bluuebunny/crossref_metadata_2025 huggingface dataset:
Shock interaction with one-dimensional array of particles in air
Authors: Sridharan P. , Jackson T. L. , Zhang J. , Balachandar S.
Published: February 2015

In this paper, we present axisymmetric numerical simulations of shock propagation in air over an aluminum particle for Mach numbers up to 10. The numerical method is a finite-volume based solver on a Cartesian grid that allows for multi-material interfaces and shocks. Validation of the solver is demonstrated by comparing to existing experimental data. We compute the unsteady inviscid drag coefficient as a function of time, and show that when normalized by post-shock conditions, the maximum drag coefficient decreases with Mach number. Furthermore, for supercritical Mach numbers, we show that the inviscid steady-state drag asymptotes to a non-zero value due to the presence of a bow shock formed just upstream of the particle. Using this information, we also present a simplified point-particle force model that can be used for mesoscale simulations. Finally, we investigate the dynamics of a shock propagating over a 1-D array of particles aligned in the flow direction. We show that the maximum drag coefficient increases as the shock travels deep into the array and then asymptotes to a final value, which can be as high as 50% more than that of the first particle, depending on Mach number and particle spacing.
A study of magnetic ordering in multiferroic hexagonal Ho1-xDyxMnO3
Authors: Magesh J. , Murugavel P. , Krishnamurthy J. , Adyam V. , Prellier W.
Published: February 2015

This paper investigates the magnetic properties of Ho1-xDyxMnO3 by considering the inter-planar Mn3+-O-O-Mn3+ interaction. The theoretical analysis shows that the asymmetric in-plane exchange interaction couples the in-plane and inter-planar Mn3+ spin structures via asymmetry parameter δ. This leads to the existence of both the in-plane and inter-planar ordering, which in turn restricted the allowed magnetic space groups to Γ1 and Γ4. The experimental studies confirmed the concomitant nature of the in-plane and the inter-planar ordering at TN, TSR, and T2. It also showed that the magnetic phase diagram is dominated by the allowed magnetic structures Γ1 and Γ4. Furthermore, an effort is made to resolve the inconsistency regarding the TSR (32 or 40 K). The studies revealed that the antiferromagnetic inter-planar interaction is switched to the ferromagnetic interaction (40 K) upon cooling, which in turn drives the spin reorientation at 32 K. The Mn3+ spin structure is seen to be coupled to rare earth sub-lattice through the modulation of the inter-planar interaction.
Experimental realization of broadband acoustic omnidirectional absorber by homogeneous anisotropic metamaterials
Authors: Gu Zhong-ming , Xue-Jiang  , Liang Bin , Li Yong , Zou Xin-ye , Yin Lei-lei , Cheng Jian-chun
Published: February 2015

We design a two-dimensional broadband acoustic omnidirectional absorber (AOA) simply comprising homogeneous anisotropic metamaterials to enlarge the absorption cross-section of a smaller core with matched acoustic impedance as the previous AOAs do, which generally involve complicated design of gradient-index or negative-index materials. Furthermore, AOAs with asymmetric/large geometrics can be realized conveniently, which will otherwise require a complex redesign of parameters. The proposed scheme is also extendable to three-dimensional cases. An implementation using angularly distributed fins was demonstrated experimentally, showing the broadband functionality of the designed absorber. Such metamaterial-based acoustic absorbers may have potential applications in various fields such as acoustic energy concentration, noise control, etc.
Properties of surface modes in one dimensional plasma photonic crystals
Authors: Shukla S. , Prasad S. , Singh V.
Published: February 2015

Properties of surface modes supported at the interface of air and a semi-infinite one dimensional plasma photonic crystal are analyzed. The surface mode equation is obtained by using transfer matrix method and applying continuity conditions of electric fields and its derivatives at the interface. It is observed that with increase in the width of cap layer, frequencies of surface modes are shifted towards lower frequency side, whereas increase in tangential component of wave-vector increases the mode frequency and total energy carried by the surface modes. With increase in plasma frequency, surface modes are found to shift towards higher frequency side. The group velocity along interface is found to control by cap layer thickness.
Electron density modification in ionospheric E layer by inserting fine dust particles
Authors: Misra Shikha , Mishra S. K.
Published: February 2015

In this paper, we have developed the kinetics of E-region ionospheric plasma comprising of fine dust grains and shown that the electron density in E-layer can purposely be reduced/enhanced up to desired level by inserting fine dust particles of appropriate physical/material properties; this may certainly be promising for preferred rf-signal processing through these layers. The analytical formulation is based on average charge theory and includes the number and energy balance of the plasma constituents along with charge balance over dust particles. The effect of varying number density, work function, and photo-efficiency of dust particles on ionospheric plasma density at different altitude in E-layer has been critically examined and presented graphically.
Layer resolved magnetic domain imaging of epitaxial heterostructures in large applied magnetic fields
Authors: Zohar S. , Choi Y. , Love D. M. , Mansell R. , Barnes C. H. W. , Keavney D. J. , Rosenberg R. A.
Published: February 2015

