bluuebunny/crossref_metadata_2025 huggingface dataset:
Time‐spatial variability observed in velocity of propagation of the internal bore in the Strait of Gibraltar
Authors: Sánchez Garrido J. C. , García Lafuente J. , Criado Aldeanueva F. , Baquerizo A. , Sannino G.
Published: July 2008

Some aspects of the time‐spatial variability of the phase speed of the internal bore generated almost every tidal cycle in Camarinal Sill, are revised using a set of high resolution experimental data collected in two different positions of the Strait during May 2003. This variability is mainly driven by the intense tidal currents, comparable with the intrinsic propagation velocity of the first mode baroclinic bore. It is shown that the importance of the diurnal tide in the Strait of Gibraltar induces a considerable diurnal inequality on the bore velocity, with an observed maximum difference of 0.7 ms−1 between the speed of two consecutives bores propagating along the eastern part of the Strait. A regularly spatial pattern has been also found: the internal bore reaches its maximum velocity in Tarifa Narrows. A theoretical estimation predicts an extreme phase speed of 2.6 ms−1 during our period of study.
Ground‐based remote sensing of precipitation in the Arctic
Authors: Zhao C. , Garrett T. J.
Published: July 2008

In this paper, a simple technique is described for application of radar to retrievals of vertical profiles of precipitation in the Arctic. The method is applied specifically to data from the DOE Atmospheric Radiation Measurement (ARM) North Slope of Alaska–Adjacent Arctic Ocean (NSA‐AAO) site near Barrow, Alaska. Profiles of precipitation characteristic size are obtained by developing a relationship between particle size and particle fall speed derived from 35 GHz Doppler radar. The relationship depends on an assumed size‐ and temperature‐dependent particle morphology tailored to the Arctic. Error analysis indicates that typical uncertainties in the precipitation retrieval rate are, to 95% confidence, about 40% for ice and 15% for liquid, although they can be as high as a factor of 2. Monthly averaged precipitation retrievals show strong seasonal variation and compare to within respective uncertainties with local ground‐based National Weather Service and ARM NSA‐AAO surface measurements. Measurements of precipitation profiles show substantial evaporation of precipitation to the atmosphere below cloud base. Associated atmospheric cooling can be several K d−1, suggesting it may be a substantial component of the boundary layer energy budget in the Arctic.
Relationship of loss, mean age of air and the distribution of CFCs to stratospheric circulation and implications for atmospheric lifetimes
Authors: Douglass A. R. , Stolarski R. S. , Schoeberl M. R. , Jackman C. H. , Gupta M. L. , Newman P. A. , Nielsen J. E. , Fleming E. L.
Published: July 2008

Projections of the recovery of the ozone layer are made with global atmospheric models using a specified time series of mixing ratios of ozone depleting substances (ODSs) at the lower boundary. This time series is calculated using atmospheric mixing ratio observations, emission rates, and an estimate for the atmospheric lifetime. ODS destruction and simulated atmospheric‐lifetime vary among models because they depend on the simulated stratospheric transport and mixing. We investigate the balance between the annual change in ODS burden, its atmospheric loss, and the annual ODS input to the atmosphere using several models. Some models produce realistic distributions for the mean age of air and some do not. Back trajectory calculations relate the fractional release (one minus the amount of ODS at a location relative to its stratospheric entry value) to the mean age through the age spectrum, showing that, for the individual spectrum elements, the maximum altitude and loss increase with age. Models with faster circulations produce “young” distributions for the age of air and fail to reproduce the observed relationship between the mean age of air and the fractional release. Models with realistic mean age of air reproduce the observed relationship. These models yield a lifetime for CFCl3 of ∼56 years, longer than the 45 year lifetime currently used to project future mixing ratios. Use of flux boundary conditions in assessment models would have several advantages, including consistency between the ODS evolution and simulated loss even if the simulated residual circulation changes due to climate change.
Magnetic signature of European margin sediments: Provenance of ice‐rafted debris and the climatic response of the British ice sheet during Marine Isotope Stages 2 and 3
Authors: Peters Clare , Walden John , Austin William E. N.
Published: July 2008

Mineral magnetic measurements are used to distinguish ice‐rafted debris (IRD) sources and climate cycles spanning Marine Isotope Stage (MIS) 3 and MIS2 in core MD95–2006, from the Barra Fan, NE Atlantic. Distinct magnetic properties are displayed by IRD from the Laurentide ice sheet (LIS) (high susceptibility (χ), low isothermal remanent magnetization (IRM), low coercivity and the Verwey transition), the British ice sheet (BIS) (high χ, high IRM, medium coercivity and suppressed Verwey transition) and the ambient background sediment (low χ and low IRM). A magnetic unmixing model quantifies proportions of the IRD sources during Greenland Stadial (GS) 16 to GS3 (57.3 to 22.6 ka B.P.) spanning Heinrich Event (H) 5 to H2. The magnetic model suggests LIS IRD is only dominant within an interval during GS9, assigned to H4. Prior to H4 low proportions of BIS IRD suggest the BIS was not able to deliver significant amounts of IRD into the marine system. Following H4, proportions of BIS IRD during stadials increase, suggesting growth of the BIS during the latter stages of MIS3, with further expansion of the BIS during MIS2. LIS IRD within H2 is masked by BIS IRD input. Climatically driven anhysteretic remanent magnetizations reflect the short Dansgaard‐Oeschger cycles between H5 and H4, while the proportions of hard magnetic minerals reflect the longer‐term Bond cycles.
Sr and Nd isotopes in river sediments from the Ganga Basin: Sediment provenance and spatial variability in physical erosion
Authors: Singh Sunil K. , Rai Santosh K. , Krishnaswami S.
Published: July 2008

