bluuebunny/crossref_metadata_2025 huggingface dataset:
The Baptismal Covenant and the Proposed Anglican Covenant
Authors: Meyers Ruth A.
Published: December 2011

An exploration of the development and meaning of the text of the Baptismal Covenant in the 1979 Book of Common Prayer of the Episcopal Church provides the basis for a discussion of the proposed Anglican Communion Covenant. The article concludes by suggesting how biblical, theological and liturgical understandings of covenant offer a perspective by which to assess the proposed Covenant for the Anglican Communion.
Attribution of water resources evolution in the highly water‐stressed Hai River Basin of China
Authors: Jia Yangwen , Ding Xiangyi , Wang Hao , Zhou Zuhao , Qiu Yaqin , Niu Cunwen
Published: December 2011

Many observations and studies have shown that water resources amount in the Hai River Basin decreased significantly over the last half of the twentieth century. This study attempts to attribute the observed changes in the water resources amount in the basin over a 40 year period (1961–2000) to different factors, including natural climate variability, climate change induced by anthropogenic forcing of greenhouse gas emissions (referred to as anthropogenic forcing hereafter), and local human activity. First, the temporal variation of the annual water resources amount in the basin during the past 40 years is analyzed by employing the moving‐average method, the linear regression method, and the Mann‐Kendall method. Second, through setting different scenarios, the effects on the water resources amount due to different factors, including natural climate variability, anthropogenic forcing, and local human activity, are obtained using the parallel climate model, the distributed hydrological model water and energy transfer processes in large river basins, and the statistical downscaling model. Third, the fingerprint‐based attribution method is used to obtain the signal strengths of observed changes in water resources amount during 1961–2000 and changes in the water resources amount under different scenarios. Finally, by comparing the signal strengths, the observed changes in water resources amount in the basin can be attributed to different factors. The results indicate that natural climate variability and local human activity may be two factors responsible for the observed changes in the water resources amount during the past 40 years in the basin, with local human activity being the main factor and accounting for about 60% of the changes.
A proof‐of‐concept balloon‐borne Global Positioning System radio occultation profiling instrument for polar studies
Authors: Haase J. S. , Maldonado‐Vargas J. , Rabier F. , Cocquerez P. , Minois M. , Guidard V. , Wyss P. , Johnson A. V.
Published: December 2011

Global warming has focused attention on the polar regions and recent changes in sea and land ice distribution. Accurate modeling of the future evolution of climate and weather in the Antarctic relies heavily on remote sensing observations. However, their reliable assimilation into numerical weather models and reanalyses is challenging because of the unique environment and sparsity of in‐situ observations for validation. We developed a stratospheric balloon‐borne GPS radio occultation system for the 2010 Concordiasi campaign to provide refractivity and derived temperature profiles for improving satellite data assimilation. The observed excess phase delay profiles agree with those simulated from model and dropsonde profiles. 711 occultations were recorded from two balloons, comparable to the number of profiles acquired by 13 driftsonde balloons. Of these profiles, 32% descended to 4 km above the surface, without open‐loop receiver tracking technology, demonstrating it is possible to retrieve useful information with relatively simple low cost instruments.
Hydraulic conductivity of the High Plains Aquifer re‐evaluated using surface drainage patterns
Authors: Luo Wei , Pederson Darryll T.
Published: December 2011

The High Plains Aquifer (HPA), underlying parts of 8 states from South Dakota to Texas, is one of the largest fresh water aquifers in the world and accounts for 30% of the groundwater used for irrigation in the US. Determining the distribution of HPA's hydraulic conductivity (K) is critical for water management and addressing water quality issues. K is traditionally estimated from well pumping data coupled with computer modeling and is known to be highly variable, spanning several orders of magnitude for the same type of rock. Here we show that applying our innovative method of determining effective horizontal K to HPA (based on surface drainage patterns and a dynamic equilibrium assumption) produced results generally consistent with those from traditional methods but reveals much more detailed spatial variation. With the exception of a few places such as the Sand Hills area, our results also show for the first time (to the best of our knowledge) a distinct relationship between surface stream drainage density and subsurface aquifer K in a major aquifer system on a regional scale. Because aquifer particle size strongly controls K, our results can be used to study patterns of past sediment movement and deposition.
The relativistic feedback discharge model of terrestrial gamma ray flashes
Authors: Dwyer Joseph R.
Published: December 2011

