bluuebunny/crossref_metadata_2025 huggingface dataset:
Redesigning the leaving group in nucleic acid polymerization
Authors: Herdewijn P. , Marlière P.
Published: March 2012

Artificial nucleic acids have the potential to propagate genetic information in vivo purposefully insulated from the canonical replication and transcription processes of cells. Natural nucleic acids are synthesized using nucleoside triphosphates as building blocks and polymerases as catalysts, pyrophosphate functioning as the universal leaving group for DNA and RNA biosynthesis. In order to avoid entanglement between the propagation of artificial nucleic acids in vivo and the cellular information processes, we promote the biosynthesis of natural and xenobiotic nucleic acids (XNA) dependent on the involvement of leaving groups distinct from pyrophosphate. The feasibility of such radically novel biochemical systems relies on the systematic exploration of the chemical diversity of nucleic acid leaving groups that can undergo the catalytic mechanism of phosphotransfer in nucleic acid polymerization. Initial forays in this research area demonstrate the wide acceptance of polymerases and augur well for in vivo implementation and integration with canonical metabolism.
Differential effects of dairy snacks on appetite, but not overall energy intake
Authors: Dougkas Anestis , Minihane Anne M. , Givens D. Ian , Reynolds Christopher K. , Yaqoob Parveen
Published: March 2012

Dietary regulation of appetite may contribute to the prevention and management of excess body weight. The present study examined the effect of consumption of individual dairy products as snacks on appetite and subsequent ad libitum lunch energy intake. In a randomised cross-over trial, forty overweight men (age 32 (sd 9) years; BMI 27 (sd 2) kg/m2) attended four sessions 1 week apart and received three isoenergetic (841 kJ) and isovolumetric (410 ml) servings of dairy snacks or water (control) 120 min after breakfast. Appetite profile was determined throughout the morning and ad libitum energy intake was assessed 90 min after the intake of snacks. Concentrations of amino acids, glucose, insulin, ghrelin and peptide tyrosine tyrosine were measured at baseline (0 min) and 80 min after the intake of snacks. Although the results showed that yogurt had the greatest suppressive effect on appetite, this could be confounded by the poor sensory ratings of yogurt. Hunger rating was 8, 10 and 24 % (P < 0·001) lower after the intake of yogurt than cheese, milk and water, respectively. Energy intake was 11, 9 and 12 % (P < 0·02) lower after the intake of yogurt, cheese and milk, respectively, compared with water (4312 (se 226) kJ). Although there was no difference in the postprandial responses of hormones, alanine and isoleucine concentrations were higher after the intake of yogurt than cheese and milk (P < 0·05). In conclusion, all dairy snacks reduced appetite and lunch intake compared with water. Yogurt had the greatest effect on suppressing subjective appetite ratings, but did not affect subsequent food intake compared with milk or cheese.
Gastrointestinal nematodes in rotationally grazing ewes in the mountainous region of central Mexico
Authors: Acevedo-Ramírez P.M.C. , Quiroz-Romero H. , Cruz-Mendoza I. , Ulloa-Arvizu R. , Ibarra-Velarde F.
Published: March 2012

The aims of this study were to determine the frequency of egg shedding (percentage of egg-positive faecal samples) and faecal egg counts (FEC) over 13 months in two different breeds of ewes, both pregnant and non-pregnant, in a mountainous region of central Mexico. Additionally, the effect of ivermectin and albendazole treatments on FEC reduction was recorded. The study also aimed to relate temperature and rainfall to FEC. The gastrointestinal nematode (GIN) third-stage larvae genera recovered from both faeces and grassland pastures in a temperate region were also assessed. Faecal samples were collected from ewes at monthly intervals for 13 months to investigate the FEC population of GIN larvae, their concentration and genera in grass samples collected from grazed and rested pastures. Egg-shedding frequency ranged from 0 to 92% and FEC from 0 to 12,000 eggs per g faeces (epg), with counts in Suffolk higher than in Dorset ewes. The identified genera were Haemonchus, Trichostrongylus, Teladorsagia, Cooperia, Oesophagostomum, Bunostomum, Nematodirus and Strongyloides. Haemonchus and Trichostrongylus were the most common genera. The number of L3 was higher in grazing lands than in those at rest. The highest FEC were recorded in the dry season due to peripartum, but the highest L3 counts were recorded in the rainy season. The coexistence of species of different geographical distributions at this site may be because there is a confluence of Nearctic and Neotropical geographic regions; thus, despite the temperate climate, tropical species can be found. Additionally, this study suggests that increasing temperatures could favour the presence of different tropical GIN species together with typical temperate-zone GIN species.
Endoscopic, assisted, modified turbinoplasty with mucosal flap
Authors: Puterman M M , Segal N , Joshua B-Z
Published: March 2012

