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The Hudson River is used as a case study for stream ecology, focusing on the effects of water level fluctuations, seasonal changes and river discharge. Flood tides were found to have substantial mixing, as did spring tides, while ebb tides produced the weakest mixing.

The gene for cherubism, an autosomal dominant disorder perhaps related to tooth development and eruption and resulting in altered facial appearance and large amounts of fibrous tissue in the jaws, has been mapped to chromosome 4p16. A genomewide search has been carried out in a 3-generation family. Three other affected families were genotyped and mapped to the locus, which is across an interval of about 22 cM.

We describe two sibling fetuses with urogenital abnormalities detected by prenatal ultrasound, in which post-delivery examination showed split hand and foot malformation, and bilateral cleft lip and palate. These findings are consistent with ectrodactyly-ectodermal dysplasia-cleft lip with or without cleft palate syndrome (EEC). Both fetuses were found to have the same missense mutation in TP63 (c.1051G > A; p.D351N). Parental clinical examinations and lymphocyte DNA analyses were normal. This report illustrates the potential severity of urogenital defects in TP63-related disorders, which may be detectable with fetal ultrasonography. It highlights the need to counsel for the possibility of germline mosaicism in TP63-associated disorders. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Neurofibromatosis type 1 (NF1) is caused by NF1 gene mutations. The phenotype is highly variable, with ‘modifiers’ being discussed as potential determinants. Mismatch repair deficiency was shown to cause NF1 mutations, but constitutional mutation of mismatch repair genes was identified only once in a NF1 patient. We aimed to analyze whether DNA methylation of mismatch repair gene promoters, known to lead to transcriptional silencing, is associated with increased tumor load in NF1 defined by the number of cutaneous neurofibromas. Leukocyte DNA of 79 controls and 79 NF1 patients was investigated for methylation of mismatch repair genes MLH1, MSH2, MSH6, and PMS2 by methylation-specific PCR and pyrosequencing. MLH1, MSH6, and PMS2 promoters were not methylated. By contrast, we found promoter methylation of MSH2 with a higher rate of methylation in NF1 patients compared with controls. Furthermore, when comparing NF1 patients with a low vs those with a high number of cutaneous neurofibromas, MSH2 promoter methylation was significantly different. In patients with a high tumor burden, methylation of two (out of six) CpGs was enhanced. This finding was not confounded by age. In conclusion, enhanced methylation involving transcription start points of mismatch repair genes, such as MSH2 in NF1, has not been described so far. Methylation-induced variability of MSH2 gene expression may lead to variable mismatch repair capacity. Our results may point toward a role of MSH2 as a modifier for NF1, although the amount of DNA methylation and subsequent gene expression in other cell types of NF1 patients needs to be elucidated. [ABSTRACT FROM AUTHOR]

Noonan syndrome (NS) and cardio-facio-cutaneous syndrome (CFCS) are related developmental disorders caused by mutations in genes encoding various components of the RAS-MAPK signaling cascade. NS is associated with mutations in the genes PTPN11, SOS1, RAF1, or KRAS, whereas CFCS can be caused by mutations in BRAF, MEK1, MEK2, or KRAS. The NS phenotype is rarely accompanied by multiple giant cell lesions (MGCL) of the jaw (Noonan-like/MGCL syndrome (NL/MGCLS)). PTPN11 mutations are the only genetic abnormalities reported so far in some patients with NL/MGCLS and in one individual with LEOPARD syndrome and MGCL. In a cohort of 75 NS patients previously tested negative for mutations in PTPN11 and KRAS, we detected SOS1 mutations in 11 individuals, four of whom had MGCL. To explore further the relevance of aberrant RAS-MAPK signaling in syndromic MGCL, we analyzed the established genes causing CFCS in three subjects with MGCL associated with a phenotype fitting CFCS. Mutations in BRAF or MEK1 were identified in these patients. All mutations detected in these seven patients with syndromic MGCL had previously been described in NS or CFCS without apparent MGCL. This study demonstrates that MGCL may occur in NS and CFCS with various underlying genetic alterations and no obvious genotype–phenotype correlation. This suggests that dysregulation of the RAS-MAPK pathway represents the common and basic molecular event predisposing to giant cell lesion formation in patients with NS and CFCS rather than specific mutation effects.European Journal of Human Genetics (2009) 17, 420–425; doi:10.1038/ejhg.2008.188; published online 15 October 2008 [ABSTRACT FROM AUTHOR]

