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  • American Meteorological Society  (8,603)
  • Annual Reviews
  • 2005-2009  (9,244)
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  • 1
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    American Meteorological Society
    In:  Journal of Climate, 19 . pp. 5667-5685.
    Publication Date: 2018-06-29
    Description: This paper analyses secular changes and interannual variability in the wind wave, swell, and significant wave height (SWH) characteristics over the North Atlantic and North Pacific on the basis of wind wave climatology derived from the visual wave observations of voluntary observing ship (VOS) officers. These data are available from the International Comprehensive Ocean–Atmosphere Data Set (ICOADS) collection of surface meteorological observations for 1958–2002, but require much more complicated preprocessing than standard meteorological variables such as sea level pressure, temperature, and wind. Visual VOS data allow for separate analysis of changes in wind sea and swell, as well as in significant wave height, which has been derived from wind sea and swell estimates. In both North Atlantic and North Pacific midlatitudes winter significant wave height shows a secular increase from 10 to 40 cm decade−1 during the last 45 yr. However, in the North Atlantic the patterns of trend changes for wind sea and swell are quite different from each other, showing opposite signs of changes in the northeast Atlantic. Trend patterns of wind sea, swell, and SWH in the North Pacific are more consistent with each other. Qualitatively the same conclusions hold for the analysis of interannual variability whose leading modes demonstrate noticeable differences for wind sea and swell. Statistical analysis shows that variability in wind sea is closely associated with the local wind speed, while swell changes can be driven by the variations in the cyclone counts, implying the importance of forcing frequency for the resulting changes in significant wave height. This mechanism of differences in variability patterns of wind sea and swell is likely more realistic than the northeastward propagation of swells from the regions from which the wind sea signal originates.
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  • 2
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    American Meteorological Society
    In:  Journal of Climate, 19 (23). pp. 6062-6067.
    Publication Date: 2017-08-23
    Description: The influence of the natural multidecadal variability of the Atlantic meridional overturning circulation (MOC) on European climate is investigated using a simulation with the coupled atmosphere–ocean general circulation model ECHAM5/Max Planck Institute Ocean Model (MPI-OM). The results show that Atlantic MOC fluctuations, which go along with changes in the northward heat transport, in turn affect European climate. Additionally, ensemble predictability experiments with ECHAM5/MPI-OM show that the probability density functions of surface air temperatures in the North Atlantic/European region are affected by the multidecadal variability of the large-scale oceanic circulation. Thus, some useful decadal predictability may exist in the Atlantic/European sector.
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  • 3
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    American Meteorological Society
    In:  Journal of Climate, 18 (19). pp. 4013-4031.
    Publication Date: 2017-08-23
    Description: Analyses of a 500-yr control integration with the non-flux-adjusted coupled atmosphere–sea ice–ocean model ECHAM5/Max-Planck-Institute Ocean Model (MPI-OM) show pronounced multidecadal fluctuations of the Atlantic overturning circulation and the associated meridional heat transport. The period of the oscillations is about 70–80 yr. The low-frequency variability of the meridional overturning circulation (MOC) contributes substantially to sea surface temperature and sea ice fluctuations in the North Atlantic. The strength of the overturning circulation is related to the convective activity in the deep-water formation regions, most notably the Labrador Sea, and the time-varying control on the freshwater export from the Arctic to the convection sites modulates the overturning circulation. The variability is sustained by an interplay between the storage and release of freshwater from the central Arctic and circulation changes in the Nordic Seas that are caused by variations in the Atlantic heat and salt transport. The relatively high resolution in the deep-water formation region and the Arctic Ocean suggests that a better representation of convective and frontal processes not only leads to an improvement in the mean state but also introduces new mechanisms determining multidecadal variability in large-scale ocean circulation.
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  • 4
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    American Meteorological Society
    In:  Journal of Physical Oceanography, 37 (4). pp. 946-961.
    Publication Date: 2018-04-11
    Description: A model of the subpolar North Atlantic Ocean is used to study different aspects of ventilation and water mass transformation during a year with moderate convection intensity in the Labrador Sea. The model realistically describes the salient features of the observed hydrographic structure and current system, including boundary currents and recirculations. Ventilation and transformation rates are defined and compared. The transformation rate of Labrador Sea Water (LSW), defined in analogy to several observational studies, is 6.3 Sv (Sv ≡ 106 m3 s−1) in the model. Using an idealized ventilation tracer, mimicking analyses based on chlorofluorocarbon inventories, an LSW ventilation rate of 10 Sv is found. Differences between both rates are particularly significant for those water masses that are partially transformed into denser water masses during winter. The main export route of the ventilated LSW is the deep Labrador Current (LC). Backward calculation of particle trajectories demonstrates that about one-half of the LSW leaving the Labrador Sea within the deep LC originates in the mixed layer during that same year. Near the offshore flank of the deep LC at about 55°W, the transformation of LSW begins in January and is at a maximum in February/March. While the export of transformed LSW out of the central Labrador Sea continues for several months, LSW generated near the boundary current is exported more rapidly, with maximum transport rates during March/April within the deep LC.
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  • 5
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    American Meteorological Society
    In:  Journal of Climate, 20 (1). pp. 131-142.
    Publication Date: 2017-08-23
    Description: An observational-based analysis of coupled variability in the equatorial Atlantic and its seasonality is presented. Regression analysis shows that the three elements of the Bjerknes positive feedback exist in the Atlantic and are spatially similar to those of the Pacific. The cross-correlation functions of the elements of the Bjerknes feedback are also similar and consistent with an ocean–atmosphere coupled mode. However, the growth rate in the Atlantic is up to 50% weaker, and explained variance is significantly lower. The Bjerknes feedback in the Atlantic is strong in boreal spring and summer, and weak in other seasons, which explains why the largest sea surface temperature anomalies (SSTAs) occur in boreal summer. Its seasonality is determined by seasonal variations in both atmospheric sensitivity to SSTA and SSTA sensitivity to subsurface temperature anomalies.
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  • 6
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    American Meteorological Society
    In:  Journal of Climate, 18 . pp. 5382-5389.
    Publication Date: 2017-08-23
    Description: The dominant pattern of atmospheric variability in the North Atlantic sector is the North Atlantic Oscillation (NAO). Since the 1970s the NAO has been well characterized by a trend toward its positive phase. Recent atmospheric general circulation model studies have linked this trend to a progressive warming of the Indian Ocean. Unfortunately, a clear mechanism responsible for the change of the NAO could not be given. This study provides further details of the NAO response to Indian Ocean sea surface temperature (SST) anomalies. This is done by conducting experiments with a coupled ocean–atmosphere general circulation model (OAGCM). The authors develop a hypothesis of how the Indian Ocean impacts the NAO.
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  • 7
    Publication Date: 2017-03-21
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  • 8
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    American Meteorological Society
    In:  Journal of Physical Oceanography, 37 . pp. 727-742.
    Publication Date: 2018-04-11
    Description: Output from an eddy-resolving model of the North Atlantic Ocean is used to estimate values for the thickness diffusivity κ appropriate to the Gent and McWilliams parameterization. The effect of different choices of rotational eddy fluxes on the estimated κ is discussed. Using the raw fluxes (no rotational flux removed), large negative values (exceeding −5000 m2 s−1) of κ are diagnosed locally, particularly in the Gulf Stream region and in the equatorial Atlantic. Removing a rotational flux based either on the suggestion of Marshall and Shutts or the more general theory of Medvedev and Greatbatch leads to a reduction of the negative values, but they are still present. The regions where κ 〈 0 correspond to regions where eddies are acting to increase, rather than decrease (as in baroclinic instability) the mean available potential energy. In the subtropical gyre, κ ranges between 500 and 2000 m2 s−1, rapidly decreasing to zero below the thermocline in all cases. Rotational fluxes and κ are also estimated using an optimization technique. In this case, |κ| can be reduced or increased by construction, but the regions where κ 〈 0 are still present and the optimized rotational fluxes also remain similar to a priori values given by the theoretical considerations. A previously neglected component (ν) of the bolus velocity is associated with the horizontal flux of buoyancy along, rather than across, the mean buoyancy contours. The ν component of the bolus velocity is interpreted as a streamfunction for eddy-induced advection, rather than diffusion, of mean isopycnal layer thickness, showing up when the lateral eddy fluxes cannot be described by isotropic diffusion only. All estimates show a similar large-scale pattern for ν, implying westward advection of isopycnal thickness over much of the subtropical gyre. Comparing ν with a mean streamfunction shows that it is about 10% of the mean in midlatitudes and even larger than the mean in the Tropics.
