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  • Food Policy  (110)
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  • 1
    Publication Date: 2022-09-25
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(4), (2022): 597–616, https://doi.org/10.1175/jpo-d-21-0121.1.
    Description: We provide a first-principles analysis of the energy fluxes in the oceanic internal wave field. The resulting formula is remarkably similar to the renowned phenomenological formula for the turbulent dissipation rate in the ocean, which is known as the finescale parameterization. The prediction is based on the wave turbulence theory of internal gravity waves and on a new methodology devised for the computation of the associated energy fluxes. In the standard spectral representation of the wave energy density, in the two-dimensional vertical wavenumber–frequency (m–ω) domain, the energy fluxes associated with the steady state are found to be directed downscale in both coordinates, closely matching the finescale parameterization formula in functional form and in magnitude. These energy transfers are composed of a “local” and a “scale-separated” contributions; while the former is quantified numerically, the latter is dominated by the induced diffusion process and is amenable to analytical treatment. Contrary to previous results indicating an inverse energy cascade from high frequency to low, at odds with observations, our analysis of all nonzero coefficients of the diffusion tensor predicts a direct energy cascade. Moreover, by the same analysis fundamental spectra that had been deemed “no-flux” solutions are reinstated to the status of “constant-downscale-flux” solutions. This is consequential for an understanding of energy fluxes, sources, and sinks that fits in the observational paradigm of the finescale parameterization, solving at once two long-standing paradoxes that had earned the name of “oceanic ultraviolet catastrophe.”
    Description: The authors gratefully acknowledge support from the ONR Grant N00014-17-1-2852. YL gratefully acknowledges support from NSF DMS Award 2009418.
    Description: 2022-09-25
    Keywords: Ocean ; Gravity waves ; Nonlinear dynamics ; Ocean dynamics ; Mixing ; Fluxes ; Isopycnal coordinates ; Nonlinear models
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  • 2
    Publication Date: 2022-08-29
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(8), (2022): 1593-1611, https://doi.org/10.1175/jpo-d-21-0180.1.
    Description: This study presents novel observational estimates of turbulent dissipation and mixing in a standing meander between the Southeast Indian Ridge and the Macquarie Ridge in the Southern Ocean. By applying a finescale parameterization on the temperature, salinity, and velocity profiles collected from Electromagnetic Autonomous Profiling Explorer (EM-APEX) floats in the upper 1600 m, we estimated the intensity and spatial distribution of dissipation rate and diapycnal mixing along the float tracks and investigated the sources. The indirect estimates indicate strong spatial and temporal variability of turbulent mixing varying from O(10−6) to O(10−3) m2 s−1 in the upper 1600 m. Elevated turbulent mixing is mostly associated with the Subantarctic Front (SAF) and mesoscale eddies. In the upper 500 m, enhanced mixing is associated with downward-propagating wind-generated near-inertial waves as well as the interaction between cyclonic eddies and upward-propagating internal waves. In the study region, the local topography does not play a role in turbulent mixing in the upper part of the water column, which has similar values in profiles over rough and smooth topography. However, both remotely generated internal tides and lee waves could contribute to the upward-propagating energy. Our results point strongly to the generation of turbulent mixing through the interaction of internal waves and the intense mesoscale eddy field.
    Description: The observations were funded through grants from the Australian Research Council Discovery Project (DP170102162) and Australia’s Marine National Facility. Surface drifters were provided by Dr. Shaun Dolk of the Global Drifter Program. AC was supported by an Australian Research Council Postdoctoral Fellowship. AC, HEP, and NLB acknowledge support from the Australian Government Department of the Environment and Energy National Environmental Science Program and the ARC Centre of Excellence in Climate Extremes. KP acknowledges the support from the National Science Foundation.
    Keywords: Diapycnal mixing ; Eddies ; Fronts ; Inertia-gravity waves ; Ocean dynamics
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  • 3
    Publication Date: 2022-09-15
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(1),(2022): 75–97, https://doi.org/10.1175/JPO-D-21-0099.1.
    Description: Mesoscale eddies contain the bulk of the ocean’s kinetic energy (KE), but fundamental questions remain on the cross-scale KE transfers linking eddy generation and dissipation. The role of submesoscale flows represents the key point of discussion, with contrasting views of submesoscales as either a source or a sink of mesoscale KE. Here, the first observational assessment of the annual cycle of the KE transfer between mesoscale and submesoscale motions is performed in the upper layers of a typical open-ocean region. Although these diagnostics have marginal statistical significance and should be regarded cautiously, they are physically plausible and can provide a valuable benchmark for model evaluation. The cross-scale KE transfer exhibits two distinct stages, whereby submesoscales energize mesoscales in winter and drain mesoscales in spring. Despite this seasonal reversal, an inverse KE cascade operates throughout the year across much of the mesoscale range. Our results are not incompatible with recent modeling investigations that place the headwaters of the inverse KE cascade at the submesoscale, and that rationalize the seasonality of mesoscale KE as an inverse cascade-mediated response to the generation of submesoscales in winter. However, our findings may challenge those investigations by suggesting that, in spring, a downscale KE transfer could dampen the inverse KE cascade. An exploratory appraisal of the dynamics governing mesoscale–submesoscale KE exchanges suggests that the upscale KE transfer in winter is underpinned by mixed layer baroclinic instabilities, and that the downscale KE transfer in spring is associated with frontogenesis. Current submesoscale-permitting ocean models may substantially understate this downscale KE transfer, due to the models’ muted representation of frontogenesis.
    Description: The OSMOSIS experiment was funded by the U.K. Natural Environment Research Council (NERC) through Grants NE/1019999/1 and NE/101993X/1. ACNG acknowledges the support of the Royal Society and the Wolfson Foundation, and XY that of a China Scholarship Council PhD studentship.
    Keywords: Ageostrophic circulations ; Dynamics ; Eddies ; Energy transport ; Frontogenesis/frontolysis ; Instability ; Mesoscale processes ; Nonlinear dynamics ; Ocean circulation ; Ocean dynamics ; Small scale processes ; Turbulence
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  • 4
    Publication Date: 2022-08-05
    Description: Author Posting. © American Meteorological Society, 2022. 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 the Atmospheric and Oceanic Technology 39(4), (2022): 491–502, https://doi.org/10.1175/jtech-d-21-0046.1.
    Description: The Air-Launched Autonomous Micro Observer (ALAMO) is a versatile profiling float that can be launched from an aircraft to make temperature and salinity observations of the upper ocean for over a year with high temporal sampling. Similar in dimensions and weight to an airborne expendable bathythermograph (AXBT), but with the same capability as Argo profiling floats, ALAMOs can be deployed from an A-sized (sonobuoy) launch tube, the stern ramp of a cargo plane, or the door of a small aircraft. Unlike an AXBT, however, the ALAMO float directly measures pressure, can incorporate additional sensors, and is capable of performing hundreds of ocean profiles compared to the single temperature profile provided by an AXBT. Upon deployment, the float parachutes to the ocean, releases the air-deployment package, and immediately begins profiling. Ocean profile data along with position and engineering information are transmitted via the Iridium satellite network, automatically processed, and then distributed by the Global Telecommunications System for use by the operational forecasting community. The ALAMO profiling mission can be modified using the two-way Iridium communications to change the profiling frequency and depth. Example observations are included to demonstrate the ALAMO’s utility.
    Description: This work was supported by the National Oceanographic and Atmospheric Administration under Grants NA13OAR4830233 (as part of CINAR Sandy Supplemental funding from the Disaster Relief Appropriations Act of 2013) and NA14OAR4320158 and by Office of Naval Research under Grants N0001416WX01384, N0001416WX01262, and N000141512293. ALAMO floats are commercially available from MRV Systems, LLC (https://www.mrvsys.com).
    Keywords: Ocean ; Hurricanes ; Ocean dynamics ; Mixed layer ; Aircraft observations ; Instrumentation/sensors
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  • 5
    Publication Date: 2022-11-01
    Description: Author Posting. © American Meteorological Society, 2022. 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 the Atmospheric and Oceanic Technology 39(5), (2022): 595–617, https://doi.org/10.1175/jtech-d-21-0039.1.
    Description: The future Surface Water and Ocean Topography (SWOT) mission aims to map sea surface height (SSH) in wide swaths with an unprecedented spatial resolution and subcentimeter accuracy. The instrument performance needs to be verified using independent measurements in a process known as calibration and validation (Cal/Val). The SWOT Cal/Val needs in situ measurements that can make synoptic observations of SSH field over an O(100) km distance with an accuracy matching the SWOT requirements specified in terms of the along-track wavenumber spectrum of SSH error. No existing in situ observing system has been demonstrated to meet this challenge. A field campaign was conducted during September 2019–January 2020 to assess the potential of various instruments and platforms to meet the SWOT Cal/Val requirement. These instruments include two GPS buoys, two bottom pressure recorders (BPR), three moorings with fixed conductivity–temperature–depth (CTD) and CTD profilers, and a glider. The observations demonstrated that 1) the SSH (hydrostatic) equation can be closed with 1–3 cm RMS residual using BPR, CTD mooring and GPS SSH, and 2) using the upper-ocean steric height derived from CTD moorings enable subcentimeter accuracy in the California Current region during the 2019/20 winter. Given that the three moorings are separated at 10–20–30 km distance, the observations provide valuable information about the small-scale SSH variability associated with the ocean circulation at frequencies ranging from hourly to monthly in the region. The combined analysis sheds light on the design of the SWOT mission postlaunch Cal/Val field campaign.
    Description: The research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004). All authors are supported by the SWOT project. J. T. Farrar was partially supported by NASA NNX16AH76G.
    Description: 2022-11-01
    Keywords: Internal waves ; Ocean dynamics ; Small scale processes ; Altimetry ; Global positioning systems (GPS) ; In situ oceanic observations ; Ship observations
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  • 6
    Publication Date: 2022-11-27
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(6), (2022): 1233-1244, https://doi.org/10.1175/jpo-d-21-0223.1.
    Description: The Sverdrup relation is the backbone of wind-driven circulation theory; it is a simple relation between the meridional transport of the wind-driven circulation in the upper ocean and the wind stress curl. However, the relation is valid for steady circulation only. In this study, a time-dependent Sverdrup relation is postulated, in which the meridional transport in a time-dependent circulation is the sum of the local wind stress curl term and a time-delayed term representing the effect of the eastern boundary condition. As an example, this time-dependent Sverdrup relation is evaluated through its application to the equatorial circulation in the Indian Ocean, using reanalysis data and a reduced gravity model. Close examination reveals that the southward Somali Current occurring during boreal winter is due to the combination of the local wind stress curl in the Arabian Sea and delayed signals representing the time change of layer thickness at the eastern boundary.
    Description: This work is supported by NSFC (41822602, 41976016, 42005035, 42076021), the Strategic Priority Research Program of Chinese Academy of Sciences (XDB42000000, XDA 20060502), Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0306), Guangdong Basic and Applied Basic Research Foundation (2021A1515011534), Youth Innovation Promotion Association CAS, ISEE2021ZD01, and LTOZZ2002. The numerical simulation is supported by the High-Performance Computing Division in the South China Sea Institute of Oceanology.
    Description: 2022-11-27
    Keywords: Ocean circulation ; Ocean dynamics ; Rossby waves ; Wind stress curl
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  • 7
    Publication Date: 2022-12-21
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(12), (2022): 2923–2933, https://doi.org/10.1175/jpo-d-22-0064.1.
    Description: The characteristics and dynamics of depth-average along-shelf currents at monthly and longer time scales are examined using 17 years of observations from the Martha’s Vineyard Coastal Observatory on the southern New England inner shelf. Monthly averages of the depth-averaged along-shelf current are almost always westward, with the largest interannual variability in winter. There is a consistent annual cycle with westward currents of 5 cm s−1 in summer decreasing to 1–2 cm s−1 in winter. Both the annual cycle and interannual variability in the depth-average along-shelf current are predominantly driven by the along-shelf wind stress. In the absence of wind forcing, there is a westward flow of ∼5 cm s−1 throughout the year. At monthly time scales, the depth-average along-shelf momentum balance is primarily between the wind stress, surface gravity wave–enhanced bottom stress, and an opposing pressure gradient that sets up along the southern New England shelf in response to the wind. Surface gravity wave enhancement of bottom stress is substantial over the inner shelf and is essential to accurately estimating the bottom stress variation across the inner shelf.
    Description: The National Science Foundation, Woods Hole Oceanographic Institution, the Massachusetts Technology Collaborative, and the Office of Naval Research have supported the construction and maintenance of MVCO. The analysis presented here was partially funded by the National Science Foundation under Grants OCE 1558874 and OCE 1655686.
    Keywords: Continental shelf/slope ; Coastal flows ; Momentum ; Ocean dynamics ; Wind stress
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  • 8
    Publication Date: 2022-12-16
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(7), (2022): 1415–1430. https://doi.org/10.1175/JPO-D-21-0147.1.
