bluuebunny/crossref_metadata_2025 huggingface dataset:
The mammalian homologue of yeast Afg1 ATPase (lactation elevated 1) mediates degradation of nuclear-encoded complex IV subunits
Authors: Cesnekova Jana , Rodinova Marie , Hansikova Hana , Houstek Josef , Zeman Jiri , Stiburek Lukas
Published: January 2016

Mitochondrial protein homeostasis is crucial for cellular function and integrity and is therefore maintained by several classes of proteins possessing chaperone and/or proteolytic activities. In the present study, we focused on characterization of LACE1 (lactation elevated 1) function in mitochondrial protein homeostasis. LACE1 is the human homologue of yeast mitochondrial Afg1 (ATPase family gene 1) ATPase, a member of the SEC18-NSF, PAS1, CDC48-VCP, TBP family. Yeast Afg1 was shown to mediate degradation of mitochondrially encoded complex IV subunits, and, on the basis of its similarity to CDC48 (p97/VCP), it was suggested to facilitate extraction of polytopic membrane proteins. We show that LACE1, which is a mitochondrial integral membrane protein, exists as part of three complexes of approximately 140, 400 and 500 kDa and is essential for maintenance of fused mitochondrial reticulum and lamellar cristae morphology. We demonstrate that LACE1 mediates degradation of nuclear-encoded complex IV subunits COX4 (cytochrome c oxidase 4), COX5A and COX6A, and is required for normal activity of complexes III and IV of the respiratory chain. Using affinity purification of LACE1–FLAG expressed in a LACE1-knockdown background, we show that the protein interacts physically with COX4 and COX5A subunits of complex IV and with mitochondrial inner-membrane protease YME1L. Finally, we demonstrate by ectopic expression of both K142A Walker A and E214Q Walker B mutants, that an intact ATPase domain is essential for LACE1-mediated degradation of nuclear-encoded complex IV subunits. Thus the present study establishes LACE1 as a novel factor with a crucial role in mitochondrial protein homeostasis.
Timeslot interchanging by efficient optical switches
Authors: Tan Xuesong Jonathan , Li Shuo‐Yen Robert , Chen Peng
Published: January 2016

A fibre memory is a serial connection of fibre‐switch blocks, each combining fibre delay lines with one optical switch. With enhanced flexibility in processing fluid optical data, fibre memories allow ramified applications in the existing literature. This study concentrates on the implementations of timeslot interchangers (TSIs) by fibre memories based on a special type of low‐complexity switches, called rotators, under periodic switching control. The proposed TSI structure achieves an economic tradeoff between control and component complexities in the construction of large‐scale optical TSIs.
Bandwidth‐allocated mechanism and its algorithm for multi‐subsystem‐based virtual passive optical network in metro‐access optical network
Authors: Xia Weidong , Gan Chaoqin , Xie Weilun , Ma Shucong
Published: January 2016

In the metro‐access optical network, bandwidth‐allocated mechanism and its algorithm are proposed for the multi‐subsystem‐based virtual passive optical network (VPON) that can implement the syncretism of multiple systems such as time division multiplexing‐PON, wavelength division multiplexing‐PON and orthogonal frequency division multiplexing‐PON. To avoid frequent bandwidth reallocation, the matrix of bandwidth‐demanded variation is introduced. According to the norm of this matrix, admission condition of bandwidth allocation for VPON users is established. To distinguish different bandwidth‐demanded variation of multiple subsystems and allocate bandwidth fairly and efficiently for VPON, the bandwidth‐allocated scheme is employed. To the increase of VPON's bandwidth demand, the multi‐granularity‐based bandwidth‐allocated algorithm is proposed to promote the admission probability of new VPONs. MATLAB is used to evaluate the performance of the proposed mechanism and algorithm. Considering the representativeness of various situations, the admission condition of bandwidth allocation for VPON users is demonstrated with ten VPONs. The bandwidth‐allocated scheme and algorithm are verified effectively in bandwidth‐utilised ratio with two original VPONs of high priority and two new VPONs of low priority, as well as in admission probability with four new VPONs.
Correlating Lagrangian structures with forcing in two-dimensional flow
Authors: Ouellette Nicholas T. , Hogg Charlie A. R. , Liao Yang
Published: January 2016

Lagrangian coherent structures (LCSs) are the dominant transport barriers in unsteady, aperiodic flows, and their role in organizing mixing and transport has been well documented. However, nearly all that is known about LCSs has been gleaned from passive observations: they are computed in a post-processing step after a flow has been observed and used to understand why the mixing and transport proceeded as it did. In many applications, the ability instead to control the presence or location of LCSs via imposed forcing would be valuable. With this goal in mind, we study the relationship between LCSs and external forcing in an experimental quasi-two-dimensional weakly turbulent flow. We find that the likelihood of finding a repelling LCS at a given location is positively correlated with the mean strain rate injected at that point and negatively correlated with the mean speed, and that it is not correlated with the vorticity. We also find that mean time between successive LCSs appearing at a fixed location is related to the structure of the forcing field. Finally, we demonstrate a surprising difference in our results between LCSs computed forward and backward in time, with forward-time (repelling) LCSs showing much more correlation with the forcing than backwards-time (attracting) LCSs.
Design of the 1.5 MW, 30-96 MHz ultra-wideband 3 dB high power hybrid coupler for Ion Cyclotron Resonance Frequency (ICRF) heating in fusion grade reactor
Authors: Yadav Rana Pratap , Kumar Sunil , Kulkarni S. V.
Published: January 2016