Congenital central hypoventilation syndrome (CCHS), a rare disorder typically presenting in the newborn period, results in over 90% of cases from PHOX2B polyalanine repeat mutations. It is characterized by alveolar hypoventilation, symptoms of autonomic nervous system dysregulation, and in a subset of cases Hirschsprung’s disease and, later, tumors of neural crest origin. We describe a preterm infant with severe phenotype of CCHS and hyperinsulinism. A novel de novo heterozygote missence mutation (Gly68Cys) in the PHOX2B gene could be identified. Based on the observation of three patients presenting with the combination of congenital hyperinsulinism and CCHS, hyperinsulinism might represent an additional clinical feature of CCHS. [ABSTRACT FROM AUTHOR]

We report on a young female patient with the clinical features of blepharophimosis-ptosis-epicanthus inversus syndrome (BPES, OMIM 110100) and a balanced chromosome translocation 46, XX, t(2;3)(q33;q23)dn.BPES is a rare autosomal dominant congenital disorder characterized by the eponymous oculo-facial features that are, in female patients, associated either with (type 1 BPES) or without (type 2 BPES) premature ovarian failure. Both types of BPES are caused by heterozygous mutations in the FOXL2 gene, which is located in chromosome band 3q23. Chromosome aberrations such as balanced rearrangements have only rarely been observed in BPES patients but can provide valuable information about regulatory regions of FOXL2. The translocation in this patient broadens our knowledge of pathogenic mechanisms in BPES and highlights the importance of conventional cytogenetic investigations in patients with negative results of FOXL2 mutation screening as a prerequisite for optimal management and genetic counseling. [ABSTRACT FROM AUTHOR]

The outflow of warm, salty, and dense water from the Red Sea into the western Gulf of Aden is numerically simulated using the Hybrid Coordinate Ocean Model (HYCOM). The pathways of the modeled overflow, temperature, salinity, velocity profiles from stations and across sections, and transport estimates are compared to those observed during the 2001 Red Sea Outflow Experiment. As in nature, the simulated outflow is funneled into two narrow channels along the seafloor. The results from the three-dimensional simulations show a favorable agreement with the observed temperature and salinity profiles along the channels. The volume transport of the modeled overflow increases with the increasing distance from the southern exit of the Bab el Mandeb Strait due to entrainment of ambient fluid, such that the modeled transport shows a reasonable agreement with that estimated from the observations. The initial propagation speed of the outflow is found to be smaller than the estimated interfacial wave speed. The slow propagation is shown to result from the roughness of the bottom topography characterized by a number of depressions that take time to be filled with outflow water. Sensitivities of the results to the horizontal grid spacing, different entrainment parameterizations, and forcing at the source location are investigated. Because of the narrow widths of the approximately 5 km of the outflow channels, a horizontal grid spacing of 1 km or less is required for model simulations to achieve a reasonable agreement with the observations. Comparison of two entrainment parameterizations, namely, TPX and K-profile parameterization (KPP), show that similar results are obtained at 1-km resolution. Overall, the simulation of the Red Sea outflow appears to be more strongly affected by the details of bottom topography and grid spacing needed to adequately resolve them than by parameterizations of diapycnal mixing. [ABSTRACT FROM AUTHOR]

Turbulence in the Red Sea outflow plume in the western Gulf of Aden was observed with an upward-looking, five-beam, 600-kHz acoustic Doppler current profiler (ADCP). The “Bottom Lander” ADCP was deployed on the seafloor in two narrow, topographically confined outflow channels south of Bab el Mandeb for periods of 18–40 h at three locations at 376-, 496-, and 772-m depths. Two deployments were taken during the winter season of maximum outflow from the Red Sea and two in the summer season of minimum outflow. These short-term observations exhibit red velocity spectra with high-frequency fluctuations of typically a few centimeters per second RMS velocity during strong plume flow as well as strong subtidal variations. In one winter season event, the plume flow was reduced by a factor of 4 over an 18-h time span. In variance-preserving form, velocity spectra show a separation at frequencies of 0.3–3 cycles per hour between low-frequency and high-frequency signals. The latter show significant coherence between horizontal and vertical velocity components; hence they carried turbulent stress. Based on a comparison with velocity spectra from atmospheric mixed-layer observations, the authors argue that large variance at frequencies of the order of 1 cph was possibly associated with bottom-generated, upward-propagating internal waves. One coherent feature that matched such waves was observed directly. Higher frequencies correspond to turbulent motions of energy-carrying scales. The turbulent Reynolds stress at heights above the bottom between 4 and 30–40 m was computed for most of the ADCP observations. Near the bottom, the streamwise turbulent stress and the streamwise velocity followed a quadratic drag law with drag coefficients ranging from 0.002 to 0.008. There was also significant spanwise stress, hinting at the three-dimensional nature of the boundary layer flow. The time–height variations of the stress and its spectrum proved to be complex, one of its most striking features being angles of up to ∼40° between the direction of the stress and that of the low-frequency flow. The turbulent shear production and eddy viscosity were also examined. On the technical side, the paper discusses the role of the fifth, center-beam velocity measurements in correcting for instrument tilt along with the effect of beam spreading in the 30° Janus configuration of the “regular” four ADCP beams. Instrumental noise and detection limits for the stress are also established. [ABSTRACT FROM AUTHOR]

