Application of a roughness-length representation to parameterize energy loss in 3-D numerical simulations of large rivers

Recent technological advances in remote sensing have enabled investigation of the morphodynamics and hydrodynamics of large rivers. However, measuring topography and flow in these very large rivers is time consuming and thus often constrains the spatial resolution and reach-length scales that can be monitored. Similar constraints exist for computational fluid dynamics (CFD) studies of large rivers, requiring maximization of mesh-or grid-cell dimensions and implying a reduction in the representation of bedform-roughness elements that are of the order of a model grid cell or less, even if they are represented in available topographic data. These ``subgrid'' elements must be parameterized, and this paper applies and considers the impact of roughness-length treatments that include the effect of bed roughness due to ``unmeasured'' topography. CFD predictions were found to be sensitive to the roughness-length specification. Model optimization was based on acoustic Doppler current profiler measurements and estimates of the water surface slope for a variety of roughness lengths. This proved difficult as the metrics used to assess optimal model performance diverged due to the effects of large bedforms that are not well parameterized in roughness-length treatments. However, the general spatial flow patterns are effectively predicted by the model. Changes in roughness length were shown to have a major impact upon flow routing at the channel scale. The results also indicate an absence of secondary flow circulation cells in the reached studied, and suggest simpler two-dimensional models may have great utility in the investigation of flow within large rivers. Citation: Sandbach, S. D. et al. (2012), Application of a roughness-length representation to parameterize energy loss in 3-D numerical simulations of large rivers, Water Resour. Res., 48, W12501, doi: 10.1029/2011WR011284.

Effects of corticosterone on innate and humoral immune functions and oxidative stress in barn owl nestlings.

The costs of coping with stressful situations are traded-off against other functions such as immune responses. This trade-off may explain why corticosterone secretion reduces immune reactions. Corticosterone differentially affects various immunity components. However, which component is suppressed varies between studies. It remains unclear whether the trade-off in energy, nutrition, autoimmunity or oxidative stress accounts for differential immunosuppression. In this study, we investigated whether corticosterone differentially affects the constitutive innate and humoral acquired immunity. We used barn owl nestlings, implanting 50% with a corticosterone-releasing pellet and the other 50% with a placebo pellet. To measure the effect on humoral immunity we vaccinated 50% of the corticosterone-nestlings and 50% of the placebo-nestlings with the antigens 'Tetravac' and the other 50% were injected with PBS. To assess the costs of elevated corticosterone, we measured body mass and resistance to oxidative stress. Administration of corticosterone increased corticosterone levels whereas vaccination induced the production of antibodies. Corticosterone reduced the production of antibodies, but it did not significantly affect the constitutive innate immunity. Corticosterone reduced body growth and resistance to oxidative stress. Under stressful conditions barn owl nestlings seem to keep the constitutive innate immunity, whereas elevated corticosterone levels negatively affected inducible immune responses. We found evidence that mounting a humoral immune reaction is not costly in terms of growth, but reduces the resistance to oxidative stress independently of corticosterone administration. We suggest that humoral immunity is suppressed because the risk of immunopathologies may be disproportionately high when mounting an antibody response under stressful situations.

Dissociation of allocentric and egocentric orientation: Effect on hippocampal place cells and place navigation

