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  • 1
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    Comparative testing of single-tree detection algorithms under different types of forest (2012)
    Oxford University Press
    In: Forestry
    Details
    Publication Date: 2012-02-11
    Description: Airborne laser scanning data and corresponding field data were acquired from boreal forests in Norway and Sweden, coniferous and broadleaved forests in Germany and tropical pulpwood plantations in Brazil. Treetop positions were extracted using six different algorithms developed in Finland, Germany, Norway and Sweden, and the accuracy of tree detection and height estimation was assessed. Furthermore, the weaknesses and strengths of the methods under different types of forest were analyzed. The results showed that forest structure strongly affected the performance of all algorithms. Particularly, the success of tree detection was found to be dependent on tree density and clustering. The differences in performance between methods were more pronounced for tree detection than for height estimation. The algorithms showed a slightly better performance in the conditions for which they were developed, while some could be adapted by different parameterization according to training with local data. The results of this study may help guiding the choice of method under different forest types and may be of great value for future refinement of the single-tree detection algorithms.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 2
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    arrayMap 2014: an updated cancer genome resource (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: Somatic copy number aberrations (CNA) represent a mutation type encountered in the majority of cancer genomes. Here, we present the 2014 edition of arrayMap ( http://www.arraymap.org ), a publicly accessible collection of pre-processed oncogenomic array data sets and CNA profiles, representing a vast range of human malignancies. Since the initial release, we have enhanced this resource both in content and especially with regard to data mining support. The 2014 release of arrayMap contains more than 64 000 genomic array data sets, representing about 250 tumor diagnoses. Data sets included in arrayMap have been assembled from public repositories as well as additional resources, and integrated by applying custom processing pipelines. Online tools have been upgraded for a more flexible array data visualization, including options for processing user provided, non-public data sets. Data integration has been improved by mapping to multiple editions of the human reference genome, with the majority of the data now being available for the UCSC hg18 as well as GRCh37 versions. The large amount of tumor CNA data in arrayMap can be freely downloaded by users to promote data mining projects, and to explore special events such as chromothripsis-like genome patterns.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    CancerPPD: a database of anticancer peptides and proteins (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: CancerPPD ( http://crdd.osdd.net/raghava/cancerppd/ ) is a repository of experimentally verified anticancer peptides (ACPs) and anticancer proteins. Data were manually collected from published research articles, patents and from other databases. The current release of CancerPPD consists of 3491 ACP and 121 anticancer protein entries. Each entry provides comprehensive information related to a peptide like its source of origin, nature of the peptide, anticancer activity, N- and C-terminal modifications, conformation, etc . Additionally, CancerPPD provides the information of around 249 types of cancer cell lines and 16 different assays used for testing the ACPs. In addition to natural peptides, CancerPPD contains peptides having non-natural, chemically modified residues and D-amino acids. Besides this primary information, CancerPPD stores predicted tertiary structures as well as peptide sequences in SMILES format. Tertiary structures of peptides were predicted using the state-of-art method, PEPstr and secondary structural states were assigned using DSSP. In order to assist users, a number of web-based tools have been integrated, these include keyword search, data browsing, sequence and structural similarity search. We believe that CancerPPD will be very useful in designing peptide-based anticancer therapeutics.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Fault activity in the epicentral area of the 1580 Dover Strait (Pas-de-Calais) earthquake (northwestern Europe) (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-07
    Description: On 1580 April 6 one of the most destructive earthquakes of northwestern Europe took place in the Dover Strait ( Pas de Calais ). The epicentre of this seismic event, the magnitude of which is estimated to have been about 6.0, has been located in the offshore continuation of the North Artois shear zone, a major Variscan tectonic structure that traverses the Dover Strait. The location of this and two other moderate magnitude historical earthquakes in the Dover Strait suggests that the North Artois shear zone or some of its fault segments may be presently active. In order to investigate the possible fault activity in the epicentral area of the AD 1580 earthquake, we have gathered a large set of bathymetric and seismic-reflection data covering the almost-entire width of the Dover Strait. These data have revealed a broad structural zone comprising several subparallel WNW–ESE trending faults and folds, some of them significantly offsetting the Cretaceous bedrock. The geophysical investigation has also shown some indication of possible Quaternary fault activity. However, this activity only appears to have affected the lowermost layers of the sediment infilling Middle Pleistocene palaeobasins. This indicates that, if these faults have been active since Middle Pleistocene, their slip rates must have been very low. Hence, the AD 1580 earthquake appears to be a very infrequent event in the Dover Strait, representing a good example of the moderate magnitude earthquakes that sometimes occur in plate interiors on faults with unknown historical seismicity.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 5