We use X-ray Excited Luminescence Microscopy to investigate the elemental and layer resolved magnetic reversal in an interlayer exchange coupled (IEC) epitaxial Fe/Cr wedge/Co heterostructure. The transition from strongly coupled parallel Co-Fe reversal for Cr thickness tCr < 0.34 nm to weakly coupled layer independent reversal for tCr > 1.5 nm is punctuated at 0.34 < tCr < 1.5 nm by a combination of IEC guided domain wall motion and stationary zig zag domain walls. Domain walls nucleated at switching field minima are guided by IEC spatial gradients and collapse at switching field maxima.
The history of wildlife camera trapping as a survey tool in Australia
Authors: Meek Paul D. , Ballard Guy-Anthony , Vernes Karl , Fleming Peter J. S.
Published: February 2015

This paper provides an historical review of the technological evolution of camera trapping as a zoological survey tool in Australia. Camera trapping in Australia began in the 1950s when purpose-built remotely placed cameras were used in attempts to rediscover the thylacine (Thylacinus cynocephalus). However, camera traps did not appear in Australian research papers and Australasian conference proceedings until 1989–91, and usage became common only after 2008, with an exponential increase in usage since 2010. Initially, Australian publications under-reported camera trapping methods, often failing to provide fundamental details about deployment and use. However, rigour in reporting of key methods has increased during the recent widespread adoption of camera trapping. Our analysis also reveals a change in camera trap use in Australia, from simple presence–absence studies, to more theoretical and experimental approaches related to population ecology, behavioural ecology, conservation biology and wildlife management. Practitioners require further research to refine and standardise camera trap methods to ensure that unbiased and scientifically rigorous data are obtained from quantitative research. The recent change in emphasis of camera trapping research use is reflected in the decreasing range of camera trap models being used in Australian research. Practitioners are moving away from less effective models that have slow reaction times between detection and image capture, and inherent bias in detectability of fauna, to more expensive brands that offer faster speeds, greater functionality and more reliability.
Making a killing: photographic evidence of predation of a Tasmanian pademelon (Thylogale billardierii) by a feral cat (Felis catus)
Authors: Fancourt Bronwyn A.
Published: February 2015

Feral cats (Felis catus) have contributed to the extinction of numerous Australian mammals and are a major threat to many species of conservation significance. Small mammals are considered to be those at greatest risk of cat predation, with risk typically inferred from dietary studies. However, dietary studies may provide only weak inference as to the risk of cat predation for some species. The most compelling evidence of predation risk comes from direct observation of killing events; however, such observations are rare and photographic evidence is even rarer. I present photographic evidence of a feral cat killing and consuming an adult female Tasmanian pademelon (Thylogale billardierii). This observation provides direct evidence that feral cats can kill prey up to 4 kg in body mass, with potential implications for the conservation of medium-sized mammals.
Bayesian analysis of direct and maternal effects for birthweight in Iranian buffaloes using Gibbs sampling
Authors: Ghavi Hossein-Zadeh Navid
Published: February 2015

Calving records from April 1994 to March 2010 comprising 8570 calving events from the first three parities of 734 buffalo herds of Iran were analysed using a linear animal model to estimate variance components and heritability for birthweight. A linear animal model including direct and maternal genetic effects with covariance between them and maternal permanent environmental effect was implemented by Gibbs sampling methodology. A single Gibbs sampling chain with 500 000 rounds was generated by the Threshold Model program. Posterior means of direct and maternal heritabilities and repeatability for birthweight were 0.21, 0.15 and 0.23, respectively. Estimate of correlation between direct and maternal genetic effects for birthweight was –0.71. Also, the ratio of permanent environmental variance to phenotypic variance was 0.02. Along with the direct genetic effects, the contribution of maternal effects to the phenotypic variance of birthweight may provide producers with information to optimally use the reported estimates when making selection decisions. The results of this study indicated that exploitable genetic variation observed for birthweight could be considered in designing future selection programs for Iranian buffaloes and improvement in birthweight could be attained by genetic selection.
Are shrubs really a sign of declining ecosystem function? Disentangling the myths and truths of woody encroachment in Australia
Authors: Eldridge David J. , Soliveres Santiago
Published: February 2015

Since European settlement, there has been a dramatic increase in the density, cover and distribution of woody plants in former grassland and open woodland. There is a widespread belief that shrub encroachment is synonymous with declines in ecosystem functions, and often it is associated with landscape degradation or desertification. Indeed, this decline in ecosystem functioning is considered to be driven largely by the presence of the shrubs themselves. This prevailing paradigm has been the basis for an extensive program of shrub removal, based on the view that it is necessary to reinstate the original open woodland or grassland structure from which shrublands are thought to have been derived. We review existing scientific evidence, particularly focussed on eastern Australia, to question the notion that shrub encroachment leads to declines in ecosystem functions. We then summarise this scientific evidence into two conceptual models aimed at optimising landscape management to maximise the services provided by shrub-encroached areas. The first model seeks to reconcile the apparent conflicts between the patch- and landscape-level effects of shrubs. The second model identifies the ecosystem services derived from different stages of shrub encroachment. We also examined six ecosystem services provided by shrublands (biodiversity, soil C, hydrology, nutrient provision, grass growth and soil fertility) by using published and unpublished data. We demonstrated the following: (1) shrub effects on ecosystems are strongly scale-, species- and environment-dependent and, therefore, no standardised management should be applied to every case; (2) overgrazing dampens the generally positive effect of shrubs, leading to the misleading relationship between encroachment and degradation; (3) woody encroachment per se does not hinder any of the functions or services described above, rather it enhances many of them; (4) no single shrub-encroachment state (including grasslands without shrubs) will maximise all services; rather, the provision of ecosystem goods and services by shrublands requires a mixture of different states; and (5) there has been little rigorous assessment of the long-term effectiveness of removal and no evidence that this improves land condition in most cases. Our review provides the basis for an improved, scientifically based understanding and management of shrublands, so as to balance the competing goals of providing functional habitats, maintaining soil processes and sustaining pastoral livelihoods.
Analysis of nutrient use efficiency (NUE) in Eucalyptus pilularis forests
Authors: Turner John , Lambert Marcia J.
Published: February 2015

