ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

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

Proceed reservation?

Export
Filter
  • Computational Methods  (26)
  • Currents  (22)
  • Land Reform  (21)
  • Oxford University Press  (47)
  • American Meteorological Society  (22)
  • MDPI Publishing
  • 2010-2014  (69)
Collection
Keywords
Publisher
Years
Year
  • 1
    facet.materialart.
    Unknown
    Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    Dynalign II: common secondary structure prediction for RNA homologs with domain insertions (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    Cooperation against theft: A test of incentives for water management In Tunisia (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-22
    Description: Water theft carried out by manipulating water meters constrains volumetric pricing in semi-arid regions. Cooperative management can reduce theft and improve incentives for efficient water use by inducing peer monitoring. Using a theoretical model, we show that theft is more likely when prices are high, punishments are weak, and cooperatives are large. We also show how cooperative membership and punishment levels are determined endogenously by constraints on monitoring. We test the model on data from Tunisia for the years 2001–2003, relying on instruments that proxy for unobservable monitoring costs. The results confirm that well-designed incentives can reduce theft, and that constraints on monitoring costs affect institutional design.
    Keywords: D82 - Asymmetric and Private Information, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q25 - Water
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 4
    facet.materialart.
    Unknown
    A Natural Resource Theory of U.S. Crop Insurance Contract Choice (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-22
    Description: A large variety of subsidized crop insurance products are available to U.S. crop growers. Distinct and perhaps puzzling patterns in the choices of insurance products and coverage levels can be discerned. Where production conditions are better and yields are less risky then ( a ) higher insurance coverage levels are chosen; and ( b ) revenue insurance is preferred over yield insurance. Also, ( c ) the extent of preference for revenue insurance is stronger in more productive areas. Assuming, as many do, that growers seek to maximize subsidy transfers, point ( a ) can be explained by the interaction between yield technology and natural resource endowments. Points ( b ) and ( c ) can be explained by location in conjunction with the "natural hedge" and a contract design bias in how revenue insurance guarantees are computed. Empirical study of Risk Management Agency data on corn, soybean, and wheat yields, and insurance contract choices lend support to our model inferences.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy, Q24 - Land
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-01
    Description: Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ~10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    Identifying RNA-binding residues based on evolutionary conserved structural and energetic features (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-11
    Description: Increasing numbers of protein structures are solved each year, but many of these structures belong to proteins whose sequences are homologous to sequences in the Protein Data Bank. Nevertheless, the structures of homologous proteins belonging to the same family contain useful information because functionally important residues are expected to preserve physico-chemical, structural and energetic features. This information forms the basis of our method, which detects RNA-binding residues of a given RNA-binding protein as those residues that preserve physico-chemical, structural and energetic features in its homologs. Tests on 81 RNA-bound and 35 RNA-free protein structures showed that our method yields a higher fraction of true RNA-binding residues (higher precision) than two structure-based and two sequence-based machine-learning methods. Because the method requires no training data set and has no parameters, its precision does not degrade when applied to ‘novel’ protein sequences unlike methods that are parameterized for a given training data set. It was used to predict the ‘unknown’ RNA-binding residues in the C-terminal RNA-binding domain of human CPEB3. The two predicted residues, F430 and F474, were experimentally verified to bind RNA, in particular F430, whose mutation to alanine or asparagine nearly abolished RNA binding. The method has been implemented in a webserver called DR_bind1, which is freely available with no login requirement at http://drbind.limlab.ibms.sinica.edu.tw .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 7
    facet.materialart.
    Unknown
    Capitalized Costs of Habitat Conservation Easements (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-05
    Description: Perpetual conservation easements permanently remove the option to convert existing habitat to more intensive agricultural production. If existing habitat is at threat of conversion, removing the option to convert will reduce land values. In this article, we estimate the land value discount resulting from perpetual habitat conservation easements by using propensity score matching. We find that on the average eased parcel, land values fall by approximately $86 per acre for every acre of eased habitat. On average, our results suggest that landowners have been adequately compensated and conservation agencies have successfully secured habitat at risk of conversion.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q24 - Land, Q57 - Ecological Economics: Ecosystem Services ; Biodiversity Conservation ; Bioeconomics
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    Agri-environmental Policy and Urban Development Patterns: A General Equilibrium Analysis (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-05
    Description: This paper investigates the spatial effects that the provision of environmental public goods have on residential location choices in a suburban context. Specifically, a spatial general equilibrium framework is developed to analyze the consequences of adopting an agri-environmental policy promoting the provision of positive farming externalities. We use a static monocentric model of an open city where agricultural bid-rents and agricultural amenities vary endogenously in space, and where the positive externalities associated with agricultural production are valued by households. Consistent with empirical evidence of the potential side effects that conservation policies may have in terms of urbanization patterns and land price changes, we show that under certain conditions implementing an agri-environmental policy may promote additional suburban development. Moreover, we demonstrate that the emergence of disconnected suburban areas may be significantly influenced by the location of land regulated by an agri-environmental policy. Finally, we discuss distributional aspects and show that while introducing an agri-environmental policy has a negative impact on most residential land value, it can have positive effects on farmland and residential land located within the regulated areas, suggesting the non-neutrality of such policies regarding the agents’ assets.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy, R13 - General Equilibrium and Welfare Economic Analysis of Regional Economies, R14 - Land Use Patterns, R21 - Housing Demand
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 9
    facet.materialart.
    Unknown
    Agricultural Rodent Control Using Barn Owls: Is It Profitable? (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-05
    Description: We develop a model to evaluate the profitability of controlling rodent damage by placing barn owl nesting boxes in agricultural areas. The model incorporates the spatial patterns of barn owl predation pressure on rodents, and the impact of this predation pressure on nesting choices and agricultural output. We apply the model to data collected in Israel and find the installation of nesting boxes profitable. While this finding indicates that economic policy instruments to enhance the adoption of this biological control method are redundant, it does support stricter regulations on rodent control using rodenticides.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy, Q57 - Ecological Economics: Ecosystem Services ; Biodiversity Conservation ; Bioeconomics
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    Complete RNA inverse folding: computational design of functional hammerhead ribozymes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-10
    Description: Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold , which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold , we design ten cis -cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis -cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/ .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 11
    facet.materialart.
    Unknown
    Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-27
    Description: While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 12
    facet.materialart.
    Unknown
    Intensive and extensive margin adjustments to water scarcity in France's Cereal Belt (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-11
    Description: Efficient water management in agriculture is becoming critical due to increasing environmental constraints and global food and bio-energy demands. Farmers may respond to increased water scarcity along three main adjustment margins: a move towards rain-fed agriculture (super-extensive margin) or towards less water-intensive crops (extensive margin), and a reduction in water intensity for irrigated crops (intensive margin). Using a positive mathematical programming model of regional supply calibrated to economic and agronomic information, we decompose the total effect of reduced water availability on these adjustment margins in Beauce, a productive cereal region that relies on a groundwater resource to meet its irrigation needs. For realistic water scarcity scenarios, 57 per cent of the total response is attributable to super-extensive margin adjustments. The extensive margin represents 28 per cent of the total response, while the intensive margin accounts for 15 per cent. Crop-level analysis reveals more subtle adaptation patterns.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q25 - Water
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 13
    facet.materialart.
    Unknown
    Encouraging Reductions in Nonpoint Source Pollution through Point-nonpoint Trading: The Roles of Baseline Choice and Practice Subsidies (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-06
    Description: Water quality regulations in the United States apply almost exclusively to point sources. In impaired watersheds where both point and nonpoint sources contribute to pollution, the U.S. Environmental Protection Agency (EPA) is encouraging the use of point-nonpoint trading to reduce the cost of point sources to meet their permit requirement, and to encourage nonpoint sources to voluntarily contribute more towards meeting overall water quality goals. The EPA guidance encourages trading programs to set a nonpoint source eligibility baseline that extracts some "extra" abatement from nonpoint sources. Research has shown that setting an eligibility baseline that is substantially more stringent than current management could discourage nonpoint source participation and significantly hinder trading. In this paper we examine how choosing the eligibility baseline for agricultural sources affects the efficiency goal of trading (reducing costs to point sources), as well as how it affects the EPA goal of encouraging nonpoint abatement. Using data from the Chesapeake Bay Watershed we find that eligibility baselines set to encourage additional nonpoint source abatement reduce the supply of credits in a market; the more stringent the baseline, the fewer the trades and the smaller the overall abatement from nonpoint sources. A subsidy to farmers for reducing the cost of meeting a baseline encourages greater nonpoint source abatement, but may not benefit the trading market.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q20 - General, Q58 - Government Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 14
    facet.materialart.
    Unknown
    An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 15
    facet.materialart.
