bluuebunny/crossref_metadata_2025 huggingface dataset:
Responses of soil‐mantled hillslopes to transient channel incision rates
Authors: Mudd Simon Marius , Furbish David Jon
Published: February 2007

Channel incision drives hillslope morphology in humid soil‐mantled landscapes. When channel incision rates change, numerous hillslope soil properties (e.g., erosion rates, soil thickness, and soil production) adjust in response to this change. Here we investigate the timescales of adjustment of hillslope soil properties when channel incision rates change in time. An idealized soil‐mantled hillslope (linear sediment flux law and soil density equal to bedrock density) is investigated, and the transient evolution of this hillslope is determined analytically. This analysis reveals two dominant adjustment timescales. The longer of these two timescales determines the rate at which the entire hillslope adjusts to a change in channel incision rates and is proportional to 4λ2/(π2D), where λ is the length of the hillslope and D is the sediment diffusivity. Numerical simulations are then used to examine responses of hillslopes that involve nonlinear behavior (e.g., hillslopes that experience nonlinear sediment transport or have soil thicknesses that respond to the soil production function). Using these numerical models, we show that the ratio between the soil density (ρs) and the density of the soil parent material (ρη) can alter the long‐term response of the hillslope such that the characteristic timescale becomes 4ρηλ2/(π2Dρs). In addition, we show that the adjustments of the soil erosion rate, the soil production rate, and the soil thickness have different characteristic response timescales. Hillslopes that experience sediment flux that is proportional to the depth slope product respond on longer timescales than hillslopes that experience a linear sediment flux law when channel incision rates increase. We illustrate how the spatial pattern of hillslope response to changes in channel incision rates can be used to constrain either channel incision histories or hillslope response timescales. If the hillslope response timescale is known, the pattern of hillslope disturbance can be used to constrain the celerity of a incision wave as it moves upstream through a channel. If the channel incision history is known, the hillslope response timescale may be evaluated on the basis of the spatial pattern of hillslope disturbance.
Recent warming of mountain permafrost in Svalbard and Scandinavia
Authors: Isaksen Ketil , Sollid Johan Ludvig , Holmlund Per , Harris Charles
Published: February 2007

Three deep boreholes (≥100 m) in mountain permafrost were recently drilled in Svalbard (Janssonhaugen) and in Scandinavia (Tarfalaryggen and Juvvasshøe) for long‐term permafrost monitoring. These holes form part of a latitudinal transect of boreholes in permafrost through Europe, established by the Permafrost and Climate in Europe (PACE) project. Six‐year thermal time series data collected from the three boreholes are presented. These data provide the first opportunity for temporal trends in permafrost temperatures in Svalbard and Scandinavia to be analyzed. Results show that the permafrost has warmed considerably at all three sites. Significant warming is detectable down to at least 60 m depth, and present decadal warming rates at the permafrost surface are on the order of 0.04°–0.07°C yr−1, with greatest warming in Svalbard and in northern Scandinavia. The present regional trend shows accelerated warming during the last decade.
Experimental investigation of the effects of copolymer surfactants on flow-induced coalescence of drops
Authors: Yoon Yosang , Hsu Adam , Leal L. Gary
Published: February 2007

Flow-induced coalescence of a pair of polymeric drops was studied at the level of individual drops, using a four-roll mill, to understand how the process is affected by the presence of a copolymer at the drop interface. The experimental system consisted of polybutadiene (PBd) drops suspended in polydimethylsiloxane (PDMS). Copolymers were produced at the drop interface by a reaction between functionalized homopolymers (PBd-COOH and PDMS-NH2). The experiments were carried out over wider ranges of parameters than our earlier studies of Hu et al. [Phys. Fluids 12, 484 (2000)] and Ha et al. [Phys. Fluids 15, 849 (2003)], in an attempt to understand the puzzling results found in our earlier studies. The experimental results were consistent with a qualitative mechanism of immobilization of the boundaries of the thin film between drops due to a flow-induced Marangoni effect. A critical or minimum copolymer interfacial coverage (Γmin) exists, above which the copolymer effect becomes independent of the coverage or the viscosity ratio. Using self-consistent mean field theory, the Γmin was found to be approximately 0.08chain∕nm2 corresponding to Δσe≅0.45mN∕m, which is around 30% of the saturation concentration, Γ∞≅0.25chain∕nm2. However, a whole new set of phenomena was discovered when the copolymer coverage is smaller (Γe<Γmin). In this case, we found that there was a strong surfactant effect at small Ca values, but that there was a transition capillary number (Cat) above which the Marangoni effect apparently becomes negligible. In this case, two critical capillary numbers for coalescence (Cac,high and Cac,low) exist, and there are two ranges of Ca and offset where coalescence is possible. The first is for Ca<Cac,low and small offsets. The second is for Cat<Ca<Cac,high, where Cac,high has almost the same values as the critical capillary number for a clean interface system. Between Cac,low and Cat, coalescence is not possible. For the copolymer systems, coalescence at Cac occurred at the angle just prior to the apparent separation of the drops in the extensional quadrant. The nonmonotonic change in Cac with copolymer concentration, found in our earlier study, is due to the fact that the separation angle increases with increased concentration, as can be seen by examination of the collision trajectory data. A copolymer with a smaller molecular weight was also used to probe the potential significance of non-hydrodynamic effects related to the molecular weight. We observed the same saturated limit for the copolymer effect (when Γe⩾Γmin) as in the case of the higher molecular weight copolymer system. We conclude that the Marangoni effect is the main mechanism for the suppression of coalescence in the current polymer/copolymer system.
Leakage current behavior in pulsed laser deposited Ba(Zr0.05Ti0.95)O3 thin films
Authors: Mukherjee Arnab , Victor P. , Parui J. , Krupanidhi S. B.
Published: February 2007