As thunderclouds charge, the large‐scale fields may approach the relativistic feedback threshold, above which the production of relativistic runaway electron avalanches becomes self‐sustaining through the generation of backward propagating runaway positrons and backscattered X‐rays. Positive intracloud (IC) lightning may force the large‐scale electric fields inside thunderclouds above the relativistic feedback threshold, causing the number of runaway electrons, and the resulting X‐ray and gamma ray emission, to grow exponentially, producing very large fluxes of energetic radiation. As the flux of runaway electrons increases, ionization eventually causes the electric field to discharge, bringing the field below the relativistic feedback threshold again and reducing the flux of runaway electrons. These processes are investigated with a new model that includes the production, propagation, diffusion, and avalanche multiplication of runaway electrons; the production and propagation of X‐rays and gamma rays; and the production, propagation, and annihilation of runaway positrons. In this model, referred to as the relativistic feedback discharge model, the large‐scale electric fields are calculated self‐consistently from the charge motion of the drifting low‐energy electrons and ions, produced from the ionization of air by the runaway electrons, including two‐ and three‐body attachment and recombination. Simulation results show that when relativistic feedback is considered, bright gamma ray flashes are a natural consequence of upward +IC lightning propagating in large‐scale thundercloud fields. Furthermore, these flashes have the same time structures, including both single and multiple pulses, intensities, angular distributions, current moments, and energy spectra as terrestrial gamma ray flashes, and produce large current moments that should be observable in radio waves.
Flower structures and Riedel shears at a step over zone along the Alpine Fault (New Zealand) inferred from 2‐D and 3‐D GPR images
Authors: Carpentier S. F. A. , Green A. G. , Langridge R. , Boschetti S. , Doetsch J. , Abächerli A. N. , Horstmeyer H. , Finnemore M.
Published: December 2011

High‐resolution GPS and ground‐penetrating radar (GPR) data are used to detect and identify hidden faults along a stretch of the transpressional Alpine Fault (South Island, New Zealand) immediately north of its junction with the Hope Fault. At this location, the Alpine Fault emerges from the basement into a sequence of variably thick late Holocene gravel deposits. Geomorphology and trenching already mapped three principal fault strands and two distinct step over zones at the study site. Our GPR images reveal numerous additional secondary fault strands throughout the region, only some of which are obvious at the surface or in the trench walls. According to the GPR data, the main fault‐generated disturbance zone has a width ranging from ∼40 to ∼200 m. The secondary fault strands outside of the step over zones likely represent the branches of positive flower structures, whereas the faulting pattern around the step over zones is best explained in terms of linked Riedel shears. Systematic northeastward increases in the width of the main fault‐generated disturbance zone and corresponding increases in principal fault‐scarp height are the likely consequences of older terraces in the northeast being disrupted and offset by more earthquakes than younger terraces in the southwest. The pattern of complex faulting in this region is distinct from the system of alternating strike‐slip and reverse faults characteristic of the Alpine Fault to the south and from the rather simple sequence of faults mapped to the north. GPR surveying has added new information on the distribution and nature of faulting at our study site.
Role of fluids in the earthquake occurrence around Aswan reservoir, Egypt
Authors: Gahalaut Kalpna , Hassoup Awad
Published: December 2011

Continuing seismicity for about 30 years near a large western embayment of the Lake Nasser, about 50 km from the Aswan High Dam in Egypt, has led to a debate about the possibility of its relation with the reservoir impoundment. The largest event in the region occurred on 14 November 1981 (M 5.3), 20 km beneath the Wadi Kalabsha embayment, a westward extension of the Lake Aswan. Since then, continuous monitoring of seismic activity has given an excellent opportunity to study the spatiotemporal distribution of seismicity in the area. Most of the immediate aftershocks of the 1981 main shock were located in the Gebel Marawa area at depths between 15 and 30 km. Depths of almost all earthquakes away from this zone were shallower than 12 km. To quantify the effect of the reservoir impoundment on the seismicity of the Aswan area, we calculated changes in stress and pore pressure due to the reservoir impoundment using Green's function approach. The change in Coulomb stress (ΔS) is calculated on the fault planes responsible for majority of the seismicity of the region. We found that for all the seismogenic faults, ΔS is negative, i.e., stabilizing, when we consider the effect of the reservoir load only, whereas it is positive, i.e., destabilizing, when we include pore pressure. For example, at the hypocenter of the main earthquake, shear stress, normal stress, and pore pressure due to reservoir operation are estimated as 5.5, 13.2, and 13.5 kPa, respectively, which suggest that ΔS is −3.1 kPa when we do not consider the effect of pore pressure and 5.7 kPa when contribution from pore pressure is considered. Hence, the seismicity in the Aswan lake region is driven by the pore pressure due to reservoir impoundment.
Typhoon‐induced phytoplankton blooms and primary productivity increase in the western North Pacific subtropical ocean
Authors: Lin I.‐I.
Published: December 2011

Using multiple satellite observations and series of numerical experiments, this work systematically studied phytoplankton blooms induced by tropical cyclones in the western North Pacific subtropical ocean (WNPSO) because WNPSO is among the world oceans where most number of intense tropical cyclones are found. All eleven typhoon cases passing the study domain in 2003 were examined in detail. It was observed that only two typhoons (18%) were able to induce phytoplankton blooms (chlorophyll‐a concentration increased from ≦0.1 mg m−3 to 0.4–0.8 mg m−3) and strong sea surface temperature cooling of −2.5 to −6°C. The other nine typhoons, including the most intense tropical cyclone on Earth in 2003 (i.e., supertyphoon Maemi), were not able to induce phytoplankton blooms and the associated sea surface temperature cooling was weak (0 to −1.5°C). Using series of numerical experiments, it was found that the presence of warm ocean eddy can effectively isolate the cold, nutrient‐rich water to be entrained to the surface ocean. Under this situation, even category 5 typhoon Maemi at its peak intensity of 150 kts could not induce phytoplankton bloom in the WNPSO. The weak responses of the other eight typhoons were due to insufficient wind intensity and transit time (caused by relatively small storm size and fast translation speed) in this deep nutricline/mixed layer ocean. As a result, the total annual primary production increase induced by typhoons in the WNPSO was estimated to be ∼3.27 × 1012 g C (0.00327 Pg), equivalent to 0.15% of the global annual anthropogenic CO2 uptake. This suggests that though WNPSO has the highest number and intensity of tropical cyclones among the world oceans, tropical cyclones in the WNPSO have little contribution to enhance biological carbon fixation in the context of global carbon‐climate system.
Coupled hydrogeophysical inversion using time‐lapse magnetic resonance sounding and time‐lapse gravity data for hydraulic aquifer testing: Will it work in practice?
Authors: Herckenrath Daan , Auken Esben , Christiansen Lars , Behroozmand Ahmad A. , Bauer‐Gottwein Peter
Published: December 2011

