bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significant Deviations in the Configurations of Homologous Tandem Repeats in Prokaryotic Genomes
Authors: Hirayama Shintaro , Mizuta Satoshi 
Published: February 2010

AbstractWe explored the possibilities of whole-genome duplication (WGD) in prokaryotic species, where we performed statistical analyses of the configurations of the central angles between homologous tandem repeats (TRs) on the circular chromosomes. At first, we detected TRs on their chromosomes and identified equivalent tandem repeat pairs (ETRPs); here, an ETRP is defined as a pair of tandem repeats sequentially similar to each other. Then we carried out statistical analyses of the central angle distributions of the detected ETRPs on each circular chromosome by way of comparisons between the detected distributions and those generated by null models. In the analyses, we estimated a P value by a simulation using the Kullback–Leibler divergence as a distance measure between two distributions. As a result, the central angle distributions for 8 out of the 203 prokaryotic species showed statistically significant deviations (P&lt;0.05). In particular, we found out the characteristic feature of one round of WGD in Photorhabdus luminescens genome and that of two rounds of WGD in Escherichia coli K12.
In SilicoCharacterization and Homology Modeling of Thylakoid Bound Ascorbate Peroxidase from a Drought Tolerant Wheat Cultivar
Authors: Katiyar A. , Lenka S.K. , Lakshmi K. , Chinnusamy V. , Bansal K.C. 
Published: February 2010

AbstractAscorbate peroxidase, a haem protein (EC 1.11.1.11), efficiently scavenges hydrogen peroxide (H2O2) in cytosol and chloroplasts of plants. In this study, a full-length coding sequence of thylakoid-bound ascorbate peroxidase cDNA (TatAPX) was cloned from a drought tolerant wheat cultivar C306. Homology modeling of the TatAPX protein was performed by using the template crystal structure of chloroplastic ascorbate peroxidase from tobacco plant (PDB: 1IYN). The model structure was further refined by molecular mechanics and dynamic methods using various tools such as PROCHECK, ProSA and Verify3D. The predicted model was then tested for docking with H2O2, the substrate for TatAPX enzyme. The results revealed that Arg233 and Glu255 in the predicted active site of the enzyme are two important amino acid residues responsible for strong hydrogen bonding affinity with H2O2, which might play an important role in scavenging of H2O2 from the plant system.
Large-Scale Analyses of Glycosylation in Cellulases
Authors: Zhou Fengfeng , Olman Victor , Xu Ying 
Published: February 2010

Abstract
Cellulases are important glycosyl hydrolases (GHs) that hydrolyze cellulose polymers into smaller oligosaccharides by breaking the cellulose β (1→4) bonds, and they are widely used to produce cellulosic ethanol from the plant biomass. N-linked and O-linked glycosylations were proposed to impact the catalytic efficiency, cellulose binding affinity and the stability of cellulases based on observations of individual cellulases. As far as we know, there has not been any systematic analysis of the distributions of N-linked and O-linked glycosylated residues in cellulases, mainly due to the limited annotations of the relevant functional domains and the glycosylated residues. We have computationally annotated the functional domains and glycosylated residues in cellulases, and conducted a systematic analysis of the distributions of the N-linked and O-linked glycosylated residues in these enzymes. Many N-linked glycosylated residues were known to be in the GH domains of cellulases, but they are there probably just by chance, since the GH domain usually occupies more than half of the sequence length of a cellulase. Our analysis indicates that the O-linked glycosylated residues are significantly enriched in the linker regions between the carbohydrate binding module (CBM) domains and GH domains of cellulases. Possible mechanisms are discussed.
A Modified Ant Colony Optimization Algorithm for Tumor Marker Gene Selection
Authors: Yu Hualong , Gu Guochang , Liu Haibo , Shen Jing , Zhao Jing 
Published: February 2010

Abstract
Microarray data are often extremely asymmetric in dimensionality, such as thousands or even tens of thousands of genes but only a few hundreds of samples or less. Such extreme asymmetry between the dimensionality of genes and samples can lead to inaccurate diagnosis of disease in clinic. Therefore, it has been shown that selecting a small set of marker genes can lead to improved classification accuracy. In this paper, a simple modified ant colony optimization (ACO) algorithm is proposed to select tumor-related marker genes, and support vector machine (SVM) is used as classifier to evaluate the performance of the extracted gene subset. Experimental results on several benchmark tumor microarray datasets showed that the proposed approach produces better recognition with fewer marker genes than many other methods. It has been demonstrated that the modified ACO is a useful tool for selecting marker genes and mining high dimension data.
Bioorganometallic mechanism of action, and inhibition, of IspH
Authors: Wang Weixue , Wang Ke , Liu Yi-Liang , No Joo-Hwan , Li Jikun , Nilges Mark J. , Oldfield Eric 
Published: February 2010