A variety of surgical methods have been developed to reduce the volume of the inferior turbinates, in order to create a more patent nasal airway. We describe a technique used in our department since February 2002 for all patients undergoing inferior turbinectomy. We resect with endoscopic assistance the lateral mucosa and bony inferior turbinate. This technique can reduce a large volume of the turbinate while preserving the mucosal continuity and the submucosa by covering the raw surface with a mucosal flap. We believe our method minimises post-operative side effects and complications such as dryness, infection, bleeding and pain.
Population increase at a calving ground of the Endangered Tibetan antelope Pantholops hodgsonii in Xinjiang, China
Authors: Buzzard Paul J. , Wong How Man , Zhang Huibin
Published: March 2012

Females in most populations of chiru or Tibetan antelope Pantholops hodgsonii migrate up to 350 km each year to summer calving grounds. These migrations characterize the Tibet–Qinghai Plateau. The Ullughusu calving grounds adjacent to the Arjinshan Nature Reserve in Xinjiang, China, are used by multiple chiru populations and this calving ground recovered from major poaching events in 1998 and 1999, with a population increase from 2001 to 2006. We used direct methods (vehicle/walking transects and radial point sampling) and an indirect method (faecal pellet counts) from 30 June to 4 July 2011 to assess the chiru population at this calving ground. We saw substantially more chiru with all methods in 2011 compared to 2006, demonstrating that the population has increased and suggesting that conservation efforts have been effective.
Theory and Praxis: Simone Weil and Marx on the Dignity of Labor
Authors: Sparling Robert
Published: March 2012

Simone Weil had an ambivalent attitude toward Marx. While she thought that the young Marx's celebration of labor had “lyrical accents,” she ultimately believed that Marx had neglected his own insights, embracing a blind worship of mechanization and a theory of history and revolution that was insufficiently attentive to the material conditions of workers. Marx, in her view, was insufficiently materialist and excessively wedded to a hierarchical model of science that maintained the domination of management. Weil and Marx's attitudes toward the dignity of labor and the necessary conditions for socialism are analyzed. The most significant cleavage between them is ultimately due to the differing manner in which they conceive of the relationship between thought and action. Through this comparison, the philosophical underpinnings of the two radically different conceptions of labor and its dignity as a human activity are explained.
Variable Phase Dark-Field Contrast—A Variant Illumination Technique for Improved Visualizations of Transparent Specimens
Authors: Piper Timm , Piper Jörg
Published: March 2012

Variable phase dark-field contrast has been developed as an illumination technique in light microscopy, which promises significant improvements and a higher variability in imaging of several transparent specimens. In this method, a phase contrast image is optically superimposed on a dark-field image so that a partial image based on the principal zeroth-order maximum (phase contrast) interferes with an image that is based on the secondary maxima (dark field). The background brightness and character of the resulting image can be continuously modulated from a phase-contrast-dominated to a dark-field-dominated character. The condenser aperture diaphragm can be used for modulations of the image's appearance. Specimens can either be illuminated concentrically or obliquely (eccentrically) when parts of the illuminating light beams are covered and blocked. Moreover, a bright-field-like partial image can be added. In this way, the illumination can be optimally adjusted to the specific properties of the specimen. The techniques described can lead to improved visual information especially in biological specimens consisting of phase structures and additional light-absorbing or -reflecting components. Moreover, the specimen's three-dimensionality can be accentuated with improved clarity because the illuminating light beams associated with phase contrast and dark field run to the specimen at different angles of incidence.
Religion and American Public Life
Authors: Olson Laura R.
Published: March 2012

In his 2000 best seller Bowling Alone: The Collapse and Revival of American Civic Community, Robert Putnam analyzed the links between social capital and civic engagement. Lamenting the decline of “civic America,” he called for a Tocquevillean renewal of voluntary association in the United States. In American Grace, Putnam and coauthor David Campbell—who also helped with the preparation of Bowling Alone—return to the analysis of American civil society, focusing their attention on America's changing religious landscape and its implications for democracy. Their basic argument is that while the United States is religiously diverse and pluralistic to a profound degree, and while in recent years it has witnessed growing religious polarization, it has also succeeded in muting religious tensions and hostilities. As they conclude: “How has America solved the puzzle of religious pluralism—the coexistence of religious diversity and devotion? And how has it done so in the wake of growing religious polarization? By creating a web of interlocking personal relationships among people of many different faiths. This is America's grace” (p. 550).

Given the importance of religion in American life and the influence of Putnam's broad agenda on much current social science research on social capital and civic engagement, we have decided to organize a symposium around the book, centered on three questions: 1) How is American Grace related to Putnam's earlier work, particularly Bowling Alone, and what are the implications of the continuities and/or discontinuities between these works? 2) What kind of a work of political science is American Grace, and how does it compare to other important recent work dealing with religion and politics in the United States? 3) What are the strengths and weaknesses of Putnam and Campbell's account of “how religion divides and unites us,” and what is the best way of thinking about the contemporary significance of religion and politics in the United States and about the ways that the religious landscape challenges U.S. politics and U.S. political science?
Teachers Unions and Public Education
Authors: Swenson Peter A.
Published: March 2012

