Effect of stratification due to suspended sediment on velocity and concentration distribution in turbulent flows

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2004.Includes bibliographical references (p. 149-152).(cont.) An examination of the effects of uncertainty in the predictive capability of our model reveals that this overshadows the slight improvement resulting from accounting for stratification. Finally, our stratification model appears to be nearly equivalent to making von Karman's constant a variable as done in the earliest attempts to account for stratification in sediment-laden flows.Sediment-induced stratification effects on velocity profiles and sediment concentration distribution in a steady, uniform turbulent flow are examined in this thesis. The early work concerning sediment stratification relates this to von Karman's constant's variability. Subsequent attempts to account for stratification were based on the stratified flow analogy, introducing the parameters α and β, whose values were assumed to be those obtained for thermally stratified flows. Following these investigators, we assume stratification effects to be expressed through these parameters. We solve the governing equations for velocity and sediment concentration for a parabolic, a simplified linear-constant and an extremely simplified linear neutral eddy viscosity model. Analytically closed form solutions are obtained. The parabolic and linear-constant models' formulae require numerical evaluation of integrals. The linear model provides excellent estimates of velocity and concentration and does not require numerical computation. We run our model against experimental data to obtain the optimal set [α, β]. For neutral conditions, β = 0 by definition, and we obtain α = 1. For stratified conditions the optimal values are α = 0.8 and β = 4.0. Accounting for stratification slightly improves the prediction of velocity and concentration in comparison with the case where we do not account for it. For predictive purposes, we need to know the movable bed roughness and the reference concentration. Analyses of experimental data sets provide predictive relationships for reference concentration and movable bed roughness in terms of sediment and flow parameters.by Julie Marine Herrmann.S.M

Mediterranean Sea response to climate change in an ensemble of twenty first century scenarios

The Mediterranean climate is expected to become warmer and drier during the twenty-first century. Mediterranean Sea response to climate change could be modulated by the choice of the socio-economic scenario as well as the choice of the boundary conditions mainly the Atlantic hydrography, the river runoff and the atmospheric fluxes. To assess and quantify the sensitivity of the Mediterranean Sea to the twenty-first century climate change, a set of numerical experiments was carried out with the regional ocean model NEMOMED8 set up for the Mediterranean Sea. The model is forced by air–sea fluxes derived from the regional climate model ARPEGE-Climate at a 50-km horizontal resolution. Historical simulations representing the climate of the period 1961–2000 were run to obtain a reference state. From this baseline, various sensitivity experiments were performed for the period 2001–2099, following different socio-economic scenarios based on the Special Report on Emissions Scenarios. For the A2 scenario, the main three boundary forcings (river runoff, near-Atlantic water hydrography and air–sea fluxes) were changed one by one to better identify the role of each forcing in the way the ocean responds to climate change. In two additional simulations (A1B, B1), the scenario is changed, allowing to quantify the socio-economic uncertainty. Our 6-member scenario simulations display a warming and saltening of the Mediterranean. For the 2070–2099 period compared to 1961–1990, the sea surface temperature anomalies range from +1.73 to +2.97 °C and the SSS anomalies spread from +0.48 to +0.89. In most of the cases, we found that the future Mediterranean thermohaline circulation (MTHC) tends to reach a situation similar to the eastern Mediterranean Transient. However, this response is varying depending on the chosen boundary conditions and socio-economic scenarios. Our numerical experiments suggest that the choice of the near-Atlantic surface water evolution, which is very uncertain in General Circulation Models, has the largest impact on the evolution of the Mediterranean water masses, followed by the choice of the socio-economic scenario. The choice of river runoff and atmospheric forcing both have a smaller impact. The state of the MTHC during the historical period is found to have a large influence on the transfer of surface anomalies toward depth. Besides, subsurface currents are substantially modified in the Ionian Sea and the Balearic region. Finally, the response of thermosteric sea level ranges from +34 to +49 cm (2070–2099 vs. 1961–1990), mainly depending on the Atlantic forcing

Characterizing, modelling and understanding the climate variability of the deep water formation in the North-Western Mediterranean Sea

