bluuebunny/crossref_metadata_2025 huggingface dataset:
A programmable broadband low frequency active vibration isolation system for atom interferometry
Authors: Tang Biao , Zhou Lin , Xiong Zongyuan , Wang Jin , Zhan Mingsheng
Published: September 2014

Vibration isolation at low frequency is important for some precision measurement experiments that use atom interferometry. To decrease the vibrational noise caused by the reflecting mirror of Raman beams in atom interferometry, we designed and demonstrated a compact stable active low frequency vibration isolation system. In this system, a digital control subsystem is used to process and feedback the vibration measured by a seismometer. A voice coil actuator is used to control and cancel the motion of a commercial passive vibration isolation platform. With the help of field programmable gate array-based control subsystem, the vibration isolation system performed flexibly and accurately. When the feedback is on, the intrinsic resonance frequency of the system will change from 0.8 Hz to about 0.015 Hz. The vertical vibration (0.01–10 Hz) measured by the in-loop seismometer is reduced by an additional factor of up to 500 on the basis of a passive vibration isolation platform, and we have proved the performance by adding an additional seismometer as well as applying it in the atom interferometry experiment.
Two soliton hierarchies associated with SO(4) and the applications of SU(2) ⊗ SU(2) ≅ SO(4)
Authors: He Baiying , Chen Liangyun , Ma Lili
Published: September 2014

Based on the six-dimensional real special orthogonal Lie algebra SO(4), we construct two different isospectral problems. And the two hierarchies of soliton equations from zero curvature equations can be generated. At last, we use the property of the isomorphism SU(2) ⊗ SU(2) ≅ SO(4), and obtain the relations between the hierarchy of SU(2) ⊗ SU(2) and the hierarchy of SO(4).
Game-theoretic characterization of antidegradable channels
Authors: Buscemi Francesco , Datta Nilanjana , Strelchuk Sergii
Published: September 2014

We introduce a guessing game involving a quantum channel, three parties—the sender, the receiver, and an eavesdropper, Eve—and a quantum public side channel. We prove that a necessary and sufficient condition for the quantum channel to be antidegradable, is that Eve wins the game. We thus obtain a complete operational characterization of antidegradable channels in a game-theoretic framework.
Interactions between inertial particles and shocklets in compressible turbulent flow
Authors: Yang Yantao , Wang Jianchun , Shi Yipeng , Xiao Zuoli , He X. T. , Chen Shiyi
Published: September 2014

Numerical simulations are conducted to investigate the dynamics of inertial particles being passively convected in a compressible homogeneous turbulence. Heavy and light particles exhibit very different types of non-uniform distributions due to their different behaviors near shocklets. Because of the relaxation nature of the Stokes drag, the heavy particles are decelerated mainly at downstream adjacent to the shocklets and form high-number-density clouds. The light particles are strongly decelerated by the added-mass effect and stay in the compression region for a relatively long time period. They cluster into thin filament structures near shocklets.
The thermal stability study and improvement of 4H-SiC ohmic contact
Authors: Liu Shengbei , He Zhi , Zheng Liu , Liu Bin , Zhang Feng , Dong Lin , Tian Lixin , Shen Zhanwei , Wang Jinze , Huang Yajun , Fan Zhongchao , Liu Xingfang , Yan Guoguo , Zhao Wanshun , Wang Lei , Sun Guosheng , Yang Fuhua , Zeng Yiping
Published: September 2014

The thermal stability of the standard Ni/SiC and a TiW/Ni/SiC Ohmic contacts was investigated and compared after being aged at 400 °C in the N2 atmosphere. The Ohmic contact was characterized using a combination of I-V measurements, the optical microscopic imaging, X-ray diffraction (XRD), and Auger electron spectroscopy (AES) techniques. It is shown that the standard Ni/SiC Ohmic contact failed after being aged at 400 °C for 20 h in the N2 atmosphere, while the TiW/Ni/SiC Ohmic contact could stand after 100 h. The TiW/Ni/SiC Ohmic contact was found kept a smooth surface morphology during the rapid thermal annealing and aging process, while the standard Ni/SiC Ohmic metal surface was found rougher. Both the Ohmic contact deteriorations after high temperature aging could be attributed to the formation of graphite which is confirmed by the XRD results. The XRD and AES results reveal that the better thermal stability of the TiW/Ni/SiC could be explained by the formation of CW3 and TiC, which deter the C atom diffusion to form graphite.
Lunar photoelectron sheath and levitation of dust
Authors: Sodha M. S. , Mishra S. K.
Published: September 2014

