ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Oxford University Press  (15,980)
  • 2010-2014  (15,980)
  • 2012  (15,980)
Collection
Years
  • 2010-2014  (15,980)
Year
  • 1
    Publication Date: 2020-11-26
    Description: So far, the role of appendicularians in the biogeochemical cycling of organic matter has been largely overlooked. Appendicularians represent only a fraction of total mesozooplankton biomass, however these ubiquitous zooplankters have very high filtration and growth rates compared to copepods, and produce numerous fecal pellets and filtering houses contributing to export production by aggregating small marine particles. To study their quantitative impact on biogeochemical flux, we have included this group in the biogeochemical flux model, using a recently developed ecophysiological model. One-dimensional annual simulations of the pelagic ecosystem including appendicularians were conducted with realistic surface forcing for the year 2000, using data from the DyFAMed open ocean station. The appendicularian grazing impact was generally low, but appendicularians increased detritus production by 8% and export production by 55% compared to a simulation without appendicularians. Therefore, current biogeochemical models lacking appendicularians probably under, or misestimate the detritus and export production by omitting the pathway from small-sized plankton to fast sinking detritus. Detritus production and export rates are 60% lower than the estimates from mesotrophic sites, showing that appendicularians’ role is lower but still significant in oligotrophic environments. The simulated annual export at 200 m exceeds sediment trap values by 44%, suggesting an intense degradation during the sinking of appendicularian detritus, supported by observations made at other sites. Thus, degradation and grazing of appendicularian detritus need better quantification if we are to accurately assess the role of appendicularia in export flux.
    Description: EU-FP6 project SESAME GOCE-036949
    Description: Published
    Description: 855-872
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: BFM ; zooplankton ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 2
    Publication Date: 2017-04-04
    Description: Crystal-rich lithic clasts occurring in volcanic deposits are key tools to understand processes of storage, cooling, and fractionation of magmas in pre-eruptive volcanic systems. These clasts, indeed, represent snapshots of the magma-chamber/host-rock interface before eruptions and provide information on crystallization, differentiation, and degrees of interaction between magma and wall-rocks. In this study, with the aim to shed light on magma-carbonate interaction and CO2 emission in volcanic areas, we focused on the petrology of cumulate and skarn rocks by using as case study a suite of mafic and calcite-bearing lithic clasts from the Colli Albani Volcanic District. By means of phase relations, bulk rock chemistry, phase compositions, and stable isotope data we have recognized different types of cumulates and skarns. Cumulates containing either clinopyroxene±olivine associated with Cr-bearing spinel or glass+phlogopite have been divided in primitive and differentiated, respectively. Primitive cumulates originate at the interface between a relatively primitive magma and carbonate-bearing rocks and show evidences of olivine instability (i.e. heteradcumulate texture) due to carbonate assimilation. Differentiated cumulates, characterized by Ca-rich olivines, phlogopite, and glass containing calcite, form from a differentiated magma in a system open to CaO-contamination. Skarns has been divided in exoskarns, characterized by xenomorphic texture and abundant calcite, and endoskarns, characterized by hypidiomorphic texture, Ca-Tschermak-rich mineral phases, and interstitial glass. Exoskarns formed by means of solid state reactions in a dolostone protolith whereas endoskarns crystallized at subliquidus temperature from a silicate melt that experienced exoskarns assimilation. Our study evidences that magma-carbonate interaction can not be considered a one step process exhausting just after the formation of skarn shells. Magma and carbonate rocks, when in contact, continuously interact leading to the formation of exoskarns, endoskarns, cumulates (primitive and differentiated ones), and differentiated melts. Finally, by means of oxygen and carbon isotope compositions of calcite in equilibrium with skarns, we demonstrate that carbonate assimilation represents a source of massive CO2 degassing mechanism due to the consumption of calcite and removing of CO2 during the decarbonation process.
    Description: Sapienza Universita' di Roma INGV-DPC [Project V 3.1, Colli Albani].
    Description: Published
    Description: 2307-2332
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: magma/carbonate interaction ; CO2 degassing ; c umulate and skarn ; Colli Albani ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 3
    facet.materialart.
    Unknown
    Oxford University Press
    In:  EPIC3Journal of Plankton Research, Oxford University Press, 34(5), pp. 399-415, ISSN: 0142-7873
    Publication Date: 2019-07-17
    Description: This study investigates the relationships between the spring phytoplankton community and environmental factors in the Brazil-Malvinas confluence region. Phytoplankton community composition was determined by the high performance liquid chromatography/CHEMTAX approach, complemented with microscopic examination. Abiotic factors included temperature, salinity, dissolved inorganic macronutrients (ammonium, nitrite, nitrate, phosphate and silicate), water column stability and upper mixed layer depth (UMLD). These environmental variables were reasonably informative to explain the variability of the phytoplankton communities (44% of variation explained). Cluster and canonical correspondence analyses allowed discrimination of four zones (coastal, Sub-Antarctic, tropical and intermediate zones), also identifiable in the T–S diagrams and in the nutrient spatial distribution patterns. The presence of nutrient-rich Sub-Antarctic waters was a major oceanographic feature, associated with diatoms and dinoflagellates. However, in the Sub-Antarctic zone, biomass was particularly low, probably as a result of grazing pressure, as suggested by chemical and biological indicators. In contrast, in oligotrophic tropical waters, phytoplankton was mainly composed by small nanoflagellates and cyanobacteria. A large intermediate zone was also dominated by nanoflagellates, mainly Phaeocystis antarctica, probably favored by strong water column stability. The coastal zone exhibited fairly similar conditions to those in the intermediate zone, but with deeper UMLD, a favorable condition for diatom growth. These results emphasize the importance of the properties of water masses and also biological processes such as grazing in structuring phytoplankton communities in the region.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): 7132-7149, doi:10.1093/nar/gks467.
    Description: The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
    Description: Office of Science (BER), U.S. Department of Energy [DE-FG02-07ER64388 to D.S. and DE-FG02- 08ER64511 to M.H.S.]; National Aeronautics and Space Administration, NASA Astrobiology Institute [NNA08CN84A to D.S.].
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 5
    Publication Date: 2012-03-09
    Description: The role played by the required level of statistical significance in the scientific method should not be seen as analogous to that played by the standard of proof in the legal process.
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 6
    Publication Date: 2012-03-09
    Description: The Supreme Court ruled in Matrixx that statistical significance is not necessary to show that a drug caused an adverse reaction. Five circuit court decisions holding otherwise preceded this decision. This paper examines the extent to which the Supreme Court’s reasoning differed from those of the circuit courts.
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 7
    Publication Date: 2012-03-09
    Description: Unlike the evaluation of single items of scientific evidence, the formal study and analysis of the joint evaluation of several distinct items of forensic evidence has to date received some punctual, rather than systematic, attention. Questions about the (i) relationships among a set of (usually unobservable) propositions and a set of (observable) items of scientific evidence, (ii) the joint probative value of a collection of distinct items of evidence as well as (iii) the contribution of each individual item within a given group of pieces of evidence still represent fundamental areas of research. To some degree, this is remarkable since both, forensic science theory and practice, yet many daily inference tasks, require the consideration of multiple items if not masses of evidence. A recurrent and particular complication that arises in such settings is that the application of probability theory, i.e. the reference method for reasoning under uncertainty, becomes increasingly demanding. The present paper takes this as a starting point and discusses graphical probability models, i.e. Bayesian networks, as framework within which the joint evaluation of scientific evidence can be approached in some viable way. Based on a review of existing main contributions in this area, the article here aims at presenting instances of real case studies from the author’s institution in order to point out the usefulness and capacities of Bayesian networks for the probabilistic assessment of the probative value of multiple and interrelated items of evidence. A main emphasis is placed on underlying general patterns of inference, their representation as well as their graphical probabilistic analysis. Attention is also drawn to inferential interactions, such as redundancy, synergy and directional change. These distinguish the joint evaluation of evidence from assessments of isolated items of evidence. Together, these topics present aspects of interest to both, domain experts and recipients of expert information, because they have bearing on how multiple items of evidence are meaningfully and appropriately set into context.
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 8
    Publication Date: 2012-03-09
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 9
    Publication Date: 2012-03-09
    Description: In its first foray into the labyrinth that causation in personal injury has become, the U.K. Supreme Court recently held obiter that statistical evidence alone could not establish causation. But in an earlier toxic tort case, the High Court had relied on epidemiological evidence to identify a cluster of birth defects arising in the vicinity of a contaminated land site. This recent British experience is then discussed within the wider context of the forensic role of ‘naked statistics’.
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 10
    Publication Date: 2012-03-09
    Description: Scales of conclusion in forensic interpretation play an important role in the interface between scientific work at a forensic laboratory and different bodies of the jurisdictional system of a country. Of particular importance is the use of a unified scale that allows interpretation of different kinds of evidence in one common framework. The logical approach to forensic interpretation comprises the use of the likelihood ratio as a measure of evidentiary strength. While fully understood by forensic scientists, the likelihood ratio may be hard to interpret for a person not trained in natural sciences or mathematics. Translation of likelihood ratios to an ordinal scale including verbal counterparts of the levels is therefore a necessary procedure for communicating evidence values to the police and in the courtroom. In this paper, we present a method to develop an ordinal scale for the value of evidence that can be applied to any type of forensic findings. The method is built on probabilistic reasoning about the interpretation of findings and the number of scale levels chosen is a compromise between a pragmatic limit and mathematically well-defined distances between levels. The application of the unified scale is illustrated by a number of case studies.
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 11
    Publication Date: 2012-03-09
    Description: In personal injury litigation, claimants may seek their compensation for future losses or expenses as a lump sum that is determined by the product of a multiplicand and a multiplier. The multiplicand represents the annual loss in earnings and other benefits, as assessed at the trial date, while the multiplier discounts future pecuniary values into a single present-day lump sum amount. At present, multipliers in the UK are calculated using actuarial methods and based on assumed mortality and interest rates. However, it is entirely possible that these assumptions are incorrect, and if they are, then all claimants who rely on the same set of actuarial multipliers will be affected. In this article, we investigate how the uncertainty surrounding mortality and interest rate assumptions affects the precision of actuarial multipliers. With the aid of stochastic models, we estimate the possible range of values that an actuarial multiplier can take.
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 12
    Publication Date: 2012-03-10
    Description: In this article we report and discuss a contextual problem solving task that was proposed to a class of 8th grade (13–14-year-old) students. These students had been developing a reasonable experience in the use of the spreadsheet to model relations within contextual problems and chose to use this tool to solve the mentioned problem, engaging in the process of translating relations between variables and combining them in chained models, while working with fractions, multiples and expressions. We intend to highlight the role of the spreadsheet in students’ processes of variable identification and translation of the problem conditions, their numerical approaches to algebraic models and their experimental forms of finding solutions to equations.