Observing, modelling and understanding the climate-scale variability of the deep water formation (DWF) in the North-Western Mediterranean Sea remains today very challenging. In this study, we first characterize the interannual variability of this phenomenon by a thorough reanalysis of observations in order to establish reference time series. These quantitative indicators include 31 observed years for the yearly maximum mixed layer depth over the period 1980–2013 and a detailed multi-indicator description of the period 2007–2013. Then a 1980–2013 hindcast simulation is performed with a fully-coupled regional climate system model including the high-resolution representation of the regional atmosphere, ocean, land-surface and rivers. The simulation reproduces quantitatively well the mean behaviour and the large interannual variability of the DWF phenomenon. The model shows convection deeper than 1000 m in 2/3 of the modelled winters, a mean DWF rate equal to 0.35 Sv with maximum values of 1.7 (resp. 1.6) Sv in 2013 (resp. 2005). Using the model results, the winter-integrated buoyancy loss over the Gulf of Lions is identified as the primary driving factor of the DWF interannual variability and explains, alone, around 50 % of its variance. It is itself explained by the occurrence of few stormy days during winter. At daily scale, the Atlantic ridge weather regime is identified as favourable to strong buoyancy losses and therefore DWF, whereas the positive phase of the North Atlantic oscillation is unfavourable. The driving role of the vertical stratification in autumn, a measure of the water column inhibition to mixing, has also been analyzed. Combining both driving factors allows to explain more than 70 % of the interannual variance of the phenomenon and in particular the occurrence of the five strongest convective years of the model (1981, 1999, 2005, 2009, 2013). The model simulates qualitatively well the trends in the deep waters (warming, saltening, increase in the dense water volume, increase in the bottom water density) despite an underestimation of the salinity and density trends. These deep trends come from a heat and salt accumulation during the 1980s and the 1990s in the surface and intermediate layers of the Gulf of Lions before being transferred stepwise towards the deep layers when very convective years occur in 1999 and later. The salinity increase in the near Atlantic Ocean surface layers seems to be the external forcing that finally leads to these deep trends. In the future, our results may allow to better understand the behaviour of the DWF phenomenon in Mediterranean Sea simulations in hindcast, forecast, reanalysis or future climate change scenario modes. The robustness of the obtained results must be however confirmed in multi-model studies

ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data.

Abstract Motivation The study of immunoglobulins and T cell receptors using next-generation sequencing has finally allowed exploring immune repertoires and responses in their immense variability and complexity. Unsurprisingly, their analysis and interpretation is a highly convoluted task. Results We thus implemented ARResT/Interrogate, a web-based, interactive application. It can organize and filter large amounts of immunogenetic data by numerous criteria, calculate several relevant statistics, and present results in the form of multiple interconnected visualizations. Availability and Implementation ARResT/Interrogate is implemented primarily in R, and is freely available at http://bat.infspire.org/arrest/interrogate/ Supplementary information Supplementary data are available at Bioinformatics online

Abnormal features of oceanographic characteristics in upwelling Vietnam waters under impact of El Niño events