Design and developmental procedure of strip-line based 1.5 MW, 30-96 MHz, ultra-wideband high power 3 dB hybrid coupler has been presented and its applicability in ion cyclotron resonance heating (ICRH) in tokamak is discussed. For the high power handling capability, spacing between conductors and ground need to very high. Hence other structural parameters like strip-width, strip thickness coupling gap, and junction also become large which can be gone upto optimum limit where various constrains like fabrication tolerance, discontinuities, and excitation of higher TE and TM modes become prominent and significantly deteriorates the desired parameters of the coupled lines system. In designed hybrid coupler, two 8.34 dB coupled lines are connected in tandem to get desired coupling of 3 dB and air is used as dielectric. The spacing between ground and conductors are taken as 0.164 m for 1.5 MW power handling capability. To have the desired spacing, each of 8.34 dB segments are designed with inner dimension of 3.6 × 1.0 × 40 cm where constraints have been significantly realized, compensated, and applied in designing of 1.5 MW hybrid coupler and presented in paper.
Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques
Authors: Fournier René , Mohareb Amir
Published: January 2016

We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0–4, n = 0–10, p = 0–2, q = 0–2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of CumSnn+ (m = 1, 2 and n = 9–12). A single GO run produced the same low-energy structures found in an earlier study where each CumSnn+ species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV.
Size effects of 109° domain walls in rhombohedral barium titanate single crystals—A molecular statics analysis
Authors: Endres Florian , Steinmann Paul
Published: January 2016

Ferroelectric functional materials are of great interest in science and technology due to their electromechanically coupled material properties. Therefore, ferroelectrics, such as barium titanate, are modeled and simulated at the continuum scale as well as at the atomistic scale. Due to recent advancements in related manufacturing technologies the modeling and simulation of smart materials at the nanometer length scale is getting more important not only to predict but also fundamentally understand the complex material behavior of such materials. In this study, we analyze the size effects of 109° nanodomain walls in ferroelectric barium titanate single crystals in the rhombohedral phase using a recently proposed extended molecular statics algorithm. We study the impact of domain thicknesses on the spontaneous polarization, the coercive field, and the lattice constants. Moreover, we discuss how the electromechanical coupling of an applied electric field and the introduced strain in the converse piezoelectric effect is affected by the thickness of nanodomains.
A high energy density relaxor antiferroelectric pulsed capacitor dielectric
Authors: Jo Hwan Ryul , Lynch Christopher S.
Published: January 2016

Pulsed capacitors require high energy density and low loss, properties that can be realized through selection of composition. Ceramic (Pb0.88La0.08)(Zr0.91Ti0.09)O3 was found to be an ideal candidate. La3+ doping and excess PbO were used to produce relaxor antiferroelectric behavior with slim and slanted hysteresis loops to reduce the dielectric hysteresis loss, to increase the dielectric strength, and to increase the discharge energy density. The discharge energy density of this composition was found to be 3.04 J/cm3 with applied electric field of 170 kV/cm, and the energy efficiency, defined as the ratio of the discharge energy density to the charging energy density, was 0.920. This high efficiency reduces the heat generated under cyclic loading and improves the reliability. The properties were observed to degrade some with temperature increase above 80 °C. Repeated electric field cycles up to 10 000 cycles were applied to the specimen with no observed performance degradation.
Performance evaluation of a lossy transmission lines based diode detector at cryogenic temperature
Authors: Villa E. , Aja B. , de la Fuente L. , Artal E.
Published: January 2016

This work is focused on the design, fabrication, and performance analysis of a square-law Schottky diode detector based on lossy transmission lines working under cryogenic temperature (15 K). The design analysis of a microwave detector, based on a planar gallium-arsenide low effective Schottky barrier height diode, is reported, which is aimed for achieving large input return loss as well as flat sensitivity versus frequency. The designed circuit demonstrates good sensitivity, as well as a good return loss in a wide bandwidth at Ka-band, at both room (300 K) and cryogenic (15 K) temperatures. A good sensitivity of 1000 mV/mW and input return loss better than 12 dB have been achieved when it works as a zero-bias Schottky diode detector at room temperature, increasing the sensitivity up to a minimum of 2200 mV/mW, with the need of a DC bias current, at cryogenic temperature.
The effect of Si content on the fracture toughness of CrAlN/Si3N4 coatings
Authors: Liu S. , Wheeler J. M. , Davis C. E. , Clegg W. J. , Zeng X. T.
Published: January 2016