Sr and Nd concentrations and isotope compositions in sediment of the Ganga River, from Gangotri to Rajmahal, and its tributaries have been measured to determine provenance and the spatial variability in physical erosion among the Ganga subbasins. Sr and Nd in silicates range from 37 to 138 and from 10 to 36 μg/g, with 87Sr/86Sr and ɛNd of 0.7474–0.8428 and −25.5 to −15.5, respectively. The results suggest that >65% of Ganga mainstream sediments are derived from the Higher Himalayan Crystallines highlighting intense physical erosion in this region. The 87Sr/86Sr values of sediments in the Gangetic plain show nearly identical trends during two seasons, with a sharp and significant decrease at Barauni downstream of Gandak confluence. This brings out the major impact of the sediment contribution from the Gandak to the Ganga mainstream. Model calculation suggests that about half of the Ganga sediment at Rajmahal is sourced from the Gandak. The erosion rates in the Himalayan subbasins of the Ganga range between 0.5 and 6 mm/a (where a is years), with the Gandak having the highest erosion rate. High relief and intense precipitation over the headwater basins of the Gandak appear to drive the rapid and focused erosion of this basin. The results of this study and those in literature suggest that the eastern syntaxis (Brahmaputra), the western syntaxis (Indus), and the Gandak have much higher physical erosion rates than the other Himalayan basins. Focused erosion in the hot spots of these river basins contributes significantly to the global riverine sediment budget and influence regional tectonics.
Bed Ribbing Instability Explanation: Testing a numerical model of ribbed moraine formation arising from coupled flow of ice and subglacial sediment
Authors: Dunlop Paul , Clark Chris D. , Hindmarsh Richard C. A.
Published: July 2008

Ribbed moraines are large (up to 16 km long) ridges of sediment produced transverse to ice flow direction that formed widely beneath palaeo‐ice sheets. Since ice sheet stability is sensitive to conditions operating at the bed, an understanding of ribbed moraine genesis will provide critical information on ice sheet dynamics. Currently, there is no consensus on ribbed moraine formation and various competing hypotheses have been presented to account for their genesis. Only one of these theories has been developed into a physically based numerical model that quantitatively describes ribbed moraine formation. This theory, known as the Bed Ribbing Instability Explanation (BRIE), argues that ribbed moraines are produced by a naturally arising instability in the coupled flow of ice and till. BRIE demonstrates that transverse subglacial ridges (i.e., ribbed moraine) spontaneously grow under certain parameter combinations, and it predicts their wavelength (spacing between ridges). The model represents a significant advance because it is the first time a theory of subglacial bedform generation has been developed to make quantitative predictions which can be formally tested. This paper discusses the types of tests that are currently possible and reports the results from the first testing of BRIE. This analysis centers on the ability of BRIE to predict the primary characteristics of ribbed moraine, which are patterning and wavelength. Results show that BRIE successfully predicts the correct ribbed moraine pattern and appropriate wavelengths. The tests fail to falsify the model, and it is concluded that BRIE remains a viable explanation of ribbed moraine formation.
Overview of the temperature response in the mesosphere and lower thermosphere to solar activity
Authors: Beig G. , Scheer J. , Mlynczak M. G. , Keckhut P.
Published: July 2008

The natural variability in the terrestrial mesosphere needs to be known to correctly quantify global change. The response of the thermal structure to solar activity variations is an important factor. Some of the earlier studies highly overestimated the mesospheric solar response. Modeling of the mesospheric temperature response to solar activity has evolved in recent years, and measurement techniques as well as the amount of data have improved. Recent investigations revealed much smaller solar signatures and in some cases revealed no significant solar signal at all. However, not much effort has been made to synthesize the results available so far. This article presents an overview of the energy budget of the mesosphere and lower thermosphere and an up‐to‐date status of solar response in temperature structure based on recently available observational data. An objective evaluation of the data sets is attempted, and important factors of uncertainty are discussed.
Remediation of Groundwater Contaminated by Nuclear Waste: A Workshop on Accelerating Development of Practical Field‐Scale Bioremediation Models; An Online Meeting, 23 January to 20 February 2008
Authors: Parker Jack , Palumbo Anthony
Published: July 2008

A Web‐based workshop sponsored by the U.S. Department of Energy Environmental Remediation Sciences Program (DOE/ERSP) was organized in early 2008 to assess the state of the science and knowledge gaps associated with the use of computer models to facilitate remediation of groundwater contaminated by wastes from Cold War era nuclear weapons development and production. Microbially mediated biological reactions offer a potentially efficient means to treat these sites, but considerable uncertainty exists in the coupled biological, chemical, and physical processes and their mathematical representation.