Public education is one of the most important “public goods” of a democratic society. In recent decades, public policy analysts, public intellectuals, and politicians have debated the state of public education in the United States and have argued about the sorts of public policies that might best promote the academic achievement, educational success, and political socialization of youth. Terry Moe and John Chubb have been important contributors to these debates. Their 1990 book, Politics, Markets, and America's Schools, set the terms of much subsequent discussion about the importance of school autonomy and “educational choice.” Moe's Special Interest extends these arguments through a more frontal critique of the role of teachers unions. This book represents an important contribution to public discussion of school reform. It also incorporates a distinctive perspective on the relationship between power and public policy, and between the role of states and that of markets in the provision of public goods and services. In this symposium, we feature a range of serious commentaries on the book's central arguments about educational policy and politics and on its approach to “engaged” or “applied” political science.
Teachers Unions and Public Education
Authors: Frymer Paul
Published: March 2012

Public education is one of the most important “public goods” of a democratic society. In recent decades, public policy analysts, public intellectuals, and politicians have debated the state of public education in the United States and have argued about the sorts of public policies that might best promote the academic achievement, educational success, and political socialization of youth. Terry Moe and John Chubb have been important contributors to these debates. Their 1990 book, Politics, Markets, and America's Schools, set the terms of much subsequent discussion about the importance of school autonomy and “educational choice.” Moe's Special Interest extends these arguments through a more frontal critique of the role of teachers unions. This book represents an important contribution to public discussion of school reform. It also incorporates a distinctive perspective on the relationship between power and public policy, and between the role of states and that of markets in the provision of public goods and services. In this symposium, we feature a range of serious commentaries on the book's central arguments about educational policy and politics and on its approach to “engaged” or “applied” political science.
The evaluation of lifestyle interventions in the Netherlands
Authors: Rappange David R. , Brouwer Werner B. F.
Published: March 2012

Current investments in preventive lifestyle interventions are relatively low, despite the significant impact of unhealthy behaviour on population health. This raises the question of whether the criteria used in reimbursement decisions about healthcare interventions put preventive interventions at a disadvantage. In this paper, we highlight the decision-making framework used in the Netherlands to delineate the basic benefits package. Important criteria in that framework are ‘necessity’ and ‘cost-effectiveness’. Several normative choices need to be made, and these choices can have an important impact on the evaluation of lifestyle interventions, especially when making these criteria operational and quantifiable. Moreover, the implementation of the decision-making framework may prove to be difficult for lifestyle interventions. Improvements of the decision-making framework in the Netherlands are required to guarantee sound evaluations of lifestyle interventions aimed at improving health.
Kinetic model of the inner magnetosphere with arbitrary magnetic field
Authors: Ilie Raluca , Liemohn Michael W. , Toth Gabor , Skoug Ruth M.
Published: March 2012

Theoretical and numerical modifications to an inner magnetosphere model—Hot Electron Ion Drift Integrator (HEIDI)—were implemented, in order to accommodate for a nondipolar arbitrary magnetic field. While the dipolar solution for the geomagnetic field during quiet times represents a reasonable assumption in the near‐Earth closed field region, during storm activity this assumption becomes invalid. HEIDI solves the time‐dependent, gyration‐ and bounce‐averaged kinetic equation for the phase space density of one or more ring current species. New equations are derived for the bounce‐averaged coefficients for the distribution function, and their numerical implementation is discussed. Also, numerically solving all the bounce‐averaged coefficients for the dipole case does not change the results significantly from the analytical approximation of Ejiri (1978). However, distorting the magnetic field changes all bounce‐averaged coefficients that make up the kinetic equation. Initial simulations show that changing the magnetic field changes the whole topology of the ring current. This is because the drifts are altered due to dayside compression and nightside stretching of the field. Therefore, at certain locations, the nondipolar magnetic drifts can dominate the convective drifts, considerably altering the pressure distribution in the equatorial plane.
The development and evaluation of the Earth Gravitational Model 2008 (EGM2008)
Authors: Pavlis Nikolaos K. , Holmes Simon A. , Kenyon Steve C. , Factor John K.
Published: March 2012

EGM2008 is a spherical harmonic model of the Earth's gravitational potential, developed by a least squares combination of the ITG‐GRACE03S gravitational model and its associated error covariance matrix, with the gravitational information obtained from a global set of area‐mean free‐air gravity anomalies defined on a 5 arc‐minute equiangular grid. This grid was formed by merging terrestrial, altimetry‐derived, and airborne gravity data. Over areas where only lower resolution gravity data were available, their spectral content was supplemented with gravitational information implied by the topography. EGM2008 is complete to degree and order 2159, and contains additional coefficients up to degree 2190 and order 2159. Over areas covered with high quality gravity data, the discrepancies between EGM2008 geoid undulations and independent GPS/Leveling values are on the order of ±5 to ±10 cm. EGM2008 vertical deflections over USA and Australia are within ±1.1 to ±1.3 arc‐seconds of independent astrogeodetic values. These results indicate that EGM2008 performs comparably with contemporary detailed regional geoid models. EGM2008 performs equally well with other GRACE‐based gravitational models in orbit computations. Over EGM96, EGM2008 represents improvement by a factor of six in resolution, and by factors of three to six in accuracy, depending on gravitational quantity and geographic area. EGM2008 represents a milestone and a new paradigm in global gravity field modeling, by demonstrating for the first time ever, that given accurate and detailed gravimetric data, asingleglobal model may satisfy the requirements of a very wide range of applications.
Ocean haline skin layer and turbulent surface convections
Authors: Zhang Y. , Zhang X.
Published: March 2012