Alternative indices to use for nutrient use efficiency (NUE) were analysed for nitrogen, phosphorus, potassium, calcium, magnesium and sulfur, using 17 Eucalyptus pilularis forest sites to test the hypothesis that NUE increases with decreasing nutrient availability. Reported indices represent different measures of nutrient use, including (1) efficiency of acquisition from soil, (2) quantities required for organic matter production, (3) organic matter production related to uptake, (4) ability to internally retranslocate nutrients and (5) physiological requirement of nutrients. Some indices are highly correlated but the highest correlations were according to age. Phosphorus, the main growth-limiting nutrient, on average, produced 6.5 and 10.9 t of organic matter per kilogram of phosphorus required and taken up from soil, respectively. Comparable estimates were made for other nutrients. NUEs of mobile nutrients increased with decreases in nutrient availability and this supported the hypotheses when age was taken into account. The NUEs of one nutrient are not independent of other nutrients. The inverse of foliage nutrient concentration is a valuable low-cost index of nutrient utilisation and correlates with net primary production/nutrient requirement, and is related to age. Resorption of nutrients, comparing new and abscised tissue, was of low value, but abscised-tissue nutrient correlations are related to a lower benchmark and are of value. The use of selected NUE indices for species comparison was discussed.
Proliferation and harvesting of secondary protocorms as a novel means for improving propagation of terrestrial orchids
Authors: Bustam Betty Mauliya , Dixon Kingsley , Bunn Eric
Published: February 2015

This study investigated optimisation of media and primary-protocorm development stages to enhance secondary-protocorm production as a novel means for propagation of terrestrial orchids, including taxa of conservation concern. Seeds of Caladenia latifolia were germinated asymbiotically on ½-strength Murashige and Skoog (MS) medium fortified with 5% (v/v) coconut water. Resulting protocorms at 3, 5 and 7 weeks of growth were subcultured to protocorm-proliferation media treatments consisting of ½-strength MS basal-salts medium with 6-benzylaminopurine (BA) and α- naphthaleneacetic acid (NAA) singly or in combination. Conversion of seeds to primary protocorms was high (87–92%). The highest percentage of secondary-protocorm proliferation was 40.1%, using 5-week-old protocorms (early Stage 4 of protocorm development) as explants and cultured on ½-strength MS with a combination of 5 µM NAA + 2 µM BA. Half-strength MS media containing a single plant-growth regulator (BA or NAA) were substantially less effective (<10% protocorm proliferation). The present study has provided a novel approach to sequential protocorm production that will be of value particularly for threatened orchids with limited seed availability. Protocorm proliferation in vitro enables a renewable supply of protocorms with which to conduct propagation, cryostorage and pilot restoration programs.
Effects of benthic substrate, nutrient enrichment and predatory fish on freshwater crayfish (kōura, Paranephrops planifrons) population characteristics in seven Te Arawa (Rotorua) lakes, North Island, New Zealand
Authors: Kusabs I. A. , Quinn J. M. , Hamilton D. P.
Published: February 2015

Populations of kōura, or freshwater crayfish (Paranephrops planifrons White, 1842), were quantified along a eutrophication gradient in seven Te Arawa lakes using the tau kōura, a traditional Māori harvesting method, in April, July and November 2009. Six of the seven lakes contained kōura. No kōura were captured in hypertrophic Lake Ōkaro. Kōura catches were highly variable and mean catch per unit effort (CPUE) varied from 1.5 to 99.3kōura per whakaweku (fern bundle) in the six lakes with kōura present. The highest abundance of kōura was recorded in eutrophic Lake Rotorua and the highest biomass in oligotrophic Lake Rotomā. Kōura orbit carapace length (OCL) ranged from 6 to 52mm, with the largest kōura recorded in lakes Rotoiti and Rotomā. Our results suggest that benthic substrate is more important in determining kōura population abundance than nutrient enrichment (using chlorophyll-a as a proxy) or predatory fish (rainbow trout abundance). Nevertheless, lake trophic status in conjunction with lake morphology appeared to indirectly affect kōura distribution in the sheltered, steep-sided lakes, through hypolimnetic deoxygenation.
Food deprivation and social inequality may lead to oxidative damage: a study on the preventive role of melatonin in the male rat reproductive system
Authors: Nasiraei-Moghadam Shiva , Parivar Kazem , Ahmadiani Abolhasan , Movahhedin Mansoureh , Mahdavi Mohammad-Reza Vaez
Published: February 2015

