, detecting SNPs in both subsets, then accepting only cross-validated SNPs increases validation rates.

Results: In the pig data set, 676 cross-validated putative SNPs were detected in a collection of 160 689 ESTs. When validating a subset of these by genotyping on MassARRAY 85.1% of SNPs were polymorphic in successful assays. In the salmon data set, 856 cross-validated putative SNPs were detected in a collection of 243 674 ESTs. Validation by genotyping showed that 81.0% of the cross-validated putative SNPs were polymorphic in successful assays.

Availability: Cross-validated SNPs are available at dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/), ss69371838-ss69372575 for the salmon SNPs and ss69372587-ss69373226 for the pig SNPs.

Contact: ben.hayes@dpi.vic.gov.au
The qualitative and time-dependent character of spatial relations in biomedical ontologies
Authors: Bittner Thomas , Goldberg Louis J.
Published: April 2007

Motivation: The formal representation of mereological aspects of canonical anatomy (parthood relations) is relatively well understood. The formal representation of other aspects of canonical anatomy, such as connectedness and adjacency relations between anatomical parts, their shape and size as well as the spatial arrangement of anatomical parts within larger anatomical structures are, however, much less well understood and represented in existing computational anatomical and bio-medical ontologies only insufficiently.

Results: In this article, we provide a methodology of how to incorporate this kind of information into anatomical and bio-medical ontologies by applying techniques of representing qualitative spatial information from Artificial Intelligence. In particular, we focus on how to explicitly take into account the qualitative and time-dependent character of these relations. As a running example, we use the human temporomandibular joint (TMJ).

Availability: Using the presented methodology, a formal ontology was developed which is accessible on http://www.ifomis.org/bfo/fol. This ontology may help to improve the logical and ontological rigor of bio-medical ontologies such as the OBO relation ontology.

Contact: bittner3@buffalo.edu
SciRoKo: a new tool for whole genome microsatellite search and investigation
Authors: Kofler Robert , Schlötterer Christian , Lelley Tamas
Published: April 2007

Summary: SciRoKo is a user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo an excellent tool for full genome analysis. Compared to other already existing tools, SciRoKo also allows the analysis of compound microsatellites.

Availability: free for use: www.kofler.or.at/Bioinformatics

Contact: robert.kofler@boku.ac.at

Supplementary information: Supplementary data are available at Bioinformatics online.
Faspad: fast signaling pathway detection
Authors: Hüffner Falk , Wernicke Sebastian , Zichner Thomas
Published: April 2007

Summary: Faspad is a user-friendly tool that detects candidates for linear signaling pathways in protein interaction networks based on an approach by Scott et al. (Journal of Computational Biology, 2006). Using recent algorithmic insights, it can solve the underlying NP-hard problem quite fast: for protein networks of typical size (several thousand nodes), pathway candidates of length up to 13 proteins can be found within seconds and with a 99.9% probability of optimality. Faspad graphically displays all candidates that are found; for evaluation and comparison purposes, an overlay of several candidates and the surrounding network context can also be shown.

Availability: Faspad is available as free software under the GPL license at http://theinf1.informatik.uni-jena.de/faspad/ and runs under Linux and Windows.

Contact: hueffner@minet.uni-jena.de
Improved seawater depth determination using corrected helicopter time‐domain electromagnetic data
Authors: Vrbancich Julian , Fullagar Peter K.
Published: April 2007

Two areas within Sydney Harbour were surveyed in 2002 with a helicopter‐borne time‐domain electromagnetic system to test its potential for bathymetric mapping in shallow seawater. As delivered, the data were improperly calibrated. Therefore a re‐calibration was performed to reconcile the measured data with ‘ground truth’. Synthetic electromagnetic transients were computed for two‐layer models representing the seawater and the sediment overlying bedrock at a number of locations within the survey area. The seawater depth in the models varied between 3 m and 70 m. The measured and calculated data were compared at each delay time, and were found to be linearly related. The slope and intercept of the line of best fit were used to correct all the measured data. Inversion of the corrected time‐domain electromagnetic data generally resolved the bathymetry to submetre accuracy down to depths of about 55 m.
Orchids of the West Indies: predictability of diversity and endemism
Authors: Ackerman J. D. , Trejo‐Torres J. C. , Crespo‐Chuy Y.
Published: April 2007

Aim We examined phytogeographical patterns of West Indian orchids, and related island area and maximum elevation with orchid species richness and endemism. We expected strong species–area relationships, but that these would differ between low and montane island groups. In so far as maximum island elevation is a surrogate for habitat diversity, we anticipated a strong relationship with maximum elevation and both species richness and endemism for montane islands.