Barium zirconium titanate [Ba(Zr0.05Ti0.95)O3, BZT] thin films were prepared by pulsed laser ablation technique and dc leakage current conduction behavior was extensively studied. The dc leakage behavior study is essential, as it leads to degradation of the data storage devices. The current-voltage (I-V) of the thin films showed an Ohmic behavior for the electric field strength lower than 7.5MV∕m. Nonlinearity in the current density-voltage (J-V) behavior has been observed at an electric field above 7.5MV∕m. Different conduction mechanisms have been thought to be responsible for the overall I-V characteristics of BZT thin films. The J-V behavior of BZT thin films was found to follow Lampert’s theory of space charge limited conduction similar to what is observed in an insulator with charge trapping moiety. The Ohmic and trap filled limited regions have been explicitly observed in the J-V curves, where the saturation prevailed after a voltage of 6.5V referring the onset of a trap-free square region. Two different activation energy values of 1.155 and 0.325eV corresponding to two different regions have been observed in the Arrhenius plot, which was attributed to two different types of trap levels present in the film, namely, deep and shallow traps.
Broadband emission in Er–Tm codoped Al2O3 films: The role of energy transfer from Er to Tm
Authors: Xiao Zhisong , Serna R. , Afonso C. N.
Published: February 2007

Er–Tm codoped a-Al2O3 thin films prepared by alternate pulsed laser deposition show a broad photoluminescence band with two characteristic peaks at 1540 and at 1640nm, respectively, related to Er3+ and Tm3+ emissions. Two series of films have been prepared. For the first series, the Tm concentration [Tm] has been increased while keeping constant the Er concentration [Er]. The results show that the photoluminescence intensity at 1640nm (I1640) to that at 1540nm (I1540) decreases and that at 1640nm (I1640) increases, i.e., the (I1640∕I1540) ratio increases as [Tm] is increased. For [Tm]∕[Er]=3, a fairly flat emission spectrum (I1640∕I1540∼1) with a full width at half maximum of 230nm is achieved. For the second series both [Tm] and [Er] are increased while keeping the [Tm]∕[Er] ratio constant. The I1640∕I1540 ratio tends to be constant with a full width at half maximum of 150nm. The lifetime values decrease in all cases as [Tm] increases. The evolution of the I1640∕I1540 and lifetimes as a function of [Tm] as well as the analysis of the latter considering Er as a donor and Tm as an acceptor evidence that there is an efficient energy transfer from Er3+ to Tm3+. These results suggest that enhanced performance with a flat broadband emission useful for planar integrated devices is achievable by further dopant engineering in the nanoscale.
Buried amorphous layers by electronic excitation in ion-beam irradiated lithium niobate: Structure and kinetics
Authors: Olivares J. , García-Navarro A. , García G. , Agulló-López F. , Agulló-Rueda F. , García-Cabañes A. , Carrascosa M.
Published: February 2007

The formation of buried heavily damaged and amorphous layers by a variety of swift-ion irradiations (F at 22MeV, O at 20MeV, and Mg at 28MeV) on congruent LiNbO3 has been investigated. These irradiations assure that the electronic stopping power Se(z) is dominant over the nuclear stopping Sn(z) and reaches a maximum value inside the crystal. The structural profile of the irradiated layers has been characterized in detail by a variety of spectroscopic techniques including dark-mode propagation, micro-Raman scattering, second-harmonic generation, and Rutherford backscattering spectroscopy∕channeling. The growth of the damage on increasing irradiation fluence presents two differentiated stages with an abrupt structural transition between them. The heavily damaged layer reached as a final stage is optically isotropic (refractive index n=2.10, independent of bombarding ion) and has an amorphous structure. Moreover, it has sharp profiles and its thickness progressively increases with irradiation fluence. The dynamics under irradiation of the amorphous-crystalline boundaries has been associated with a reduction of the effective amorphization threshold due to the defects created by prior irradiation (cumulative damage). The kinetics of the two boundaries of the buried layer is quite different, suggesting that other mechanisms aside from the electronic stopping power should play a role on ion-beam damage.
Photodefinable organofunctionalized inorganic dielectric for organic thin film transistors
Authors: Choi Se-Jin , Lee Sangwoon , Han Keon-Kook , Lee Kwanghee , Kim Dongbum , Kim Jongchul , Lee Hong H.
Published: February 2007