Individuals from academia and DOE laboratories with expertise in modeling or microbiology and experience involving groundwater bioremediation participated in the workshop, which involved 10 hours of online meetings over a 5‐week period in early 2008 via linked audio and video communication. The objective of the workshop was to narrow the communication gap between modelers and microbiologists, engineers, and scientists, who tend to look at problems from different and sometimes divergent perspectives.
Geophysical Fluid Dynamics Program Receives Excellence in Geophysical Education Award
Authors: Whitehead John A. , Veronis George
Published: July 2008

The Geophysical Fluid Dynamics program received the Excellence in Geophysical Education Award at the 2008 Joint Assembly Honors Ceremony, which was held on 29 May 2008 in Fort Lauderdale, Fla. The award honors “a sustained commitment to excellence in geophysical education by a team, individual, or group.” George Veronis, cofounder of the Geophysical Fluid Dynamics program, accepted the award.
Greenhouse gas fluxes from natural ecosystems
Authors: Dalal Ram C. , Allen Diane E.
Published: July 2008

Besides water vapour, greenhouse gases CO2, CH4, O3 and N2O contribute ~60%, 20%, 10% and 6% to global warming, respectively; minor contribution is made by chlorofluorocarbons and volatile organic compounds (VOC). We present CO2, CH4 and N2O fluxes from natural and relatively unmanaged soil–plant ecosystems (the ecosystems minimally disturbed by direct human or human-induced activities). All natural ecosystems are net sinks for CO2, although tundra and wetlands (including peatlands) are large sources of CH4, whereas significant N2O emissions occur mainly from tropical and temperate forests. Most natural ecosystems decrease net global warming potential (GWP) from –0.03 ± 0.35 t CO2-e ha–1 y–1 (tropical forests) to –0.90 ± 0.42 t CO2-e ha–1 y–1 (temperate forests) and –1.18 ± 0.44 t CO2-e ha–1 y–1 (boreal forests), mostly as CO2 sinks in phytobiomass, microbial biomass and soil C. But net GWP contributions from wetlands are very large, which is primarily due to CH4 emissions. Although the tropical forest system provides a large carbon sink, the negligible capacity of tropical forests to reduce GWP is entirely due to N2O emissions, possibly from rapid N mineralisation under favourable temperature and moisture conditions. It is estimated that the natural ecosystems reduce the net atmospheric greenhouse gas (GHG) emissions by 3.55 ± 0.44 Gt CO2-e y–1 or ~0.5 ppmv CO2-e y–1, hence, the significant role of natural and relatively unmanaged ecosystems in slowing global warming and climate change. However, the impact of increasing N deposition on natural ecosystems is poorly understood, and further understanding is required regarding the use of drainage as a management tool, to reduce CH4 emissions from wetlands and to increase GHG sink from the restoration of degraded lands, including saline and sodic soils. Data on GHG fluxes from natural and relatively unmanaged ecosystems are further compounded by large spatial and temporal heterogeneity, limited sensitivity of current instruments, few and poor global distribution of monitoring sites and limited capacity of models that could integrate GHG fluxes across ecosystems, atmosphere and oceans and include feedbacks from biophysical variables governing these fluxes.
UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases
Authors: Takaya Tomohisa , Su Charlene , de La Harpe Kimberly , Crespo-Hernández Carlos E. , Kohler Bern
Published: July 2008

Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)
4
, and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution.
The architecture of the DNA replication origin recognition complex in
Saccharomyces cerevisiae
Authors: Chen Zhiqiang , Speck Christian , Wendel Patricia , Tang Chunyan , Stillman Bruce , Li Huilin
Published: July 2008

The origin recognition complex (ORC) is conserved in all eukaryotes. The six proteins of the
Saccharomyces cerevisiae
ORC that form a stable complex bind to origins of DNA replication and recruit prereplicative complex (pre-RC) proteins, one of which is Cdc6. To further understand the function of ORC we recently determined by single-particle reconstruction of electron micrographs a low-resolution, 3D structure of
S. cerevisiae
ORC and the ORC–Cdc6 complex. In this article, the spatial arrangement of the ORC subunits within the ORC structure is described. In one approach, a maltose binding protein (MBP) was systematically fused to the N or the C termini of the five largest ORC subunits, one subunit at a time, generating 10 MBP-fused ORCs, and the MBP density was localized in the averaged, 2D EM images of the MBP-fused ORC particles. Determining the Orc1–5 structure and comparing it with the native ORC structure localized the Orc6 subunit near Orc2 and Orc3. Finally, subunit–subunit interactions were determined by immunoprecipitation of ORC subunits synthesized
in vitro
. Based on the derived ORC architecture and existing structures of archaeal Orc1–DNA structures, we propose a model for ORC and suggest how ORC interacts with origin DNA and Cdc6. The studies provide a basis for understanding the overall structure of the pre-RC.
Integrated one- and two-photon imaging platform reveals clonal expansion as a major driver of mutation load
Authors: Wiktor-Brown Dominika M. , Kwon Hyuk-Sang , Nam Yoon Sung , So Peter T. C. , Engelward Bevin P.
Published: July 2008