Temporal changes in water content can be directly related to the time‐lapse signals retrieved using magnetic resonance sounding (TL‐MRS) and relative gravimetry (TL‐RG). Previous studies suggest that TL‐RG measurements can potentially provide accurate estimates of aquifer characteristics in an aquifer pumping test experiment when used in a coupled hydrogeophysical inversion approach. However, these studies considered highly idealized conditions. The aim of this paper is twofold: first, we investigate three major issues which likely limit the practical utility of TL‐RG for pumping test monitoring: partially penetrating pumping wells in anisotropic aquifers, delayed drainage effects, and typical data errors for TL‐RG. Second, we introduce TL‐MRS in a similar coupled hydrogeophysical inversion framework and compare the performance of TL‐MRS and TL‐RG for pumping test monitoring. For this purpose we consider a virtual pumping test, for which we generate synthetic drawdown, TL‐MRS and TL‐RG observations, and subsequently determine the aquifer parameters in an inverse parameter estimation approach. The inclusion of TL‐RG and TL‐MRS data did slightly improve parameter estimates for the specific yield and hydraulic conductivity when considering a fully penetrating well and minimal data error. Using more conservative TL‐RG and TL‐MRS data error estimates according our own field experience strongly limited the informative value of the TL‐RG data; TL‐MRS data was less affected by this. For a partially penetrating well under anisotropic conditions, parameter uncertainty could be reduced more effectively compared to a fully penetrating well. Delayed drainage effects did not limit the ability of the TL‐MRS and TL‐RG data to reduce parameter uncertainty significantly. The incorporation of representative measurement error correlation in the TL‐RG data did not affect its informative value. A local sensitivity analysis showed that observations were most sensitive to the pumping rate and the thickness, specific yield, and hydraulic conductivity of the aquifer. The inclusion of TL‐MRS data proved to be more effective to constrain the aquifer parameters compared with TL‐RG. The inclusion of both TL‐RG and TL‐MRS had limited added value compared to TL‐MRS only. We conclude that this particular application of coupled hydrogeophysical inversion has limited potential for TL‐RG, while TL‐MRS appears to be a more promising method.
Prediction of sediment transport in step‐pool channels
Authors: Yager E. M. , Dietrich W. E. , Kirchner J. W. , McArdell B. W.
Published: December 2011

In mountainous drainage networks, sediment mobilized on hillslopes must first pass through steep streams before reaching lower‐gradient channels. The bed of steep channels is typically composed of large, relatively immobile boulders and finer, more mobile gravel. Most sediment transport equations overpredict sediment flux in steep streams by several orders of magnitude because they do not account for the stress borne by immobile grains and the limited availability of the more mobile sediment. We previously developed and tested (in flume experiments) a sediment transport equation that accounts for these two effects. Here we modify the Parker (1990) bed load equation to include the resistance borne by steps and selective transport of the relatively mobile sediment using a range of hiding functions. We test a number of resistance equations and hiding functions, combined with our modified and the original Parker equations, against measured flow and sediment transport in three steep channels. Our modified sediment transport equation generally predicts the transported sediment volumes to within an order of magnitude of the measured values, whereas the unmodified equations do not. The most accurate sediment flux predictions were obtained from using our modified equation, combined with a hiding function that calculates highly selective transport of the relatively mobile sediment. Furthermore, this hiding function has a critical Shields stress that is similar to those reported for lower gradient channels. The effects of the immobile steps on flow and sediment transport are not adequately captured by simply increasing the critical Shields stress to values reported in steep streams.
Semi‐analytical solutions for solute transport and exchange in fractured porous media
Authors: Roubinet Delphine , de Dreuzy J.‐R. , Tartakovsky Daniel M.
Published: December 2011

Fracture‐matrix interactions can significantly affect solute transport in fractured porous media and rocks, even when fractures are major (or sole) conduits of flow. We develop a semi‐analytical solution for transport of conservative solutes in a single fracture. Our solution accounts for two‐dimensional dispersion in the fracture, two‐dimensional diffusion in the ambient matrix, and fully coupled fracture‐matrix exchange, without resorting to simplifying assumptions regarding any of these transport mechanisms. It also enables one to deal with arbitrary initial and boundary conditions, as well as with distributed and point sources. We investigate the impact of transverse dispersion in a fracture and longitudinal diffusion in the ambient matrix on the fracture‐matrix exchange, both of which are neglected in standard models of transport in fractured media.
A New General Allometric Biomass Model
Authors: Zeng Wei Sheng , Tang Shou Zheng
Published: December 2011