Location The West Indies.

Methods Our data included 49 islands and 728 species. Islands were classified as either montane (≥ 300 m elevation) or low (< 300 m). Linear and multivariate regression analyses were run to detect relationships between either area or maximum island elevation and species richness or the number of island endemic species.

Results For all 49 islands, the species–area relationship was strong, producing az‐value of 0.47 (slope of the regression line) and explaining 46% of the variation. For 18 relatively homogeneous, low islands we found a non‐significant slope ofz = −0.01 that explained only 0.1% of the variation. The 31 montane islands had a highly significant species–area relationship, withz = 0.49 and accounting for 65% of the variation. Species numbers were also strongly related to maximum island elevation. For all islands < 750 km2, we found a small‐island effect, which reduced the species–area relationship to a non‐significantz = 0.16, with only 5% of the variation explained by the model. Species–area relationships for montane islands of at least 750 km2were strong and significant, but maximum elevation was the best predictor of species richness and accounted for 79% of the variation. The frequency of single‐island endemics was high (42%) but nearly all occurred on just nine montane islands (300 species). The taxonomic distribution of endemics was also skewed, suggesting that seed dispersability, while remarkable in some taxa, is very limited in others. Montane island endemics showed strong species–area and species–elevation relationships.

Main conclusions Area and elevation are good predictors of orchid species diversity and endemism in the West Indies, but these associations are driven by the extraordinarily strong relationships of large, montane islands. The species richness of low islands showed no significant relationship with either variable. A small‐island effect exists, but the montane islands had a significant relationship between species diversity and maximum elevation. Thus, patterns of Caribbean orchid diversity are dependent on an interplay between area and topographic diversity.
An artificial prosthesis to reconstruct donor defects following facial transplantation
Authors: Renshaw Anthony , Chooneea Teerathraj , Clarke Alex , Butler Peter E.
Published: April 2007

Abstract:  Post‐harvest donor facial appearance is likely to have an impact on both the donor family and the transplant harvest team. We describe a method of fabricating a donor‐specific artificial prosthesis, which can be constructed within the time frame of the facial graft harvest.
Different mechanisms can lead to the same altered HLA class I phenotype in tumors
Authors: Rodriguez T. , Aptsiauri N. , Méndez R. , Jimenez P. , Ruiz‐Cabello F. , Garrido F
Published: April 2007

Human leukocyte antigen (HLA) class I plays an important role in tumor recognition and rejection. Total or selective losses of HLA class I antigens (classified into seven HLA class I altered phenotypes) represent one of the main routes of tumor escape from immune surveillance. Abnormal expression of HLA class I has been reported in different human tumor samples with distinct underlying mechanisms. Notably, different molecular mechanisms can generate the same altered HLA class I phenotype. Here, we describe various molecular mechanisms that can lead to HLA total loss or downregulation (phenotype I) in melanoma, colorectal carcinoma and bladder cancer.
Clinical significance of donor–recipient HLA matching on survival after myeloablative hematopoietic cell transplantation from unrelated donors
Authors: Petersdorf E. W. , Gooley T. , Malkki M. , Horowitz M. ,   for The International Histocompatibility Working Group in Hematopoietic Cell Transplantation
Published: April 2007

The application of unrelated donor hematopoietic cell transplantation can be expanded with the use of mismatched donors if human leukocyte antigen (HLA) disparity does not lead to increased morbidity and mortality. The rules that govern permissibility of HLA mismatches are not well defined. The International Histocompatibility Working Group in hematopoietic cell transplantation measured the risks associated with locus‐specific disparity in 4796 patients transplanted for low, intermediate, or high‐risk hematologic diseases. The permissibility of a given HLA mismatch is in part defined by the locus and by disease risk.
Cloning and sequencing alleles of the KIR2DL4 gene from genomic DNA samples
Authors: Roberts C. H. , Madrigal J. A. , Marsh S. G. E.
Published: April 2007

