bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancement of tunneling magnetoresistance by inserting a diffusion barrier in L1-FePd perpendicular magnetic tunnel junctions
Authors: Zhang De-Lin , Schliep Karl B. , Wu Ryan J. , Quarterman P. , Reifsnyder Hickey Danielle , Lv Yang , Chao Xiaohui , Li Hongshi , Chen Jun-Yang , Zhao Zhengyang , Jamali Mahdi , Mkhoyan K. Andre , Wang Jian-Ping
Published: April 2018

We studied the tunnel magnetoresistance (TMR) of L10-FePd perpendicular magnetic tunnel junctions (p-MTJs) with an FePd free layer and an inserted diffusion barrier. The diffusion barriers studied here (Ta and W) were shown to enhance the TMR ratio of the p-MTJs formed using high-temperature annealing, which are necessary for the formation of high quality L10-FePd films and MgO barriers. The L10-FePd p-MTJ stack was developed with an FePd free layer with a stack of FePd/X/Co20Fe60B20, where X is the diffusion barrier, and patterned into micron-sized MTJ pillars. The addition of the diffusion barrier was found to greatly enhance the magneto-transport behavior of the L10-FePd p-MTJ pillars such that those without a diffusion barrier exhibited negligible TMR ratios (<1.0%), whereas those with a Ta (W) diffusion barrier exhibited TMR ratios of 8.0% (7.0%) at room temperature and 35.0% (46.0%) at 10 K after post-annealing at 350 °C. These results indicate that diffusion barriers could play a crucial role in realizing high TMR ratios in bulk p-MTJs such as those based on FePd and Mn-based perpendicular magnetic anisotropy materials for spintronic applications.
Shock temperature dependent rate law for plastic bonded explosives
Authors: Aslam Tariq D.
Published: April 2018

A reactive flow model for the tri-amino-tri-nitro-benzene (TATB) based plastic bonded explosive PBX 9502 (95% TATB, 5% polymeric binder Kel-F 800) is presented. This newly devised model is based primarily on the shock temperature of the material, along with local pressure, and accurately models a broader range of detonation and initiation scenarios. Specifically, sensitivity changes to the initial explosive temperature are accounted for naturally and with a single set of parameters. The equation of state forms for the reactants and products, as well as the thermodynamic closure of pressure and temperature equilibration, are carried over from the Wescott-Stewart-Davis (WSD) model [Wescott et al., J. Appl. Phys. 98, 053514 (2005) and “Modeling detonation diffraction and dead zones in PBX-9502,” in Proceedings of the Thirteenth International Detonation Symposium (2006)]. This newly devised model, with Arrhenius state dependence on the shock temperature, based on the WSD equation of states, is denoted by AWSD. Modifying an existing implementation of the WSD model to the AWSD model in a hydrocode is a rather straightforward procedure.
Mesoscopic electrohydrodynamic simulations of binary colloidal suspensions
Authors: Rivas Nicolas , Frijters Stefan , Pagonabarraga Ignacio , Harting Jens
Published: April 2018

A model is presented for the solution of electrokinetic phenomena of colloidal suspensions in fluid mixtures. We solve the discrete Boltzmann equation with a Bhatnagar-Gross-Krook collision operator using the lattice Boltzmann method to simulate binary fluid flows. Solvent-solvent and solvent-solute interactions are implemented using a pseudopotential model. The Nernst-Planck equation, describing the kinetics of dissolved ion species, is solved using a finite difference discretization based on the link-flux method. The colloids are resolved on the lattice and coupled to the hydrodynamics and electrokinetics through appropriate boundary conditions. We present the first full integration of these three elements. The model is validated by comparing with known analytic solutions of ionic distributions at fluid interfaces, dielectric droplet deformations, and the electrophoretic mobility of colloidal suspensions. Its possibilities are explored by considering various physical systems, such as breakup of charged and neutral droplets and colloidal dynamics at either planar or spherical fluid interfaces.
Stress-induced reversible and irreversible ferroelectric domain switching
Authors: Chen Zibin , Huang Qianwei , Wang Feifei , Ringer Simon P. , Luo Haosu , Liao Xiaozhou
Published: April 2018