The ocean haline skin layer is of great interest to oceanographic applications, while its attribute is still subject to considerable uncertainty due to observational difficulties. By introducing Batchelor micro‐scale, a turbulent surface convection model is developed to determine the depths of various ocean skin layers with same model parameters. These parameters are derived from matching cool skin layer observations. Global distributions of salinity difference across ocean haline layers are then simulated, using surface forcing data mainly from OAFlux project and ISCCP. It is found that, even though both thickness of the haline layer and salinity increment across are greater than the early global simulations, the microwave remote sensing error caused by the haline microlayer effect is still smaller than that from other geophysical error sources. It is shown that forced convections due to sea surface wind stress are dominant over free convections driven by surface cooling in most regions of oceans. The free convection instability is largely controlled by cool skin effect for the thermal microlayer is much thicker and becomes unstable much earlier than the haline microlayer. The similarity of the global distributions of temperature difference and salinity difference across cool and haline skin layers is investigated by comparing their forcing fields of heat fluxes. The turbulent convection model is also found applicable to formulating gas transfer velocity at low wind.
Sensitivity of the shortwave radiative effect of dust on particle shape: Comparison of spheres and spheroids
Authors: Haapanala Päivi , Räisänen Petri , Kahnert Michael , Nousiainen Timo
Published: March 2012

The sensitivity of direct shortwave radiative effects of dust (DRE) to assumed particle shape is investigated. Radiative transfer simulations are conducted using optical properties of either spheres, mass‐equivalent spheroids (mass‐conserving case), or (mass‐equivalent) spheroids whose number concentration is modified so that they have the same midvisible optical thickness (τ(545 nm)) as spheres (τ‐conserving case). The impact of particle shape on DRE is investigated for different dust particle effective radii, optical thickness of the dust cloud, solar zenith angle, and spectral surface albedo (ocean, grass, and desert). It is found that the influence of particle shape on the DRE is strongest over ocean. It also depends very strongly on the shape distribution of spheroids used, to a degree that the results for two distributions of spheroids may deviate more from each other than from those for spheres. Finally, the effects of nonsphericity largely depend on whether the mass‐ orτ‐conserving case is considered. For example, when using a shape distribution of spheroids recommended in a recent study for approximating the single‐scattering properties of dust, the DRE at the surface differs at most 5% from that from spherical particles in the mass‐conserving case. This stems from compensating nonsphericity effects on optical thickness, asymmetry parameter, and single‐scattering albedo. However, in theτ‐conserving case, the negative DRE at the surface can be up to 15% weaker for spheroids than spheres.
Peat accumulation in drained thermokarst lake basins in continuous, ice‐rich permafrost, northern Seward Peninsula, Alaska
Authors: Jones Miriam C. , Grosse Guido , Jones Benjamin M. , Walter Anthony Katey
Published: March 2012

Thermokarst lakes and peat‐accumulating drained lake basins cover a substantial portion of Arctic lowland landscapes, yet the role of thermokarst lake drainage and ensuing peat formation in landscape‐scale carbon (C) budgets remains understudied. Here we use measurements of terrestrial peat thickness, bulk density, organic matter content, and basal radiocarbon age from permafrost cores, soil pits, and exposures in vegetated, drained lake basins to characterize regional lake drainage chronology, C accumulation rates, and the role of thermokarst‐lake cycling in carbon dynamics throughout the Holocene on the northern Seward Peninsula, Alaska. Most detectable lake drainage events occurred within the last 4,000 years with the highest drainage frequency during the medieval climate anomaly. Peat accumulation rates were highest in young (50–500 years) drained lake basins (35.2 g C m−2 yr−1) and decreased exponentially with time since drainage to 9 g C m−2 yr−1 in the oldest basins. Spatial analyses of terrestrial peat depth, basal peat radiocarbon ages, basin geomorphology, and satellite‐derived land surface properties (Normalized Difference Vegetation Index (NDVI); Minimum Noise Fraction (MNF)) from Landsat satellite data revealed significant relationships between peat thickness and mean basin NDVI or MNF. By upscaling observed relationships, we infer that drained thermokarst lake basins, covering 391 km2 (76%) of the 515 km2 study region, store 6.4–6.6 Tg organic C in drained lake basin terrestrial peat. Peat accumulation in drained lake basins likely serves to offset greenhouse gas release from thermokarst‐impacted landscapes and should be incorporated in landscape‐scale C budgets.
Contrasting rift and subduction‐related plagiogranites in the Jinshajiang ophiolitic mélange, southwest China, and implications for the Paleo‐Tethys
Authors: Zi Jian‐Wei , Cawood Peter A. , Fan Wei‐Ming , Wang Yue‐Jun , Tohver Eric
Published: March 2012