    Unknown
    Individual and Cooperative Management of Invasive Species in Human-mediated Landscapes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-13
    Description: As a bioinvasion spreads across a landscape from its point of introduction, damages rise roughly with the square of the distance from the original invasion. It is thus generally beneficial, at the landscape scale, to apply eradication or containment controls early if not immediately upon discovery. However, an individual property owner only has incentives to consider the costs and benefits of control on his/her own property rather than potential landscape-scale damages. Bioinvasions will therefore generally be under-controlled in a landscape of independent owners operating under a laissez-faire system. A mechanism is thus needed to induce early cooperative contributions to control costs from beneficiaries who would, without them, be invaded later. We develop a spatially-explicit, integrated model of invasion spread and human behavior to examine how different degrees of spatial cooperation affect patterns of invasion spread and the total costs and damages imposed. We compare individual laissez-faire, cooperative control by adjacent neighbors, and cooperative control by groups including more distant but nearby neighbors. As expected, private laissez-faire control decisions tend to under-control the invasion relative to socially optimal control under most circumstances. But a reasonably high fraction of first best payoffs can be achieved with only a modest geographical reach of cooperation. We also find that less extensive cooperation is needed to control invasions whose costs and damages otherwise lead to the largest externalities (circumstances with costs that are relatively low compared with damages). This suggests that even small amounts of cooperation to control bioinvasions can provide large social benefits.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q24 - Land, Q57 - Ecological Economics: Ecosystem Services ; Biodiversity Conservation ; Bioeconomics
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 16
    facet.materialart.
    Unknown
    Farmland Protection and Agricultural Land Values at the Urban-Rural Fringe: British Columbia's Agricultural Land Reserve (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-13
    Description: Farmland conservation policies typically use zoning and differentiated taxes to prevent urban development of farmland, but little is known about the effectiveness of these policies. This study adds to current knowledge by examining the impact of British Columbia's Agricultural Land Reserve (ALR), established in 1973, which severely restricts subdivision and nonagricultural uses for more than 4.7 million hectares of farmland. To determine the extent to which the ALR preserves farmland by reducing or removing the development option, a multilevel hedonic pricing model is used to estimate the impact of land use, geographic, and zoning characteristics on farmland value near the capital city of Victoria on Vancouver Island. Using sales data from 1974 through 2008, the model demonstrates a changing ALR impact over time that varies considerably by improved and unimproved land types. In 2008, landowners paid 19% less for the typical improved farmland parcel within the ALR versus that outside it. This suggests that would-be developers expect permanency in the zoning law, and prefer non-ALR zoned land. However, ALR land that is unimproved has a premium of 55%, suggesting that this land is more valuable for agriculture than for development. Farmland located closer to the city or the commuting highway commands a premium if it has a residence on it, with a residence also explaining why smaller agricultural properties sell at higher prices. However, it appears that zoning by itself is insufficient to protect farmland; other policies likely need to be implemented in conjunction with zoning to protect agricultural land.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q28 - Government Policy, R14 - Land Use Patterns
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 17
    facet.materialart.
    Unknown
    Capitalized Amenity Value of Native Vegetation in a Multifunctional Rural Landscape (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-13
    Description: In many parts of the world, natural vegetation has been cleared to allow agricultural production. To ensure a long-term flow of ecosystem services without compromising agricultural activities, restoring the environment requires a balance between public and private benefits and costs. Information about private benefits generated by environmental assets can be utilized to identify conservation opportunities on private lands, evaluate environmental projects, and design effective policy instruments. We use a spatio-temporal hedonic model to estimate the private benefits of native vegetation on rural properties in the state of Victoria, Australia. Specifically, we estimate the marginal value of native vegetation on private land and examine how it varies with the extent of vegetation on a property and across a range of property types and sizes. Private benefits of native vegetation are greater per unit area on small and medium-sized properties and smaller on large production-oriented farms. Native vegetation exhibits diminishing marginal benefits as its proportion of a property increases. The current extent of native vegetation cover is lower than the extent that would maximize the amenity value to many landowners. There is scope for improved targeting of investment in the study region by incorporating private benefits of environmental projects into environmental planning processes. Landowners with high marginal private benefits from revegetation would be more willing to participate in a revegetation program. Targeting these landowners would likely provide higher value for money because such projects could be implemented at lower public cost.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q57 - Ecological Economics: Ecosystem Services ; Biodiversity Conservation ; Bioeconomics
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 18
    facet.materialart.
    Unknown
    Strain/species identification in metagenomes using genome-specific markers (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-01
    Description: Shotgun metagenome sequencing has become a fast, cheap and high-throughput technology for characterizing microbial communities in complex environments and human body sites. However, accurate identification of microorganisms at the strain/species level remains extremely challenging. We present a novel k -mer-based approach, termed GSMer, that identifies genome-specific markers (GSMs) from currently sequenced microbial genomes, which were then used for strain/species-level identification in metagenomes. Using 5390 sequenced microbial genomes, 8 770 321 50-mer strain-specific and 11 736 360 species-specific GSMs were identified for 4088 strains and 2005 species (4933 strains), respectively. The GSMs were first evaluated against mock community metagenomes, recently sequenced genomes and real metagenomes from different body sites, suggesting that the identified GSMs were specific to their targeting genomes. Sensitivity evaluation against synthetic metagenomes with different coverage suggested that 50 GSMs per strain were sufficient to identify most microbial strains with ≥0.25 x coverage, and 10% of selected GSMs in a database should be detected for confident positive callings. Application of GSMs identified 45 and 74 microbial strains/species significantly associated with type 2 diabetes patients and obese/lean individuals from corresponding gastrointestinal tract metagenomes, respectively. Our result agreed with previous studies but provided strain-level information. The approach can be directly applied to identify microbial strains/species from raw metagenomes, without the effort of complex data pre-processing.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 19
    facet.materialart.
    Unknown
    The Effects of Energy Prices on Agricultural Groundwater Extraction from the High Plains Aquifer (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: We examine the effects of energy prices on groundwater extraction using an econometric model of a farmer's irrigation water pumping decision that accounts for both the intensive and extensive margins. Our results show that energy prices have an effect on both types of margins. Increasing energy prices would affect crop selection decisions, crop acreage allocation decisions, and farmers’ demand for water. Our estimated total marginal effect, which sums the effects on the intensive and extensive margins, suggests that a $1 per million btu increase in the energy price would decrease water extraction by an individual farmer by 5.89 acre-feet per year, a decrease of 3.6 percent of the average annual extraction rate. Our estimated elasticity of water extraction with respect to energy price is –0.26.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q40 - General
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 20
    facet.materialart.
    Unknown
    Do Wealth Gains from Land Appreciation Cause Farmers to Expand Acreage or Buy Land? (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: Recent increases in farm real estate values in the United States have increased farm equity. By exploiting periods of high and low appreciation that caused various increases in wealth for farmers owning various shares of their farmland, we examine whether U.S. grain farmers expanded their acres harvested or acres owned in response to an increase in their land wealth. We find that land wealth had little effect on farm size. However, for similarly-sized farms, a larger ownership share (10 percentage points) led to an increase in the growth of land owned (2 percentage points). Because older farmers own more of the land that they farm, greater land appreciation slows the rate at which younger farmers acquire land relative to older farmers.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 21
    facet.materialart.
    Unknown
    Characterizing RNA ensembles from NMR data with kinematic models (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 22
    facet.materialart.
    Unknown
    Quantitative models for accelerated protein dissociation from nucleosomal DNA (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: Binding of transcription factors to their binding sites in promoter regions is the fundamental event in transcriptional gene regulation. When a transcription factor binding site is located within a nucleosome, the DNA has to partially unwrap from the nucleosome to allow transcription factor binding. This reduces the rate of transcription factor binding and is a known mechanism for regulation of gene expression via chromatin structure. Recently a second mechanism has been reported where transcription factor off-rates are dramatically increased when binding to target sites within the nucleosome. There are two possible explanations for such an increase in off-rate short of an active role of the nucleosome in pushing the transcription factor off the DNA: (i) for dimeric transcription factors the nucleosome can change the equilibrium between monomeric and dimeric binding or (ii) the nucleosome can change the equilibrium between specific and non-specific binding to the DNA. We explicitly model both scenarios and find that dimeric binding can explain a large increase in off-rate while the non-specific binding model cannot be reconciled with the large, experimentally observed increase. Our results suggest a general mechanism how nucleosomes increase transcription factor dissociation to promote exchange of transcription factors and regulate gene expression.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 23
    facet.materialart.
    Unknown
    SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-15
    Description: High-throughput sequencing technologies, including RNA-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. Furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. While many statistical methods have been proposed for identifying novel transcriptional events with RNA-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. Few tools exist for the unsupervised discovery of such events without class labels. In this paper, we present SigFuge for identifying genomic loci exhibiting differential transcription patterns across many RNA-seq samples. SigFuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. We apply SigFuge to RNA-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the Cancer Genome Atlas, and identify several cases of differential isoform usage including CDKN2A , a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 24
    facet.materialart.
    Unknown
    The role of crop land during economic development: evidence from rural Vietnam (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-02
    Description: Under economic structural changes, some households intensify farming while others reduce it, resulting in significant changes in landholding. This paper studies the link between such changes in landholding and household well-being during a period of rapid economic transformation in Vietnam. Using a rural household panel data set, we find a U-shaped relationship between landholding and well-being: both accumulating crop land and moving out of farming are associated with higher household income and expenditure. Notably, these relationships are greater in communes that are less developed, suggesting that the benefits of structural transformation may diminish at higher levels of development.
    Keywords: I30 - General, I32 - Measurement and Analysis of Poverty, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 25
    facet.materialart.
    Unknown
    Land Markets and the Value of Water: Hedonic Analysis Using Repeat Sales of Farmland (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-23
    Description: The lack of robust water markets makes it difficult to value irrigation water. Because water rights are appurtenant to land, it is possible to infer the value of water from observed differences in the market price of land. We use panel data on repeat farmland sales in California's San Joaquin Valley to estimate a hedonic regression equation with parcel fixed effects. This controls for sources of omitted variables bias and allows us to recover the value of irrigation water to landowners in our sample. We show that a more traditional cross-sectional regression results in an artificially low value of irrigation water.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q24 - Land, Q25 - Water
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 26
    facet.materialart.