We have investigated the mechanism of action of
Aquifex aeolicus
IspH [E-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) reductase], together with its inhibition, using a combination of site-directed mutagenesis (
K

M

,
V
max
), EPR and
1
H,
2
H,
13
C,
31
P, and
57
Fe-electron-nuclear double resonance (ENDOR) spectroscopy. On addition of HMBPP to an (unreactive) E126A IspH mutant, a reaction intermediate forms that has a very similar EPR spectrum to those seen previously with the HMBPP “parent” molecules, ethylene and allyl alcohol, bound to a nitrogenase FeMo cofactor. The EPR spectrum is broadened on
57
Fe labeling and there is no evidence for the formation of allyl radicals. When combined with ENDOR spectroscopy, the results indicate formation of an organometallic species with HMBPP, a
π
/
σ
“metallacycle” or
η
2
-alkenyl complex. The complex is poised to interact with H
+
from E126 (and H124) in reduced wt IspH, resulting in loss of water and formation of an
η
1
-allyl complex. After reduction, this forms an
η
3
-allyl
π
-complex (i.e. containing an allyl anion) that on protonation (at C2 or C4) results in product formation. We find that alkyne diphosphates (such as propargyl diphosphate) are potent IspH inhibitors and likewise form metallacycle complexes, as evidenced by
1
H,
2
H, and
13
C ENDOR, where hyperfine couplings of approximately 6 MHz for
13
C and 10 MHz for
1
H, are observed. Overall, the results are of broad general interest because they provide new insights into IspH catalysis and inhibition, involving organometallic species, and may be applicable to other Fe
4
S
4
-containing proteins, such as IspG.
A new emission inventory for nonagricultural open fires in Asia from 2000 to 2009
Authors: Song Yu , Chang Di , Liu Bing , Miao Weijie , Zhu Lei , Zhang Yuanhang 
Published: February 2010

Open fires play a significant role in atmospheric pollution and climatic change. This work aims to develop an emission inventory for nonagricultural open fires in Asia using the newly released MODIS (Moderate Resolution Imaging Spectroradiometer) burned area product (MCD45A1), as the MODIS sensor cannot efficiently detect field crop residue burning. Country-level or province-specific biomass density data were used as fuel loads. Moisture contents were taken into account when calculating combustion factors for grass fuel. During the nine fire years 2000–2008, both burned areas and fire emissions clearly presented spatial and seasonal variations. Extensive nonagricultural open fires were concentrated in the months of February and March, while another peak was between August and October. Indonesia was the most important contributor to fire emission, which was largely attributable to peat burning. Myanmar, India, and Cambodia together contributed approximately half of the total burned area and emission. The annual emissions for CO2, CO, CH4, NMHCs, NOx, NH3, SO2, BC, OC, PM2.5, and PM10were 83 (69–103), 6.1 (4.6–8.2), 0.38 (0.24–0.57), 0.64 (0.36–1.0), 0.085 (0.074–0.10), 0.31 (0.17–0.48), 0.030 (0.024–0.037), 0.023 (0.020–0.028), 0.27 (0.22–0.33), 2.0 (1.6–2.6), and 2.2 (1.7–2.9) Tg yr− 1, respectively. This inventory has a daily temporal resolution and 500 m spatial resolution, and covers a long period, from April 2000 to February 2009. It could be used in global and regional air quality modeling.
DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data
Authors: Hollunder Jens , Friedel Maik , Kuiper Martin , Wilhelm Thomas 
Published: February 2010