    Print ISSN: 0268-3679
    Electronic ISSN: 1471-6976
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 13
    Publication Date: 2012-03-10
    Print ISSN: 0268-3679
    Electronic ISSN: 1471-6976
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 14
    Publication Date: 2012-03-10
    Description: This theoretical study is an attempt to explore the potential of the dynamic and interactive mathematics learning environments (DIMLE) in relation to the technological pedagogical content knowledge (TPACK) framework. DIMLE are developed with intent to support learning mathematics through free exploration in a less constrained environment. A typical DIMLE software package has interactivity and dynamism as key affordances; these are especially suitable for enhancing learning and teaching with technology of the essentially dynamic mathematics concepts. Moreover, we propose that DIMLE and their affordances should be studied under the TPACK framework because this framework is explicit in considering technology-supported mathematics learning as a qualitative add-on as contrasted to what would be a simple totalling of technological, pedagogical and mathematical knowledge. As an example, we focus in our discussion on using a DIMLE in order to support learner in development of the limit concept.
    Print ISSN: 0268-3679
    Electronic ISSN: 1471-6976
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 15
    Publication Date: 2012-03-10
    Description: The present article reports a study concerning the analysis of 19 activity plans (we call them ‘scenarios’) developed by mathematics teacher educators-in-training for the pedagogical use of digital tools. The development of these scenarios took place during their training program and was designed as an activity for increasing reflection, for expressing creative pedagogical ideas and for an active engagement in the design of curricula enriched with the use of technology. Our analysis showed that the trainee teacher educators deconstructed and reconstructed respective parts of the formal curriculum regarding the mathematical concepts they chose to embody in their scenarios.
    Print ISSN: 0268-3679
    Electronic ISSN: 1471-6976
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 16
    Publication Date: 2012-03-10
    Description: In this research we present the use of some technologies in problem solving activities (at different secondary school grades), aimed at finding a model for a geometric configuration, and representing this model in various ways: through a construction, through a Cartesian graph, etc. The task is part of a teaching experiment, in which students used paper and pencil, and technological tools: a sensor and a calculator (at a lower grade), GeoGebra and TI-Nspire (at a higher grade). We show results in terms of the passage from static to dynamic representations and back, to observe how technology may foster dynamic thinking for students solving mathematical problems. Data suggest that the dynamic features of technology support the genesis of conjectures, and their validation or refutation, along with the choice of independent and dependent variables. Results are used to prepare materials for teacher training in an e-learning Moodle platform (Comenius EdUmatics Project).
    Print ISSN: 0268-3679
    Electronic ISSN: 1471-6976
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 17
    Publication Date: 2012-02-22
    Description: SUMMARY In the absence of seismological measurements, observations of the topography and gravity fields of solid planets are the primary constraints on their internal structure. To compute the synthetic geoid and topography induced by the dynamics of planetary interiors, we introduce a 3-D numerical tool describing mantle convection beneath an elastic lithosphere. Although the energy conservation is treated in the whole spherical domain, the deformation aspect is solved using a hybrid technique (finite volume method for the viscous flow, spectral method for elastic deformation). The mechanical coupling is achieved via the imposition of the traction at the surface of the viscous flow as a basal boundary condition for the elastic deformation. We present both response functions and full thermal convection cases computed with our new method for planetary bodies of varying dimensions: the filtering effect of the lithosphere on the dynamic topography and geoid is specific for each planetary body, justifying the importance of such a tool. Furthermore, since our approach specifically focuses on the mechanical coupling at the base of the lithosphere, it will permit future, more elaborate, rheological treatments. It also enables to discriminate between the radial and tangential components of the viscous traction. The latter is found to have a significant influence on the elastic deformation. The effect on geoid is prominent. More specifically, while a thin elastic lithosphere is usually considered to play little role on the dynamic topography and geoid of Venus, a ∼35 per cent reduction is obtained for geoid height in the numerical example we propose. On a planet with thicker elastic lithosphere such as Mars, the consequence of this filtering effect is to rule out the possibility of a dynamical support for the Tharsis Rise, even for the lowest admissible values of elastic thickness in this region.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 18
    Publication Date: 2012-02-22
    Description: SUMMARY The Central Iran plateau appears aseismic during the last few millenniums based on instrumental and historical seismic records. Nevertheless, it is sliced by several strike-slip faults that are hundreds of kilometres long. These faults display along-strike, horizontal offsets of intermittent gullies that suggest the occurrence of earthquakes in the Holocene. Establishing this is crucial for accurately assessing the regional seismic hazard. The first palaeoseismic study performed on the 200-km long, NS striking Anar fault shows that this right-lateral fault hosted three large ( M w ≈ 7) earthquakes during the Holocene or possibly Uppermost Pleistocene for the older one. These three seismic events are recorded within a sedimentary succession, which is not older than 15 ka, suggesting an average recurrence of at most 5 ka. The six optically stimulated luminescence ages available provide additional constraints and allow estimating that the three earthquakes have occurred within the following time intervals: 4.4 ± 0.8, 6.8 ± 1 and 9.8 ± 2 ka. The preferred age of the more recent event, ranging between 3600 and 5200 yr, suggests that the fault is approaching the end of its seismic cycle and the city of Anar could be under the threat of a destructive earthquake in the near future. In addition, our results confirm a previous minimum slip rate estimate of 0.8 ± 0.1 mm yr −1 for the Anar fault indicating that the westernmost prominent right-lateral faults of the Central Iran plateau are characterized by slip rates close to 1 mm yr −1 . These faults, which have repeatedly produced destructive earthquakes with large magnitudes and long recurrence interval of several thousands of years during the Holocene, show that the Central Iran plateau does not behave totally as a rigid block and that its moderate internal deformation is nonetheless responsible for a significant seismic hazard.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 19
    Publication Date: 2012-03-13
    Description: SUMMARY Passive seismic interferometry is a new promising methodology for seismic exploration. Interferometry allows information about the subsurface structure to be extracted from ambient seismic noise. In this study, we apply the cross-correlation technique to approximately 25 hr of recordings of ambient seismic noise at the Ketzin experimental CO 2 storage site, Germany. Common source gathers were generated from the ambient noise for all available receivers along two seismic lines by cross-correlation of noise records. This methodology isolates the interstation Green's functions that can be directly compared to active source gathers. We show that the retrieved response includes surface waves, refracted waves and reflected waves. We use the dispersive behaviour of the retrieved surface waves to infer geological properties in the shallow subsurface and perform passive seismic imaging of the subsurface structure by processing the retrieved reflected waves.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 20
    Publication Date: 2012-03-13
    Print ISSN: 1471-678X
    Electronic ISSN: 1471-6798
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 21
    Publication Date: 2012-03-14
    Description: SUMMARY Normal mode observations play an important role in studying broad-scale lateral variations in the Earth. Such studies require the calculation of accurate synthetic spectra in realistic earth models, and this remains a computationally challenging problem. Here, we describe a new implementation of the direct solution method for calculating normal mode spectra in laterally heterogeneous earth models. In this iterative direct solution method , the mode-coupling equations are solved in the frequency-domain using the preconditioned biconjugate gradient algorithm, and the time-domain solution is recovered using a numerical inverse Fourier transform. A number of example calculations are presented to demonstrate the accuracy and efficiency of the method for performing large ‘full coupling’ calculations as compared to methods based on matrix diagonalization and the traditional direct solution method.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 22
    Publication Date: 2012-03-14
    Description: Telomeres, the ends of linear chromosomes, safeguard against genome instability. The enzyme responsible for extension of the telomere 3' terminus is the ribonucleoprotein telomerase. Whereas telomerase activity can be reconstituted in vitro with only the telomerase RNA (hTR) and telomerase reverse transcriptase (TERT), additional components are required in vivo for enzyme assembly, stability and telomere extension activity. One such associated protein, dyskerin, promotes hTR stability in vivo and is the only component to co-purify with active, endogenous human telomerase. We used oligonucleotide-based affinity purification of hTR followed by native gel electrophoresis and in-gel telomerase activity detection to query the composition of telomerase at different purification stringencies. At low salt concentrations (0.1 M NaCl), affinity-purified telomerase was ‘supershifted’ with an anti-dyskerin antibody, however the association with dyskerin was lost after purification at 0.6 M NaCl, despite the retention of telomerase activity and a comparable yield of hTR. The interaction of purified hTR and dyskerin in vitro displayed a similar salt-sensitive interaction. These results demonstrate that endogenous human telomerase, once assembled and active, does not require dyskerin for catalytic activity. Native gel electrophoresis may prove useful in the characterization of telomerase complexes under various physiological conditions.
    Keywords: Protein-nucleic acid interaction, Miscellaneous/other
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 23
    Publication Date: 2012-03-14
    Description: We describe an inexpensive and efficient method for generating functional pools of Dicer-substrate small interfering RNAs (siRNAs) in a single reaction tube. The method exploits a highly active form of the enzyme Dicer from Giardia lamblia , which is capable of accurately processing double-stranded RNA (dsRNA) into 25–27 nt RNA pools during in vitro transcription. The small RNAs produced function as substrates of human Dicer in vitro and induce gene silencing with potency equivalent to traditional siRNAs when introduced into mammalian cells. The overall reaction is simple, can be carried out in any laboratory with access to a PCR machine, and is amenable to high-throughput processes.