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    Bio/chemoinformatics in India: an outlook (2015)
    Oxford University Press
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    Publication Date: 2015-07-15
    Description: With the advent of significant establishment and development of Internet facilities and computational infrastructure, an overview on bio/chemoinformatics is presented along with its multidisciplinary facts, promises and challenges. The Government of India has paved the way for more profound research in biological field with the use of computational facilities and schemes/projects to collaborate with scientists from different disciplines. Simultaneously, the growth of available biomedical data has provided fresh insight into the nature of redundant and compensatory data. Today, bioinformatics research in India is characterized by a powerful grid computing systems, great variety of biological questions addressed and the close collaborations between scientists and clinicians, with a full spectrum of focuses ranging from database building and methods development to biological discoveries. In fact, this outlook provides a resourceful platform highlighting the funding agencies, institutes and industries working in this direction, which would certainly be of great help to students seeking their career in bioinformatics. Thus, in short, this review highlights the current bio/chemoinformatics trend, educations, status, diverse applicability and demands for further development.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 6
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    Slow repair of lipid peroxidation-induced DNA damage at p53 mutation hotspots in human cells caused by low turnover of a DNA glycosylase (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-15
    Description: Repair of oxidative stress- and inflammation-induced DNA lesions by the base excision repair (BER) pathway prevents mutation, a form of genomic instability which is often observed in cancer as ‘mutation hotspots’. This suggests that some sequences have inherent mutability, possibly due to sequence-related differences in repair. This study has explored intrinsic mutability as a consequence of sequence-specific repair of lipid peroxidation-induced DNA adduct, 1, N 6 -ethenoadenine (A). For the first time, we observed significant delay in repair of A at mutation hotspots in the tumor suppressor gene p53 compared to non-hotspots in live human hepatocytes and endothelial cells using an in-cell real time PCR-based method. In-cell and in vitro mechanism studies revealed that this delay in repair was due to inefficient turnover of N -methylpurine-DNA glycosylase (MPG), which initiates BER of A. We determined that the product dissociation rate of MPG at the hotspot codons was 5–12-fold lower than the non-hotspots, suggesting a previously unknown mechanism for slower repair at mutation hotspots and implicating sequence-related variability of DNA repair efficiency to be responsible for mutation hotspot signatures.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Osteopontin is indispensible for AP1-mediated angiotensin II-related miR-21 transcription during cardiac fibrosis (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-22
    Description: Aims Osteopontin (OPN) is a multifunctional cytokine critically involved in cardiac fibrosis. However, the underlying mechanisms are unresolved. Non-coding RNAs are powerful regulators of gene expression and thus might mediate this process. Methods and results OPN and miR-21 were significantly increased in cardiac biopsies of patients with myocardial fibrosis. Ang II infusion via osmotic minipumps led to specific miRNA regulations with miR-21 being strongly induced in wild-type (WT) but not OPN knockout (KO) mice. This was associated with enhanced cardiac collagen content, myofibroblast activation, ERK-MAP kinase as well as AKT signalling pathway activation and a reduced expression of Phosphatase and Tensin Homologue (PTEN) as well as SMAD7 in WT but not OPN KO mice. In contrast, cardiotropic AAV9-mediated overexpression of OPN in vivo further enhanced cardiac fibrosis. In vitro , Ang II induced expression of miR-21 in WT cardiac fibroblasts, while miR-21 levels were unchanged in OPN KO fibroblasts. As pri-miR-21 was also increased by Ang II, we studied potential involved upstream regulators; Electrophoretic Mobility Shift and Chromatin Immunoprecipitation analyses confirmed activation of the miR-21 upstream-transcription factor AP-1 by Ang II. Recombinant OPN directly activated miR-21, enhanced fibrosis, and activated the phosphoinositide 3-kinase pathway. Locked nucleic acid-mediated miR-21 silencing ameliorated cardiac fibrosis development in vivo . Conclusion In cardiac fibrosis related to Ang II, miR-21 is transcriptionally activated and targets PTEN/SMAD7 resulting in increased fibroblast survival. OPN KO animals are protected from miR-21 increase and fibrosis development due to impaired AP-1 activation and fibroblast activation.