Hydrographic, direct velocity, and subsurface float observations from the 2001 Red Sea Outflow Experiment (REDSOX) are analyzed to investigate the gravitational and dynamical adjustment of the Red Sea Outflow Water (RSOW) where it is injected into the open ocean in the western Gulf of Aden. During the winter REDSOX cruise, when outflow transport was large, several intermediate-depth salinity maxima (product waters) were formed from various bathymetrically confined branches of the outflow plume, ranging in depth from 400 to 800 m and in potential density from 27.0 to 27.5 σθ, a result of different mixing intensity along each branch. The outflow product waters were not dense enough to sink to the seafloor during either the summer or winter REDSOX cruises, but analysis of previous hydrographic and mooring data and results from a one-dimensional plume model suggest that they may be so during wintertime surges of strong outflow currents, or about 20% of the time during winter. Once vertically equilibrated in the Gulf of Aden, the shallowest RSOW was strongly influenced by mesoscale eddies that swept it farther into the gulf. The deeper RSOW was initially more confined by the walls of the Tadjura Rift, but eventually it escaped from the rift and was advected mainly southward along the continental slope. There was no evidence of a continuous boundary undercurrent of RSOW similar to the Mediterranean Undercurrent in the Gulf of Cadiz. This is explained by considering 1) the variability in outflow transport and 2) several different criteria for separation of a jet at a sharp corner, which indicate that the outflow currents should separate from the boundary where they are injected into the gulf. [ABSTRACT FROM AUTHOR]

When the salty and heavy water of the Red Sea exits from the Strait of Bab el Mandeb, it continues downslope into the Gulf of Aden mainly along two channels. The 130-km-long “Northern Channel” (NC) is topographically confined and is typically only 5 km wide. In it, the Red Sea plume shows unanticipated patterns of vertical structure, turbulent mixing, and entrainment. Above the seafloor a 25–120-m-thick weakly stratified layer shows little dilution along the channel. Hence this bottom layer undergoes only weak entrainment. In contrast, a 35–285-m-thick interfacial layer shows stronger entrainment and is shown in a companion paper to undergo vigorous turbulent mixing. It is thus the interface that exhibits the bulk of entrainment of the Red Sea plume in the NC. The interfacial layer also carries most of the overall plume transport, increasingly so with downstream distance. The “Southern Channel” (SC) is wider than the NC and is accessed from the latter by a sill about 33 m above the floor of the NC. Entrainment into the bottom layer of the SC is diagnosed to be strong near the entry into the SC such that the near-bottom density and salinity are smaller in the SC than in the NC at the same distance from Bab el Mandeb. In comparison with winter conditions, the authors encountered weaker outflow with shallower equilibration depths during the summer cruise. Bulk Froude numbers computed for the whole plume varied within the range 0.2–1. Local maxima occurred in relatively steep channel sections and coincided with locations of significant entrainment. [ABSTRACT FROM AUTHOR]