Spermatogenic cells are susceptible to oxidative stress and apoptosis. Food deprivation (FD) has been reported as a stressor that could increase reactive oxygen species. In the present study, FD-induced oxidative stress and apoptosis, as well as the protective effects of melatonin, were evaluated in the testes. Wistar rats in the control group were fed a standard diet, whereas a sham group was administered saline as the melatonin vehicle. A third group received daily injections of melatonin (5 mg kg–1 bodyweight). These rats were further divided into four groups of rats that were either subjected to FD, FD + isolation, FD + melatonin injection and FD + melatonin injection + isolation. Testicular tissues were evaluated for malondialdehyde (MDA) and reduced glutathione (GSH) concentrations, as well as and DNA damage. FD increased MDA and reduced GSH concentrations, whereas melatonin treatment improved these parameters. Immunohistochemistry for capsase-3 and terminal deoxyribonucleotidyl transferase-mediated dUTP–digoxigenin nick end-labelling revealed that the number of apoptotic cells was increased in rats subjected to FD alone. Melatonin treatment offset the number of apoptotic cells following FD. The results provide evidence that FD can increase oxidative stress, leading to activation of apoptosis, and that melatonin has the ability to protect the testes against oxidative damage induced by FD.
Maternal control of early embryogenesis in mammals
Authors: Zhang Kun , Smith George W.
Published: February 2015

Oocyte quality is a critical factor limiting the efficiency of assisted reproductive technologies (ART) and pregnancy success in farm animals and humans. ART success is diminished with increased maternal age, suggesting a close link between poor oocyte quality and ovarian aging. However, the regulation of oocyte quality remains poorly understood. Oocyte quality is functionally linked to ART success because the maternal-to-embryonic transition (MET) is dependent on stored maternal factors, which are accumulated in oocytes during oocyte development and growth. The MET consists of critical developmental processes, including maternal RNA depletion and embryonic genome activation. In recent years, key maternal proteins encoded by maternal-effect genes have been determined, primarily using genetically modified mouse models. These proteins are implicated in various aspects of early embryonic development, including maternal mRNA degradation, epigenetic reprogramming, signal transduction, protein translation and initiation of embryonic genome activation. Species differences exist in the number of cell divisions encompassing the MET and maternal-effect genes controlling this developmental window. Perturbations of maternal control, some of which are associated with ovarian aging, result in decreased oocyte quality.
Gα
i/o
-coupled receptor signaling restricts pancreatic β-cell expansion
Authors: Berger Miles , Scheel David W. , Macias Hector , Miyatsuka Takeshi , Kim Hail , Hoang Phuong , Ku Greg M. , Honig Gerard , Liou Angela , Tang Yunshuo , Regard Jean B. , Sharifnia Panid , Yu Lisa , Wang Juehu , Coughlin Shaun R. , Conklin Bruce R. , Deneris Evan S. , Tecott Laurence H. , German Michael S.
Published: February 2015

Significance

This paper shows that a class of receptors known to modulate insulin release by pancreatic β cells also regulates the proliferation of these cells and restrains the perinatal β-cell expansion that establishes adult β-cell mass, suggesting that alterations in signaling by these receptors could contribute to the decreased β-cell numbers seen in patients with type 2 diabetes. Further, inhibition of signaling through these receptors potentially could be used to generate more β cells for people with diabetes.
Mechanistic links between cellular trade-offs, gene expression, and growth
Authors: Weiße Andrea Y. , Oyarzún Diego A. , Danos Vincent , Swain Peter S.
Published: February 2015

Significance

Cells have finite resources. Committing resources to one task therefore reduces the amount of resources available to others. These trade-offs are often overlooked but potentially modify all cellular processes. Building a mathematical cell model that respects such trade-offs and describes the mechanisms of protein synthesis and how cells extract resources from their environment, we quantitatively recover the typical behavior of an individual growing cell and of a population of cells. As trade-offs are experienced by all cells and because growth largely determines cellular fitness, a predictive understanding of how biochemical processes affect others and affect growth is important for diverse applications, such as the use of microbes for biotechnology, the inhibition of antibiotic resistance, and the growth of cancers.
Structure of a left-handed DNA G-quadruplex
Authors: Chung Wan Jun , Heddi Brahim , Schmitt Emmanuelle , Lim Kah Wai , Mechulam Yves , Phan Anh Tuân
Published: February 2015

Significance

DNA can adopt diverse structural conformations including duplexes, triplexes, and quadruplexes. Four-stranded structures known as G-quadruplexes have been implicated in cellular processes and found potential applications in therapeutics and nanotechnology. G-quadruplex structures are highly polymorphic, but so far, only right-handed helical forms have been observed. Here we present the NMR solution and X-ray crystal structures of an unprecedented left-handed DNA G-quadruplex, containing structural features that can be exploited as unique recognition elements.
Judicial Selection and the Democratization of Justice
Authors: Driscoll Amanda , Nelson Michael J.
Published: February 2015