Navigation by means of cognitive maps appears to require the hippocampus; hippocampal place cells (PCs) appear to store spatial memories because their discharge is confined to cell-specific places called firing fields (FFs). Experiments with rats manipulated idiothetic and landmark-related information to understand the relationship between PC activity and spatial rotation. Rotating a circular arena in the caused a discrepancy between these cuse. This discrepancy caused most FFs to disappear in both the arena and room reference frames. However, FFs persisted in the rotating arena frame when the discrepancy was reduced by darkness or by a card in the arena. The discrepancy was increased by "field clamping" the rat in a room-defined FF location by rotations that countered its locomotion. Most FFs disspared and reappeared an hour or more after the clamp. Place-avoidance experiments showed that navigation uses independent idiothetic and exteroceptive memories. Rats learned to avoid the unmarked footshock region within a circular arena. When acquired on the stable arena in the light, the location of the punishment was learned by using both room and idiothetic cues; extinction in the dark transferred to the following session in the light. If, however, extinction occured during rotation, only the arena-frame avoidance was extinguished in darkness; the room-defined location was avoided when the light were turned back on. Idiothetic memory of room-defined avoidance was not formed during rotation in light; regardless of rotation with a randomly dispersed pellet. The resulting behaviour alternated between random pellet searching and target-directed navigation, making it possible to examine PC correlates of these two classes of spatial behaviour. The independence of idiothetic and exteroceptive spatial memories and the disruption of PC firing during rotation suggest that PCs may not be necessary for spatial cognition; this idea can be tested by recording during place-avoidance and preference tasks.

Regulation of free corticosterone and CBG capacity under different environmental conditions in altricial nestlings.

The concentration of circulating glucocorticoids is regulated in response to environmental and endogenous conditions. Total circulating corticosterone, the main glucocorticoid in birds, consists of a fraction which is bound to corticosterone-binding globulins (CBG) and a free fraction. There is increasing evidence that the environment modulates free corticosterone levels through varying the concentration of CBG, but experimental evidence is lacking. To test the hypothesis that the regulation of chronic stress in response to endogenous and environmental conditions involves variation in both corticosterone release and CBG capacity, we performed an experiment with barn owl (Tyto alba) nestlings in two different years with pronounced differences in environmental conditions and in nestlings experimentally fed ad libitum. In half of the individuals we implanted a corticosterone-releasing pellet to artificially increase corticosterone levels and in the other half we implanted a placebo pellet. We then repeatedly collected blood samples to measure the change in total and free corticosterone levels as well as CBG capacity. The increase in circulating total corticosterone after artificial corticosterone administration varied with environmental conditions and with the food regime of the nestlings. The highest total corticosterone levels were found in nestlings growing up in poor environmental conditions and the lowest in ad libitum fed nestlings. CBG was highest in the year with poor environmental conditions, so that, contrary to total corticosterone, free corticosterone levels were low under poor environmental conditions. When nestlings were fed ad libitum total corticosterone, CBG and free corticosterone did not increase when administering corticosterone. These results suggest that depending on the individual history an animal experienced during development the HPA-axis is regulated differently.

The cervico-thoracic outlet compression syndrome. Analysis of surgical treatment.

Surgical treatment of the thoracic outlet compression syndrome is being presently reconsidered. Until these last few years, there was the choice between two interventions only: scalenotomy, a simple operation entailing no complication, but with a 60% recurrence rate--or the resection of the first rib through an axillary approach, an efficacious intervention which caused, however, serious nervous complications in 14% of treated cases. The follow-up of 75 cases operated for a TOCS reveals to the authors that--all techniques taken into account--results are unsatisfactory in 33% of cases. These failures are due either to technical deficiencies, or to a complication arising in the course of the operation, or to an erroneous diagnosis. The authors resort to surgery only to treat serious vascular syndromes (absolute indication) or invalidating neurological compression syndromes, after failure of physical therapy (relative indication). They propose a cervical approach--the only one enabling a safe dissection of the brachial plexus--a partial scalenectomy, resection of all fibrous bands pressing on nervous trunks, or the resection of a cervical rib. Should the costo-clavicular space appear anatomically too narrow, the first rib, already partially freed by the cervical approach, will be resected through the axillary route.

Localization in sucrose gradients of the pyrophosphate-dependent proton transport of maize root membranes.