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  • 9
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    American Meteorological Society
    In:  Journal of Climate, 19 (16). pp. 3973-3987.
    Publication Date: 2017-08-23
    Description: The influence of phytoplankton on the seasonal cycle and the mean global climate is investigated in a fully coupled climate model. The control experiment uses a fixed attenuation depth for shortwave radiation, while the attenuation depth in the experiment with biology is derived from phytoplankton concentrations simulated with a marine biogeochemical model coupled online to the ocean model. Some of the changes in the upper ocean are similar to the results from previous studies that did not use interactive atmospheres, for example, amplification of the seasonal cycle; warming in upwelling regions, such as the equatorial Pacific and the Arabian Sea; and reduction in sea ice cover in the high latitudes. In addition, positive feedbacks within the climate system cause a global shift of the seasonal cycle. The onset of spring is about 2 weeks earlier, which results in a more realistic representation of the seasons. Feedback mechanisms, such as increased wind stress and changes in the shortwave radiation, lead to significant warming in the midlatitudes in summer and to seasonal modifications of the overall warming in the equatorial Pacific. Temperature changes also occur over land where they are sometimes even larger than over the ocean. In the equatorial Pacific, the strength of interannual SST variability is reduced by about 10%–15% and phase locking to the annual cycle is improved. The ENSO spectral peak is broader than in the experiment without biology and the dominant ENSO period is increased to around 5 yr. Also the skewness of ENSO variability is slightly improved. All of these changes lead to the conclusion that the influence of marine biology on the radiative budget of the upper ocean should be considered in detailed simulations of the earth’s climate.
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  • 10
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    American Meteorological Society
    In:  Journal of Physical Oceanography, 35 (4). pp. 489-511.
    Publication Date: 2018-04-11
    Description: The Labrador Sea is one of the few regions of the World Ocean where deep convection takes place. Several moorings across the Labrador continental slope just north of Hamilton Bank show that convection does take place within the Labrador Current. Mixing above the lower Labrador slope is facilitated by the onshore along-isopycnal intrusions of low-potential-vorticity eddies that weaken the stratification, combined with baroclinic instability that sustains slanted mixing while restratifying the water column through horizontal fluxes. Above the shelf break, the Irminger seawater core is displaced onshore while the stratification weakens with the increase in isopycnal slope. The change in stratification is partially due to the onshore shift of the “classical” Labrador Current, baroclinic instability, and possibly slantwise convection.
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  • 11
    Publication Date: 2017-08-23
    Description: Recent observations show dramatic changes of the Arctic atmosphere–ice–ocean system. Here the authors demonstrate, through the analysis of a vast collection of previously unsynthesized observational data, that over the twentieth century the central Arctic Ocean became increasingly saltier with a rate of freshwater loss of 239 ± 270 km3 decade−1. In contrast, long-term (1920–2003) freshwater content (FWC) trends over the Siberian shelf show a general freshening tendency with a rate of 29 ± 50 km3 decade−1. These FWC trends are modulated by strong multidecadal variability with sustained and widespread patterns. Associated with this variability, the FWC record shows two periods in the 1920s–30s and in recent decades when the central Arctic Ocean was saltier, and two periods in the earlier century and in the 1940s–70s when it was fresher. The current analysis of potential causes for the recent central Arctic Ocean salinification suggests that the FWC anomalies generated on Arctic shelves (including anomalies resulting from river discharge inputs) and those caused by net atmospheric precipitation were too small to trigger long-term FWC variations in the central Arctic Ocean; to the contrary, they tend to moderate the observed long-term central-basin FWC changes. Variability of the intermediate Atlantic Water did not have apparent impact on changes of the upper–Arctic Ocean water masses. The authors’ estimates suggest that ice production and sustained draining of freshwater from the Arctic Ocean in response to winds are the key contributors to the salinification of the upper Arctic Ocean over recent decades. Strength of the export of Arctic ice and water controls the supply of Arctic freshwater to subpolar basins while the intensity of the Arctic Ocean FWC anomalies is of less importance. Observational data demonstrate striking coherent long-term variations of the key Arctic climate parameters and strong coupling of long-term changes in the Arctic–North Atlantic climate system. Finally, since the high-latitude freshwater plays a crucial role in establishing and regulating global thermohaline circulation, the long-term variations of the freshwater content discussed here should be considered when assessing climate change and variability.
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  • 12
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    American Meteorological Society
    In:  Journal of Climate, 20 (10). pp. 2058-2075.
    Publication Date: 2017-08-23
    Description: In this paper, a version of the European Centre for Medium-Range Weather Forecasts (ECMWF) operational model is used to (i) diagnose the diabatic heating associated with the winter North Atlantic Oscillation (NAO) and (ii) assess the role of this heating in the dynamics of the NAO in the model. Over the North Atlantic sector, the NAO-related diabatic heating is dominated above the planetary boundary layer by the latent heat release associated with precipitation, and within the boundary layer by vertical diffusion associated with sensible heat flux from the ocean. An association between La Niña–El Niño–type conditions in the tropical Pacific and the positive/negative NAO is found in model runs using initial conditions and sea surface temperature (SST) lower boundary conditions from the period 1982–2001, but not in a companion set of model runs for the period 1962–81. Model experiments are then described in which the NAO-related diabatic heating diagnosed from the 1982–2001 control run is applied as a constant forcing in the model temperature equation using both 1982–2001 and 1962–81 model setups. To assess the local feedback from the diabatic heating, the specified forcing is first restricted to the North Atlantic sector alone. In this case, the model response (in an ensemble mean sense) is suggestive of a weak negative feedback, but exhibits more baroclinic structure and has its centers of action shifted compared to those of the NAO. On the other hand, forcing with only the tropical Pacific part of the diabatic heating leads to a robust model response in both the 1982–2001 and 1962–81 model setups. The model response projects on to the NAO with the same sign as that used to diagnose the forcing, arguing that the link between the tropical Pacific and the NAO is real in the 1982–2001 control run. The missing link in the corresponding run for 1962–81 is a result of a change in the tropical forcing between the two periods, and not the extratropical flow regime.
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  • 13
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    American Meteorological Society
    In:  Journal of Physical Oceanography, 36 (1). pp. 43-63.
    Publication Date: 2017-11-15
    Description: The circulation of the northeastern Atlantic Ocean at intermediate depths is characterized by watermass transformation processes that involve Iceland–Scotland Overflow Water (ISOW) from the northeast, Labrador Sea Water (LSW) from the west, and Mediterranean Water from the south. Field observations were carried out with 89 eddy-resolving floats (RAFOS and MARVOR types). The data coverage achieved is remarkably high and enables a comprehensive study of the eastern basins between Iceland and the Azores. The trajectories show typical pathways of the water masses involved and the role that the complex bottom topography plays in defining them. The ISOW paths tend to lean against the slopes of the Reykjanes Ridge and Rockall Plateau. Westward escapes through multiple gaps in the ridge are possible, superimposed on a sustained southward flow in the eastern basin along the Mid-Atlantic Ridge. LSW pathways leading to the eastern basins are subject to high variability in flow direction and eddy activity. In addition to a selection of characteristic trajectories, maps of the horizontal distributions of Lagrangian eddy kinetic energy and integral time scales are presented. These reveal distinct areas of intensified mixing in the Iceland Basin, as well as the sharp contrast between the subpolar and subtropical dynamics. A self-contained eddy detection scheme is applied to obtain statistics on individual eddy properties and their abundance. It is suggested that much of the intensified mixing can be related to cyclonic activity, particularly in the subpolar region.
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  • 14
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    American Meteorological Society
    In:  Journal of Climate, 22 (18). pp. 4939-4952.