    Unknown
    Strengthening of the Pacific Equatorial Undercurrent in the SODA reanalysis : mechanisms, ocean dynamics, and implications (2014)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 27 (2014): 2405–2416, doi:10.1175/JCLI-D-13-00359.1.
    Description: Several recent studies utilizing global climate models predict that the Pacific Equatorial Undercurrent (EUC) will strengthen over the twenty-first century. Here, historical changes in the tropical Pacific are investigated using the Simple Ocean Data Assimilation (SODA) reanalysis toward understanding the dynamics and mechanisms that may dictate such a change. Although SODA does not assimilate velocity observations, the seasonal-to-interannual variability of the EUC estimated by SODA corresponds well with moored observations over a ~20-yr common period. Long-term trends in SODA indicate that the EUC core velocity has increased by 16% century−1 and as much as 47% century−1 at fixed locations since the mid-1800s. Diagnosis of the zonal momentum budget in the equatorial Pacific reveals two distinct seasonal mechanisms that explain the EUC strengthening. The first is characterized by strengthening of the western Pacific trade winds and hence oceanic zonal pressure gradient during boreal spring. The second entails weakening of eastern Pacific trade winds during boreal summer, which weakens the surface current and reduces EUC deceleration through vertical friction. EUC strengthening has important ecological implications as upwelling affects the thermal and biogeochemical environment. Furthermore, given the potential large-scale influence of EUC strength and depth on the heat budget in the eastern Pacific, the seasonal strengthening of the EUC may help reconcile paradoxical observations of Walker circulation slowdown and zonal SST gradient strengthening. Such a process would represent a new dynamical “thermostat” on CO2-forced warming of the tropical Pacific Ocean, emphasizing the importance of ocean dynamics and seasonality in understanding climate change projections.
    Description: EJDis supported by NSFGrantsOCE-1031971 and OCE-1233282. KBK is supported by NSF Grant OCE-1233282.
    Description: 2014-09-15
    Keywords: Tropics ; Currents ; Ocean dynamics ; Atmosphere-ocean interaction ; Climate variability ; Reanalysis data
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 27
    facet.materialart.
    Unknown
    The Equatorial Undercurrent and TAO sampling bias from a decade at SEA (2014)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 21 (2014): 2015–2025, doi:10.1175/JTECH-D-13-00262.1.
    Description: The NOAA Tropical Atmosphere Ocean (TAO) moored array has, for three decades, been a valuable resource for monitoring and forecasting El Niño–Southern Oscillation and understanding physical oceanographic as well as coupled processes in the tropical Pacific influencing global climate. Acoustic Doppler current profiler (ADCP) measurements by TAO moorings provide benchmarks for evaluating numerical simulations of subsurface circulation including the Equatorial Undercurrent (EUC). Meanwhile, the Sea Education Association (SEA) has been collecting data during repeat cruises to the central equatorial Pacific Ocean (160°–126°W) throughout the past decade that provide useful cross validation and quantitative insight into the potential for stationary observing platforms such as TAO to incur sampling biases related to the strength of the EUC. This paper describes some essential sampling characteristics of the SEA dataset, compares SEA and TAO velocity measurements in the vicinity of the EUC, shares new insight into EUC characteristics and behavior only observable in repeat cross-equatorial sections, and estimates the sampling bias incurred by equatorial TAO moorings in their estimates of the velocity and transport of the EUC. The SEA high-resolution ADCP dataset compares well with concurrent TAO measurements (RMSE = 0.05 m s−1; R2 = 0.98), suggests that the EUC core meanders sinusoidally about the equator between ±0.4° latitude, and reveals a mean sampling bias of equatorial measurements (e.g., TAO) of the EUC’s zonal velocity of −0.14 ± 0.03 m s−1 as well as a ~10% underestimation of EUC volume transport. A bias-corrected monthly record and climatology of EUC strength at 140°W for 1990–2010 is presented.
    Description: The authors thank the NSF Physical Oceanography program (OCE-1233282) and the WHOI Academic Programs Office for funding.
    Description: 2015-03-01
    Keywords: Pacific Ocean ; Tropics ; Currents ; Ocean dynamics ; Buoy observations ; Sampling
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 28
    facet.materialart.
    Unknown
    Four current meter models compared in strong currents in Drake Passage (2014)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 30 (2013): 2465–2477, doi:10.1175/JTECH-D-13-00032.1.
    Description: Seven current meters representing four models on a stiffly buoyed mooring were placed for an 11-month deployment to intercompare their velocity measurements: two vector-measuring current meters (VMCMs), two Aanderaa recording current meter (RCM) 11s, two Aanderaa SEAGUARDs, and a Nortek Aquadopp. The current meters were placed 6-m apart from each other at about 4000-m depth in an area of Drake Passage expected to have strong currents, nearly independent of depth near the bottom. Two high-current events occurred in bursts of semidiurnal pulses lasting several days, one with peak speeds up to 67 cm s−1 and the other above 35 cm s−1. The current-speed measurements all agreed within 7% of the median value when vector averaged over simultaneous time intervals. The VMCMs, chosen as the reference measurements, were found to measure the median of the mean-current magnitudes. The RCM11 and SEAGUARD current speeds agreed within 2% of the median at higher speeds (35–67 cm s−1), whereas in lower speed ranges (0–35 cm s−1) the vector-averaged speeds for the RCM11 and SEAGUARD were 4%–5% lower and 3%–5% higher than the median, respectively. The shorter-record Aquadopp current speeds were about 6% higher than the VMCMs over the range (0–40 cm s−1) encountered.
    Description: This work was supported by U.S. National Science Foundation Grants ANT-0635437 and ANT-0636493.
    Description: 2014-04-01
    Keywords: Currents ; Acoustic measurements/effects ; In situ oceanic observations ; Instrumentation/sensors
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 29
    facet.materialart.
    Unknown
    Eulerian and Lagrangian correspondence of high-frequency radar and surface drifter data : effects of radar resolution and flow components (2014)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 31 (2014): 945–966, doi:10.1175/JTECH-D-13-00146.1.
    Description: This study investigated the correspondence between the near-surface drifters from a mass drifter deployment near Martha’s Vineyard, Massachusetts, and the surface current observations from a network of three high-resolution, high-frequency radars to understand the effects of the radar temporal and spatial resolution on the resulting Eulerian current velocities and Lagrangian trajectories and their predictability. The radar-based surface currents were found to be unbiased in direction but biased in magnitude with respect to drifter velocities. The radar systematically underestimated velocities by approximately 2 cm s−1 due to the smoothing effects of spatial and temporal averaging. The radar accuracy, quantified by the domain-averaged rms difference between instantaneous radar and drifter velocities, was found to be about 3.8 cm s−1. A Lagrangian comparison between the real and simulated drifters resulted in the separation distances of roughly 1 km over the course of 10 h, or an equivalent separation speed of approximately 2.8 cm s−1. The effects of the temporal and spatial radar resolution were examined by degrading the radar fields to coarser resolutions, revealing the existence of critical scales (1.5–2 km and 3 h) beyond which the ability of the radar to reproduce drifter trajectories decreased more rapidly. Finally, the importance of the different flow components present during the experiment—mean, tidal, locally wind-driven currents, and the residual velocities—was analyzed, finding that, during the study period, a combination of tidal, locally wind-driven, and mean currents were insufficient to reliably reproduce, with minimal degradation, the trajectories of real drifters. Instead, a minimum combination of the tidal and residual currents was required.
    Description: I.R. was supported by the WHOI Coastal Ocean Institute Project 27040148 and by the WHOI Access to the Sea Program 27500036. I.R. and A.K. acknowledge support fromthe NSF project 83264600. A.K. acknowledges support from the Massachusetts Clean Energy Center (MassCEC) via the New England Marine Renewable Energy Center (MREC).
    Description: 2014-10-01
    Keywords: Coastal flows ; Currents ; Lagrangian circulation/transport ; Trajectories ; Radars/Radar observations
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 30
    facet.materialart.
    Unknown
    TrAp: a tree approach for fingerprinting subclonal tumor composition (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide only an overview of the aggregate of numerous cells. Computational approaches to de-mix a collective signal composed of the aberrations of a mixed cell population of a tumor sample into its individual components are not available. We propose an evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. We have developed an algorithm (TrAp) for solving this mixture problem. In silico analyses show that TrAp correctly deconvolves mixed subpopulations when the number of subpopulations and the measurement errors are moderate. We demonstrate the applicability of the method using tumor karyotypes and somatic hypermutation data sets. We applied TrAp to Exome-Seq experiment of a renal cell carcinoma tumor sample and compared the mutational profile of the inferred subpopulations to the mutational profiles of single cells of the same tumor. Finally, we deconvolve sequencing data from eight acute myeloid leukemia patients and three distinct metastases of one melanoma patient to exhibit the evolutionary relationships of their subpopulations.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 31
    facet.materialart.
    Unknown
    Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-02
    Description: MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5' tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 32
    facet.materialart.
    Unknown
    Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense–antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 33
    facet.materialart.