The authors present an organic functionalized inorganic dielectric for use as a gate dielectric of organic thin film transistors (OTFTs). This inorganic-organic hybrid material is not only solution processable but also directly definable by photolithography. The gate dielectric can thus be patterned in the process of forming the dielectric layer. The organic functional moieties incorporated into inorganic siloxane backbone allow photocurability and development in aqueous solvents. Fabrication of pentacene-based OTFTs with the gate dielectric results in a device performance that is better than that of the device fabricated with spin-coatable inorganic dielectric such as spin on glass.
Influence of growth conditions on irradiation induced defects in low doped 4H-SiC epitaxial layers
Authors: Pintilie I. , Grossner U. , Svensson B. G. , Irmscher K. , Thomas B.
Published: February 2007

Nitrogen doped 4H-SiC epitaxial layers were investigated by deep level transient spectroscopy after irradiation with 6MeV electrons. The influence of C∕Si ratio, N doping level, and growth rate on the behavior of the prominent Z1,2 and EH6,7 levels during irradiation and subsequent annealing was studied. Both Z1,2 and EH6,7 increase in concentration with the N doping as well as with the C∕Si ratio. It is demonstrated that the growth conditions play a decisive role for the annihilation of the EH6,7 level and a possible identity of the EH6,7 defect is discussed.
Perfectly tetragonal, tensile-strained Ge on Ge1−ySny buffered Si(100)
Authors: Fang Y.-Y. , Tolle J. , Roucka R. , Chizmeshya A. V. G. , Kouvetakis John , D’Costa V. R. , Menéndez José
Published: February 2007

High-quality, tensile-strained Ge layers with variable thickness (>30nm) have been deposited at low temperature (350–380°C) on Si(100) via fully relaxed Ge1−ySny buffers. The precise strain state of the epilayers is controlled by varying the Sn content of the buffer, yielding tunable tensile strains up to 0.25% for y=0.025. Combined Raman analysis and high resolution x-ray diffraction using multiple off-axis reflections reveal unequivocally that the symmetry of tensile Ge is perfectly tetragonal, while the strain state of the buffer (∼200nm thick) remains essentially unchanged. A downshift of the direct gap consistent with tensile strain has been observed.
Plasticity of genetic interactions in metabolic networks of yeast
Authors: Harrison Richard , Papp Balázs , Pál Csaba , Oliver Stephen G. , Delneri Daniela
Published: February 2007

Why are most genes dispensable? The impact of gene deletions may depend on the environment (plasticity), the presence of compensatory mechanisms (mutational robustness), or both. Here, we analyze the interaction between these two forces by exploring the condition-dependence of synthetic genetic interactions that define redundant functions and alternative pathways. We performed systems-level flux balance analysis of the yeast (
Saccharomyces cerevisiae
) metabolic network to identify genetic interactions and then tested the model's predictions with
in vivo
gene-deletion studies. We found that the majority of synthetic genetic interactions are restricted to certain environmental conditions, partly because of the lack of compensation under some (but not all) nutrient conditions. Moreover, the phylogenetic cooccurrence of synthetically interacting pairs is not significantly different from random expectation. These findings suggest that these gene pairs have at least partially independent functions, and, hence, compensation is only a byproduct of their evolutionary history. Experimental analyses that used multiple gene deletion strains not only confirmed predictions of the model but also showed that investigation of false predictions may both improve functional annotation within the model and also lead to the discovery of higher-order genetic interactions. Our work supports the view that functional redundancy may be more apparent than real, and it offers a unified framework for the evolution of environmental adaptation and mutational robustness.
Telomere dysfunction as a cause of genomic instability in Werner syndrome
Authors: Crabbe Laure , Jauch Anna , Naeger Colleen M. , Holtgreve-Grez Heidi , Karlseder Jan
Published: February 2007

Werner syndrome (WS) is a rare human premature aging disease caused by mutations in the gene encoding the RecQ helicase WRN. In addition to the aging features, this disorder is marked by genomic instability, associated with an elevated incidence of cancer. Several lines of evidence suggest that telomere dysfunction is associated with the aging phenotype of the syndrome; however, the origin of the genomic instability observed in WS cells and the reason for the high incidence of cancer in WS have not been established. We previously proposed that WRN helicase activity was necessary to prevent dramatic telomere loss during DNA replication. Here we demonstrate that replication-associated telomere loss is responsible for the chromosome fusions found in WS fibroblasts. Moreover, using metaphase analysis we show that telomere elongation by telomerase can significantly reduce the appearance of new chromosomal aberrations in cells lacking WRN, similar to complementation of WS cells with WRN. Our results suggest that the genome instability in WS cells depends directly on telomere dysfunction, linking chromosome end maintenance to chromosomal aberrations in this disease.
Loop formation in unfolded polypeptide chains on the picoseconds to microseconds time scale
Authors: Fierz Beat , Satzger Helmut , Root Christopher , Gilch Peter , Zinth Wolfgang , Kiefhaber Thomas
Published: February 2007