The Jinshajiang ophiolitic mélange zone in southwest China represents a remnant of the eastern Paleo‐Tethys Ocean. Field, geochronological and geochemical studies have identified two distinct suites of plagiogranites within the mélange, the Dongzhulin trondhjemite and Jiyidu tonalite, which represent rift and subduction settings, respectively, related to opening and closing of the ocean. SHRIMP U‐Pb analysis on zircons extracted from the Dongzhulin trondhjemite yields a mean 206Pb/238U age of 347 ± 7 Ma. REE and isotopic characteristics suggest an origin from low pressure partial melting of an amphibolitic protolith. Highly variable Hf isotopic compositions for zircons from this body may indicate a heterogenous source involving both depleted mantle and enriched continental components. This, together with geologic relations, suggests formation near an embryonic spreading center in a continent‐ocean transition setting. The Jiyidu tonalite has a U‐Pb zircon age of 283 ± 3 Ma, and geochemical data indicates high Sr/Y, (La/Yb)N, Nb/Ta and low Y, and marked heavy REE depletion. These signatures suggest derivation from low degree partial melting of subducted slab at pressure high enough to stabilize garnet and rutile. A slab‐melt origin is also supported by in situ Hf and O data for zircon that show isotopic compositions comparable with typical altered oceanic crust. Thus, the crystallization age of the Jiyidu high Sr/Y tonalite provides a constraint for the subduction of the Jinshajiang ocean floor. The rift‐related Dongzhulin trondhjemite and subduction‐related Jiyidu high‐Sr/Y tonalite constrain the timing and setting of opening and closing of this segment of the Paleo‐Tethys Ocean.
Derivation of site‐specific relationships between hydraulic parameters and p‐wave velocities based on hydraulic and seismic tomography
Authors: Brauchler R. , Doetsch J. , Dietrich P. , Sauter M.
Published: March 2012

In this study, hydraulic and seismic tomographic measurements were used to derive a site‐specific relationship between the geophysical parameter p‐wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p‐wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the Simultaneous Iterative Reconstruction Technique algorithm, using a ray tracing technique with curved trajectories. The experimental set up was designed such that the p‐wave velocity tomogram overlaps the hydraulic tomograms by half. The experiments were performed at a well‐characterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct‐push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site‐specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p‐wave velocities into hydraulic properties was undertaken using a k‐means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.
Influence of hydrogen on the electronic states of olivine: Implications for electrical conductivity
Authors: Wang Duojun , Karato Shun‐ichiro , Liu Zaiyang
Published: March 2012

The influence of hydrogen on the electronic states in olivine was investigated by the first‐principle calculations combined with the models of the mobility of electrons. We find that the dissolution of hydrogen modifies the electronic states when hydrogen is dissolved as charged defects but there is little modifications to the electronic structure when hydrogen is dissolved as a neutral defect such as two protons at M‐site. In the former case an impurity state is created just above the valence band providing a mechanism of impurity conduction. The electrical conductivity calculated from this model using a model of the mobility appropriate for “polaron” mechanism of conduction shows a good agreement with the experimental observations on hydrated olivine. We conclude that the enhanced electrical conductivity in olivine by the dissolution of hydrogen may partly due to the enhancement of electronic conduction. Possible implications for high‐temperature creep are also discussed.
Environmental susceptibility model for predicting forest fire occurrence in the Western Ghats of India
Authors: Renard Quentin , Pélissier Raphaël , Ramesh B. R. , Kodandapani Narendran
Published: March 2012

Forest fires are a recurrent management problem in the Western Ghats of India. Although most fires occur during the dry season, information on the spatial distribution of fires is needed to improve fire prevention. We used the MODIS Hotspots database and Maxent algorithm to provide a quantitative understanding of the environmental controls regulating the spatial distribution of forest fires over the period 2003–07 in the entire Western Ghats and in two nested subregions with contrasting characteristics. We used hierarchical partitioning to assess the independent contributions of climate, topography and vegetation to the goodness-of-fit of models and to build the most parsimonious fire susceptibility model in each study area. Results show that although areas predicted as highly prone to forest fires were mainly localised on the eastern slopes of the Ghats, spatial predictions and model accuracies differed significantly between study areas. We suggest accordingly a two-step approach to identify: first, large fire-prone areas by paying special attention to the climatic conditions of the monsoon season before the fire season, which determine the fuels moisture content during the fire season; second, the most vulnerable sites within the fire-prone areas using local models mainly based on the type of vegetation.
Relevance of soil seed bank and seed rain to immediate seed supply after a large wildfire
Authors: Rodrigo Anselm , Arnan Xavier , Retana Javier
Published: March 2012