In 2011, Bolivia became the first modern country to directly elect national judges. Reformers heralded the adoption of judicial elections as a “democratization of justice,” by which institutional independence would be assured, public confidence in the judiciary might be expanded, and various maladies of the judicial system would find resolution. We evaluate the elections in light of these objectives. We show candidates were advantaged when voters shared their partisan and demographic traits, resulting in unprecedented diversity on the national courts. Also, public confidence in the judiciary increased among government supporters but declined overall. We offer preliminary reflections for would-be reformers.
When Judging Is Power
Authors: Remiche Adélaïde
Published: February 2015

This article examines the feminization of the judiciary in France and in the United States through the prism of the “imagined judge,” that is, the judge as he or she is represented in a specific legal culture. The French imagined judge is a knowledgeable automaton mechanically applying the law entirely created by the parliament, while his or her American counterpart is a decision maker well equipped to solve social problems. Interpreting the gender composition of the judiciary through the intellectual device of the imagined judge leads to a crucial observation: there is a correlation between the conceptualization of the imagined judge as a being exercising power, as in the United States, and the continued underrepresentation of women on the bench. From this observation comes an important hypothesis: the conceptualization of judging as an act of power works to keep women off the bench.prism
Judicial Contributions to US National Policy Change since 1945
Authors: Grossmann Matt , Swedlow Brendon
Published: February 2015

How often, at what times, and on what issues do courts directly make policy or indirectly influence policy making by other branches of government? We assess the judicial contribution to policy change using 268 policy histories covering 14 issue areas of US domestic policy making from 1945 to 2004. Contrary to the prominent view that courts are relatively inconsequential policy-making institutions, we find that federal courts made or influenced nearly one in four significant federal policy changes. Courts directly made almost as many significant policies as the executive branch and indirectly influenced about as many significant policies in other branches as Congress. We also find that judicial policy making and influence are concentrated in a few time periods and issue areas.
Uniqueness of the fixed point of nonexpansive semidifferentiable maps
Authors: Akian Marianne , Gaubert Stéphane , Nussbaum Roger
Published: February 2015

We consider semidifferentiable (possibly nonsmooth) maps, acting on a subset of a Banach space, that are nonexpansive either in the norm of the space or in Hilbert’s or Thompson’s metric inherited from a convex cone. We show that the global uniqueness of the fixed point of the map, as well as the geometric convergence of every orbit to this fixed point, can be inferred from the semidifferential of the map at this point. In particular, we show that the geometric convergence rate of the orbits to the fixed point can be bounded in terms of Bonsall’s nonlinear spectral radius of the semidifferential. We derive similar results concerning the uniqueness of the eigenline and the geometric convergence of the orbits to it, in the case of positively homogeneous maps acting on the interior of a cone, or of additively homogeneous maps acting on an AM-space with unit. This is motivated in particular by the analysis of dynamic programming operators (Shapley operators) of zero-sum stochastic games.
Weighted local estimates for singular integral operators
Authors: Poelhuis Jonathan , Torchinsky Alberto
Published: February 2015

A local median decomposition is used to prove that a weighted mean of a function is controlled locally by the weighted mean of its local sharp maximal function. Together with the estimate

M

0
,
s

♯

(
T
f
)
(
x
)
≤
c

M
f
(
x
)

M^{\sharp }_{0,s}(Tf)(x) \le c\,Mf(x)

for Calderón-Zygmund singular integral operators, this allows us to express the local weighted control of

T
f

Tf

by

M
f

Mf

. Similar estimates hold for

T
T

replaced by singular integrals with kernels satisfying Hörmander-type conditions or integral operators with homogeneous kernels, and

M
M

replaced by an appropriate maximal function

M
T

M_T

. Using sharper bounds in the local median decomposition we prove two-weight,

L
v
p

−

L
w
q

L^p_v-L^q_w

estimates for the singular integral operators described above for

1
>
p
≤
q
>
∞

1>p\le q>\infty

and a range of

q
q

. The local nature of the estimates leads to results involving weighted generalized Orlicz-Campanato and Orlicz-Morrey spaces.
Specific interaction with the nuclear transporter importin α2 can modulate paraspeckle protein 1 delivery to nuclear paraspeckles
Authors: Major Andrew T. , Hogarth Cathryn A. , Miyamoto Yoichi , Sarraj Mai A. , Smith Catherine L. , Koopman Peter , Kurihara Yasuyuki , Jans David A. , Loveland Kate L.
Published: February 2015

Importin (IMP) superfamily members mediate regulated nucleocytoplasmic transport, which is central to key cellular processes. Although individual IMPα proteins exhibit dynamic synthesis and subcellular localization during cellular differentiation, including during spermatogenesis, little is known of how this affects cell fate. To investigate how IMPαs control cellular development, we conducted a yeast two-hybrid screen for IMPα2 cargoes in embryonic day 12.5 mouse testis, a site of peak IMPα2 expression coincident with germ-line masculization. We identified paraspeckle protein 1 (PSPC1), the original defining component of nuclear paraspeckles, as an IMPα2-binding partner. PSPC1-IMPα2 binding in testis was confirmed in immunoprecipitations and pull downs, and an enzyme-linked immunosorbent assay–based assay demonstrated direct, high-affinity PSPC1 binding to either IMPα2/IMPβ1 or IMPα6/IMPβ1. Coexpression of full-length PSPC1 and IMPα2 in HeLa cells yielded increased PSPC1 localization in nuclear paraspeckles. High-throughput image analysis of >3500 cells indicated IMPα2 levels can directly determine PSPC1-positive nuclear speckle numbers and size; a transport-deficient IMPα2 isoform or small interfering RNA knockdown of IMPα2 each reduced endogenous PSPC1 accumulation in speckles. This first validation of an IMPα2 nuclear import cargo in fetal testis provides novel evidence that PSPC1 delivery to paraspeckles, and consequently paraspeckle function, may be controlled by modulated synthesis of specific IMPs.
Mitotic entry in the presence of DNA damage is a widespread property of aneuploidy in yeast
Authors: Blank Heidi M. , Sheltzer Jason M. , Meehl Colleen M. , Amon Angelika
Published: February 2015