Intrachain loop formation allows unfolded polypeptide chains to search for favorable interactions during protein folding. We applied triplet–triplet energy transfer between a xanthone moiety and naphthylalanine to directly measure loop formation in various unfolded polypeptide chains with loop regions consisting of polyserine, poly(glycine–serine) or polyproline. By combination of femtosecond and nanosecond laserflash experiments loop formation could be studied over many orders of magnitude in time from picoseconds to microseconds. The results reveal processes on different time scales indicating motions on different hierarchical levels of the free energy surface. A minor (<15%) very fast reaction with a time constant of ≈3 ps indicates equilibrium conformations with donor and acceptor in contact at the time of the laserflash. Complex kinetics of loop formation were observed on the 50- to 500-ps time scale, which indicate motions within a local well on the energy landscape. Conformations within this well can form loops by undergoing local motions without having to cross major barriers. Exponential kinetics observed on the 10- to 100-ns time scale are caused by diffusional processes involving large-scale motions that allow the polypeptide chain to explore the complete conformational space. These results indicate that the free energy landscape for unfolded polypeptide chains and native proteins have similar properties. The presence of local energy minima reduces the conformational space and accelerates the conformational search for energetically favorable local intrachain contacts.
Functional Properties and Convergence in Biology
Authors: Couch Mark B.
Published: February 2007

Evolutionary convergence is often appealed to in support of claims about multiple realization. The idea is that convergence shows that the same function can be realized by different kinds of structures. I argue here that the nature of convergence is more complicated than it might appear at first look. Broad claims about convergence are made by biologists during general discussions of the mechanisms of evolution. In their specialized work, though, biologists are often more limited in the claims they make. I will examine a standard example to show how claims about convergence can be oversimplified.
Pearson's Wrong Turning: Against Statistical Measures of Causal Efficacy
Authors: Northcott Robert
Published: February 2007

Standard statistical measures of strength of association, although pioneered by Pearson deliberately to be acausal, nowadays are routinely used to measure causal efficacy. But their acausal origins have left them ill suited to this latter purpose. I distinguish between two different conceptions of causal efficacy, and argue that: (1) Both conceptions can be useful; (2) The statistical measures only attempt to capture the first of them; (3) They are not fully successful even at this; (4) An alternative definition based more squarely on causal thinking not only captures the second conception, but also can capture the first one better too.
Relativistic Quantum Mechanics through Frame-Dependent Constructions
Authors: Barrett Jeffrey A.
Published: February 2007

This paper is concerned with the possibility and nature of relativistic hidden-variable formulations of quantum mechanics. Both ad hoc teleological constructions and frame-dependent constructions of spacetime maps are considered. While frame-dependent constructions are clearly preferable, a many-maps theory based on such constructions fails to provide dynamical explanations for local quantum events. Here the hidden-variable dynamics used in the frame-dependent constructions is just a rule that serves to characterize the set of all possible spacetime maps. While not having dynamical explanations of the values of quantum-mechanical measurement records is a significant cost, it may prove too much to ask for dynamical explanations in relativistic quantum mechanics.
Consensus, Dissensus, and Democracy: What Is at Stake in Feminist Science Studies?
Authors: Grebowicz Margret
Published: February 2007

If feminists argue for the irreducibility of the social dimensions of science, then they ought to embrace the idea that feminist and non-feminist scientists are not in collaboration, but in fact defenddifferentinterests. Instead, however, contemporary feminist science studies literature argues that feminist research improves particular, existing scientific enterprises, both epistemically (truer claims) and politically (more democratic methodologies and applications). I argue that the concepts of empirical success and democracy at work in this literature from Longino (1994) and Harding (1996), to Longino (2002), Gilbert and Rader (2001), and Keller (2001) are not sufficiently critical, and fail to do justice to the truly revolutionary work done by feminist scientists. I offer the beginnings of an epistemology of dissensus (as opposed to consensus), using the work of Haraway (1978), Lyotard (1984, 1998), and Ziarek (2001). How would such an epistemology relate to feminist discussions of the possibility of democratic, responsible knowledge?
Newcomb's Problem and Repeated Prisoners’ Dilemmas
Authors: Schmidt-Petri Christoph
Published: February 2007

I present a game-theoretic way to understand the situation describing Newcomb's Problem (NP) which helps to explain the intuition of both one-boxers and two-boxers. David Lewis has shown that the NP may be modelled as a Prisoner's Dilemma game (PD) in which ‘cooperating’ corresponds to ‘taking one box’. Adopting relevant results from game theory, this means that one should take just one box if the NP is repeated an indefinite number of times, but both boxes if it is a one-shot game. Causal decision theorists thus give the right answer for the one-shot situation, whereas the one-boxers’ solution applies to the indefinitely iterated case. Because Nozick's set-up of the NP is ambiguous between a one-shot and a repeated game, both of these solutions may appear plausible—depending on whether one conceives of the situation as one-off or repeated. If the players’ aim is to maximize their payoffs, the symmetric structure of the PD implies that the two players will behave alike both when the game is one-shot and when it is played repeatedly. Therefore neither the observed outcome of both players selecting the same strategy (in the PD) nor, correspondingly, the predictor's accurate prediction of this outcome (in the NP) is at all surprising. There is no need for a supernatural predictor to explain the NP phenomena.
Contemporary Nativism, Scientific Texture, and the Moral Limits of Free Inquiry
Authors: Cordero Alberto
Published: February 2007