The decision to launch Luna Glob and Luna Resus satellites, carrying instrumentation to investigate the structure of photoelectron sheath and levitation of dust particles in the sheath, adjacent to the surface of the moon has intensified interest in this exciting area. The present analysis incorporates the following novel features: (i) In contrast to intuitive half Maxwellian (M) distribution of velocities of the photoelectrons, emitted from the surface of the moon, which corresponds to an arbitrary temperature, a well-established half Fermi Dirac (F-D) distribution [R. H. Fowler, Phys. Rev. 38, 45 (1931)] has been used, (ii) the profiles for electric potential, electric field, and electron density have been derived (not a priori assumed), (iii) an expression for the rate of electron accretion on a positively charged dust particle, which takes account of the anisotropic flux of electrons has been derived and used in the analysis, and (iv) a derived (rather than intuitive) expression for the rate of photoelectron emission from a positively charged dust particle has been used for the first time in such analyses. The profiles of the electric potential, electric field, and electron density in the photoelectric sheath have been evaluated for typical lunar environment and used to obtain the profile of the radius of a dust particle for levitation. The dependence of the electric potential on the surface of the moon on the parameters of the solar wind and photo-efficiency of the material of moon's surface has also been discussed. It is seen that the results based on half F-D distribution are significantly different from those obtained on the basis of M-distribution.
Comparative study of amplified spontaneous emission and short pre-pulse impacts onto fast electron generation at sub-relativistic femtosecond laser-plasma interaction
Authors: Ivanov K. A. , Shulyapov S. A. , Ksenofontov P. A. , Tsymbalov I. N. , Volkov R. V. , Savel'ev A. B. , Brantov A. V. , Bychenkov V. Yu. , Turinge A. A. , Lapik A. M. , Rusakov A. V. , Djilkibaev R. M. , Nedorezov V. G.
Published: September 2014

This paper describes the study of hot electron generation under the action of intense (∼1018 W/cm2) femtosecond pulses onto the surface of a solid target, in the presence of a long pre-plasma, which varied with different spatial extents and densities. The corona was formed by pre-pulses with varied intensities and temporal profiles (amplified spontaneous emission (ASE) and short pre-pulses). The most efficient fast electron acceleration, to energies well beyond the ponderomotive potential, was observed if the ASE was able to form to the extent of ∼100 μm a slightly undercritical plasma. Energy of accelerated electrons underwent further growth if the laser pulse duration increased from ∼45 to ∼350 fs at constant energy fluence. The experimental results were supported by numerical simulations using 3D3V Mandor PIC code.
Capsule-like voids in SiC single crystal: Phase contrast imaging and computer simulations
Authors: Kohn V. G. , Argunova T. S. , Je J. H.
Published: September 2014

The results of observation of capsule-like voids in silicon carbide (6H-SiC) single crystal by means of a phase contrast imaging technique with synchrotron radiation at the Pohang Light Source as well as computer simulations of such images are presented. A pink beam and a monochromated beam were used. The latter gives more pronounced images but they still are smoothed due to a finite detector resolution and the spatial coherence of the beam. Sizes and a structure of far field images are different from these of the objects. The computer simulations allow us to reproduce a shape and a size of the capsule-like void.
Dual-band infrared metasurface thermal emitter for CO2 sensing
Authors: Miyazaki H. T. , Kasaya T. , Iwanaga M. , Choi B. , Sugimoto Y. , Sakoda K.
Published: September 2014

Polarization- and angle-independent, dual-band metasurface thermal emitter was developed. The metasurface emits radiation at 4.26 μm and 3.95 μm, conventionally used for CO2 sensing. The metasurface is based on a planar Au/Al2O3/Au structure, in which orthogonal rectangular Au patches are arrayed alternately, and generates nearly perfect blackbody radiation with an emittance as high as 0.97. The metasurface is integrated on a resistive heater mounted on a SiN membrane, so that the infrared waves are produced by applying a voltage. The metasurface emitter was incorporated into an actual CO2 sensing system and was demonstrated to reduce the electric power needed by about 30% compared with a conventional blackbody emitter by suppressing unnecessary radiation.
Measuring Changing Ethnic Separations in England: A Spatial Discontinuity Approach
Authors: Harris Richard
Published: September 2014

This paper investigates claims of decreased segregation yet also a declining number of White British residents in English cities during the period from 2001 to 2011. It does so by supplementing a traditional measure of segregation—the dissimilarity index—with a related measure comparing differences between adjoining or closely located small areas. It discusses the methodological basis for the measure and uses it in conjunction with the original index and a measure of spatial clustering to consider both the amount and spatial configuration of ‘segregation’ between various ethnic groups in English local authorities. Further analysis identifies neighbouring places with the greatest difference in their ethnic compositions in 2001 and shows that, in the main, those differences had decreased by 2011. The explanation for the reduction is seen as partly due to processes of migration/diffusion by ‘minority’ groups but also as a consequence of the reduction in the White British population locally. There is some suggestion that whilst preexisting differences diminish, they are replaced by greater differences between neighbouring locations elsewhere.
Globalization, Science, and the Making of an Environmental Discourse on the Wild Coast, South Africa
Authors: Kepe Thembela
Published: September 2014