We examined the density and composition of the immediate seed supply (i.e. instant potential post-fire germination from soil seed bank and off-site seed rain) after a large wildfire in a sub-Mediterranean pine forest. We also tested the effects of fire severity and distance from unburned edges on the density and composition of the seed bank and the immediate off-site seed rain. Our results showed that although seed density did not differ between them, their composition was markedly different. The soil seed bank was dominated by species from the Fabaceae family with limited dispersal mechanisms such as autochory and barochory, whereas the seed rain was mainly composed of species from the Asteraceae family with wind-dispersed seeds. These patterns were not affected either by fire severity or distance from the fire edge. The main conclusion of the study is that both the soil seed bank and the seed rain play an important role in providing seeds for immediate regeneration after a large wildfire throughout the burned area. We suggest that the role of seed rain on immediate post-fire recovery of Mediterranean plant communities might be more important than has previously been thought. However, the effective role of this group of species on the longer term should be evaluated.
Collaboration in social networks
Authors: Dall’Asta Luca , Marsili Matteo , Pin Paolo
Published: March 2012

The very notion of social network implies that linked individuals interact repeatedly with each other. This notion allows them not only to learn successful strategies and adapt to them, but also to condition their own behavior on the behavior of others, in a strategic forward looking manner. Game theory of repeated games shows that these circumstances are conducive to the emergence of collaboration in simple games of two players. We investigate the extension of this concept to the case where players are engaged in a local contribution game and show that rationality and credibility of threats identify a class of Nash equilibria—that we call “collaborative equilibria”—that have a precise interpretation in terms of subgraphs of the social network. For large network games, the number of such equilibria is exponentially large in the number of players. When incentives to defect are small, equilibria are supported by local structures whereas when incentives exceed a threshold they acquire a nonlocal nature, which requires a “critical mass” of more than a given fraction of the players to collaborate. Therefore, when incentives are high, an individual deviation typically causes the collapse of collaboration across the whole system. At the same time, higher incentives to defect typically support equilibria with a higher density of collaborators. The resulting picture conforms with several results in sociology and in the experimental literature on game theory, such as the prevalence of collaboration in denser groups and in the structural hubs of sparse networks.
Identification of a cis-acting element that localizes mRNA to synapses
Authors: Meer Elliott J. , Wang Dan Ohtan , Kim Sangmok , Barr Ian , Guo Feng , Martin Kelsey C.
Published: March 2012

Messenger RNA (mRNA) localization and regulated translation can spatially restrict gene expression to each of the thousands of synaptic compartments formed by a single neuron. Although cis-acting RNA elements have been shown to direct localization of mRNAs from the soma into neuronal processes, less is known about signals that target transcripts specifically to synapses. In
Aplysia
sensory-motor neuronal cultures, synapse formation rapidly redistributes the mRNA encoding the peptide neurotransmitter sensorin from neuritic shafts into synapses. We find that the export of sensorin mRNA from soma to neurite and the localization to synapse are controlled by distinct signals. The 3′ UTR is sufficient for export into distal neurites, whereas the 5′ UTR is required for concentration of reporter mRNA at synapses. We have identified a 66-nt element in the 5′ UTR of sensorin that is necessary and sufficient for synaptic mRNA localization. Mutational and chemical probing analyses are consistent with a role for secondary structure in this process.
The ancestral SgrS RNA discriminates horizontally acquired
Salmonella
mRNAs through a single G-U wobble pair
Authors: Papenfort Kai , Podkaminski Dimitri , Hinton Jay C. D. , Vogel Jörg
Published: March 2012

SgrS RNA is a model for the large class of Hfq-associated small RNAs that act to posttranscriptionally regulate bacterial mRNAs. The function of SgrS is well-characterized in nonpathogenic
Escherichia coli
, where it was originally shown to counteract glucose-phosphate stress by acting as a repressor of the
ptsG
mRNA, which encodes the major glucose transporter. We have discovered additional SgrS targets in
Salmonella
Typhimurium, a pathogen related to
E. coli
that recently acquired one-quarter of all genes by horizontal gene transfer. We show that the conserved short seed region of SgrS that recognizes
ptsG
was recruited to target the
Salmonella
-specific
sopD
mRNA of a secreted virulence protein. The SgrS–
sopD
interaction is exceptionally selective; we find that
sopD2
mRNA, whose gene arose from
sopD
duplication during
Salmonella
evolution, is deaf to SgrS because of a nonproductive G-U pair in the potential SgrS-
sopD2
RNA duplex vs. G-C in SgrS-
sopD
. In other words, SgrS discriminates the two virulence factor mRNAs at the level of a single hydrogen bond. Our study suggests that bacterial pathogens use their large suites of conserved Hfq-associated regulators to integrate horizontally acquired genes into existing posttranscriptional networks, just as conserved transcription factors are recruited to tame foreign genes at the DNA level. The results graphically illustrate the importance of the seed regions of bacterial small RNAs to select new targets with high fidelity and suggest that target predictions must consider all or none decisions by individual seed nucleotides.
‘Coming out’ in therapy? Perceived risks and benefits of self‐disclosure of sexual orientation by gay and lesbian therapists to straight clients
Authors: Moore Jo , Jenkins Peter
Published: March 2012