Some thinkers distrust Darwinist explorations of complex human behaviors, particularly investigations into possible differences in valued skills between genders, races or classes. Such projects, it is claimed, tend to have adverse effects on people who are already disadvantaged. A recent argument by Philip Kitcher both clarifies and generalizes this charge to cover a wider genre of scientific projects. In this paper I try to spell out and analyze Kitcher's argument. The argument fails, I suggest, because some of its key premises fail to convince. My analysis focuses on relevant facts about the role of inquiry in fallibilist contexts, the texture of belief in contemporary natural science, and the moral dimension of scientific research.
Does Black Hole Complementarity Answer Hawking's Information Loss Paradox?
Authors: Bokulich Peter
Published: February 2007

A proper understanding of black hole complementarity as a response to the information loss paradox requires recognizing the essential role played by arguments for the applicability and limitations of effective semiclassical theories. I argue that this perspective sheds important light on the arguments advanced by Susskind, Thorlacius, and Uglum—although ultimately I argue that their position is unsatisfactory. I also consider the argument offered by 't Hooft for the breakdown of microcausality around black holes, and conclude that it relies on a mistaken treatment of measurement collapse. There is, however, a legitimate argumentative role for black hole complementarity, exemplified by the position of Kiem, Verlinde, and Verlinde, that calls for a more subtle analysis of the limitations facing our effective theories.
Theory of Nanosecond Pulse Generation by a Parallel Plate Capacitor Discharged in the Centre
Authors: L Hellström  , N R Nilsson  , H Wilhelmsson
Published: February 2007

The discharge of a transmission line in the form of a plate capacitor is studied theoretically. The aim of the present investigation is to find out how to achieve a short rise time of the generated electromagnetic pulse. Applying Laplace transform technique the mixed initial boundary value problem for the wave equation is solved for the case where the resistance of the spark is a constant. The corresponding problem for a time dependent resistance is treated by means of a computer. It is demonstrated that the rise time of the pulse essentially depends on (a) the geometry of the system, (b) the dispersive properties of the insulating dielectric medium, and (c) the time dependence of the spark resistance.
Spectrum and Term System of Doubly Ionized Fluorine, F III
Authors: Hans P Palenius
Published: February 2007

The analysis of the spectrum of doubly ionized fluorine, F III, has been revised and extended by using a sliding spark as a light-source. Many new lines (about 700) are identified, particularly in the regions 742-2 206 Å and 3 436-9 078 Å, where no lines were previously known. The nf and ng levels have been found and compared with those derived from the theoretical expressions for pair coupling. Altogether about 150 new energy levels are established. The sextet terms are connected with the other terms, giving for the quantity x in "Atomic Energy Levels" the value +21.6 cm-1. The first ionization limit (3
P
0) has been determined to 505 777 ± 5 cm-1.
Evidence for an Isomeric 29/2+ Level in 211At
Authors: I Bergström  , B Fant  , C J Herrlander  , K Wikström  , J Blomqvist
Published: February 2007

A 70 ns isomeric state at 2 641 keV has been produced in the 209Bi(α,2n)211 At reaction and interpreted as the 29/2+ state of the h
9/2
2
i
13/2 proton configuration. It decays to the states (h
9/2
2
f
7/2)23/2, (h
9/2
3)21/2, (h
9/2
3)17/2, (h
9/2
3)13/2 and (h
9/2
3)9/2 by a straight cascade of transitions with energies (multipolarities) 713.3 keV (E3), 511.6 keV (M1), 96.0 keV (E2), 253.4 keV (E2), and 1 066.9 keV (E2). There is also indirect evidence for a 24.4 keV (E2) branch to a (h
9/2
2
i
13/2)25/2 state followed by a 688.9 keV (E1) transition to the 21/2- state. The reduced transition rate B(E3, 29/2+ → 23/2-) = 51 000 e
2 fm6 can be reproduced by taking the value 0.9 MeV for the particle-phonon coupling matrix element ⟨i
13/2, 3-; 7/2|H
coupl|f
7/2⟩.
Additions to the B I Term System Based on Infrared Observations
Authors: Ulf Litzén
Published: February 2007

The wavelengths of twelve B I lines in the extra-photographic infrared have been measured with an accuracy better than 0.01 cm-1, giving the positions of the previously unknown 4p, 4f and 5f terms.
Using ghost lineages to identify diversification events in the fossil record
Authors: Cavin Lionel , Forey Peter L
Published: February 2007