    Publication Date: 2017-08-24
    Description: A characteristic feature of global warming is the land-sea contrast, with stronger warming over land than over oceans. Recent studies find that this land-sea contrast also exists in equilibrium global change scenarios, and it is caused by differences in the availability of surface moisture over land and oceans. In this study it is illustrated that this land-sea contrast exists also on interannual time scales and that the ocean-land interaction is strongly asymmetric. The land surface temperature is more sensitive to the oceans than the oceans are to the land surface temperature, which is related to the processes causing the land-sea contrast in global warming scenarios. It suggests that the ocean's natural variability and change is leading to variability and change with enhanced magnitudes over the continents, causing much of the longer-time-scale (decadal) global-scale continental climate variability. Model simulations illustrate that continental warming due to anthropogenic forcing (e. g., the warming at the end of the last century or future climate change scenarios) is mostly (80%-90%) indirectly forced by the contemporaneous ocean warming, not directly by local radiative forcing.
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  • 15
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    American Meteorological Society
    In:  Journal of Climate, 22 (18). pp. 4930-4938.
    Publication Date: 2017-08-24
    Description: Several recent general circulation model studies discuss the predictability of the Indian Ocean dipole (IOD) mode, suggesting that it is predictable because of coupled ocean-atmosphere interactions in the Indian Ocean. However, it is not clear from these studies how much of the predictability is due to the response to El Nino. It is shown in this note that a simple statistical model that treats the Indian Ocean as a red noise process forced by tropical Pacific SST shows forecast skills comparable to those of recent general circulation model studies. The results also indicate that some of the eastern tropical Indian Ocean SST predictability in recent studies may indeed be beyond the skill of the simple model proposed in this note, indicating that dynamics in the Indian Ocean may have caused this improved predictability in this region. The model further indicates that the IOD index may be the least predictable index of Indian Ocean SST variability. The model is proposed as a null hypothesis for Indian Ocean SST predictions.
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  • 16
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.
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  • 17
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The recent development of new techniques to manipulate single DNA molecules has opened new opportunities for the study of the enzymes that control DNA topology: the type I and II topoisomerases. These single-molecule assays provide a unique way to study the uncoiling of single supercoiled DNA molecules and the unlinking of two intertwined DNAs. They allow for a detailed characterization of the activity of topoisomerases, including the processivity, the chiral discrimination, and the dependence of their enzymatic rate on ATP concentration, degree of supercoiling, and the tension in the molecule. These results shed new light on the mechanism of these enzymes and their function in vivo.
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  • 18
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    ISSN: 1523-9829
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Technology , Medicine
    Notes: We review the history of DNA mechanics and its analysis. We evaluate several methods to analyze the structures of superhelical DNA molecules, each predicated on the assumption that DNA can be modeled with reasonable accuracy as an extended, linearly elastic polymer. Three main approaches are considered: mechanical equilibrium methods, which seek to compute minimum energy conformations of topologically constrained molecules; statistical mechanical methods, which seek to compute the Boltzmann distribution of equilibrium conformations that arise in a finite temperature environment; and dynamic methods, which seek to compute deterministic trajectories of the helix axis by solving equations of motion. When these methods include forces of self-contact, which prevent strand passage and preserve the topological constraint, each predicts plectonemically interwound structures. On the other hand, the extent to which these mechanical methods reliably predict energetic and thermodynamic properties of superhelical molecules is limited, in part because of their inability to account explicitly for interactions involving solvent. Monte Carlo methods predict the entropy associated with supercoiling to be negative, in conflict with a body of experimental evidence that finds it is large and positive, as would be the case if superhelical deformations significantly disrupt the ordering of ambient solvent molecules. This suggests that the large-scale conformational properties predicted by elastomechanical models are not the only ones determining the energetics and thermodynamics of supercoiling. Moreover, because all such models that preserve the topological constraint correctly predict plectonemic interwinding, despite these and other limitations, this constraint evidently dominates energetic and thermodynamic factors in determining supercoil geometry. Therefore, agreement between predicted structures and structures obtained experimentally, for example, by electron microscopy, does not in itself provide evidence for the correctness or completeness of any given model of DNA mechanics.
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  • 19
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The ATP-binding cassette (ABC) superfamily of genes encode membrane proteins that transport a diverse set of substrates across membranes. Mutations in ABC transporters cause or contribute to many different Mendelian and complex disorders including adrenoleukodystrophy, cystic fibrosis, retinal degeneration, hypercholesterolemia, and cholestasis. The genes play important roles in protecting organisms from xenobiotics and transport compounds across the intestine, blood-brain barrier, and the placenta. There are 48 ABC genes in the human genome divided into seven subfamilies based on amino acid sequence similarities and phylogeny. These seven subfamilies are represented in all eukaryotic genomes and are therefore of ancient origin. Sequencing the genomes of numerous vertebrate organisms has allowed the complement of ABC transporters to be characterized and the evolution of the genes to be assessed. Most ABC transporters are conserved in all vertebrates, but there are also several examples of recent duplication and gene loss. For genes with a conserved ortholog, animal models have been identified or developed that can be used to probe the function and regulation of selected genes. Genes that are restricted to a specific group of animals may represent specialized functions that could provide insight into unique biological properties of that organism. Further characterization of all ABC transporters from the human genome and from model organisms will lead to additional insights into normal physiology and human disease.
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  • 20
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
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  • 21
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Glaucoma describes a group of diseases that kill retinal ganglion cells. There are different types of glaucoma, and each appears to be genetically heterogeneous. Different glaucoma genes have been identified, but these genes account for only a small proportion of glaucoma. Most glaucoma cases appear to be multifactorial, and are likely affected by multiple interacting loci. A number of genetic susceptibility factors have been suggested to contribute to glaucoma. These factors fit into two broad groups, those affecting intraocular pressure and those important in modulating retinal ganglion cell viability. Defining the complex genetics of glaucoma will require significant further study of the human disease and animal models. Genetic approaches are essential and will be enhanced by recently developed genomic and proteomic technologies. These technologies will provide valuable clues about pathogenesis for subsequent testing. In this review, we focus on endogenous genetic susceptibility factors and on how experimental studies will be valuable for dissecting the multifactorial complexity of their interactions.
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  • 22
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The availability of complete genome sequences and the wealth of large-scale biological data sets now provide an unprecedented opportunity to elucidate the genetic basis of rare and common human diseases. Here we review some of the emerging genomics technologies and data resources that can be used to infer gene function to prioritize candidate genes. We then describe some computational strategies for integrating these large-scale data sets to provide more faithful descriptions of gene function, and how such approaches have recently been applied to discover genes underlying Mendelian disorders. Finally, we discuss future prospects and challenges for using integrative genomics to systematically discover not only single genes but also entire gene networks that underlie and modify human disease.
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  • 23
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.
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  • 24
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Mammalian X chromosome inactivation is one of the most striking examples of epigenetic gene regulation. Early in development one of the pair of Đ♯160-Mb X chromosomes is chosen to be silenced, and this silencing is then stably inherited through subsequent somatic cell divisions. Recent advances have revealed many of the chromatin changes that underlie this stable silencing of an entire chromosome. The key initiator of these changes is a functional RNA, XIST, which is transcribed from, and associates with, the inactive X chromosome, although the mechanism of association with the inactive X and recruitment of facultative heterochromatin remain to be elucidated. This review describes the unique evolutionary history and resulting genomic structure of the X chromosome as well as the current understanding of the factors and events involved in silencing an X chromosome in mammals.
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  • 25
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Cystic fibrosis (CF) is the most common lethal autosomal recessive disorder in the Caucasian population, affecting about 30,000 individuals in the United States. The gene responsible for CF, the CF transmembrane conductance regulator (CFTR), was identified 15 years ago. Substantial variation in the many aspects of the CF phenotype among individuals with the same CFTR genotype demonstrates that factors independent of CFTR exert considerable influence on outcome in CF. To date, the majority of published studies investigating the cause of disease variability in CF report associations between candidate genes and some aspect of the CF phenotype. However, a definitive modifier gene for CF remains to be identified. Despite the challenges posed by searches for modifier effects, studies of affected twins and siblings indicate that genetic factors play a substantial role in intestinal manifestations. Identifying the factors contributing to variation in pulmonary disease, the primary cause of mortality, remains a challenge for CF research.
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  • 26
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 37 (2005), S. 263-293 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The large-scale dynamics of the extratropical stratosphere are reviewed. The role of Rossby waves and vortex dynamics in shaping the winter stratospheric circulation and the dynamics of the longitudinal mean flow are first discussed separately. The important effects of two-way interaction between waves and mean flow are then described, with emphasis on how mechanisms discovered in simple models can be followed through to models that are closer to the real stratosphere. A final topic is the possible effect of the stratosphere on the troposphere, with emphasis on dynamical mechanisms for such an effect.