Primary objective: The study's primary objective was to investigate the experiences of gay and lesbian therapists, when considering self‐disclosure of their sexual orientation to straight (i.e. heterosexual) clients. This qualitative study set out to ascertain the key factors gay therapists take into account when considering this decision and to explore the effects this self‐disclosure may have on themselves, their clients and their therapeutic relationships. Research design: The research design was based on the use of semi‐structured interviews, undertaken with a non‐random, purposive sample of counsellors and psychotherapists (n=8) in current practice. The rationale for this method was to aid exploration of therapists' experiences of the process of self‐disclosure. Methods and procedures: Inclusion criteria were for therapists who self‐identified as being gay or lesbian, and who were experienced in clinical work with straight clients. Transcribed data was analysed using inductive thematic analysis. Main outcomes and results: Some therapists reported being confident with self‐disclosure relating to their own sexual orientation. However, a common theme related to the reportedly high levels of anxiety and vulnerability, which therapists identified. Key themes emerged around: respondents' fears of client judgement; a need for therapist self‐protection; self‐awareness of the potential impact of their own fears and prejudices on the therapeutic relationship; and the potential relevance of internalised homophobia, as an overall constraining factor. Conclusions: Self‐disclosure of their sexual orientation to straight clients is constructed, in this initial survey, as being potentially problematic and risky for some gay therapists.
Accentuating the positive: The gendered identities of male problem‐drinkers, and the questions these pose for the counselling profession
Authors: Owen-Pugh Valerie , Allen Julie
Published: March 2012

Background: Few published studies have addressed the male experience of alcohol dependency. Aim: This paper seeks to address this deficiency and to highlight aspects of the male experience relevant to the counselling and psychotherapy profession. Methods: Six men in recovery from alcohol dependency participated in semi‐structured interviews. Findings: A grounded theory analysis elicited five core categories, Beginning to Drink, Paying for Gain with Pain, Reaching Rock Bottom, Struggling to Recover and Leading a New Life. Despite the pain they had experienced, participants' narratives were matter‐of‐fact and goal‐oriented. Low self‐esteem was expressed indirectly. Conclusions: These findings are consistent with socialisation models of alcoholism. Counsellors, and the wider profession, must be alert for the male under‐reporting of emotional distress.
Analysis of electron heat transport with off-axis modulated ECRH in Tore Supra
Authors: Song S.D. , Zou X.L. , Giruzzi G. , Xiao W.W. , Ding X.T. , Ding B.J. , Ségui J.L. , Elbèze D. , Clairet F. , Fenzi C. , Aniel T. , Artaud J.F. , Basiuk V. , Bouquey F. , Magne R. , Corbel E.
Published: March 2012

Experiments to study inward heat transport phenomena have been performed in the Tore Supra tokamak with off-axis electron cyclotron resonance heating (ECRH). Both power balance and perturbation transport analysis have been done for low-frequency (1 Hz) ECRH modulation experiments. Heat diffusivity and heat pinch have been separately determined by fitting the experimental data of the amplitude and phase of the Fourier transform of the modulated temperature with a linear transport model including convection term. Comparison with the critical gradient model has shown that the heat pinch previously obtained could include a pseudo-pinch due to the non-linearity of the diffusivity and an additional non-diffusive heat pinch. The pinch effect is reduced for higher densities.
Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays
Authors: Aghaeepour Nima , Chattopadhyay Pratip K. , Ganesan Anuradha , O'Neill Kieran , Zare Habil , Jalali Adrin , Hoos Holger H. , Roederer Mario , Brinkman Ryan R.
Published: March 2012

Motivation: Polychromatic flow cytometry (PFC), has enormous power as a tool to dissect complex immune responses (such as those observed in HIV disease) at a single cell level. However, analysis tools are severely lacking. Although high-throughput systems allow rapid data collection from large cohorts, manual data analysis can take months. Moreover, identification of cell populations can be subjective and analysts rarely examine the entirety of the multidimensional dataset (focusing instead on a limited number of subsets, the biology of which has usually already been well-described). Thus, the value of PFC as a discovery tool is largely wasted.

Results: To address this problem, we developed a computational approach that automatically reveals all possible cell subsets. From tens of thousands of subsets, those that correlate strongly with clinical outcome are selected and grouped. Within each group, markers that have minimal relevance to the biological outcome are removed, thereby distilling the complex dataset into the simplest, most clinically relevant subsets. This allows complex information from PFC studies to be translated into clinical or resource-poor settings, where multiparametric analysis is less feasible. We demonstrate the utility of this approach in a large (n=466), retrospective, 14-parameter PFC study of early HIV infection, where we identify three T-cell subsets that strongly predict progression to AIDS (only one of which was identified by an initial manual analysis).