Observed rises in taxic diversity could reflect bias of the fossil record or a genuine diversification. Here we outline a new method that attempts to differentiate between these two possible explanations. The method is based on the calculations of average ghost lineage duration through successive intervals of time. Biases due to variation in preservational conditions affect taxa independently from their position in the tree of life. A genuine radiation event will affect some parts of the tree of life more than others. During periods of rapid diversification, there will be a high proportion of new taxa showing short ghost lineages and therefore the average ghost lineage duration will drop as diversity rises, allowing us to distinguish such events from preservational bias during which ghost lineage duration remains unchanged. We test the method on Aptian–Maastrichtian (Cretaceous) ray-finned fish diversity. The result shows that a peak of diversity in the Cenomanian is associated with a drop in average ghost lineage duration, indicating that a genuine biological radiation occurred at that time.
Exceptional preservation of nerve and muscle tissues in Late Devonian placoderm fish and their evolutionary implications
Authors: Trinajstic Kate , Marshall Carina , Long John , Bifield Kat
Published: February 2007

In this paper, we show exceptional three-dimensionally preserved fossilized muscle tissues in 380–384 Myr old placoderm fish (Late Devonian), offering new morphological evidence supporting the hypothesis that placoderms are the sister group to all other gnathostomes. We describe the oldest soft tissue discovered in gnathostomes, which includes striated muscle fibres, circulatory and nerve tissues, preserved as phosphatized structures precipitated by microbial infilling of small, protected areas under the headshield of the arthrodire,
Eastmanosteus calliaspis
. Muscle impressions have also been found in the ptyctodontid,
Austroptyctodus gardineri
. The specimens display primitive vertebrate muscle structures; in particular, shallow W-shaped muscle blocks such as those observed in lampreys. New information from fossilized soft tissues thus elucidates the affinities of the placoderms and provides new insights into the evolution and radiation of gnathostomes.
The evolutionary epidemiology of vaccination
Authors: Gandon Sylvain , Day Troy
Published: February 2007

Vaccination leads to dramatic perturbations of the environment of parasite populations and this can have both demographic and evolutionary consequences. We present a theoretical framework for modelling the short- and long-term epidemiological and evolutionary consequences of vaccination. This framework integrates previous theoretical studies of vaccine-induced parasite evolution, and it allows one to make some useful qualitative predictions regarding the outcome of the competition between different types of vaccine-favoured variants. It can also be used to make quantitative predictions about the speed of such evolutionary processes. This work may help define the relevant parameters that need to be measured in specific parasite populations in order to evaluate the potential evolutionary consequences of vaccination. In particular, we argue that more work should be done evaluating the nature and magnitude of parasite fitness costs associated with adaptation to vaccinated hosts.
Observations of the plume generated by the December 2005 oil depot explosions and prolonged fire at Buncefield (Hertfordshire, UK) and associated atmospheric changes
Authors: Mather T.A , Harrison R.G , Tsanev V.I , Pyle D.M , Karumudi M.L , Bennett A.J , Sawyer G.M , Highwood E.J
Published: February 2007

The explosions and subsequent fire at the Buncefield oil depot in December 2005 afforded a rare opportunity to study the atmospheric consequences of a major oil fire at close range, using ground-based remote-sensing instruments. Near-source measurements (less than 10 km) suggest that plume particles were approximately 50% black carbon (BC) with refractive index 1.73−0.42i, effective radius (
R
eff
) 0.45–0.85 μm and mass loading approximately 2000 μg m
−3
. About 50 km downwind, particles were approximately 60–75% BC with refractive index between 1.80−0.52i and 1.89−0.69i,
R
eff
∼1.0 μm and mass loadings 320–780 μg m
−3
. Number distributions were almost all monomodal with peak at
r
<0.1 μm. Near-source UV spectroscopy revealed elevated trace gas concentrations of SO
2
(70 ppbv), NO
2
(140 ppbv), HONO (20 ppbv), HCHO (160 ppbv) and CS
2
(40 ppbv). Our measurements are consistent with others of the Buncefield plume, and with studies of the 1991 Kuwaiti oil-fire plumes; differences from the latter reflecting in part contrasts in combustion efficiency and source composition (refined fuels versus crude oils) leading to important potential differences in atmospheric impacts. Other measurements made as the plume passed overhead approximately 50 km downwind showed a reduced solar flux reaching the surface, but little effect on the atmospheric potential gradient (electric field). The wind speed data from the day of the explosion hint at a possible explosion signature.
Rapid courtship evolution in grouse (Tetraonidae): contrasting patterns of acceleration between the Eurasian and North American polygynous clades
Authors: Spaulding Allen
Published: February 2007

Sexual selection is thought to be a powerful diversifying force, based on large ornamental differences between sexually dimorphic species. This assumes that unornamented phenotypes represent evolution without sexual selection. If sexual selection is more powerful than other forms of selection, then two effects would be: rapid divergence of sexually selected traits and a correlation between these divergence rates and variance in mating success in the ornamented sex. I tested for these effects in grouse (Tetraonidae). For three species pairs, within and among polygynous clades, male courtship characters had significantly greater divergence than other characters. This was most pronounced for two species in
Tympanuchus
. In the Eurasian polygynous clade, relative courtship divergence gradually increased with nucleotide divergence, suggesting a less dramatic acceleration. Increase in relative courtship divergence was associated with mating systems having higher variance in male mating success. These results suggest that sexual selection has accelerated courtship evolution among grouse, although the microevolutionary details appear to vary among clades.
On the lack of evidence that non-human animals possess anything remotely resembling a ‘theory of mind’
Authors: Penn Derek C , Povinelli Daniel J
Published: February 2007