    Unknown
    r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-16
    Description: The coupling of chromosome conformation capture (3C) with next-generation sequencing technologies enables the high-throughput detection of long-range genomic interactions, via the generation of ligation products between DNA sequences, which are closely juxtaposed in vivo . These interactions involve promoter regions, enhancers and other regulatory and structural elements of chromosomes and can reveal key details of the regulation of gene expression. 3C-seq is a variant of the method for the detection of interactions between one chosen genomic element (viewpoint) and the rest of the genome. We present r3Cseq , an R/Bioconductor package designed to perform 3C-seq data analysis in a number of different experimental designs. The package reads a common aligned read input format, provides data normalization, allows the visualization of candidate interaction regions and detects statistically significant chromatin interactions, thus greatly facilitating hypothesis generation and the interpretation of experimental results. We further demonstrate its use on a series of real-world applications.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 34
    facet.materialart.
    Unknown
    Profit-Maximizing Land-Use Revisited: The Testable Implications of Non-joint Crop Production Under Land Constraint (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-22
    Description: This article derives new implications for the land allocation and production decisions of profit-maximizing farm-firms where production of different crops is non-joint but subject to a constraint on the total land area. These implications are observable and thus subject to empirical scrutiny. An estimable model of crop production, land allocation, and input-use decisions is derived that permits joint production and enables the implications of non-joint but land-constrained production to be tested. This may improve econometric estimates of cross-price elasticities of supply by linking models of land use and production decisions, and allowing non-jointness to be imposed where appropriate.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 35
    facet.materialart.
    Unknown
    Comparison of GHG-Emission Indicators for Dairy Farms with Respect to Induced Abatement Costs, Accuracy, and Feasibility (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-22
    Description: There is broad debate about including agriculture in greenhouse gas (GHG) reduction efforts such as the European Emissions Trading Scheme. Since most agricultural GHG emissions originate from non-point sources, they cannot be directly measured, and therefore have to be derived by calculation schemes (indicators). We designed five such GHG indicators for dairy farms and analyzed the trade-offs between their feasibility, measurement accuracy, and level of induced abatement costs. Analyses of induced abatement costs and calculation accuracy are based on emission reduction simulations with a highly-detailed single-farm optimization model. Feasibility is discussed in a qualitative manner. Our results indicate that the trade-offs depend on both farm characteristics and the targeted reduction level. In particular, the advantages of detailed indicators decrease for higher abatement levels. Only the least feasible indicator led to abatement costs that would result in emission efforts at given prices in the European Emissions Trading Scheme, although with a rather small potential. Our results thus suggest little potential for including dairy production into market-based reduction policies.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 36
    facet.materialart.
    Unknown
    Production Incentives from Static Decoupling: Land Use Exclusion Restrictions (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-22
    Description: Many agricultural support payments are based on past production with restrictions on how land may currently be used. When support payments to field crops are analyzed in a static framework, they do not directly impact current production decisions. However, over time, as relative profits change, these payments affect current output. The payments may keep land in less profitable production of program crops through restrictions prohibiting potentially more profitable endeavors such as cultivating fruits and vegetables. These payments have the potential to lead to production and trade distortions similar in magnitude to the distortions associated with direct production subsidies.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 37
    facet.materialart.
    Unknown
    When Is Reliance on Voluntary Approaches in Agriculture Likely to Be Effective? (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-05
    Description: Voluntary approaches have been used in a variety of contexts and for a variety of purposes in agriculture, including voluntary conservation programs and product labeling. This paper provides an overview of some of the general principles that emerge from the literature on voluntary approaches and their application in agriculture. The literature suggests that, to be effective, voluntary approaches must provide sufficiently strong participation incentives to a targeted population, clearly identify standards for behavior or performance that ensure additionality and avoid slippage, and monitor outcomes. Thus, reliance on voluntary approaches in agriculture is likely to be effective only if there is sufficient market demand for certain product characteristics, significant public funds are committed to pay for voluntary actions, or the political will exists to impose regulations if voluntary approaches fail.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q20 - General, Q50 - General
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 38
    facet.materialart.
    Unknown
    Wind-driven cross-equatorial flow in the Indian Ocean (2013)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 2234–2253, doi:10.1175/JPO-D-12-033.1.
    Description: Meridional velocity, mass, and heat transport in the equatorial oceans are difficult to estimate because of the nonapplicability of the geostrophic balance. For this purpose a steady-state model is utilized in the equatorial Indian Ocean using NCEP wind stress and temperature and salinity data from the World Ocean Atlas 2005 (WOA05) and Argo. The results show a Somali Current flowing to the south during the winter monsoon carrying −11.5 ± 1.3 Sv (1 Sv ≡ 106 m3 s−1) and −12.3 ± 0.3 Sv from WOA05 and Argo, respectively. In the summer monsoon the Somali Current reverses to the north transporting 16.8 ± 1.2 Sv and 19.8 ± 0.6 Sv in the WOA05 and Argo results. Transitional periods are considered together and in consequence, there is not a clear Somali Current present in this period. Model results fit with in situ measurements made around the region, although Argo data results are quite more realistic than WOA05 data results.
    Description: This study has been partly funded by the MOC Project (CTM 2008- 06438) and the Spanish contribution to the Argo network (AC2009 ACI2009-0998), financed by the Spanish Government and Feder.
    Description: 2013-06-01
    Keywords: Indian Ocean ; Subtropics ; Currents ; Ocean circulation ; Transport ; Wind stress
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 39
    facet.materialart.
    Unknown
    Decoupling of agricultural support payments: the impact on land market participation decisions (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-03
    Description: This paper analyses the impact of the recent decision by the European Union to ‘decouple’ agricultural support payments from agricultural production on Irish farmers' land market decisions. The land market participation decisions of Irish farmers are modelled using a dynamic probit model, while the extent of participation decisions is modelled using a dynamic tobit model. Decoupling does not appear to have significantly altered farmers' land market decisions. One likely explanation for this is the cross-compliance obligation for farmers to maintain land in a state fit for agricultural production in order to receive their full payments.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 40
    facet.materialart.
    Unknown
    Efficient motif search in ranked lists and applications to variable gap motifs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Sequence elements, at all levels—DNA, RNA and protein, play a central role in mediating molecular recognition and thereby molecular regulation and signaling. Studies that focus on measuring and investigating sequence-based recognition make use of statistical and computational tools, including approaches to searching sequence motifs. State-of-the-art motif searching tools are limited in their coverage and ability to address large motif spaces. We develop and present statistical and algorithmic approaches that take as input ranked lists of sequences and return significant motifs. The efficiency of our approach, based on suffix trees, allows searches over motif spaces that are not covered by existing tools. This includes searching variable gap motifs—two half sites with a flexible length gap in between—and searching long motifs over large alphabets. We used our approach to analyze several high-throughput measurement data sets and report some validation results as well as novel suggested motifs and motif refinements. We suggest a refinement of the known estrogen receptor 1 motif in humans, where we observe gaps other than three nucleotides that also serve as significant recognition sites, as well as a variable length motif related to potential tyrosine phosphorylation.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 41
    facet.materialart.
    Unknown
    Inference of modules associated to eQTLs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Cataloging the association of transcripts to genetic variants in recent years holds the promise for functional dissection of regulatory structure of human transcription. Here, we present a novel approach, which aims at elucidating the joint relationships between transcripts and single-nucleotide polymorphisms (SNPs). This entails detection and analysis of modules of transcripts, each weakly associated to a single genetic variant, together exposing a high-confidence association signal between the module and this ‘main’ SNP. To explore how transcripts in a module are related to causative loci for that module, we represent such dependencies by a graphical model. We applied our method to the existing data on genetics of gene expression in the liver. The modules are significantly more, larger and denser than found in permuted data. Quantification of the confidence in a module as a likelihood score, allows us to detect transcripts that do not reach genome-wide significance level. Topological analysis of each module identifies novel insights regarding the flow of causality between the main SNP and transcripts. We observe similar annotations of modules from two sources of information: the enrichment of a module in gene subsets and locus annotation of the genetic variants. This and further phenotypic analysis provide a validation for our methodology.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 42
    facet.materialart.
    Unknown
    Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonization (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Phase variation of surface structures occurs in diverse bacterial species due to stochastic, high frequency, reversible mutations. Multiple genes of Campylobacter jejuni are subject to phase variable gene expression due to mutations in polyC/G tracts. A modal length of nine repeats was detected for polyC/G tracts within C. jejuni genomes. Switching rates for these tracts were measured using chromosomally-located reporter constructs and high rates were observed for cj1139 (G8) and cj0031 (G9). Alteration of the cj1139 tract from G8 to G11 increased mutability 10-fold and changed the mutational pattern from predominantly insertions to mainly deletions. Using a multiplex PCR, major changes were detected in ‘on/off’ status for some phase variable genes during passage of C. jejuni in chickens. Utilization of observed switching rates in a stochastic, theoretical model of phase variation demonstrated links between mutability and genetic diversity but could not replicate observed population diversity. We propose that modal repeat numbers have evolved in C. jejuni genomes due to molecular drivers associated with the mutational patterns of these polyC/G repeats, rather than by selection for particular switching rates, and that factors other than mutational drift are responsible for generating genetic diversity during host colonization by this bacterial pathogen.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 43
    facet.materialart.