Availability: The ‘flowType: Phenotyping Multivariate PFC Assays’ package is available through Bioconductor. Additional documentation and examples are available at: www.terryfoxlab.ca/flowsite/flowType/

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  rbrinkman@bccrc.ca
Seabirds, set-nets, and conservation management: assessment of conflict potential and vulnerability of birds to bycatch in gillnets
Authors: Sonntag Nicole , Schwemmer Henriette , Fock Heino Ove , Bellebaum Jochen , Garthe Stefan
Published: March 2012

Sonntag, N., Schwemmer, H., Fock, H.O., Bellebaum, J., and Garthe, S. 2012. Seabirds, set-nets, and conservation management: assessment of conflict potential and vulnerability of birds to bycatch in gillnets. – ICES Journal of Marine Science, 69: 578–589. We addressed the issue of bird bycatch in set-nets in the southern Baltic Sea by (i) assessing the vulnerability of diving birds to drowning by developing a vulnerability index based on weighted bird abundance, (ii) providing information on set-net fishing activities, and (iii) using a spatial overlap approach to indicate the potential conflicts between diving birds and fishing activities. Birds and fisheries concentrated in the same areas. Vulnerability and potential conflict were highest during winter and spring in coastal waters and around shallow offshore grounds. Local bycatch studies validated the usefulness of our approach, which can provide a valuable tool for conservation purposes. Although the conflict analysis outlined the current extent of overlap between birds and fisheries, the vulnerability index indicated important areas and periods in terms of diving bird abundance, irrespective of fisheries, and enabled the development of appropriate conservation and management options. A suite of measures including temporal or spatial restrictions can be derived, despite a scarcity of real data for bycatch rates. This approach is particularly useful for assessing impacts that are difficult to monitor and where mortality cannot be properly addressed, as in artisanal gillnet fisheries. It is also generally applicable to any marine area or species worldwide.
Revisiting the marine migration of US Atlantic salmon using historical Carlin tag data
Authors: Miller Alicia S. , Sheehan Timothy F. , Renkawitz Mark D. , Meister Alfred L. , Miller Timothy J.
Published: March 2012

Miller, A. S., Sheehan, T. F., Renkawitz, M. D., Meister, A. L., and Miller, T. J. 2012. Revisiting the marine migration of US Atlantic salmon using historical Carlin tag data. – ICES Journal of Marine Science, 69: 1609–1615. The development of a fishery for Atlantic salmon (Salmo salar) in the sea at West Greenland in the early 1960s prompted the start of a US tagging programme in 1962. Between 1962 and 1996, more than 1.5 million salmon from New England rivers, primarily hatchery-reared smolts, were tagged and released. Overall, the rate of tag recovery was 0.55%, with 23.2% of the tags recovered from Canada, 26.0% from Greenland, and 50.8% from the United States. A generalized additive model was used to analyse marine survival based on returns of tagged salmon to the Penobscot River. The month and year of release, sea age, smolt age, and environmental variables, such as the North Atlantic Oscillation (NAO) and Atlantic Multidecadal Oscillation (AMO) indices and local sea surface temperatures (SSTs), were assessed to explain the variability in the return rate. The AMO and NAO indices, SST, sea age, and time across years all affected survival assessed in terms of returns to the Penobscot River. The results provide information to support the management of Atlantic salmon stocks on a spatial and temporal scale in US rivers and the fishery at West Greenland.
Residual methylprednisolone suppresses human T-cell responses to spleen, but not islet, extracts from deceased organ donors
Authors: Joffe Max , Necula Andra S. , Chand Rochna , McWhinney Brett C. , Krishnamurthy Balasubramanian , Loudovaris Tom , Goodman David , Thomas Helen E. , Kay Thomas W. H. , Mannering Stuart I.
Published: March 2012

Pancreatic islets, transplanted into recipients with type 1 diabetes, are exposed to allogenic and auto-immune T-cell responses. We set out to develop an assay to measure these responses using PBMC. Our approach was to prepare spleen extract from the islet donors (allo-antigen) and islet extracts (auto-antigen). To our surprise, we found that spleen extracts potently inhibited the proliferation of human T cells driven by antigen (tetanus toxoid) and mitogen (anti-CD3 mAb, OKT3), whereas extracts prepared from pancreatic islets from the same donor did not suppress T-cell proliferation. Suppression mediated by spleen extracts was unaffected by blocking mAbs against the IL-10R, transforming growth factor-β or CD152 (CTLA-4). It was also unaffected by denaturing the spleen extracts by heating, exposing to reducing agents or protease digestion. Because deceased organ donors are commonly given the immunosuppressive glucocorticoid methylprednisolone prior to death, we hypothesized that suppression was due to residual methylprednisolone in the spleen extracts. Methylprednisolone could be detected by mass spectrometry in spleen extracts at concentrations that suppress T-cell proliferation. Finally, the glucocorticoid receptor antagonist mifepristone completely reversed the suppression caused by the spleen extracts. We conclude that extracts of human spleen, but not islets, from deceased organ donors contain sufficient residual methylprednisolone to suppress the proliferation of T-cells in vitro.