    Keywords: Microarray Technology, Nucleic Acid Enzymology
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 24
    Publication Date: 2012-03-14
    Description: Microglial cells are the main HIV-1 targets in the central nervous system (CNS) and constitute an important reservoir of latently infected cells. Establishment and persistence of these reservoirs rely on the chromatin structure of the integrated proviruses. We have previously demonstrated that the cellular cofactor CTIP2 forces heterochromatin formation and HIV-1 gene silencing by recruiting HDAC and HMT activities at the integrated viral promoter. In the present work, we report that the histone demethylase LSD1 represses HIV-1 transcription and viral expression in a synergistic manner with CTIP2. We show that recruitment of LSD1 at the HIV-1 proximal promoter is associated with both H3K4me3 and H3K9me3 epigenetic marks. Finally, our data suggest that LSD1-induced H3K4 trimethylation is linked to hSET1 recruitment at the integrated provirus.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 25
    Publication Date: 2012-03-14
    Description: This short review aims at presenting some recent illustrative examples of spontaneous nucleolipids self-assembly. High-resolution structural investigations reveal the diversity and complexity of assemblies formed by these bioinspired amphiphiles, resulting from the interplay between aggregation of the lipid chains and base–base interactions. Nucleolipids supramolecular assemblies are promising soft drug delivery systems, particularly for nucleic acids. Regarding prodrugs, squalenoylation is an innovative concept for improving efficacy and delivery of nucleosidic drugs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 26
    Publication Date: 2012-03-14
    Description: Determining the underlying haplotypes of individual human genomes is an essential, but currently difficult, step toward a complete understanding of genome function. Fosmid pool-based next-generation sequencing allows genome-wide generation of 40-kb haploid DNA segments, which can be phased into contiguous molecular haplotypes computationally by Single Individual Haplotyping (SIH). Many SIH algorithms have been proposed, but the accuracy of such methods has been difficult to assess due to the lack of real benchmark data. To address this problem, we generated whole genome fosmid sequence data from a HapMap trio child, NA12878, for which reliable haplotypes have already been produced. We assembled haplotypes using eight algorithms for SIH and carried out direct comparisons of their accuracy, completeness and efficiency. Our comparisons indicate that fosmid-based haplotyping can deliver highly accurate results even at low coverage and that our SIH algorithm, ReFHap, is able to efficiently produce high-quality haplotypes. We expanded the haplotypes for NA12878 by combining the current haplotypes with our fosmid-based haplotypes, producing near-to-complete new gold-standard haplotypes containing almost 98% of heterozygous SNPs. This improvement includes notable fractions of disease-related and GWA SNPs. Integrated with other molecular biological data sets, this phase information will advance the emerging field of diploid genomics.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 27
    Publication Date: 2012-03-14
    Description: RNA tetraloops can recognize receptors to mediate long-range interactions in stable natural RNAs. In vitro selected GNRA tetraloop/receptor interactions are usually more ‘G/C-rich’ than their ‘A/U-rich’ natural counterparts. They are not as widespread in nature despite comparable biophysical and chemical properties. Moreover, while AA, AC and GU dinucleotide platforms occur in natural GAAA/11 nt receptors, the AA platform is somewhat preferred to the others. The apparent preference for ‘A/U-rich’ GNRA/receptor interactions in nature might stem from an evolutionary adaptation to avoid folding traps at the level of the larger molecular context. To provide evidences in favor of this hypothesis, several riboswitches based on natural and artificial GNRA receptors were investigated in vitro for their ability to prevent inter-molecular GNRA/receptor interactions by trapping the receptor sequence into an alternative intra-molecular pseudoknot. Extent of attenuation determined by native gel-shift assays and co-transcriptional assembly is correlated to the G/C content of the GNRA receptor. Our results shed light on the structural evolution of natural long-range interactions and provide design principles for RNA-based attenuator devices to be used in synthetic biology and RNA nanobiotechnology.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 28
    Publication Date: 2012-03-14
    Description: Many types of DNA structures are generated in response to DNA damage, repair and recombination that require processing via specialized nucleases. DNA hairpins represent one such class of structures formed during V(D)J recombination, palindrome extrusion, DNA transposition and some types of double-strand breaks. Here we present biochemical and genetic evidence to suggest that Pso2 is a robust DNA hairpin opening nuclease in budding yeast. Pso2 (SNM1A in mammals) belongs to a small group of proteins thought to function predominantly during interstrand crosslink (ICL) repair. In this study, we characterized the nuclease activity of Pso2 toward a variety of DNA substrates. Unexpectedly, Pso2 was found to be an efficient, structure-specific DNA hairpin opening endonuclease. This activity was further shown to be required in vivo for repair of chromosomal breaks harboring closed hairpin ends. These findings provide the first evidence that Pso2 may function outside ICL repair and open the possibility that Pso2 may function at least in part during ICL repair by processing DNA intermediates including DNA hairpins or hairpin-like structures.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 29
    Publication Date: 2012-03-14
    Description: The mom gene of bacteriophage Mu encodes an enzyme that converts adenine to N 6 -(1-acetamido)-adenine in the phage DNA and thereby protects the viral genome from cleavage by a wide variety of restriction endonucleases. Mu-like prophage sequences present in Haemophilus influenzae Rd (FluMu), Neisseria meningitidis type A strain Z2491 (Pnme1) and H. influenzae biotype aegyptius ATCC 11116 do not possess a Mom-encoding gene. Instead, at the position occupied by mom in Mu they carry an unrelated gene that encodes a protein with homology to DNA adenine N 6 -methyltransferases ( hin1523 , nma1821 , hia5 , respectively). Products of the hin1523 , hia5 and nma1821 genes modify adenine residues to N 6 -methyladenine, both in vitro and in vivo . All of these enzymes catalyzed extensive DNA methylation; most notably the Hia5 protein caused the methylation of 61% of the adenines in DNA. Kinetic analysis of oligonucleotide methylation suggests that all adenine residues in DNA, with the possible exception of poly(A)-tracts, constitute substrates for the Hia5 and Hin1523 enzymes. Their potential ‘sequence specificity’ could be summarized as AB or BA (where B = C, G or T). Plasmid DNA isolated from Escherichia coli cells overexpressing these novel DNA methyltransferases was resistant to cleavage by many restriction enzymes sensitive to adenine methylation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 30
    Publication Date: 2012-03-14
    Description: The influenza A virus genome consists of eight viral RNAs (vRNAs) that form viral ribonucleoproteins (vRNPs). Even though evidence supporting segment-specific packaging of vRNAs is accumulating, the mechanism ensuring selective packaging of one copy of each vRNA into the viral particles remains largely unknown. We used electron tomography to show that the eight vRNPs emerge from a common ‘transition zone’ located underneath the matrix layer at the budding tip of the virions, where they appear to be interconnected and often form a star-like structure. This zone appears as a platform in 3D surface rendering and is thick enough to contain all known packaging signals. In vitro , all vRNA segments are involved in a single network of intermolecular interactions. The regions involved in the strongest interactions were identified and correspond to known packaging signals. A limited set of nucleotides in the 5' region of vRNA 7 was shown to interact with vRNA 6 and to be crucial for packaging of the former vRNA. Collectively, our findings support a model in which the eight genomic RNA segments are selected and packaged as an organized supramolecular complex held together by direct base pairing of the packaging signals.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 31
    Publication Date: 2012-03-14
    Description: Anti-miRs are oligonucleotide inhibitors complementary to miRNAs that have been used extensively as tools to gain understanding of specific miRNA functions and as potential therapeutics. We showed previously that peptide nucleic acid (PNA) anti-miRs containing a few attached Lys residues were potent miRNA inhibitors. Using miR-122 as an example, we report here the PNA sequence and attached amino acid requirements for efficient miRNA targeting and show that anti-miR activity is enhanced substantially by the presence of a terminal-free thiol group, such as a Cys residue, primarily due to better cellular uptake. We show that anti-miR activity of a Cys-containing PNA is achieved by cell uptake through both clathrin-dependent and independent routes. With the aid of two PNA analogues having intrinsic fluorescence, thiazole orange (TO)-PNA and [bis- o -(aminoethoxy)phenyl]pyrrolocytosine (BoPhpC)-PNA, we explored the subcellular localization of PNA anti-miRs and our data suggest that anti-miR targeting of miR-122 may take place in or associated with endosomal compartments. Our findings are valuable for further design of PNAs and other oligonucleotides as potent anti-miR agents.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 32
    Publication Date: 2012-03-14
    Description: Translation initiation factor eIF3 acts as the key orchestrator of the canonical initiation pathway in eukaryotes, yet its structure is greatly unexplored. We report the 2.2 Å resolution crystal structure of the complex between the yeast seven-bladed β-propeller eIF3i/TIF34 and a C-terminal α-helix of eIF3b/PRT1, which reveals universally conserved interactions. Mutating these interactions displays severe growth defects and eliminates association of eIF3i/TIF34 and strikingly also eIF3g/TIF35 with eIF3 and 40S subunits in vivo . Unexpectedly, 40S-association of the remaining eIF3 subcomplex and eIF5 is likewise destabilized resulting in formation of aberrant pre-initiation complexes (PICs) containing eIF2 and eIF1, which critically compromises scanning arrest on mRNA at its AUG start codon suggesting that the contacts between mRNA and ribosomal decoding site are impaired. Remarkably, overexpression of eIF3g/TIF35 suppresses the leaky scanning and growth defects most probably by preventing these aberrant PICs to form. Leaky scanning is also partially suppressed by eIF1, one of the key regulators of AUG recognition, and its mutant sui1 G107R but the mechanism differs. We conclude that the C-terminus of eIF3b/PRT1 orchestrates co-operative recruitment of eIF3i/TIF34 and eIF3g/TIF35 to the 40S subunit for a stable and proper assembly of 48S pre-initiation complexes necessary for stringent AUG recognition on mRNAs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 33
    Publication Date: 2012-03-14
    Description: The misreplication of damaged DNA is an important biological process that produces numerous adverse effects on human health. This report describes the synthesis and characterization of a non-natural nucleotide, designated 3-ethynyl-5-nitroindolyl-2'-deoxyriboside triphosphate (3-Eth-5-NITP), as a novel chemical reagent that can probe and quantify the misreplication of damaged DNA. We demonstrate that this non-natural nucleotide is efficiently inserted opposite an abasic site, a commonly formed and potentially mutagenic non-instructional DNA lesion. The strategic placement of the ethynyl moiety allows the incorporated nucleoside triphosphate to be selectively tagged with an azide-containing fluorophore using ‘click’ chemistry. This reaction provides a facile way to quantify the extent of nucleotide incorporation opposite non-instructional DNA lesions. In addition, the incorporation of 3-Eth-5-NITP is highly selective for an abasic site, and occurs even in the presence of a 50-fold molar excess of natural nucleotides. The biological applications of using 3-Eth-5-NITP as a chemical probe to monitor and quantify the misreplication of non-instructional DNA lesions are discussed.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 34
    Publication Date: 2012-03-16
    Description: SUMMARY We report on a unique set of infrasound observations from a single earthquake, the 2011 January 3 Circleville earthquake ( M w 4.7, depth of 8 km), which was recorded by nine infrasound arrays in Utah. Based on an analysis of the signal arrival times and backazimuths at each array, we find that the infrasound arrivals at six arrays can be associated to the same source and that the source location is consistent with the earthquake epicentre. Results of propagation modelling indicate that the lack of associated arrivals at the remaining three arrays is due to path effects. Based on these findings we form the working hypothesis that the infrasound is generated by body waves causing the epicentral region to pump the atmosphere, akin to a baffled piston. To test this hypothesis, we have developed a numerical seismoacoustic model to simulate the generation of epicentral infrasound from earthquakes. We model the generation of seismic waves using a 3-D finite difference algorithm that accounts for the earthquake moment tensor, source time function, depth and local geology. The resultant acceleration–time histories on a 2-D grid at the surface then provide the initial conditions for modelling the near-field infrasonic pressure wave using the Rayleigh integral. Finally, we propagate the near-field source pressure through the Ground-to-Space atmospheric model using a time-domain Parabolic Equation technique. By comparing the resultant predictions with the six epicentral infrasound observations from the 2011 January 3, Circleville earthquake, we show that the observations agree well with our predictions. The predicted and observed amplitudes are within a factor of 2 (on average, the synthetic amplitudes are a factor of 1.6 larger than the observed amplitudes). In addition, arrivals are predicted at all six arrays where signals are observed, and importantly not predicted at the remaining three arrays. Durations are typically predicted to within a factor of 2, and in some cases much better. These results suggest that measured infrasound from the Circleville earthquake is consistent with the generation of infrasound from body waves in the epicentral region.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 35