The clonal expansion of mutant cells is hypothesized to be an important first step in cancer formation. To understand the earliest stages of tumorigenesis, a method to identify and analyze clonal expansion is needed. We have previously described transgenic Fluorescent Yellow Direct Repeat (FYDR) mice in which cells that have undergone sequence rearrangements (via homologous recombination events) express a fluorescent protein, enabling fluorescent labeling of phenotypically normal cells. Here, we develop an integrated one- and two-photon imaging platform that spans four orders of magnitude to permit rapid quantification of clonal expansion in the FYDR pancreas
in situ
. Results show that as mice age there is a significant increase in the number of cells within fluorescent cell clusters, indicating that pancreatic cells can clonally expand with age. Importantly, >90% of fluorescent cells in aged mice result from clonal expansion, rather than
de novo
sequence rearrangements at the FYDR locus. The spontaneous frequency of sequence rearrangements at the FYDR locus is on par with that of other classes of mutational events. Therefore, we conclude that clonal expansion is one of the most important mechanisms for increasing the burden of mutant cells in the mouse pancreas.
Evolution of sequence specificity in a restriction endonuclease by a point mutation
Authors: Saravanan Matheshwaran , Vasu Kommireddy , Nagaraja Valakunja
Published: July 2008

Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed with exquisite sequence specificity. REases have originated from the ancestral proteins and evolved new sequence specificities by genetic recombination, gene duplication, replication slippage, and transpositional events. They are also speculated to have evolved from nonspecific endonucleases, attaining a high degree of sequence specificity through point mutations. We describe here an example of generation of exquisitely site-specific REase from a highly-promiscuous one by a single point mutation.
Parallel memory processing by the CA1 region of the dorsal hippocampus and the basolateral amygdala
Authors: Cammarota Martín , Bevilaqua Lia R. , Rossato Janine I. , Lima Ramón H. , Medina Jorge H. , Izquierdo Iván
Published: July 2008

There is abundant literature on the role of the basolateral amygdala (BLA) and the CA1 region of the hippocampus in memory formation of inhibitory avoidance (IA) and other behaviorally arousing tasks. Here, we investigate molecular correlates of IA consolidation in the two structures and their relation to NMDA receptors (NMDArs) and β-adrenergic receptors (β-ADrs). The separate posttraining administration of antagonists of NMDAr and β-ADr to BLA and CA1 is amnesic. IA training is followed by an increase of the phosphorylation of calcium and calmodulin-dependent protein kinase II (CaMKII) and ERK2 in CA1 but only an increase of the phosphorylation of ERK2 in BLA. The changes are blocked by NMDAr antagonists but not β-ADr antagonists in CA1, and they are blocked by β-ADr but not NMDAr antagonists in BLA. In addition, the changes are accompanied by increased phosphorylation of tyrosine hydroxylase in BLA but not in CA1, suggesting that β-AD modulation results from local catecholamine synthesis in the former but not in the latter structure. NMDAr blockers in CA1 do not alter the learning-induced neurochemical changes in BLA, and β-ADr blockade in BLA does not hinder those in CA1. When put together with other data from the literature, the present findings suggest that CA1 and BLA play a role in consolidation, but they operate to an extent in parallel, suggesting that each is probably involved with different aspects of the task studied.
Prevalence of acute reactions to iopromide: postmarketing surveillance study of 74,717 patients
Authors: Kopp A. F. , Mortele K. J. , Cho Y. D. , Palkowitsch P. , Bettmann M. A. , Claussen C. D.
Published: July 2008

Background: Iodinated X-ray contrast media (CM) are recognized worldwide to be among the safest and most widely used injectable drugs. However, adverse drug reactions (ADRs) may still occur, ranging in severity from minor disturbances to severe and potentially fatal complications.

Purpose: To prospectively determine the incidence and characteristics of acute ADRs during clinical utilization of a single nonionic monomeric contrast agent, iopromide, in routine radiological practice in a large number of nonselected patients.

Material and Methods: 74,717 patients were enrolled in a prospective international postmarketing surveillance registry with iopromide (Ultravist; Bayer Schering Pharma AG, Berlin, Germany). A standardized questionnaire was used to collect the following patient information from 762 centers in 27 countries: baseline demographics, risk factors, premedication regimen, type of examination, route of injection, volume and selected concentration of iopromide, and overall tolerance to CM (utilizing specific criteria and descriptors).

Results: The overall rate of ADRs, including tolerance indicators (TI) (i.e., heat sensation and pain at the injection site), was 2%; when TIs were excluded, the rate was 1.5%. Fourteen serious adverse reactions were reported (rate 0.02%), of which none were fatal. There was a higher incidence of ADRs among women and for the age group ranging between 18 and 30 years. Patients with established risk factors, such as a history of previous CM reaction or allergic diathesis (7.4% and 4.1%, respectively), were at an increased risk for developing an ADR when compared to patients without risk factors (1.2%). The incidence of ADRs was not altered by the use of premedication.