This paper uses the case of the proposed Pondoland National Park in South Africa, which is in the center of policy debates about biodiversity conservation, development, and resource rights in the Wild Coast area of South Africa. It explores whether the making of the case for the conservation of the Wild Coast, which relies on global environmental discourses, has ideologically and practically clarified local poor people's resource rights. It does this by tracing the genealogy of the Pondoland National Park discourse, which originates from scientific research and individual and group lobbying, to help explain the disjuncture between post-apartheid environmental policy discourses and what takes place in practice. The paper concludes that the reliance on global environmental discourses in research done in support for the Pondoland National Park complicates the role of the nation-state in terms of environmental governance, and that this can negatively affect the poor and powerless residents of the area in question.
Local Ties and Family Migration
Authors: Mulder Clara H , Malmberg Gunnar
Published: September 2014

The migration of couples and families has thus far been approached mainly from human-capital and gender perspectives. In this paper, we investigate how the male and female partner's local ties influence the likelihood of family migration. Our hypotheses are that local ties to work and family strongly decrease the likelihood of migrating; that, given the dominating gender structures, ties to the man's work are more influential than ties to the woman's work; and that ties to the woman's family are more influential than ties to the man's family. We used data from the ASTRID microdatabase for Sweden, based on administrative information about the entire Swedish population. Logistic regression analysis was applied to moves that exceeded a distance of 50 km for two-gender couples who did not separate in the period December 2004–December 2005. With regard to the likelihood of migrating, we find marked negative associations in the following: working close to home, the presence of parents and siblings nearby, and whether someone lives near the place of birth. The man's ties to work seem to be more important to the likelihood of migrating than the woman's, but we find hardly any gender differences in the impact of ties to family.
A Cosmopolitics of Energy: Diverging Materialities and Hesitating Practices
Authors: Gabrys Jennifer
Published: September 2014

Numerous proposals, analyses, and strategies now exist for materializing energy in order to influence environmental participation and reduce energy use. This paper asks how specific materialities of energy are articulated across social science and creative practice projects, and how these distinct renderings of materiality perform environmental change. Drawing on work by Stengers, the paper moves to consider the diverging materialities and speculative practices that might emerge through more cosmopolitical approaches to energy. A range of creative practice projects that materialize energy and perform environmental change in different registers is discussed, with attention given to considering how what counts as materiality, participation, and environmental matters of concern shifts within these differently configured engagements. The paper asks how alternative materialities of energy might be articulated that work through experimental registers of environmental practice, and that may not always be clearly directed toward instrumental ends. How might environmental practices attend to the speculative qualities of performativity, which engage not just with energy as actuality but also with energy as potentiality?
Articulating Social Science in the Wild of Global Natures? On Economics and Anthropology in Transnational Environmental Politics
Authors: Blok Anders
Published: September 2014

Building on multisited ethnographic case studies, this paper seeks to contrastively compare the demonstration and articulation formats of two social science expert cultures—economics and anthropology—enrolled ‘in the wild’ of transnational environmental politics. How, the paper asks, do different social sciences come to be configured within, and do performative work upon, heterogeneous assemblages of global natures? In the first case US economists translate carbon markets into a world of Indian ecoprofessionals, across serious North–South conflicts in climate politics. In the second case a group of anthropologists, mobilized by Japanese bureaucratic elites, deploy their methods to assemble whaling cultures, as part of global biodiversity conflicts. Whereas the first case builds on existing arguments on the ‘performativity of economics' (Callon), the second case expands this agenda, noting how the noneconomic social sciences (eg, anthropology) may also be consequential in enacting particular nature-cultures. Theoretically, the paper situates these inquiries at the intersection of science and technology studies (STS) and political anthropology, in addressing the question—important to environmental expertise and politics—of how ‘local’ (particular) and ‘global’ (universal) claims are linked in efficacious ways in ‘other-than-Western’ contexts? Here, the argument will be that, despite their differences, economic and anthropological performances of global natures share certain formal (aesthetic) similarities, related to credible expert demonstrations in transnational environmental contexts. The paper concludes by discussing the implications of this claim for STS self-reflection on its politics of methods.
Synchronous monoecy in Ecdeiocoleaceae (Poales), in Western Australia
Authors: Briggs Barbara G. , Tinker Allan
Published: September 2014

The Western Australian plant family Ecdeiocoleaceae includes only three species but DNA data show them as the closest living sister-group of the Poaceae. Ecdeiocoleaceae are wind-pollinated and monoecious; spikes produce separate zones of pistillate and staminate flowers, in acropetal succession. Spikes of Ecdeiocolea have up to 45 flowers, with a sequence of zones up the spike, commonly pistillate–staminate–pistillate–staminate–pistillate, with potentially high fruit set in both of the lower pistillate zones. Rainfall in their habitats in semiarid south-western Australia is highly variable and shorter spikes with fewer zones are formed in drought conditions. Georgeantha, with fewer flowers per spike, shows the same general pattern but fewer switches. Synchrony of zonal flowering gives an effective barrier to self-pollination, a form of ‘temporal dioecy’. All spikes on many stems of a plant flower with the conspicuous white stigmas of a pistillate zone or, at a different time, all with the yellow anthers of a staminate zone. Such synchrony is between the many spikes on the plant, not between plants in a population. Features of vegetative and flowering structures and habitat are briefly mentioned.
How much wetland has the world lost? Long-term and recent trends in global wetland area
Authors: Davidson Nick C.
Published: September 2014