    Publication Date: 2012-03-16
    Description: SUMMARY We present new dedicated core surface field models spanning the decade from 2000.0 to 2010.0. These models, called gufm-sat , are based on CHAMP, Ørsted and SAC-C satellite observations along with annual differences of processed observatory monthly means. A spatial parametrization of spherical harmonics up to degree and order 24 and a temporal parametrization of sixth-order B-splines with 0.25 yr knot spacing is employed. Models were constructed by minimizing an absolute deviation measure of misfit along with measures of spatial and temporal complexity at the core surface. We investigate traditional quadratic or maximum entropy regularization in space, and second or third time derivative regularization in time. Entropy regularization allows the construction of models with approximately constant spectral slope at the core surface, avoiding both the divergence characteristic of the crustal field and the unrealistic rapid decay typical of quadratic regularization at degrees above 12. We describe in detail aspects of the models that are relevant to core dynamics. Secular variation and secular acceleration are found to be of lower amplitude under the Pacific hemisphere where the core field is weaker. Rapid field evolution is observed under the eastern Indian Ocean associated with the growth and drift of an intense low latitude flux patch. We also find that the present axial dipole decay arises from a combination of subtle changes in the southern hemisphere field morphology.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 36
    Publication Date: 2012-03-16
    Description: SUMMARY We present a novel frequency-domain inverse solution to recover the 3-D electrical conductivity distribution in the mantle. The solution is based on analysis of local C -responses. It exploits an iterative gradient-type method—limited-memory quasi-Newton method—for minimizing the penalty function consisting of data misfit and regularization terms. The integral equation code is used as a forward engine to calculate responses and data misfit gradients during inversion. An adjoint approach is implemented to compute misfit gradients efficiently. Further improvements in computational load come from parallelizing the scheme with respect to frequencies, and from setting the most time-consuming part of the forward calculations—calculation of Green’s tensors—apart from the inversion loop. Convergence, performance, and accuracy of our 3-D inverse solution are demonstrated with a synthetic numerical example. A companion paper applies the strategy set forth here to real data.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 37
    Publication Date: 2012-02-02
    Description: This paper presents a benchmarking, performance analysis and optimization study of the OP2 ‘active’ library, which provides an abstraction framework for the parallel execution of unstructured mesh applications. OP2 aims to decouple the scientific specification of the application from its parallel implementation, and thereby achieve code longevity and near-optimal performance through re-targeting the application to execute on different multi-core/many-core hardware. Runtime performance results are presented for a representative unstructured mesh application on a variety of many-core processor systems, including traditional X86 architectures from Intel (Xeon based on the older Penryn and current Nehalem micro-architectures) and GPU offerings from NVIDIA (GTX260, Tesla C2050). Our analysis demonstrates the contrasting performance between the use of CPU (OpenMP) and GPU (CUDA) parallel implementations for the solution of an industrial-sized unstructured mesh consisting of about 1.5 million edges. Results show the significance of choosing the correct partition and thread-block configuration, the factors limiting the GPU performance and insights into optimizations for improved performance.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 38
    Publication Date: 2012-02-02
    Description: In this paper, we describe the integrated power, area and thermal modeling framework in the structural simulation toolkit (SST) for large-scale high performance computer simulation. It integrates various power and thermal modeling tools and computes run-time energy dissipation for core, network on chip, memory controller and shared cache. It also provides functionality to update the leakage power as temperature changes. We illustrate the utilization of the framework by applying it to explore interconnect options in manycore systems with consideration of temperature variation and leakage feedback. We compare power, energy-delay-area product (EDAP) and energy-delay product (EDP) of four manycore configurations-1 core, 2 cores, 4 cores and 8 cores per cluster. Results from simulation with or without consideration of temperature variation both show that the 4-core per cluster configuration has the best EDAP and EDP. Even so, considering that temperature variation increases total power dissipation, we demonstrate the importance of considering temperature variation in the design flow. With this power, area and thermal modeling capability, the SST can be used for hardware/software co-design of future exascale systems.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 39
    Publication Date: 2012-02-02
    Description: With the advent of heterogeneous computing systems consisting of multi-core central processing units (CPUs) and many-core graphics processing units (GPUs), robust methods are needed to facilitate fair benchmark comparisons between different systems. In this paper, we present a benchmarking methodology for measuring a number of performance metrics for heterogeneous systems. Methods for comparing performance and energy efficiency are included. Consideration is given to further metrics, such as associated running costs and carbon emissions. We give a case study for these metrics applied to Bristol University Docking engine, a molecular mechanics-based docking application that has been ported to open computing language at the University of Bristol. Results are included for both AMD and NVIDIA GPUs, and for a highly optimized code on the latest x86 CPUs.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 40
    Publication Date: 2012-02-02
    Description: Java embedded systems often include Java middleware classes installed on the client device. For higher performance, they can be compiled into machine code before runtime using an ahead-of-time compiler (AOTC). There are many approaches to AOTC, yet a bytecode-to-C (b-to-C) AOTC which translates the bytecode into the C code and then compiles it using an existing optimizing compiler such as gcc would be the most straightforward one. This paper explores a few important design and optimization issues of a b-to-C AOTC, including the compilation form for the translated C code, the call interfaces among translated and interpreted Java methods, and Java-specific optimizations by the AOTC that can complement the gcc optimizations. We evaluate these issues with our b-to-C AOTC implemented on the MIPS platform for the Sun's CDC VM to understand their performance impact.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 41
    Publication Date: 2012-02-02
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 42
    Publication Date: 2012-02-07
    Print ISSN: 0272-4960
    Electronic ISSN: 1464-3634
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 43
    Publication Date: 2012-02-08
    Description: Let K be a convex body in R n . We introduce a new affine invariant, which we call K , that can be found in three different ways: as a limit of normalized L p -affine surface areas; as the relative entropy of the cone measure of K and the cone measure of K °; as the limit of the volume difference of K and L p -centroid bodies. We investigate properties of K and of related new invariant quantities. In particular, we show new affine isoperimetric inequalities and we show an ‘information inequality’ for convex bodies.
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 44
    Publication Date: 2012-02-08
    Description: We establish the precise bounds for the amount of determinacy provable in second-order arithmetic. We show that, for every natural number n , second-order arithmetic can prove that determinacy holds for Boolean combinations of n many classes, but it cannot prove that all finite Boolean combinations of classes are determined. More specifically, we prove that , but that , where is the n th level in the difference hierarchy of classes. We also show some conservativity results that imply that reversals for the theorems above are not possible. We prove that, for every true 1 4 sentence T (as, for instance, -DET) and every and .
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 45
    Publication Date: 2012-02-11
    Description: Longitudinal or hierarchical data are often observed in forestry, which can pose both challenges and opportunities when performing statistical analyses. The current standard approach for analysing these types of data is mixed-effects models under the frequentist paradigm. Bayesian techniques have several advantages when compared with traditional approaches, but their use in forestry has been relatively limited. In this paper, we propose a Bayesian solution to non-linear mixed-effects models for longitudinal data in forestry. We demonstrate the Bayesian modelling process using individual tree height–age data for balsam fir ( Abies balsamea (L.)) collected from eastern Maine. Due to its frequent utilization in modelling dominant tree height growth over time, we choose to examine models based on the Chapman–Richards function. We established four different model formulations, each having varying subject-specific parameters, which we estimated using both frequentist and Bayesian approaches. We found the estimation results to be quite close between the two methods. In addition, an important feature of the Bayesian method is the unified manner in which estimation and prediction are handled. Specifically, local parameters can be predicted for a new dataset after setting the posterior distributions from the estimation stage as new priors in the prediction phase.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 46
    Publication Date: 2012-02-11
    Description: This study compares the financial return of converting old-growth boreal stands into even-aged stands to that of two approaches of selection cutting in Quebec (Canada). In this region, old-growth stands are usually harvested by completely removing the canopy while protecting the abundant advance regeneration, an approach known as careful logging around advance growth (CLAAG). These approaches were compared using a time frame of over 200 years. Consideration is given to the majority of the operating costs leading to end products. The financial analysis integrates Monte Carlo simulations, making it possible to consider the uncertainty associated with variables. The net present values (NPVs) are then associated with a distribution of probabilities. The results show that the probabilities of obtaining positive NPVs are high for all treatments, suggesting that selection cutting approaches can be appropriate alternatives to CLAAG for some stands. Depending on the criteria used, the CLAAG cut or one of the selection cuts show the best performances. In fact, the results of the financial study show that in the future, selection cutting approaches will be more profitable than CLAAG but still less than present CLAAG operations. This occurs because, according to the current yield curves and rotation ages, future stands managed with CLAAG will have smaller and less valuable trees than in the primary forest and in stands managed with the selection system.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 47
    Publication Date: 2012-02-11
    Description: There is a growing interest in the feasibility of establishing ‘Carbon’ forests where carbon sinks are created by maintaining forest stands out to considerable ages. In New Zealand, Pinus radiata (D. Don) is usually grown over 25- to 30-year rotations; the main aim of this paper is to examine the potential to maintain stands to 60 years or more. There were over 140 permanent sample plots in New Zealand that were maintained for at least 50 years. These data were examined to verify that growth can be sustained over this period. Net basal area per hectare and mean-top-height are graphically demonstrated to follow expected growth paths with no signs of senescence occurring. Stems per hectare loss is shown to be sometimes high, especially with dense stockings, but virtually all dying trees are small suppressed stems, so the impact on basal area yield at maturity is minimal. It is concluded that growing radiata pine on a rotation of 60 years is feasible, and it may be possible to use much longer rotations.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 48
    Publication Date: 2012-02-11