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    Annual Review of Fluid Mechanics 37 (2005), S. 151-182 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Early work and recent advances in feedback control of combustion oscillations are described. The physics of combustion oscillations, most commonly caused by a coupling between acoustic waves and unsteady heat release, are discussed, and the concept of using feedback control to interrupt these interactions is introduced. Factors affecting practical implementation of feedback control, including sensors, actuators, and controller design are described, and the historical development of control strategy for combustion oscillations is reviewed. Finally, demonstrations of feedback control on full-scale combustion systems are described, and it is concluded that there is potential to apply more systematic controller designs at full scale.
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    Annual Review of Fluid Mechanics 37 (2005), S. 393-423 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Gravity-driven bubbly flows are a specific class of flows, where all action is provided by gravity. An industrial example is formed by the so-called bubble column: a vertical cylinder filled with liquid through which bubbles flow that are introduced at the bottom of the cylinder. On the bubble scale, gravity gives rise to buoyancy of individual bubbles. On larger scales, gravity acts on nonuniformities in the spatial bubble distribution present in the bubbly mixture. The gravity-induced flow and flow structures can increase the inhomogeneity of the bubble distribution, leading to a turbulent flow. In this flow, specific scales are identified: a large-scale circulation with the liquid flowing upward in the center of the column and downward close to the wall. On the intermediate scale there are vortical structures; eddies of liquid, with a size on the order of the diameter of the column, that stir the liquid and radially transport the bubbles. On the small scale there is the local stirring of the bubbles. We describe the ideas developed over time and identify some open questions. We discuss the experimental findings on the turbulence generated, the stability of the flow, axial dispersion, and the similarities between bubble columns and air lifts. Especially for higher gas fractions, many questions still lack accurate answers. The lateral lift force in bubble swarms and the structure of the turbulence in the bubbly mixture are important examples of inadequately understood physical phenomena, providing many challenges for fundamental and applied research on bubbly flows.
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    Annual Review of Fluid Mechanics 37 (2005), S. 211-238 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Efficiently and accurately solving the equations governing fluid flow in oil reservoirs is very challenging because of the complex geological environment and the intricate properties of crude oil and gas at high pressure. We present these challenges and review successful and promising solution approaches. We discuss in detail the modeling of fluid flow in reservoirs with strongly varying rock properties. This requires subgrid-scale models that accurately represent the flow physics due to fine-scale fluctuations. A second focus is on the complex multiphase, multicomponent systems that describe miscible gas injection processes for enhanced oil recovery and CO2 sequestration.
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    Annual Review of Fluid Mechanics 37 (2005), S. 425-455 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Development and optimization of multifunctional devices for fluidic manipulation of films, drops, and bubbles require detailed understanding of interfacial phenomena and microhydrodynamic flows. Systems are distinguished by a large surface to volume ratio and flow at small Reynolds, capillary, and Bond numbers are strongly influenced by boundary effects and therefore amenable to control by a variety of surface treatments and surface forces. We review the principles underlying common techniques for actuation of droplets and films on homogeneous, chemically patterned, and topologically textured surfaces by modulation of normal or shear stresses.
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    Annual Review of Fluid Mechanics 37 (2005), S. 183-210 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: "What force does an insect wing generate?" Finding answers to this enduring question is an essential step toward our understanding of interactions of moving objects with fluids that enable most living species such as insects, birds, and fish to travel efficiently and us to follow similar suit with sails, oars, and airfoils. We give a brief history of research in insect flight and discuss recent findings in unsteady aerodynamics of flapping flight at intermediate range Reynolds numbers ( 10Đ??104 ). In particular, we examine the unsteady mechanisms in uniform and accelerated motions, forward and hovering flight, as well as passive flight of free-falling objects. The results obtained by "taking the insects apart" helped us to resolve previous puzzles about the force estimates in hovering insects, to ellucidate basic mechanisms essential to flapping flight, and to gain insights about the efficieny of flight.
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    Annual Review of Fluid Mechanics 37 (2005), S. 295-328 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Chaotic advection and, more generally, ideas from dynamical systems, have been fruitfully applied to a diverse, and varied, collection of mixing and transport problems arising in engineering applications over the past 20 years. Indeed, the "dynamical systems approach" was developed, and tested, to the point where it can now be considered a standard tool for understanding mixing and transport issues in many disciplines. This success for engineering-type flows motivated an effort to apply this approach to transport and mixing problems in geophysical flows. However, there are fundamental difficulties arising in this endeavor that must be properly understood and overcome. Central to this approach is that the starting point for analysis is a velocity field (i.e., the "dynamical system"). In many engineering applications this can be obtained sufficiently accurately, either analytically or computationally, so that it describes particle trajectories for the actual flow. However, in geophysical flows (and we concentrate here almost exclusively on oceanographic flows), the wide range of dynamically significant time and length scales makes the justification of any velocity field, in the sense of reproducing particle trajectories for the actual flow, a much more difficult matter. Nevertheless, the case for this approach is compelling due to the advances in observational capabilities in oceanography (e.g., drifter deployments, remote sensing capabilities, satellite imagery, etc.), which reveal space-time structures that are highly suggestive of the structures one visualizes in the global, geometrical study of dynamical systems theory. This has been pursued in recent years through a combination of laboratory studies, kinematic models, and dynamically consistent models that have all been compared with observational data. During the course of these studies it has become apparent that a new type of dynamical system is necessary to consider in these studies (i.e., a finite time, aperiodically time-dependent velocity field defined as a data set), which requires the development of new analytical and computational tools, as well as the necessity to discard some of the standard ideas and results from dynamical systems theory. In this article we review a number of the key developments to date in this young, but rapidly developing, area at the interface between geophysical fluid dynamics and applied and computational mathematics. We also describe the wealth of new directions for research that this approach unlocks.
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    Annual Review of Fluid Mechanics 37 (2005), S. 71-98 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The flow in turbomachines is unsteady due to the relative motion of the rows of blades. In the low-pressure turbine, the wakes from the upstream bladerows provide the dominant source of unsteadiness. Because much of the blade-surface boundary-layer flow is laminar, one of the most important consequences of this unsteadiness is the interaction of the wakes with the suction-side boundary layer of a downstream blade. This is important because the blade suctionĐ??side boundary layers are responsible for most of the loss of efficiency and because the combined effects of random (wake turbulence) and periodic disturbances (wake velocity defect and pressure fields) cause the otherwise laminar boundary layer to undergo transition and eventually become turbulent. This article summarizes the process of wake-induced boundary-layer transition in low-pressure turbines and the loss generation processes that result. Particular emphasis is placed on how the effects of wakes may be exploited to control loss generation and how this has enabled successful development of ultra-high-lift low-pressure turbines.
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    Annual Review of Fluid Mechanics 37 (2005), S. 329-356 
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    Annual Review of Fluid Mechanics 38 (2006), S. 251-276 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: We review recent advances in understanding, modeling, and controlling oscillations in the flow past a cavity. The fundamental mechanisms underlying cavity flow oscillations have been known for at least 40 years, but suppressing these oscillations in a reliable and robust way is still a challenge today. Interest in controlling the flow past a cavity is motivated by aerospace applications, but in addition, cavity flows provide an attractive canonical problem for exploring general flow control techniques. The focus is on recent advances in modeling these flows, and in controlling them, using both open-loop and closed-loop techniques. A relatively new perspective is that cavity oscillations may not always be self-sustained, but under some flow conditions may be lightly damped resonances, sustained by external disturbances such as boundary layer turbulence. Areas in which our understanding is incomplete, and which deserve further study, are discussed, in particular the effects of high-frequency open-loop forcing, fundamental limitations of feedback control for a given configuration of sensors and actuators, and the development of a feedback design methodology that respects the limited range of validity of the available dynamical models.