CrAlN/Si3N4 nanocomposite coatings with different Si contents were deposited to understand how Si influences the microstructure and mechanical behaviour of the coatings, in particular, the fracture toughness. The coating composition, chemical bonding, microstructure, and mechanical properties were studied by energy dispersive spectroscopy, x-ray photoelectron spectroscopy, x-ray diffraction, and nanoindentation, respectively. Using a micro double cantilever beam sample, it was found that the fracture toughness of CrAlN/Si3N4 coatings was higher than that of both the CrN and CrAlN coatings and increased with increasing Si content. Cross-sectional transmission electron microscopy suggested that this was caused by the suppression of cracking at columnar boundaries.
Surface sensitivity of optical and magneto-optical and ellipsometric properties in magnetoplasmonic nanodisks
Authors: Herreño-Fierro César A. , Patiño Edgar J. , Armelles Gaspar , Cebollada Alfonso
Published: January 2016

The optical, ellipsometric, and magneto-optical surface sensitivity to dielectric environment of magnetoplasmonic nanodisks is experimentally studied. Here, the shift of the corresponding spectral structures as a function of the thickness of a coating SiO2 layer is characterized. Our results reveal that the so called pseudo-Brewster Angle, easily identified in the ellipsometric phase (Δ) spectrum, is up to four times more sensitive than the conventional features used in surface plasmon resonance based sensors. These results highlight the need of investigating the factual implementation of this technique to develop improved ellipsometric-phase based transducers for bio-chemical sensing purposes.
Volume coil based on hybridized resonators for magnetic resonance imaging
Authors: Jouvaud C. , Abdeddaim R. , Larrat B. , de Rosny J.
Published: January 2016

We present an electromagnetic device based on hybridization of four half-wavelength dipoles which increases the uniformity and the strength of the radio-frequency (RF) field of a Magnetic Resonant Imaging (MRI) apparatus. Numerical results show that this Hybridized Coil (HC) excited with a classical loop coil takes advantage of the magnetic hybrid modes. The distribution of the RF magnetic field is experimentally confirmed on a 7-T MRI with a gelatin phantom. Finally, the HC is validated in vivo by imaging the head of an anesthetized rat. We measure an overall increase of the signal to noise ratio with up to 2.4 fold increase in regions of interest far from the active loop coil.
Defects in solution-processed dithienylsilole-based small-molecule photovoltaic thin-films
Authors: Muntasir Tanvir , Chaudhary Sumit
Published: January 2016

DTS-(FBTTh2)2 is a prominent solution-processable small-molecule donor for donor-acceptor bulk-heterojunction organic photovoltaics. Power conversion efficiency of DTS-(FBTTh2)2 based photovoltaic devices exceeds 8%. This paper reports on the distribution of sub-bandgap trap states in DTS-(FBTTh2)2. Trap states were probed using admittance spectroscopy and low-frequency capacitance-voltage profiling and analyzed using established theoretical models. Three distributions were revealed in the trap density of states energy spectra. Key observations were (1) thicker solution-processed films with higher drying time had 55% less traps than thinner films that dried relative faster (2) blending of DTS-(FBTTh2)2 with the acceptor PC70BM introduced traps at the center of the donor-acceptor interfacial bandgap. Charge carrier dynamics in DTS-(FBTTh2)2 based thin-films was also characterized using impedance spectroscopy.
Bright and multicolor luminescent colloidal Si nanocrystals prepared by pulsed laser irradiation in liquid
Authors: Nakamura Toshihiro , Yuan Ze , Watanabe Kanta , Adachi Sadao
Published: January 2016

We reported the preparation of bright and multicolor luminescent colloidal Si nanocrystal (Si-nc) by pulsed UV laser irradiation to porous Si (PSi) in an organic solvent. The different-luminescence-color (different-sized) colloidal Si-nc was produced by the pulsed laser-induced fragmentation of different-sized porous nanostructures. The colloidal Si-nc samples were found to have higher photoluminescence quantum efficiencies (20%–23%) than the PSi samples (1%–3%). The brighter emission of the colloidal Si-nc was attributed to an enhanced radiative band-to-band transition rate due to the presence of a surface organic layer formed by UV laser-induced hydrosilylation.
Precise parameterization of the recombination velocity at passivated phosphorus doped surfaces
Authors: Kimmerle Achim , Momtazur Rahman Md. , Werner Sabrina , Mack Sebastian , Wolf Andreas , Richter Armin , Haug Halvard
Published: January 2016