A maize (Zea mays L. cv LG 11) root homogenate was prepared and centrifuged to sediment the mitochondria. The pellet (6 KP) and the supernatant (6 KS) were collected and fractionated on linear sucrose density gradients. Marker enzymes were used to study the distribution of the different cell membranes in the gradients. The distribution of the ATP- and pyrophosphate-dependent proton pumping activities was similar after 3 hours of centrifugation of the 6 KS or the 6 KP fraction. The pumps were clearly separated from the mitochondrial marker cytochrome c oxidase and the plasmalemma marker UDP-glucose-sterolglucosyl-transferase. The pyrophosphate-dependent proton pump might be associated with the tonoplast, as the ATP-dependent pump, despite the lack of a specific marker for this membrane. However, under all the conditions tested, the two pumps overlapped the Golgi markers latent UDPase and glucan synthase I and the ER marker NADH-cytochrome c reductase. It is therefore not possible to exclude the presence of proton pumping activities on the Golgi or the ER of maize root cells. The two pumps (but especially the pyrophosphate-dependent one) were more active (or more abundant) in the tip than in the basal part of maize roots, indicating that these activities might be important in growth processes.

Anti-Nogo-A Antibody Treatment Promotes Recovery of Manual Dexterity after Unilateral Cervical Lesion in Adult Primates--re-examination and Extension of Behavioral Data.

In rodents and nonhuman primates subjected to spinal cord lesion, neutralizing the neurite growth inhibitor Nogo-A has been shown to promote regenerative axonal sprouting and functional recovery. The goal of the present report was to re-examine the data on the recovery of the primate manual dexterity using refined behavioral analyses and further statistical assessments, representing secondary outcome measures from the same manual dexterity test. Thirteen adult monkeys were studied; seven received an anti-Nogo-A antibody whereas a control antibody was infused into the other monkeys. Monkeys were trained to perform the modified Brinkman board task requiring opposition of index finger and thumb to grasp food pellets placed in vertically and horizontally oriented slots. Two parameters were quantified before and following spinal cord injury: (i) the standard 'score' as defined by the number of pellets retrieved within 30 s from the two types of slots; (ii) the newly introduced 'contact time' as defined by the duration of digit contact with the food pellet before successful retrieval. After lesion the hand was severely impaired in all monkeys; this was followed by progressive functional recovery. Remarkably, anti-Nogo-A antibody-treated monkeys recovered faster and significantly better than control antibody-treated monkeys, considering both the score for vertical and horizontal slots (Mann-Whitney test: P = 0.05 and 0.035, respectively) and the contact time (P = 0.008 and 0.005, respectively). Detailed analysis of the lesions excluded the possibility that this conclusion may have been caused by differences in lesion properties between the two groups of monkeys.

The contribution of patch topology and demographic parameters to PVA predictions: the case of the European tree frog

Population viability analyses (PVA) are increasingly used in metapopulation conservation plans. Two major types of models are commonly used to assess vulnerability and to rank management options: population-based stochastic simulation models (PSM such as RAMAS or VORTEX) and stochastic patch occupancy models (SPOM). While the first set of models relies on explicit intrapatch dynamics and interpatch dispersal to predict population levels in space and time, the latter is based on spatially explicit metapopulation theory where the probability of patch occupation is predicted given the patch area and isolation (patch topology). We applied both approaches to a European tree frog (Hyla arborea) metapopulation in western Switzerland in order to evaluate the concordances of both models and their applications to conservation. Although some quantitative discrepancies appeared in terms of network occupancy and equilibrium population size, the two approaches were largely concordant regarding the ranking of patch values and sensitivities to parameters, which is encouraging given the differences in the underlying paradigms and input data.

Diagnostic performance of &supl;⁸F-fluorodeoxyglucose positron emission tomography in giant cell arteritis: a systematic review and meta-analysis.