Conclusion: The safety of iopromide in routine clinical practice was shown to be comparable to the published safety profiles of other nonionic iodinated contrast agents. Adverse drug reaction rates were affected by age, gender, and risk factors (especially previous CM reactions or allergies), but not by premedication.
Numerical analysis of the effect of fast-ion losses on plasma rotation in a tokamak with toroidal field ripple
Authors: Honda M. , Takizuka T. , Fukuyama A. , Yoshida M. , Ozeki T.
Published: July 2008

The effect of fast-ion losses due to the toroidal field ripple on the toroidal rotation is studied through numerical simulations. The simulations are carried out by utilizing a multi-fluid one-dimensional transport code, TASK/TX, with a ripple transport model suitable for implementing one-dimensional transport codes. Simulation results are qualitatively consistent with the experiments in JT-60U. It is shown that the return current associated with the outward radial fast-ion current due to the ripple loss flows inwards in the bulk plasma and the resultant
torque drives the plasma toroidally in the counter direction of the plasma current. The equilibrium value of the toroidal rotation velocity is determined by the balance between the perpendicular viscosity and the total torque.
Comparison of motional Stark effect diagnostic approaches for equilibrium reconstruction
Authors: Foley E.L. , Levinton F.M. , Yuh H.Y. , Zakharov L.E.
Published: July 2008

The motional Stark effect (MSE) diagnostic has been successfully applied to many tokamak plasmas to yield internal magnetic field measurements which contribute significant information to equilibrium reconstruction. As commonly implemented, the diagnostic measures the line polarization of a single component of the Stark spectrum and returns a spatially resolved profile of the magnetic field pitch angle. The line shifts in the Stark spectrum contain information about the magnetic field magnitude which is not typically exploited, and has not previously been used in equilibrium reconstruction. In this paper, we examine the utility of the MSE line shift (LS) measurement as compared with the MSE line polarization (LP) by analysis with the equilibrium and stability code (ESC)–equilibrium reconstruction variance (ERV) code system, a program which employs the theory of variances to evaluate the relationship between specified diagnostics and equilibrium reconstruction. Comparisons of the code results are made for an analytic solution of a toroidal plasma with circular cross-section and high aspect ratio, and for previous experimental results of q-profile reconstruction using VMEC on TFTR. ESC–ERV is then used to evaluate MSE-LS and MSE-LP in conditions like those expected in ITER, and for a configuration similar to the National Spherical Torus experiment. The analysis suggests that both the MSE-LP and the MSE-LS approaches, given sufficient measurement accuracy, can be used for reconstruction of q-profiles and pressure profiles.
Analytical modelling of Kirschner wires in Ilizarov circular external fixator as pretensioned slender beams
Authors: Zamani A.R , Oyadiji S.O
Published: July 2008

Transfixing thin Kirschner wires (K-wires) are the key components of the Ilizarov fixator regarding its axial stiffness, which affects the mechanobiological environment in which bone is healed. Mechanically speaking, K-wires are slender beams that are axially tensioned, then fixed and transversely loaded. The existing solutions to such a problem either do not accommodate any axial loading prior to transverse loading, or do not account for the change in the axial load (reaction) due to transverse loading. Their applicability is also limited vis-à-vis applied loads and beam dimensions. This work seeks to address those problems by providing a mathematical formulation for a pretensioned slender beam that accounts for the change in the beam tension due to lateral loading. Central loading of a pretensioned beam was studied and new polynomial equations have been derived, the roots of which yield the final tension for a (i) long, slender and heavily loaded beam and (ii) relatively thicker beam subjected to a lower load. Results were produced and discussed for the specific application of pretensioned K-wires in circular (ring) external fixators in orthopaedics (such as Ilizarov's), which were checked (validated) via two- and three-dimensional finite-element analyses.
Directionality in the evolution of influenza A haemagglutinin
Authors: Kryazhimskiy Sergey , Bazykin Georgii A , Plotkin Joshua , Dushoff Jonathan
Published: July 2008

The evolution of haemagglutinin (HA), an important influenza virus antigen, has been the subject of intensive research for more than two decades. Many characteristics of HA's sequence evolution are captured by standard Markov chain substitution models. Such models assign equal fitness to all accessible amino acids at a site. We show, however, that such models strongly underestimate the number of homoplastic amino acid substitutions during the course of HA's evolution, i.e. substitutions that repeatedly give rise to the same amino acid at a site. We develop statistics to detect individual homoplastic events and find that they preferentially occur at positively selected epitopic sites. Our results suggest that the evolution of the influenza A HA, including evolution by positive selection, is strongly affected by the long-term site-specific preferences for individual amino acids.
Aggressive monopolization of mobile carers by young of a cooperative breeder
Authors: Gilchrist J.S
Published: July 2008