The summer upwelling that occurs in coastal waters of South Central Vietnam is one of the major hydrographic features in the South China Sea. A weakening of the upwelling after major El Niño events was observed in the literature for previous El Nino events and was verified here from the analysis of new satellite image data sets of sea surface temperature (SST) and surface wind. The analysis of empirical orthogonal function (EOF) from of monthly SST as well as of temporal and spatial variations of SST and wind force allow us to identify abnormal characteristics in ocean surface water that happened after El Niño episode, in agreement with previous studies. Those abnormal characteristics in Vietnam upwelling waters appeared mainly during the summers of 1998, 2003, 2010 and 2016 years for the El Niño decline phase. The upwelling weakening during El Niño decline episodes is associated with the following signals: (1) Wind force and Ekman pump are very weak; (2) the cold  and high chlorophyll-a  tongue is shifted northward but not extended eastward; (3) for years when El Nino occurs, SST strongly increases and reaches a peak in May or early June of next year, during the declining phase of El Niño episode; (4) upwelling phenomenon typically occurs during August and not July. Using a reanalysis dataset derived from the HYCOM/NCODA system coupled with a local Finite Element Model (FEM) allow us to complete our knowledge about the abnormal oceanographic characteristics of deeper water layers after El Niño episodes. The analysis of spatial variations of oceanography fields derived from HYCOM/NCODA/FEM system along zonal and meridional sections and vertical profiles as well as the results obtained from water mass analysis allow us to identify in details the abnormal oceanic characteristics of deeper water layers during the declining  El Niño phase. Those are; (5) Sea water in both surface and deeper water layers were transported dominantly northward  but not eastward; (6) The thermo-halocline layer in South Vietnam upwelling center was deeper (about 90 -100m), compared with previous El Nino and normal years (50-60 m and 35-40 m, respectively); (7) Extreme global warming in recent years (2012-2016) pressed the thermo-halocline layer in upwelling center deeper (90-100 m) during summer. Under the influence of the ocean global warming, this process should progress continuously, the depth of thermo-halocline layer should become therefore deeper and deeper in next years.References Barthel, K., R. Rosland, and N. C. Thai, 2009. Modelling the circulation on the continental shelf of the province Khanh Hoa in Vietnam, J. Mar. Syst., 77(1-2), 89-113. Bui Hong Long, Tran Van Chung, 2009. Calculations of currents in the upwelling region along south-central Vietnamese coast, using three dimensions (3-D) nonlinear model”, Journal of Marine Science and Technology - VAST, 9(2), 01-25 (in Vietnamese). Bui Hong Long, Tran Van Chung, 2017. Preliminary studies on the impact of climate change on the upwelling region south Central Vietnam in summer.  Journal of Marine Science and Technology - VAST , 17(1), 01-19 (in Vietnamese). Colling, A., 2001. Ocean Circulation, Open University Course Team. Second Edition. ISBN 978-0-7506-5278-0. Dippner, J. W., and N. Loick-Wilde, 2011. A redefinition of water masses in the Vietnamese upwelling area, J. Mar. Syst., 84(1-2), 42-47. Hale, W.G, Margham, J.P,  and Sauder, V.A, 2005. Collins Dictionary of  Biology 3rd . London: Collin. Huang, Q.-Z.,W.-Z. Wang, Y. S. Li, and C. W. Li, 1994. Current characteristics of the South China Sea, in Oceanology of China Sea, edited by D. Zhou, Y.-B. Liang, and C. K. Tsebgm, 39-47, Kluwer Acad., Norwell, Mass. H.E. Hurlburt, E.P. Chassignet, J.A. Cummings, A.B. Kara, E.J. Metzger, J.F. Shriver, O.M. Smedstad, A.J. Wallcraft, and C.N. Barron, 2008. Eddy-resolving Global Ocean Prediction, in M. Hecht and H. Hasumi, eds., Ocean Modeling in an Eddying Regime, Geophysical Monograph 177 (American Geophysical Union, Washington, DC ). Knauss, J.A., 2005. Introduction to Physical Oceanography, Waveland Press. Second Edition. ISBN 978-1-57766-429-1. Kuo. N. J, Zheng. Q, Ho C. R, 2004.  