    Description: Strong subinertial variability near a seamount at the Xisha Islands in the South China Sea was revealed by mooring observations from January 2017 to January 2018. The intraseasonal deep flows presented two significant frequency bands, with periods of 9–20 and 30–120 days, corresponding to topographic Rossby waves (TRWs) and deep eddies, respectively. The TRW and deep eddy signals explained approximately 60% of the kinetic energy of the deep subinertial currents. The TRWs at the Ma, Mb, and Mc moorings had 297, 262, and 274 m vertical trapping lengths, and ∼43, 38, and 55 km wavelengths, respectively. Deep eddies were independent from the upper layer, with the largest temperature anomaly being 〉0.4°C. The generation of the TRWs was induced by mesoscale perturbations in the upper layer. The interaction between the cyclonic–anticyclonic eddy pair and the seamount topography contributed to the generation of deep eddies. Owing to the potential vorticity conservation, the westward-propagating tilted interface across the eddy pair squeezed the deep-water column, thereby giving rise to negative vorticity west of the seamount. The strong front between the eddy pair induced a northward deep flow, thereby generating a strong horizontal velocity shear because of lateral friction and enhanced negative vorticity. Approximately 4 years of observations further confirmed the high occurrence of TRWs and deep eddies. TRWs and deep eddies might be crucial for deep mixing near rough topographies by transferring mesoscale energy to small scales.
    Description: This work was supported by the National Natural Science Foundation of China (92158204, 91958202, 42076019, 41776036, 91858203), the Open Project Program of State Key Laboratory of Tropical Oceanography (project LTOZZ2001), and Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0304).
    Description: 2022-12-16
    Keywords: Abyssal circulation ; Ocean circulation ; Ocean dynamics ; Intraseasonal variability
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  • 9
    Publication Date: 2023-02-01
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(8), (2022): 1927-1943, https://doi.org/10.1175/jpo-d-21-0124.1.
    Description: The Galápagos Archipelago lies on the equator in the path of the eastward flowing Pacific Equatorial Undercurrent (EUC). When the EUC reaches the archipelago, it upwells and bifurcates into a north and south branch around the archipelago at a latitude determined by topography. Since the Coriolis parameter (f) equals zero at the equator, strong velocity gradients associated with the EUC can result in Ertel potential vorticity (Q) having sign opposite that of planetary vorticity near the equator. Observations collected by underwater gliders deployed just west of the Galápagos Archipelago during 2013–16 are used to estimate Q and to diagnose associated instabilities that may impact the Galápagos Cold Pool. Estimates of Q are qualitatively conserved along streamlines, consistent with the 2.5-layer, inertial model of the EUC by Pedlosky. The Q with sign opposite of f is advected south of the Galápagos Archipelago when the EUC core is located south of the bifurcation latitude. The horizontal gradient of Q suggests that the region between 2°S and 2°N above 100 m is barotropically unstable, while limited regions are baroclinically unstable. Conditions conducive to symmetric instability are observed between the EUC core and the equator and within the southern branch of the undercurrent. Using 2-month and 3-yr averages, e-folding time scales are 2–11 days, suggesting that symmetric instability can persist on those time scales.
    Description: This work was supported by the National Science Foundation (Grants OCE-1232971 and OCE-1233282), the NASA Earth and Space Science Fellowship Program (Grant 80NSSC17K0443), and the Global Ocean Monitoring and Observing Program of the National Oceanographic and Atmospheric Administration (NA13OAR4830216). Color maps are from Thyng et al. (2016).
    Description: 2023-02-01
    Keywords: Currents ; In situ oceanic observations ; Instability ; Mixing ; Ocean dynamics ; Pacific Ocean ; Potential vorticity ; Tropics
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  • 10
    Publication Date: 2023-02-01
    Description: Author Posting. © American Meteorological Society, 2022. 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 the Atmospheric and Oceanic Technology 39(8), (2022): 1183-1198, https://doi.org/10.1175/jtech-d-21-0068.1.
    Description: Horizontal kinematic properties, such as vorticity, divergence, and lateral strain rate, are estimated from drifter clusters using three approaches. At submesoscale horizontal length scales O(1–10)km, kinematic properties become as large as planetary vorticity f, but challenging to observe because they evolve on short time scales O(hourstodays). By simulating surface drifters in a model flow field, we quantify the sources of uncertainty in the kinematic property calculations due to the deformation of cluster shape. Uncertainties arise primarily due to (i) violation of the linear estimation methods and (ii) aliasing of unresolved scales. Systematic uncertainties (iii) due to GPS errors, are secondary but can become as large as (i) and (ii) when aspect ratios are small. Ideal cluster parameters (number of drifters, length scale, and aspect ratio) are determined and error functions estimated empirically and theoretically. The most robust method—a two-dimensional, linear least squares fit—is applied to the first few days of a drifter dataset from the Bay of Bengal. Application of the length scale and aspect-ratio criteria minimizes errors (i) and (ii), and reduces the total number of clusters and so computational cost. The drifter-estimated kinematic properties map out a cyclonic mesoscale eddy with a surface, submesoscale fronts at its perimeter. Our analyses suggest methodological guidance for computing the two-dimensional kinematic properties in submesoscale flows, given the recently increasing quantity and quality of drifter observations, while also highlighting challenges and limitations.
    Description: This research was supported by the Office of Naval Research (ONR) Departmental Research Initiative ASIRI under Grant N00014-13-1-0451 (SE and AM) and Grant N00014-13-1-0477 (VH and LC). The authors thank the captain and crew of the R/V Roger Revelle, and Andrew Lucas with the Multiscale Ocean Dynamics group at the Scripps Institution for Oceanography for providing the FastCTD data collected in 2015, which was supported by ONR Grant N00014-13-1-0489, as well as Eric D’Asaro for helpful discussions and Lance Braasch for assistance with the drifter dataset. AM and SE further thank NSF (Grant OCE-I434788) and ONR (Grant N00014-16-1-2470) for support. VH and LC were additionally supported by ONR Grants N00014-15-1-2286, N00014-14-1-0183, N00014-19-1-26-91 and NOAA Global Drifter Program (GDP) Grant NA15OAR4320071.
    Description: 2023-02-01
    Keywords: Indian Ocean ; Eddies ; Frontogenesis/frontolysis ; Fronts ; Lagrangian circulation/transport ; Ocean circulation ; Ocean dynamics
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  • 11
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    American Meteorological Society
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 50(9), (2020): 2491-2506, doi:10.1175/JPO-D-20-0056.1.
    Description: An idealized two-layer shallow water model is applied to the study of the dynamics of the Arctic Ocean halocline. The model is forced by a surface stress distribution reflective of the observed wind stress pattern and ice motion and by an inflow representing the flow of Pacific Water through Bering Strait. The model reproduces the main elements of the halocline circulation: an anticyclonic Beaufort Gyre in the western basin (representing the Canada Basin), a cyclonic circulation in the eastern basin (representing the Eurasian Basin), and a Transpolar Drift between the two gyres directed from the upwind side of the basin to the downwind side of the basin. Analysis of the potential vorticity budget shows a basin-averaged balance primarily between potential vorticity input at the surface and dissipation at the lateral boundaries. However, advection is a leading-order term not only within the anticyclonic and cyclonic gyres but also between the gyres. This means that the eastern and western basins are dynamically connected through the advection of potential vorticity. Both eddy and mean fluxes play a role in connecting the regions of potential vorticity input at the surface with the opposite gyre and with the viscous boundary layers. These conclusions are based on a series of model runs in which forcing, topography, straits, and the Coriolis parameter were varied.
    Description: This study was supported by National Science Foundation Grant OPP-1822334. Comments and suggestions from two anonymous referees greatly helped to improve the paper.
    Description: 2021-02-17
    Keywords: Eddies ; Ekman pumping/transport ; Ocean circulation ; Ocean dynamics ; Potential vorticity ; Shallow-water equations
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  • 12
    Publication Date: 2022-05-27
    Description: Author Posting. © American Meteorological Society, 2020. 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 50(11), (2020): 3235–3251, https://doi.org/10.1175/JPO-D-20-0095.1.
    Description: The dense outflow through Denmark Strait is the largest contributor to the lower limb of the Atlantic meridional overturning circulation, yet a description of the full velocity field across the strait remains incomplete. Here we analyze a set of 22 shipboard hydrographic–velocity sections occupied along the Látrabjarg transect at the Denmark Strait sill, obtained over the time period 1993–2018. The sections provide the first complete view of the kinematic components at the sill: the shelfbreak East Greenland Current (EGC), the combined flow of the separated EGC, and the North Icelandic Jet (NIJ), and the northward-flowing North Icelandic Irminger Current (NIIC). The total mean transport of overflow water is 3.54 ± 0.29 Sv (1 Sv ≡ 106 m3 s−1), comparable to previous estimates. The dense overflow is partitioned in terms of water mass constituents and flow components. The mean transports of the two types of overflow water—Atlantic-origin Overflow Water and Arctic-origin Overflow Water—are comparable in Denmark Strait, while the merged NIJ–separated EGC transports 55% more water than the shelfbreak EGC. A significant degree of water mass exchange takes place between the branches as they converge in Denmark Strait. There are two dominant time-varying configurations of the flow that are characterized as a cyclonic state and a noncyclonic state. These appear to be wind-driven. A potential vorticity analysis indicates that the flow through Denmark Strait is subject to symmetric instability. This occurs at the top of the overflow layer, implying that the mixing/entrainment process that modifies the overflow water begins at the sill.
    Description: Funding for the study was provided by National Science Foundation (NSF) Grants OCE-1259618, OCE-1756361, and OCE-1558742. The German research cruises were financially supported through various EU Projects (e.g. THOR, NACLIM) and national projects (most recently TRR 181 “Energy Transfer in Atmosphere and Ocean” funded by the German Research Foundation and RACE II “Regional Atlantic Circulation and Global Change” funded by the German Federal Ministry for Education and Research). GWKM acknowledges the support of the Natural Sciences and Engineering Research Council of Canada. LP was supported by NSF Grant OCE-1657870.
    Keywords: Currents ; Instability ; Ocean circulation ; Ocean dynamics ; Potential vorticity
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  • 13
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 33(17), (2020): 7697-7714, https://doi.org/10.1175/JCLI-D-20-0115.1.
    Description: The decadal to multidecadal mixed layer variability is investigated in a region south of the Kuroshio Extension (130°E–180°, 25°–35°N), an area where the North Pacific subtropical mode water forms, during 1948–2012. By analyzing the mixed layer heat budget with different observational and reanalysis data, here we show that the decadal to multidecadal variability of the mixed layer temperature and mixed layer depth is covaried with the Atlantic multidecadal oscillation (AMO), instead of the Pacific decadal oscillation (PDO). The mixed layer temperature has strong decadal to multidecadal variability, being warm before 1970 and after 1990 (AMO positive phase) and cold during 1970–90 (AMO negative phase), and so does the mixed layer depth. The dominant process for the mixed layer temperature decadal to multidecadal variability is the Ekman advection, which is controlled by the zonal wind changes related to the AMO. The net heat flux into the ocean surface Qnet acts as a damping term and it is mainly from the effect of latent heat flux and partially from sensible heat flux. While the wind as well as mixed layer temperature decadal changes related to the PDO are weak in the western Pacific Ocean. Our finding proposes the possible influence of the AMO on the northwestern Pacific Ocean mixed layer variability, and could be a potential predictor for the decadal to multidecadal climate variability in the western Pacific Ocean.
    Description: Xiaopei Lin is supported by the China’s national key research and development projects (2016YFA0601803) and the National Natural Science Foundation of China (41925025 and U1606402). Baolan Wu is supported by the China Scholarship Council (201806330010). Lisan Yu thanks NOAA for support for her study on climate change and variability.
    Keywords: Atmosphere-ocean interaction ; Boundary currents ; Hadley circulation ; Ocean dynamics ; Teleconnections
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  • 14
    Publication Date: 2022-05-27
    Description: Author Posting. © American Meteorological Society, 2021. 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 51(8),(2021): 2425–2441, https://doi.org/10.1175/JPO-D-20-0317.1.
    Description: The frequency and latitudinal dependence of the midlatitude wind-driven meridional overturning circulation (MOC) is studied using theory and linear and nonlinear applications of a quasigeostrophic numerical model. Wind forcing is varied either by changing the strength of the wind or by shifting the meridional location of the wind stress curl pattern. At forcing periods of less than the first-mode baroclinic Rossby wave basin crossing time scale, the linear response in the middepth and deep ocean is in phase and opposite to the Ekman transport. For forcing periods that are close to the Rossby wave basin crossing time scale, the upper and deep MOC are enhanced, and the middepth MOC becomes phase shifted, relative to the Ekman transport. At longer forcing periods the deep MOC weakens and the middepth MOC increases, but eventually for long enough forcing periods (decadal) the entire wind-driven MOC spins down. Nonlinearities and mesoscale eddies are found to be important in two ways. First, baroclinic instability causes the middepth MOC to weaken, lose correlation with the Ekman transport, and lose correlation with the MOC in the opposite gyre. Second, eddy thickness fluxes extend the MOC beyond the latitudes of direct wind forcing. These results are consistent with several recent studies describing the four-dimensional structure of the MOC in the North Atlantic Ocean.