Ferroelectric materials have been extensively explored for applications in electronic devices because of their ferroelectric/ferroelastic domain switching behaviour under electric bias or mechanical stress. Recent findings on applying mechanical loading to manipulate reversible logical signals in non-volatile ferroelectric memory devices make ferroelectric materials more attractive to scientists and engineers. However, the dynamical microscopic structural behaviour of ferroelectric domains under stress is not well understood, which limits the applications of ferroelectric/ferroelastic switching in memory devices. Here, the kinetics of reversible and irreversible ferroelectric domain switching induced by mechanical stress in relaxor-based ferroelectrics was explored. In-situ transmission electron microscopy investigation revealed that 90° ferroelastic and 180° ferroelectric domain switching can be induced by low and high mechanical stresses. The nucleation and growth of nanoscale domains overwhelm the defect-induced pinning effect on the stable micro-domain walls. This study provides deep insights for exploring the mechanical kinetics for ferroelectric/ferroelastic domains and a clear pathway to overcome the domain pinning effect of defects in ferroelectrics.
Heteroepitaxial growth of ε-(AlxGa1−x)2O3 alloy films on c-plane AlN templates by mist chemical vapor deposition
Authors: Tahara Daisuke , Nishinaka Hiroyuki , Morimoto Shota , Yoshimoto Masahiro
Published: April 2018

In this study, ε-(AlxGa1−x)2O3 alloy films were grown on c-plane AlN templates by mist chemical vapor deposition. The Al content of two samples was determined by Rutherford backscattering analysis. The lattice constant of the ε-(AlxGa1−x)2O3 alloy films followed Vegard's law, and the Al contents of other samples were determined to be as high as x = 0.395 by Vegard's law. The direct bandgap was obtained in the range of 5.0–5.9 eV by transmittance measurements. The valence-band offset between ε-(Al0.395Ga0.605)2O3 and ε-Ga2O3 was analyzed to be 0.2 eV, and the conduction-band offset was calculated to be 0.7 eV by X-ray photoelectron spectroscopy. The ε-(AlxGa1−x)2O3/ε-Ga2O3 interface band discontinuity was type I. Our experimental results will be important for the actual application of ε-(AlxGa1−x)2O3/ε-Ga2O3 heterojunction devices.
Scalable, large area compound array refractive lens for hard X-rays
Authors: Reich Stefan , dos Santos Rolo Tomy , Letzel Alexander , Baumbach Tilo , Plech Anton
Published: April 2018

We demonstrate the fabrication of a 2D Compound Array Refractive Lens (CARL) for multi-contrast X-ray imaging. The CARL consists of six stacked polyimide foils with each displaying a 2D array of lenses with a 65 μm pitch aiming for a sensitivity on sub-micrometer structures with a (few-)micrometer resolution in sensing through phase and scattering contrast at multiple keV. The parabolic lenses are formed by indents in the foils by a paraboloid needle. The ability for fast single-exposure multi-contrast imaging is demonstrated by filming the kinetics of pulsed laser ablation in liquid. The three contrast channels, absorption, differential phase, and scattering, are imaged with a time resolution of 25 μs. By changing the sample-detector distance, it is possible to distinguish between nanoparticles and microbubbles.
Open circuit potential monitored digital photocorrosion of GaAs/AlGaAs quantum well microstructures
Authors: Aithal Srivatsa , Dubowski Jan J.
Published: April 2018

Nanostructuring of semiconductor wafers with an atomic level depth resolution is a challenging task, primarily due to the limited availability of instruments for in situ monitoring of such processes. Conventional digital etching relies on calibration procedures and cumbersome diagnostics applied between or at the end of etching cycles. We have developed a photoluminescence (PL) based process for monitoring in situ digital photocorrosion (DPC) of GaAs/AlGaAs microstructures at rates below 0.2 nm per cycle. In this communication, we demonstrate that DPC of GaAs/AlGaAs microstructures could be monitored with open circuit potential (OCP) measured between the photocorroding surface of a microstructure and an Ag/AgCl reference electrode installed in the sample chamber. The excellent correlation between the position of both PL and OCP maxima indicates that the DPC process could be monitored in situ for materials that do not necessarily exhibit measurable PL emission.
Shock-induced microstructural response of mono- and nanocrystalline SiC ceramics
Authors: Branicio Paulo S. , Zhang Jingyun , Rino José P. , Nakano Aiichiro , Kalia Rajiv K. , Vashishta Priya
Published: April 2018

