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  • Articles  (22)
  • American Geophysical Union  (11)
  • Wiley  (8)
  • Oxford University Press  (3)
  • American Meteorological Society (AMS)
  • Paleontological Society
  • Journal of Geophysical Research JGR - Oceans  (6)
  • Nucleic Acids Research  (3)
  • Journal of Geophysical Research: Oceans  (2)
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  • Articles  (22)
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  • American Geophysical Union  (11)
  • Wiley  (8)
  • Oxford University Press  (3)
  • American Meteorological Society (AMS)
  • Paleontological Society
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  • 1
    Publication Date: 2012-10-17
    Description: Analyses of field observations and numerical model results have identified that sediment transport in the Hudson River estuary is laterally segregated between channel and shoals, features frontal trapping at multiple locations along the estuary, and varies significantly over the spring-neap tidal cycle. Lateral gradients in depth, and therefore baroclinic pressure gradient and stratification, control the lateral distribution of sediment transport. Within the saline estuary, sediment fluxes are strongly landward in the channel and seaward on the shoals. At multiple locations, bottom salinity fronts form at bathymetric transitions in width or depth. Sediment convergences near the fronts create local maxima in suspended-sediment concentration and deposition, providing a general mechanism for creation of secondary estuarine turbidity maxima at bathymetric transitions. The lateral bathymetry also affects the spring-neap cycle of sediment suspension and deposition. In regions with broad, shallow shoals, the shoals are erosional and the channel is depositional during neap tides, with the opposite pattern during spring tides. Narrower, deeper shoals are depositional during neaps and erosional during springs. In each case, the lateral transfer is from regions of higher to lower bed stress, and depends on the elevation of the pycnocline relative to the bed. Collectively, the results indicate that lateral and along-channel gradients in bathymetry and thus stratification, bed stress, and sediment flux lead to an unsteady, heterogeneous distribution of sediment transport and trapping along the estuary rather than trapping solely at a turbidity maximum at the limit of the salinity intrusion.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
    Publication Date: 2019
    Description: ABSTRACT Modifications for navigation since the late 1800s have increased channel depth (H) in the lower Hudson River estuary by 10‐30%, and at the mouth the depth has more than doubled. Observations along the lower estuary show that both salinity and stratification have increased over the past century. Model results comparing pre‐dredging bathymetry from the 1860s with modern conditions indicate an increase in the salinity intrusion of about 30%, which is roughly consistent with the H5/3 scaling expected from theory for salt flux dominated by steady exchange. While modifications including a recent deepening project have been concentrated near the mouth, the changes increase salinity and threaten drinking water supplies more than 100 km landward. The deepening has not changed the responses to river discharge (Qr) of the salinity intrusion (~Qr‐1/3) or mean stratification (Qr2/3). Surprisingly, the increase in salinity intrusion with channel deepening results in almost no change in the estuarine circulation. This contrasts sharply with local scaling based on local dynamics of an H2 dependence, but it is consistent with a steady state salt balance that allows scaling of the estuarine circulation based on external forcing factors and is independent of depth. In contrast, the observed and modeled increases in stratification are opposite of expectations from the steady state balance, which could be due to reduction in mixing with loss of shallow subtidal regions. Overall, the mean shift in estuarine parameter space due to channel deepening has been modest compared with the monthly‐to‐seasonal variability due to tides and river discharge.
    Print ISSN: 2169-9275
    Electronic ISSN: 2169-9291
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
    Publication Date: 2014-11-09
    Description: ABSTRACT The outflowing currents from tidal inlets are influenced both by the morphology of the ebb-tide shoal and interaction with incident surface gravity waves. Likewise, the propagation and breaking of incident waves are affected by the morphology and the strength and structure of the outflowing current. The 3D COAWST (Coupled Ocean-Atmosphere-Wave-Sediment Transport) modeling system is applied to numerically analyze the interaction between currents, waves, and bathymetry in idealized inlet configurations. The bathymetry is found to be a dominant controlling variable. In the absence of an ebb shoal and with weak wave forcing, a narrow outflow jet extends seaward with little lateral spreading. The presence of an ebb-tide shoal produces significant pressure gradients in the region of the outflow, resulting in enhanced lateral spreading of the jet. Incident waves cause lateral spreading and limit the seaward extent of the jet, due both to conversion of wave momentum flux and enhanced bottom friction. The interaction between the vorticity of the outflow jet and the wave stokes drift is also an important driving force for the lateral spreading of the plume. For weak outflows, the outflow jet is actually enhanced by strong waves when there is a channel across the bar, due to the “return current” effect. For both strong and weak outflows, waves increase the along-shore transport in both directions from the inlet due to the wave-induced set-up over the ebb shoal. Wave-breaking is more influenced by the topography of the ebb shoal than by wave-current interaction, although strong outflows show intensified breaking at the head of the main channel.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 4