    Description: This study was supported by National Science Foundation Grant OCE-1947290.
    Description: 2022-01-13
    Keywords: Eddies ; Large-scale motions ; Meridional overturning circulation ; Ocean dynamics ; Planetary waves
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  • 15
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 50(9), (2020): 2669-2688, doi:10.1175/JPO-D-19-0077.1
    Description: The scale-dependent variance of tracer properties in the ocean bears the imprint of the oceanic eddy field. Anomalies in spice (which combines anomalies in temperature T and salinity S on isopycnal surfaces) act as passive tracers beneath the surface mixed layer (ML). We present an analysis of spice distributions along isopycnals in the upper 200 m of the ocean, calculated with over 9000 vertical profiles of T and S measured along ~4800 km of ship tracks in the Bay of Bengal. The data are from three separate research cruises—in the winter monsoon season of 2013 and in the late and early summer monsoon seasons of 2015 and 2018. We present a spectral analysis of horizontal tracer variance statistics on scales ranging from the submesoscale (~1 km) to the mesoscale (~100 km). Isopycnal layers that are closer to the ML-base exhibit redder spectra of tracer variance at scales ≲10 km than is predicted by theories of quasigeostrophic turbulence or frontogenesis. Two plausible explanations are postulated. The first is that stirring by submesoscale motions and shear dispersion by near-inertial waves enhance effective horizontal mixing and deplete tracer variance at horizontal scales ≲10 km in this region. The second is that the spice anomalies are coherent with dynamical properties such as potential vorticity, and not interpretable as passively stirred.
    Description: We are grateful to the captain and crew of the R/V Roger Revelle and the R/V Thomas G. Thompson, and all ASIRI-OMM and MISO-BOB scientists. We thank Prof. Andrew Thompson and an anonymous reviewer for suggestions that improved the manuscript. This work was carried out under the Office of Naval Research’s Air-Sea Interaction Regional Initiative (ASIRI) and Monsoon Intra-Seasonal Oscillations in the Bay of Bengal (MISO-BOB) research initiatives, in collaboration with the Indian Ministry of Earth Science’s Ocean Mixing and Monsoons (OMM) initiative supported by the Monsoon Mission. Support came from ONR Grants N00014-16-1-2470, N00014-13-1-0451, N00014-17-1-2390 (G.S.J. and A.M.), N00014-14-1-0455 (J.M. and J.N), N00014-17-1-2511 (J.M.), N00014-13-1-0489, N00014-17-1-2391 (A.L.), N00014-15-1-2634 (E.S.), N00014-13-1-0456, N00014-17-1-2355 (A.T.), and N00014-13-1-0453, N00014-17-1-2880 (J.F.).
    Description: 2021-02-28
    Keywords: Ocean dynamics ; Thermocline ; Water masses/storage ; In situ oceanic observations ; Tracers ; Spectral analysis/models/distribution
    Repository Name: Woods Hole Open Access Server
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  • 16
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. 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 49(7), (2019): 1889-1904, doi:10.1175/JPO-D-19-0053.1.
    Description: A high-resolution numerical model, together with in situ and satellite observations, is used to explore the nature and dynamics of the dominant high-frequency (from one day to one week) variability in Denmark Strait. Mooring measurements in the center of the strait reveal that warm water “flooding events” occur, whereby the North Icelandic Irminger Current (NIIC) propagates offshore and advects subtropical-origin water northward through the deepest part of the sill. Two other types of mesoscale processes in Denmark Strait have been described previously in the literature, known as “boluses” and “pulses,” associated with a raising and lowering of the overflow water interface. Our measurements reveal that flooding events occur in conjunction with especially pronounced pulses. The model indicates that the NIIC hydrographic front is maintained by a balance between frontogenesis by the large-scale flow and frontolysis by baroclinic instability. Specifically, the temperature and salinity tendency equations demonstrate that the eddies act to relax the front, while the mean flow acts to sharpen it. Furthermore, the model reveals that the two dense water processes—boluses and pulses (and hence flooding events)—are dynamically related to each other and tied to the meandering of the hydrographic front in the strait. Our study thus provides a general framework for interpreting the short-time-scale variability of Denmark Strait Overflow Water entering the Irminger Sea.
    Description: MAS was supported by the National Science Foundation (NSF) under Grants OCE-1558742 and OCE-1534618. RSP, PL, and DM were supported by NSF under Grants OCE-1558742 and OCE-1259618. WJvA was supported by the Helmholtz Infrastructure Initiative FRAM. TWNH and MA were supported by NSF under Grants OCE-1633124 and OCE-118123.
    Description: 2020-07-01
    Keywords: Baroclinic flows ; Frontogenesis/frontolysis ; Meridional overturning circulation ; Ocean dynamics ; Topographic effects
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  • 17
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    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 643-646, doi:10.1175/JPO-D-17-0240.1.
    Description: A simple oceanic model is presented for source–sink flow on the β plane to discuss the pathways from source to sink when transport boundary layers have large enough Reynolds numbers to be inertial in their dynamics. A representation of the flow as a Fofonoff gyre, suggested by prior work on inertial boundary layers and eddy-driven circulations in two-dimensional turbulent flows, indicates that even when the source and sink are aligned along the same western boundary the flow must intrude deep into the interior before exiting at the sink. The existence of interior pathways for the flow is thus an intrinsic property of an inertial circulation and is not dependent on particular geographical basin geometry.
    Description: 2018-09-12
    Keywords: Abyssal circulation ; Bottom currents ; Nonlinear dynamics ; Ocean circulation ; Ocean dynamics ; Potential vorticity
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  • 18
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 4847-4863, doi:10.1175/JCLI-D-17-0802.1.
    Description: The sensitivity of sea ice to the temperature of inflowing Atlantic water across the Greenland–Scotland Ridge is investigated using an eddy-resolving configuration of the Massachusetts Institute of Technology General Circulation Model with idealized topography. During the last glacial period, when climate on Greenland is known to have been extremely unstable, sea ice is thought to have covered the Nordic seas. The dramatic excursions in climate during this period, seen as large abrupt warming events on Greenland and known as Dansgaard–Oeschger (DO) events, are proposed to have been caused by a rapid retreat of Nordic seas sea ice. Here, we show that a full sea ice cover and Arctic-like stratification can exist in the Nordic seas given a sufficiently cold Atlantic inflow and corresponding low transport of heat across the Greenland–Scotland Ridge. Once sea ice is established, continued sea ice formation and melt efficiently freshens the surface ocean and makes the deeper layers more saline. This creates a strong salinity stratification in the Nordic seas, similar to today’s Arctic Ocean, with a cold fresh surface layer protecting the overlying sea ice from the warm Atlantic water below. There is a nonlinear response in Nordic seas sea ice to Atlantic water temperature with simulated large abrupt changes in sea ice given small changes in inflowing temperature. This suggests that the DO events were more likely to have occurred during periods of reduced warm Atlantic water inflow to the Nordic seas.
    Description: The research was supported by the Centre for Climate Dynamics at the Bjerknes Centre for Climate Research. The research leading to these results is part of the ice2ice project funded by the European Research Council under the European Community Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 610055.
    Keywords: Ocean ; Arctic ; Sea ice ; Ocean dynamics ; Paleoclimate ; General circulation models
    Repository Name: Woods Hole Open Access Server
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  • 19
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    Unknown
    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 163-174, doi:10.1175/JPO-D-17-0161.1.
    Description: The general problem of exchange from a shallow shelf across sharp topography to the deep ocean forced by narrow, cross-shelf wind jets is studied using quasigeostrophic theory and an idealized primitive equation numerical model. Interest is motivated by katabatic winds that emanate from narrow fjords in southeast Greenland, although similar topographically constrained wind jets are found throughout the world’s oceans. Because there is no net vorticity input by the wind, the circulation is largely confined to the region near the forcing. Circulation over the shelf is limited by bottom friction for weakly stratified flows, but stratification allows for much stronger upper-layer flows that are regulated by weak coupling to the lower layer. Over the sloping topography, the topographic beta effect limits the deep flow, while, for sufficient stratification, the upper-layer flow can cross the topography to connect the shelf to the open ocean. This can be an effective transport mechanism even for short, strong wind events because damping of the upper-layer flow is weak. A variety of transients are generated for an abrupt onset of winds, including short topography Rossby waves, long topographic Rossby waves, and inertial waves. Using parameters representative of southeast Greenland, katabatic wind events will force an offshore transport of O(0.4) Sv (1 Sv ≡ 106 m3 s−1) that, when considered for 2 days, will result in an offshore flux of O(5 × 1010) m3.
    Description: MAS was supported by the National Science Foundation under Grant OCE-1533170.
    Description: 2018-07-18
    Keywords: Coastal flows ; Downslope winds ; Ocean dynamics
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  • 20
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1375-1384, doi:10.1175/JPO-D-17-0266.1.
    Description: The relationship between net mixing and the estuarine exchange flow may be quantified using a salinity variance budget. Here “mixing” is defined as the rate of destruction of volume-integrated salinity variance, and the exchange flow is quantified using the total exchange flow. These concepts are explored using an idealized 3D model estuary. It is shown that in steady state (e.g., averaging over the spring–neap cycle) the volume-integrated mixing is approximately given by Mixing ≅ SinSoutQr, where Sin and Sout are the representative salinities of in- and outflowing layers at the mouth and Qr is the river volume flux. This relationship provides an extension of the familiar Knudsen relation, in which the exchange flow is diagnosed based on knowledge of these same three quantities, quantitatively linking mixing to the exchange flow.
    Description: The work was supported by the National Science Foundation through Grants OCE-1736242 to PM and OCE-1736539 to WRG and by the German Research Foundation through Grants TRR 181 and GRK 2000 to HB.
    Keywords: Coastal flows ; Diapycnal mixing ; Ocean dynamics ; Streamflow ; Diagnostics ; Isopycnal coordinates
    Repository Name: Woods Hole Open Access Server
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  • 21
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. 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 30 (2017): 1739-1751, doi:10.1175/JCLI-D-16-0200.1.
    Description: The Indian Ocean has sustained robust surface warming in recent decades, but the role of multidecadal variability remains unclear. Using ocean model hindcasts, characteristics of low-frequency Indian Ocean temperature variations are explored. Simulated upper-ocean temperature changes across the Indian Ocean in the hindcast are consistent with those recorded in observational products and ocean reanalyses. Indian Ocean temperatures exhibit strong warming trends since the 1950s limited to the surface and south of 30°S, while extensive subsurface cooling occurs over much of the tropical Indian Ocean. Previous work focused on diagnosing causes of these long-term trends in the Indian Ocean over the second half of the twentieth century. Instead, the temporal evolution of Indian Ocean subsurface heat content is shown here to reveal distinct multidecadal variations associated with the Pacific decadal oscillation, and the long-term trends are thus interpreted to result from aliasing of the low-frequency variability. Transmission of the multidecadal signal occurs via an oceanic pathway through the Indonesian Throughflow and is manifest across the Indian Ocean centered along 12°S as westward-propagating Rossby waves modulating thermocline and subsurface heat content variations. Resulting low-frequency changes in the eastern Indian Ocean thermocline depth are associated with decadal variations in the frequency of Indian Ocean dipole (IOD) events, with positive IOD events unusually common in the 1960s and 1990s with a relatively shallow thermocline. In contrast, the deeper thermocline depth in the 1970s and 1980s is associated with frequent negative IOD and rare positive IOD events. Changes in Pacific wind forcing in recent decades and associated rapid increases in Indian Ocean subsurface heat content can thus affect the basin’s leading mode of variability, with implications for regional climate and vulnerable societies in surrounding countries.
    Description: This research was supported by a Research Fellowship by the Alexander von Humboldt Foundation, as well as the Ocean Climate Change Institute and the Investment in Science Fund at WHOI.
    Description: 2017-08-15
    Keywords: Indian Ocean ; Ocean dynamics ; Climate variability ; Multidecadal variability ; Pacific decadal oscillation
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  • 22
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. 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 47 (2017): 2251-2265, doi:10.1175/JPO-D-17-0042.1.