After decades of effort by some of our brightest human and non-human minds, there is still little consensus on whether or not non-human animals understand anything about the unobservable mental states of other animals or even what it would mean for a non-verbal animal to understand the concept of a ‘mental state’. In the present paper, we confront four related and contentious questions head-on: (i) What exactly would it mean for a non-verbal organism to have an ‘understanding’ or a ‘representation’ of another animal's mental state? (ii) What should (and should not) count as compelling empirical evidence that a non-verbal cognitive agent has a system for understanding or forming representations about mental states in a functionally adaptive manner? (iii) Why have the kind of experimental protocols that are currently in vogue failed to produce compelling evidence that non-human animals possess anything even remotely resembling a theory of mind? (iv) What kind of experiments could, at least in principle, provide compelling evidence for such a system in a non-verbal organism?
AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12
Authors: Babcock Melanie , Yatsenko Svetlana , Stankiewicz Pawel , Lupski James R. , Morrow Bernice E.
Published: February 2007

Low copy repeats (LCRs; segmental duplications) constitute ∼5% of the sequenced human genome. Nonallelic homologous recombination events between LCRs during meiosis can lead to chromosomal rearrangements responsible for many genomic disorders. The 22q11.2 region is susceptible to recurrent and nonrecurrent deletions, duplications as well as translocations that are mediated by LCRs termed LCR22s. One particular DNA structural element, a palindromic AT-rich repeat (PATRR) present within LCR22-3a, is responsible for translocations. Similar AT-rich repeats are present within the two largest LCR22s, LCR22-2 and LCR22-4. We provide direct sequence evidence that the AT-rich repeats have altered LCR22 organization during primate evolution. The AT-rich repeats are surrounded by a subtype of human satellite I (HSAT I), and an AluSc element, forming a 2.4-kb tripartite structure. Besides 22q11.2, FISH and PCR mapping localized the tripartite repeat within heterochromatic, unsequenced regions of the genome, including the pericentromeric regions of the acrocentric chromosomes and the heterochromatic portion of Yq12 in humans. The repeat is also present on autosomes but not on chromosome Y in other hominoid species, suggesting that it has duplicated on Yq12 after speciation of humans from its common ancestor. This demonstrates that AT-rich repeats have shaped or altered the structure of the genome during evolution.
Identification of muscle-specific regulatory modules inCaenorhabditis elegans
Authors: Zhao Guoyan , Schriefer Lawrence A. , Stormo Gary D.
Published: February 2007

Transcriptional regulation is the major regulatory mechanism that controls the spatial and temporal expression of genes during development. This is carried out by transcription factors (TFs), which recognize and bind to their cognate binding sites. Recent studies suggest a modular organization of TF-binding sites, in which clusters of transcription-factor binding sites cooperate in the regulation of downstream gene expression. In this study, we report our computational identification and experimental verification of muscle-specificcis-regulatory modules inCaenorhabditis elegans. We first identified a set of motifs that are correlated with muscle-specific gene expression. We then predicted muscle-specific regulatory modules based on clusters of those motifs with characteristics similar to a collection of well-studied modules in other species. The method correctly identifies 88% of the experimentally characterized modules with a positive predictive value of at least 65%. The prediction accuracy of muscle-specific expression on an independent test set is highly significant (P< 0.0001). We performed in vivo experimental tests of 12 predicted modules, and 10 of those drive muscle-specific gene expression. These results suggest that our method is highly accurate in identifying functional sequences important for muscle-specific gene expression and is a valuable tool for guiding experimental designs.
The Role of Renin—Angiotensin System Blockade in the Management of Hypertension Associated With the Cardiometabolic Syndrome
Authors: Sharma Arya M. , Engeli Stefan
Published: February 2007

The mounting epidemic of overweight and obesity has made understanding the relationship between excess weight and associated comorbidities more urgent. Obesity is one of the strongest predictors of the development of hypertension and is an independent risk factor for cardiovascular disease, renal disease, and diabetes mellitus. The concomitant presence of obesity and hypertension, as commonly occurs in the cardiometabolic syndrome, magnifies the risk for cardiovascular and renal disease. The term “obesity—hypertension” thus serves to underscore the link between these two deleterious conditions and to emphasize the imperative for clinical intervention. Adipose tissue is now known to produce hormones and cytokines that promote inflammation, lipid accumulation, and insulin resistance. In addition, adipose tissue contains all the components of the renin—angiotensin system (RAS), which is upregulated in the presence of obesity. Evidence implicates activation of the systemic and adipose tissue RAS, as well as the sympathetic nervous system, as key obesity‐related mechanisms of hypertension and other components of the cardiometabolic syndrome. RAS blockade therefore becomes a potential therapeutic strategy in patients with obesity‐related hypertension and in persons with the cardiometabolic syndrome. Clinical trials of angiotensin‐converting enzyme inhibitors and angiotensin II receptor blockers conducted in predominantly overweight/obese populations have demonstrated significant reductions in cardiovascular and renal disease risk among a range of at‐risk patients. RAS blockade also is associated with a reduced risk of new‐onset diabetes compared with other classes of antihypertensive therapy. Randomized, controlled trials conducted specifically in patients with obesity and hypertension are needed to determine the optimal therapeutic approach for these patients.
Trajectories of adolescent alcohol and cannabis use into young adulthood
Authors: Patton George C. , Coffey Carolyn , Lynskey Michael T. , Reid Sophie , Hemphill Sheryl , Carlin John B. , Hall Wayne
Published: February 2007