    Publication Date: 2015-03-14
    Description: The Cdk12/CycK complex promotes expression of a subset of RNA polymerase II genes, including those of the DNA damage response. CDK12 is among only nine genes with recurrent somatic mutations in high-grade serous ovarian carcinoma. However, the influence of these mutations on the Cdk12/CycK complex and their link to cancerogenesis remain ill-defined. Here, we show that most mutations prevent formation of the Cdk12/CycK complex, rendering the kinase inactive. By examining the mutations within the Cdk12/CycK structure, we find that they likely provoke structural rearrangements detrimental to Cdk12 activation. Our mRNA expression analysis of the patient samples containing the CDK12 mutations reveals coordinated downregulation of genes critical to the homologous recombination DNA repair pathway. Moreover, we establish that the Cdk12/CycK complex occupies these genes and promotes phosphorylation of RNA polymerase II at Ser2. Accordingly, we demonstrate that the mutant Cdk12 proteins fail to stimulate the faithful DNA double strand break repair via homologous recombination. Together, we provide the molecular basis of how mutated CDK12 ceases to function in ovarian carcinoma. We propose that CDK12 is a tumor suppressor of which the loss-of-function mutations may elicit defects in multiple DNA repair pathways, leading to genomic instability underlying the genesis of the cancer.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2019
    Description: Abstract Since the late nineteenth century, channel depths have more than doubled in parts of New York Harbor and the tidal Hudson River, wetlands have been reclaimed and navigational channels widened, and river flow has been regulated. To quantify the effects of these modifications, observations and numerical simulations using historical and modern bathymetry are used to analyze changes in the barotropic dynamics. Model results and water level records for Albany (1868 to present) and New York Harbor (1844 to present) recovered from archives show that the tidal amplitude has more than doubled near the head of tides, whereas increases in the lower estuary have been slight (〈10%). Channel deepening has reduced the effective drag in the upper tidal river, shifting the system from hyposynchronous (tide decaying landward) to hypersynchronous (tide amplifying). Similarly, modeling shows that coastal storm effects propagate farther landward, with a 20% increase in amplitude for a major event. In contrast, the decrease in friction with channel deepening has lowered the tidally averaged water level during discharge events, more than compensating for increased surge amplitude. Combined with river regulation that reduced peak discharges, the overall risk of extreme water levels in the upper tidal river decreased after channel construction, reducing the water level for the 10‐year recurrence interval event by almost 3 m. Mean water level decreased sharply with channel modifications around 1930, and subsequent decadal variability has depended both on river discharge and sea level rise. Channel construction has only slightly altered tidal and storm surge amplitudes in the lower estuary.
    Print ISSN: 2169-9275
    Electronic ISSN: 2169-9291
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
    Publication Date: 2012-06-28
    Description: The Drosophila Suppressor of Hairy-wing [Su(Hw)] protein is a globally expressed, multi-zinc finger (ZnF) DNA-binding protein. Su(Hw) forms a classic insulator when bound to the gypsy retrotransposon and is essential for female germline development. These functions are genetically separable, as exemplified by Su(Hw) f that carries a defective ZnF10, causing a loss of insulator but not germline function. Here, we completed the first genome-wide analysis of Su(Hw)-binding sites (SBSs) in the ovary, showing that tissue-specific binding is not responsible for the restricted developmental requirements for Su(Hw). Mapping of ovary Su(Hw) f SBSs revealed that female fertility requires binding to only one third of the wild-type sites. We demonstrate that Su(Hw) f retention correlates with binding site affinity and partnership with Modifier of (mdg4) 67.2 protein. Finally, we identify clusters of co-regulated ovary genes flanked by Su(Hw) f bound sites and show that loss of Su(Hw) has limited effects on transcription of these genes. These data imply that the fertility function of Su(Hw) may not depend upon the demarcation of transcriptional domains. Our studies establish a framework for understanding the germline Su(Hw) function and provide insights into how chromatin occupancy is achieved by multi-ZnF proteins, the most common transcription factor class in metazoans.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2013-05-01
    Description: ABSTRACT A 3D hydrodynamic model (ROMS) is used to investigate the dynamics and structure of hyperpycnal river plumes over sloping continental shelves. The focus is on the plume's response to varying slopes and settling velocities ( w s ). The idealized model is configured to represent small mountainous river systems during a flood event. A hyperpycnal sediment concentration of 60 (g/l) is specified at the river mouth such that the sediment-freshwater mixture is denser than the seawater, causing the plumes to traverse the shelves as undercurrents. A realistic range of shelf slope of 0.001-0.03 is chosen. The settling velocity is varied based on river's carrying capacity. The model-derived velocity profiles and the entrainment rate compare favorably against prior laboratory experiments. Both cross-shore and along-shore momentum balances are primarily between gravitational forcing and bottom friction. But, the Coriolis deflection is significant at the plume core in the along-shore momentum budget (i.e., Ekman balance). As the slope increases and settling velocity decreases, hyperpycnal plumes transition from depositional to autosuspending regime. An estimate of critical slope governed by a dimensionless parameter ( q b is buoyancy input) reasonably captures the regime transition. In the depositional regime, the plume's runout (cross-shore penetration) scales with advective distance: increasing slopes and discharge enhance the gravitational forcing and plume velocity, leading to an increase in runout. In contrast, increasing settling velocity shortens the vertical settling time, thereby reducing the plume's horizontal footprint. For the range of parameters considered, the runout of depositional plumes is confined within 15 km from the mouth, whereas the penetration of autosuspending plumes is essentially unlimited.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 8