It has been frequently stated, but without provision of supporting evidence, that the world has lost 50% of its wetlands (or 50% since 1900 AD). This review of 189 reports of change in wetland area finds that the reported long-term loss of natural wetlands averages between 54–57% but loss may have been as high as 87% since 1700 AD. There has been a much (3.7 times) faster rate of wetland loss during the 20th and early 21st centuries, with a loss of 64–71% of wetlands since 1900 AD. Losses have been larger and faster for inland than coastal natural wetlands. Although the rate of wetland loss in Europe has slowed, and in North America has remained low since the 1980s, the rate has remained high in Asia, where large-scale and rapid conversion of coastal and inland natural wetlands is continuing. It is unclear whether the investment by national governments in the Ramsar Convention on Wetlands has influenced these rates of loss. There is a need to improve the knowledge of change in wetland areas worldwide, particularly for Africa, the Neotropics and Oceania, and to improve the consistency of data on change in wetland areas in published papers and reports.
Impacts of fire on soil organic carbon stocks in a grazed semi-arid tropical Australian savanna: accounting for landscape variability
Authors: Allen D. E. , Bloesch P. M. , Cowley R. A. , Orton T. G. , Payne J. E. , Dalal R. C.
Published: September 2014

Fire and grazing are commonplace in Australian tropical savannas and the effects of these management practices on soil organic carbon stocks (SOC) is not well understood. A long-term (20 years) experiment studying the effects of fire on a grazed semi-arid tropical savanna was used to increase this understanding. Treatments, including frequency of fire (every 2, 4 and 6 years), season of fire [early (June) vs late (October) dry season] and unburnt control plots, were imposed on Vertosol grassland and Calcarosol woodland sites, which were grazed. Additionally long-term enclosures [unburnt (except the Calcarosol in 2001) and ungrazed since 1973] on each soil type adjacent to each site were sampled, although not included in statistical analyses. SOC stocks were measured to a soil depth of 0.3 m using a wet oxidation method (to avoid interference by carbonates) and compared on an equivalent soil mass basis. Significant treatment differences in SOC stocks were tested for, while accounting for spatial background variation within each site. SOC stocks (0–0.3 m soil depth) ranged between 10.1 and 28.9 t ha–1 (Vertosol site) and 20.7 and 54.9 t ha–1 (Calcarosol site). There were no consistent effects of frequency or season of fire on SOC stocks, possibly reflecting the limited statistical power of the study and inherent spatial variability observed. Differences in the response to frequency and season of fire observed between these soils may have been due to differences in clay type, plant species composition and/or preferential grazing activity associated with fire management. There may also have been differences in C input between treatments and sites due to differences in the herbage mass and post-fire grazing activity on both sites and changed pasture composition, higher herbage fuel load, and a reduction in woody cover on the Vertosol site. This study demonstrated the importance of accounting for background spatial variability and treatment replication (in the absence of baseline values) when assessing SOC stocks in relation to management practices. Given the absence of baseline SOC values and the potentially long period required to obtain changes in SOC in rangelands, modelling of turnover of SOC in relation to background spatial variability would enable management scenarios to be considered in relation to landscape variation that may be unrelated to management. These considerations are important for reducing uncertainty in C-flux accounting and to provide accurate and cost-effective methods for land managers considering participation in the C economy.
Improvements are Needed in Reporting of Accuracy Studies for Diagnostic Tests Used for Detection of Finfish Pathogens
Authors: Gardner Ian A. , Burnley Timothy , Caraguel Charles
Published: September 2014

Indices of test accuracy, such as diagnostic sensitivity and specificity, are important considerations in test selection for a defined purpose (e.g., screening or confirmation) and affect the interpretation of test results. Many biomedical journals recommend that authors clearly and transparently report test accuracy studies following the Standards for Reporting of Diagnostic Accuracy (STARD) guidelines (www.stard-statement.org). This allows readers to evaluate overall study validity and assess potential bias in diagnostic sensitivity and specificity estimates. The purpose of the present study was to evaluate the reporting quality of studies evaluating test accuracy for finfish diseases using the 25 items in the STARD checklist. Based on a database search, 11 studies that included estimates of diagnostic accuracy were identified for independent evaluation by three reviewers. For each study, STARD checklist items were scored as “yes,” “no,” or “not applicable.” Only 10 of the 25 items were consistently reported in most (≥80%) papers, and reporting of the other items was highly variable (mostly between 30% and 60%). Three items (“number, training, and expertise of readers and testers”; “time interval between index tests and reference standard”; and “handling of indeterminate results, missing data, and outliers of the index tests”) were reported in less than 10% of papers. Two items (“time interval between index tests and reference standard” and “adverse effects from testing”) were considered minimally relevant to fish health because test samples usually are collected postmortem. Modification of STARD to fit finfish studies should increase use by authors and thereby improve the overall reporting quality regardless of how the study was designed. Furthermore, the use of STARD may lead to the improved design of future studies.