    Description: The effects of site preparation practices (drainage, mounding and fertilization) on the fluxes from the soil surface of carbon dioxide (CO 2 ), methane (CH 4 ) and nitrous oxide (N 2 O) were studied on an organic-rich peaty gley soil at Harwood Forest, north-east England. Drained plots had significantly higher CO 2 fluxes but significantly lower CH 4 fluxes compared with undrained plots, while N 2 O emissions were not affected by drainage. Mounding caused significantly higher CH 4 emissions, while it significantly reduced N 2 O emissions. Fertilization caused significant increases in emissions of CO 2 , CH 4 and N 2 O. In terms of overall greenhouse warming potential, drainage and fertilization increased CO 2 -equivalent emissions by ~18–29 and 7–23 per cent, respectively, while mounding reduced CO 2 -equivalent emissions by ~8 per cent in year 1, but had no effect on emissions in year 2 of study. Soil temperature was the main environmental variable controlling CO 2 emissions, while CH 4 was controlled primarily by water table depth. Nitrous oxide emissions responded to changes in soil temperature and water table depth. In the short term, drainage and fertilization contributed to accelerating greenhouse gas emissions significantly, although their long-term effects are likely moderated by accelerating carbon accumulation in the tree biomass. Long-term studies are required to assess the cumulative impacts of site preparation practices during the whole rotation cycle.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 49
    Publication Date: 2012-02-11
    Description: As signatories to the United Nation Framework Convention on Climate Change, the US has been estimating standing dead tree (SDT) carbon (C) stocks using a model based on live tree attributes. The USDA Forest Service began sampling SDTs nationwide in 1999. With comprehensive field data now available, the objective of this study was to compare field- and model-based estimates of SDT C stocks across the US to evaluate potential directions for improving National Greenhouse Gas Inventory (NGHGI) reporting and C dynamics research. Field inventory data indicated that most forests have relatively little SDT C stocks (〈1 Mg/ha), whereas large SDT C stocks (〉25 Mg/ha) are infrequent. Models used for past NGHGIs to predict SDT C stocks do not accurately reflect what was observed in inventory plots, resulting in an overestimation (~100 per cent) of SDT C stocks at the national scale. These results indicate that the current estimate of the Nation’s total forest C stock is overestimated by ~4.2 per cent due to overestimation of SDT C stocks that are a relatively small component of the total forest C stock. A field-based approach is suggested for use in future C reporting efforts to reduce estimation bias.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 50
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 51
    Publication Date: 2012-02-11
    Description: Silvicultural systems which retain canopy cover during the regeneration phase have become an increasingly important form of management, but their effectiveness in controlling weed species has not been extensively studied. The development of bramble, which is a widespread competitive weed species, was observed within a c . 35-year-old Corsican pine stand thinned to remove 10, 20, 40 and 80 per cent of basal area. Cover, height and numbers of inflorescences and berries were recorded in each of the 3 years following thinning and were generally ranked according to intensity of thinning, but there were no significant differences between treatments. Shoot length, estimated using a grid-intersection method, was significantly lower in the 10 per cent compared with the 40 and 80 per cent thinning treatments. The initial length of bramble shoot present, and basal area and number of trees remaining could be used in various combinations to predict cover, height and shoot length. Although the bramble thicket was generally less well developed in the less-intense thinning treatments, these did not appear to enhance the establishment of trees. Seedlings grew best in the 80 per cent treatment and overall their mean heights were generally lower than that of bramble. Retention of overstorey cover in order to suppress bramble growth and promote tree seedling establishment during forest regeneration may not succeed.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 52
    Publication Date: 2012-02-11
    Description: Three experiments were established in the 1990s to examine the impact of complete residue (brash) and above-ground biomass removal (i.e. ‘whole-tree harvesting’, WTH) at clearfelling on the subsequent growth and yield of replanted Sitka spruce ( Picea sitchensis ). The sites were of varying fertility; two would now be considered to be of ‘medium’ risk for brash removal, while one would be a ‘high’-risk site. The interactions between brash removal and regular remedial fertilizer applications and weed control regimes were also investigated at each site. After 10 years, trees had been successfully established at all sites, and in most cases, the treatments were close to canopy closure. The main effects observed at all sites were due to brash retention and fertilizer application. The benefits from the former were not evident until the last stages of the establishment period, whereas benefits from fertilizer application were evident once the trees had reached 5–6 years of age. The impacts of weed control were inconsistent, providing temporary benefits on the more fertile sites, and having a negative effect on the poorest site, primarily because the herbicide regime favoured the development of ericaceous vegetation which competed with the planted trees for nutrients. After 10 years at the two medium-risk sites, the difference in growth between plots with brash retained and those where brash was removed was 5–9 per cent for height growth and 5–7 per cent for diameter. However, at the poorest site, the equivalent differences were ~9 per cent and 19 per cent. The results show that the impact of brash removal due to WTH are significantly affected by site type and soil fertility and also that it may take nearly a decade before the impacts of such practices are evident.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 53
    Publication Date: 2012-02-11
    Description: Policy makers, scientists and civil society are involved in the development of criteria and indicators for sustainable forest management (SFM), reflecting the growing worldwide demand for addressing sustainable development and environmental governance management goals. Such frameworks have been largely derived from expert-led or community-based approaches. This article details the identification process of criteria and indicators (C & I) based on the international principles of SFM through the analysis of a hybrid approach that uses both a top-down (TD) and a bottom-up (BU) approach. The aim of this article is to discuss how the two approaches have worked to incorporate the different views, opinions and experiences of experts and stakeholders. National-level C & I are then compared with those at the local level, making specific reference to sustainable community forest (CF) management. For the TD approach, a Delphi survey was conducted where 121 experts shared their knowledge, experience and judgements in assessing a set of 72 indicators with regard to the applicability, practicality and importance of national, regional and CF management in Nepal. For the BU approach, C & I for CF management were developed with the direct involvement of various stakeholders. It was shown that such a hybrid approach is feasible from a methodological point of view, but a framework is needed by the government to more fully utilize the opportunities of the C & I development process in the SFM context. The results of this study also help to bridge the gap between the ad hoc planning of decision makers and the requirement for a holistic management system, which includes participatory processes. Based on the conclusions of this study, general recommendations for the methodological design of C & I development in similar studies are given.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 54
    facet.materialart.
    Unknown
    Oxford University Press
    In: Forestry
    Publication Date: 2012-02-11
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 55
    Publication Date: 2012-02-14
    Description: SUMMARY In places where sedimentation and erosion compete at fast rates, part of the record of past earthquakes on faults may be buried, hence hidden, in the first few metres below the surface. We developed a novel form of palaeoseismology, of geophysical type, based on the use of a dense pseudo-3-D Ground Penetrating Radar (GPR) survey to investigate such possible buried earthquake traces, on a long, fast-slipping strike-slip fault (Hope fault, New Zealand), at a site (Terako) where marked alluvial conditions prevail. We first used LiDAR data to analyse the ground surface morphology of the 2 km 2 site at the greatest resolution. Nineteen morphological markers were observed, mainly alluvial terrace risers and small stream channels that are all dextrally offset by the fault by amounts ranging between 3 and 200 m. The measurements document about 10 past earthquake slip events with a mean coseismic slip of 3.3 ± 1 m, with the most recent earthquake event having a slip of 3 ± 0.5 m. We then investigated a detailed area of the site (400 × 600 m 2 ) with pseudo-3-D GPR. We measured 56, ≈ 400 m long, 5–10 m spaced GPR profiles (250 MHz), parallel to the fault and evenly distributed on either side. The analysis revealed the existence of a palaeosurface buried at about 3 m depth, corresponding to the top of alluvial terraces of different ages. That buried surface is incised by a dense network of stream channels that are all dextrally offset by the fault. We measured 48 lateral offsets in the buried channel network, more than twice than at the surface. These offsets range between 6 and 108 m, as observed at the surface, yet provide a more continuous record of the fault slip. The similarity of the successive slip increments suggests a slip per event averaging 4.4 ± 1 m, fairly similar to that estimated from surface data. From the total ‘surface and buried’ 67 offset collection, we infer that a minimum of 30 large earthquakes have broken the Hope fault at the Terako site in the last about 6–7 kyr, with an average coseismic slip of 3.2 ± 1 m, a minimum average recurrence time of about 200 yr, and a magnitude of at least M w 7.0–7.4. Our study therefore confirms that part of the record of past earthquakes may indeed reside in the first few metres below the surface, where it may be explored with geophysical, GPR-based palaeoseismology. Developing such a new palaeoseismological tool should provide rich information that may complement surface observations and help to document the past earthquakes on faults.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 56
    Publication Date: 2012-02-14
    Description: Not simply set out in accompaniment of the Greek geometrical text, the diagram also is coaxed into existence manually (using straightedge and compasses) by commands in the text. The marks that a diligent reader thus sequentially produces typically sum, however, to a figure more complex than the provided one and also not (as it is) artful for being synoptically instructive. To provide a figure artfully is to balance multiple desiderata, interlocking the timelessness of insight with the temporality of construction. Our account of the diagram complements those of Manders and Macbeth by more strongly emphasizing practical synthesis.
    Print ISSN: 0031-8019
    Electronic ISSN: 1744-6406
    Topics: Mathematics , Philosophy
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 57
    Publication Date: 2012-02-14
    Description: Tennenbaum's Theorem yields an elegant characterisation of the standard model of arithmetic. Several authors have recently claimed that this result has important philosophical consequences: in particular, it offers us a way of responding to model-theoretic worries about how we manage to grasp the standard model. We disagree. If there ever was such a problem about how we come to grasp the standard model, then Tennenbaum's Theorem does not help. We show this by examining a parallel argument, from a simpler model-theoretic result.
    Print ISSN: 0031-8019
    Electronic ISSN: 1744-6406
    Topics: Mathematics , Philosophy
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 58
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2012-02-14
    Description: The paper discusses Husserl's phenomenology of mathematics in his Formal and Transcendental Logic (1929). In it Husserl seeks to provide descriptive foundations for mathematics. As sciences and mathematics are normative activities Husserl's attempt is also to describe the norms at work in these disciplines. The description shows that mathematics can be given in several different ways. The phenomenologist's task is to examine whether a given part of mathematics is genuine according to the norms that pertain to the approach in question. The paper will then examine the intuitionistic, formalistic, and structural features of Husserl's philosophy of mathematics.
    Print ISSN: 0031-8019
    Electronic ISSN: 1744-6406
    Topics: Mathematics , Philosophy
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 59
    Publication Date: 2012-02-14
    Print ISSN: 0031-8019
    Electronic ISSN: 1744-6406
    Topics: Mathematics , Philosophy
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 60
    Publication Date: 2012-02-14
    Print ISSN: 0031-8019
    Electronic ISSN: 1744-6406
    Topics: Mathematics , Philosophy
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 61
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2012-02-14
    Description: Linnebo and Pettigrew's critique in this journal of categorical foundations well emphasizes that the particulars of various categorical foundations matter, and that mathematical practice must be a major consideration. But several categorists named by the authors as proposing categorical foundations do not propose foundations, notably Awodey, and the article's description of current textbook practice seems inaccurate. They say that categorical foundations have justificatory autonomy if and only if mathematics can be justified simply by its practice. Do they seriously believe philosophers may be able to justify some currently unpractised mathematics better than current practice justifies itself?