To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(~2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M and D (diameter on breast height). Secondly, using five datasets of aboveground biomass which consisted of 1441 M-D pairs of sample trees, the new general biomass allometric model was validated. Finally, the relationship between parameter a and wood density p was analyzed, and the linear regression was developed. The new model, which is not only simple but also species-specific, offers a feasible approach on establishment of generalized biomass models for regional and national forest biomass estimation.
Axl Deficiency Does Not Affect Adipogenesis or Adipose Tissue Development
Authors: Scroyen Ilse , Frederix Liesbeth , Lijnen H Roger
Published: December 2011

To evaluate a potential role of Axl, the high‐affinity receptor of growth arrest‐specific protein 6 (GAS6) in adiposity, murine embryonic fibroblasts (MEF) derived from mice with genetic deficiency of Axl (Axl−/−) or wild‐type littermates (Axl+/+) were differentiated into mature adipocytes. In addition, Axl−/− and Axl+/+ mice were kept on standard fat diet (SFD) or on high‐fat diet (HFD) for 15 weeks. Deficiency of Axl in MEF did not affect differentiation, as shown by a similar uptake of Oil Red O and expression of the adipogenic markers aP2 and peroxisome proliferator activator receptor γ (PPARγ) at the end of the differentiation. In the first 7 weeks of HFD feeding, Axl−/− mice gained less weight than their wild‐type littermates. Weight gain for both genotypes on either SFD of HFD over 15 weeks was, however, not significantly different, resulting in comparable body weights, as well as subcutaneous (s.c.) and gonadal (GON) fat mass. Adipocyte size in the fat tissues was not affected by Axl deficiency. Gene expression analysis indicated that the absence of Axl in vivo may be compensated for by the other TAM family members Mer and Tyro3. Glucose and insulin tolerance tests (ITT) in Axl−/− and Axl+/+ mice did not reveal significant differences in glucose homeostasis. Thus, Axl deficiency had no significant effect on adipogenesis in vitro or in vivo.
Endocavitary Contrast Enhanced Ultrasound (CEUS) – Work in Progress
Authors: Heinzmann A. , Müller T. , Leitlein J. , Braun B. , Kubicka S. , Blank W.
Published: December 2011

Ziel: Darstellung der diagnostischen Möglichkeiten der endokavitären Anwendung von Ultraschallkontrastmittel über Drainagen, im biliären System sowie bei oraler Gabe zur Untersuchung des GI-Traktes.

Material und Methoden: Kochsalzlösung unter Zumischung eines Tropfens SonoVue® wurde über die Drainage bzw. pro-/retrograd in das biliäre System eingebracht. Bei der oralen Anwendung wurden unterschiedliche Mischungsverhältnisse von Wasser mit SonoVue® verabreicht.

Ergebnisse: Die Kontrastmittelzumischung in Kochsalzlösung erleichtert die Lagekontrolle der Drainage und liefert zusätzliche Informationen zur Ausdehnung des zu drainierenden Prozesses. Komplikationen wie Fisteln zu den Gallengängen, Gefäßen, Darmschlingen, anderen Organen oder in die freie Bauchhöhle sind sensitiv erkennbar. Das biliäre System lässt sich gut darstellen. Bei der Gabe per os lässt sich das Kontrastmittel im Gastrointestinaltrakt verfolgen. Auch lassen sich Anastomoseninsuffizienzen und Perforationsstellen erkennen.

Schlussfolgerung: Die Gabe eines verdünnten Ultraschallkontrastmittels über eine Drainage bringt wertvolle Informationen über Lage, die Ausdehnung und Kommunikation des drainierten Prozesses zur Umgebung. Das biliäre System ist darstellbar. Die Gabe von Ultraschallkontrastverstärker per os ist möglich und kann Anastomoseninsuffizienzen und Perforationsstellen darstellen.
Spatial Aggregation and Compactness of Census Areas with a Multiobjective Genetic Algorithm: A Case Study in Canada
Authors: Datta Dilip , Malczewski Jacek , Figueira José Rui
Published: December 2011

The paper focuses on a case study of delineating census tracts (CTs) in the Census Metropolitan area of London, Ontario, Canada. The procedure for defining the actual pattern of CTs by a local committee and Statistics Canada has involved such consideration as the compactness of CTs and their population-based and area-based uniformity as well as some subjective aspects. The actual pattern shows that compactness of CTs has been achieved at the expense of uniformity in population and areal sizes. The paper proposes an integer-coded multiobjective genetic algorithm for aggregating census units with the expectation of obtaining a higher level of compactness and population/area uniformity of CTs through an optimization technique. Square-shape and circular-shape compactness of CTs are examined under different scenarios. The results indicate that the proposed genetic algorithm can provide solutions that are considerably better in terms of the Pareto-optimality principle than the actual pattern of CTs.
Synchrotron Infrared Spectroscopy of Cells and Tissue
Authors: McNaughton Don , Wood Bayden R.
Published: December 2011