    Unknown
    eIF4E-binding protein regulation of mRNAs with differential 5'-UTR secondary structure: a polyelectrostatic model for a component of protein-mRNA interactions (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-13
    Description: Control of translation in eukaryotes is complex, depending on the binding of various factors to mRNAs. Available data for subsets of mRNAs that are translationally up- and down-regulated in yeast eIF4E-binding protein (4E-BP) deletion mutants are coupled with reported mRNA secondary structure measurements to investigate whether 5'-UTR secondary structure varies between the subsets. Genes with up-regulated translational efficiencies in the caf20 mutant have relatively high averaged 5'-UTR secondary structure. There is no apparent wide-scale correlation of RNA-binding protein preferences with the increased 5'-UTR secondary structure, leading us to speculate that the secondary structure itself may play a role in differential partitioning of mRNAs between eIF4E/4E-BP repression and eIF4E/eIF4G translation initiation. Both Caf20p and Eap1p contain stretches of positive charge in regions of predicted disorder. Such regions are also present in eIF4G and have been reported to associate with mRNA binding. The pattern of these segments, around the canonical eIF4E-binding motif, varies between each 4E-BP and eIF4G. Analysis of gene ontology shows that yeast proteins containing predicted disordered segments, with positive charge runs, are enriched for nucleic acid binding. We propose that the 4E-BPs act, in part, as differential, flexible, polyelectrostatic scaffolds for mRNAs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 44
    facet.materialart.
    Unknown
    Identification of activated cryptic 5' splice sites using structure profiles and odds measure (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-23
    Description: The activation of cryptic 5' splice sites (5' SSs) is often related to human hereditary diseases. The DNA-based mutation screening strategies are commonly used to recognize the cryptic 5' SSs, because features of the local DNA sequence can influence the choice of cryptic 5' SSs. To improve the identification of the cryptic 5' SSs, we developed a structure-based method, named SPO (structure profiles and odds measure), which combines two parameters, the structural feature derived from hydroxyl radical cleavage pattern and odds measure, to assess the likelihood of a cryptic 5' SS activation in competing with its paired authentic 5' SS. Compared to the current tools for identifying activated cryptic 5' SSs, the SPO algorithm achieves higher prediction accuracy than the other methods, including MaxEnt, MDD, Markov model, weight matrix model, Shapiro and Senapathy matrix, R i and G . In addition, the predicted SPO scores from the SPO algorithm exhibited a greater degree of correlation with the strength of cryptic 5' SS activation than that measured from the other seven methods. In conclusion, the SPO algorithm provides an optimal identification of cryptic 5' SSs, can be applied in designing mutagenesis experiments for various splicing events and may be helpful to investigate the relationship between structural variants and human hereditary diseases.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 45
    facet.materialart.
    Unknown
    Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-10
    Description: The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 46
    facet.materialart.
    Unknown
    Automated 3D structure composition for large RNAs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-08
    Description: Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 47
    facet.materialart.
    Unknown
    Spacer-length dependence of programmed -1 or -2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-27
    Description: Programmed –1 ribosomal frameshifting is employed in the expression of a number of viral and cellular genes. In this process, the ribosome slips backwards by a single nucleotide and continues translation of an overlapping reading frame, generating a fusion protein. Frameshifting signals comprise a heptanucleotide slippery sequence, where the ribosome changes frame, and a stimulatory RNA structure, a stem–loop or RNA pseudoknot. Antisense oligonucleotides annealed appropriately 3' of a slippery sequence have also shown activity in frameshifting, at least in vitro . Here we examined frameshifting at the U 6 A slippery sequence of the HIV gag/pol signal and found high levels of both –1 and –2 frameshifting with stem–loop, pseudoknot or antisense oligonucleotide stimulators. By examining –1 and –2 frameshifting outcomes on mRNAs with varying slippery sequence-stimulatory RNA spacing distances, we found that –2 frameshifting was optimal at a spacer length 1–2 nucleotides shorter than that optimal for –1 frameshifting with all stimulatory RNAs tested. We propose that the shorter spacer increases the tension on the mRNA such that when the tRNA detaches, it more readily enters the –2 frame on the U 6 A heptamer. We propose that mRNA tension is central to frameshifting, whether promoted by stem–loop, pseudoknot or antisense oligonucleotide stimulator.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 48
    facet.materialart.
    Unknown
    Co-clustering phenome-genome for phenotype classification and disease gene discovery (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-24
    Description: Understanding the categorization of human diseases is critical for reliably identifying disease causal genes. Recently, genome-wide studies of abnormal chromosomal locations related to diseases have mapped 〉2000 phenotype–gene relations, which provide valuable information for classifying diseases and identifying candidate genes as drug targets. In this article, a regularized non-negative matrix tri-factorization (R-NMTF) algorithm is introduced to co-cluster phenotypes and genes, and simultaneously detect associations between the detected phenotype clusters and gene clusters. The R-NMTF algorithm factorizes the phenotype–gene association matrix under the prior knowledge from phenotype similarity network and protein–protein interaction network, supervised by the label information from known disease classes and biological pathways. In the experiments on disease phenotype–gene associations in OMIM and KEGG disease pathways, R-NMTF significantly improved the classification of disease phenotypes and disease pathway genes compared with support vector machines and Label Propagation in cross-validation on the annotated phenotypes and genes. The newly predicted phenotypes in each disease class are highly consistent with human phenotype ontology annotations. The roles of the new member genes in the disease pathways are examined and validated in the protein–protein interaction subnetworks. Extensive literature review also confirmed many new members of the disease classes and pathways as well as the predicted associations between disease phenotype classes and pathways.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 49
    facet.materialart.
    Unknown
    A global sampling approach to designing and reengineering RNA secondary structures (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-04
    Description: The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign , a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 50
    facet.materialart.
    Unknown
    Functional impact bias reveals cancer drivers (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-25
    Description: Identifying cancer driver genes and pathways among all somatic mutations detected in a cohort of tumors is a key challenge in cancer genomics. Traditionally, this is done by prioritizing genes according to the recurrence of alterations that they bear. However, this approach has some known limitations, such as the difficulty to correctly estimate the background mutation rate, and the fact that it cannot identify lowly recurrently mutated driver genes. Here we present a novel approach, Oncodrive-fm, to detect candidate cancer drivers which does not rely on recurrence. First, we hypothesized that any bias toward the accumulation of variants with high functional impact observed in a gene or group of genes may be an indication of positive selection and can thus be used to detect candidate driver genes or gene modules. Next, we developed a method to measure this bias (FM bias) and applied it to three datasets of tumor somatic variants. As a proof of concept of our hypothesis we show that most of the highly recurrent and well-known cancer genes exhibit a clear FM bias. Moreover, this novel approach avoids some known limitations of recurrence-based approaches, and can successfully identify lowly recurrent candidate cancer drivers.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 51
    facet.materialart.
    Unknown
    Improving HF radar estimates of surface currents using signal quality metrics, with application to the MVCO high-resolution radar system (2012)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 29 (2012): 1377–1390, doi:10.1175/JTECH-D-11-00160.1.
    Description: Estimates of surface currents over the continental shelf are now regularly made using high-frequency radar (HFR) systems along much of the U.S. coastline. The recently deployed HFR system at the Martha’s Vineyard Coastal Observatory (MVCO) is a unique addition to these systems, focusing on high spatial resolution over a relatively small coastal ocean domain with high accuracy. However, initial results from the system showed sizable errors and biased estimates of M2 tidal currents, prompting an examination of new methods to improve the quality of radar-based velocity data. The analysis described here utilizes the radial metric output of CODAR Ocean Systems’ version 7 release of the SeaSonde Radial Site Software Suite to examine both the characteristics of the received signal and the output of the direction-finding algorithm to provide data quality controls on the estimated radial currents that are independent of the estimated velocity. Additionally, the effect of weighting spatial averages of radials falling within the same range and azimuthal bin is examined to account for differences in signal quality. Applied to two month-long datasets from the MVCO high-resolution system, these new methods are found to improve the rms difference comparisons with in situ current measurements by up to 2 cm s−1, as well as reduce or eliminate observed biases of tidal ellipses estimated using standard methods.
    Description: 2013-03-01
    Keywords: Coastal flows ; Currents ; Data processing ; Data quality control ; In situ atmospheric observations ; Remote sensing
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 52
    facet.materialart.
    Unknown
    How do agricultural policies influence farm size inequality? The example of France (2011)
    Oxford University Press
    Details
    Publication Date: 2011-12-27
    Description: We investigate farm size inequality in France using agricultural censuses and farm structure surveys at the NUTS3 level (‘départements’) during the period 1970–2007. Using calculated Gini coefficients, we show that farm size inequality has not systematically increased in France. An econometric analysis of the determinants of farm size inequality reveals that policy measures significantly affected farm size inequality, with most of the measures considered decreasing it. Empirical results suggest that the main contributor was the activity of the SAFER (Société d'Aménagement Foncier et d'Etablissement Rural), a specific feature of the French farm structural policy aimed at regulating rural land management. Besides, this research highlights the great complexity of the dynamics underlying the evolution of farm size distribution.
    Keywords: D30 - General, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 53
    facet.materialart.
    Unknown
    Optimisation of implementation policies of environmental quota trade (2011)
    Oxford University Press
    Details
    Publication Date: 2011-12-27
    Description: This paper analyses implementation policies of environmental quota trade, with the Flemish nutrient production rights as an example. Implementation policies concern the transaction quantity, quota reduction and prevention of speculation. They are analysed with a static and a dynamic multi-agent quota trade model. The static model with discrete non-auctioned quota trade shows that the obligation for quota sellers to entirely stop their production stimulates structural change. The dynamic model version indicates that a flat rate reduction on traded quota and measures taken to prevent speculation combined with too low penalties for overuse stimulate the total production.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 54
    facet.materialart.