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    Annual Review of Fluid Mechanics 38 (2006), S. 371-394 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Mammalian fertilization requires the coordinated activity of motile spermatozoa, muscular contractions of the uterus and oviduct, as well as ciliary beating. These elastic structures generate forces that drive fluid motion, but their configurations are, in turn, determined by the fluid dynamics. We review the basic fluid mechanical aspects of reproduction, including flagellar/ciliary beating and peristalsis. We report on recent biological studies that have shed light on the relative importance of the mechanical ingredients of reproduction. In particular, we examine sperm motility in the reproductive tract, ovum pickup and transport in the oviduct, as well as sperm-egg interactions. We review recent advances in understanding the internal mechanics of cilia and flagella, flagellar surface interaction, sperm motility in complex fluids, and the role of fluid dynamics in embryo transfer. We outline promising computational fluid dynamics frameworks that may be used to investigate these complex, fluid-structure interactions.
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    Annual Review of Fluid Mechanics 38 (2006), S. 339-369 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: We consider the hydrodynamics of creatures capable of sustaining themselves on the water surface by means other than flotation. Particular attention is given to classifying water walkers according to their principal means of weight support and lateral propulsion. The various propulsion mechanisms are rationalized through consideration of energetics, hydrodynamic forces applied, or momentum transferred by the driving stroke. We review previous research in this area and suggest directions for future work. Special attention is given to introductory discussions of problems not previously treated in the fluid mechanics literature, with hopes of attracting physicists, applied mathematicians, and engineers to this relatively unexplored area of fluid mechanics.
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    Notes: The fluid mechanics of artificial blood pumps has been studied since the early 1970s in an attempt to understand and mitigate hemolysis and thrombus formation by the device. Pulsatile pumps are characterized by inlet jets that set up a rotational "washing" pattern during filling. Strong regurgitant jets through the closed artificial heart valves have Reynolds stresses on the order of 10,000 dynes/cm2 and are the most likely cause of red blood cell damage and platelet activation. Although the flow in the pump chamber appears benign, low wall shear stresses throughout the pump cycle can lead to thrombus formation at the wall of the smaller pumps (10Đ??50 cc). The local fluid mechanics is critical. There is a need to rapidly measure or calculate the wall shear stress throughout the device so that the results may be easily incorporated into the design process.
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    Annual Review of Fluid Mechanics 38 (2006), S. 87-110 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Homeland security involves many applications of fluid mechanics and offers many opportunities for research and development. This review explores a wide selection of fluids topics in counterterrorism and suggests future directions. Broad topics range from preparedness and deterrence of impending terrorist attacks to detection, response, and recovery. Specific topics include aircraft hardening, blast mitigation, sensors and sampling, explosive detection, microfluidics and labs-on-a-chip, chemical plume dispersal in urban settings, and building ventilation. Also discussed are vapor plumes and standoff detection, nonlethal weapons, airborne disease spread, personal protective equipment, and decontamination. Involvement in these applications requires fluid dynamicists to think across the traditional boundaries of the field and to work with related disciplines, especially chemistry, biology, aerosol science, and atmospheric science.
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    Annual Review of Fluid Mechanics 38 (2006), S. 159-192 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The review deals with drop impacts on thin liquid layers and dry surfaces. The impacts resulting in crown formation are referred to as splashing. Crowns and their propagation are discussed in detail, as well as some additional kindred, albeit nonsplashing, phenomena like drop spreading and deposition, receding (recoil), jetting, fingering, and rebound. The review begins with an explanation of various practical motivations feeding the interest in the fascinating phenomena of drop impact, and the above-mentioned topics are then considered in their experimental, theoretical, and computational aspects.
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    Annual Review of Physiology 67 (2005), S. 69-98 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Intracellular calcium release channels are present on sarcoplasmic and endoplasmic reticuli (SR, ER) of all cell types. There are two classes of these channels: ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R). RyRs are required for excitation-contraction (EC) coupling in striated (cardiac and skeletal) muscles. RyRs are made up of macromolecular signaling complexes that contain large cytoplasmic domains, which serve as scaffolds for proteins that regulate the function of the channel. These regulatory proteins include calstabin1/calstabin2 (FKBP12/FKBP12.6), a 12/12.6 kDa subunit that stabilizes the closed state of the channel and prevents aberrant calcium leak from the SR. Kinases and phosphatases are targeted to RyR2 channels and modulate RyR2 function in response to extracellular signals. In the classic fight or flight stress response, phosphorylation of RyR channels by protein kinase A reduces the affinity for calstabin and activates the channels leading to increased SR calcium release. In heart failure, a cardiac insult causes a mismatch between blood supply and metabolic demands of organs. The chronically activated fight or flight response leads to leaky channels, altered calcium signaling, and contractile dysfunction and cardiac arrhythmias.
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    Annual Review of Physiology 67 (2005), S. 99-145 
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    Topics: Medicine , Biology
    Notes: Blood flow in the microcirculation is regulated by physiological oxygen (O2) gradients that are coupled to vasoconstriction or vasodilation, the domain of nitric oxide (NO) bioactivity. The mechanism by which the O2 content of blood elicits NO signaling to regulate blood flow, however, is a major unanswered question in vascular biology. While the hemoglobin in red blood cells (RBCs) would appear to be an ideal sensor, conventional wisdom about its chemistry with NO poses a problem for understanding how it could elicit vasodilation. Experiments from several laboratories have, nevertheless, very recently established that RBCs provide a novel NO vasodilator activity in which hemoglobin acts as an O2 sensor and O2-responsive NO signal transducer, thereby regulating both peripheral and pulmonary vascular tone. This article reviews these studies, together with biochemical studies, that illuminate the complexity and adaptive responsiveness of NO reactions with hemoglobin. Evidence for the pivotal role of S-nitroso (SNO) hemoglobin in mediating this response is discussed. Collectively, the reviewed work sets the stage for a new understanding of RBC-derived relaxing activity in auto-regulation of blood flow and O2 delivery and of RBC dysfunction in disorders characterized by tissue O2 deficits, such as sickle cell disease, sepsis, diabetes, and heart failure.
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    Annual Review of Physiology 67 (2005), S. 203-223 
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    Topics: Medicine , Biology
    Notes: Comparative developmental physiology spans genomics to physiological ecology and evolution. Although not a new discipline, comparative developmental physiology's position at the convergence of development, physiology and evolution gives it prominent new significance. The contributions of this discipline may be particularly influential as physiologists expand beyond genomics to a true systems synthesis, integrating molecular through organ function in multiple organ systems. This review considers how developing physiological systems are directed by genes yet respond to environment and how these characteristics both constrain and enable evolution of physiological characters. Experimental approaches and methodologies of comparative developmental physiology include studying event sequences (heterochrony and heterokairy), describing the onset and progression of physiological regulation, exploiting scaling, expanding the list of animal models, using genetic engineering, and capitalizing on new miniaturized technologies for physiological investigation down to the embryonic level. A synthesis of these approaches is likely to generate a more complete understanding of how physiological systems and, indeed, whole animals develop and how populations evolve.
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    Annual Review of Physiology 67 (2005), S. 225-257 
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    Notes: The cellular stress response is a universal mechanism of extraordinary physiological/pathophysiological significance. It represents a defense reaction of cells to damage that environmental forces inflict on macromolecules. Many aspects of the cellular stress response are not stressor specific because cells monitor stress based on macromolecular damage without regard to the type of stress that causes such damage. Cellular mechanisms activated by DNA damage and protein damage are interconnected and share common elements. Other cellular responses directed at re-establishing homeostasis are stressor specific and often activated in parallel to the cellular stress response. All organisms have stress proteins, and universally conserved stress proteins can be regarded as the minimal stress proteome. Functional analysis of the minimal stress proteome yields information about key aspects of the cellular stress response, including physiological mechanisms of sensing membrane lipid, protein, and DNA damage; redox sensing and regulation; cell cycle control; macromolecular stabilization/repair; and control of energy metabolism. In addition, cells can quantify stress and activate a death program (apoptosis) when tolerance limits are exceeded.
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    Annual Review of Physiology 67 (2005), S. 285-308 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Tremendous progress has been made in elucidating numerous critical aspects of estrogen signaling. New tools and techniques have enabled detailed molecular analysis of components that direct estrogen responses. At the other end of the spectrum, generation of a multiplicity of transgenic animals has allowed analysis of the physiological roles of the estrogen-signaling components in biologically relevant models. Here, we review the ever-increasing body of knowledge in the field of estrogen biology, especially as applied to the female reproductive processes.