We investigate the surface recombination velocity Sp at the silicon-dielectric interface of phosphorus-doped surfaces for two industrially relevant passivation schemes for crystalline silicon solar cells. A broad range of surface dopant concentrations together with a high accuracy of evaluating the latter is achieved by incremental back-etching of the surface. The analysis of lifetime measurements and the simulation of the surface recombination consistently apply a set of well accepted models, namely, the Auger recombination by Richter et al. [Phys. Rev. B 86, 1–14 (2012)], the carrier mobility by Klaassen [Solid-State Electron. 35, 953–959 (1992); 35, 961–967 (1992)], the intrinsic carrier concentration for undoped silicon by Altermatt et al. [J. Appl. Phys. 93, 1598–1604 (2003)], and the band-gap narrowing by Schenk [J. Appl. Phys. 84, 3684–3695 (1998)]. The results show an increased Sp at textured in respect to planar surfaces. The obtained parameterizations are applicable in modern simulation tools such as EDNA [K. R. McIntosh and P. P. Altermatt, in Proceedings of the 35th IEEE Photovoltaic Specialists Conference, Honolulu, Hawaii, USA (2010), pp. 1–6], PC1Dmod [Haug et al., Sol. Energy Mater. Sol. Cells 131, 30–36 (2014)], and Sentaurus Device [Synopsys, Sentaurus TCAD, Zürich, Switzerland] as well as in the analytical solution under the assumption of local charge neutrality by Cuevas et al. [IEEE Trans. Electron Devices 40, 1181–1183 (1993)].
Pasture mixes with lucerne (Medicago sativa) increase yields and water-use efficiencies over traditional pastures based on subterranean clover (Trifolium subterraneum)
Authors: McCaskill M. R. , Raeside M. C. , Clark S. G. , MacDonald C. , Clark B. , Partington D. L.
Published: January 2016

Pastures sown to lucerne (Medicago sativa L.) with a perennial non-legume could increase feed supply relative to traditional pastures based on subterranean clover (Trifolium subterraneum L.). Such mixtures might also be preferable to pure lucerne pastures, which are prone to weed invasion. Yield and water-use efficiency (harvested dry matter per unit evapotranspiration) of mixtures with lucerne or subterranean clover were compared a field experiment established under rainfed conditions at Hamilton, Victoria. Soil moisture and dry matter production were measured over 2 years. Treatments included chicory (Cichorium intybus L.), cocksfoot (Dactylis glomerata L.) and tall fescue (Festuca arundinacea Shreb.) with either lucerne or subterranean clover; pure lucerne; and phalaris (Phalaris aquatica L.) and perennial ryegrass (Lolium perenne L.) with only subterranean clover. In the second year, dry matter production from lucerne mixtures exceeded that of equivalent mixtures with subterranean clover in spring, summer and winter. In spring, the lucerne component continued producing for longer than the clover component through its use of deeper stored soil water, and in summer, lucerne continued to grow slowly after the grass component had entered a drought-induced dormancy. In winter, the contribution from the lucerne component complemented, rather than competed with, that from the non-legume component. Water-use efficiencies during winter–spring ranged from 4 kg ha–1 mm–1 for chicory–clover to 27 kg ha–1 mm–1 for a fescue–lucerne mixture, and during summer–autumn from nil for cocksfoot–clover to 13 kg ha–1 mm–1 for a fescue–lucerne mixture. This study demonstrates that lucerne-based mixtures can increase forage supply per unit water use relative to traditional pastures based on subterranean clover.
Towards a new paradigm in fire severity research using dose–response experiments
Authors: Smith Alistair M. S. , Sparks Aaron M. , Kolden Crystal A. , Abatzoglou John T. , Talhelm Alan F. , Johnson Daniel M. , Boschetti Luigi , Lutz James A. , Apostol Kent G. , Yedinak Kara M. , Tinkham Wade T. , Kremens Robert J.
Published: January 2016

Most landscape-scale fire severity research relies on correlations between field measures of fire effects and relatively simple spectral reflectance indices that are not direct measures of heat output or changes in plant physiology. Although many authors have highlighted limitations of this approach and called for improved assessments of severity, others have suggested that the operational utility of such a simple approach makes it acceptable. An alternative pathway to evaluate fire severity that bridges fire combustion dynamics and ecophysiology via dose–response experiments is presented. We provide an illustrative example from a controlled nursery combustion laboratory experiment. In this example, severity is defined through changes in the ability of the plant to assimilate carbon at the leaf level. We also explore changes in the Differenced Normalised Differenced Vegetation Index (dNDVI) and the Differenced Normalised Burn Ratio (dNBR) as intermediate spectral indices. We demonstrate the potential of this methodology and propose dose–response metrics for quantifying severity in terms of carbon cycle processes.
Gender agreement with animate nouns in French
Authors: Ihsane Tabea , Sleeman Petra
Published: January 2016

Grammatical gender and semantic gender do not always go hand in hand. In French such mismatches can be observed outside the strict DP. To account for such phenomena and for gender more generally, we propose that gender is expressed in two positions within DP: on N as an uninterpretable feature accounting for grammatical gender and on the head of a Gender Phrase as a feature accounting for semantic gender. To account for the mismatches we discuss, we propose that the gender of the nouns involved is unspecified inside DP and that it can be specified in D later in the derivation.We further show that inside the strict DP, grammatical gender agreement between Gen and NP is stricter than in the ‘looser’ DP (partitive), which is in turn stricter than the agreeing/referring relation with elements outside DP, reflecting Corbett’s agreement hierarchy, to which we add a partitive position.
On null objects and ellipses in Brazilian Portuguese
Authors: Lopes Ruth E.V. , Cyrino Sonia M. L.
Published: January 2016