The dynamic behavior of mono- and nanocrystalline SiC ceramics under plane shock loading is revealed using molecular-dynamics simulations. The generation of shock-induced elastic compression, plastic deformation, and structural phase transformation is characterized at different crystallographic directions as well as on a 5-nm grain size nanostructure at 10 K and 300 K. Shock profiles are calculated in a wide range of particle velocities 0.1–6.0 km/s. The predicted Hugoniot agree well with experimental data. Results indicate the generation of elastic waves for particle velocities below 0.8–1.9 km/s, depending on the crystallographic direction. In the intermediate range of particle velocities between 2 and 5 km/s, the shock wave splits into an elastic precursor and a zinc blende-to-rock salt structural transformation wave, which is triggered by shock pressure over the ∼90 GPa threshold value. A plastic wave, with a strong deformation twinning component, is generated ahead of the transformation wave for shocks in the velocity range between 1.5 and 3 km/s. For particle velocities greater than 5–6 km/s, a single overdriven transformation wave is generated. Surprisingly, shocks on the nanocrystalline sample reveal the absence of wave splitting, and elastic, plastic, and transformation wave components are seamlessly connected as the shock strength is continuously increased. The calculated strengths 15.2, 31.4, and 30.9 GPa for ⟨001⟩, ⟨111⟩, and ⟨110⟩ directions and 12.3 GPa for the nanocrystalline sample at the Hugoniot elastic limit are in excellent agreement with experimental data.
Acoustic emission by self-organising effects of micro-hollow cathode discharges
Authors: Kotschate Daniel , Gaal Mate , Kersten Holger
Published: April 2018

We designed micro-hollow cathode discharge prototypes under atmospheric pressure and investigated their acoustic characteristics. For the acoustic model of the discharge, we correlated the self-organisation effect of the current density distribution with the ideal model of an acoustic membrane. For validation of the obtained model, sound particle velocity spectroscopy was used to detect and analyse the acoustic emission experimentally. The results have shown a behaviour similar to the ideal acoustic membrane. Therefore, the acoustic excitation is decomposable into its eigenfrequencies and predictable. The model was unified utilising the gas exhaust velocity caused by the electrohydrodynamic force. The results may allow a contactless prediction of the current density distribution by measuring the acoustic emission or using the micro-discharge as a tunable acoustic source for specific applications as well.
Impact of phenomenological theory of turbulence on pragmatic approach to fluvial hydraulics
Authors: Ali Sk Zeeshan , Dey Subhasish
Published: April 2018

The phenomenological theory of turbulence (PTT) remains a long-standing and fascinating theory in turbulence research. In this review article, we highlight the state-of-the-science of the impact of the PTT on the pragmatic approach to fluvial hydraulics, explored over recent decades, discussing the salient and the subtle roles that the turbulence plays in governing many physical processes. To acquire a theoretical explanation of this pragmatic approach necessitates an intuitive thought that can bring together the background mechanisms of all the physical processes under one law—a thought that is capable of finding their inextricable links with the turbulent energy spectrum. We begin here with emphasizing the spectral and the co-spectral origin of the well-recognized laws of the wall, the resistance equation, and the turbulence intensities by portraying the typical momentum transfer mechanism of eddies in a turbulent flow. Next, we focus on the scaling laws of key fluvial processes derived from the perspective of the PTT, enlightening their physical insight and ability to judge how far the so-called empirical formulas can be used with confidence. The PTT has been able to disclose the origin of several primeval empirical formulas that have been used over many years without having any theoretical clarification and confirmation. Finally, we make an effort to describe some unsolved issues to be resolved as a future scope of research.
Light-induced forces push optically trapped nanoparticles and reveal molecules’ light absorption
Authors: Fellet Melissae
Published: April 2018

A new method of detecting forces to monitor molecular light absorption under ambient conditions may eventually be extended to spectroscopic monitoring of single molecules in solution.
Theoretical model offers more complete account of robotic gripping physics
Authors: Cesare Chris
Published: April 2018

Mean-field approach provides a mathematical basis for the dependence of surface adhesion and friction on an applied voltage.
Does foliage metal accumulation influence plant–insect interactions? A field study of two sympatric tree metallophytes
Authors: Fernando Denise R. , Smith Chaya S. , Steinbauer Martin J. , Farnier Kevin , Watson Simon J. , Green Peter T.
Published: April 2018

Gossia (Myrtaceae) is a highly restricted tree genus most speciose in New Caledonia and eastern Australia. The latter group accumulates above-normal foliar manganese (Mn) concentrations, with some individuals exhibiting the rare Mn-hyperaccumulative trait. Whether foliar metals contribute to chemical defence has been addressed via numerous feeding experiments and very few field studies. This investigation exploited specifically different insect activities on the foliage of sympatric Gossia grayi (N.Snow & Guymer) and Gossia shepherdii (F.Muell.) N.Snow & Guymer, endemic to north-eastern Australia, to test for direct and indirect effects of foliar Mn enrichment on plant–insect interactions. Leaf organic and inorganic chemistries, specific weight, surface damage, gall infestation and occupancy were quantified. Discovery that both species are Mn hyperaccumulators augments the world listing by 5–7%. Highly elevated gall-Mn concentrations coupled with negligible gall parasitisation suggested chemical fortification and adaptation by the host insect – a Cecidomyiidae fly. Linear mixed modelling (LMM) showed differences in leaf Mn, phenolics, toughness and surface damage across tree species and leaf age. There was no direct relationship between leaf Mn and insect impact. However, LMM did resolve indirect effects, i.e. between insect impact and certain foliar elements, consistent with nutritional dynamics in a physiologically novel plant system where Mn is vastly overaccumulated.
How Spartina alterniflora adapts to a new environment created by embankment reclamation through C-N-P stoichiometry in the coastal wetlands of eastern China
Authors: Qiao Yajun , Yang Wen , Zhao Yuxuan , Jeelani Nasreen , Xu Lingqian , Zhao Hui , Zhang Yanan , An Shuqing , Leng Xin
Published: April 2018