Competition between young of the same brood or litter is of particular interest in the fields of behavioural and evolutionary ecology, because the competing individuals are likely to be closely related, where evolutionary theory predicts a greater degree of cooperation. Studies of cooperative breeding species typically concentrate on who contributes care to rearing young, and assume a passive role of the young. Relatively, little attention has been devoted to considering how intralitter competition between young affects the distribution of care in cooperative breeders. In banded mongoose (Mungos mungo) groups, the majority of pups each form a stable exclusive one-to-one association with an adult group member (its ‘escort’) that is its principal care provider. This paper presents experimental evidence that each pup aggressively defends access to its escort, preventing other pups approaching, and therefore monopolizes the care provided by its escort. Each pup travels with the group and follows its escort, around which its exclusion zone is fixed: a form of mobile territoriality. This represents a novel system of care of young in a mammal species, but has general implications for the study of the distribution of care of young, particularly in cooperative breeding species. Parents and helpers may provide biased care to young, not due to preference but due to the competitive actions of the young within the brood or litter.
A high incidence of parthenogenesis in agricultural pests
Authors: Hoffmann Ary A , Tracy Reynolds K , Nash Michael A , Weeks Andrew R
Published: July 2008

Parthenogenetic species are assumed to represent evolutionary dead ends, yet parthenogenesis is common in some groups of invertebrates particularly in those found in relatively constant environments. This suggests that parthenogenetic reproduction might be common in pest invertebrates from uniform agricultural environments. Based on the evaluations of two databases from North America and Italy, we found that parthenogenetic species comprised 45 per cent (North America) or 48 per cent (Italy) of pest species derived from genera where parthenogenesis occurred, compared with an overall incidence of 10 per cent or 16 per cent in these genera. In establishing these patterns, we included only genera containing at least some member species that reproduced by parthenogenesis. The high incidence of parthenogenesis in pest species is spread across different families and several insect orders. Parthenogenetic reproduction may be favoured in agricultural environments when particular clones have a high fitness across multiple generations. Increasing the complexity and variability of agricultural environments represents one way of potentially controlling parthenogenetic pest species.
Dinosaurs and the Cretaceous Terrestrial Revolution
Authors: Lloyd Graeme T , Davis Katie E , Pisani Davide , Tarver James E , Ruta Marcello , Sakamoto Manabu , Hone David W.E , Jennings Rachel , Benton Michael J
Published: July 2008

The observed diversity of dinosaurs reached its highest peak during the mid- and Late Cretaceous, the 50 Myr that preceded their extinction, and yet this explosion of dinosaur diversity may be explained largely by sampling bias. It has long been debated whether dinosaurs were part of the Cretaceous Terrestrial Revolution (KTR), from 125–80 Myr ago, when flowering plants, herbivorous and social insects, squamates, birds and mammals all underwent a rapid expansion. Although an apparent explosion of dinosaur diversity occurred in the mid-Cretaceous, coinciding with the emergence of new groups (e.g. neoceratopsians, ankylosaurid ankylosaurs, hadrosaurids and pachycephalosaurs), results from the first quantitative study of diversification applied to a new supertree of dinosaurs show that this apparent burst in dinosaurian diversity in the last 18 Myr of the Cretaceous is a sampling artefact. Indeed, major diversification shifts occurred largely in the first one-third of the group's history. Despite the appearance of new clades of medium to large herbivores and carnivores later in dinosaur history, these new originations do not correspond to significant diversification shifts. Instead, the overall geometry of the Cretaceous part of the dinosaur tree does not depart from the null hypothesis of an equal rates model of lineage branching. Furthermore, we conclude that dinosaurs did not experience a progressive decline at the end of the Cretaceous, nor was their evolution driven directly by the KTR.
Complex food webs prevent competitive exclusion among producer species
Authors: Brose Ulrich
Published: July 2008

Herbivorous top-down forces and bottom-up competition for nutrients determine the coexistence and relative biomass patterns of producer species. Combining models of predator–prey and producer–nutrient interactions with a structural model of complex food webs, I investigated these two aspects in a dynamic food-web model. While competitive exclusion leads to persistence of only one producer species in 99.7% of the simulated simple producer communities without consumers, embedding the same producer communities in complex food webs generally yields producer coexistence. In simple producer communities, the producers with the most efficient nutrient-intake rates increase in biomass until they competitively exclude inferior producers. In food webs, herbivory predominantly reduces the biomass density of those producers that dominated in producer communities, which yields a more even biomass distribution. In contrast to prior analyses of simple modules, this facilitation of producer coexistence by herbivory does not require a trade-off between the nutrient-intake efficiency and the resistance to herbivory. The local network structure of food webs (top-down effects of the number of herbivores and the herbivores' maximum consumption rates) and the nutrient supply (bottom-up effect) interactively determine the relative biomass densities of the producer species. A strong negative feedback loop emerges in food webs: factors that increase producer biomasses also increase herbivory, which reduces producer biomasses. This negative feedback loop regulates the coexistence and biomass patterns of the producers by balancing biomass increases of producers and biomass fluxes to herbivores, which prevents competitive exclusion.
Behavioural phenotype affects social interactions in an animal network
Authors: Pike Thomas W , Samanta Madhumita , Lindström Jan , Royle Nick J
Published: July 2008