Brazilian Portuguese (BP) is known to license anaphoric null objects (ANO), that is, null objects with a linguistic antecedent. It also licenses VP ellipsis (VPE), with auxiliaries, modals and main verbs, the latter a case of V-stranding VPE (V-VPE), the one with which we will be concerned. Although ANOs and V-VPE may have identical surface strings in BP, we propose that they do not have the same structure. To achieve that we examine the properties of the ANOs and compare them to V-VPE, arguing the first are cases of DP ellipsis. We present evidence for an analysis of the ANO as a base-generated empty phrase-marker that will be reconstructed in LF. We also propose that ANOs and VPE are licensed by a lexicalized aspectual head, as a consequence of the loss of generalized verb movement in BP.
The phonology of postverbal pronouns in Romance languages
Authors: Repetti Lori
Published: January 2016

In many Romance varieties, the verb in imperative verb + (postverbal) pronoun phrases retains primary stress: Italian/Spanish: [kómpra]/[kómpra-melo] ‘buy!’/‘buy me it!’. However, in others varieties, stress in these phrases may be realized on a different syllable: [kompra-meló], [kompra-mélo], [kompra-mélozo]. In this paper, I address questions that have puzzled linguists for some time: Why is there a stress shift when enclitic pronouns are added to the imperative verb? How is the position of the stressed syllable determined? I propose that many factors are involved, including morpho-syntactic factors (the presence of a weak or a clitic pronoun, which are prosodized differently), phonological processes (the mapping of syntactic to prosodic structure), and phonetic processes (tonal association to metrically prominent syllables).
Emotive Interjections in British English
Authors: Stange Ulrike
Published: January 2016

Emotive Interjections in British English: A corpus-based study on variation in acquisition, function and usage constitutes the first in-depth corpus-based study on the use of emotive interjections in Present Day British English. In a novel approach, it systematically distinguishes between child and adult speakers, providing new insights into how they use Ow!, Ouch!, Ugh!, Yuck!, Whoops!, Whoopsadaisy! and Wow! in everyday spoken language. It studies in detail their acquisition by children and pinpoints changes and developments in their use throughout early childhood. The study highlights particularities displayed by child and adult speakers in general and identifies crucial differences regarding how adults use emotive interjections depending on whether they are interacting with children or other adults. This book thus offers an exhaustive overview on the functions of emotive interjections based on thorough empirical research and will appeal to linguists concerned with pragmatics, child language acquisition, the expression of emotion and interjections.
Third Person References
Authors: Dumont Jenny
Published: January 2016

This volume, a case study on the grammar of third person references in two genres of spoken Ecuadorian Spanish, examines from a discourse-analytic perspective how genre affects linguistic patterns and how researchers can look for and interpret genre effects. This marks a timely contribution to corpus linguistics, as many linguists are choosing to work with empirical data. Corpus based approaches have many advantages and are useful in the comparison of different languages as well as varieties of the same language, but what is often overlooked in such comparisons is the genre of language under examination. As this case study shows, genre is an important factor in interpreting patterns and distributions of forms.

The book also contributes toward theories of anaphora, referentiality and Preferred Argument Structure. It is relevant for scholars who work with referentiality, genre differences, third person references, and interactional linguistics, as well as those interested in Spanish morphosyntax.
Rustenburg's labour recruitment regime: shifts and new meanings
Authors: Forrest Kally
Published: January 2016

In South Africa's democracy, the dismantling of the apartheid low-wage migrant labour system has been a stated goal of the state and trade unions. Through an investigation of the recruitment regime on the Rustenburg platinum belt, this article demonstrates how mine managements have responded to the goal of guaranteeing a continued supply of cheap and plentiful labour, how it has manipulated the unionised labour market, how it has ensured labour's consent in its project and how this has impacted on workers. Using Michael Burawoy's (1983) conceptual distinction between ‘despotic’ and ‘hegemonic’ labour regimes which embraces the idea of the politics of production, the article demonstrates how migrant labour recruitment patterns contain continuities, but have also fractured under the impact of neoliberal flexible labour patterns, the state's transformational laws which particularly impact on non-South African labour, and the local labour market characterised by deep structural unemployment. Workers have in some measure benefited from changed recruitment patterns, but for many it has rendered their position increasingly precarious and has simultaneously segmented the solidarity of labour, resulting in some segments of mine labour belonging to the new democratic dispensation more than others.
No local double exponential gradient growth in hyperbolic flow for the 2d Euler equation
Authors: Hoang Vu , Radosz Maria
Published: January 2016

We consider smooth, double-odd solutions of the two-dimensional Euler equation in

[
−
1
,
1

)
2

[-1, 1)^2

with periodic boundary conditions. This situation is a possible candidate to exhibit strong gradient growth near the origin. We analyze the flow in a small box around the origin in a strongly hyperbolic regime and prove that the compression of the fluid induced by the hyperbolic flow alone is not sufficient to create double-exponential growth of the gradient.
Injury, reflex impairment, and survival of beam-trawled flatfish
Authors: Uhlmann Sebastian S. , Theunynck Ruben , Ampe Bart , Desender Marieke , Soetaert Maarten , Depestele Jochen
Published: January 2016