    Description: The problem of localized dense water formation over a sloping bottom is considered for the general case in which the topography forms a closed contour. This class of problems is motivated by topography around islands or shallow shoals in which convection resulting from brine rejection or surface heat loss reaches the bottom. The focus of this study is on the large-scale circulation that is forced far from the region of surface forcing. The authors find that a cyclonic current is generated around the topography, in the opposite sense to the propagation of the dense water plume. In physical terms, this current results from the propagation of low sea surface height from the region of dense water formation anticyclonically along the topographic contours back to the formation region. This pressure gradient is then balanced by a cyclonic geostrophic flow. This basic structure is well predicted by a linear quasigeostrophic theory, a primitive equation model, and in rotating tank experiments. For sufficiently strong forcing, the anticyclonic circulation of the dense plume meets this cyclonic circulation to produce a sharp front and offshore advection of dense water at the bottom and buoyant water at the surface. This nonlinear limit is demonstrated in both the primitive equation model and in the tank experiments.
    Description: MAS was supported by the National Science Foundation under Grant OCE-1534618. Support for CC was given by the WHOI Ocean Climate Change Institute Proposal 27071273.
    Description: 2018-03-20
    Keywords: Bottom currents ; Buoyancy ; Ocean dynamics ; Density currents
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  • 23
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2016. 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 29 (2016): 8317-8331, doi:10.1175/JCLI-D-16-0109.1.
    Description: A simple analytic model is developed to represent the offshore decay of cold sea surface temperature (SST) signals that originate from wind-driven upwelling at a coastal boundary. The model couples an oceanic mixed layer to an atmospheric boundary layer through wind stress and air–sea heat exchange. The primary mechanism that controls SST is a balance between Ekman advection and air–sea exchange. The offshore penetration of the cold SST signal decays exponentially with a length scale that is the product of the ocean Ekman velocity and a time scale derived from the air–sea heat flux and the radiative balance in the atmospheric boundary layer. This cold SST signal imprints on the atmosphere in terms of both the boundary layer temperature and surface wind. Nonlinearities due to the feedback between SST and atmospheric wind, baroclinic instability, and thermal wind in the atmospheric boundary layer all slightly modify this linear theory. The decay scales diagnosed from two-dimensional and three-dimensional eddy-resolving numerical ocean models are in close agreement with the theory, demonstrating that the basic physics represented by the theory remain dominant even in these more complete systems. Analysis of climatological SST off the west coast of the United States also shows a decay of the cold SST anomaly with scale roughly in agreement with the theory.
    Description: MASwas supported by the Andrew W. Mellon Foundation Endowed Fund for Innovative Research and the National Science Foundation under Grant OCE-1433170 and PLR-1415489. NS was supported by the National Aeronautics and Space Administration under Grant NNX14AL83G, the Department of Energy, Office of Science Grant DE-SC0006766, and the Japan Agency for Marine-Earth Science and Technology as part of the JAMSTEC-IPRC Joint Investigations.
    Description: 2017-05-03
    Keywords: Coastal flows ; Ekman pumping/transport ; Ocean dynamics
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  • 24
    Publication Date: 2017-01-05
    Description: New National School Lunch Program (NSLP) guidelines aim to reduce sodium and saturated fats, limit calories, and eliminate trans-fat and whole milk. This paper provides a novel approach to understanding how the healthfulness of NSLP participants’ entrée selections varies across socioeconomic and demographic groups. Unlike previous studies that rely on dietary recalls, we use a mixed logit model to examine students’ entrée choices in a school cafeteria. We estimate the likelihood that an entrée is selected from the available lunch choices as a function of the entrée’s nutrients (fat, carbohydrate, protein, and sodium) and entrée’s taste profile characteristics (e.g., Mexican, Pizza-like), as well as the student’s socio-economic and demographic characteristics. Using these estimates, we examine how changing the nutritional content of an offering impacts the probability of selecting each of the offerings. Free lunch recipients are more likely to choose entrées higher in fat but lower in sodium than other students. Full-price lunch recipients are the most responsive to changes in nutritional content of the offerings and are most likely to respond to changes in the nutritional content of the offered entrées by substituting a lunch brought from home for the school-purchased lunch. Replacing less healthy menu items with popular but healthier items reduces the selection of total calories, calories from fat, and sodium by approximately 4%, 18%, and 8%, respectively, over the study period. The new guidelines should be effective at improving the nutrition of school-age children, and potentially reducing childhood obesity, provided NSLP participation does not decline appreciably.
    Keywords: D12 - Consumer Economics: Empirical Analysis, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 25
    Publication Date: 2017-01-05
    Description: We estimate the effects of changes in cotton adoption on children’s schooling and child labor in rural Burkina Faso. Using time and spatial variations, we find evidence that expansion of cotton farming has led to an increase in enrollment and to a reduction of participation in child labor for girls. There are, however, no detectable effects on boys. In theory, cotton adoption could increase household income, leading to increased demand for schooling and reduced child labor. On the other hand, because children are productive on cotton farms, adoption of cotton could increase the opportunity cost of child time and the demand for child labor. We provide suggestive evidence showing that boys are more productive than girls on cotton farms. Taken together, the results suggest that the income effect from cotton adoption might have been larger than the wage effect for girls, hence the overall positive impacts on school enrollment for girls.
    Keywords: O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, O15 - Human Resources ; Human Development ; Income Distribution ; Migration, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 26
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2913–2932, doi:10.1175/JPO-D-14-0179.1.
    Description: The oceanic deep circulation is shared between concentrated deep western boundary currents (DWBCs) and broader interior pathways, a process that is sensitive to seafloor topography. This study investigates the spreading and deepening of Denmark Strait overflow water (DSOW) in the western subpolar North Atlantic using two ° eddy-resolving Atlantic simulations, including a passive tracer injected into the DSOW. The deepest layers of DSOW transit from a narrow DWBC in the southern Irminger Sea into widespread westward flow across the central Labrador Sea, which remerges along the Labrador coast. This abyssal circulation, in contrast to the upper levels of overflow water that remain as a boundary current, blankets the deep Labrador Sea with DSOW. Farther downstream after being steered around the abrupt topography of Orphan Knoll, DSOW again leaves the boundary, forming cyclonic recirculation cells in the deep Newfoundland basin. The deep recirculation, mostly driven by the meandering pathway of the upper North Atlantic Current, leads to accumulation of tracer offshore of Orphan Knoll, precisely where a local maximum of chlorofluorocarbon (CFC) inventory is observed. At Flemish Cap, eddy fluxes carry ~20% of the tracer transport from the boundary current into the interior. Potential vorticity is conserved as the flow of DSOW broadens at the transition from steep to less steep continental rise into the Labrador Sea, while around the abrupt topography of Orphan Knoll, potential vorticity is not conserved and the DSOW deepens significantly.
    Description: This work is supported by ONR Award N00014-09-1-0587, the NSF Physical Oceanography Program, and NASA Ocean Surface Topography Science Team Program.
    Description: 2016-06-01
    Keywords: Circulation/ Dynamics ; Abyssal circulation ; Boundary currents ; Ocean circulation ; Ocean dynamics ; Potential vorticity ; Topographic effects
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 27
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. 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 46 (2016): 361–367, doi:10.1175/JPO-D-15-0171.1.
    Description: Idealized laboratory experiments investigate the glacier–ocean boundary dynamics near a vertical glacier in a two-layer stratified fluid. Discharge of meltwater runoff at the base of the glacier (subglacial discharge) enhances submarine melting. In the laboratory, the effect of multiple sources of subglacial discharge is simulated by introducing freshwater at freezing temperature from two point sources at the base of an ice block representing the glacier. The buoyant plumes of cold meltwater and subglacial discharge water entrain warm ambient water, rise vertically, and interact within a layer of depth H2 if the distance between the sources x0 is smaller than H2α/0.35, where α is the entrainment constant. The plume water detaches from the glacier face at the interface between the two layers and/or at the free surface, as confirmed by previous numerical studies and field observations. A plume model is used to explain the observed nonmonotonic dependence of submarine melting on the sources’ separation. The distance between the two sources influences the entrainment of warm water in the plumes and consequently the amount of submarine melting and the final location of the meltwater within the water column. Two interacting plumes located very close together are observed to melt approximately half as much as two independent plumes. The inclusion, or parameterization, of the dynamics regulating multiple plumes’ interaction is therefore necessary for a correct estimate of submarine melting. Hence, the distribution and number of sources of subglacial discharge may play an important role in glacial melt rates and fjord stratification and circulation.
    Description: Support to C.C. was given by the NSF Project OCE-1130008 and OCE-1434041. V.M.G. received support from the “Gori” Fellowship.
    Description: 2016-07-01
    Keywords: Geographic location/entity ; Glaciers ; Circulation/ Dynamics ; Buoyancy ; Entrainment ; Ocean dynamics ; Small scale processes ; Models and modeling ; Laboratory/physical models
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  • 28
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PeerJ 4 (2016): e1839, doi:10.7717/peerj.1839.
    Description: High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.
    Description: This work was supported by the Frank R. Lillie Research Innovation Award, and startup funds from the University of Chicago.
    Keywords: Genomics ; Assembly ; Curation ; Visualization ; Contamination ; HGT
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  • 29
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    Unknown
    American Meteorological Society
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2016. 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 46 (2016): 1277-1284, doi:10.1175/JPO-D-16-0027.1.
    Description: The contemporary Arctic Ocean differs markedly from midlatitude, ice-free, and relatively warm oceans in the context of density-compensating temperature and salinity variations. These variations are invaluable tracers in the midlatitudes, revealing essential fundamental physical processes of the oceans, on scales from millimeters to thousands of kilometers. However, in the cold Arctic Ocean, temperature variations have little effect on density, and a measure of density-compensating variations in temperature and salinity (i.e., spiciness) is not appropriate. In general, temperature is simply a passive tracer, which implies that most of the heat transported in the Arctic Ocean relies entirely on the ocean dynamics determined by the salinity field. It is shown, however, that as the Arctic Ocean warms up, temperature will take on a new role in setting dynamical balances. Under continued warming, there exists the possibility for a regime shift in the mechanisms by which heat is transported in the Arctic Ocean. This may result in a cap on the storage of deep-ocean heat, having profound implications for future predictions of Arctic sea ice.
    Description: Support was provided by the National Science Foundation Division of Polar Programs Award 1350046 and Office of Naval Research Grant Number N00014-12-1-0110.
    Description: 2016-10-05
    Keywords: Geographic location/entity ; Arctic ; Circulation/ Dynamics ; Ocean dynamics
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  • 30
    Publication Date: 2016-07-09
    Description: Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 31
    Publication Date: 2016-07-28
    Description: Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.
    Keywords: Genomics
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    Topics: Biology
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  • 32
    Publication Date: 2016-01-09
    Description: Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.
    Keywords: Genomics
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  • 33
    Publication Date: 2016-08-20
    Description: Concerns about the growing prevalence of obesity worldwide have led researchers and policy makers to investigate the potential health impact of fiscal policies such as taxes on unhealthy foods. A common instrument used to measure the relationship between food prices and food consumption is the price elasticity of demand. Using meta-regression analysis we assessed how differences in methodological approaches to estimating demand affected food price elasticities. Most methodological differences had a statistically significant impact on elasticity estimates, which stresses the importance of using meta-estimates or testing the sensitivity of simulation outcomes to a range of elasticity parameters before drawing policy conclusions.
    Keywords: D11 - Consumer Economics: Theory, H31 - Household, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 34
    Publication Date: 2016-08-20
    Description: Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an i ntegrative and d iscriminative e pigenome a nnotation s ystem, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.
    Keywords: Genomics
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  • 35
    Publication Date: 2016-09-03
    Description: A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 x 10 –4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 x 10 –5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS 1 , IS 2 , IS 5 and IS 186 . Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS 186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.
    Keywords: Genomics
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  • 36
    Publication Date: 2016-08-20
    Description: This paper reviews the situation in the agricultural sector and food security in Cuba, and particularly the transformations that have (not) taken place since 1990. We compare the Cuban transition with transitions in other "transition countries" and show that Cuba does not easily fit into one of the transition patterns, and, in a way, has characteristics of "a bit of everything". To conclude, we discuss the (potential) effects of the recent policy changes and the new economic reforms that were announced.
    Keywords: O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, P21 - Planning, Coordination, and Reform, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 37
    Publication Date: 2016-07-09
    Description: If agricultural subsidies are largely capitalized into farmland values through their effect on rental rates, then expanding support for agriculture may not benefit farmers who rent the land they farm. Existing evidence on the incidence of subsidies on cash rental rates is mixed. Identification is obscured by unobserved or imprecisely measured factors that tend to be correlated with subsidies, especially land quality and time-varying factors like commodity prices and adverse weather events. A problem that has received less attention is the fact that subsidies and land quality on rented land may differ from owned land. Since most farms possess both rented and owned acreage, farm-level measures of subsidies, land values, and rental rates may bias estimated incidence. Using a new, field-level data set that, for the first time, precisely links subsidies to land parcels, we show that this bias is considerable: where farm-level estimates suggest an incidence of 42–49 cents of the marginal subsidy dollar, field-level estimates from the same farms indicate that landlords capture just 20–28 cents. The size of the farm and the duration of the rental arrangement have substantial effects. Incidence falls by 5–15 cents when doubling total operated acres, and the incidence falls by 0.1–0.8 cents with each additional year of the rental arrangement. Low incidence of subsidies on rents combined with the farm-size and duration effects suggest that farmers renting land have monopsony power.