PURPOSE: The aim of this study was to conduct a systematic review and perform a meta-analysis on the diagnostic performances of (18)F-fluorodeoxyglucose positron emission tomography (FDG PET) for giant cell arteritis (GCA), with or without polymyalgia rheumatica (PMR). METHODS: MEDLINE, Embase and the Cochrane Library were searched for articles in English that evaluated FDG PET in GCA or PMR. All complete studies were reviewed and qualitatively analysed. Studies that fulfilled the three following criteria were included in a meta-analysis: (1) FDG PET used as a diagnostic tool for GCA and PMR; (2) American College of Rheumatology and Healey criteria used as the reference standard for the diagnosis of GCA and PMR, respectively; and (3) the use of a control group. RESULTS: We found 14 complete articles. A smooth linear or long segmental pattern of FDG uptake in the aorta and its main branches seems to be a characteristic pattern of GCA. Vessel uptake that was superior to liver uptake was considered an efficient marker for vasculitis. The meta-analysis of six selected studies (101 vasculitis and 182 controls) provided the following results: sensitivity 0.80 [95% confidence interval (CI) 0.63-0.91], specificity 0.89 (95% CI 0.78-0.94), positive predictive value 0.85 (95% CI 0.62-0.95), negative predictive value 0.88 (95% CI 0.72-0.95), positive likelihood ratio 6.73 (95% CI 3.55-12.77), negative likelihood ratio 0.25 (95% CI 0.13-0.46) and accuracy 0.84 (95% CI 0.76-0.90). CONCLUSION: We found overall valuable diagnostic performances for FDG PET against reference criteria. Standardized FDG uptake criteria are needed to optimize these diagnostic performances.