    Print ISSN: 0031-8019
    Electronic ISSN: 1744-6406
    Topics: Mathematics , Philosophy
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 62
    Publication Date: 2012-02-14
    Print ISSN: 0031-8019
    Electronic ISSN: 1744-6406
    Topics: Mathematics , Philosophy
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 63
    Publication Date: 2012-02-14
    Print ISSN: 0031-8019
    Electronic ISSN: 1744-6406
    Topics: Mathematics , Philosophy
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 64
    Publication Date: 2012-02-14
    Description: Given a Calderón–Zygmund singular integral operator, it is an open question whether the Fefferman inequality holds true with u as an arbitrary weight. This inequality is known as the Muckenhoupt–Wheeden conjecture. In this paper we prove that, for a wider class of operators called Rubio de Francia operators, if || u || ≤1, then where the function is slightly bigger than the identity. Applications of this inequality in the setting of rearrangement invariant spaces are given.
    Print ISSN: 0033-5606
    Electronic ISSN: 1464-3847
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 65
    Publication Date: 2012-02-14
    Description: We show that whenever m ≤ n , the space of all continuous rational maps from CP m to CP n has the same homology as the space of all continuous maps between these spaces in dimensions smaller than d (2 n – 2 m + 1) – 1. This improves the result of the paper ‘Spaces of rational maps and the Stone–Weierstrass theorem’ ( Topology 45 (2006), 281–293).
    Print ISSN: 0033-5606
    Electronic ISSN: 1464-3847
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 66
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2012-02-14
    Description: A theorem of Davenport, Mirsky, Newman and Rado shows that there does not exist an exact covering system with distinct moduli. Motivated by this, we raise the question whether or not this is true for covering systems in algebraic number fields. We provide an affirmative answer for certain quadratic fields.
    Print ISSN: 0033-5606
    Electronic ISSN: 1464-3847
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 67
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2012-02-14
    Description: The caustic of a smooth surface in the Euclidean 3-space is the envelope of the normal rays to the surface. It is also the locus of the centres of curvature (the focal points) of the surface. This is why it is also referred to as the focal set of the surface. It has Lagrangian singularities and its generic models are given in [V. I. Arnol’d, S. M. Gusein-Zade and A. N. Varchenko, Singularities of Differentiable Maps , Vol. I, Birkhäuser, Boston, 1986]. The aim of this paper is to define the caustic C ( M ) of a smooth surface M embedded in the Minkowski 3-space and to study its geometry. We denote by the locus of degeneracy (LD) the locus of points on M where the metric is degenerate. If M is a closed surface then its LD is not empty. At a point on the LD the ‘normal’ line to M is lightlike and is tangent to M . Also, the focal set of M is not defined at points on the LD. We define the caustic of M as the bifurcation set of the family of distance-squared functions on M . Then C ( M ) coincides with the focal set of M \ LD and provides an extension of the focal set to the LD. We study the local behaviour of the metric on C ( M ).
    Print ISSN: 0033-5606
    Electronic ISSN: 1464-3847
    Topics: Mathematics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 68
    Publication Date: 2012-02-15
    Description: SUMMARY The M w 9.0 off northeast Japan (Tohoku-oki) earthquake occurred on 2011 March 11 at the interface between the North American (NA) and Pacific (PA) plates. The occurrence of interplate earthquakes can be regarded as the sudden release of tectonic stress accumulated by the interseismic gradual increase of slip deficit in source regions. The inversion analysis of GPS velocity data for a seismically calm period (1996–2000) before the Tohoku-oki earthquake has revealed the existence of five remarkable slip-deficit zones distributed on the NA–PA plate interface along the southern Kuril-Japan trench. We analysed coseismic GPS displacement data for the Tohoku-oki earthquake with the same inversion method, and obtained the bimodal distribution of coseismic slip spreading over the southern two, Miyagi-oki and Fukushima-oki, interseismic slip-deficit zones. The maximum slip is 32 m for the Miyagi-oki slip-deficit zone but only 7 m for the Fukushima-oki slip-deficit zone. The extraordinarily large coseismic slip in the Miyagi-oki slip-deficit zone, where ordinarily large earthquakes with about 3 m coseismic slips have repeated every 40 yr in the past two centuries, suggests the total rupture of a 300-km-long basement asperity underlying much smaller-scale local asperities.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 69
    Publication Date: 2012-02-16
    Description: SUMMARY A combined palaeodirectional and palaeointensity study of a representative collection of plutonic rocks from the Antarctic Peninsula batholith from the western part of the Antarctic Peninsula, near the Ukrainian Antarctic base 'Academik Vernadsky' were carried out. Petrographically, the collection includes gabbros, diorites and quartz diorites, tonalities, granodiorites and granites. The ages of igneous complex emplacement vary from 50 to 117 Ma with most of the rocks belonging to the Cretaceous Normal Superchron. The characteristic remanent magnetizations were isolated by stepwise thermal demagnetization over the temperature interval 440–590°C and their intensities amount to 95 per cent of the NRM. The geographic positions of palaeopoles do not contradict the ‘key poles’ of the Antarctic Peninsula between 90 and 60 Ma. A significant part of the collection was subjected to Coe-modified Thellier palaeointensity experiments with the pTRM checks, which yielded seven reliable palaeointensity determinations for seven different locations. The obtained VDMs are relatively low for all sites, being on average about half of the present day VDM. The analysis of available palaeointensity data for the Cretaceous, Miocene and Middle Jurassic indicates the existence of strong correlations between the mean VDM and VDM scatter versus the rate of reversals. However, due to the shortage of data, the correlations are not significant at the 5 per cent significance level.
    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).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 70
    Publication Date: 2012-02-17
    Description: Rosen, S., Engås, A., Fernö, A., and Jörgensen, T. 2012. The reactions of shoaling adult cod to a pelagic trawl: implications for commercial trawling. – ICES Journal of Marine Science, 69: 303–312. The reactions of shoaling adult Atlantic cod to a pelagic trawl were measured during fishing off the north coast of Norway. Cod remaining in the trawl track dived at rates as fast as 0.35 m s –1 following vessel passage and swam away from the vessel, in the direction of the approaching trawl, at an average rate of 0.6 m s –1 . They did not attempt to swim ahead of the trawl as documented previously, but passed into the lower half of the trawl entrance and swam slowly in the direction of trawling at a rate of 0.2–0.5 m s –1 as the trawl's greater speed through water carried them deeper into the trawl. Shoals compressed vertically once inside the trawl, suggesting that packing density increased at least fourfold. Fish remained in the lower part of the trawl as they moved through its tapered section towards the codend, with little to no clearance above the bottom panel, but significant clearance beneath the top panel. Catches were sufficient to support commercial harvest, and the behaviour observed suggests that changes in trawl design and fishing strategy might improve fuel economy and species selectivity.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 71
    Publication Date: 2012-02-17
    Description: Shackell, N. L., Bundy, A., Nye, J. A., and Link, J. S. 2012. Common large-scale responses to climate and fishing across Northwest Atlantic ecosystems. – ICES Journal of Marine Science, 69: 151–152. Investigating whether there were common biological responses to climate and fishing across seven Northwest Atlantic ecosystems, a minimum/maximum autocorrelation factor analysis of biological indicators for each region revealed a common primary multivariate trend of a rapid change during the 1980s and early 1990s. There was a strong common pattern in the biological indicators responsible for the primary multivariate temporal trend in the five more northerly regions: an increase in the abundance of phytoplankton, an increase in biomass at mid-trophic levels, and a decline in predatory groundfish size. The common associations between patterns and drivers were fishing indices and the Atlantic Multidecadal Oscillation, but all associations weakened when co-varying drivers were held constant. The results are consistent with known long-term effects of intense fishing, such as a decline in average fish size and changes in species composition. Less fishing pressure has allowed some regions to recover to former predatory biomass levels since the late 1990s, but the bulk of the biomass consists of fewer species. However, fishing was not the only driver, and a more mechanistic understanding of how the climate affects lower trophic levels is needed to contextualize climate effects in heavily fished ecosystems.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 72
    Publication Date: 2012-02-17
    Description: Deporte, N., Ulrich, C., Mahévas, S., Demanèche, S., and Bastardie, F. 2012. Regional métier definition: a comparative investigation of statistical methods using a workflow applied to international otter trawl fisheries in the North Sea. – ICES Journal of Marine Science, 69: 331–342. The European Common Fisheries Policy recognizes the importance of accounting for heterogeneity in fishing practices, and métier-based sampling is now at the core of the EU Data Collection Framework. The implementation of such an approach would require Member States to agree on the standard regional métier definitions and on practical rules to categorize logbook records into métiers. Several alternative approaches have been used in the past to categorize landings profiles, but no consensus has yet emerged. A generic open-source workflow is developed to test and compare a selection of methods, including principal components analysis (PCA), hierarchical agglomerative clustering (HAC), K -means, and Clustering LARge Applications (CLARA), and to provide simple allocation rules. This workflow is applied to a unique regional dataset consisting of bottom-trawl logbooks of five North Sea countries. No method proved to be infallible, but combining PCA with either CLARA or HAC performed best. For 2008, a hierarchical classification with 14 species assemblages is proposed. Discriminant analysis proved more robust than simple ordination methods for allocating a new logbook record into an existing métier. The whole approach is directly operational and could contribute to defining more objective and consistent métiers across European fisheries.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 73
    Publication Date: 2012-02-17
    Description: Greenstreet, S. P. R., Rogers, S. I., Rice, J. C., Piet, G. J., Guirey, E. J., Fraser, H. M., and Fryer, R. J. 2012. A reassessment of trends in the North Sea Large Fish Indicator and a re-evaluation of earlier conclusions. – ICES Journal of Marine Science, 69: 343–345. Previous analysis of the Large Fish Indicator, the basis for the North Sea "fish communities" EcoQO, suggested a strong recovery between 2001 and 2008. Discovery of a mistake in this earlier analysis now suggests that this recovery is not as strong as first thought, but reanalysis of the corrected data still supports the majority of conclusions drawn in the original paper.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 74
    Publication Date: 2012-02-17
    Description: Xie, Y., Michielsens, C. G. J., and Martens, F. J. 2012. Classification of fish and non-fish acoustic tracks using discriminant function analysis. – ICES Journal of Marine Science, 69: 313–322. Hydroacoustic data acquired for estimating fish populations contain information on both fish and non-fish targets, so sonar technicians traditionally rely on their knowledge of fish behaviour and experience with hydroacoustics to remove non-fish targets from the hydroacoustic data. This process is often labour-intensive and time-consuming, making real-time assessment of fish populations difficult. Simple solutions are not always available for all circumstances. However, the split-beam sonar data collected in the lower Fraser River, British Columbia, Canada, showed distinct signatures between actively swimming fish and non-fish objects such as drifting debris, surface bubbles, and stationary objects in the water column and off the river bottom. Acoustic tracks of fish and non-fish targets were characterized by differentiable statistical patterns that were amenable to discriminant function analysis (DFA). An application of DFA to segregate fish and non-fish targets detected by a split-beam sonar system in the lower Fraser River is presented, characteristics of user-identified fish and non-fish acoustic tracks being utilized as learning samples for the DFA. Also, a method to rank the discriminating power of individual variables is presented, providing guidance for constructing efficient and effective discriminant functions with variables that offer high discriminating power. The DFA yielded classification accuracies of 96% for fish and 91% for non-fish tracks and reduced the manual sorting time by 50–75%.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 75
    Publication Date: 2012-02-17
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 76
    Publication Date: 2012-02-17