    Keywords: H22 - Incidence, Q14 - Agricultural Finance, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
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    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 38
    Publication Date: 2016-07-09
    Description: Many countries adjust their trade policies counter-cyclically with food prices, to the extent that the use of restrictions by food-exporting countries has occasionally threatened the food security of food-importing countries. These trade policies are inconsistent with the terms-of-trade motivation often retained to characterize the payoff frontier of self-enforcing trade agreements, as they can worsen the terms of trade of the countries that apply them. This article analyzes trade policy coordination when trade policies are driven by terms-of-trade effects and a desire to reduce domestic food price volatility. This framework implies that importing and exporting countries have incentives to deviate from cooperation at different periods: the latter when prices are high and the former when prices are low. Since staple food prices tend to have asymmetric distributions, with more prices below than above the mean but with occasional spikes, a self-enforcing agreement generates asymmetric outcomes. Without cooperation, an importing country uses its trade policy more frequently because of the concentration of prices below the mean, but an exporting country has a greater incentive to deviate from a cooperative trade policy because positive deviations from the mean price are larger than negative ones. Thus, the asymmetry of the distribution of commodity prices can make it more difficult to discipline export taxes than tariffs in trade agreements.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 39
    Publication Date: 2016-07-09
    Description: We analyze the effects of the interactions that the two pillars of the European Union Common Agricultural Policy—market support and rural development—have on farmers’ uptake of organic farming practices. Special attention is given to the 2003 reform, which substantially altered the relative importance of the two types of support by decoupling direct agricultural payments from the production of a specific crop. In our empirical analysis we study the case of Sweden, making use of the variation in the timing of farmers’ decisions regarding participation in support programs. We estimate a dynamic non-linear unobserved effects probit model to account for unobserved individual heterogeneity and state dependence. Our results indicate the existence of a negative effect of the market support system in place when organic farming techniques were adopted before the 2003 reform. However, this effect is reversed by the introduction of decoupling. Furthermore, the effects of support differ between certified and non-certified organic production: both pillars have significant effects on non-certified organic farming, whereas certified organic farming is exclusively driven by agro-environmental subsidies.
    Keywords: C23 - Models with Panel Data, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 40
    Publication Date: 2016-02-20
    Description: Genetic variants in or near miRNA genes can have profound effects on miRNA expression and targeting. As user-friendly software for the impact prediction of miRNA variants on a large scale is still lacking, we created a tool called miRVaS. miRVaS automates this prediction by annotating the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) and by annotating all predicted structural changes within the miRNA due to the variant. In addition, the tool defines the most important region that is predicted to have structural changes and calculates a conservation score that is indicative of the reliability of the structure prediction. The output is presented in a tab-separated file, which enables fast screening, and in an html file, which allows visual comparison between wild-type and variant structures. All separate images are provided for downstream use. Finally, we tested two different approaches on a small test set of published functionally validated genetic variants for their capacity to predict the impact of variants on miRNA expression.
    Keywords: Genomics
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  • 41
    Publication Date: 2016-02-20
    Description: Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts ( trans -spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (〉98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans -spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans -spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
    Keywords: Genomics
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  • 42
    Publication Date: 2016-05-20
    Description: Visualization of chromosomal dynamics is important for understanding many fundamental intra-nuclear processes. Efficient and reliable live-cell multicolor labeling of chromosomal loci can realize this goal. However, the current methods are constrained mainly by insufficient labeling throughput, efficiency, flexibility as well as photostability. Here we have developed a new approach to realize dual-color chromosomal loci imaging based on a modified single-guide RNA (sgRNA) of the CRISPR/Cas9 system. The modification of sgRNA was optimized by structure-guided engineering of the original sgRNA, consisting of RNA aptamer insertions that bind fluorescent protein-tagged effectors. By labeling and tracking telomeres, centromeres and genomic loci, we demonstrate that the new approach is easy to implement and enables robust dual-color imaging of genomic elements. Importantly, our data also indicate that the fast exchange rate of RNA aptamer binding effectors makes our sgRNA-based labeling method much more tolerant to photobleaching than the Cas9-based labeling method. This is crucial for continuous, long-term tracking of chromosomal dynamics. Lastly, as our method is complementary to other live-cell genomic labeling systems, it is therefore possible to combine them into a plentiful palette for the study of native chromatin organization and genome ultrastructure dynamics in living cells.
    Keywords: Genomics
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  • 43
    Publication Date: 2016-05-19
    Description: Whether direct farmer-to-consumer outlets compete with supermarkets on produce prices remains an empirical question; marketing costs are not consistently higher in one retail channel or the other. This study compared prices of 29 fruits and vegetables across North Carolina farmers’ markets, roadside stands, and supermarkets. Larger farmers’ markets had higher prices: three fruits and one vegetable were cheaper at a direct outlet, while four vegetables were cheaper at supermarkets. Weighting item prices by consumption share attenuated differences in mean price across outlets. Direct-retail outlets are price competitive and should be considered among other tools to boost fresh fruit and vegetable intake.
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 44
    Publication Date: 2016-05-19
    Description: This paper investigates how the Fresh Fruit and Vegetable Program (FFVP), a nutrition assistance program that provides funding for the distribution of free fresh fruits and vegetables to students in participating schools, affects childhood obesity using a panel data set of Arkansas public schoolchildren with two different approaches. First, we combine matching methodology and difference-in-differences (DID) analysis. Second, we use the synthetic control method to compare each FFVP participating school to a similar, albeit synthetic, control school. Both analyses show that FFVP program causes an economically meaningful reduction in the obesity outcome of participating children.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 45
    Publication Date: 2016-05-19
    Description: This study considers the transition into farming and growth of new farmers in U.S. agriculture by examining land ownership and leasing trends. Our approach is to characterize the entire distribution by farmer age and farmer experience rather than using young versus old and beginning versus established farmer categories. We also use a linked-farms longitudinal approach to show trends over time in farmland expansion and contraction. We find that farms operated by older beginning farmers tend to be smaller and do not tend to grow over time. Our results show that it is mostly young farmers as opposed to all beginning farmers who rapidly expand their farm operations after entering agriculture. Our findings inform policy makers about the strategies that young and beginning farmers use to start their businesses and expand over time, and suggest more effective approaches for targeting loan programs to both young and beginning farmers.
    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
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 46
    Publication Date: 2016-04-24
    Description: We estimate the impact of Malawi's Farm Input Subsidy Program using an economy-wide approach. This approach yields benefit-cost ratios about 60% higher than existing partial equilibrium studies, a result of our accounting for indirect benefits. Fertilizer response rates remain the determining parameter for benefit-cost ratio levels. Even with lower-end response rates, the program is pro-poor and generates double-dividends through higher and more drought-resilient yields. Overall, for macro-economically significant programs, our approach strongly complements survey-based evaluations. For Malawi, our results buttress arguments for a focus on program improvements.
    Keywords: C68 - Computable General Equilibrium Models, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, O22 - Project Analysis, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 47
    Publication Date: 2016-04-24
    Description: "Agriculture by contract" ( $\hbox {A}\times \hbox {C}$ ) is the main Mexican government program aimed at mitigating price risks for agricultural producers in Mexico. $\hbox {A} \times \hbox {C}$ has unique features involving forward contracts and the provision of basis subsidies and subsidized exchange-traded futures options for both producers and intermediaries. A simulation model is developed to analyze the market and welfare effects of $\hbox {A}\times \hbox {C}$ . When applied to corn, results show that $\hbox {A}\times \hbox {C}$ exerts substantial impacts and causes large transfers across sectors. Even if $\hbox {A}\times \hbox {C}$ reduced intermediaries' market power to the largest extent feasible, results indicate that it would still cause important losses in aggregate welfare.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 48
    Publication Date: 2016-03-31
    Description: The Agricultural Act of 2014 solidified insurance as the cornerstone of U.S. agricultural policy. The Congressional Budget Office (2014) estimates that this act will increase spending on agricultural insurance programs by $5.7 billion to a total of $89.8 billion over the next decade. In light of the sizable resources directed toward these programs, accurate rating of insurance contracts is of the utmost importance to producers, private insurance companies, and the federal government. Unlike most forms of insurance, agricultural insurance is plagued by a paucity of spatially correlated data. A novel interpretation of Bayesian Model Averaging is used to estimate a set of possibly similar densities that offers greater efficiency if the set of densities are similar while seemingly not losing any if the set of densities are dissimilar. Simulations indicate that finite sample performance—in particular small sample performance—is quite promising. The proposed approach does not require knowledge of the form or extent of any possible similarities, is relatively easy to implement, admits correlated data, and can be used with either parametric or nonparametric estimators. We use the proposed approach to estimate U.S. crop insurance premium rates for area-type programs and develop a test to evaluate its efficacy. An out-of-sample game between private insurance companies and the federal government highlights the policy implications for a variety of crop-state combinations. Consistent with the simulation results, the performance of the proposed approach with respect to rating area-type insurance—in particular small sample performance—remains quite promising.
    Keywords: Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 49
    Publication Date: 2016-03-31
    Description: Distributing healthy food is an important goal for hunger relief agencies, but they face many challenges in meeting it. Budgets for purchasing food are limited, and hunger relief agencies often have little influence over the nutritional quality of food they receive through donations. In a recent study, Healthy Eating Index (HEI) scores were calculated monthly using electronic invoice data for food shelves served by two major food banks in Minnesota. While the HEI is directly related to nutrition guidelines and provides great detail in its scoring, implementation requires careful measurement and classification of foods and a rather complex set of calculations. In addition, a significant portion of food distributed by food banks is mixed pallets of free "miscellaneous" that cannot readily be included in HEI calculations. We propose and test a less data- and labor-intensive measure for characterizing the healthfulness of food distributed by hunger relief agencies. This new measure, the Hunger Relief Nutrition Index (HRNI), facilitates nutritional assessment of miscellaneous foods, allows for easy aggregation of healthfulness scores across food sources and time periods, and correlates well with the HEI.
    Keywords: C81 - Methodology for Collecting, Estimating, and Organizing Microeconomic Data, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 50
    Publication Date: 2016-03-31
    Description: Gleaning is increasingly attracting the attention of food safety networks, including food banks, as a valuable tool that simultaneously reduces food loss and alleviates food insecurity. However, managing gleaning operations can be challenging because the arrival of gleaning opportunities and the attendance of gleaner volunteers are both stochastic. We develop a stochastic optimization model to characterize and optimize a gleaning operation. The food bank chooses the gleaning schedule, which affects the gleaner capacity and the number of gleaning opportunities scheduled. In a specific field study of the Food Bank of the Southern Tier in New York, we analyze the tradeoff between call and volume service levels to find the optimum schedule that maximizes the expected total volume gleaned. Moreover, we find that increasing the gleaning window and increasing slot availability can be used as substitute mechanisms for increasing the total volume gleaned. Additionally, we use our model to assess the impact of recruiting more volunteer gleaners.
    Keywords: C61 - Optimization Techniques ; Programming Models ; Dynamic Analysis, C63 - Computational Techniques, D24 - Production ; Cost ; Capital and Total Factor Productivity ; Capacity, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 51
    Publication Date: 2016-02-10
    Description: The longstanding "cash versus food" debate has received renewed attention in both research and practice. This paper reviews key issues shaping the debate and presents new evidence from randomized and quasi-experimental evaluations that deliberately compare cash and in-kind food transfers in ten developing counties. Findings show that relative effectiveness cannot be generalized: although some differences emerge in terms of food consumption and dietary diversity, average impacts tend to depend on context, specific objectives, their measurement, and program design. Costs for cash transfers and vouchers tend to be significantly lower relative to in-kind food. Yet the consistency and robustness of methods for efficiency analyses varies greatly.
    Keywords: D61 - Allocative Efficiency ; Cost-Benefit Analysis, H53 - Government Expenditures and Welfare Programs, O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0257-3032
    Electronic ISSN: 1564-6971
    Topics: Economics
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  • 52
    Publication Date: 2016-10-28
    Description: Many smallholder families are exceptionally prone to potentially catastrophic decreases in their incomes and access to food. Over the past decade, therefore, policy makers and economists have increasingly focused on potential mechanisms for expanding risk management strategies available to those families. Commercially provided weather-based index insurance products, perhaps partially funded by subsidies, have been of particular interest because of their apparent potential to provide payments to smallholder families when they are most in need of help. However, the empirical evidence from a wide range of studies indicates that, absent relatively substantial subsidies, small holder farmers will not purchase commercially priced index products or even "all risk" products where payments are tied to the farm's crop losses. There are three important reasons why this is the case. First, smallholder farmers already have many ways of managing their risks, including informal community-based initiatives, on-farm production decisions and off-farm work. Second, index insurance schemes are subject to considerable basis risk; families often do not receive an index insurance indemnity when they experience a substantial crop loss on their farms. Third, the fixed costs of delivering crop insurance to smallholders make such coverage expensive. The potential market for weather index insurance therefore may be limited to insuring relatively large groups of farmers, either directly or indirectly though providing micro finance and other lending institution with coverage against widespread loan defaults associated with catastrophic events like major droughts. Alternatively, weather indexes could simply be used to more accurately target emergency aid.