    Unknown
    Shelf circulation and cross-shelf transport out of a bay driven by eddies from an open-ocean current. Part I : interaction between a barotropic vortex and a steplike topography (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 41 (2011): 889–910, doi:10.1175/2010JPO4496.1.
    Description: This paper examines interaction between a barotropic point vortex and a steplike topography with a bay-shaped shelf. The interaction is governed by two mechanisms: propagation of topographic Rossby waves and advection by the forcing vortex. Topographic waves are supported by the potential vorticity (PV) jump across the topography and propagate along the step only in one direction, having higher PV on the right. Near one side boundary of the bay, which is in the wave propagation direction and has a narrow shelf, waves are blocked by the boundary, inducing strong out-of-bay transport in the form of detached crests. The wave–boundary interaction as well as out-of-bay transport is strengthened as the minimum shelf width is decreased. The two control mechanisms are related differently in anticyclone- and cyclone-induced interactions. In anticyclone-induced interactions, the PV front deformations are moved in opposite directions by the point vortex and topographic waves; a topographic cyclone forms out of the balance between the two opposing mechanisms and is advected by the forcing vortex into the deep ocean. In cyclone-induced interactions, the PV front deformations are moved in the same direction by the two mechanisms; a topographic cyclone forms out of the wave–boundary interaction but is confined to the coast. Therefore, anticyclonic vortices are more capable of driving water off the topography. The anticyclone-induced transport is enhanced for smaller vortex–step distance or smaller topography when the vortex advection is relatively strong compared to the wave propagation mechanism.
    Description: Y. Zhang acknowledges the support of theMIT-WHOI Joint Programin Physical Oceanography, NSF OCE-9901654 and OCE-0451086. J. Pedlosky acknowledges the support of NSF OCE- 9901654 and OCE-0451086.
    Keywords: Transport ; Eddies ; Barotropic flow ; Topographic effects ; Vortices ; Currents ; Potential vorticity ; Rossby waves
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 55
    facet.materialart.
    Unknown
    Observing the Galápagos–EUC interaction : insights and challenges (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2010. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 40 (2010): 2768–2777, doi:10.1175/2010JPO4461.1.
    Description: Although sustained observations yield a description of the mean equatorial current system from the western Pacific to the eastern terminus of the Tropical Atmosphere Ocean (TAO) array, a comprehensive observational dataset suitable for describing the structure and pathways of the Equatorial Undercurrent (EUC) east of 95°W does not exist and therefore climate models are unconstrained in a region that plays a critical role in ocean–atmosphere coupling. Furthermore, ocean models suggest that the interaction between the EUC and the Galápagos Islands (92°W) has a striking effect on the basic state and coupled variability of the tropical Pacific. To this end, the authors interpret historical measurements beginning with those made in conjunction with the discovery of the Pacific EUC in the 1950s, analyze velocity measurements from an equatorial TAO mooring at 85°W, and analyze a new dataset from archived shipboard ADCP measurements. Together, the observations yield a possible composite description of the EUC structure and pathways in the eastern equatorial Pacific that may be useful for model validation and guiding future observation.
    Description: Karnauskas acknowledges the WHOI Penzance Endowed Fund in Support of Assistant Scientists.
    Keywords: Atmosphere-ocean interaction ; Currents ; In situ observations ; Model evaluation/performance ; Pacific Ocean ; Tropics
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 56
    facet.materialart.
    Unknown
    Transport and dynamics of the Panay Sill overflow in the Philippine Seas (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2010. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 40 (2010): 2679–2695, doi:10.1175/2010JPO4395.1.
    Description: Observations of stratification and currents between June 2007 and March 2009 reveal a strong overflow between 400- and 570-m depth from the Panay Strait into the Sulu Sea. The overflow water is derived from approximately 400 m deep in the South China Sea. Temporal mean velocity is greater than 0.75 m s−1 at 50 m above the 570-m Panay Sill. Empirical orthogonal function analysis of a mooring time series shows that the flow is dominated by the bottom overflow current with little seasonal variance. The overflow does not descend below 1250 m in the Sulu Sea but rather settles above high-salinity deep water derived from the Sulawesi Sea. The mean observed overflow transport at the sill is 0.32 × 106 m3 s−1. The observed transport was used to calculate a bulk diapycnal diffusivity of 4.4 × 10−4 m2 s−1 within the Sulu Sea slab (575–1250 m) ventilated from Panay Strait. Analysis of Froude number variation across the sill shows that the flow is hydraulically controlled. A suitable hydraulic control model shows overflow transport equivalent to the observed overflow. Thorpe-scale estimates show turbulent dissipation rates up to 5 × 10−7 W kg−1 just downstream of the supercritical to subcritical flow transition, suggesting a hydraulic jump downstream of the sill.
    Description: This work was supported by the Office of Naval Research Grant N00014-09-1-0582 to Lamont-Doherty Earth Observatory of Columbia University; Grants ONR-13759000 and N00014-09-1-0582 to the Woods Hole Oceanographic Institution; Grant ONR-N00014-06-1-0690 to Scripps Institute of Oceanography; and a National Defense Science and Engineering Graduate Fellowship.
    Keywords: Transport ; Dynamics ; Topographic effects ; Currents ; Empirical orthogonal functions
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 57
    facet.materialart.
    Unknown
    Near-surface transport pathways in the north Atlantic Ocean : looking for throughput from the subtropical to the subpolar gyre (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 41 (2011): 911–925, doi:10.1175/2011JPO4498.1.
    Description: Motivated by discrepancies between Eulerian transport estimates and the behavior of Lagrangian surface drifters, near-surface transport pathways and processes in the North Atlantic are studied using a combination of data, altimetric surface heights, statistical analysis of trajectories, and dynamical systems techniques. Particular attention is paid to the issue of the subtropical-to-subpolar intergyre fluid exchange. The velocity field used in this study is composed of a steady drifter-derived background flow, upon which a time-dependent altimeter-based perturbation is superimposed. This analysis suggests that most of the fluid entering the subpolar gyre from the subtropical gyre within two years comes from a narrow region lying inshore of the Gulf Stream core, whereas fluid on the offshore side of the Gulf Stream is largely prevented from doing so by the Gulf Stream core, which acts as a strong transport barrier, in agreement with past studies. The transport barrier near the Gulf Stream core is robust and persistent from 1992 until 2008. The qualitative behavior is found to be largely independent of the Ekman drift.
    Description: This work was supported by the National Science Foundation Grants CMG-82469600 and CMG-82579600 and by the Office of Naval Research Grant ONR-13108700.
    Keywords: Atlantic Ocean ; Transport ; Gyres ; Lagrangian circulation/transport ; Tracers ; Currents ; Meridional overturning circulation
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 58
    facet.materialart.
    Unknown
    Influence of the meridional shifts of the Kuroshio and the Oyashio Extensions on the atmospheric circulation (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2011. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 24 (2011): 762-777, doi:10.1175/2010JCLI3731.1.
    Description: The meridional shifts of the Oyashio Extension (OE) and of the Kuroshio Extension (KE), as derived from high-resolution monthly sea surface temperature (SST) anomalies in 1982–2008 and historical temperature profiles in 1979–2007, respectively, are shown based on lagged regression analysis to significantly influence the large-scale atmospheric circulation. The signals are independent from the ENSO teleconnections, which were removed by seasonally varying, asymmetric regression onto the first three principal components of the tropical Pacific SST anomalies. The response to the meridional shifts of the OE front is equivalent barotropic and broadly resembles the North Pacific Oscillation/western Pacific pattern in a positive phase for a northward frontal displacement. The response may reach 35 m at 250 hPa for a typical OE shift, a strong sensitivity since the associated SST anomaly is 0.5 K. However, the amplitude, but not the pattern or statistical significance, strongly depends on the lag and an assumed 2-month atmospheric response time. The response is stronger during fall and winter and when the front is displaced southward. The response to the northward KE shifts primarily consists of a high centered in the northwestern North Pacific and hemispheric teleconnections. The response is also equivalent barotropic, except near Kamchatka, where it tilts slightly westward with height. The typical amplitude is half as large as that associated with OE shifts.
    Description: This work was supported in part by the L’Institut universitaire de France (CF), the WHOI Heyman fellowship, and the NASAGrant withAwardNNX09AF35G(Y.-O. K), and grants through NOAA’s Climate Variability and Predictability Program (MAA).
    Keywords: Atmospheric circulation ; Currents
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 59
    facet.materialart.
    Unknown
    Diapycnal mixing in the Antarctic Circumpolar Current (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2011. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 41 (2011): 241-246, doi:10.1175/2010JPO4557.1.
    Description: The vertical dispersion of a tracer released on a density surface near 1500-m depth in the Antarctic Circumpolar Current west of Drake Passage indicates that the diapycnal diffusivity, averaged over 1 yr and over tens of thousands of square kilometers, is (1.3 ± 0.2) × 10−5 m2 s−1. Diapycnal diffusivity estimated from turbulent kinetic energy dissipation measurements about the area occupied by the tracer in austral summer 2010 was somewhat less, but still within a factor of 2, at (0.75 ± 0.07) × 10−5 m2 s−1. Turbulent diapycnal mixing of this intensity is characteristic of the midlatitude ocean interior, where the energy for mixing is believed to derive from internal wave breaking. Indeed, despite the frequent and intense atmospheric forcing experienced by the Southern Ocean, the amplitude of finescale velocity shear sampled about the tracer was similar to background amplitudes in the midlatitude ocean, with levels elevated to only 20%–50% above the Garrett–Munk reference spectrum. These results add to a long line of evidence that diapycnal mixing in the interior middepth ocean is weak and is likely too small to dictate the middepth meridional overturning circulation of the ocean.