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    Annual Review of Physiology 67 (2005), S. 377-409 
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    Notes: In many species the pancreatic duct epithelium secretes HCO3 ions at a concentration of around 140 mM by a mechanism that is only partially understood. We know that HCO3 uptake at the basolateral membrane is achieved by Na+-HCO3 cotransport and also by a H+-ATPase and Na+/H+ exchanger operating together with carbonic anhydrase. At the apical membrane, the secretion of moderate concentrations of HCO3 can be explained by the parallel activity of a Cl/HCO3 exchanger and a Cl conductance, either the cystic fibrosis transmembrane conductance regulator (CFTR) or a Ca2+-activated Cl channel (CaCC). However, the sustained secretion of HCO3 into a HCO3 -rich luminal fluid cannot be explained by conventional Cl/HCO3 exchange. HCO3 efflux across the apical membrane is an electrogenic process that is facilitated by the depletion of intracellular Cl, but it remains to be seen whether it is mediated predominantly by CFTR or by an electrogenic SLC26 anion exchanger.
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    Annual Review of Physiology 67 (2005), S. 515-529 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: The primary cilium, an organelle largely ignored by physiologists, functions both as a mechano-sensor and a chemo-sensor in renal tubular epithelia. This forgotten structure is critically involved in the determination of left-right sidedness during development and is a key factor in the development of polycystic kidney disease, as well as a number of other abnormalities. This review provides an update of our current understanding about the function of primary cilia. Much new information obtained in the past five years has been stimulated, in part, by discoveries of the primary cilium's key role in the genesis of polycystic kidney disease as well as its involvement in determination of left-right axis asymmetry. Here we focus on the various functions of the primary cilium rather than on its role in pathology.
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    Annual Review of Physiology 67 (2005), S. 663-696 
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    Topics: Medicine , Biology
    Notes: Surfactant protein C (SP-C) is a hydrophobic 35-amino acid peptide that co-isolates with the phospholipid fraction of lung surfactant. SP-C represents a structurally and functionally challenging protein for the alveolar type 2 cell, which must synthesize, traffic, and process a 191Đ??197-amino acid precursor protein through the regulated secretory pathway. The current understanding of SP-C biosynthesis considers the SP-C proprotein (proSP-C) as a hybrid molecule that incorporates structural and functional features of both bitopic integral membrane proteins and more classically recognized luminal propeptide hormones, which are subject to post-translational processing and regulated exocytosis. Adding to the importance of a detailed understanding of SP-C biosynthesis has been the recent association of mutations in the proSP-C sequence with chronic interstitial pneumonias in children and adults. Many of these mutations involve either missense or deletion mutations located in a region of the proSP-C molecule that has structural homology to the BRI family of proteins linked to inherited degenerative dementias. This review examines the current state of SP-C biosynthesis with a focus on recent developments related to molecular and cellular mechanisms implicated in the emerging role of SP-C mutations in the pathophysiology of diffuse parenchymal lung disease.
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    Annual Review of Physiology 67 (2005), S. 759-778 
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    Topics: Medicine , Biology
    Notes: Numerous Cl channels have been identified in the kidney using physiological approaches and thus are thought to be involved in a range of physiological processes, including vectorial transepithelial Cl transport, cell volume regulation, and vesicular acidification. In addition, expression of genes from several Cl channel gene families has also been observed. However, the molecular characteristics of a number of Cl channels within the kidney are still unknown, and the physiological roles of Cl channels identified by molecular means remain to be determined. A gene knockout approach using mice might shed further light on the characteristics of these various Cl channels. In addition, study of diseases involving Cl channels (channelopathies) might clarify the physiological role of specific Cl channels. To date, more is known about CLC Cl channels than any other Cl channels within the kidney. This review focuses on the physiological roles of CLC Cl channels within the kidney, particularly kidney-specific ClC-K Cl channels, as well as the recently identified maxi anion channel in macula densa, which is involved in tubulo-glomerular feedback.
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    Notes: The physical removal of viruses and bacteria on the mucociliary escalator is an important aspect of the mammalian lung's innate defense mechanism. The volume of airway surface liquid (ASL) present in the respiratory tract is a critical determinant of both mucus hydration and the rate of mucus clearance from the lung. ASL volume is maintained by the predominantly ciliated epithelium via coordinated regulation of (a) absorption, by the epithelial Na+ channel, and (b) secretion, by the Ca2+ -activated Cl channel (CaCC) and CFTR. This review provides an update on our current understanding of how shear stress regulates ASL volume height in normal and cystic fibrosis (CF) airway epithelia through extracellular ATP- and adenosine (ADO)-mediated pathways that modulate ion transport and ASL volume homeostasis. We also discuss (a) how derangement of the ADO-CFTR pathway renders CF airways vulnerable to viral infections that deplete ASL volume and produce mucus stasis, and (b) potential shear stressĐ??dependent therapies for CF.
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    Annual Review of Physiology 68 (2006), S. 375-401 
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    Topics: Medicine , Biology
    Notes: Cyclic nucleotideĐ??activated ion channels play a fundamental role in a variety of physiological processes. By opening in response to intracellular cyclic nucleotides, they translate changes in concentrations of signaling molecules to changes in membrane potential. These channels belong to two families: the cyclic nucleotideĐ??gated (CNG) channels and the hyperpolarization-activated cyclic nucleotideĐ??modulated (HCN) channels. The two families exhibit high sequence similarity and belong to the superfamily of voltage-gated potassium channels. Whereas HCN channels are activated by voltage and CNG channels are virtually voltage independent, both channels are activated by cyclic nucleotide binding. Furthermore, the channels are thought to have similar channel structures, leading to similar mechanisms of activation by cyclic nucleotides. However, although these channels are structurally and behaviorally similar, they have evolved to perform distinct physiological functions. This review describes the physiological roles and biophysical behavior of CNG and HCN channels. We focus on how similarities in structure and activation mechanisms result in common biophysical models, allowing CNG and HCN channels to be viewed as a single genre.
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    Annual Review of Physiology 68 (2006), S. 461-490 
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    Topics: Medicine , Biology
    Notes: The serum/glucocorticoid-induced kinase Sgk1 plays an important role in the regulation of epithelial ion transport. This kinase is very rapidly regulated at the transcriptional level as well as via posttranslational modifications involving phosphorylation by the MAP or PI-3 kinase pathways and/or ubiquitylation. Although Sgk1 is a cell survival kinase, its primary role likely concerns the regulation of epithelial ion transport, as suggested by the phenotype of Sgk1-null mice, which display a defect in Na+ homeostasis owing to disturbed renal tubular Na+ handling. In this review we first discuss the molecular, cellular, and regulatory aspects of Sgk1 and its paralogs. We then discuss its roles in the physiology and pathophysiology of epithelial ion transport.
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    Annual Review of Anthropology 34 (2005), S. 317-341 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This essay reviews recent anthropological attention to the "beginnings" and "endings" of life. A large literature since the 1990s highlights the analytic trends and innovations that characterize anthropological attention to the cultural production of persons, the naturalization of life, and the emergence of new life forms. Part I of this essay outlines the coming-into-being, completion and attenuation of personhood and how life and death are attributed, contested, and enacted. Dominant themes include how connections are forged or severed between the living and the dead and the socio-politics of dead, dying, and decaying bodies. The culture of medicine is examined for its role in organizing and naming life and death. Part II is organized by the turn to biopolitical analyses stimulated by the work of Foucault. It encompasses the ways in which the biosciences and biotechnologies, along with state practices, govern forms of living and dying and new forms of life such as the stem cell, embryo, comatose, and brain dead, and it emphasizes the production of value. Much of this scholarship is informed by concepts of liminality (a period and state of being between social statuses) and subjectification (in which notions of self, citizenship, life and its management are linked to the production of knowledge and political forms of regulation).
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    Annual Review of Anthropology 34 (2005), S. 13 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Scholarly interest in body size has increased in concert with recent efforts to shape and assess bodies in particular ways within industrialized social contexts. Attending to both overt and covert references to Eurocentric body projects, this chapter reviews literature in anthropology, sociology, and cultural studies that addresses the cultural politics of body size in various parts of the world. It begins with a discussion of biocultural paradigms, which accept certain biomedical categories even when challenging or reconfiguring their hegemonic power. Next is a survey of works analyzing body size within "non-Western" groups as well as European and North American subgroups. These studies often employ culturally powerful "Western" constructs as foils, an approach that risks cultural othering. The analysis then turns to the extensive literature that unpacks dominant Euro-American body practices and discourses. Here, diverse perspectives on several key concerns in sociocultural anthropology are considered; concepts of culture and power, theories of the body and embodiment, and understandings of human agency vary in instructive ways. The chapter concludes with a review of scholarship on postcolonial processes and representations that incorporates a critical perspective on Eurocentric preoccupations with body size.