    Description: Rey, F. 2012. Declining silicate concentrations in the Norwegian and Barents Seas. – ICES Journal of Marine Science, 69: 208–212. Since 1990, a decline in silicate concentrations together with increasing salinities has been observed in the Atlantic water of the Norwegian and Barents Seas. This decline in silicate has been found to be related to the relative proportion in which eastern and western source water masses from the northeastern North Atlantic enter the Norwegian Sea.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 77
    Publication Date: 2012-02-17
    Description: Zhou, S., Milton, D. A., and Fry, G. C. 2012. Integrated risk analysis for rare marine species impacted by fishing: sustainability assessment and population trend modelling. – ICES Journal of Marine Science, 69: 271–280. Risk assessment and conservation management of rare species are challenging due to a lack of data. We developed an integrated risk assessment approach to assess human impact on population sustainability of rare species. The approach involved two components: a quantitative sustainability assessment coupled with modelling trends in relative abundance. Both components took nil catches into account through zero-inflated statistical distributions that simultaneously modelled the zero and non-zero catches separately in submodels. The sustainability assessment used detection–non-detection data for population estimation and linked sustainability to easily collected life-history traits. This component provides an assessment of population sustainability at one point in time. The trend modelling applied zero-inflated negative binomial models to temporal trends in density and dispersion of species. It provided a complement to the static sustainability assessment. We applied this integrated approach to assess the risk to 14 species of rare, protected sea snakes incidentally caught in the Australian Northern Prawn Fishery. This approach can be applicable for risk assessment of many species with limited abundance data, a large number of absences and some presence–absence information only.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 78
    Publication Date: 2012-02-17
    Description: Frid, C. L. J., and Paramor, O. A. L. 2012. Feeding the world: what role for fisheries? – ICES Journal of Marine Science, 69: 145–150. Fisheries (wild capture and aquaculture) deliver more than 110 million tonnes of food and around 15% of the dietary protein to the 7 billion people currently living on the planet. With the global population expected to peak at 9 billion by 2050, and 〉80% of global fish stocks currently fully or overexploited (and aquaculture is at least in part dependent on capture fisheries), the contribution of fisheries looks set to decline. The challenge is therefore determining how better management, an ecosystem perspective, and more efficient utilization of fisheries waste can support fisheries products continuing to contribute significantly to "feeding the world" up to and beyond the population peak.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 79
    Publication Date: 2012-02-17
    Description: Boström, M. K., Östman, Ö., Bergenius, M. A. J., and Lunneryd, S-G. 2012. Cormorant diet in relation to temporal changes in fish communities. – ICES Journal of Marine Science, 69: 175–183. The stomach contents of 229 great cormorants ( Phalacrocorax carbo sinensis ) shot between March and October 2009 along the Swedish east coast were analysed for differences in diet between gender, age, and breeding phase. Sticklebacks ( Gasterosteus aculeatus and Pungitius pungitius ) were the most common prey, followed by eelpout ( Zoarces viviparus ), herring ( Clupea harengus membras ), and cyprinids (Cyprinidae). Diet did not differ between age and gender, but changed over the breeding season. The different phases explained around 10% of the total variation in stomach content between cormorants, suggesting no major shift in diet over the breeding season. The diet of cormorants in 2009 was compared with the results of a study conducted in the same area in 1992. There were evident changes in the diet between 1992 and 2009, with less perch ( Perca fluviatilis ) and cyprinids and more eelpout and herring in 2009. This change in diet could partly be related to changes in the fish community. The seasonal changes in diet composition of whole stomachs were less notable than in many previous studies, but long-term changes in the fish communities may induce changes in cormorant diet. It is clearly important to use stomach contents in areas with many small fish species for a comprehensive assessment of cormorant diet.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 80
    Publication Date: 2012-02-17
    Description: Cañás, L., Stransky, C., Schlickeisen, J., Sampedro, M. P., and Fariña, A. C. 2012. Use of the otolith shape analysis in stock identification of anglerfish ( Lophius piscatorius ) in the Northeast Atlantic. – ICES Journal of Marine Science, 69: 250–256. The geographical variability in the anglerfish Lophius piscatorius otolith shape was investigated to examine biological evidence for the current separation into Northern and Southern stocks of L. piscatorius established in the Southwest European waters (Southern Shelf area) by the International Council for the Exploration of the Sea (ICES). In all, 629 otoliths of L. piscatorius (12–90 cm total length) from commercial fishing and research surveys were collected in two consecutive years, 2008 and 2009. The otolith shape was compared between stocks for differences in univariate descriptors using non-parametric analysis of covariance, as well as elliptical Fourier shape descriptors, through a metric multidimensional scaling and a linear discriminant analysis (LDA). The differences found in the otolith shape between Northern and Southern stocks were not large enough to hold the current status of L. piscatorius regarding stock definition in the Southern Shelf area, although homogeneous mixing between both stocks is not expected as there were significant differences between three univariate descriptors and the LDA was significant. These results are in agreement with the previous L. piscatorius stock identification studies (genetics, body morphology, and migratory behaviour), which do not support the current separation of these stocks but found substructures within the area.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 81
    Publication Date: 2012-02-17
    Description: Low-temperature methane and methanol steam-reforming catalysts Ni/Al 2 O 3 , Cu/Al 2 O 3 and Ni–Cu/Al 2 O 3 with various loadings of Ni and Cu were prepared using a wet impregnation method. The samples were characterized using scanning electron microscope, surface area (BET) test, X-ray diffraction (XRD), infrared test, CO chemisorption test and temperature-programmed reduction tests. XRD testing showed that NiO and CuO were present. Ni–Cu-alloyed catalyst shows a significant change in the catalyst characteristics compared with those of individual metals. The results presented in this paper show the main changes in the catalyst properties using ex situ testing.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 82
    Publication Date: 2012-02-17
    Description: In this paper we report the synthesis of a series of new Mn/Ti containing perovskites, La 1– x Mn x Mn 1– x Ti x O 3– , for investigation of their potential for use as solid oxide fuel cell electrodes, particularly anodes. Single-phase samples could be achieved for x ≤ 0.4. Above this level, La 2 Ti 2 O 7 impurities were found. Conductivity measurements showed electronic conductivity up to a maximum of 12 S cm –1 at 850°C in air. While the samples were shown to be stable in both air and 5% H 2 /N 2 , the conductivities in the latter were significantly lower (0.4 S cm –1 ), which would be an issue for potential anode applications.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 83
    Publication Date: 2012-02-17
    Description: Motivation: High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein-bound nucleic acids. Results: We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation. Availability: Artemis is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute websites: http://www.sanger.ac.uk/resources/software/artemis/ . Contact: artemis@sanger.ac.uk ; tjc@sanger.ac.uk
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 84
    Publication Date: 2012-02-17
    Description: : microRibonucleic acid (miRNAs) are small regulatory molecules that act by mRNA degradation or via translational repression. Although many miRNAs are ubiquitously expressed, a small subset have differential expression patterns that may give rise to tissue-specific complexes. Motivation: This work studies gene targeting patterns amongst miRNAs with differential expression profiles, and links this to control and regulation of protein complexes. Results: We find that, when a pair of miRNAs are not expressed in the same tissues, there is a higher tendency for them to target the direct partners of the same hub proteins. At the same time, they also avoid targeting the same set of hub-spokes. Moreover, the complexes corresponding to these hub-spokes tend to be specific and nonoverlapping. This suggests that the effect of miRNAs on the formation of complexes is specific. Contact: wongls@comp.nus.edu.sg Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 85
    Publication Date: 2012-02-17
    Description: Motivation: Small interfering RNAs (siRNAs) are produced from much longer sequences of double-stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterization of the precursors from which they are derived. Results: High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated datasets. Availability: Our methods are available as the Bioconductor ( www.bioconductor.org ) package segmentSeq (version 1.5.6 and above). Contact: tjh48@cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 86
    Publication Date: 2012-02-17
    Description: Motivation: Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome for high-throughput applications. Results: In this work, we present an ensemble of protein disorder predictors called ESpritz. These are based on bidirectional recursive neural networks and trained on three different flavors of disorder, including a novel NMR flexibility predictor. ESpritz can produce fast and accurate sequence-only predictions, annotating entire genomes in the order of hours on a single processor core. Alternatively, a slower but slightly more accurate ESpritz variant using sequence profiles can be used for applications requiring maximum performance. Two levels of prediction confidence allow either to maximize reasonable disorder detection or to limit expected false positives to 5%. ESpritz performs consistently well on the recent CASP9 data, reaching a S w measure of 54.82 and area under the receiver operator curve of 0.856. The fast predictor is four orders of magnitude faster and remains better than most publicly available CASP9 methods, making it ideal for genomic scale predictions. Conclusions: ESpritz predicts three flavors of disorder at two distinct false positive rates, either with a fast or slower and slightly more accurate approach. Given its state-of-the-art performance, it can be especially useful for high-throughput applications. Availability: Both a web server for high-throughput analysis and a Linux executable version of ESpritz are available from: http://protein.bio.unipd.it/espritz/ Contact: silvio.tosatto@unipd.it Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 87
    Publication Date: 2012-02-17
    Description: Motivation: Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories. Results: We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors—which were introduced by Røgen and co-workers—and subsequently performing K-means clustering. Conclusions: Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50 000 structures, can be clustered within seconds to minutes. Contact: thamelry@binf.ku.dk ; harder@binf.ku.dk Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 88
    Publication Date: 2012-02-17
    Description: Motivation: Transmembrane β barrel proteins (TMBs) are found in the outer membrane of Gram-negative bacteria, chloroplast and mitochondria. They play a major role in the translocation machinery, pore formation, membrane anchoring and ion exchange. TMBs are also promising targets for antimicrobial drugs and vaccines. Given the difficulty in membrane protein structure determination, computational methods to identify TMBs and predict the topology of TMBs are important. Results: Here, we present BOCTOPUS; an improved method for the topology prediction of TMBs by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and HMMs account for local and global residue preferences, respectively. Based on a 10-fold cross-validation test, BOCTOPUS performs better than all existing methods, reaching a Q3 accuracy of 87%. Further, BOCTOPUS predicted the correct number of strands for 83% proteins in the dataset. BOCTOPUS might also help in reliable identification of TMBs by using it as an additional filter to methods specialized in this task. Availability: BOCTOPUS is freely available as a web server at: http://boctopus.cbr.su.se/ . The datasets used for training and evaluations are also available from this site. Contact: arne@bioinfo.se Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 89
    Publication Date: 2012-02-17
    Description: Motivation: High-dimensional data such as microarrays have created new challenges to traditional statistical methods. One such example is on class prediction with high-dimension, low-sample size data. Due to the small sample size, the sample mean estimates are usually unreliable. As a consequence, the performance of the class prediction methods using the sample mean may also be unsatisfactory. To obtain more accurate estimation of parameters some statistical methods, such as regularizations through shrinkage, are often desired. Results: In this article, we investigate the family of shrinkage estimators for the mean value under the quadratic loss function. The optimal shrinkage parameter is proposed under the scenario when the sample size is fixed and the dimension is large. We then construct a shrinkage-based diagonal discriminant rule by replacing the sample mean by the proposed shrinkage mean. Finally, we demonstrate via simulation studies and real data analysis that the proposed shrinkage-based rule outperforms its original competitor in a wide range of settings. Contact: tongt@hkbu.edu.hk