Received September 24, 2013; accepted May 15, 2014
Perceptual‐cognitive skill training and its transfer to expert performance in the field: Future research directions
Authors: Broadbent David P. , Causer Joe , Williams A. Mark , Ford Paul R.
Published: September 2014

Perceptual‐cognitive skills training provides a potentially valuable method for training athletes on key skills, such as anticipation and decision‐making. It can be used when athletes are unable to physically train or are unable to experience repeated key situations from their sport. In this article, we review research on perceptual‐cognitive skills training and describe future research areas focusing on a number of key theories and principles. The main aim of any training intervention should be the efficacy of retention and transfer of learning from training to field situations, which should be the key consideration when designing the representative tasks used in perceptual‐cognitive skills training. We review the principles that seek to create practice tasks that replicate those found in the field, so as to increase the amount of transfer that occurs. These principles are perception–action coupling, the contextual interference effect and contextual information, which suggest there should be a high level of similarity between training and real‐life performance when designing perceptual‐cognitive skills training. In the final section, we discuss the transfer of retained skill acquisition from perceptual‐cognitive skills training to field performance, which we suggest to be the key area for future research in this area.
Identifying biochemical phenotypic differences between cryptic species
Authors: Liebeke Manuel , Bruford Michael W. , Donnelly Robert K. , Ebbels Timothy M. D. , Hao Jie , Kille Peter , Lahive Elma , Madison Rachael M. , Morgan A. John , Pinto-Juma Gabriela A. , Spurgeon David J. , Svendsen Claus , Bundy Jacob G.
Published: September 2014

Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthwormLumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such asNε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status.
What drives activation-dependent shifts in the force–length curve?
Authors: Holt Natalie C. , Azizi E.
Published: September 2014

Skeletal muscles are rarely recruited maximally during movement. However, much of our understanding of muscle properties is based on studies using maximal activation. The effect of activation level on skeletal muscle properties remains poorly understood. Muscle optimum length increases with decreased activation; however, the mechanism responsible is unclear. Here, we attempted to determine whether length-dependent calcium effects, or the effect of absolute force underpin this shift. Fixed-end contractions were performed in frog plantaris muscles at a range of lengths using maximal tetanic (high force, high calcium), submaximal tetanic (low force, high calcium) and twitch (low force, low calcium) stimulation conditions. Peak force and optimum length were determined in each condition. Optimum length increased with decreasing peak force, irrespective of stimulation condition. Assuming calcium concentration varied as predicted, this suggests that absolute force, rather than calcium concentration, underpins the effect of activation level on optimum length. We suggest that the effect of absolute force is due to the varying effect of the internal mechanics of the muscle at different activation levels. These findings have implications for our understanding of
in vivo
muscle function and suggest that mechanical interactions within muscle may be important determinants of force at lower levels of activation.
Self-preservation strategies during bacterial biomineralization with reference to hydrozincite and implications for fossilization of bacteria
Authors: Ngwenya Bryne T. , Magennis Marisa , Podda Francesca , Gromov Andrei
Published: September 2014

The induction of mineralization by microbes has been widely demonstrated but whether induced biomineralization leads to distinct morphologies indicative of microbial involvement remains an open question. For calcium carbonate, evidence suggests that microbial induction enhances sphere formation, but the mechanisms involved and the role of microbial surfaces are unknown. Here, we describe hydrozincite biominerals from Sardinia, Italy, which apparently start life as smooth globules on cyanobacterial filaments, and evolve to spheroidal aggregates consisting of nanoplates. Complementary laboratory experiments suggest that organic compounds are critical to produce this morphology, possibly by inducing aggregation of nanoscopic crystals or nucleation within organic globules produced by metabolizing cells. These observations suggest that production of extracellular polymeric substances by microbes may constitute an effective mechanism to enhance formation of porous spheroids that minimize cell entombment while also maintaining metabolite exchange. However, the high porosity arising from aggregation-based crystal growth probably facilitates rapid oxidation of entombed cells, reducing their potential to be fossilized.
A robotic crawler exploiting directional frictional interactions: experiments, numerics and derivation of a reduced model
Authors: Noselli Giovanni , DeSimone Antonio
Published: September 2014

We present experimental and numerical results for a model crawler which is able to extract net positional changes from reciprocal shape changes, i.e. ‘breathing-like’ deformations, thanks to directional, frictional interactions with a textured solid substrate, mediated by flexible inclined feet. We also present a simple reduced model that captures the essential features of the kinematics and energetics of the gait, and compare its predictions with the results from experiments and from numerical simulations.
An introduction to the mechanics of the lasso
Authors: Brun Pierre-Thomas , Ribe Neil , Audoly Basile
Published: September 2014