Background  Both alcohol and cannabis use carry health risks. Both are commonly initiated in adolescence. To date little research has described trajectories of adolescent cannabis or alcohol use or compared their respective consequences in young adulthood.

Methods  The design was a 10‐year eight‐wave cohort study of a state‐wide community sample of 1943 Victorians initially aged 14–15 years. Moderate‐ and high‐risk alcohol use was defined according to total weekly alcohol consumption. Moderate‐ and high‐risk cannabis use were defined as weekly and daily use, respectively.

Results  Around 90% of young adults used either alcohol or cannabis. Although an association existed between alcohol and cannabis use, there was a tendency for heavy users to use one substance predominantly at any one time. Weekly or more frequent cannabis use in the absence of moderate‐risk alcohol use in teenagers predicted a sevenfold higher rate of daily cannabis use in young adults but only a twofold increase in high‐risk alcohol use. Conversely, moderate‐risk adolescent alcohol use in the absence of weekly cannabis predicted an approximately threefold increased rate of both high‐risk drinking and daily cannabis use in young adulthood. Selective heavy cannabis use in both adolescence and young adulthood was associated with greater illicit substance use and poorer social outcomes in young adulthood than selective alcohol use.

Conclusions  Heavier teenage cannabis users tend to continue selectively with cannabis use. Considering their poor young adult outcomes, regular adolescent cannabis users appear to be on a problematic trajectory.
Does childhood sexual abuse have an effect on young adults' nicotine disorder (dependence or withdrawal)? Evidence from a birth cohort study
Authors: Al Mamun Abdullah , Alati Rosa , O'Callaghan Michael , Hayatbakhsh Mohammad R. , O'Callaghan Frances V. , Najman Jake M. , Williams Gail M. , Bor William
Published: February 2007

Aims  To examine whether there is evidence of an independent association between childhood sexual abuse (CSA) and nicotine disorder in youth and to explore the mechanisms underlying this association in a prospective cohort study.

Design  Birth cohort study followed‐up to 21 years.

Setting  One of two major obstetric hospitals in Brisbane, Australia.

Participants  The Mater‐University of Queensland Study of Pregnancy involves a prospective birth cohort from a population‐based sample involving 7223 singletons whose mothers were enrolled between 1981 and 1984 at the first antenatal visit. The present cohort consisted of a subgroup of 2571 youth who completed the life‐time version of the Composite International Diagnostic Interview—computerized version (CIDI‐Auto) at the 21‐year follow‐up.

Measurements  Nicotine disorder was measured based on Diagnostic and Statistical Manual version IV (DSM‐IV) diagnostic criteria and measures of CSA, including retrospective self‐reports of rape, were obtained at 21 years.

Results  Of 2571 young adults, 16.6% met the criteria for either dependence (12.8%) or withdrawal (8.5%). Non‐penetrative sexual abuse was reported by 15.5% of respondents and 8.0% reported penetrative sexual abuse. For any types of sexual abuse including non‐penetrative, penetrative and self‐reported rape before age 16 years, young adults had significantly higher rates of nicotine disorder than young adults who did not experience CSA. This relationship was independent and appeared direct after adjustment for a range of potential confounding and mediating factors.

Conclusions  This study shows that CSA is associated with young adult nicotine disorder. The results extend the public health significance of findings in this area and highlight the importance of not only intensifying public health efforts to address substance use problems among those who have experienced CSA, but of early intervention, so that emerging risky behaviours may be targeted in the earliest stages.
Can we accurately interpret drawings of ears with retractions?
Authors: Pothier D.D. , Awad Z.
Published: February 2007

Keypoints

• Retraction pockets of the pars tensa and flaccida are commonly drawn to monitor the condition.

• The clinical value of such drawings has not been assessed.

• This study shows that the ability to recognise an identical ear to a reference photograph from a drawing is poor.

• Using a drawing to identify the relative stage of a retraction from a drawing is unreliable.

• Otoendoscopic photographs are likely to be more reliable.
Not just music but medicine. Podcasting surgical procedures in otolaryngology
Authors: Whitehead D.E.J. , Bray D. , Harries M.
Published: February 2007

Keypoints

• Audiovisual teaching material can now be watched using a personal computer or portable media device.

• The cost of delivering video across the Internet has fallen considerably in recent years.

• Podcasting technology automates the distribution of audio and video across the Internet.

• Podcasting technology, with the Internet, has the potential to improve learning.

• To access podcasts all you need is a computer, free software and an Internet connection.