Although embankment reclamation is a recurring activity in the coastal wetlands of China, the effect of embankment construction on plant growth has attracted little attention. Leaf carbon, nitrogen and phosphorus stoichiometry (C-N-P stoichiometry) of a plant can be used to reflect plant adaptation to new environments created by reclamation. In the present study we investigated the biomass and leaf C-N-P stoichiometry of Spartina alterniflora Loisel., soil C-N-P stoichiometry and soil moisture, salinity, bulk density and pH in both embankment-reclaimed and natural S. alterniflora salt marshes in eastern China. Plant biomass, leaf P content, soil salinity and soil moisture were significantly lower in the reclaimed compared with natural marsh. The decrease in leaf P content is possibly attributed to changes in soil salinity, soil moisture and soil organic C and N content in the reclaimed marsh. The results of the present study indicate that the decreased aboveground biomass in the reclaimed marsh is likely to be correlated with an increase in the leaf N:P ratio, in accordance with the ‘growth rate hypothesis’. However, previously published threshold values of the N:P ratio as indicators of N or P limitation of plant growth may not be applicable to S. alterniflora at our study site.
Chemical trends in ocean islands explained by plume–slab interaction
Authors: Dannberg Juliane , Gassmöller Rene
Published: April 2018

Significance

The composition of ocean island basalts is known to correlate with zones in the lowermost mantle almost 3,000 km below, thought to represent piles of hot, dense material. One important open question in the Earth sciences is the mechanism behind this link between the surface and Earth’s deep interior. Here, we use high-resolution 3D geodynamic models with a realistic subduction history, plate geometries, and plate motions to identify a dynamically feasible mechanism for how rising hot material can inherit the lower-mantle geochemical structure despite variations in material density. Our findings provide a framework for mapping chemical anomalies at the surface to the deep mantle and illuminate the composition of one of the least well-understood regions of the Earth.
Tradeoffs between immune function and childhood growth among Amazonian forager-horticulturalists
Authors: Urlacher Samuel S. , Ellison Peter T. , Sugiyama Lawrence S. , Pontzer Herman , Eick Geeta , Liebert Melissa A. , Cepon-Robins Tara J. , Gildner Theresa E. , Snodgrass J. Josh
Published: April 2018

Significance

The energetic impact of immune function on human growth remains unclear. Using data from Amazonian forager-horticulturalists, we show that diverse, low-level immune activity predicts reduced childhood growth over periods of competing energy use ranging from 1 wk to 20 mo. We also demonstrate that modest body fat stores (i.e., energy reserves) protect children from the particularly detrimental impact of acute inflammation on growth. These findings provide evidence for considerable energetic tradeoffs between immune function and growth among humans, highlighting the energy constraint of childhood and the characteristic ability of our species to respond sensitively to dynamic environmental conditions. We outline the possible role of immune-related tradeoffs in driving patterns of human growth faltering, developmental metabolic plasticity, and life history evolution.
Extracting neuronal functional network dynamics via adaptive Granger causality analysis
Authors: Sheikhattar Alireza , Miran Sina , Liu Ji , Fritz Jonathan B. , Shamma Shihab A. , Kanold Patrick O. , Babadi Behtash
Published: April 2018

Significance

Probing functional interactions among the nodes in a network is crucial to understanding how complex systems work. Existing methodologies widely assume static network structures or Gaussian statistics or do not take account of likely sparse interactions. They are therefore not well-suited to neuronal spiking data with rapid task-dependent dynamics, binary statistics, and sparse functional dependencies. We develop an inference framework for extracting functional network dynamics from neuronal data by integrating techniques from adaptive filtering, compressed sensing, point processes, and high-dimensional statistics. We derive efficient estimation algorithms and precise statistical inference procedures. We apply our proposed techniques to experimentally recorded neuronal data to probe the neuronal functional networks underlying attentive behavior. Our techniques provide substantial gains in computation, resolution, and statistical robustness.
Fermentation of dihydroxyacetone by engineered
Escherichia coli
and
Klebsiella variicola
to products
Authors: Wang Liang , Chauliac Diane , Rhee Mun Su , Panneerselvam Anushadevi , Ingram Lonnie O. , Shanmugam K. T.
Published: April 2018