This paper reviews work carried out in the Centre for Biospectroscopy, Monash University, at the Infrared Microspectroscopy Beamline on the Australian Synchrotron since the first synchrotron light. It discusses the attributes and advantages of the beamline for chemical spectroscopy and imaging of cellular and tissue samples and briefly summarizes new techniques that will come online in the near future.
Recovery dynamics of rainfed winter wheat after livestock grazing 1. Growth rates, grain yields, soil water use and water-use efficiency
Authors: Harrison Matthew T. , Evans John R. , Dove Hugh , Moore Andrew D.
Published: December 2011

Detailed information on the growth dynamics, yield responses and soil water use of dual-purpose cereal crops after grazing is often required to devise guidelines for profitable grazing management. To increase the availability of such data, grazing experiments with winter wheat (Triticum aestivum) were conducted near Canberra, Australia. In 2007, cultivar Mackellar was grazed at low-short (LS, 33 sheep/ha for 31 days), heavy-short (HS, 67 sheep/ha for 31 days) or low-long (LL, 33 sheep/ha for 62 days) intensity-durations. In 2008, cultivars Mackellar and Naparoo were grazed at the HS intensity-duration. Aboveground net primary production (ANPP) of ungrazed Mackellar crops averaged 1181 g/m2. LS and HS grazing did not affect ANPP in 2007, but LL grazing in 2007 and HS grazing in 2008 treatments reduced ANPP by 20% (which included biomass removed by livestock). Average grain yield (381 g/m2) was not significantly affected by grazing. Grazing increased the proportion of water lost through soil evaporation but decreased transpiration, reducing shoot dry matter production per unit evapotranspiration by up to 22%. However, grazing did not affect grain yield per unit evapotranspiration. For rainfed wheat crops grown in temperate environments, greater biomass production occurred with shorter rather than longer grazing durations, irrespective of grazing intensities.
Spatial characteristics and species niche attributes modulate the response by aquatic passive dispersers to habitat degradation
Authors: Gascón Stéphanie , Machado Margarida , Sala Jordi , Cancela da Fonseca Luís , Cristo Margarida , Boix Dani
Published: December 2011

The relative influences of local and regional factors on the distribution of passive dispersers may be altered by habitat degradation, partly via differential effects on species depending on their niche breadths. To study this, we compared the effects of local (pond, water and vegetation characteristics) and regional (Moran’s eigenvector maps) factors on passively dispersing large branchiopod crustaceans from two areas of the Iberian Peninsula differing in habitat condition (i.e. well preserved vs impacted). Species were arranged from generalists to specialists based on niche breadth. We hypothesised that (1) habitat degradation would favour functional homogenisation, resulting in higher occurrences of generalist species in the impacted area; because generalist species are likely to be less dependent on local factors, we also hypothesised that (2) regional factors would be more important in the impacted area. As predicted, the most generalist species had higher occurrences in the impacted area, resulting in functional homogenisation. Ultimately, this process affected metacommunity dynamics that were more influenced by regional than local factors because generalist species were widely distributed regardless of habitat degradation.
Fruit development in eucalypts (Myrtaceae: Eucalypteae)
Authors: Bohte Ann , Drinnan Andrew N.
Published: December 2011

Developmental anatomy of eucalypt flower buds from flower to mature fruits was investigated using light microscopy. Several important features contribute to the maturity of flower and fruit. The epidermis of the flower in many species is replaced by periderm in the fruit. Brachysclereid idioblasts develop in the parenchymatous zone beneath the epidermis; fibres develop from cambium-like activity in the vascular bundles located in the mid-region of the ovary wall; and cells adjacent to the locule lining mature as transversely oriented filiform sclereids. The initiation of these features in relation to anthesis varies among taxa, and this influences flower and fruit anatomy and morphology. In taxa where sclereids and fibres are initiated following anthesis, there is substantial post-anthesis growth and fruits are larger than flowers. When these features are developed before anthesis, the flowers are essentially pre-fruits that exhibit little or no further growth in the fruit stage apart from additional cell-wall lignification. Several other anatomical features, such as oil ducts and the distribution of oil glands and crystal layers, are not developmentally variable, but are phylogenetically informative within the eucalypt group.
Re-evaluating species limits in Uncinia angustifolia, U. caespitosa s.str., U. rupestris, U. viridis and U. zotovii (Cyperaceae)
Authors: Lehnebach C. A.
Published: December 2011