Under the “high survival” exemption of the European landing obligation or discard ban, monitoring vitality and survival of European flatfish becomes relevant to a discard-intensive beam trawl fishery. The reflex action mortality predictor (RAMP) method may be useful in this context. It involves scoring for the presence or absence of natural animal reflexes to generate an impairment score which is then correlated with post-release or discard mortality. In our first experiment, we determined suitable candidate reflexes for acclimated, laboratory-held European plaice (Pleuronectes platessa) and common sole (Solea solea). In a second experiment, we quantified reflex impairment of commercially trawled-and-handled plaice and sole in response to commercial fishing stressors. In a third experiment, we tested whether a combined reflex impairment and injury (vitality) score of plaice was correlated with delayed post-release mortality to establish RAMP. Five-hundred fourteen trawled-and-discarded plaice and 176 sole were assessed for experimentally confirmed reflexes such as righting, evasion, stabilise, and tail grab, among others. Of these fish, 316 plaice were monitored for at least 14 d in captivity, alongside 60 control plaice. All control fish survived, together with an average of 50% (±29 SD) plaice after being trawled from conventional, 60 min trawls and sorted on-board a coastal beam trawler. Stressors such as trawl duration, wave height, air, and seawater temperature were not as relevant as a vitality score and total length in predicting post-release survival probability. In the second experiment where survival was not assessed, reflex impairment of plaice became more frequent with prolonged air exposure. For sole, a researcher handling-and-reflex scoring bias rather than a fishing stressor may have confounded results. Scoring a larger number of individuals for injuries and reflexes from a representative selection of trawls and trips may allow for a fleet-scale discard survival estimate to facilitate implementation of the discard ban.
Near-infrared spectroscopy of M dwarfs. III. Carbon and oxygen abundances in late M dwarfs, including the dusty rapid rotator 2MASSI J1835379+325954
Authors: Tsuji Takashi , Nakajima Tadashi
Published: January 2016

Carbon and oxygen abundances of eight late M dwarfs are determined based on the near-infrared spectra of medium resolution (R = λ/Δ λ ≈ 20000). In late M dwarfs, dust forms in their photospheres for Teff below about 2600 K, and this case applies to the M8.5 dwarf 2MASSI J1835379+325954 (hereafter 2MASS 1835+32) whose Teff is 2275 K. The other seven objects with Teff above 2600 K are analyzed with dust-free models. For the case of 2MASS 1835+32 analyzed with the dusty model, the surface temperature is higher by about 600 K due to the blanketing effect of the dust grains, mainly composed of iron grains, and the carbon and oxygen abundances are higher by 0.25 and 0.15 dex, respectively, compared to the analysis by the dust-free model. Once dust forms in the photosphere, the dust works as a kind of thermostat and the temperatures of the surface layers remain nearly the same as the condensation temperatures of the dust grains. For this reason, the temperatures of the surface layers of dusty dwarfs are relatively insensitive to the fundamental parameters, including Teff. In addition, it appears that 2MASS 1835+32 is a rapid rotator, for which its equivalent widths (EWs) are thought to remain unchanged by the rotational broadening. This is, however, true only when the true continuum is well defined. Otherwise, the pseudo-continuum level depends on the rotational velocity and hence the EWs as well. For this reason, the derived abundances depend on the rotational velocity assumed: for the values of Vrotsin i = 37.6 and 44.0 km s−1 available in the literature, the derived carbon and oxygen abundances differ by 0.23 and 0.14 dex, respectively, and we find that the higher value provides a better account of the observed spectrum. The resulting carbon and oxygen abundances in the eight late M dwarfs show no systematic difference from our results for the early and middle M dwarfs, and confirm the higher AO/AC ratio at the lower metallicity. In late M dwarfs, CO and H2O remain as excellent abundance indicators of carbon and oxygen, respectively, except for additional uncertainty due to complexity associated with dust formation in the latest M dwarfs.
The fern cavitation catapult: mechanism and design principles
Authors: Llorens C. , Argentina M. , Rojas N. , Westbrook J. , Dumais J. , Noblin X.
Published: January 2016

Leptosporangiate ferns have evolved an ingenious cavitation catapult to disperse their spores. The mechanism relies almost entirely on the annulus, a row of 12–25 cells, which successively: (i) stores energy by evaporation of the cells’ content, (ii) triggers the catapult by internal cavitation, and (iii) controls the time scales of energy release to ensure efficient spore ejection. The confluence of these three biomechanical functions within the confines of a single structure suggests a level of sophistication that goes beyond most man-made devices where specific structures or parts rarely serve more than one function. Here, we study in detail the three phases of spore ejection in the sporangia of the fernPolypodium aureum. For each of these phases, we have written the governing equations and measured the key parameters. For the opening of the sporangium, we show that the structural design of the annulus is particularly well suited to inducing bending deformations in response to osmotic volume changes. Moreover, the measured parameters for the osmoelastic design lead to a near-optimal speed of spore ejection (approx. 10 m s–1). Our analysis of the trigger mechanism by cavitation points to a critical cavitation pressure of approximately −100 ± 14 bar, a value that matches the most negative pressures recorded in the xylem of plants. Finally, using high-speed imaging, we elucidated the physics leading to the sharp separation of time scales (30 versus 5000 µs) in the closing dynamics. Our results highlight the importance of the precise tuning of the parameters without which the function of the leptosporangium as a catapult would be severely compromised.
Evolving random fractal Cantor superlattices for the infrared using a genetic algorithm
Authors: Bossard Jeremy A. , Lin Lan , Werner Douglas H.
Published: January 2016