Abstract
Summary: Many large ‘omics’ datasets have been published and many more are expected in the near future. New analysis methods are needed for best exploitation. We have developed a graphical user interface (GUI) for easy data analysis. Our discovery of all significant substructures (DASS) approach elucidates the underlying modularity, a typical feature of complex biological data. It is related to biclustering and other data mining approaches. Importantly, DASS-GUI also allows handling of multi-sets and calculation of statistical significances. DASS-GUI contains tools for further analysis of the identified patterns: analysis of the pattern hierarchy, enrichment analysis, module validation, analysis of additional numerical data, easy handling of synonymous names, clustering, filtering and merging. Different export options allow easy usage of additional tools such as Cytoscape.
Availability: Source code, pre-compiled binaries for different systems, a comprehensive tutorial, case studies and many additional datasets are freely available at http://www.ifr.ac.uk/dass/gui/. DASS-GUI is implemented in Qt.
Contact: jehol@psb.vib-ugent.be; thomas.wilhelm@bbsrc.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
A meta-analysis of two-dimensional electrophoresis pattern of the Parkinson's disease-related protein DJ-1
Authors: Natale Massimo , Bonino Dario , Consoli Paolo , Alberio Tiziana , Ravid Rivka G. , Fasano Mauro , Bucci Enrico M. 
Published: February 2010

AbstractMotivation: The two-dimensional electrophoresis (2-DE) pattern of proteins is thought to be specifically related to the physiological or pathological condition at the moment of sample preparation. On this ground, most proteomic studies move to identify specific hallmarks for a number of different conditions. However, the information arising from these investigations is often incomplete due to inherent limitations of the technique, to extensive protein post-translational modifications and sometimes to the paucity of available samples.The meta-analysis of proteomic data can provide valuable information pertinent to various biological processes that otherwise remains hidden.Results: Here, we show a meta-analysis of the PD protein DJ-1 in heterogeneous 2-DE experiments. The protein was shown to segregate into specific clusters associated with defined conditions.Interestingly, the DJ-1 pool from neural tissues displayed a specific and characteristic molecular weight and isoelectric point pattern. Moreover, changes in this pattern have been related to neurodegenerative processes and aging. These results were experimentally validated on human brain specimens from control subjects and PD patients.Availability: ImageJ is a public domain image processing program developed by the National Institutes of Health and is freely available at http://rsbweb.nih.gov/ij. All the ImageJ macros used in this study are available as supplementary material and upon request at info@biodigitalvalley.com. XLSTAT can be purchased online at http://www.xlstat.com/en/home/ at a current cost of ∼300 EUR.Contact: enrico.bucci@biodigitalvalley.comSupplementary information: Supplementary data are available at Bioinformatics online.
Adherence to the medical regime in patients with heart failure
Authors: Muzzarelli Stefano , Brunner‐La Rocca Hanspeter , Pfister Otmar , Foglia Pietro , Moschovitis Giorgio , Mombelli Giorgio , Stricker Hans 
Published: February 2010

AimsTo assess adherence to medical treatment in patients with heart failure (HF) using a specific questionnaire and measurement of the serum concentration of digoxin.Methods and resultsForty patients with symptomatic HF and a clinical indication for digoxin were included in this pilot study. The assessment of adherence to the medical regime was based on two different methods: (i) the CARDIA‐Questionnaire and (ii) the measurement of serum digoxin concentration (SDC) at 1 and 6 months. All patients were placed on digoxin treatment (target SDC 0.6–0.8 ng/mL) at baseline. Poor adherence was defined if the patient self‐reported taking ≤75% of the prescribed HF medication or had an SDC < 0.4 ng/mL (subtherapeutic range) at the follow‐up visits. During the entire follow‐up, the proportion of patients with poor adherence was 15% as assessed by the questionnaire, 20% as assessed by the SDC, and 25% if both methods were combined.ConclusionAlthough HF is a symptomatic disease, the proportion of patients with poor adherence to the medical regime in our study was high (up to 25%). The objective methodology based on the measurement of the SDC identified a higher number of patients with poor adherence when compared with the CARDIA‐Questionnaire.
Tracing Cadmium from Culture to Spikelet: Noninvasive Imaging and Quantitative Characterization of Absorption, Transport, and Accumulation of Cadmium in an Intact Rice Plant
Authors: Fujimaki Shu , Suzui Nobuo , Ishioka Noriko S. , Kawachi Naoki , Ito Sayuri , Chino Mitsuo , Nakamura Shin-ichi 
Published: February 2010