South of the Strait of Bab el Mandeb, saline Red Sea Water flows downslope into the Gulf of Aden mainly along the narrow 130-km-long “Northern Channel” (NC) and the shorter and wider “Southern Channel” (SC). In the NC, the Red Sea plume simultaneously exhibited weak entrainment into a 35–120-m-thick, weakly stratified bottom layer while a 35–285-m-thick interfacial layer above showed signs of vigorous mixing, overturns up to 30 m thick, and extensive zones of gradient Richardson numbers below 1/4. Turbulent overturning scales, or Thorpe scales, are extracted from regular CTD profiles and equated to Ozmidov scales. On this basis, interfacial mixing is quantified in terms of estimated turbulent dissipation rates, vertical turbulent salt flux, and interfacial stress. Even though these estimates are subject to significant uncertainty, they demonstrate the intensity of mixing during strong winter outflow in terms of eddy diffusivities Kρ on the order of 10-2 m2 s-1. The large Kρ occur in strong stratification such that vertical turbulent salt fluxes are also large. Along the NC, relative maxima of Kρ correspond to maxima in the bulk Froude number. Direct short-term measurements of the Reynolds stress just above the seafloor at two locations, one in the NC and one in the SC, allow comparisons of the bottom stress τb with the interfacial turbulent stress τi. The ratio τi/τb shows large scatter in a small sample, with maximum values on the order of 1. Anoutlines procedures of making and reducing lowered acoustic Doppler current profiler measurements optimized for observing descending plumes. [ABSTRACT FROM AUTHOR]

Presents a simple, two-equation turbulence closure. Extra energy sink in the turbulent kinetic energy equation; Transfer of energy from turbulent kinetic energy to internal waves and other nonturbulent motions; Turbulent time scale; Turbulent dissipation rate; Buoyancy period; Onset of the collapse of turbulence into nonturbulence.

Spatial variations of vertical turbulent mixing along a stretch of the Hudson River estuary are examined with focus on the vicinity of a “hydraulic control point” at the George Washington Bridge at which the cross section narrows and the thalweg takes a bend. Richardson numbers are lowered and mixing is enhanced downstream of this “modest” morphological feature, qualitatively following predictions based on hydraulic theory by Chant and Wilson. The enhancement in the viscous dissipation rate ℇ is only a modest factor of 2–3, however, extending over 2 km along the river. Upon averaging over tidal and fortnightly cycles and multiple cruises, streamwise variations of ℇ along the probed 15-km stretch of the estuary are surprisingly small, given that individual depth averages of ℇ across the halocline vary by over three orders of magnitude. The principal result is that the observed part of the Hudson River showed strong broadly distributed mixing everywhere, with little local concentration. [ABSTRACT FROM AUTHOR]

Given the motivation that overflow processes, which supply source waters for most of the deep and intermediate water masses in the ocean, pose significant numerical and dynamical challenges for ocean general circulation models, an intercomparison study is conducted between field data collected in the Red Sea overflow and a high-resolution, nonhydrostatic process model. The investigation is focused on the part of the outflow that flows along a long narrow channel, referred to as the “northern channel,” that naturally restricts motion in the lateral direction such that the use of a two-dimensional model provides a reasonable approximation to the dynamics. This channel carries about two-thirds of the total Red Sea overflow transport, after the overflow splits into two branches in the western Gulf of Aden. The evolution of the overflow in the numerical simulations can be characterized in two phases: the first phase is highly time dependent, during which the density front associated with the overflow propagates along the channel. The second phase corresponds to that of a statistically steady state. The primary accomplishment of this study is that the model adequately captures the general characteristics of the system: (i) the gradual thickening of the overflow with downstream distance, (ii) the advection of high salinity and temperature signals at the bottom along the channel with little dilution, and (iii) ambient water masses sandwiched between the overflow and surface mixed layer. To quantify mixing of the overflow with the ambient water masses, an entrainment parameter is determined from the transport increase along the slope and is expressed explicitly as a function of mean slope angle. Bulk Richardson numbers are estimated both from data and model and are related to the entrainment parameter. The range of entrainment parameter and its functional dependence on bulk Richardson number in this study are found to be in reasonable agreement with those reported from various laboratory experiments and that based on measurements of the Mediterranean overflow. The results reveal a complex dynamical interaction between shear-induced mixing and internal waves and illustrate the high computational and modeling requirements for numerical simulation of overflows to capture (at least in part) turbulent transports explicitly. [ABSTRACT FROM AUTHOR]

Characterizes the coastal ocean environment at the South Florida Ocean Measurement Center, using observations from very high frequency (VHF) radar. Background on the concept of using high frequency and VHF radar pulses to probe surface ocean currents; Description of the experimental design using the VHF radar; Surface current observations.