Ordered and chaotic superlattices have been identified in Nature that give rise to a variety of colours reflected by the skin of various organisms. In particular, organisms such as silvery fish possess superlattices that reflect a broad range of light from the visible to the UV. Such superlattices have previously been identified as ‘chaotic’, but we propose that apparent ‘chaotic’ natural structures, which have been previously modelled as completely random structures, should have an underlying fractal geometry. Fractal geometry, often described as the geometry of Nature, can be used to mimic structures found in Nature, but deterministic fractals produce structures that are too ‘perfect’ to appear natural. Introducing variability into fractals produces structures that appear more natural. We suggest that the ‘chaotic’ (purely random) superlattices identified in Nature are more accurately modelled by multi-generator fractals. Furthermore, we introduce fractal random Cantor bars as a candidate for generating both ordered and ‘chaotic’ superlattices, such as the ones found in silvery fish. A genetic algorithm is used to evolve optimal fractal random Cantor bars with multiple generators targeting several desired optical functions in the mid-infrared and the near-infrared. We present optimized superlattices demonstrating broadband reflection as well as single and multiple pass bands in the near-infrared regime.
A curve shortening flow rule for closed embedded plane curves with a prescribed rate of change in enclosed area
Authors: Dallaston Michael C. , McCue Scott W.
Published: January 2016

Motivated by a problem from fluid mechanics, we consider a generalization of the standard curve shortening flow problem for a closed embedded plane curve such that the area enclosed by the curve is forced to decrease at a prescribed rate. Using formal asymptotic and numerical techniques, we derive possible extinction shapes as the curve contracts to a point, dependent on the rate of decreasing area; we find there is a wider class of extinction shapes than for standard curve shortening, for which initially simple closed curves are always asymptotically circular. We also provide numerical evidence that self-intersection is possible for non-convex initial conditions, distinguishing between pinch-off and coalescence of the curve interior.
On the existence of a unique class of yield and failure criteria comprising Tresca, von Mises, Drucker–Prager, Mohr–Coulomb, Galileo–Rankine, Matsuoka–Nakai and Lade–Duncan
Authors: Lagioia R. , Panteghini A.
Published: January 2016

In this paper, it is mathematically demonstrated that classical yield and failure criteria such as Tresca, von Mises, Drucker–Prager, Mohr–Coulomb, Matsuoka–Nakai and Lade–Duncan are all defined by the same equation. This can be seen as one of the three solutions of a cubic equation of the principal stresses and suggests that all such criteria belong to a more general class of non-convex formulations which also comprises a recent generalization of the Galileo–Rankine criterion. The derived equation is always convex and can also provide a smooth approximation of continuity of at least class
C
2
of the original Tresca and Mohr–Coulomb criteria. It is therefore free from all the limitations which restrain the use of some of them in numerical analyses. The mathematical structure of the presented equation is based on a separate definition of the meridional and deviatoric sections of the graphical representation of the criteria. This enables the use of an efficient implicit integration algorithm which results in a very short machine runtime even when demanding boundary value problems are analysed.
Pleiotropic effects of juvenile hormone in ant queens and the escape from the reproduction–immunocompetence trade-off
Authors: Pamminger Tobias , Treanor David , Hughes William O. H.
Published: January 2016

The ubiquitous trade-off between survival and costly reproduction is one of the most fundamental constraints governing life-history evolution. In numerous animals, gonadotropic hormones antagonistically suppressing immunocompetence cause this trade-off. The queens of many social insects defy the reproduction–survival trade-off, achieving both an extraordinarily long life and high reproductive output, but how they achieve this is unknown. Here we show experimentally, by integrating quantification of gene expression, physiology and behaviour, that the long-lived queens of the ant
Lasius niger
have escaped the reproduction–immunocompetence trade-off by decoupling the effects of a key endocrine regulator of fertility and immunocompetence in solitary insects, juvenile hormone (JH). This modification of the regulatory architecture enables queens to sustain a high reproductive output without elevated JH titres and suppressed immunocompetence, providing an escape from the reproduction–immunocompetence trade-off that may contribute to the extraordinary lifespan of many social insect queens.
RASLseqTools: open-source methods for designing and analyzing RNA-mediated oligonucleotide Annealing, Selection, and, Ligation sequencing (RASL-seq) experiments
Authors: Scott Erick R. , Larman H. Benjamin , Torkamani Ali , Schork Nicholas J. , Wineinger Nathan , Nanis Max , Thompson Ryan C. , Beheshti Zavareh Reza B. , Lairson Luke L. , Schultz Peter G. , Su Andrew I.
Published: January 2016