Abstract
We characterized the absorption and short-term translocation of cadmium (Cd) in rice (Oryza sativa ‘Nipponbare’) quantitatively using serial images observed with a positron-emitting tracer imaging system. We fed a positron-emitting 107Cd (half-life of 6.5 h) tracer to the hydroponic culture solution and noninvasively obtained serial images of Cd distribution in intact rice plants at the vegetative stage and at the grain-filling stage every 4 min for 36 h. The rates of absorption of Cd by the root were proportional to Cd concentrations in the culture solution within the tested range of 0.05 to 100 nm. It was estimated that the radial transport from the culture to the xylem in the root tissue was completed in less than 10 min. Cd moved up through the shoot organs with velocities of a few centimeters per hour at both stages, which was obviously slower than the bulk flow in the xylem. Finally, Cd arrived at the panicles 7 h after feeding and accumulated there constantly, although no Cd was observed in the leaf blades within the initial 36 h. The nodes exhibited the most intensive Cd accumulation in the shoot at both stages, and Cd transport from the basal nodes to crown root tips was observed at the vegetative stage. We conclude that the nodes are the central organ where xylem-to-phloem transfer takes place and play a pivotal role in the half-day travel of Cd from the soil to the grains at the grain-filling stage.
Nonhost Resistance of Barley to Different Fungal Pathogens Is Associated with Largely Distinct, Quantitative Transcriptional Responses
Authors: Zellerhoff Nina , Himmelbach Axel , Dong Wubei , Bieri Stephane , Schaffrath Ulrich , Schweizer Patrick 
Published: February 2010

Abstract
Nonhost resistance protects plants against attack by the vast majority of potential pathogens, including phytopathogenic fungi. Despite its high biological importance, the molecular architecture of nonhost resistance has remained largely unexplored. Here, we describe the transcriptional responses of one particular genotype of barley (Hordeum vulgare subsp. vulgare ‘Ingrid’) to three different pairs of adapted (host) and nonadapted (nonhost) isolates of fungal pathogens, which belong to the genera Blumeria (powdery mildew), Puccinia (rust), and Magnaporthe (blast). Nonhost resistance against each of these pathogens was associated with changes in transcript abundance of distinct sets of nonhost-specific genes, although general (not nonhost-associated) transcriptional responses to the different pathogens overlapped considerably. The powdery mildew- and blast-induced differences in transcript abundance between host and nonhost interactions were significantly correlated with differences between a near-isogenic pair of barley lines that carry either the Mlo wild-type allele or the mutated mlo5 allele, which mediates basal resistance to powdery mildew. Moreover, during the interactions of barley with the different host or nonhost pathogens, similar patterns of overrepresented and underrepresented functional categories of genes were found. The results suggest that nonhost resistance and basal host defense of barley are functionally related and that nonhost resistance to different fungal pathogens is associated with more robust regulation of complex but largely nonoverlapping sets of pathogen-responsive genes involved in similar metabolic or signaling pathways.
TheArabidopsisRNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci
Authors: Havecker Ericka R. , Wallbridge Laura M. , Hardcastle Thomas J. , Bush Maxwell S. , Kelly Krystyna A. , Dunn Ruth M. , Schwach Frank , Doonan John H. , Baulcombe David C. 
Published: February 2010

AbstractArgonaute (AGO) effectors of RNA silencing bind small RNA (sRNA) molecules and mediate mRNA cleavage, translational repression, or epigenetic DNA modification. In many organisms, these targeting mechanisms are devolved to different products of AGO multigene families. To investigate the basis of AGO functional diversification, we characterized three closely related Arabidopsis thaliana AGOs (AGO4, AGO6, and AGO9) implicated in RNA-directed DNA methylation. All three AGOs bound 5′ adenosine 24-nucleotide sRNAs, but each exhibited different preferences for sRNAs from different heterochromatin-associated loci. This difference was reduced when AGO6 and AGO9 were expressed from the AGO4 promoter, indicating that the functional diversification was partially due to differential expression of the corresponding genes. However, the AGO4-directed pattern of sRNA accumulation and DNA methylation was not fully recapitulated with AGO6 or AGO9 expressed from the AGO4 promoter. Here, we show that sRNA length and 5′ nucleotide do not account for the observed functional diversification of these AGOs. Instead, the selectivity of sRNA binding is determined by the coincident expression of the AGO and sRNA-generating loci, and epigenetic modification is influenced by interactions between the AGO protein and the different target loci. These findings highlight the importance of tissue specificity and AGO-associated proteins in influencing epigenetic modifications.
Design and analysis for an innovative scheme of SINS/GPS ultra‐tight integration
Authors: Jie Yu , Xinlong Wang , Jiaxing Ji 
Published: February 2010