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    Annual Review of Anthropology 34 (2005), S. 549-573 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This review examines literature on indigenous movements in Latin America from 1992 to 2004. It addresses ethnic identity and ethnic activism, in particular the reindianization processes occurring in indigenous communities throughout the region. We explore the impact that states and indigenous mobilizing efforts have had on each other, as well as the role of transnational nongovernmental organizations and para-statal organizations, neoliberalism more broadly, and armed conflict. Shifts in ethnoracial, political, and cultural indigenous discourses are examined, special attention being paid to new deployments of rhetorics concerned with political imaginaries, customary law, culture, and identity. Self-representational strategies will be numerous and dynamic, identities themselves multiple, fluid, and abundantly positional. The challenges these dynamics present for anthropological field research and ethnographic writing are discussed, as is the dialogue between scholars, indigenous and not, and activists, indigenous and not. Conclusions suggest potentially fruitful research directions for the future.
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    Annual Review of Anthropology 34 (2005), S. 619-638 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: The mapping of indigenous lands to secure tenure, manage natural resources, and strengthen cultures is a recent phenomenon, having begun in Canada and Alaska in the 1960s and in other regions during the last decade and a half. A variety of methodologies have made their appearance, ranging from highly participatory approaches involving village sketch maps to more technical efforts with geographic information systems (GIS) and remote sensing. In general, indigenous mapping has shown itself to be a powerful tool and it has spread rapidly throughout the world. The distribution of mapping projects is uneven, as opportunities are scarce in many parts of the world. This review covers the genesis and evolution of indigenous mapping, the different methodologies and their objectives, the development of indigenous atlases and guidebooks for mapping indigenous lands, and the often uneasy mix of participatory community approaches with technology. This last topic is at the center of considerable discussion as spatial technologies are becoming more available and are increasingly used in rural areas. The growth of GIS laboratories among tribes in the United States and Canada, who frequently have both financial and technical support, is in sharp contrast to groups in the SouthĐ??primarily Africa, Asia, and Latin AmericaĐ??where resources are in short supply and permanent GIS facilities are rare.
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    Annual Review of Anthropology 34 (2005), S. 599-617 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Over the past decade, the field of biocultural diversity has arisen as an area of transdisciplinary research concerned with investigating the links between the world's linguistic, cultural, and biological diversity as manifestations of the diversity of life. The impetus for the emergence of this field came from the observation that all three diversities are under threat by some of the same forces and from the perception that loss of diversity at all levels spells dramatic consequences for humanity and the earth. Accordingly, the field of biocultural diversity has developed with both a theoretical and a practical side, the latter focusing on on-the-ground work and policy, as well as with an ethics and human rights component. This review provides some background on the historical antecedents and beginnings of this field and on its philosophical and ethical underpinnings, and then surveys the key literature on biocultural diversity, concentrating on three main aspects: global and regional studies on the links between linguistic, cultural, and biological diversity; the measurement and assessment of biocultural diversity; and the protection and maintenance of biocultural diversity. The review concludes with some considerations about future prospects for this emerging field.
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    Annual Review of Anthropology 34 (2005), S. 717-739 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Throughout the twentieth century, social and cultural policies toward indigenous peoples in Latin America have been closely related to indigenismo, an ideological movement that denounced the exploitation of aboriginal groups and strove for the cultural unity and the extension of citizenship through social integration and "acculturation." This review traces the colonial and nineteenth-century roots of indigenismo and places it in the context of the populist tendencies in most Latin American states from the 1920s to the 1970s, which favored economic protectionism and used agrarian reform and the provision of services as tools for governance and legitimacy. Also examined is the role of anthropological research in its relation to state hegemony as well as the denunciation of indigenista policies by ethnic intellectuals and organizations. In recent decades, the dismantling of populist policies has given rise to a new official "neoliberal" discourse that extols multiculturalism. However, the widespread demand for multicultural policies is also seen as the outcome of the fight by militant indigenous organizations for a new type of citizenship.
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    Annual Review of Anthropology 34 (2005), S. 253-268 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This review article addresses the following question: Given the transformed social, political, and intellectual conditions for ethnographic research among indigenous peoples in North America, what forms has such research come to take at the turn of the twenty-first century? The review considers significant trends and innovations in research sites and topics, research methodologies, theoretical orientations, and forms of representation. It also assesses the distinctive strengths and limitations posed by ethnographic research for scholars engaging with significant dimensions of contemporary indigenous life, including struggles for rights, resources, recognition, and language vitality in both the national and international arenas; the repatriation and sovereignty movements; the development of tribal casinos, tourist complexes, cultural centers, and media outlets; continued social and economic marginalization of many indigenous peoples; and challenges posed by neoliberalism and globalization to tribal governments and economies.
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    Annual Review of Anthropology 34 (2005), S. 429-449 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Archaeology has been linked to colonialist attitudes and scientific imperialism. But what are the perspectives of Indigenous groups concerning the practice of archaeology? Numerous organizations recognize the distinctive needs of Indigenous communities throughout the world and have adopted agreements and definitions that govern their relationships with those populations. The specific name by which Indigenous groups are known varies from country to country, as local governments are involved in determining the appropriateness of particular definitions to populations within their borders. This paper begins with an examination of the various aspects that have been used to determine whether or not a group of people might be considered "indigenous" under various definitions, and then uses the history of the relationships between North American archaeologists and Indigenous populations as a background for the examination of some of the political aspects of archaeology that have impacted Indigenous populations. It then proceeds to discuss perspectives on archaeology offered by members of various Indigenous populations throughout the World.
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    Annual Review of Anthropology 34 (2005), S. 85-104 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: In a number of countries in Latin America, recent changes in the constitutional and legislative environment under which indigenous people hold or claim land and natural resource rights have triggered a number of processes and projects to demarcate, legalize, or otherwise consolidate indigenous lands. This review begins with a look at Nicaragua and goes on to examine five of the South American processes, allegedly with the most favorable legal and policy environments, and concludes that they suffer from common problems related to (a) the amount of land and resources being claimed by relatively small numbers of people, (b) the contestation of the claims by non-indigenous sectors, and (c) the nature of indigenous organizations and the NGOs that support them. The confrontation between policy and reality yields some lessons for the future.
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    Annual Review of Anthropology 34 (2005), S. 1-11 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: In the twentieth century, many anthropological comparisons were mounted on the base of the synchronic societal ethnographies being produced at the time. That work produced a valuable inventory of the range of variations and differences. Now, following quite a different track, and defining the task anew, a remarkable number of ethnographies consist of observations of processes of change as they go along. The considerable obstacles to comparing such temporally oriented, processual case histories distinguishes them from earlier studies of tradition and custom. In this review, five abbreviated case histories of ongoing development projects illustrate the difference of approach. The process by which plans to control particular aspects of a social field are designed, implemented, altered, and diverted are the object of these ethnographic studies. The cultures of control employed by the planners are noted, but the dynamic of the societal context into which projects are introduced is shown to be equally important to the outcome. No less than a redefinition of the anthropological field of observation is involved in this approach.
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    Annual Review of Anthropology 34 (2005), S. 67-83 
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    Notes: This paper synthesizes research on linguistic practice and critically examines the legacy of Pierre Bourdieu from the perspective of linguistic anthropology. Bourdieu wrote widely about language and linguistics, but his most far reaching engagement with the topic is in his use of linguistic reasoning to elaborate broader sociological concepts including habitus, field, standardization, legitimacy, censorship, and symbolic power. The paper examines and relates habitus and field in detail, tracing the former to the work of Erwin Panofsky and the latter to structuralist discourse semantics. The principles of relative autonomy, boundedness, homology, and embedding apply to fields and their linkage to habitus. Authority, censorship, and euphemism are traced to the field, and symbolic power is related to misrecognition. And last, this chapter relates recent work in linguistic anthropology to practice and indicates lines for future research.