    Description: This material is based upon work supported by the National Science Foundation Grants OCE-0622825,OCE-0622670, OCE-0622630, and OCE-0623177.
    Keywords: Diapycnal mixing ; Currents ; Antarctica ; Ocean circulation ; Meridional overturning circulation
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 60
    facet.materialart.
    Unknown
    Response to a steady poleward outflow. Part I : the linear, quasigeostrophic problem (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 1541-1550, doi:10.1175/2008JPO3999.1.
    Description: The response of a zonal channel to a uniform, switched-on but subsequently steady poleward outflow is presented. An eastward coastal current with a Kelvin wave’s cross-shore structure is found to be generated instantly upon initiation of the outflow. The current is essentially in geostrophic balance everywhere except for the vicinity of the outflow channel mouth, where the streamlines must cross planetary vorticity contours to feed the current. The adjustment of this region generates a plume that propagates westward at Rossby wave speeds. The cross-shore structure of the plume varies with longitude, and at any given longitude it evolves with time. The authors show that the plume evolution can be understood both conceptually and quantitatively as the westward propagation of the Kelvin current’s meridional spectrum, with each spectral element propagating at its own Rossby wave group velocity.
    Description: This work was completed at Woods Hole Oceanographic Institution while T.S. Durland was supported by the Ocean and Climate Change Institute. M.A. Spall was supported by NSF Grant OCE-0423975, and J. Pedlosky by NSF Grant OCE-0451086. T.S. Durland acknowledges additional report preparation support from NASA Grant NNG05GN98G.
    Keywords: Coastal flows ; Estuaries ; Currents ; Vorticity ; Plumes
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 61
    facet.materialart.
    Unknown
    Performance of a new generation of acoustic current meters (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 37 (2007): 148–161, doi:10.1175/JPO3003.1.
    Description: As part of a program aimed at developing a long-duration, subsurface mooring, known as Ultramoor, several modern acoustic current meters were tested. The instruments with which the authors have the most experience are the Aanderaa RCM11 and the Nortek Aquadopp, which measure currents using the Doppler shift of backscattered acoustic signals, and the Falmouth Scientific ACM, which measures changes in travel time of acoustic signals between pairs of transducers. Some results from the Doppler-based Sontek Argonaut and the travel-time-based Nobska MAVS are also reported. This paper concentrates on the fidelity of the speed measurement but also presents some results related to the accuracy of the direction measurement. Two procedures were used to compare the instruments. In one, different instruments were placed close to one another on three different deep-ocean moorings. These tests showed that the RCM11 measures consistently lower speeds than either a vector averaging current meter or a vector measuring current meter, both more traditional instruments with mechanical velocity sensors. The Aquadopp in use at the time, but since updated to address accuracy problems in low scattering environments, was biased high. A second means of testing involved comparing the appropriate velocity component of each instrument with the rate of change of pressure when they were lowered from a ship. Results from this procedure revealed no depth dependence or measurable bias in the RCM11 data, but did show biases in both the Aquadopp and Argonaut Doppler-based instruments that resulted from low signal-to-noise ratios in the clear, low scattering conditions beneath the thermocline. Improvements in the design of the latest Aquadopp have reduced this bias to a level that is not significant.
    Description: This material is based upon work supported by the National Science Foundation under Grant 9810641.
    Keywords: Currents ; Acoustic measurements ; In situ sensors
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 62
    facet.materialart.
    Unknown
    Laboratory experiments on the interaction of a buoyant coastal current with a canyon : application to the East Greenland Current (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 1258-1271, doi:10.1175/2008JPO4028.1.
    Description: This paper presents a set of laboratory experiments focused on how a buoyant coastal current flowing over a sloping bottom interacts with a canyon and what controls the separation, if any, of the current from the upstream canyon bend. The results show that the separation of a buoyant coastal current depends on the current width W relative to the radius of curvature of the bathymetry ρc. The flow moved across the mouth of the canyon (i.e., separated) for W/ρc 〉 1, in agreement with previous results. The present study extends previous work by examining both slope-controlled and surface-trapped currents, and using a geometry specific to investigating buoyant current–canyon interaction. The authors find that, although bottom friction is important in setting the position of the buoyant front, the separation process driven by the inertia of the flow could overcome even the strongest bathymetric influence. Application of the laboratory results to the East Greenland Current (EGC), an Arctic-origin buoyant current that is observed to flow in two branches south of Denmark Strait, suggests that the path of the EGC is influenced by the large canyons cutting across the shelf, as the range of W/ρc in the ocean spans those observed in the laboratory. What causes the formation of a two-branched EGC structure downstream of the Kangerdlugssuaq Canyon (68°N, 32°W) is still unclear, but potential mechanisms are discussed.
    Description: This work was partially funded by NSF Grant OCE-0450658. DS also received support from the Academic Programs Office of the Woods Hole Oceanographic Institution, while CC had partial support from NSF OCE-0350891.
    Keywords: Coastal flows ; Buoyancy ; Currents ; Experimental design ; Topographic effects
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 63
    facet.materialart.
    Unknown
    Interannual variability in the pathways of the North Atlantic Current over the Mid-Atlantic Ridge and the impact of topography (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 38 (2008): 104–120, doi:10.1175/2007JPO3686.1.
    Description: Recent studies have indicated that the North Atlantic Ocean subpolar gyre circulation undergoes significant interannual-to-decadal changes in response to variability in atmospheric forcing. There are also observations, however, suggesting that the southern limb of the subpolar gyre, namely, the eastward-flowing North Atlantic Current (NAC), may be quasi-locked to particular latitudes in the central North Atlantic by fracture zones (gaps) in the Mid-Atlantic Ridge. This could constrain the current’s ability to respond to variability in forcing. In the present study, subsurface float trajectories at 100–1000 m collected during 1997–99 and satellite-derived surface geostrophic velocities from 1992 to 2006 are used to provide an improved description of the detailed pathways of the NAC over the ridge and their relationship to bathymetry. Both the float and satellite observations indicate that in 1997–99, the northern branch of the NAC was split into two branches as it crossed the ridge, one quasi-locked to the Charlie–Gibbs Fracture Zone (CGFZ; 52°–53°N) and the other to the Faraday Fracture Zone (50°–51°N). The longer satellite time series shows, however, that this pattern did not persist outside the float sampling period and that other branching modes persisted for one or more years, including an approximately 12-month time period in 2002–03 when the strongest eastward flow over the ridge was at 49°N. Schott et al. showed how northward excursions of the NAC can temporarily block the westward flow of the Iceland–Scotland Overflow Water through the CGFZ. From the 13-yr time series of surface geostrophic velocity, it is estimated that such blocking may occur on average 6% of the time, although estimates for any given 12-month period range from 0% to 35%.
    Description: This research was supported by National Science Foundation Grants OCE-9531877 to the Woods Hole Oceanographic Institution (WHOI) and OCE-9906775 to the University of Rhode Island, by the WHOI Summer Student Fellowship Program, and by the Lawrence J. Pratt and Melinda M. Hall Endowed Fund for Interdisciplinary Research at the Woods Hole Oceanographic Institution.
    Keywords: Currents ; Topographic effects ; Interannual variability ; Forcing ; Gyres
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 64
    facet.materialart.
    Unknown
    Observations and a model of the mean circulation over the Middle Atlantic Bight continental shelf (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 38 (2008): 1203–1221, doi:10.1175/2007JPO3768.1.
    Description: Analyses of current time series longer than 200 days from 33 sites over the Middle Atlantic Bight continental shelf reveal a consistent mean circulation pattern. The mean depth-averaged flow is equatorward, alongshelf, and increases with increasing water depth from 3 cm s−1 at the 15-m isobath to 10 cm s−1 at the 100-m isobath. The mean cross-shelf circulation exhibits a consistent cross-shelf and vertical structure. The near-surface flow is typically offshore (positive, range −3 to 6 cm s−1). The interior flow is onshore and remarkably constant (−0.2 to −1.4 cm s−1). The near-bottom flow increases linearly with increasing water depth from −1 cm s−1 (onshore) in shallow water to 4 cm s−1 (offshore) at the 250-m isobath over the slope, with the direction reversal near the 50-m isobath. A steady, two-dimensional model (no along-isobath variations in the flow) reproduces the main features of the observed circulation pattern. The depth-averaged alongshelf flow is primarily driven by an alongshelf pressure gradient (sea surface slope of 3.7 × 10−8 increasing to the north) and an opposing mean wind stress that also drives the near-surface offshore flow. The alongshelf pressure gradient accounts for both the increase in the alongshelf flow with water depth and the geostrophic balance onshore flow in the interior. The increase in the near-bottom offshore flow with water depth is due to the change in the relative magnitude of the contributions from the geostrophic onshore flow that dominates in shallow water and the offshore flow driven by the bottom stress that dominates in deeper water.
    Description: This research was funded by Ocean Sciences Division of the National Science Foundation under Grants OCE-820773, OCE-841292, and OCE-848961.