Genetic instability is a hallmark of aneuploidy in budding and fission yeast. All aneuploid yeast strains analyzed to date harbor elevated levels of Rad52-GFP foci, a sign of DNA damage. Here we investigate how continuously elevated levels of DNA damage affect aneuploid cells. We show that Rad52-GFP foci form during S phase, consistent with the observation that DNA replication initiation and elongation are impaired in some aneuploid yeast strains. We furthermore find that although DNA damage is low in aneuploid cells, it nevertheless has dramatic consequences. Many aneuploid yeast strains adapt to DNA damage and undergo mitosis despite the presence of unrepaired DNA leading to cell death. Wild-type cells exposed to low levels of DNA damage exhibit a similar phenotype, indicating that adaptation to low levels of unrepaired DNA is a general property of the cell's response to DNA damage. Our results indicate that by causing low levels of DNA damage, whole-chromosome aneuploidies lead to DNA breaks that persist into mitosis. Such breaks provide the substrate for translocations and deletions that are a hallmark of cancer.
The microtubule cross-linker Feo controls the midzone stability, motor composition, and elongation of the anaphase B spindle inDrosophilaembryos
Authors: Wang Haifeng , Brust-Mascher Ingrid , Scholey Jonathan M.
Published: February 2015

Chromosome segregation during anaphase depends on chromosome-to-pole motility and pole-to-pole separation. We propose that in Drosophila embryos, the latter process (anaphase B) depends on a persistent kinesin-5–generated interpolar (ip) microtubule (MT) sliding filament mechanism that “engages” to push apart the spindle poles when poleward flux is turned off. Here we investigated the contribution of the midzonal, antiparallel MT-cross-linking nonmotor MAP, Feo, to this “slide-and-flux-or-elongate” mechanism. Whereas Feo homologues in other systems enhance the midzone localization of the MT-MT cross-linking motors kinesin-4, -5 and -6, the midzone localization of these motors is respectively enhanced, reduced, and unaffected by Feo. Strikingly, kinesin-5 localizes all along ipMTs of the anaphase B spindle in the presence of Feo, including at the midzone, but the antibody-induced dissociation of Feo increases kinesin-5 association with the midzone, which becomes abnormally narrow, leading to impaired anaphase B and incomplete chromosome segregation. Thus, although Feo and kinesin-5 both preferentially cross-link MTs into antiparallel polarity patterns, kinesin-5 cannot substitute for loss of Feo function. We propose that Feo controls the organization, stability, and motor composition of antiparallel ipMTs at the midzone, thereby facilitating the kinesin-5–driven sliding filament mechanism underlying proper anaphase B spindle elongation and chromosome segregation.
A novel statistical method for quantitative comparison of multiple ChIP-seq datasets
Authors: Chen Li , Wang Chi , Qin Zhaohui S. , Wu Hao
Published: February 2015

Motivation: ChIP-seq is a powerful technology to measure the protein binding or histone modification strength in the whole genome scale. Although there are a number of methods available for single ChIP-seq data analysis (e.g. ‘peak detection’), rigorous statistical method for quantitative comparison of multiple ChIP-seq datasets with the considerations of data from control experiment, signal to noise ratios, biological variations and multiple-factor experimental designs is under-developed.

Results: In this work, we develop a statistical method to perform quantitative comparison of multiple ChIP-seq datasets and detect genomic regions showing differential protein binding or histone modification. We first detect peaks from all datasets and then union them to form a single set of candidate regions. The read counts from IP experiment at the candidate regions are assumed to follow Poisson distribution. The underlying Poisson rates are modeled as an experiment-specific function of artifacts and biological signals. We then obtain the estimated biological signals and compare them through the hypothesis testing procedure in a linear model framework. Simulations and real data analyses demonstrate that the proposed method provides more accurate and robust results compared with existing ones.

Availability and implementation: An R software package ChIPComp is freely available at http://web1.sph.emory.edu/users/hwu30/software/ChIPComp.html.