Morphology of New Zealand hook sedges Uncinia angustifolia Hamlin, U. rupestris Raoul and U. zotovii Hamlin overlaps considerably, making species identification difficult. All three species have a complicated taxonomic history. U. angustifolia has been considered a variety of U. rupestris, which, in turn, has been considered a variety of U. caespitosa Boot or included in two other species. As for U. zotovii, this was originally part of U. caespitosa along with the grassland species U. viridis (C.B.Clarke) Edgar. The present study re-examines historical and recently collected material, and re-evaluates species limits for these five species using multivariate statistic analyses of morphological characters. Results confirm the circumscription of U. caespitosa s.str. and the segregation of U. viridis and U. zotovii from U. caespitosa s.lat., but they also indicate that current species descriptions are inaccurate and based on material of mixed identity. Results also suggest that U. angustifolia, U. rupestris and U. zotovii should be considered as three different species. U. viridis and U. rupestris are conspecific; the latter name has priority and should be maintained. An identification key, revised descriptions, new synonymy and distribution maps for the species recognised here are also presented.
Successful use of a passive integrated transponder (PIT) system for below-ground detection of plethodontid salamanders
Authors: Connette Grant M. , Semlitsch Raymond D.
Published: December 2011

Context
Passive integrated transponder (PIT) technology allows for permanent and unambiguous marking of animals and has recently been adapted for locating tagged individuals in the field with portable detection systems.

Aims
We seek to assess the effects of PIT tagging on the growth and survival of plethodontid salamanders in the laboratory and to evaluate the effectiveness of this method for subterranean detection of salamanders in the field.

Methods
In a laboratory experiment, we assigned 36 Plethodon shermani to either a PIT tag or control group and compared survival and growth rates over the course of 9 weeks. For the field study, we implanted six Plethodon metcalfi with PIT tags and conducted surveys so as to determine their below-ground positions with a portable detector.

Key results
We found no effect of PIT tagging on either growth or survival in the laboratory. In the field, PIT telemetry resulted in an overall detection efficiency of 44%, with nighttime surveys yielding a greater detection efficiency than daytime surveys. This technique provided a significant improvement over traditional hand-capture because detected salamanders were rarely visible on the ground surface.

Key conclusions
Our study indicates that even these relatively small-bodied salamanders (range: 2.14–5.18 g) are capable of bearing PIT tag implants and confirms the results of previous studies that found no effect of PIT tagging on the health or survival of amphibians. This study further demonstrates that the use of a portable PIT detector can be an effective method for locating below-ground salamanders.

Implications
Because of the small size and long lifespan of PIT tags, we believe portable PIT detectors can provide researchers with an unprecedented level of detail for studies of the movement behaviour, spatial ecology and management of species that are small or otherwise challenging to detect and monitor with other techniques.
Checkpoint kinase 1 (Chk1)-short is a splice variant and endogenous inhibitor of Chk1 that regulates cell cycle and DNA damage checkpoints
Authors: Pabla Navjotsingh , Bhatt Kirti , Dong Zheng
Published: December 2011

Checkpoint kinase 1 (Chk1) is a key regulator of checkpoint signaling in both the unperturbed cell cycle and DNA damage response. Under these conditions, Chk1 becomes active to prevent premature CDK1 activation and mitotic entry until DNA is properly replicated or repaired. It is unclear how Chk1 activity is controlled in the unperturbed cell cycle. During DNA damage, Chk1 is activated by ataxia telangiectasia and Rad3 related (ATR)-mediated phosphorylation; however, it is not entirely clear how this phosphorylation results in Chk1 activation. Here we report an N-terminally truncated alternative splice variant of Chk1, Chk1-S. Importantly, we show that Chk1-S is an endogenous repressor and regulator of Chk1. In the unperturbed cell cycle, Chk1-S interacts with and antagonizes Chk1 to promote the S-to-G2/M phase transition. During DNA damage, Chk1 is phosphorylated, which disrupts the Chk1–Chk1-S interaction, resulting in free, active Chk1 to arrest the cell cycle and facilitate DNA repair. Higher levels of Chk1-S are expressed, along with Chk1, in fetal and cancer tissues than in normal tissues. However, forced overexpression of Chk1-S in cultured cells and tumor xenografts induces premature mitotic entry, mitotic catastrophe, and reduction of tumor growth. The identification of Chk1-S as a unique splice variant and key regulator of Chk1 provides insights into cell cycle regulation and DNA damage response.
Site-specific ubiquitination is required for relieving the transcription factor Miz1-mediated suppression on TNF-α–induced JNK activation and inflammation
Authors: Liu Jing , Yan Jie , Jiang Shan , Wen Jing , Chen Long , Zhao Yingming , Lin Anning
Published: December 2011

The transcription factor zinc-finger protein Miz1 represses TNF-α–induced JNK activation and the repression is relieved upon TNF-α stimulation. However, the underlying mechanism is incompletely understood. Here we report that Miz1 interferes with the ubiquitin conjugating enzyme (E2) Ubc13 for binding to the RING domain of TNF-receptor associated factor 2 (TRAF2), thereby inhibiting the ubiquitin ligase (E3) activity of TRAF2 and suppressing TNF-α–induced JNK activation. Upon TNF-α stimulation, Miz1 rapidly undergoes K48-linked polyubiquitination at Lys388 and Lys472 residues and subsequent proteasomal degradation in a TRAF2-dependent manner. Replacement of Lysine 388 and Lysine 472 by arginines generates a nondegradable Miz1 mutant, which significantly suppresses TNF-α–induced JNK1 activation and inflammation. Thus, our results reveal a molecular mechanism by which the repression of TNF-α–induced JNK activation by Miz1 is de-repressed by its own site-specific ubiquitination and degradation, which may account for the temporal control of TNF-α–JNK signaling.
Modularity of a carbon-fixing protein organelle
Authors: Bonacci Walter , Teng Poh K. , Afonso Bruno , Niederholtmeyer Henrike , Grob Patricia , Silver Pamela A. , Savage David F.
Published: December 2011