    Keywords: D61 - Allocative Efficiency ; Cost-Benefit Analysis, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0257-3032
    Electronic ISSN: 1564-6971
    Topics: Economics
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  • 53
    Publication Date: 2016-11-01
    Description: Presence of excess unaltered, wild-type (WT) DNA providing no information of biological or clinical value often masks rare alterations containing diagnostic or therapeutic clues in cancer, prenatal diagnosis, infectious diseases or organ transplantation. With the surge of high-throughput technologies there is a growing demand for removing unaltered DNA over large pools-of-sequences. Here we present nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO), a single-step approach with broad genome coverage that can remove WT-DNA from numerous sequences simultaneously, prior to genomic analysis. NaME-PrO employs a double-strand-DNA-specific nuclease and overlapping oligonucleotide-probes interrogating WT-DNA targets and guiding nuclease digestion to these sites. Mutation-containing DNA creates probe-DNA mismatches that inhibit digestion, thus subsequent DNA-amplification magnifies DNA-alterations at all selected targets. We demonstrate several-hundred-fold mutation enrichment in diverse human samples on multiple clinically relevant targets including tumor samples and circulating DNA in 50-plex reactions. Enrichment enables routine mutation detection at 0.01% abundance while by adjusting conditions it is possible to sequence mutations down to 0.00003% abundance, or to scan tumor-suppressor genes for rare mutations. NaME-PrO introduces a simple and highly parallel process to remove un-informative DNA sequences and unmask clinically and biologically useful alterations.
    Keywords: Genomics
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  • 54
    Publication Date: 2016-08-20
    Description: How much has food abundance, attributable to U.S. public agricultural R&D, contributed to high and rising U.S. obesity rates? In this paper we investigate the effects of public investment in agricultural R&D on food prices, per capita calorie consumption, adult body weight, obesity, public healthcare expenditures related to obesity, and consumer welfare. We find that a 10% increase in the stream of annual U.S. public investment in agricultural R&D in the latter half of the twentieth century would have caused a modest increase in the average daily calorie consumption of American adults, resulting in small increases in public healthcare expenditures related to obesity. On the other hand, such an increase in spending would have generated very substantial consumer benefits, and net national benefits, given the very large benefit-cost ratios for agricultural R&D. This implies that current policy objectives of revising agricultural R&D priorities to pursue obesity objectives are likely to be comparatively unproductive and socially wasteful. Moreover, R&D lags of decades mean that such an approach would be totally ineffective in the immediate horizon.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 55
    Publication Date: 2016-12-07
    Description: This article reports spending results for the USDA's Healthy Incentives Pilot (HIP), which tested a 30% incentive on fruit and vegetable purchases with Supplemental Nutrition Assistance Program (SNAP) benefits. Self-reported mean usual monthly spending for all fruits and vegetables was $6.15 higher for randomly assigned HIP participant households than for a control group. Much of the additional spending appears to have taken place in ways that did not earn the incentive—spending with non-SNAP resources or in retailers that did not participate in HIP. This article investigates mechanisms that might explain the HIP impact on fruit and vegetable purchases that did not earn the incentive.
    Keywords: Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 56
    Publication Date: 2016-12-01
    Description: The RAG1/RAG2 endonuclease initiates V(D)J recombination at antigen receptor loci but also binds to thousands of places outside of these loci. RAG2 localizes directly to lysine 4 trimethylated histone 3 (H3K4me3) through a plant homeodomain (PHD) finger. The relative contribution of RAG2-dependent and RAG1-intrinsic mechanisms in determining RAG1 binding patterns is not known. Through analysis of deep RAG1 ChIP-seq data, we provide a quantitative description of the forces underlying genome-wide targeting of RAG1. Surprisingly, sequence-specific DNA binding contributes minimally to RAG1 targeting outside of antigen receptor loci. Instead, RAG1 binding is driven by two distinct modes of interaction with chromatin: the first is driven by H3K4me3, promoter-focused and dependent on the RAG2 PHD, and the second is defined by H3K27Ac, enhancer-focused and dependent on ‘non-core’ portions of RAG1. Based on this and additional chromatin and genomic features, we formulated a predictive model of RAG1 targeting to the genome. RAG1 binding sites predicted by our model correlate well with observed patterns of RAG1-mediated breaks in human pro-B acute lymphoblastic leukemia. Overall, this study provides an integrative model for RAG1 genome-wide binding and off-target activity and reveals a novel role for the RAG1 non-core region in RAG1 targeting.
    Keywords: Genomics
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    Topics: Biology
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  • 57
    Publication Date: 2016-12-07
    Description: The food packages provided by the Supplemental Nutrition Program for Women, Infants, and Children (WIC) program changed in 2009. This article examines purchases of whole grain products before and after the change. Nielsen Homescan panel data from 2008 to 2010 provide information on households’ food purchases, demographics, and self-reported WIC participation status. We estimate the effect of WIC participation and the 2009 package change on whole grains purchases using a difference-in-difference method, and find that participation in the WIC program was associated with more whole grain purchases during the observed period; the package change in 2009 roughly doubled the associated effect of WIC participation on the purchases of whole grain products. These results are consistent with recommendations in the Dietary Guidelines for Americans and suggest that moderate innovations in the design of food assistance programs can lead to beneficial dietary choices.
    Keywords: D10 - General, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 58
    Publication Date: 2016-12-07
    Description: As US beef and pork prices approached record high levels in 2014, industry analysts expressed surprised at consumer response. Because the relative price swings have occurred only recently, traditional approaches to demand analysis that rely on historical data series may be less useful than is typically the case. Employing one of the largest and longest-running choice experiments, we analyze data on 110,295 choices made by 12,255 consumers observed over a year-long time period coinciding with historically high meat prices. Our findings reveal nonlinear demands for meat products, with demand being more inelastic at higher prices. Ground beef, steak, and pork chop demands are more sensitive to changes in chicken breast price than the reverse. Moreover, cross-price elasticities between disaggregate meat products shrink as prices rise. Consumers' incomes significantly affect demand inter-relationships. Higher income consumers are more likely to choose steak and chicken breasts and are less likely to choose ground beef, chicken wings, and deli ham than are lower income consumers. High-income consumers tend to be less responsive to own-price changes and more responsive to cross-price changes than lower income consumers. This analysis provides estimates of structural demand parameters that help explain current meat expenditure patterns, and the results have implications for the assumption of linearity often invoked in policy analyses. 
    Keywords: C83 - Survey Methods ; Sampling Methods, D12 - Consumer Economics: Empirical Analysis, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q18 - Agricultural Policy ; Food Policy
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    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 59
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 1410–1425, doi:10.1175/JPO-D-14-0192.1.
    Description: The west-to-east crossover of boundary currents has been seen in mean circulation schemes from several past models of the Red Sea. This study investigates the mechanisms that produce and control the crossover in an idealized, eddy-resolving numerical model of the Red Sea. The authors also review the observational evidence and derive an analytical estimate for the crossover latitude. The surface buoyancy loss increases northward in the idealized model, and the resultant mean circulation consists of an anticyclonic gyre in the south and a cyclonic gyre in the north. In the midbasin, the northward surface flow crosses from the western boundary to the eastern boundary. Numerical experiments with different parameters indicate that the crossover latitude of the boundary currents changes with f0, β, and the meridional gradient of surface buoyancy forcing. In the analytical estimate, which is based on quasigeostrophic, β-plane dynamics, the crossover is predicted to lie at the latitude where the net potential vorticity advection (including an eddy component) is zero. Various terms in the potential vorticity budget can be estimated using a buoyancy budget, a thermal wind balance, and a parameterization of baroclinic instability.
    Description: This work is supported by Award USA 00002, KSA 00011, and KSA 00011/02 made by King Abdullah University of Science and Technology (KAUST), by National Science Foundation Grants OCE0927017, OCE1154641, and OCE85464100, and by the Woods Hole Oceanographic Institution Academic Program Office.
    Description: 2015-11-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Buoyancy ; Ocean circulation ; Ocean dynamics
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 60
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 1822–1842, doi:10.1175/JPO-D-14-0147.1.
    Description: Influences of time-dependent precipitation on water mass transformation and heat budgets in an idealized marginal sea are examined using theoretical and numerical models. The equations proposed by Spall in 2012 are extended to cases with time-dependent precipitation whose form is either a step function or a sinusoidal function. The theory predicts the differences in temperature and salinity between the convective water and the boundary current as well as the magnitudes of heat fluxes into the marginal sea and across the sea surface. Moreover, the theory reveals that there are three inherent time scales: relaxation time scales for temperature and salinity and a precipitation time scale. The relaxation time scales are determined by a steady solution of the theoretical model with steady precipitation. The relaxation time scale for temperature is always smaller than that for salinity as a result of not only the difference in the form of fluxes at the surface but also the variation in the eddy transport from the boundary current. These three time scales and the precipitation amplitude determine the strength of the ocean response to changes in precipitation and the phase relation between precipitation, changes in salinity and temperature, and changes in heat fluxes. It is demonstrated that the theoretical predictions agree qualitatively well with results from the eddy-resolving numerical model. This demonstrates the fundamental role of mesoscale eddies in the ocean response to time-dependent forcing and provides a framework with which to assess the extent to which observed variability in marginal sea convection and water mass transformation are consistent with an external forcing by variations in precipitation.
    Description: This work was initiated at the 2013 WHOI Geophysical Fluid Dynamics Summer Program, which was supported by the National Science Foundation and the Office of Naval Research. This work was also supported by Grant-in-Aid for Research Fellow (25·8466) of the Ministry of Education, Culture, Sports and Technology (MEXT), Japan, the Program for Leading Graduate Schools, MEXT, Japan (YY), and by the National Science Foundation Grant OCE-1232389 (MAS).
    Description: 2016-01-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Deep convection ; Eddies ; Ocean dynamics ; Atm/Ocean Structure/ Phenomena ; Precipitation
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 61
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2806–2819, doi:10.1175/JPO-D-15-0061.1.
    Description: An eastward-flowing current of a homogeneous fluid with velocity U, contained in a channel of width L, impinges on an island of width of O(L), and the resulting interaction and dynamics are studied for values of the supercriticality parameter, b = βL2/U, both larger and smaller than π2. The former case is subcritical with respect to Rossby waves, and the latter is supercritical. The nature of the flow field depends strongly on b, and in particular, the nature of the flow around the island and the proportion of the flow passing to the north or south of the island are sensitive to b and to the position of the island in the channel. The problem is studied analytically in a relatively simple, nonlinear quasigeostrophic and adiabatic framework and numerically with a shallow-water model that allows a qualitative extension of the results to the equator. Although the issues involved are motivated by the interaction of the Equatorial Undercurrent and the Galapagos Islands, the analysis presented here focuses on the fundamental issue of the distinctive nature of the flow as a function of Rossby wave criticality.
    Description: Supported by the National Science Foundation Grant OCE-0959381.
    Description: 2016-05-01
    Keywords: Circulation/ Dynamics ; Ocean circulation ; Ocean dynamics ; Waves, oceanic
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 62
    Publication Date: 2015-08-11
    Description: The Special Supplemental Nutrition Program for Women, Infants and Children (WIC) Program is a key part of America's safety net, but its structure fails to incentivize participants to be cost-conscious in their purchases and may cause retailers to attach excessive markups to WIC products. We investigate cost containment in the WIC Program, with a focus on California. Results show that smaller vendors often charge considerably higher prices for WIC foods than their larger counterparts. However, larger vendors do not mark up WIC foods more or promote them less than comparable control products. Cost containment can be improved by targeting WIC Program sales to larger vendors when it is possible to do so without compromising participant access, and using large-vendor prices as a benchmark to limit prices set by smaller vendors.
    Keywords: D12 - Consumer Economics: Empirical Analysis, I38 - Government Policy ; Provision and Effects of Welfare Programs, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 63
    Publication Date: 2015-09-19
    Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 64
    Publication Date: 2015-08-29
    Description: Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.
    Keywords: Genomics
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  • 65
    Publication Date: 2015-05-29
    Description: A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines G enomic O rigins T hrough T axonomic CHA llenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.