Die Töpferin und der Schmied : Basel-Gasfabrik, Grabung 1989/5

RésuméDie Grabung 1989/5 der Archäologischen Bodenforschung Basel-Stadt im Zentrum der Siedlung Basel-Gasfabrik umfasste eine Fläche von etwa 900 m2. Auf etwa 370 m2 konnten intakte latènezeitliche Strukturen festgestellt werden. Der ehemalige Gehhorizont und die darunter liegende Siedlungsschicht waren jedoch nirgends erhalten geblieben.Die in den gewachsenen Boden eingetieften Pfostengrub en erlaubten die Rekonstrulction von zwei rechteckigen Häusern mit je vier Eckpfosten, die als Wohngebäude gedeutet werden.Über das ganze Areal verteilt wurden 14 Gruben unterschiedlicher Form und Grösse ganz oder teilweise ausgegraben. Bei der flachen Grube 261 handelt es sich wohl um den eingetieften Bereich eines kleinen Grubenhauses, das für nicht näher bestimmbare handwerkliche Aktivitäten genutzt wurde. Die beiden mit einem Pfostenbau überdeckten Gruben 258 und 259 können hingegen mit grosser Wahrscheinlichkeit als Schmiedegruben gedeutet werden. In Grube 258 waren gar die Reste von zwei Feuerstellen und der Unterbau eines kaminartigen Abzugs in situ erhalten. Die Gruben 253, 254A, 254B, 255,256 und 257 mit Resten von Lehmausideidungen dienten vermutlich als Getreidesilos. Sie liegen alle im Zentrum des Grabungsareals im Bereich einer anstehenden Lehmschicht. Bei einigen weiteren Gruben könnte es sich um Keller handeln.Im Westen der Grabungsfläche kamen die Heizkanäle von zwei Töpferöfen zum Vorschein. Es handelt sich um einfache Kuppelöfen mit gegenständiger Feuerung. In geringer Entfernung lagen drei kleine Gruben, die vielleicht zur Aufbereitung des Töpferlehms dienten. Aufgrund der klimatischen Verhältnisse ist mit einem saisonalen Betrieb der Töpferöfen während der Sommermonate zu rechnen. Die notwendigen Arbeiten wurden mit grosser Wahrscheinlichkeit von Frauen ausgeführt, da die Männer während dieser Jahreszeit in der Landwirtschaft beschäftigt waren. Der Töpfereibetrieb produzierte grössere Serien scheibengedrehter, reduzierend gebrannter Feinkeramik, von der im Bereich der Öfen zahlreiche Scherben gefunden wurden.Die räumliche Organisation der Bebauung zeugt von einer einheitlichen und wohl kontinuierlichen Nutzung der Grabungsfläche. ImWesten gruppieren sich Haus 1 und die Einrichtungen des Töpfereibetriebs um eine unbebaute Hofzone. Nach Osten zu folgt dann die Zone mit den Getreidesilos. Das östliche Bauensemble besteht aus Haus 2, den Schmiedegruben, dem Grubenhaus sowie einer mutmasslichen Kellergrube. Stratigra-phische Überschneidungen von Befunden sind nur im Bereich der Töpferöfen vorhanden.Die Grubenfüllungen erwiesen sich als sehr fundreich. Die gegen 20000 Keramikscherben repräsentieren das gesamte Spektrum der aus Basel-Gasfabrik bekannten einheimischen Grobund Feinkeramik. Bei den seltenen Scherben von Graphittonkeramik handelt es sich um Importe aus dem ostkeltischen Bereich.Die zahlreichen Amphorenscherben stammen von mindestens 35 verschiedenen Gefässindividuen des Typs Dressel 1A, von denen aber immer nur ein kleiner Prozentsatz vorhanden war. Die Typologie und die Datierung der Befunde zeigen, dass der Amphorenimport erst im Laufe von LT D1 einsetzte.Unter den Kleinfunden verdienen die zahlreichen Silber- und Potinmünzen sowie die Glasfunde besondere Erwähnung. Das Fragment eines möglicherweise latènezeitlichen Glasgefässes stammt leider aus einem unsicheren Fundzusammenhang.Die über 70 Fibeln und Fibelteile sind zu 70% aus Bronze gefertigt. Das Fibelspektrum wird von den Nauheimer Fibeln dominiert. Besonders bei den Eisenfibeln konnten aber auch typologisch ältere Typen identifiziert werden, welche in die Stufen LT C2 und LT D1a gehören. Bei den Glasarmringen machen mittellatènezeitliche Typen gegen 20 % der Fundmenge aus.Von besonderer Bedeutung sind die 23 Menschenknochen von 19 verschiedenen Individuen. Es handelt sich dabei um einen fast vollständigen Schädel, Schädelteile und Fragmente von Langknochen sowie wenige weitere Skelettteile. Die Zusammensetzung des Ensembles und der Zustand der Einzelknochen lässt sich sehr gut mit den Menschenknochen aus den Altgrabungen von Basel-Gasfabrik und aus Manching vergleichen. Eine detaillierte Untersuchung zeigt, dass die Knochen am Ende eines langwierigen Totenrituals, das aufgrund ethno - logischer Vergleiche als mehrstufige Bestattung bezeichnet werden kann, in der Siedlung vergraben wurden. In der Umgebung der Menschenknochen wurden in einigen Fällen auffallend viele Amphorenscherben gefunden, die bezeugen, dass der importierte Wein bei diesen Riten eine bedeutende Rolle spielte. Wahrscheinlich wurden diese Knochen auch als Ahnenrelikte verehrt.Neben den mehrstufigen Bestattungen konnten auch zwei Säuglingsbestattungen identifiziert werden.Die Analyse von Fundmenge und Fundverteilung in den Gruben zeigt, dass die Funde nicht direkt, sondern auf dem Umweg über primäre Deponien in die Gruben gelangten. In den pri-mären Deponien wurden Funde über längere Zeit akkumuliert und mit verschiedenen Erdmaterialien intensiv vermischt.Für den Grossteil der Funde wird eine profane Deutung als Abfälle vorgeschlagen. Daneben können aber auch einige Funde als gezielte Deponierungen angesprochen werden. Ver-schiedene Fibelpaare und wahrscheinlich auch Münzen wurden wohl als Opfergaben in die Gruben gegeben. Ein Zusammenhang dieser Opfergaben mit den Bestattungen von Men-schenknochen ist nicht erkennbar.Die Datierung der Funde zeigt einen Siedlungsbeginn in LT C2 und ein Ende noch vor dem Beginn der Stufe LT D2. Die Kombination dieser Datierungen mit den stratigraphischen Überschneidungen einiger Befunde erlaubt eine Rekonstruktion der Besiedlungsentwicklung auf dem Grabungsareal. Die Gruben 259 und 260 wurden bereits in LT C2 verfüllt, die Schmiedegrube 259 anschliessend durch Grube 258 ersetzt. Die beiden Töpferöfen waren nacheinander in LT D1 in Betrieb. Die beiden Häuser können leider nicht genauer datiert werden.Die Besiedlung des Area's setzte noch vor 150 V. Chr. ein und dauerte maximal 80 Jahre.Die Synthese aller Untersuchungen zeigt, dass auf dem Grabungsareal eine Gruppe von etwa 15 Personen ansässig war, die sich v. a. der Landwirtschaft widmete. Die handwerkliche Tätigkeit (Töpferei, Metallverarbeitung) erreichte keinen vollberuflichen Standard.Die dörfliche Siedlungsgemeinschaft bestand aus bäuerlichen Selbstversorgern, mit anderen Gemeinschaften wurden jedoch Keramik, Handwerksprodukte und Schlachtvieh ausge-tauscht. Von besonderer Bedeutung war offenbar das Getreide, das in grossen Mengen in der Siedlung gelagert wurde und mit grosser Wahrscheinlichkeit für den Export bestimmt war. Die Herkunft dieses Getreides und die sozialen Strukturen hinter diesem Austausch sind nicht ldar, aber mit hoher Wahrscheinlichkeit wurden durch den Getreideexport die Importe wie Salz, Rohstoffe (Metall) und Wein ermöglicht.