    Publication Date: 2017-05-17
    Description: Estuarine mixing is often intensified in regions where topographic forcing leads to hydraulic transitions. Observations in the salt-wedge estuary of the Connecticut River indicate that intense mixing occurs during the ebb tide in regions of supercritical flow that is accelerated by lateral expansion of the channel. The zones of mixing are readily identifiable based on echo-sounding images of large-amplitude shear instabilities. The gradient Richardson number (Ri) averaged across the mixing layer decreases to a value very close to 0.25 during most of the active mixing phase. The along-estuary variation in internal Froude number and interface elevation are roughly consistent with a steady, inviscid, two-layer hydraulic representation, and the fit is improved when a parameterization for interfacial stress is included. The analysis indicates that the mixing results from lateral straining of the shear layer, and that the rapid development of instabilities maintains the overall flow near the mixing threshold value of Ri=0.25, even with continuous, active mixing. The entrainment coefficient can be estimated from salt conservation within the interfacial layer, based on the finding that the mixing maintains Ri=0.25. This approach leads to a scaling estimate for the interfacial mixing coefficient based on the lateral spreading rate and the aspect ratio of the flow, yielding estimates of turbulent dissipation within the pycnocline that are consistent with estimates based on turbulence-resolving measurements.
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    Topics: Geosciences , Physics
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  • 9
    Publication Date: 2016-12-23
    Description: The Connecticut River is a tidal salt wedge estuary, where advection of sharp salinity gradients through channel constrictions and over steeply sloping bathymetry leads to spatially heterogeneous stratification and mixing. A 3-d unstructured-grid finite-volume hydrodynamic model (FVCOM) was evaluated against shipboard and moored observations, and mixing by both the turbulent closure and numerical diffusion were calculated. Excessive numerical mixing in regions with strong velocities, sharp salinity gradients, and steep bathymetry reduced model skill for salinity. Model calibration was improved by optimizing both the bottom roughness ( z 0 ), based on comparison with the barotropic tidal propagation, and the mixing threshold in the turbulence closure (steady-state Richardson number, Ri st ), based on comparison with salinity. Whereas a large body of evidence supports a value of Ri st ∼ 0.25, model skill for salinity improved with Ri st ∼ 0.1. With Ri st = 0.25, numerical mixing contributed about 1/2 the total mixing, while with Ri st = 0.10 it accounted for ∼2/3, but salinity structure was more accurately reproduced. The combined contributions of numerical and turbulent mixing were quantitatively consistent with high-resolution measurements of turbulent mixing. A coarser grid had increased numerical mixing, requiring further reductions in turbulent mixing and greater bed friction to optimize skill. The optimal Ri st for the fine grid case was closer to 0.25 than for the coarse grid, suggesting that additional grid refinement might correspond with Ri st approaching the theoretical limit. Numerical mixing is rarely assessed in realistic models, but comparisons with high-resolution observations in this study suggest it is an important factor. This article is protected by copyright. All rights reserved.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 10
    Publication Date: 2014-07-04
    Description: The bromodomain protein Brd4 regulates the transcription of signal-inducible genes. This is achieved by recruiting the positive transcription elongation factor P-TEFb to promoters by its P-TEFb interaction domain (PID). Here we show that Brd4 stimulates the kinase activity of P-TEFb for phosphorylation of the C-terminal domain (CTD) of RNA polymerase II over basal levels. The CTD phosphorylation saturation levels, the preferences for pre-phosphorylated substrates, and the phosphorylation specificity for Ser5 of the CTD however remain unchanged. Inhibition of P-TEFb by Hexim1 is relieved by Brd4, although no mutual displacement with the Cyclin T-binding domain of Hexim1 was observed. Brd4 PID shows a surprising sequence motif similarity to the trans -activating Tat protein from HIV-1, which includes a core RxL motif, a polybasic cluster known as arginine-rich motif, and a C-terminal leucine motif. Mutation of these motifs to alanine significantly diminished the stimulatory effect of Brd4 and fully abrogated its activation potential in presence of Hexim1. Yet the protein was not found to bind Cyclin T1 as Tat, but only P-TEFb with a dissociation constant of 0.5 μM. Our data suggest a model where Brd4 acts on the kinase subunit of P-TEFb to relieve inhibition and stimulate substrate recognition.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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