Bacterial microcompartments are proteinaceous complexes that catalyze metabolic pathways in a manner reminiscent of organelles. Although microcompartment structure is well understood, much less is known about their assembly and function in vivo. We show here that carboxysomes, CO2-fixing microcompartments encoded by 10 genes, can be heterologously produced inEscherichia coli. Expression of carboxysomes inE. coliresulted in the production of icosahedral complexes similar to those from the native host. In vivo, the complexes were capable of both assembling with carboxysomal proteins and fixing CO2. Characterization of purified synthetic carboxysomes indicated that they were well formed in structure, contained the expected molecular components, and were capable of fixing CO2in vitro. In addition, we verify association of the postulated pore-forming protein CsoS1D with the carboxysome and show how it may modulate function. We have developed a genetic system capable of producing modular carbon-fixing microcompartments in a heterologous host. In doing so, we lay the groundwork for understanding these elaborate protein complexes and for the synthetic biological engineering of self-assembling molecular structures.
Social selection and peer influence in an online social network
Authors: Lewis Kevin , Gonzalez Marco , Kaufman Jason
Published: December 2011

Disentangling the effects of selection and influence is one of social science's greatest unsolved puzzles: Do people befriend others who are similar to them, or do they become more similar to their friends over time? Recent advances in stochastic actor-based modeling, combined with self-reported data on a popular online social network site, allow us to address this question with a greater degree of precision than has heretofore been possible. Using data on the Facebook activity of a cohort of college students over 4 years, we find that students who share certain tastes in music and in movies, but not in books, are significantly likely to befriend one another. Meanwhile, we find little evidence for the diffusion of tastes among Facebook friends—except for tastes in classical/jazz music. These findings shed light on the mechanisms responsible for observed network homogeneity; provide a statistically rigorous assessment of the coevolution of cultural tastes and social relationships; and suggest important qualifications to our understanding of both homophily and contagion as generic social processes.
Genetic adaptation to captivity can occur in a single generation
Authors: Christie Mark R. , Marine Melanie L. , French Rod A. , Blouin Michael S.
Published: December 2011

Captive breeding programs are widely used for the conservation and restoration of threatened and endangered species. Nevertheless, captive-born individuals frequently have reduced fitness when reintroduced into the wild. The mechanism for these fitness declines has remained elusive, but hypotheses include environmental effects of captive rearing, inbreeding among close relatives, relaxed natural selection, and unintentional domestication selection (adaptation to captivity). We used a multigenerational pedigree analysis to demonstrate that domestication selection can explain the precipitous decline in fitness observed in hatchery steelhead released into the Hood River in Oregon. After returning from the ocean, wild-born and first-generation hatchery fish were used as broodstock in the hatchery, and their offspring were released into the wild as smolts. First-generation hatchery fish had nearly double the lifetime reproductive success (measured as the number of returning adult offspring) when spawned in captivity compared with wild fish spawned under identical conditions, which is a clear demonstration of adaptation to captivity. We also documented a tradeoff among the wild-born broodstock: Those with the greatest fitness in a captive environment produced offspring that performed the worst in the wild. Specifically, captive-born individuals with five (the median) or more returning siblings (i.e., offspring of successful broodstock) averaged 0.62 returning offspring in the wild, whereas captive-born individuals with less than five siblings averaged 2.05 returning offspring in the wild. These results demonstrate that a single generation in captivity can result in a substantial response to selection on traits that are beneficial in captivity but severely maladaptive in the wild.
Exploring one-state downhill protein folding in single molecules
Authors: Liu Jianwei , Campos Luis A. , Cerminara Michele , Wang Xiang , Ramanathan Ravishankar , English Douglas S. , Muñoz Victor
Published: December 2011

A one-state downhill protein folding process is barrierless at all conditions, resulting in gradual melting of native structure that permits resolving folding mechanisms step-by-step at atomic resolution. Experimental studies of one-state downhill folding have typically focused on the thermal denaturation of proteins that fold near the speed limit (
ca.
10
6
 s
-1
) at their unfolding temperature, thus being several orders of magnitude too fast for current single-molecule methods, such as single-molecule FRET. An important open question is whether one-state downhill folding kinetics can be slowed down to make them accessible to single-molecule approaches without turning the protein into a conventional activated folder. Here we address this question on the small helical protein BBL, a paradigm of one-state downhill thermal (un)folding. We decreased 200-fold the BBL folding-unfolding rate by combining chemical denaturation and low temperature, and carried out free-diffusion single-molecule FRET experiments with 50-μs resolution and maximal photoprotection using a recently developed Trolox-cysteamine cocktail. These experiments revealed a single conformational ensemble at all denaturing conditions. The chemical unfolding of BBL was then manifested by the gradual change of this unique ensemble, which shifts from high to low FRET efficiency and becomes broader at increasing denaturant. Furthermore, using detailed quantitative analysis, we could rule out the possibility that the BBL single-molecule data are produced by partly overlapping folded and unfolded peaks. Thus, our results demonstrate the one-state downhill folding regime at the single-molecule level and highlight that this folding scenario is not necessarily associated with ultrafast kinetics.
Activation in the neural network responsible for categorization and recognition reflects parameter changes
Authors: Nosofsky Robert M. , Little Daniel R. , James Thomas W.
Published: December 2011