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 90
    Publication Date: 2012-02-17
    Description: Motivation: The advent of high-throughput sequencing technologies is revolutionizing our ability in discovering and genotyping DNA copy number variants (CNVs). Read count-based approaches are able to detect CNV regions with an unprecedented resolution. Although this computational strategy has been recently introduced in literature, much work has been already done for the preparation, normalization and analysis of this kind of data. Results: Here we face the many aspects that cover the detection of CNVs by using read count approach. We first study the characteristics and systematic biases of read count distributions, focusing on the normalization methods designed for removing these biases. Subsequently, we compare the algorithms designed to detect the boundaries of CNVs and we investigate the ability of read count data to predict the exact number of DNA copy. Finally, we review the tools publicly available for analysing read count data. To better understand the state of the art of read count approaches, we compare the performance of the three most widely used sequencing technologies (Illumina Genome Analyzer, Roche 454 and Life Technologies SOLiD) in all the analyses that we perform. Contact: albertomagi@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 91
    Publication Date: 2012-02-17
    Description: Motivation: We investigate and quantify the generalizability of the white blood cell (WBC) transcriptome to the general, multiorgan transcriptome. We use data from the NCBI's Gene Expression Omnibus (GEO) public repository to define two datasets for comparison, WBC and OO (Other Organ) sets. Results: Comprehensive pair-wise correlation and expression level profiles are calculated for both datasets (with sizes of 81 and 1463, respectively). We have used mapping and ranking across the Gene Ontology (GO) categories to quantify similarity between the two sets. GO mappings of the most correlated and highly expressed genes from the two datasets tightly match, with the notable exceptions of components of the ribosome, cell adhesion and immune response. That is, 10 877 or 48.8% of all measured genes do not change 〉10% of rank range between WBC and OO; only 878 (3.9%) change rank 〉50%. Two trans -tissue gene lists are defined, the most changing and the least changing genes in expression rank. We also provide a general, quantitative measure of the probability of expression rank and correlation profile in the OO system given the expression rank and correlation profile in the WBC dataset. Contact: vvaltchinov@partners.org Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 92
    Publication Date: 2012-02-17
    Description: Motivation: The understanding of the molecular sources for diseases like cancer can be significantly improved by computational models. Recently, Boolean networks have become very popular for modeling signaling and regulatory networks. However, such models rely on a set of Boolean functions that are in general not known. Unfortunately, while detailed information on the molecular interactions becomes available in large scale through electronic databases, the information on the Boolean functions does not become available simultaneously and has to be included manually into the models, if at all known. Results: We propose a new Boolean approach which can directly utilize the mechanistic network information available through modern databases. The Boolean function is implicitly defined by the reaction mechanisms. Special care has been taken for the treatment of kinetic features like inhibition. The method has been applied to a signaling model combining the Wnt and MAPK pathway. Availability: A sample C++ implementation of the proposed method is available for Linux and compatible systems through http://code.google.com/p/libscopes/wiki/Paper2011 Contact: handorf@physik.hu-berlin.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 93
    Publication Date: 2012-02-17
    Description: Motivation: Multiple sequence alignment (MSA) is a core method in bioinformatics. The accuracy of such alignments may influence the success of downstream analyses such as phylogenetic inference, protein structure prediction, and functional prediction. The importance of MSA has lead to the proliferation of MSA methods, with different objective functions and heuristics to search for the optimal MSA. Different methods of inferring MSAs produce different results in all but the most trivial cases. By measuring the differences between inferred alignments, we may be able to develop an understanding of how these differences (i) relate to the objective functions and heuristics used in MSA methods, and (ii) affect downstream analyses. Results: We introduce four metrics to compare MSAs, which include the position in a sequence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel) event occurs. We use both real and synthetic data to explore the information given by these metrics and demonstrate how the different metrics in combination can yield more information about MSA methods and the differences between them. Availability: MetAl is a free software implementation of these metrics in Haskell. Source and binaries for Windows, Linux and Mac OS X are available from http://kumiho.smith.man.ac.uk/whelan/software/metal/ . Contact: simon.whelan@manchester.ac.uk
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 94
    Publication Date: 2012-02-17
    Description: Motivation: Peptide detection is a crucial step in mass spectrometry (MS) based proteomics. Most existing algorithms are based upon greedy isotope template matching and thus may be prone to error propagation and ineffective to detect overlapping peptides. In addition, existing algorithms usually work at different charge states separately, isolating useful information that can be drawn from other charge states, which may lead to poor detection of low abundance peptides. Results: BPDA2d models spectra as a mixture of candidate peptide signals and systematically evaluates all possible combinations of possible peptide candidates to interpret the given spectra. For each candidate, BPDA2d takes into account its elution profile, charge state distribution and isotope pattern, and it combines all evidence to infer the candidate's signal and existence probability. By piecing all evidence together—especially by deriving information across charge states—low abundance peptides can be better identified and peptide detection rates can be improved. Instead of local template matching, BPDA2d performs global optimization for all candidates and systematically optimizes their signals. Since BPDA2d looks for the optimal among all possible interpretations of the given spectra, it has the capability in handling complex spectra where features overlap. BPDA2d estimates the posterior existence probability of detected peptides, which can be directly used for probability-based evaluation in subsequent processing steps. Our experiments indicate that BPDA2d outperforms state-of-the-art detection methods on both simulated data and real liquid chromatography–mass spectrometry data, according to sensitivity and detection accuracy. Availability: The BPDA2d software package is available at http://gsp.tamu.edu/Publications/supplementary/sun11a/ Contact: Michelle.Zhang@utsa.edu ; edward@ece.tamu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 95
    Publication Date: 2012-02-17
    Description: Motivation: The continued progress in developing technological platforms, availability of many published experimental datasets, as well as different statistical methods to analyze those data have allowed approaching the same research question using various methods simultaneously. To get the best out of all these alternatives, we need to integrate their results in an unbiased manner. Prioritized gene lists are a common result presentation method in genomic data analysis applications. Thus, the rank aggregation methods can become a useful and general solution for the integration task. Results: Standard rank aggregation methods are often ill-suited for biological settings where the gene lists are inherently noisy. As a remedy, we propose a novel robust rank aggregation (RRA) method. Our method detects genes that are ranked consistently better than expected under null hypothesis of uncorrelated inputs and assigns a significance score for each gene. The underlying probabilistic model makes the algorithm parameter free and robust to outliers, noise and errors. Significance scores also provide a rigorous way to keep only the statistically relevant genes in the final list. These properties make our approach robust and compelling for many settings. Availability: All the methods are implemented as a GNU R package R obust R ank A ggreg , freely available at the Comprehensive R Archive Network http://cran.r-project.org/ . Contact: vilo@ut.ee Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 96
    Publication Date: 2012-02-17
    Description: : CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation. Availability: CLARE is freely accessible at http://clare.dcode.org/ . Contact: taherl@ncbi.nlm.nih.gov ; ovcharen@nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 97
    Publication Date: 2012-02-17
    Description: Motivation: We present a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for methylated DNA immunoprecipitation (MeDIP)-sequence datasets. This is the first MeDIP-seq-specific analytic pipeline that starts at the output of the sequencers. This pipeline will reduce the data analysis load on staff and allows the easy and straightforward analysis of sequencing data for DNA methylation. The pipeline integrates customized scripting and several existing tools, which can deal with both paired and single end data. Availability: The package and extensive documentation, and comparison to public data is available at http://life.tongji.edu.cn/meqa/ Contact: jhuang@cephb.fr
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 98
    Publication Date: 2012-02-17
    Description: Motivation: A plethora of bioinformatics analysis has led to the discovery of numerous gene sets, which can be interpreted as discrete measurements emitted from latent signaling pathways. Their potential to infer signaling pathway structures, however, has not been sufficiently exploited. Existing methods accommodating discrete data do not explicitly consider signal cascading mechanisms that characterize a signaling pathway. Novel computational methods are thus needed to fully utilize gene sets and broaden the scope from focusing only on pairwise interactions to the more general cascading events in the inference of signaling pathway structures. Results: We propose a gene set based simulated annealing (SA) algorithm for the reconstruction of signaling pathway structures. A signaling pathway structure is a directed graph containing up to a few hundred nodes and many overlapping signal cascades, where each cascade represents a chain of molecular interactions from the cell surface to the nucleus. Gene sets in our context refer to discrete sets of genes participating in signal cascades, the basic building blocks of a signaling pathway, with no prior information about gene orderings in the cascades. From a compendium of gene sets related to a pathway, SA aims to search for signal cascades that characterize the optimal signaling pathway structure. In the search process, the extent of overlap among signal cascades is used to measure the optimality of a structure. Throughout, we treat gene sets as random samples from a first-order Markov chain model. We evaluated the performance of SA in three case studies. In the first study conducted on 83 KEGG pathways, SA demonstrated a significantly better performance than Bayesian network methods. Since both SA and Bayesian network methods accommodate discrete data, use a ‘search and score’ network learning strategy and output a directed network, they can be compared in terms of performance and computational time. In the second study, we compared SA and Bayesian network methods using four benchmark datasets from DREAM. In our final study, we showcased two context-specific signaling pathways activated in breast cancer. Availibility: Source codes are available from http://dl.dropbox.com/u/16000775/sa_sc.zip Contact: dzhu@wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 99
    Publication Date: 2012-02-17
    Description: : We provide a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies. It includes detection of outliers and biases, inefficient immuno-precipitation and overamplification artifacts, de novo identification of read-rich genomic regions and visualization of the location and coverage of genomic region lists. Availability: www.bioconductor.org Contact: david.rossell@irbbarcelona.org Supplementary information: Supplementary data available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 100
    Publication Date: 2012-02-17
    Description: Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes p L induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004). Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O ( n 2 D ln), where n is the sequence length, is the number of local minima in the partial landscape p L under consideration and D is the maximum number of steepest descent steps in attraction basins associated with p L . Contact: a.albrecht@qub.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...