    Keywords: Genomics
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  • 66
    Publication Date: 2015-05-26
    Description: With the enactment of Regulation (EC) No. 1924/2006, 20 December 2006, ‘ On nutrition and health claims made on foods ’ several health claims can no longer be used on food products in European markets. We simulate the overall impact of the regulation on consumers and producers using the Italian yogurt market as a case study, and data prior to the introduction of the policy. We quantify welfare losses incurred if accepted claims were false, and simulate scenarios where rejected truthful health claims are removed, considering also the case where the products carrying them exit the market. We find that consumers can incur large welfare losses if approved claims are untruthful; if truthful claims are instead denied both consumers and producers may incur losses, with consumers being penalised more than producers.
    Keywords: L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, M38 - Government Policy and Regulation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 67
    Publication Date: 2015-05-12
    Description: China has long struggled to achieve food security. In the era of a planned economy, local self-sufficiency was dictated by policy. With China's transition to a market economy, however, different policy schemes have been utilized, with greater emphasis placed on the role of market forces, especially in conjunction with China's accession to the World Trade Organization in 2001. Nevertheless, self-sufficiency in grain production remains a deeply rooted goal, and interventionist measures geared towards its achievement are still viewed as the most direct and effective means of food security. This paper examines how the well-being of China's rural population, proxied by measures of food consumption, is affected by the promotion of grain production. Our findings suggest that targeted households bear a disproportionate burden of food security policy, as it is currently implemented.
    Keywords: O12 - Microeconomic Analyses of Economic Development, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 68
    Publication Date: 2015-05-12
    Description: Policymakers have dedicated increasing attention to whether Americans have access to healthful food. As a result, various methods for measuring food store access at the national level have been developed to identify areas that lack access. However, these methods face definitional, data, and methodological limitations. The focus on neighborhoods instead of individuals underestimates the barriers that some individuals face in accessing healthy food, and overestimates the problem in other neighborhoods. This paper reviews and critiques currently available national-level measures of food access. While multiple measures of food access are needed to understand the problem, we recommend greater attention be paid to individual measures of food store access.
    Keywords: I14 - Health and Inequality, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 69
    Publication Date: 2015-05-12
    Description: The Canadian farm share for five crop-based products and seven livestock-based products from 1997 to 2010 is calculated using a supply chain IO analysis. Significant differences exist in farm shares across food commodities with higher farm shares for livestock products and lower farm shares for grain-based products. The decline in the Canadian farm share for food consumed at home is driven in large part by the food purchasing habits of consumers. This paper also addresses the hypothesis that the decline in the Canadian farm share could be partially driven by rising input costs in post-farmgate processes or rising input costs that have greater impact on downstream sectors than primary agricultural producers. Three experiments were conducted to assess the impact of an increase in the cost of corn, energy, and farm labor would have on commodity output prices, farm returns, food expenditure, and farm share. In all three cases, the overall farm share increases, albeit by a small amount, suggesting that these shocks have a larger relative impact on the prices of agricultural commodities than the prices of marketing commodities used in post-farmgate activities. A two-period comparison of these simulations shows that energy (corn and farm labour) price shocks would have had a greater (lower) impact on the farm share in 2007 than 1997.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 70
    Publication Date: 2015-05-12
    Description: Household food insecurity in the United States has reached its highest levels to date. As public and private initiatives have emerged to help improve diets by fostering access to food, the availability of more food stores may result in lower levels of food insecurity. In this article, we assess the relationship between adult food insecurity and food store density in metropolitan areas of the United States. We find that while small grocery/convenience stores show a mitigating effect on adult food insecurity across different samples of households, the effects of large supermarkets/grocery stores and supercenters vary. We also find that Supplemental Nutrition Assistance Program participation and food access can have a simultaneously beneficial effect in reducing adult food insecurity. Implications for policies aiming to improve food security by fostering access to food stores are discussed.
    Keywords: I14 - Health and Inequality, L81 - Retail and Wholesale Trade ; e-Commerce, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 71
    Publication Date: 2015-04-02
    Description: With read lengths of currently up to 2 x 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.
    Keywords: Genomics
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  • 72
    Publication Date: 2015-04-02
    Description: RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se , other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
    Keywords: Genomics
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  • 73
    Publication Date: 2015-12-29
    Description: This article empirically investigates the impact of trade barriers on the world wine trade focusing on trade costs impeding exports, including transport, tariffs, technical barriers and sanitary and phytosanitary (SPS) standards. A gravity model is estimated using data from the main importing and exporting countries for the years 1997–2010. The Poison pseudo-maximum likelihood estimator accounts for heteroskedasticity and the presence of zero trade flows. Our results identify which regulations can adversely affect trade providing useful information to policy-makers involved in negotiations on trade frictions. While SPS measures do not seem to obstruct exports, technical barriers have a varying impact on trade. A decreasing trend for tariffs has largely been compensated by more stringent technical barriers. The overall result is that frictions in the world wine trade have not changed during the past 15 years.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
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    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 74
    Publication Date: 2015-08-29
    Description: Any given human individual carries multiple genetic variants that disrupt protein-coding genes, through structural variation, as well as nucleotide variants and indels. Predicting the phenotypic consequences of a gene disruption remains a significant challenge. Current approaches employ information from a range of biological networks to predict which human genes are haploinsufficient (meaning two copies are required for normal function) or essential (meaning at least one copy is required for viability). Using recently available study gene sets, we show that these approaches are strongly biased towards providing accurate predictions for well-studied genes. By contrast, we derive a haploinsufficiency score from a combination of unbiased large-scale high-throughput datasets, including gene co-expression and genetic variation in over 6000 human exomes. Our approach provides a haploinsufficiency prediction for over twice as many genes currently unassociated with papers listed in Pubmed as three commonly-used approaches, and outperforms these approaches for predicting haploinsufficiency for less-studied genes. We also show that fine-tuning the predictor on a set of well-studied ‘gold standard’ haploinsufficient genes does not improve the prediction for less-studied genes. This new score can readily be used to prioritize gene disruptions resulting from any genetic variant, including copy number variants, indels and single-nucleotide variants.
    Keywords: Genomics
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  • 75
    Publication Date: 2015-07-10
    Description: In many developing countries, supermarkets are expanding rapidly. This affects farmers’ marketing options. Previous studies have analyzed welfare effects of smallholder participation in supermarket channels from a static perspective, using cross-section data. We develop a conceptual framework and use panel data to better understand participation and impact dynamics. The analysis focuses on vegetable producers in Kenya. Participation in supermarket channels is associated with income gains. However, many farmers have dropped out of the supermarket channel due to various constraints. The initial income gains cannot be sustained when returning to the traditional market. Organizational support may be needed to avoid widening income disparities.
    Keywords: L24 - Contracting Out ; Joint Ventures ; Technology Licensing, O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 76
    Publication Date: 2015-07-12
    Description: Meta-analysis of gene expression has enabled numerous insights into biological systems, but current methods have several limitations. We developed a method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. To demonstrate the utility of our method, we conducted a meta-analysis of lung cancer gene expression based on publicly available data. Using 629 samples from five data sets, we trained a multinomial classifier to distinguish between four lung cancer subtypes. Our meta-analysis-derived classifier included 58 genes and achieved 91% accuracy on leave-one-study-out cross-validation and on three independent data sets. Our method makes meta-analysis of gene expression more systematic and expands the range of questions that a meta-analysis can be used to address. As the amount of publicly available gene expression data continues to grow, our method will be an effective tool to help distill these data into knowledge.
    Keywords: Genomics
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  • 77
    Publication Date: 2015-07-15
    Description: Although the importance of diet quality for improving child health is widely recognized, the roles of environmental factors and the absorption of nutrients for children's physical growth and morbidity have not been adequately integrated into a policy framework. Moreover, nutrient intakes gradually affect child health, so it is helpful to use alternative tools to evaluate short-term interventions versus long-term food policies. This article emphasizes the role of diet quality reflected in the intake of nutrients such as protein, calcium, and iron for children's physical growth. Vitamins A and C are important for reducing morbidity. Children's growth and morbidity affect their cognitive development, which is critical for the future supply of skilled labor and economic growth. Evidence on these issues from countries such as Bangladesh, India, Kenya, the Philippines, and Tanzania is summarized. The supply of nutritious foods is appraised from the viewpoint of improving diet quality. Finally, the roles of educational campaigns and indirect taxes on unhealthy processed foods consumed by the affluent in developing countries are discussed.
    Keywords: O12 - Microeconomic Analyses of Economic Development, I15 - Health and Economic Development, I25 - Education and Economic Development, J10 - General, Q01 - Sustainable Development, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0257-3032
    Electronic ISSN: 1564-6971
    Topics: Economics
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  • 78
    Publication Date: 2015-04-21
    Description: Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact .
    Keywords: Genomics
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  • 79
    Publication Date: 2015-05-20
    Description: Analysis of rewired upstream subnetworks impacting downstream differential gene expression aids the delineation of evolving molecular mechanisms. Cumulative statistics based on conventional differential correlation are limited for subnetwork rewiring analysis since rewiring is not necessarily equivalent to change in correlation coefficients. Here we present a computational method ChiNet to quantify subnetwork rewiring by statistical heterogeneity that enables detection of potential genotype changes causing altered transcription regulation in evolving organisms. Given a differentially expressed downstream gene set, ChiNet backtracks a rewired upstream subnetwork from a super-network including gene interactions known to occur under various molecular contexts. We benchmarked ChiNet for its high accuracy in distinguishing rewired artificial subnetworks, in silico yeast transcription-metabolic subnetworks, and rewired transcription subnetworks for Candida albicans versus Saccharomyces cerevisiae , against two differential-correlation based subnetwork rewiring approaches. Then, using transcriptome data from tolerant S. cerevisiae strain NRRL Y-50049 and a wild-type intolerant strain, ChiNet identified 44 metabolic pathways affected by rewired transcription subnetworks anchored to major adaptively activated transcription factor genes YAP1 , RPN4 , SFP1 and ROX1 , in response to toxic chemical challenges involved in lignocellulose-to-biofuels conversion. These findings support the use of ChiNet in rewiring analysis of subnetworks where differential interaction patterns resulting from divergent nonlinear dynamics abound.
    Keywords: Genomics
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    Topics: Biology
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  • 80
    Publication Date: 2015-05-26
    Description: The European Union (EU) is the world's largest wine producer, as well as the world's most regulated wine market. In 2007, the EU decided on a major reform of its wine policy. A crucial element was the abolishment of a system of planting rights to limit the planting of vineyards. However, after intense lobbying by opponents of the liberalisation, this decision was reversed in 2013. Despite the importance of planting rights in European (and hence global) wine production, and despite the fierce debates surrounding the reforms, no model exists to study the effects of this policy. We develop the first theoretical model of planting rights, integrating the markets for land, planting rights and wine to analyse efficiency and distributional effects. We use the model to study the effects of differences among EU member states in restrictions on trade in planting rights, the role of government reserves and the impact of imperfect enforcement.
    Keywords: Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 81
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2015-04-18
    Description: The prospects for plant variety protection to deliver improved varieties of self-pollinating crops is assessed using the experience of the Australian wheat breeding sector as a natural experiment. The analysis is based on detailed new data on the agronomic performance of all wheat varieties released by Australian breeders between 1976 and 2011. The results indicate that plant variety protection, and associated reforms, led to a substantial fall in breeder output. Qualitative evidence indicates that this was caused by a combination of fewer research spillovers, lower release standards, and a possible fall in total investment in breeding.
    Keywords: O34 - Intellectual Property Rights, Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 82
    Publication Date: 2015-06-24
    Description: Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein–RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein–rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a ‘proof of concept’ that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites.
    Keywords: Genomics
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  • 83
    Publication Date: 2015-02-18
    Description: The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins , implemented in Python and C and supported on Linux and Mac OS X.
    Keywords: Genomics
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  • 84
    Publication Date: 2015-02-18
    Description: Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 85
    Publication Date: 2015-02-11
    Description: Excess returns to producers insured by the Federal Crop Insurance Corporation can arise due to asymmetric information or from the design of the insurance programs themselves. Using unique, unit-level crop insurance contract data for major crops such as corn, soybeans, and wheat in five growing regions, we find evidence that producers in most regions may profit by selecting optional units, buy-up coverage, or by using transitional yields to participate in the federal crop insurance program. We also find evidence that advantages increase with land resource heterogeneity. However, the results do not support hypotheses that producers profit by selecting revenue insurance, nor that high levels of government "incompetence" exist in the design and administration of the crop insurance system.