Killer‐cell immunoglobulin‐like receptor (KIR) genes are highly polymorphic and polymorphisms have been found in all KIR exons. Although less is known of the introns, these also appear to be polymorphic. To generate a comprehensive database of KIR genomic sequences, which will aid in the design of KIR typing reagents, we have established a method for cloning and sequencing of KIR genes from genomic DNA. We cloned and sequenced the entire KIR2DL4 gene from genomic DNA using long template touchdown PCR and high capacity cloning vectors. Overlapping secondary amplicons were modified to include a nucleotide analogue that reduced sequencing problems associated with secondary structure formation in the KIR sequence. Using a modified sequencing chemistry we were able to sequence approximately 11,000 bases confirming the previously published KIR2DL4*005 allele sequence.
Functions of HLA‐G in the immune system
Authors: Favier B. , LeMaoult J. , Carosella E. D.
Published: April 2007

Human leukocyte antigen (HLA)‐G is a nonclassical HLA class I molecule that has tolerogenic functions and acts on cells of both innate and adaptive immunity. The molecular mechanism leading to tolerance involves the interaction between HLA‐G and inhibitory receptors that are expressed at the surface of immune cells. In this review, we will briefly summarize the key advances on the relationships between HLA‐G and the immune system and their consequences in pathology.
14th International HLA and Immunogenetics Workshop: Report on joint study on MHC and infection
Authors: Mehra N. K. , Kaur G.
Published: April 2007

The ‘MHC and Infection’ study of the 14th International HLA and Immunogenetics Workshop was undertaken to evaluate the contribution of specific variants of major histocompatibility complex (MHC) and non‐MHC genes that are specifically associated with higher probabilities of infection, disease severity, and progression in different populations.
Schirmer tear test, phenol red thread tear test, eye blink frequency and corneal sensitivity in the guinea pig
Authors: Trost Katrin , Skalicky M. , Nell Barbara
Published: April 2007

Objective To establish reference values for Schirmer tear tests (STT) I and II, phenol red thread (PRT) tear test and eye blink frequency, and to determine corneal sensitivity for normal guinea pigs.

Animals studied One hundred and eight eyes of 54 adult Duncan‐Hartley guinea pigs.

Procedure Schirmer tear test (STT) I and then STT II were performed in 36 guinea pigs. PRT and STT I were compared in 18 adult Duncan‐Hartley guinea pigs. Corneal sensitivity was determined in 23 guinea pigs by evaluating the corneal touch threshold (CTT) of five different regions using a Cochet‐Bonnet esthesiometer. Eye blink frequency was measured in 10 guinea pigs over a period of 20 min and in 17 guinea pigs over a period of 10 min.

Results Mean STT I was 0.36 mm ± 1.09 mm (wetting/min) and mean STT II was 0.43 mm ± 1.29 mm (wetting/min). There was no significant difference between mean STT I and mean STT II (P = 0.79). The mean PRT‐value was 16 ± 4.7 mm (wetting/15 s), and the mean STT I‐value in the same guinea pigs was 0.6 ± 1.83 mm (wetting/min). Corneal sensitivity was significantly higher in the center than in the four limbal regions. The mean CTT for central, ventral, nasal, temporal and dorsal regions was 2, 1.7, 1.7, 1.7 and 1.6 cm or 3.7, 5.2, 5.6, 5.7 and 6.4 g/mm2, respectively. Eye blink frequency was between two to five (mean 3.4 ± 1.04) blinks per eye over 20 min in guinea pigs in their home environment, while in handheld and restrained guinea pigs eye blink frequency showed a variation between 0 and 17 blinks per eye (mean 3.24 ± 3.64 blinks per eye) over 10 min.

Conclusions As there were no significant differences between STT I and STT II results, reflex tear secretion in the guinea pig may not exist. The most likely explanation is a lower corneal sensitivity in the guinea pig than in other species, such as cats, dogs and horses. Because of the small amount of tears, PRT is the preferred test for tear measurement in the guinea pig.
International Trade with a Public Intermediate Good and the Gains from Trade*
Authors: Suga Nobuhito , Tawada Makoto
Published: April 2007

This paper presents a one‐primary factor, two‐consumer good, and two‐country model of international trade where each country’s government supplies a country‐specific public intermediate good so as to attain efficient production. By introducing the Marshallian adjustment process, it is demonstrated that the country with larger factor endowment exports the good whose productivity is more sensitive to the public intermediate good. Our normative analysis of free trade shows the following results. First, at least one country gains from trade. Secondly, if a country incompletely specializes in the trading equilibrium, the country necessarily loses from trade.