Animal social networks can be extremely complex and are characterized by highly non-random interactions between group members. However, very little is known about the underlying factors affecting interaction preferences, and hence network structure. One possibility is that behavioural differences between individuals, such as how bold or shy they are, can affect the frequency and distribution of their interactions within a network. We tested this using individually marked three-spined sticklebacks (Gasterosteus aculeatus), and found that bold individuals had fewer overall interactions than shy fish, but tended to distribute their interactions more evenly across all group members. Shy fish, on the other hand, tended to associate preferentially with a small number of other group members, leading to a highly skewed distribution of interactions. This was mediated by the reduced tendency of shy fish to move to a new location within the tank when they were interacting with another individual; bold fish showed no such tendency and were equally likely to move irrespective of whether they were interacting or not. The results show that animal social network structure can be affected by the behavioural composition of group members and have important implications for understanding the spread of information and disease in social groups.
The influence of psychological factors on breastfeeding duration
Authors: O’Brien Maxine , Buikstra Elizabeth , Hegney Desley
Published: July 2008

Title.  The influence of psychological factors on breastfeeding duration.

Aim.  This paper reports on a study examining the relationship between women’s psychological characteristics and breastfeeding duration, after controlling for socio‐demographic factors.

Background.  The literature suggests that psychological factors may influence breastfeeding behaviour, but studies are few. Existing evidence and the results of phase 1 of our study were used to construct a list of psychological factors, which were tested for their association with breastfeeding duration in the current design.

Method.  Participants were postnatal inpatients in one of two regional hospitals between October and December 2005 and they completed the initial questionnaire within 14 days of giving birth (n = 375). Infant feeding method at 6 months and the timing of introduction of other food(s), where relevant, were ascertained by telephone interview.

Findings.  Forty‐four per cent of the sample showed signs of postnatal distress in the 14 days following the birth. Breastfeeding duration was statistically significantly associated with psychological factors including dispositional optimism, breastfeeding self‐efficacy, faith in breastmilk, breastfeeding expectations, anxiety, planned duration of breastfeeding and the time of the infant feeding decision. As a set, these psychological factors were more predictive of breastfeeding duration than was the set of socio‐demographic characteristics. The duration of any breastfeeding was uniquely predicted by faith in breastmilk, planned breastfeeding duration and breastfeeding self‐efficacy.

Conclusion.  This increased knowledge of the factors influencing breastfeeding will assist in identifying women at risk of early weaning and in constructing programmes capable of increasing the length of time for which women breastfeed.
Focal adhesion interactions with topographical structures: a novel method for immuno‐SEM labelling of focal adhesions in S‐phase cells
Authors: BIGGS M.J.P. , RICHARDS R.G. , WILKINSON C.D.W. , DALBY M.J.
Published: July 2008

Current understanding of the mechanisms involved in osseointegration following implantation of a biomaterial has led to adhesion quantification being implemented as an assay of cytocompatibility. Such measurement can be hindered by intra‐sample variation owing to morphological changes associated with the cell cycle. Here we report on a new scanning electron microscopical method for the simultaneous immunogold labelling of cellular focal adhesions and S‐phase nuclei identified by BrdU incorporation. Prior to labelling, cellular membranes are removed by tritonization and antigens of non‐interest blocked by serum incubation. Adhesion plaque–associated vinculin and S‐phase nuclei were both separately labelled with a 1.4 nm gold colloid and visualized by subsequent colloid enhancement via silver deposition. This study is specifically concerned with the effects microgroove topographies have on adhesion formation in S‐phase osteoblasts. By combining backscattered electron (BSE) imaging with secondary electron (SE) imaging it was possible to visualize S‐phase nuclei and the immunogold‐labelled adhesion sites in one energy ‘plane’ and the underlying nanotopography in another. Osteoblast adhesion to these nanotopographies was ascertained by quantification of adhesion complex formation.
Quantitative image correction and calibration for confocal fluorescence microscopy using thin reference layers and SIPchart‐based calibration procedures
Authors: ZWIER J.M. , OOMEN L. , BROCKS L. , JALINK K. , BRAKENHOFF G.J.
Published: July 2008

The fluorescence intensity image of an axially integrated through‐focus series of a thin standardized uniform fluorescent layer can be used for image intensity correction and calibration in sectioning microscopy. This intensity image is in fact available from the earlier introduced Sectioned Imaging Property (SIP) charts (Brakenhoff et al., 2005). It is shown that the integrated intensity of a z‐stack from a biological sample, imaged under identical conditions as the layer, can be calibrated in terms of fluorescence layer units of the calibration layer. The imaging after such calibration becomes, as a first approximation, independent of the microscope system and imaging conditions. This is demonstrated on axially integrated images of standard fluorescent beads and standard BPAE Fluorocells. Corrections on the microscope imaging conditions include shading effects, imaging with different magnifications and objectives, and using different microscope systems. It is also shown that with the present approach the actual underlying three‐dimensional (3D) fluorescence data set itself can be corrected for variations in point spread function (PSF) imaging efficiency over the imaging data cube. Realizing such calibration between imaging conditions or systems requires basically only the 2D fluorescer molecule density of the reference layers and the section distances with which the layer data are collected.
Application of wavelet denoising to improve compression efficiency while preserving integrity of digital micrographs
Authors: BERNAS T. , ASEM E.K. , ROBINSON J.P. , RAJWA B.
Published: July 2008