The place preference task: a new tool for studying the relation between behavior and place cell activity in rats

This study describes a task that combines random searching with goal directed navigation. The testing was conducted on a circular elevated open field (80 cm in diameter), with an unmarked target area (20 cm in diameter) in the center of 1 of the 4 quadrants. Whenever the rat entered the target area, the computerized tracking system released a pellet to a random point on the open field. Rats were able to learn the task under light and in total darkness, and on a stable or a rotating arena. Visual information was important in light, but idiothetic information became crucial in darkness. Learning of a new position was quicker under light than in total darkness on a rotating arena. The place preference task should make it possible to study place cells (PCs) when the rats use an allothetic (room frame) or idiothetic (arena frame) representation of space and to compare the behavioral response with the PCs' activity.

Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach.

AbstractText BACKGROUND: Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim's epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim's DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim's fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim's fraction, and then digest the residual victim's DNA with a nuclease. METHODS: The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases. RESULTS: For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles. CONCLUSIONS: In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods.

Granulomatous uveitis and congenital cataract: a rare association.

INTRODUCTION: The association of a granulomatous uveitis and congenital cataract and is rarely observed in newborn children. We describe the history of two patients presenting simultaneously with these two features in the absence of a TORCH infection. PATIENTS AND METHODS: The first patient, a boy born in 1997, presented to our hospital two days after birth with multiples Koeppe's and Busacca's nodules and bilateral cataract. The second patient, a boy born in 2006, was referred two weeks after birth. He presented with a severe unilateral granulomatous uveitis, multiples iris nodules, a high intraocular pressure of 45 mmHg and a congenital cataract. THERAPY AND OUTCOME: Lens extraction produced a rapid resolution of uveitis in these two patients. TORCH infection was ruled out in both children by history, extensive serologies performed simultaneously in mother and child or PCR of ocular fluids. CONCLUSIONS: A congenital cataract associated with a granulomatous uveitis is an extremely rare association. The removal of the lens resulted in complete resolution of the inflammation: a phacogenic mechanism could be at the origin of ocular inflammation in both cases.