Trick roping evolved from humble origins as a cattle-catching tool into a sport that delights audiences all over the world with its complex patterns or ‘tricks’. Its fundamental tool is the lasso, formed by passing one end of a rope through a small loop (the honda) at the other end. Here, we study the mechanics of the simplest rope trick, the
Flat Loop
, in which the rope is driven by the steady circular motion of the roper's hand in a horizontal plane. We first consider the case of a fixed (non-sliding) honda. Noting that the rope's shape is steady in the reference frame rotating with the hand, we analyse a string model in which line tension is balanced by the centrifugal force and the rope's weight. We use numerical continuation to classify the steadily rotating solutions in a bifurcation diagram and analyse their stability. In addition to
Flat Loops
, we find planar ‘coat-hanger’ solutions, and whirling modes in which the loop collapses onto itself. Next, we treat the more general case of a honda that can slide due to a finite coefficient of friction of the rope on itself. Using matched asymptotic expansions, we resolve the shape of the rope in the boundary layer near the honda where the rope's bending stiffness cannot be neglected. We use this solution to derive a macroscopic criterion for the sliding of the honda in terms of the microscopic Coulomb static friction criterion. Our predictions agree well with rapid-camera observations of a professional trick roper and with laboratory experiments using a ‘robo-cowboy’.
Early evolution of limb regeneration in tetrapods: evidence from a 300-million-year-old amphibian
Authors: Fröbisch Nadia B. , Bickelmann Constanze , Witzmann Florian
Published: September 2014

Salamanders are the only tetrapods capable of fully regenerating their limbs throughout their entire lives. Much data on the underlying molecular mechanisms of limb regeneration have been gathered in recent years allowing for new comparative studies between salamanders and other tetrapods that lack this unique regenerative potential. By contrast, the evolution of animal regeneration just recently shifted back into focus, despite being highly relevant for research designs aiming to unravel the factors allowing for limb regeneration. We show that the 300-million-year-old temnospondyl amphibianMicromelerpeton, a distant relative of modern amphibians, was already capable of regenerating its limbs. A number of exceptionally well-preserved specimens from fossil deposits show a unique pattern and combination of abnormalities in their limbs that is distinctive of irregular regenerative activity in modern salamanders and does not occur as variants of normal limb development. This demonstrates that the capacity to regenerate limbs is not a derived feature of modern salamanders, but may be an ancient feature of non-amniote tetrapods and possibly even shared by all bony fish. The finding provides a new framework for understanding the evolution of regenerative capacity of paired appendages in vertebrates in the search for conserved versus derived molecular mechanisms of limb regeneration.
Abnormal X Chromosome Inactivation in Females with Major Psychiatric Disorders
Authors: Ji Baohu , Higa Kerin K. , Kelsoe John R. , Zhou Xianjin
Published: September 2014

Bipolar disorder, major depression and schizophrenia are severe brain disorders. No biological hallmark has been identified for any of these disorders. Here, we report that abnormal X chromosome inactivation (XCI) often presents in lymphoblastoid cells of female patients with different major psychiatric disorders in the general population. X chromosome inactivation is well preserved in human lymphoblastoid cells.XIST,KDM5C,and other X-linked genes are over-expressed in the lymphoblastoid cells of female patients, suggesting an abnormal XCI. Trimethylation of lysine 27 on histone 3 (H3K27me3) is significantly increased at bothXISTandKDM5Cgene loci. We found thatXISTandKDM5Cexpression can be used as a potential diagnostic hallmark for major psychiatric disorders in a large sub-population of female patients. Preliminary studies also suggest an increasedXISTexpression in postmortem brains from female patients with schizophrenia, bipolar disorder, and major depression. An increased gene dosage from some X-linked genes may contribute to the development of psychiatric disorders, as functional disomy of partial X chromosome have been suggested to cause mental retardation and other developmental abnormalities. Additionally, patients with Klinefelter syndrome (XXY) or Triple X syndrome (XXX) frequently display psychiatric disorders due to an extra X chromosome. Mutation of theKDM5Cgene was reported to cause X-linked syndromic mental retardation. Our studies suggest that abnormal X chromosome inactivation could play a causal role in development of major psychiatric disorders in females. Correction of abnormal X chromosome inactivation may prevent and/or cure major psychiatric disorders in a sub-population of female patients in the future.
Genetic and environmental exposures constrain epigenetic drift over the human life course
Authors: Shah Sonia , McRae Allan F. , Marioni Riccardo E. , Harris Sarah E. , Gibson Jude , Henders Anjali K. , Redmond Paul , Cox Simon R. , Pattie Alison , Corley Janie , Murphy Lee , Martin Nicholas G. , Montgomery Grant W. , Starr John M. , Wray Naomi R. , Deary Ian J. , Visscher Peter M.
Published: September 2014