Contact:  hao.wu@emory.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Testing a passive deterrent on longlines to reduce sperm whale depredation in the Gulf of Alaska
Authors: O'Connell Victoria , Straley Janice , Liddle Joe , Wild Lauren , Behnken Linda , Falvey Dan , Thode Aaron
Published: February 2015

In Alaska, sperm whale (Physeter macrocephalus) depredation on longline sets has increased since implementation of the Individual Fishing Quota programme in 1995. A collaborative effort (SEASWAP) between longliners, scientists, and managers has undertaken research to evaluate this depredation with a primary objective to develop and test a passive deterrent that would reduce depredation without reducing catch rate of sablefish (Anoplopoma fimbria). Commercial longliners, fishing for their own sablefish quotas during the regular season, deployed beaded gear (25 mm lucite beads attached to gangions) with control gear and set recorders to collect acoustic data. Beaded and control gear were randomly assigned by skate quad (672 hooks) with 5 quads in each longline set. Acoustic recorders were used to document sperm whale creak–pause events, representative of depredation of the longline gear. Although there were more sablefish per skate quad on the beaded gear and there was a decrease in depredation events on the beaded gear compared with the control, neither effect was significant (p = 0.205 and 0.364, respectively). The SEASWAP project is testing other deterrent strategies including gear modifications and the establishment of a sighting network to improve avoidance.
A barrier to gene flow in the Asian paddle crab, Charybdis japonica, in the Yellow Sea
Authors: Han Zhiqiang , Zheng Wei , Zhu Wenbin , Yu Cungen , Shui Bonian , Gao Tianxiang
Published: February 2015

Three primary factors affecting genetic patterns of marine species in the Northwestern Pacific Ocean have been proposed: isolation and population expansion during Pleistocene glacial cycles, ocean currents facilitating the gene flow, and the Yangtze River outflow imposing a physical barrier to gene flow. Here, we examined these factors affecting population structuring of the Asian paddle crab, Charybdis japonica, in the Yellow Sea, East China Sea, and adjacent areas. Genetic variation in nine populations of C. japonica (n = 169) was determined from partial mitochondrial cytochrome c oxidase subunit I sequences. Among the 14 haplotypes identified, a dominant haplotype H1 was present in all populations, and a relatively abundant localized haplotype H2 was found in four of the northern populations. Furthermore, the frequency of the common haplotype H1 decreased from south to north. A genetic discontinuity was detected in Haizhou Bay, which divided species into two groups (north group and south group). The lack of genetic structure in the south and north groups indicates high dispersal of C. japonica within groups. Local marine gyres in Haizhou Bay might be responsible for the divergence of the north and south groups. Our study highlights the importance of local marine gyres for influencing genetic structure in marine coastal species in the Northwestern Pacific, especially in species spawning inshore.
Spectroscopic analysis of myoglobin and cytochrome
c
dynamics in isolated cardiomyocytes during hypoxia and reoxygenation
Authors: Almohammedi A. , Kapetanaki S. M. , Wood B. R. , Raven E. L. , Storey N. M. , Hudson A. J.
Published: February 2015

Raman microspectroscopy was applied to monitor the intracellular redox state of myoglobin and cytochrome
c
from isolated adult rat cardiomyocytes during hypoxia and reoxygenation. The nitrite reductase activity of myoglobin leads to the production of nitric oxide in cells under hypoxic conditions, which is linked to the inhibition of mitochondrial respiration. In this work, the subsequent reoxygenation of cells after hypoxia is shown to lead to increased levels of oxygen-bound myoglobin relative to the initial levels observed under normoxic conditions. Increased levels of reduced cytochrome
c
in
ex vivo
cells are also observed during hypoxia and reoxygenation by Raman microspectroscopy. The cellular response to reoxygenation differed dramatically depending on the method used in the preceding step to create hypoxic conditions in the cell suspension, where a chemical agent, sodium dithionite, leads to reduction of cytochromes in addition to removal of dissolved oxygen, and bubbling-N
2
gas leads to displacement of dissolved oxygen only. These results have an impact on the assessment of experimental simulations of hypoxia in cells. The spectroscopic technique employed in this work will be used in the future as an analytical method to monitor the effects of varying levels of oxygen and nutrients supplied to cardiomyocytes during either the preconditioning of cells or the reperfusion of ischaemic tissue.
Ectoparasitism shortens the breeding season in a colonial bird
Authors: Brown Charles R. , Brown Mary Bomberger
Published: February 2015

When blood-feeding parasites increase seasonally, their deleterious effects may prevent some host species, especially those living in large groups where parasites are numerous, from reproducing later in the summer. Yet the role of parasites in regulating the length of a host's breeding season—and thus the host's opportunity for multiple brooding—has not been systematically investigated. The highly colonial cliff swallow (Petrochelidon pyrrhonota), a temperate-latitude migratory songbird in the western Great Plains, USA, typically has a relatively short (eight to nine week) breeding season, with birds rarely nesting late in the summer. Colonies at which ectoparasitic swallow bugs (Oeciacus vicarius) were experimentally removed by fumigation were over 45 times more likely to have birds undertake a second round of nesting than were colonies exposed to parasites. Late nesting approximately doubled the length of the breeding season, with some birds raising two broods. Over a 27 year period the percentage of birds engaging in late nesting each year increased at a colony site where parasites were removed annually. This trend could not be explained by changes in group size, climate or nesting phenology during the study. The results suggest that ectoparasitism shortens the cliff swallow's breeding season and probably prevents many individuals from multiple brooding. When this constraint is removed, selection may rapidly favour late nesting.
FGF/MAPK signaling sets the switching threshold of a bistable circuit controlling cell fate decisions in ES cells
Authors: Schröter Christian , Rué Pau , Mackenzie Jonathan P , Martinez Arias Alfonso
Published: February 2015