    Print ISSN: 0195-668X
    Electronic ISSN: 1522-9645
    Topics: Medicine
    Published by Oxford University Press
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  • 8
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    Three-dimensional velocity structure around Tehri region of the Garhwal Lesser Himalaya: constraints on geometry of the underthrusting Indian plate (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-18
    Description: We investigate the upper crustal velocity structure beneath the Tehri region of the Garhwal Himalaya. The investigated region is situated within the 700-km-long central seismic gap of the Himalaya that has experienced three gap-filling earthquakes since 1991 including the recent 2015 Nepal earthquake ( M w 7.8). The local tomographic inversion is based on a data set of 1365 events collected from 2008 January to 2012 December by a 12-station local network that covers an area of about 100  x  80 km around Tehri Dam. We perform a simultaneous inversion for P- and S -wave velocity anomalies. Tomograms are interpreted in the backdrop of the regional geological and tectonic framework of the region. The spatial distribution of relocated events from the 3-D velocity model has shed new light on the pattern of seismicity in the vicinity of the Main Central thrust (MCT), and has elucidated the structure of the underthrusting Indian plate. Our model exhibits a significant negative velocity anomaly up to ~5 per cent beneath the central part of the Garhwal Inner Lesser Himalaya, and a P -wave low velocity anomaly near the Chamoli region. The seismicity zone around the Chamoli region may be attributed to the presence of fluid-filled rocks. Furthermore, an area with ~3–4 per cent positive velocity anomaly is delineated to the northwest of the Uttarkashi thrust in the vicinity of the MCT. Significant findings of the study include: a flat-ramp-flat-type subsurface geometry of the underthrusting Indian plate below the Garhwal Himalaya, high-velocity images representing the trend and configuration of Delhi–Haridwar ridge below the Sub Himalaya and Lesser Himalaya and a seismically active zone representing geometrical asperity on the basement thrust in the vicinity of the MCT.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 9
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    Gender Disparity and Mutation Burden in Metastatic Melanoma (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-23
    Description: Gender differences in melanoma incidence and outcome have been consistently observed but remain biologically unexplained. We hypothesized that tumors are genetically distinct between men and women and analyzed the mutation spectra in 266 metastatic melanomas (102 women and 164 men) from The Cancer Genome Atlas (TCGA). We found a statistically significantly greater burden of missense mutations among men (male median 298 vs female median = 211.5; male-to-female ratio [M:F] = 1.85, 95% confidence interval [CI] = 1.44 to 2.39). We validated these initial findings using available data from a separate melanoma exome cohort (n = 95) and found a similar increase in missense mutations among men (male median 393 vs female median 259; M:F = 1.59, 95% CI = 1.12 to 2.27). In addition, we found improved survival with increasing log-transformed missense mutation count (univariate hazard ratio = 0.82, 95% CI = 0.69 to 0.98) for TCGA samples. Our analyses demonstrate for the first time a gender difference in mutation burden in cutaneous melanoma.
    Electronic ISSN: 1460-2105
    Topics: Medicine
    Published by Oxford University Press
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  • 10
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    The RNA world in the 21st century--a systems approach to finding non-coding keys to clinical questions (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-19
    Description: There was evidence that RNAs are a functionally rich class of molecules not only since the arrival of the next-generation sequencing technology. Non-coding RNAs (ncRNA) could be the key to accelerated diagnosis and enhanced prediction of disease and therapy outcomes as well as the design of advanced therapeutic strategies to overcome yet unsatisfactory approaches. In this review, we discuss the state of the art in RNA systems biology with focus on the application in the systems biomedicine field. We propose guidelines for analysing the role of microRNAs and long non-coding RNAs in human pathologies. We introduce RNA expression profiling and network approaches for the identification of stable and effective RNomics-based biomarkers, providing insights into the role of ncRNAs in disease regulation. Towards this, we discuss ways to model the dynamics of gene regulatory networks and signalling pathways that involve ncRNAs. We also describe data resources and computational methods for finding putative mechanisms of action of ncRNAs. Finally, we discuss avenues for the computer-aided design of novel RNA-based therapeutics.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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