Epigenetic mechanisms such as DNA methylation (DNAm) are essential for regulation of gene expression. DNAm is dynamic, influenced by both environmental and genetic factors. Epigenetic drift is the divergence of the epigenome as a function of age due to stochastic changes in methylation. Here we show that epigenetic drift may be constrained at many CpGs across the human genome by DNA sequence variation and by lifetime environmental exposures. We estimate repeatability of DNAm at 234,811 autosomal CpGs in whole blood using longitudinal data (2–3 repeated measurements) on 478 older people from two Scottish birth cohorts—the Lothian Birth Cohorts of 1921 and 1936. Median age was 79 yr and 70 yr, and the follow-up period was ∼10 yr and ∼6 yr, respectively. We compare this to methylation heritability estimated in the Brisbane Systems Genomics Study, a cross-sectional study of 117 families (offspring median age 13 yr; parent median age 46 yr). CpG repeatability in older people was highly correlated (0.68) with heritability estimated in younger people. Highly heritable sites had strong underlying cis-genetic effects. Thirty-seven and 1687 autosomal CpGs were associated with smoking and sex, respectively. Both sets were strongly enriched for high repeatability. Sex-associated CpGs were also strongly enriched for high heritability. Our results show that a large number of CpGs across the genome, as a result of environmental and/or genetic constraints, have stable DNAm variation over the human lifetime. Moreover, at a number of CpGs, most variation in the population is due to genetic factors, despite some sites being highly modifiable by the environment.
Rapid Identification of a Natural Knockout Allele of ARMADILLO REPEAT-CONTAINING KINESIN1 That Causes Root Hair Branching by Mapping-By-Sequencing
Authors: Rishmawi Louai , Sun Hequan , Schneeberger Korbinian , Hülskamp Martin , Schrader Andrea
Published: September 2014

In Arabidopsis (Arabidopsis thaliana), branched root hairs are an indicator of defects in root hair tip growth. Among 62 accessions, one accession (Heiligkreuztal2 [HKT2.4]) displayed branched root hairs, suggesting that this accession carries a mutation in a gene of importance for tip growth. We determined 200- to 300-kb mapping intervals using a mapping-by-sequencing approach of F2 pools from crossings of HKT2.4 with three different accessions. The intersection of these mapping intervals was 80 kb in size featuring not more than 36 HKT2.4-specific single nucleotide polymorphisms, only two of which changed the coding potential of genes. Among them, we identified the causative single nucleotide polymorphism changing a splicing site in ARMADILLO REPEAT-CONTAINING KINESIN1. The applied strategies have the potential to complement statistical methods in high-throughput phenotyping studies using different natural accessions to identify causative genes for distinct phenotypes represented by only one or a few accessions.
Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element
Authors: Narasimhan Kamesh , Hilbig Antonia , Udayasuryan Barath , Jayabal Sriram , Kolatkar Prasanna R. , Jauch Ralf
Published: September 2014

Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based onin vitrooptimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind their target DNA elements with different binding modes/topologies, however this hypothesis has not yet been structurally explored. One of the most extensively studied DNA target elements of the Pax6 paired domain is the eye-lens specific DC5 (δ-crystallin) enhancer element. In order to shed light on Pax6–DC5 DNA interactions, the related paired-domain prototype Pax9 was crystallized with the minimal δ-crystallin DC5 enhancer element and preliminary X-ray diffraction analysis was attempted. A 3.0 Å resolution native data set was collected at the National Synchrotron Light Source (NSLS), Brookhaven from crystals grown in a solution consisting of 10%(w/v) PEG 20K, 20%(v/v) PEG 550 MME, 0.03 MNaNO3, 0.03 MNa2HPO4, 0.03 MNH2SO4, 0.1 MMES/imidazole pH 6.5. The data set was indexed and merged in space groupC2221, with unit-cell parametersa= 75.74,b= 165.59,c= 70.14 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of one Pax9 paired domain bound to duplex DNA in the asymmetric unit.
Human carbonic anhydrase II–cyanate inhibitor complex: putting the debate to rest
Authors: West Dayne , Pinard Melissa A. , Tu Chingkuang , Silverman David N. , McKenna Robert
Published: September 2014

The binding of anions to carbonic anhydrase II (CA II) has been attributed to high affinity for the active-site zinc. An anion of interest is cyanate, for which contrasting binding modes have been reported in the literature. Previous spectroscopic data have shown cyanate behaving as an inhibitor, directly binding to the zinc, in contrast to previous crystallographic data that implied that cyanate acts as a substrate mimic that is not directly bound to the zinc but overlaps with the binding site of the substrate CO2. Wild-type and the V207I variant of CA II have been expressed and X-ray crystal structures of their cyanate complexes have been determined to 1.7 and 1.5 Å resolution, respectively. The rationale for the V207I CA II variant was its close proximity to the CO2-binding site. Both structures clearly show that the cyanate binds directly to the zinc. In addition, inhibition constants (∼40 µM) were measured using18O-exchange mass spectrometry for wild-type and V207I CA II and were similar to those determined previously (Supuranet al., 1997). Hence, it is concluded that under the conditions of these experiments the binding of cyanate to CA II is directly to the zinc, displacing the zinc-bound solvent molecule, and not in a site that overlaps with the CO2substrate-binding site.
Crystallization and preliminary X-ray diffraction analysis of the BRPF1 bromodomain in complex with its H2AK5ac and H4K12ac histone-peptide ligands
Authors: Lubula Mulu Y. , Poplawaski Amanda , Glass Karen C.
Published: September 2014