According to various influential formal models of cognition, perceptual categorization and old−new recognition recruit the same memory system. By contrast, the prevailing view in the cognitive neuroscience literature is that separate neural systems mediate perceptual categorization and recognition. A direct form of evidence is that separate brain regions are activated when observers engage in categorization and recognition tasks involving the same types of stimuli. However, even if the same memory-based comparison processes underlie categorization and recognition, one would not expect to see identical patterns of brain activity across the tasks; the reason is that observers would adjust parameter settings (e.g., vary criterion settings) across the tasks to satisfy the different task goals. In this fMRI study, we conducted categorization and recognition tasks in which stimulus conditions were held constant, and in which observers were induced to vary hypothesized parameter settings across conditions. A formal exemplar model was fitted to the data to track the changes in parameters to help interpret the fMRI results. We observed systematic effects of changes in parameters on patterns of brain activity, which were interpretable in terms of differing forms of evidence accumulation that resulted from the changed parameter settings. After controlling for stimulus and parameter-related differences, we found little evidence that categorization and recognition recruit separate memory systems.
Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target
Authors: Libri Valentina , Helwak Aleksandra , Miesen Pascal , Santhakumar Diwakar , Borger Jessica G. , Kudla Grzegorz , Grey Finn , Tollervey David , Buck Amy H.
Published: December 2011

Individual microRNAs (miRNAs) are rapidly down-regulated during conditions of cellular activation and infection, but factors mediating miRNA turnover are poorly understood. Infection of mouse cells with murine cytomegalovirus (MCMV) induces the rapid down-regulation of an antiviral cellular miRNA, miR-27. Here, we identify a transcript produced by MCMV that binds to miR-27 and mediates its degradation. UV-crosslinking and high-throughput sequencing [CRAC (UV-crosslinking and analysis of cDNA)] identified MCMV RNA segments associated with the miRNA-binding protein Argonaute 2 (Ago2). A cluster of hits mapped to a predicted miR-27-binding site in the 3′UTR of the previously uncharacterized ORF, m169. The expression kinetics of the m169 transcript correlated with degradation of miR-27 during infection, and m169 expression inhibited miR-27 functional activity in a reporter assay. siRNA knockdown of m169 demonstrated its requirement for miR-27 degradation following infection and did not affect other host miRNAs. Substitution of the miR-27-binding site in m169 to create complementarity to a different cellular miRNA, miR-24, resulted in down-regulation of only miR-24 following infection. The m169 transcript is cytoplasmic, capped, polyadenylated, and interacts with miRNA-27 through seed pairing: characteristic features of the normal messenger RNA (mRNA) targets of miRNAs. This virus–host interaction reveals a mode of miRNA regulation in which a mRNA directs the degradation of a miRNA. We speculate that RNA-mediated miRNA degradation could be a more general viral strategy for manipulating host cells.
Structural basis and evolution of redox regulation in plant adenosine-5′-phosphosulfate kinase
Authors: Ravilious Geoffrey E. , Nguyen Amelia , Francois Julie A. , Jez Joseph M.
Published: December 2011

Adenosine-5′-phosphosulfate (APS) kinase (APSK) catalyzes the phosphorylation of APS to 3′-phospho-APS (PAPS). In
Arabidopsis thaliana
, APSK is essential for reproductive viability and competes with APS reductase to partition sulfate between the primary and secondary branches of the sulfur assimilatory pathway; however, the biochemical regulation of APSK is poorly understood. The 1.8-Å resolution crystal structure of APSR from
A. thaliana
(AtAPSK) in complex with β,γ-imidoadenosine-5′-triphosphate, Mg
2+
, and APS provides a view of the Michaelis complex for this enzyme and reveals the presence of an intersubunit disulfide bond between Cys86 and Cys119. Functional analysis of AtAPSK demonstrates that reduction of Cys86-Cys119 resulted in a 17-fold higher
k
cat
/
K
m
and a 15-fold increase in
K
i
for substrate inhibition by APS compared with the oxidized enzyme. The C86A/C119A mutant was kinetically similar to the reduced WT enzyme. Gel- and activity-based titrations indicate that the midpoint potential of the disulfide in AtAPSK is comparable to that observed in APS reductase. Both cysteines are invariant among the APSK from plants, but not other organisms, which suggests redox-control as a unique regulatory feature of the plant APSK. Based on structural, functional, and sequence analyses, we propose that the redox-sensitive APSK evolved after bifurcation of the sulfur assimilatory pathway in the green plant lineage and that changes in redox environment resulting from oxidative stresses may affect partitioning of APS into the primary and secondary thiol metabolic routes by having opposing effects on APSK and APS reductase in plants.