ABSTRACT Turbulent mixing in the water column was observed with a microstructure profiler in the Hudson River estuary during two cruises in summer and fall 1995. The focus is on the estimation of turbulent salt flux and turbulent stress from measured viscous dissipation rates (e), and on the tidal and fortnightly variability of these fluxes. In estimating eddy viscosity (K[sub m]) and eddy diffusivity (K[sub p]), the authors follow measurement/modeling techniques of Busch and Osborn, while prescribing a variable flux Richardson number (R[sub j]) dependent upon the gradient Richardson number (Ri). It is argued that a steady-state production-dissipation balance holds in the turbulent kinetic energy budget. All turbulence characteristics varied strongly over semidiurnal tidal cycles and over the fortnightly cycle. Subject to complications arising from nontidal flows, the "strongest" mixing occurred during flood on neap tides, and during ebb on spring tides. In the lower part of the water column during floods and spring ebb K[sub m] and K[sub p] reached maxima of 1-5 (x 10[sup -2] m[sup 2] s[sup -1]) and decreased roughly exponentially with increasing height by 1-3 decades. The smallest eddy coefficients occurred in the halocline during neap tide with K[sub m] Is equivalent to 10[sup 4] m[sup 2] s[sup -1] and K[sub p] Is approximately equal to 10[sup -5] m[sup 2] s[sup -1]. Mostly, the internal turbulent stress (tau[sub y]) was close to 0 in the upper third of the water column and approached the bottom shear stress with decreasing height. Neap ebb had small |tau[sub y]| even close to... [ABSTRACT FROM AUTHOR]

We screened a total of 92 unrelated patients with neurofibromatosis type 1 (NF1) for mutations in exon 37 of the NF1 gene, by using temperature gradient gel electrophoresis. Two novel mutations were found: a 4 bp deletion in a so-called quasi-symmetric element (6789delTTAC) and a recurrent nonsense mutation, which was identified in two unrelated patients, at codon 2264 (C6792A). The independent origin of the latter mutation in two families was confirmed by haplotype analysis. The nonsense mutation and the 4 bp deletion are both predicted to lead to a truncated protein product lacking the Cterminal 20% (aproximately) of its sequence. The occurrence of three independent mutations among 92 NF1 patients at codons 2263-2264 (exon 37) suggests that a specific search for mutations in this area should be undertaken in screening programs for NF1 mutations. [ABSTRACT FROM AUTHOR]

Neurofibromatosis type I (NF1) is a common familial tumour syndrome with multiple clinical features such as neurofibromas, caf´-au-lait spots (CLS), iris Lisch nodules, axillary freckling, optic glioma, specific bone lesions and an increased risk of malignant tumours. It is caused by a wide spectrum of mutations affecting the NF1 gene. Most mutations result in the loss of one allele at the DNA, mRNA or protein level and thus in the loss of any function of the gene product neurofibromin. The idea of the simultaneous loss of several different neurofibromin functions has been postulated to explain the pleiotropic effects of its loss. However, we have identified a novel missense mutation in a family with a classical multi-symptomatic NF1 phenotype, including a malignant schwannoma, that specifically abolishes the Ras-GTPase-activating function of neurofibromin. In this family, Arg1276 had mutated into proline. Based on complex biochemical studies as well as the analysis of the crystal structure of the GTPaseactivating protein (GAP) domain of p120GAP in the presence of Ras, we unequivocally identified this amino acid as the arginine finger of the neurofibromin GAP-related domain (GRD)—the most essential catalytic element for RasGAP activity. Here, we present data demonstrating that the mutation R1276P, unlike previously reported missense mutations of the GRD region, does not impair the secondary and tertiary protein structure. It neither reduces the level of cellular neurofibromin nor influences its binding to Ras substantially, but it does completely disable GAP activity. Our findings provide direct evidence that failure of neurofibromin GAP activity is the critical element of NF1 pathogenesis. Thus, therapeutic approaches aimed at the reduction of Ras. GTP levels in neural crest-derived cells can be expected to relieve most of the NF1 symptoms. [ABSTRACT FROM AUTHOR]

Cherubism (MIM 118400) is an autosomal dominant inherited syndrome characterized by excessive bone degradation of the upper and lower jaws followed by development of fibrous tissue masses, which causes a characteristic facial swelling. Here we describe seven mutations in the SH3-binding protein SH3BP2 (MIM 602104) on chromosome 4p16.3 that cause cherubism. [ABSTRACT FROM AUTHOR]

The article informs that the author claims of a better fit to laboratory data of turbulent length scales than that found in BPO4. It can be achieved either with a traditional model or with a modification of the BPO4 closure, and he finally argues that there is no need for BPO4's explicit term of energy transfer from turbulence to internal waves. The notation herein is that of K05 and BPO4 and needs no specific definitions. BPO4 deliberately refrained from tuning and optimizing parameters. This closure is not tunable; its body and its parameter values form a unity.