The bromodomain-PHD finger protein 1 (BRPF1) is an essential subunit of the monocytic leukemia zinc (MOZ) histone acetyltransferase (HAT) complex and is required for complex formation and enzymatic activation. BRPF1 contains a structurally conserved bromodomain, which recognizes specific acetyllysine residues on histone proteins. The MOZ HAT plays a direct role in hematopoiesis, and deregulation of its activity is linked to the development of acute myeloid leukemia. However, the molecular mechanism of histone-ligand recognition by the BRPF1 bromodomain is currently unknown. The 117-amino-acid BRPF1 bromodomain was overexpressed inEscherichia coliand purified to homogeneity. Crystallization experiments of the BRPF1 bromodomain in complex with its H4K12ac and H2AK5ac histone ligands yielded crystals that were suitable for high-resolution X-ray diffraction analysis. The BRPF1 bromodomain–H4K12ac crystals belonged to the tetragonal space groupP43212, with unit-cell parametersa= 75.1,b= 75.1,c= 86.3 Å, and diffracted to a resolution of 1.94 Å. The BRPF1 bromodomain–H2AK5ac crystals grew in the monoclinic space groupP21, with unit-cell parametersa= 60.9,b= 55.6,c= 82.1 Å, β = 93.6°, and diffracted to a resolution of 1.80 Å. Complete data sets were collected from both crystal forms using synchrotron radiation on beamline X29 at Brookhaven National Laboratory (BNL).
Crystallization and preliminary X-ray diffraction analyses of the redox-controlled complex of terminal oxygenase and ferredoxin components in the Rieske nonhaem iron oxygenase carbazole 1,9a-dioxygenase
Authors: Matsuzawa Jun , Aikawa Hiroki , Umeda Takashi , Ashikawa Yuji , Suzuki-Minakuchi Chiho , Kawano Yoshiaki , Fujimoto Zui , Okada Kazunori , Yamane Hisakazu , Nojiri Hideaki
Published: September 2014

The initial reaction in bacterial carbazole degradation is catalyzed by carbazole 1,9a-dioxygenase, which consists of terminal oxygenase (Oxy), ferredoxin (Fd) and ferredoxin reductase components. The electron-transfer complex between reduced Oxy and oxidized Fd was crystallized at 293 K using the hanging-drop vapour-diffusion method with PEG 3350 as the precipitant under anaerobic conditions. The crystal diffracted to a maximum resolution of 2.25 Å and belonged to space groupP21, with unit-cell parametersa= 97.3,b= 81.6,c= 116.2 Å, α = γ = 90, β = 100.1°. TheVMvalue is 2.85 Å3 Da−1, indicating a solvent content of 56.8%.
Crystallization and preliminary X-ray diffraction analysis of cyclolavandulyl diphosphate synthase, a new member of thecis-isoprenyl diphosphate synthase superfamily
Authors: Tomita Takeo , Ozaki Taro , Matsuda Kenichi , Nishiyama Makoto , Kuzuyama Tomohisa
Published: September 2014

Cyclolavandulyl diphosphate synthase (CLDS; estimated molecular weight 23.1 kDa) from the soil bacteriumStreptomycessp. CL190 is an enzyme that catalyzes both the condensation of two molecules of C5dimethylallyl diphosphate (DMAPP) and the subsequent cyclization. CLDS was crystallized in the absence and the presence of the substrate DMAPP. Diffraction data were collected at a synchrotron source and the crystals diffracted to 2.00 and 1.73 Å resolution, respectively. The crystal obtained in the absence of DMAPP belonged to space groupP212121, with unit-cell parametersa= 39.0,b= 87.5,c= 113.6 Å. The crystal obtained in the presence of DMAPP belonged to space groupP1, with unit-cell parametersa= 46.9,b= 61.7,c= 82.2 Å, α = 74.0, β = 84.5, γ = 86.0°.
Enhancing ubiquitin crystallization through surface-entropy reduction
Authors: Loll Patrick J. , Xu Peining , Schmidt John T. , Melideo Scott L.
Published: September 2014

Ubiquitin has many attributes suitable for a crystallization chaperone, including high stability and ease of expression. However, ubiquitin contains a high surface density of lysine residues and the doctrine of surface-entropy reduction suggests that these lysines will resist participating in packing interactions and thereby impede crystallization. To assess the contributions of these residues to crystallization behavior, each of the seven lysines of ubiquitin was mutated to serine and the corresponding single-site mutant proteins were expressed and purified. The behavior of these seven mutants was then compared with that of the wild-type protein in a 384-condition crystallization screen. The likelihood of obtaining crystals varied by two orders of magnitude within this set of eight proteins. Some mutants crystallized much more readily than the wild type, while others crystallized less readily. X-ray crystal structures were determined for three readily crystallized variants: K11S, K33S and the K11S/K63S double mutant. These structures revealed that the mutant serine residues can directly promote crystallization by participating in favorable packing interactions; the mutations can also exert permissive effects, wherein crystallization appears to be driven by removal of the lysine rather than by addition of a serine. Presumably, such permissive effects reflect the elimination of steric and electrostatic barriers to crystallization.