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    Notes: The past 15 years have brought an upsurge of "autochthony." It has become an incendiary political slogan in many parts of the African continent as an unexpected corollary of democratization and the new style of development policies ("by-passing the state" and decentralization). The main agenda of the new autochthony movements is the exclusion of supposed "strangers" and the unmasking of "fake" autochthons, who are often citizens of the same nation-state. However, Africa is no exception in this respect. Intensified processes of globalization worldwide seem to go together with a true "conjuncture of belonging" (T.M. Li 2000 ) and increasingly violent attempts to exclude "allochthons." This article compares studies of the upsurge of autochthony in Africa with interpretations of the rallying power of a similar discourse in Western Europe. How can the same discourse appear "natural" in such disparate circumstances? Recent studies highlight the extreme malleability of the apparently self-evident claims of autochthony. These discourses promise the certainty of belonging, but in practice, they raise basic uncertainties because autochthony is subject to constant redefinition against new "others" and at ever-closer range.
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    Notes: The description and explanation of racial and ethnic health disparities are major initiatives of the public health research establishment. Black Americans suffer on nearly every measure of health in relation to white Americans. Five theoretical models have been proposed to explain these disparities: a racial-genetic model, a health-behavior model, a socioeconomic status model, a psychosocial stress model, and a structural-constructivist model. We selectively review literature on health disparities, emphasizing research on low birth weight and high blood pressure. The psychosocial stress model and the structural-constructivist model offer greatest promise to explain disparities. In future research, theoretical elaboration and operational specificity are needed to distinguish among three distinct factors: (a) genetic variants contributing to disease risk; (b) ethnoracial or folk racial categories masquerading as biology; and (c) ethnic group membership. Such elaboration is necessary to move beyond the conflation of these three distinct constructs that characterizes much of current research.
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    Annual Review of Anthropology 34 (2005), S. 33-42 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This chapter introduces the reader to the areas of previous investigation in creole studies, while outlining new directions the field is taking. The first section shows that, although the chief areas of interest have essentially remained the same for the past few decades, methodologies have changed toward a more comprehensive multilayered approach aimed at a better understanding of how individual creole languages emerge, evolve and function. The second section focuses particularly on cognitive processes involved in creole formation, such as restructuring, relexification, reanalysis, and dialectal leveling. In the third and last section, I critically evaluate the current state of affairs and point out potential obstacles and promising interdisciplinary trends.
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    Annual Review of Anthropology 34 (2005), S. 43-65 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Ecologists have increasingly turned to history, including human history, to explain and manage modern ecosystems and landscapes. The imprint of past land use can persist even in seemingly pristine areas. Archaeology provides a long-term perspective on human actions and their environmental consequences that can contribute to conservation and restoration efforts. Case studies illustrate examples of the human history of seemingly pristine landscapes, forest loss and recovery, and the creation or maintenance of places that today are valued habitats. Finally, as archaeologists become more involved in research directed at contemporary environmental issues, they need to consider the potential uses and abuses of their findings in management and policy debates.
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    Annual Review of Anthropology 34 (2005), S. 253-268 
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    Topics: Ethnic Sciences , Biology
    Notes: This review article addresses the following question: Given the transformed social, political, and intellectual conditions for ethnographic research among indigenous peoples in North America, what forms has such research come to take at the turn of the twenty-first century? The review considers significant trends and innovations in research sites and topics, research methodologies, theoretical orientations, and forms of representation. It also assesses the distinctive strengths and limitations posed by ethnographic research for scholars engaging with significant dimensions of contemporary indigenous life, including struggles for rights, resources, recognition, and language vitality in both the national and international arenas; the repatriation and sovereignty movements; the development of tribal casinos, tourist complexes, cultural centers, and media outlets; continued social and economic marginalization of many indigenous peoples; and challenges posed by neoliberalism and globalization to tribal governments and economies.
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    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Airborne geophysics has been used to identify more than 100 lakes beneath the ice sheets of Antarctica. The largest, Lake Vostok, is more than 250 km in length and 1 km deep. Subglacial lakes occur because the ice base is kept warm by geothermal heating, and generated meltwater collects in topographic hollows. For lake water to be in equilibrium with the ice sheet, its roof must slope ten times more than the ice sheet surface. This slope causes differential temperatures and melting/freezing rates across the lake ceiling, which excites water circulation. The exploration of subglacial lakes has two goals: to find and understand the life that may inhabit these unique environments and to measure the climate records that occur in sediments on lake floors. The technological developments required for in situ measurements mean, however, that direct studies of subglacial lakes may take several years to happen.
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    Notes: Microbes are recognized as important components of the Earth system, playing key roles in controlling the composition of the atmosphere and surface waters, forming the basis of the marine food web, and the cycling of chemicals in the ocean. A revolution in microbial ecology has occurred in the past 15Đ??20 years with the advent of rapid methods for discovering and sequencing the genes of uncultivated microbes from natural environments. Initially based on sequences from the 16S rRNA gene, this revolution made it possible to identify microorganisms without first cultivating them, to discover and characterize the immense previously unsuspected diversity of the microbial world, and to reconstruct the evolutionary relationships among microbes. Subsequent focus on functional genes, those that encode enzymes that catalyze biogeochemical transformations, and current work on larger DNA fragments and entire genomes make it possible to link microbial diversity to ecosystem function. These approaches have yielded insights into the regulation of microbial activity and proof of the microbial role in biogeochemical processes previously unknown. Questions raised by the molecular revolution, which are now the focus of microbial ecology research, include the significance of microbial diversity and redundancy to biogeochemical processes and ecosystem function.
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    Notes: Stable cratons and stable continental platforms are salient features of the Earth. Mantle xenoliths provide detailed data on deep structure. Cratonal lithosphere is about 200 km thick. It formed in the Archean by processes analogous to modern tectonics and has been stable beneath the larger cratons since that time. Its high viscosity, high yield strength, and chemical buoyancy protected it from being entrained by underlying stagnant lid convection and by subduction. Chemically buoyant mantle does not underlie platforms. Platform lithosphere has gradually thickened with time as convection waned as the Earth's interior cooled. The thermal contraction associated with this thickening causes platforms to subside relative to cratons. At present, the thickness of platform lithosphere is comparable to that of cratonal lithosphere.
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    Notes: Earthquake triggering is the process by which stress changes associated with an earthquake can induce or retard seismic activity in the surrounding region or trigger other earthquakes at great distances. Calculations of static Coulomb stress changes associated with earthquake slip have proven to be a powerful tool in explaining many seismic observations, including aftershock distributions, earthquake sequences, and the quiescence of broad, normally active regions following large earthquakes. Delayed earthquake triggering, which can range from seconds to decades, can be explained by a variety of time-dependent stress transfer mechanisms, such as viscous relaxation, poroelastic rebound, or afterslip, or by reductions in fault friction, such as predicted by rate and state constitutive relations. Rapid remote triggering of earthquakes at great distances (from several fault lengths to 1000s of km) is best explained by the passage of transient (dynamic) seismic waves, which either immediately induce Coulomb-type failure or initiate a secondary mechanism that induces delayed triggering. The passage of seismic waves may also play a significant role in the triggering of near-field earthquakes.
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    Notes: Ichthyosaurs were a group of Mesozoic marine reptiles that evolved fish-shaped body outlines. They are unique in several anatomical characters, including the possession of enormous eyeballs sometimes exceeding 25 cm and an enlarged manus with sometimes up to 20 bones in a single digit, or 10 digits per manus. They are also unique in that their biology has been studied from the perspective of physical constraints, which allowed estimation of such characteristics as optimal cruising speed, visual sensitivity, and even possible basal metabolic rate ranges. These functional inferences, although based on physical principles, obviously contain errors arising from the limitations of fossilized data, but are necessarily stronger than the commonly made inferences based on superficial correlations among quantities without mechanical or optical explanations for why such correlations exist.
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    Notes: The Ediacara biota (575Đ??542 Ma) marks the first appearance of large, architecturally complex organisms in Earth history. Present evidence suggests that the Ediacara biota included a mixture of stem- and crown-group radial animals, stem-group bilaterian animals, "failed experiments" in animal evolution, and perhaps representatives of other eukaryotic kingdoms. These soft-bodied organisms were preserved under (or rarely within) event beds of sand or volcanic ash, and fo