Modern microscopy methods require efficient image compression techniques owing to collection of up to thousands of images per experiment. Current irreversible techniques such as JPEG and JPEG2000 are not optimized to preserve the integrity of the scientific data as required by 21 CFR part 11. Therefore, to construct an irreversible, yet integrity‐preserving compression mechanism, we establish a model of noise as a function of signal in our imaging system. The noise is then removed with a wavelet shrinkage algorithm whose parameters are adapted to local image structure. We ascertain the integrity of the denoised images by measuring changes in spatial and intensity distributions of registered light in the biological images and estimating changes of the effective microscope MTF. We demonstrate that the proposed denoising procedure leads to a decrease in image file size when a reversible JPEG2000 coding is used and provides better fidelity than irreversible JPEG and JPEG2000 at the same compression ratio. We also demonstrate that denoising reduces image artefacts when used as a pre‐filtering step prior to irreversible image coding.
Fluorescence resonance energy transfer of GFP and YFP by spectral imaging and quantitative acceptor photobleaching
Authors: DINANT C. , VAN ROYEN M. E. , VERMEULEN W. , HOUTSMULLER A. B.
Published: July 2008

To study protein–protein interactions by fluorescence energy transfer (FRET), the proteins of interest are tagged with either a donor or an acceptor fluorophore. For efficient FRET, fluorophores need to have a reasonable overlap of donor emission and acceptor excitation spectra. However, given the relatively small Stokes shift of conventional fluorescent proteins, donor and acceptor pairs with high FRET efficiencies have emission spectra that are difficult to separate. GFP and YFP are widely used in fluorescence microscopy studies. The spectral qualities of GFP and YFP make them one of the most efficient FRET donor–acceptor couples available. However, the emission peaks of GFP (510 nm) and YFP (527 nm) are spectrally too close for separation by conventional fluorescence microscopy. Difficulties in simultaneous detection of GFP and YFP with a fluorescence microscope are eliminated when spectral imaging and subsequent linear unmixing are applied. This allows FRET microscopy using these tags to study protein–protein interactions. We adapted the linear unmixing procedure from commercially available software (Zeiss) for use with acceptor photobleaching FRET using GFP and YFP as FRET pair. FRET efficiencies up to 52% for a GFP‐YFP fusion protein were measured. To investigate the applicability of the procedure, we used two constituents of the nucleotide excision repair system, which removes UV‐induced single‐strand DNA damage. ERCC1 and XPF form a heterodimeric 5′ endonuclease in nucleotide excision repair. FRET between ERCC1‐GFP and XPF‐YFP occurs with an efficiency of 30%.
Electron microscopy study of different stages of oxidation of Ti‐47Al‐2Nb‐2Cr‐0.15B and Ti‐45Al‐15Nb at 900°C
Authors: LU W. , CHEN C. , HE L. , WANG F.
Published: July 2008

The initial stage of oxidation of Ti‐47Al‐2Nb‐2Cr‐0.15B and Ti‐45Al‐15Nb alloys was studied. Studies reveal that the X and NbCr2 phases will form in advance in the transition layer of the 2Nb2Cr alloy compared with the 15Nb alloy. The adherence between the nitride layer and underling layer is good. However, an obvious boundary exists between the mixed layer and the inner layer. The recrystallizing of the base alloy leads to an increase of the volume fraction of grain boundaries that can increase the oxidation rate at the initial oxidation stage. An Nb‐based compound forms in the transition layer, which can prevent the formation of X phase.
Total internal reflection microscopy for live imaging of cellular uptake of sub‐micron non‐fluorescent particles
Authors: BYRNE G. D. , PITTER M. C. , ZHANG J. , FALCONE F. H. , STOLNIK S. , SOMEKH M. G.
Published: July 2008

This paper presents a simple, high‐resolution, non‐fluorescent imaging technique called total internal reflection microscopy (TIRM) and demonstrates its potential application to real‐time imaging of live cellular events. In addition, a novel instrument is introduced that combines the simplicity of TIRM with the specificity afforded by dual‐colour total internal reflection fluorescence (TIRF) microscopy and allows sequential imaging with the two modalities. The key design considerations necessary to apply these imaging modes in a single instrument are discussed. The application of TIRM alone yielded high‐resolution live images of cell adherence to a poly‐l‐lysine modified substrate, whereby fine cellular structures are imaged. Non‐fluorescent imaging of the uptake of sub‐micron–sized polymeric particles by live cells is also demonstrated. Finally, images of fluorescently labelled cells were obtained in TIRF mode, sequentially to images obtained of the same cell in TIRM mode. Visual information gained using TIRF is compared with TIRM to demonstrate that the level of cell structure information obtainable with our total internal reflection microscope is comparable with the TIRF technique.