RNA-mediated oligonucleotide Annealing, Selection, and Ligation (RASL-seq) is a method to measure the expression of hundreds of genes in thousands of samples for a fraction of the cost of competing methods. However, enzymatic inefficiencies of the original protocol and the lack of open source software to design and analyze RASL-seq experiments have limited its widespread adoption. We recently reported an Rnl2-based RASL-seq protocol (RRASL-seq) that offers improved ligation efficiency and a probe decoy strategy to optimize sequencing usage. Here, we describe an open source software package, RASLseqTools, that provides computational methods to design and analyze RASL-seq experiments. Furthermore, using data from a large RRASL-seq experiment, we demonstrate how normalization methods can be used for characterizing and correcting experimental, sequencing, and alignment error. We provide evidence that the three principal predictors of RRASL-seq reproducibility are barcode/probe sequence dissimilarity, sequencing read depth, and normalization strategy. Using dozens of technical and biological replicates across multiple 384-well plates, we find simple normalization strategies yield similar results to more statistically complex methods.
PEDLA: predicting enhancers with a deep learning-based algorithmic framework
Authors: Liu Feng , Li Hao , Ren Chao , Bo Xiaochen , Shu Wenjie
Published: January 2016

Transcriptional enhancers are non-coding segments of DNA that play a central role in the spatiotemporal regulation of gene expression programs. However, systematically and precisely predicting enhancers remain a major challenge. Although existing methods have achieved some success in enhancer prediction, they still suffer from many issues. We developed a deep learning-based algorithmic framework named PEDLA (https://github.com/wenjiegroup/PEDLA), which can directly learn an enhancer predictor from massively heterogeneous data and generalize in ways that are mostly consistent across various cell types/tissues. We first trained PEDLA with 1,114-dimensional heterogeneous features in H1 cells, and we demonstrated that our PEDLA framework integrates diverse heterogeneous features and gives state-of-the-art performance relative to five existing methods for enhancer prediction. We further extended PEDLA to iteratively learn from 22 training cell types/tissues. Our results showed that PEDLA manifested superior performance consistency in both training and independent test sets. On average, PEDLA achieved 95.0% accuracy and a 96.8% geometric mean (GM) across 22 training cell types/tissues, as well as 95.7% accuracy and a 96.8% GM across 20 independent test cell types/tissues. Together, our work illustrates the power of harnessing state-of-the-art deep learning techniques to consistently identify regulatory elements at a genome-wide scale from massively heterogeneous data across diverse cell types/tissues.
Genome-wide identification and characterisation of HOT regions in the human genome
Authors: Li Hao , Liu Feng , Ren Chao , Bo Xiaochen , Shu Wenjie
Published: January 2016

HOT (high-occupancy target) regions, which are bound by a surprisingly large number of transcription factors, are considered to be among the most intriguing findings of recent years. An improved understanding of the roles that HOT regions play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying HOT regions across the spectrum of human cell types. We characterised and validated HOT regions in embryonic stem cells (ESCs) and produced a catalogue of HOT regions in a broad range of human cell types. We found that HOT regions are associated with genes that control and define the developmental processes of the respective cell and tissue types. We also showed evidence of the developmental persistence of HOT regions at primitive enhancers and demonstrate unique signatures of HOT regions that distinguish them from typical enhancers and super-enhancers. Finally, we performed an epigenetic analysis to reveal the dynamic epigenetic regulation of HOT regions upon H1 differentiation. Taken together, our results provide a resource for the functional exploration of HOT regions and extend our understanding of the key roles of HOT regions in development and differentiation.
A bacterial parasite effector mediates insect vector attraction in host plants independently of developmental changes
Authors: Orlovskis Zigmunds , Hogenhout Saskia A
Published: January 2016

Parasites can take over their hosts and trigger dramatic changes in host appearance and behaviour that are typically interpreted as extended phenotypes to promote parasite survival and fitness. For example, Toxoplasma gondii manipulates the behaviour of infected rodents to aid transmission to cats and parasitic trematodes of the genus Ribeiroia alter limb development in their amphibian hosts to facilitate predation by birds. Plant parasites and pathogens also reprogram host development and morphology. Phytoplasma parasites of plants induce extensive leaf-like flower phenotype (phyllody) in their host plants, presumably to attract insect vectors on which these bacteria depend for transmission. However, it remains debatable whether morphological phenotypes, such as phyllody, are directly beneficial to the parasites or are side-products of parasite infection. Previously, we found that phytoplasma virulence protein (effector) SAP54 binds and mediates degradation of host MADS-box transcription factors (MTFs), regulatory hubs of plant development and hormone physiology, to induce phyllody and promote insect vector colonisation. Here we show that plants heterologously expressing SAP54 are strongly attractive to insects, but surprisingly, insect attraction was independent of the presence of leaf-like flowers. Moreover, plants that produce leaf-like flowers in the absence of SAP54 did not attract insects. We conclude that the SAP54 effector mediates insect vector attraction in host plants by exploiting the role of its MTF targets in insect defence and that perturbation of floral development may be a secondary effect of the effector activity.