Response of Vietnam coastal upwelling to the 1997-1998 ENSO event observed by multisensor data, Remote sensing of Environment, 15 January, 89(1), 106-115. Le Phuoc Trinh, Nguyen Tien Dung, Nguyen Van Minh, Le Minh Tan, Nguyen Kim Vinh, 1981. A proposal of studies on the upwelling of Southeastern coast of Vietnam, Collection of Marine Research Works, 2(2), 13-31 (in Vietnamese). Nguyen Van Long and Vo. Si  Tuan, 2010. Status of coral reefs in Vietnam following the 2010 coral bleaching event. In: Kimura T, Tun K (eds) Status of Coral Reefs in East Asian Seas Region: Ministry of the Environment, Japan, 29-49. NOAA National Centers for Environmental Information, State of the Climate: Global Analysis for Annual 2010, published online January 2011, retrieved on March 25, 2017 from http://www.ncdc.noaa.gov/sotc/global/201013. Ose, T., Y. Song, and A. Kitoh, 1997. Sea surface temperature in the South China Sea: An index for the Asian monsoon and ENSO system, J. Meteorol. Soc. Japan., 75, 1091-1107. Pohlmann, T., 1987. A three dimensional circulation model of the South China Sea., 245-268. In Three-Dimensional Models of Marine and Estuarine Dynamics, ed. by J. J. Nihoul and B. M. Jamart, Elsevier, New York. Qu, T,  Kim, Y.Y, Yaremchuk, M., Tozuka. T, Ishida, A, Yamagata, T., 2004. Can Luzon strait transport play a role in conveying the impact of ENSO to the South China Sea J. Clim. 17, 3644-3657 Shaw, P. T., and S. Y. Chao, 1994.  Surface Circulation in the South China Sea, Deep-Sea Res., I(41), 1663-1683. Siswanto, E., H. Ye, D. Yamazaki, and D.L. Tang 2017. Detailed spatiotemporal impacts of El Niño on phytoplankton biomass in the South China Sea, J. Geophys. Res. Oceans, 122, doi:10.1002/2016JC012276. Sverdrup, H.U., M.W. Johnson and Fleming, R.H., 1942. The Oceans: their physics, chemistry and general biology. Prentice Hall, New York, 1087p. Tang D. L., H. Kawamura, H. Doan Nhu, and W. Takahashi, 2004. Remote sensing oceanography of a harmful algal bloom off the coast of southeastern Vietnam, J. Geophys. Res., 109, C03014, doi:10.1029/ 2003JC002045. Thai Minh Quang, 2016. Studies on influence of  2016.  El Niño event to coral bleaching phenomena in coastal waters in Ninh Hai - Ninh Thuan province. Technical report of  basic research pro­ject funded by Institute of Oceanography - the Vietnam Academy of Science and Technology (in Vietnamese). Tong Phuoc Hoang Son, Vo Van Lanh and Lau Va Khin, 2005. Application of empirical orthogonal function (EOF) for studying thermal structure in sea surface water in South China Sea. The 26th Asian Remote sensing Conference, 7-11 November 2005 in Hanoi. Tran Van Chung, Bui Hong Long, 2016. Effect of temperature field and anomalies of sea water level in East Vietnam Sea in relationship to global climate change - Journal of Marine Science and Technology - VAST, 16(3), 255-266 (in Vietnamese). Vo Van Lanh, 1995. The environmental characteristics of strongly upwelling waters in south of Vietnam and its ecological impacts. Technical report of National project KT03.05. Institute of Oceanography, 480p (in Vietnamese). Vo Si Tuan, 2000. The corals at Con Dao archipelago (South Vietnam): before, during and after the bleaching event in 1998. In: Proceeding of 9th International Coral Reef Symposium, Bali, Indonesia, 23rd-27th October, 895-899. Wang B., An S., 2005. A method for detecting season-dependent modes of climate variability: S-EOF analysis. Geophys. Res. Lett., 32, L15710. Wyrtki K., 1961. Physical oceanography of the Southeast Asian waters, Naga Rep. 2, 195p, Scripps Inst. of Oceanogr., La Jolla, Calif. Xie S.-P., Q. Xie, D. Wang and W. T. Liu, 2003. Summer upwelling in the South China Sea and its role in regional climate variations, J. Geophys. Res., 108(C8), 3261, doi:10.1029/2003JC001867. Xie S.-P., C.-H. Chang, Q. Xie and D. Wang, 2007. Intraseasonal variability in the summer South China Sea: Wind jet, cold filament, and recirculations, J. Geophys. Res., 112, C10008, doi:10.1029/2007JC004238