    Keywords: Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 86
    Publication Date: 2015-02-11
    Description: We analyze the various welfare costs, transfers, trade, and employment consequences of the current U.S. sugar program for U.S. consumers, other sugar users, sugar refiners, cane and beet growing and processing industries, other associated agricultural sectors, and world markets. The removal of the sugar program would increase U.S. consumers' welfare by $2.9 to $3.5 billion each year and generate a modest job creation of 17,000 to 20,000 new jobs in food manufacturing and related industries. Imports of sugar containing products would fall dramatically, especially confectioneries substituting for domestic inputs under the sugar program. Sugar imports would rise substantially to 5–6 million short tons raw sugar equivalent. World sugar price increases would be minor, equivalent to about 1 cent per pound.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 87
    Publication Date: 2015-07-10
    Description: Existing analyses of market participation are based on a "double-hurdle" modeling approach. Such models are appropriate only when all members of the population of interest actually produce the good. In some contexts, however (e.g., smallholder farmers), many members of the population do not produce particular goods that they could produce and that their neighbors do produce. Policies influencing market participation among producers may thus also induce additional farmers to become producers. Previous double-hurdle approaches do not allow explicitly for this possibility. To address these limitations, this article presents a "triple-hurdle" approach with an initial stage that includes nonproducers. The model is used to identify the factors associated with Kenyan smallholder farmers choosing to participate in dairy production, and the role that these producers choose to play (or not) in the marketplace. In the midst of debates underway over the privatization of the parastatal Kenya Creameries Company, new knowledge about smallholder participation in dairy could be an important contribution. Results suggest the importance of rural electrification, training, and improved grazing practices. We find that expected net sales are significantly higher when farmers have access to informal private markets. We also describe a version of the ordered tobit model that includes nonproducers and is nested in our triple-hurdle model. A likelihood ratio test shows the latter to be a significantly better fit to our data. We discuss how insights gained from this study differ from the insights that would come from a double-hurdle ordered tobit that also includes nonproducers.
    Keywords: C51 - Model Construction and Estimation, C81 - Methodology for Collecting, Estimating, and Organizing Microeconomic Data, O12 - Microeconomic Analyses of Economic Development, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 88
    Publication Date: 2015-07-10
    Description: This article argues that the structure of the Vietnamese rice export system is, in political economy terms, a rational response to the volatility present in the international rice market. In particular, it is argued that the Vietnamese Food Agency, along with VINAFOOD-1 and VINAFOOD-2, have been structured so that they can benefit from the domestic demands for export restrictions anticipated to occur as a consequence of international price volatility and the psychological demand of consumers for price stability. In turn, the actions of these agencies also contribute to international price volatility and the resulting demand for export restrictions. Since the political and economic elite in Vietnam obtain both political and economic power from this system, it is unlikely to be replaced with more effective and efficient policies to combat domestic price volatility. Thus, continued volatility in the price of rice can be expected.
    Keywords: N55 - Asia including Middle East, P26 - Political Economy ; Property Rights, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 89
    Publication Date: 2015-07-10
    Description: The dimensions that define a food product have expanded rapidly to include characteristics of the production process, marketing arrangements, and implications that production and consumption of the product have for the environment. Some market intermediaries have responded by requiring that their suppliers abide by restrictive production practices. We examine the economic effects of such restrictions and apply this analysis to limitations on the use of antibiotics in U.S. pork production. Results from conceptual and simulation analyses show that, in the absence of demand growth, less pork is sold due to higher costs in the restricted segment, and both pork consumers (on average) and producers are harmed. Demand growth of between 6–11% from adding new consumers who will consume the restricted (antibiotic-free) product but not the conventional product is needed to return consumer surplus to the level in the base case, and between 2–4% demand growth was required to return producer surplus to base. When restricted and conventional products are modeled using a vertical differentiation framework, results depend importantly on the ease with which consumers can switch to a seller who offers their desired product type. Significant distributional impacts among consumers are present when switching costs are prohibitive.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 90
    Publication Date: 2015-09-12
    Description: This article examines bilateral trade patterns in the Asia-Pacific using a new model in which comparative advantage within the agricultural sector is linked to agro-ecological characteristics, and trade costs are product-specific. Bilateral market share is a function of productivity and trade costs. However, countries with similar land and climate characteristics systematically have high productivity in similar products making them disproportionately sensitive to changes in each other's trade costs. We use a random coefficients logit model to estimate a parametric distribution of comparative advantage and trade costs across products and calculate regional trade liberalization elasticities for each exporter in each import market. Unlike most existing models, the value of the elasticity depends on the degree to which liberalization includes competitors with similar comparative advantage within the agricultural sector. We find disproportionately larger trade elasticities under China-led liberalization relative to U.S.-led liberalization among close U.S. competitors compared to countries whose agricultural products are unlikely to compete head-to-head with U.S. exports. For the United States, we find that the "lost opportunity" cost of exclusion from regional liberalization is increasing in the extent to which its close competitors gain new access.
    Keywords: F13 - Trade Policy ; International Trade Organizations, F14 - Country and Industry Studies of Trade, F15 - Economic Integration, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 91
    Publication Date: 2015-09-12
    Description: Contracts between farmers and intermediaries and crop insurers are important means for farmers to mitigate risks in modern U.S. agriculture. In this paper, we investigate the effect of crop insurance enrollment on contract terms and farmers’ participation in marketing contracts. Following Ligon (2003) , we set up a mechanism design framework to demonstrate an intermediary's contract design problem, where farmers are assumed to be utility maximizing agents. We depict farmers’ optimal choices of insurance coverage using the specification developed by Babcock (2012) . Our model shows that improved terms of crop insurance (lower premiums, higher subsidies) make contracts less appealing to farmers as mechanisms for mitigating risk. Therefore, intermediaries may revise their contract offers so that they are more attractive. However, improvements in contract terms are limited by their cost to the intermediaries and will not lead to expanded participation in contracts.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 92
    Publication Date: 2015-10-31
    Description: We consider how cost heterogeneity and market power affect voting power in producer referenda for mandatory agricultural marketing organisations with generic promotion programmes in the United States. We measure voting power using the Banzhaf Power Index and propose a new version of this index based on the profit-maximising theory of the firm that provides an improved estimate of voting power. Examining several types of demand shifts and voting rules, we find that both Banzhaf Power and our new measure vary considerably depending on the market structure and level of cost heterogeneity.
    Keywords: D71 - Social Choice ; Clubs ; Committees ; Associations, D72 - Models of Political Processes: Rent-Seeking, Elections, Legislatures, and Voting Behavior, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 93
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2015-11-06
    Description: I compare the distribution of risk attitudes of farm owners in the United States to nonfarm business owners and the general population using a measure of risk tolerance collected from national surveys. I find that farmers are significantly more tolerant of risk than the general population, though they are significantly less tolerant of risk than nonfarm business owners. Once demographic differences are controlled, farm and nonfarm business owners are more similar in their risk attitudes and both groups remain significantly more risk tolerant than the general population. First-generation farmers display greater risk tolerance than farmers who inherit operations from family members, as do farmers who have just begun operating a farm; neither pattern emerges among nonfarm business owners. The most risk tolerant farmers are young and male with larger operations, higher incomes, less formal education and close proximity to metropolitan centers. Among farmers, those with less diversified operations and those with specialty enterprises are more risk tolerant than other types of farmers. Crop farmers are less risk tolerant than fruit and vegetable farmers or farmers with specialty enterprises, while farmers who receive government payments or buy enterprise insurance are not significantly different in risk tolerance from farmers who eschew such opportunities. These findings stimulate questions about how farm programs and the distinct challenges of entry in the production agriculture sector shape the underlying distribution of key farmer characteristics such as risk tolerance.
    Keywords: D81 - Criteria for Decision-Making under Risk and Uncertainty, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 94
    Publication Date: 2015-12-02
    Description: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.
    Keywords: Genomics
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    Topics: Biology
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  • 95
    Publication Date: 2015-12-13
    Description: Families in low-income neighborhoods sometimes lack access to supermarkets that provide a broad range of healthy foods. We investigate whether these so called "food deserts" play a role in childhood obesity using a statewide panel data set of Arkansas elementary schoolchildren. We use fixed-effects panel data regression models to estimate the average food desert effect. We next compare children who left (entered) food deserts to children who were always (never) in food deserts and homogenize samples for those whose food desert status changed as a result of a change in residence and those whose status changed only as a consequence of the entry or exit of a supermarket. We present evidence that exposure to food deserts is associated with higher z-scores for body mass index. On average, this is in the neighborhood of 0.04 standard deviations. The strongest evidence and largest association is among urban students and especially those that transition into food deserts from non-deserts. Our food desert estimates are similar in magnitude to findings reported in earlier work on diet and lifestyle interventions targeting similarly aged schoolchildren. That said, we are unable to conclude that the estimated food desert effect is causal because many of the transitions into or out of food deserts result from a change in residence, an event that is endogenous to the child's household. However, there is evidence that food deserts are a risk indicator and that food desert areas may be obesogenic in ways that other low-income neighborhoods are not.
    Keywords: I14 - Health and Inequality, I19 - Other, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 96
    Publication Date: 2015-03-14
    Description: This study examines the relationship between the use of modern food retailers and health outcomes using data from a survey of 1,180 urban households in Indonesia. The dependent variables include adult and child body-mass index and the share of individuals overweight and obese. After controlling for individual and household characteristics and using standard and Lewbel instrumental variable approaches to control for unobservable characteristics, we do not find a statistically significant relationship between use of supermarkets and adult nutrition measures. On the other hand, there is mixed evidence for a negative effect of supermarkets on child nutrition, particularly for those in high-income households.
    Keywords: I15 - Health and Economic Development, P46 - Consumer Economics ; Welfare and Poverty, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 97
    Publication Date: 2015-03-14
    Description: This paper investigates the effect of items’ physical position in the best-worst scaling technique. Although the best-worst scaling technique has been widely used in many fields, the literature has largely overlooked the phenomenon of consumers’ adoption of processing strategies while making their best-worst choices. We examine this issue in the context of consumers’ trust in institutions to provide information about a new food technology, nanotechnology, and its use in food processing. Our results show that approximately half of the consumers used position as a schematic cue when making choices. We find the position bias was particularly strong when consumers chose their most trustworthy institution compared to their least trustworthy institution. In light of our findings, we recommend that researchers in the field be aware of the possibility of position bias when designing best-worst scaling surveys. We also encourage researchers who have already collected best-worst data to investigate whether their data shows such heuristics.
    Keywords: C25 - Discrete Regression and Qualitative Choice Models, D12 - Consumer Economics: Empirical Analysis, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 98
    Publication Date: 2015-03-14
    Description: Methods to interpret personal genome sequences are increasingly required. Here, we report a novel framework (EvoTol) to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation of protein sequences and can incorporate tissue-specific gene expression data. We apply this framework to the analysis of whole-exome sequence data in epilepsy and congenital heart disease, and demonstrate EvoTol's ability to identify known disease-causing genes is unmatched by competing methods. Application of EvoTol to the human interactome revealed networks enriched for genes intolerant to protein sequence variation, informing novel polygenic contributions to human disease.
    Keywords: Genomics
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    Topics: Biology
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  • 99
    Publication Date: 2015-03-14
    Description: Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo . However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. However, technical limitations of these methods prevent them from being applied broadly, especially in clinical settings. We conducted a comprehensive survey involving multiple cell lines, TFs, and methylation types and found that there are intimate relationships between TF binding and methylation level changes around the binding sites. Exploiting the connection between DNA methylation and TF binding, we proposed a novel supervised learning approach to predict TF–DNA interaction using data from base-resolution whole-genome methylation sequencing experiments. We devised beta-binomial models to characterize methylation data around TF binding sites and the background. Along with other static genomic features, we adopted a random forest framework to predict TF–DNA interaction. After conducting comprehensive tests, we saw that the proposed method accurately predicts TF binding and performs favorably versus competing methods.
    Keywords: Genomics
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  • 100
    Publication Date: 2015-08-18
    Description: Copy-number variants (CNVs) are a major form of genetic variation and a risk factor for various human diseases, so it is crucial to accurately detect and characterize them. It is conceivable that allele-specific reads from high-throughput sequencing data could be leveraged to both enhance CNV detection and produce allele-specific copy number (ASCN) calls. Although statistical methods have been developed to detect CNVs using whole-genome sequence (WGS) and/or whole-exome sequence (WES) data, information from allele-specific read counts has not yet been adequately exploited. In this paper, we develop an integrated method, called AS-GENSENG, which incorporates allele-specific read counts in CNV detection and estimates ASCN using either WGS or WES data. To evaluate the performance of AS-GENSENG, we conducted extensive simulations, generated empirical data using existing WGS and WES data sets and validated predicted CNVs using an independent methodology. We conclude that AS-GENSENG not only predicts accurate ASCN calls but also improves the accuracy of total copy number calls, owing to its unique ability to exploit information from both total and allele-specific read counts while accounting for various experimental biases in sequence data. Our novel, user-friendly and computationally efficient method and a complete analytic protocol is freely available at https://sourceforge.net/projects/asgenseng/ .
    Keywords: Genomics
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    Topics: Biology
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