    Keywords: Ocean models ; Ocean circulation ; Continental shelf ; Currents ; In situ observations
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 65
    facet.materialart.
    Unknown
    Western Arctic shelfbreak eddies : formation and transport (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 38 (2008): 1644-1668, doi:10.1175/2007JPO3829.1.
    Description: The mean structure and time-dependent behavior of the shelfbreak jet along the southern Beaufort Sea, and its ability to transport properties into the basin interior via eddies are explored using high-resolution mooring data and an idealized numerical model. The analysis focuses on springtime, when weakly stratified winter-transformed Pacific water is being advected out of the Chukchi Sea. When winds are weak, the observed jet is bottom trapped with a low potential vorticity core and has maximum mean velocities of O(25 cm s−1) and an eastward transport of 0.42 Sv (1 Sv ≡ 106 m3 s−1). Despite the absence of winds, the current is highly time dependent, with relative vorticity and twisting vorticity often important components of the Ertel potential vorticity. An idealized primitive equation model forced by dense, weakly stratified waters flowing off a shelf produces a mean middepth boundary current similar in structure to that observed at the mooring site. The model boundary current is also highly variable, and produces numerous strong, small anticyclonic eddies that transport the shelf water into the basin interior. Analysis of the energy conversion terms in both the mooring data and the numerical model indicates that the eddies are formed via baroclinic instability of the boundary current. The structure of the eddies in the basin interior compares well with observations from drifting ice platforms. The results suggest that eddies shed from the shelfbreak jet contribute significantly to the offshore flux of heat, salt, and other properties, and are likely important for the ventilation of the halocline in the western Arctic Ocean. Interaction with an anticyclonic basin-scale circulation, meant to represent the Beaufort gyre, enhances the offshore transport of shelf water and results in a loss of mass transport from the shelfbreak jet.
    Description: This study was supported by the National Science Foundation Office of Polar Programs under Grants 0421904 and 035268 (MS), and by the Office of Naval Research Grant N00014-02-1-0317 (RP and PF). Analysis by AJP was supported by the Office of Naval Research under Grant N00014-97-1-0135 and by the National Science Foundation under Grant OPP-9815303.
    Keywords: Arctic ; Eddies ; Transport ; Currents ; Jets
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 66
    facet.materialart.
    Unknown
    The western North Atlantic shelfbreak current system in summer (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography. 37 (2007): 2509-2533, doi:10.1175/JPO3123.1.
    Description: Twelve years of historical hydrographic data, spanning the period 1990–2001, are analyzed to examine the along-stream evolution of the western North Atlantic Ocean shelfbreak front and current, following its path between the west coast of Greenland and the Middle Atlantic Bight. Over 700 synoptic sections are used to construct a mean three-dimensional description of the summer shelfbreak front and to quantify the along-stream evolution in properties, including frontal strength and grounding position. Results show that there are actually two fronts in the northern part of the domain—a shallow front located near the shelf break and a deeper front centered in the core of Irminger Water over the upper slope. The properties of the deeper Irminger front erode gradually to the south, and the front disappears entirely near the Grand Banks of Newfoundland. The shallow shelfbreak front is identifiable throughout the domain, and its properties exhibit large variations from north to south, with the largest changes occurring near the Tail of the Grand Banks. Despite these structural changes, and large variations in topography, the foot of the shelfbreak front remains within 20 km of the shelf break. The hydrographic sections are also used to examine the evolution of the baroclinic velocity field and its associated volume transport. The baroclinic velocity structure consists of a single velocity core that is stronger and penetrates deeper where the Irminger front is present. The baroclinic volume transport decreases by equal amounts at the southern end of the Labrador Shelf and at the Tail of the Grand Banks. Overall, the results suggest that the Grand Banks is a geographically critical location in the North Atlantic shelfbreak system.
    Description: This work was supported by the National Science Foundation under Grants OCE00- 95261 (PF) and OCE-0450658 (RP).
    Keywords: Continental shelf ; Currents ; Atlantic Ocean ; Fronts ; Transport
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 67
    facet.materialart.
    Unknown
    Anisotropic material transport by eddies and eddy-driven currents in a model of the North Atlantic (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 3162-3175, doi:10.1175/2009JPO4239.1.
    Description: This study analyzes anisotropic properties of the material transport by eddies and eddy-driven zonal jets in a general circulation model of the North Atlantic through the analysis of Lagrangian particle trajectories. Spreading rates—defined here as half the rate of change in the particle dispersion—in the zonal direction systematically exceed the meridional rates by an order of magnitude. Area-averaged values for the upper-ocean zonal and meridional spreading rates are approximately 8100 and 1400 m2 s−1, respectively, and in the deep ocean they are 2400 and 200 m2 s−1. The results demonstrate that this anisotropy is mainly due to the action of the transient eddies and not to the shear dispersion associated with the time-mean jets. This property is consistent with the fact that eddies in this study have zonally elongated shapes. With the exception of the upper-ocean subpolar gyre, eddies also cause the superdiffusive zonal spreading, significant variations in the spreading rate in the vertical and meridional directions, and the difference between the westward and eastward spreading.
    Description: Funding for IK was provided by NSF Grants OCE 0346178, 0749722, and 0842834. Funding for PB was provided by NSF Grants OCE 0344094 and OCE 0725796 and by the research grant from the Newton Trust of the University of Cambridge. For JP the acknowledgement is to NSF OCE-0451086.
    Keywords: Eddies ; Transport ; Currents ; North Atlantic Ocean
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 68
    facet.materialart.
    Unknown
    An oceanic current against the wind : how does Taiwan island steer warm water into the East China Sea? (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 37 (2007): 2563-2569, doi:10.1175/JPO3134.1.
    Description: Along the Taiwan Strait (〈100 m in depth) a northeastward flow persists in all seasons despite the annually averaged wind stress that is strongly southwestward. The forcing mechanism of this countercurrent is examined by using a simple ocean model. The results from a suite of experiments demonstrate that it is the Kuroshio that plays the deciding role for setting the flow direction along the Taiwan Strait. The momentum balance along the strait is mainly between the wind stress, friction, and pressure gradient. Since both wind stress and friction act against the northward flow, it is most likely the pressure gradient that forces the northward flow, as noted in some previous studies. What remains unknown is why there is a considerable pressure difference between the southern and northern strait. The Kuroshio flows along the east coast of Taiwan, and thus the western boundary current layer dynamics applies there. Integrating the momentum equation along Taiwan’s east coast shows that there must be a pressure difference between the southern and the northern tip of Taiwan to counter a considerable friction exerted by the mighty Kuroshio. This same pressure difference is also felt on the other side of the island where it forces the northward flow through Taiwan Strait. The model shows that the local wind stress acts to dampen this northward flow. This mechanism can be illustrated by an integral constraint for flow around an island.
    Description: This study has been supported by National Science Foundation through Grant OCE-0351055.
    Keywords: Ocean circulation ; Wind ; Currents
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 69
    facet.materialart.
    Unknown
    Role of the Gulf Stream and Kuroshio–Oyashio systems in large-scale atmosphere–ocean interaction : a review (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2010. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 23 (2010): 3249-3281, doi:10.1175/2010JCLI3343.1.
    Description: Ocean–atmosphere interaction over the Northern Hemisphere western boundary current (WBC) regions (i.e., the Gulf Stream, Kuroshio, Oyashio, and their extensions) is reviewed with an emphasis on their role in basin-scale climate variability. SST anomalies exhibit considerable variance on interannual to decadal time scales in these regions. Low-frequency SST variability is primarily driven by basin-scale wind stress curl variability via the oceanic Rossby wave adjustment of the gyre-scale circulation that modulates the latitude and strength of the WBC-related oceanic fronts. Rectification of the variability by mesoscale eddies, reemergence of the anomalies from the preceding winter, and tropical remote forcing also play important roles in driving and maintaining the low-frequency variability in these regions. In the Gulf Stream region, interaction with the deep western boundary current also likely influences the low-frequency variability. Surface heat fluxes damp the low-frequency SST anomalies over the WBC regions; thus, heat fluxes originate with heat anomalies in the ocean and have the potential to drive the overlying atmospheric circulation. While recent observational studies demonstrate a local atmospheric boundary layer response to WBC changes, the latter’s influence on the large-scale atmospheric circulation is still unclear. Nevertheless, heat and moisture fluxes from the WBCs into the atmosphere influence the mean state of the atmospheric circulation, including anchoring the latitude of the storm tracks to the WBCs. Furthermore, many climate models suggest that the large-scale atmospheric response to SST anomalies driven by ocean dynamics in WBC regions can be important in generating decadal climate variability. As a step toward bridging climate model results and observations, the degree of realism of the WBC in current climate model simulations is assessed. Finally, outstanding issues concerning ocean–atmosphere interaction in WBC regions and its impact on climate variability are discussed.
    Description: Funding for LT was provided by the NASA-sponsored Ocean Surface Topography Science Team, under Contract 1267196 with the University of Washington, administered by the Jet Propulsion Laboratory. HN was supported in part by the Grant-in-Aid 18204044 by the Japan Society for Promotion for Science (JSPS) and the Global Environment Research Fund (S-5) of the Japanese Ministry of Environment. YK was supported by the Kerr Endowed Fund and Penzance Endowed Fund.
    Keywords: Currents ; Sea surface temperature ; Anomalies ; Large-scale motions ; Oceanic mixed layer ; Northern Hemisphere
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...