Corneal Alterations during Combined Therapy with Cyclodextrin/Allopregnanolone and Miglustat in a Knock-Out Mouse Model of NPC1 Disease

BACKGROUND: Niemann Pick disease type C1 is a neurodegenerative disease caused by mutations in the NPC1 gene, which result in accumulation of unesterified cholesterol and glycosphingolipids in the endosomal-lysosomal system as well as limiting membranes. We have previously shown the corneal involvement in NPC1 pathology in form of intracellular inclusions in epithelial cells and keratocytes. The purpose of the present study was to clarify if these inclusions regress during combined substrate reduction- and by-product therapy (SRT and BPT). METHODOLOGY/PRINCIPAL FINDINGS: Starting at postnatal day 7 (P7) and thereafter, NPC1 knock-out mice (NPC1(-/-)) and wild type controls (NPC1(+/+)) were injected with cyclodextrin/allopregnanolone weekly. Additionally, a daily miglustat injection started at P10 until P23. Starting at P23 the mice were fed powdered chow with daily addition of miglustat. The sham group was injected with 0.9% NaCl at P7, thereafter daily starting at P10 until P23, and fed powdered chow starting at P23. For corneal examination, in vivo confocal laser-scanning microscopy (CLSM) was performed one day before experiment was terminated. Excised corneas were harvested for lipid analysis (HPLC/MS) and electron microscopy. In vivo CLSM demonstrated a regression of hyperreflective inclusions in all treated NPC1(-/-)mice. The findings varied between individual mice, demonstrating a regression, ranging from complete absence to pronounced depositions. The reflectivity of inclusions, however, was significantly lower when compared to untreated and sham-injected NPC1(-/-) mice. These confocal findings were confirmed by lipid analysis and electron microscopy. Another important CLSM finding revealed a distinct increase of mature dendritic cell number in corneas of all treated mice (NPC1(-/-) and NPC1(+/+)), including sham-treated ones. CONCLUSIONS/SIGNIFICANCE: The combined substrate reduction- and by-product therapy revealed beneficial effects on the cornea. In vivo CLSM is a non-invasive tool to monitor disease progression and treatment effects in NPC1 disorder

Data Descriptor : Collocated observations of cloud condensation nuclei, particle size distributions, and chemical composition

Cloud condensation nuclei (CCN) number concentrations alongside with submicrometer particle number size distributions and particle chemical composition have been measured at atmospheric observatories of the Aerosols, Clouds, and Trace gases Research InfraStructure (ACTRIS) as well as other international sites over multiple years. Here, harmonized data records from 11 observatories are summarized, spanning 98,677 instrument hours for CCN data, 157,880 for particle number size distributions, and 70,817 for chemical composition data. The observatories represent nine different environments, e.g., Arctic, Atlantic, Pacific and Mediterranean maritime, boreal forest, or high alpine atmospheric conditions. This is a unique collection of aerosol particle properties most relevant for studying aerosol-cloud interactions which constitute the largest uncertainty in anthropogenic radiative forcing of the climate. The dataset is appropriate for comprehensive aerosol characterization (e.g., closure studies of CCN), model-measurement intercomparison and satellite retrieval method evaluation, among others. Data have been acquired and processed following international recommendations for quality assurance and have undergone multiple stages of quality assessment.Peer reviewe

The Evolution of Primate Short-Term Memory.

Short-term memory is implicated in a range of cognitive abilities and is critical for understanding primate cognitive evolution. To investigate the effects of phylogeny, ecology and sociality on short-term memory, we tested the largest and most diverse primate sample to date (421 non-human primates across 41 species) in an experimental delayed-response task. Our results confirm previous findings that longer delays decrease memory performance across species and taxa. Our analyses demonstrate a considerable contribution of phylogeny over ecological and social factors on the distribution of short-term memory performance in primates; closely related species had more similar short-term memory abilities. Overall, individuals in the branch of Hominoidea performed better compared to Cercopithecoidea, who in turn performed above Platyrrhini and Strepsirrhini. Interdependencies between phylogeny and socioecology of a given species presented an obstacle to disentangling the effects of each of these factors on the evolution of short-term memory capacity. However, this study offers an important step forward in understanding the interspecies and individual variation in short-term memory ability by providing the first phylogenetic reconstruction of this trait’s evolutionary history. The dataset constitutes a unique resource for studying the evolution of primate cognition and the role of short-term memory in other cognitive abilities.info:eu-repo/semantics/publishedVersio