PurposeThe purpose of this paper is to improve the tracking performance of the carrier phase lock loop (PLL) in the strapdown inertial navigation system/global positioning system (SINS/GPS) integrated system with an innovative scheme of ultra‐tight integration.Design/methodology/approachFirst, providing the Doppler frequency for PLL using SINS velocity could enlarge the loop equivalent bandwidth and reduce the dynamic effect on the carrier loop. Meanwhile, lowering the filter bandwidth could increase the immunity to noise. Second, the relationships between the PLL and SINS errors have been analyzed, and then the PLL error model is established to eliminate the correlation between the pseudo‐range‐rate error and SINS velocity error. Third, the carrier frequency is regulated to improve the tracking accuracy, according to the error estimations of Kalman filter.FindingsThe innovative ultra‐tightly integrated system could not only enhance the anti‐jamming capability and the dynamic tracking performance of the tracking loops, but also improve the pseudo‐range‐rate measurements accuracy for the integrated filter.Originality/valueThis paper provides further study on the method of enhancing the carrier‐tracking performance and improving the integration mode in the ultra‐tightly integrated system based on the software‐defined GPS receiver.
Induced rolling moment for NACA4412 plain and flapped wing
Authors: Elsayed Omer A. , Kwon Kijung , Asrar Waqar , Omar Ashraf A. 
Published: February 2010

PurposeThe paper aims to compute rolling moments on a follower aircraft wing due to vortices generated by a plain and flapped NACA4412 wing using experimental particle image velocimetery (PIV) data.Design/methodology/approachThis paper describes the detailed variation of the induced rolling moment on a follower aircraft wing derived from a PIV velocity field measurement. A rectangular wing of a subsonic wall interference model is used as a vortex generator in two different configurations: plain wing of NACA4412 cross‐section profile; and flapped wing with trailing edge flap of NACA0012 cross‐section profile extended at 20°.FindingsResults obtained showed that the maximum induced rolling moment coefficient depends on the strength of the vortex produced by the generating aircraft wing and increases linearly with the increment of the angle of attack.Originality/valueThis paper provides an insight on the effects of different angles of attacks for plain and flapped wings on the induced rolling moment coefficient and therefore, the hazard imposed on the following aircraft can be estimated.
Fuzzy logic‐based detection scheme for pilot fatigue
Authors: Perhinschi M.G. , Smith B. , Betoney P. 
Published: February 2010

PurposeThe paper aims to present the development of a detection scheme for pilot fatigue using fuzzy logic. Evaluation parameters based on the dynamic response of the pilot/aircraft system are to be defined and criteria for online fatigue detection to be formulated.Design/methodology/approachThe approach is based on the idea that, while performing the same task, under otherwise identical conditions, the dynamic signatures of the pilot/aircraft system are different depending on the pilot condition, “rested” or “tired.” Tests performed on a 6 degrees‐of‐freedom (DOF) flight simulator with pilots at two extreme levels of alertness are used to define parameters based on aircraft states and pilot input measurements that can serve as pilot fatigue detectors at steady state flight conditions. These parameters are computed using the statistics of the tracking errors (TE), state and control time histories, and the Fourier transforms of the TE. Fuzzy logic is used to evaluate the pilot condition based on composite detection parameters.FindingsValidation tests on a 6 DOF flight simulator showed that the proposed detection scheme has promising capabilities for safety monitoring purposes and design of control laws that can accommodate for pilot abnormal conditions.Research limitations/implicationsThe pilot fatigue detection algorithm presented in this paper can be used as a starting point for future research in the following directions: development of safety monitoring systems for warning and/or triggering of automatic control compensation; development of pilot fault‐tolerant control laws; development of human pilot models for simulation, handling qualities assessment, and control laws design.Practical implicationsThe approach for pilot fatigue detection proposed in this paper is a viable alternative to existing methods based on physiological measurements such as electrical activity of the brain, pulse, body temperature, etc. which imply direct and permanent connection of the pilot to the measurement system and interfere adversely with pilot comfort and his/her ability to perform the task. The proposed approach eliminates this drawback and does not require on‐board additional heavy equipment.Originality/valuePilot fatigue assessment from measurements of pilot/aircraft dynamic parameters has not yet been investigated as an alternative to the physiological approach.