Intracellular transcriptional regulators and extracellular signaling pathways together regulate the allocation of cell fates during development, but how their molecular activities are integrated to establish the correct proportions of cells with particular fates is not known. Here we study this question in the context of the decision between the epiblast (Epi) and the primitive endoderm (PrE) fate that occurs in the mammalian preimplantation embryo. Using an embryonic stem (ES) cell model, we discover two successive functions of FGF/MAPK signaling in this decision. First, the pathway needs to be inhibited to make the PrE-like gene expression program accessible for activation by GATA transcription factors in ES cells. In a second step, MAPK signaling levels determine the threshold concentration of GATA factors required for PrE-like differentiation, and thereby control the proportion of cells differentiating along this lineage. Our findings can be explained by a simple mutual repression circuit modulated by FGF/MAPK signaling. This may be a general network architecture to integrate the activity of signal transduction pathways and transcriptional regulators, and serve to balance proportions of cell fates in several contexts.
A list of organometallic kryptoracemates
Authors: Bernal Ivan , Watkins Steven
Published: February 2015

The vast majority of racemic solutions of chiral compounds apparently crystallize at room temperature in non-Sohncke space groups as racemic crystals. However, kryptoracemic crystals composed of nearly enantiomeric pairs occasionally crystallize at room temperature, or appear as low-temperature phases, in Sohncke space groups. As a complement to the previously published catalog of organic kryptoracemates [Fábián & Brock (2010).Acta Cryst.B66, 94–103], 1412 chiral organometallic crystal structures have now been extracted from the Cambridge Structural Database and analyzed. 26 are listed herein as credible kryptoracemates. The possible influence of temperature is discussed, together with some problems in characterizing and classifying these structures.
Crystallization and preliminary X-ray crystallographic analysis of human myotubularin-related protein 1
Authors: Bong Seoung Min , Yang Seung Won , Choi Ji-Woong , Kim Seung Jun , Lee Byung Il
Published: February 2015

Myotubularin-related protein 1 is a phosphatase that dephosphorylates phospholipids such as phosphatidylinositol 3-phosphate or phosphatidylinositol 3,5-bisphosphate. In this study, human MTMR1 was overexpressed inEscherichia coli, purified and crystallized at 277 K using polyethylene glycol 20 000 as a precipitant. Diffraction data were collected to 2.0 Å resolution using synchrotron radiation. The crystals belonged to space groupP1, with unit-cell parametersa= 67.219,b= 96.587,c= 97.581 Å, α = 87.597, β = 86.072, γ = 77.327°. Assuming the presence of four molecules in the asymmetric unit, the calculated Matthews coefficient value was 2.61 Å3 Da−1and the corresponding solvent content was 52.9%.
Purification, crystallization and preliminary X-ray diffraction studies of the β-catenin homolog HMP-2 fromCaenorhabditis elegans
Authors: Choi Hee-Jung , Weis William I.
Published: February 2015

β-Catenin is a multifunctional protein involved in both cell adhesion and Wnt signaling in metazoans. The nematodeCaenorhabditis elegansis unusual in that it expresses four β-catenin paralogs with separate functions.C. elegansHMP-2 participates in cell adhesion but not in Wnt signaling, so structural and biochemical studies of this protein will help in understanding its unusual specialization and the evolution of β-catenin. HMP-2 was expressed, purified and crystallized in two different salt conditions. Crystals grown from a sodium formate condition diffracted to a resolution of 2 Å and belonged to space groupC2, with unit-cell parametersa= 165.2,b= 39.0,c= 101.1 Å, β = 116.7°. Crystals obtained from a lithium sulfate condition diffracted to 3 Å resolution and belonged to space groupP43, with unit-cell parametersa=b= 85.3,c= 138.7 Å. Diffraction data were collected and processed from both crystal forms and the structure was solved by molecular replacement. Model refinement is in progress.
Production, crystallization and X-ray diffraction analysis of a complex between a fragment of the TssM T6SS protein and a camelid nanobody
Authors: Nguyen Van Son , Spinelli Silvia , Desmyter Aline , Le Thi Thu Hang , Kellenberger Christine , Cascales Eric , Cambillau Christian , Roussel Alain
Published: February 2015

The type VI secretion system (T6SS) is a machine evolved by Gram-negative bacteria to deliver toxin effectors into target bacterial or eukaryotic cells. The T6SS is functionally and structurally similar to the contractile tail of theMyoviridaefamily of bacteriophages and can be viewed as a syringe anchored to the bacterial membrane by a transenvelope complex. The membrane complex is composed of three proteins: the TssM and TssL inner membrane components and the TssJ outer membrane lipoprotein. The TssM protein is central as it interacts with both TssL and TssJ, therefore linking the membranes. Using controlled trypsinolysis, a 32.4 kDa C-terminal fragment of enteroaggregativeEscherichia coliTssM (TssM32Ct) was purified. A nanobody obtained from llama immunization, nb25, exhibited subnanomolar affinity for TssM32Ct. Crystals of the TssM32Ct–nb25 complex were obtained and diffracted to 1.9 Å resolution. The crystals belonged to space groupP64, with unit-cell parametersa = b = 95.23,c= 172.95 Å. Molecular replacement with a model nanobody indicated the presence of a dimer of TssM32Ct–nb25 in the asymmetric unit.