Significance

World-wide natural gas production in 2016 was 3.55 trillion cubic meters, and the natural gas flared is estimated to contribute about 350 million tons of CO
2
. The global warming potential of CH
4
is several orders of magnitude higher than that of CO
2
. Upgrading CH
4
to chemicals and liquid fuels converts low-cost natural gas to high-value products and traps it from release into atmosphere. Current chemical technology can produce dihydroxyacetone (DHA) from CH
4
provided a microorganism can ferment this growth-inhibitory sugar. Here we report metabolically engineered microorganisms that ferment DHA to products. Combining the existing technology of chemical conversion of CH
4
to DHA and the fermentation of this sugar is a strategy to transform inexpensive CH
4
to chemicals and liquid fuels.
Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt of
Pseudomonas aeruginosa
Authors: Lee Mijoon , Batuecas María T. , Tomoshige Shusuke , Domínguez-Gil Teresa , Mahasenan Kiran V. , Dik David A. , Hesek Dusan , Millán Claudia , Usón Isabel , Lastochkin Elena , Hermoso Juan A. , Mobashery Shahriar
Published: April 2018

Significance

β-Lactam antibiotics are currently the most broadly used class of antibiotics. These antibiotics prevent bacterial cell wall from cross-linking, which leads to the accumulation of long non–cross-linked strands of peptidoglycan.
Pseudomonas aeruginosa
, a nefarious bacterial pathogen, attempts to repair this aberrantly formed peptidoglycan by the function of the lytic transglycosylase Slt. We document in the present report that Slt turns over the peptidoglycan by both scission of the glycosidic bonds from a terminus or in the middle of the peptidoglycan. In a series of seven X-ray crystal structures, we provide structural context to how these two reactions take place. These results disclose the details of bacterial response to the β-lactam antibiotic challenge.
Software Tools for Big Data Resources in Family Names Dictionaries
Authors: Rambousek Adam , Parkin Harry , Horak Ales
Published: April 2018

This paper describes the design and development of specific software tools used during the creation of Family Names in Britain and Ireland (FaNBI) research project, started by the University of the West of England in 2010 and finished successfully in 2016. First, the overview of the project and methodology is provided. Next section contains the description of dictionary management tools and software tools to combine input data resources.
Microstructure and mechanical properties of as-cast Mg-4Zn-0.5Zr-0.2Cu-0.2Ce alloy
Authors: He M. L. , Luo T. J. , Zhou J. X. , Yang Y. S.
Published: April 2018

In this study, an approach is proposed to improve the microstructure and mechanical properties of Mg-4Zn-0.5Zr alloy by combining trace Cu and rare earth Ce addition. The results showed that Cu and Ce additions led to obvious grain refinement and the formation of Mg-Zn-Cu and Mg-Zn-Ce phases. The Mg-Zn-Ce phase was identified to have an orthorhombic structure. The length of the [0001]α rods in the Cu-containing alloys remarkably decreased. The yield strength increased slightly after Cu and Ce co-addition, which was attributed to grain refinement and precipitation strengthening. The coarse Mg-Zn-Ce phase distributed at the grain boundaries would reduce the ductility by promoting crack propagation during tensile processes.
Improving the specific antitumor efficacy of ONC by fusion with N-terminal domain of transferrin
Authors: Qi Jianying , Ye Xianlong , Li Lingling , Bai Haijing , Xu Cunshuan
Published: April 2018

Onconase (ONC) as a novel anti-tumor drug has a significant killing effect on a variety of tumor cells. Drug delivery system mediated by transferrin (TF) and TF receptor (TfR), which can significantly increase the amount of drug uptake in the tumor cells, enhance the initiative target efficiency of drugs and reduce its toxic side effects. It has been widely used in drug delivery and clinical trials. In this study, the rONC-TFn was expressed in Escherichia coli by linking ONC with the N-terminal domain of TF (TFn). ELISA and competitive binding analysis demonstrated that rONC-TFn can bind to TfR. The rONC-TFn protein showed much higher cytotoxicity to the cultured HepG2 and Hela cells than rONC. These results suggested that the N-terminal domain protein of TF promoted the tumor targeting of ONC, and thus the rONC-TFn fusion protein may be further developed as a potential targeted anti-tumor drug.
A novel carbohydrate-binding surface layer protein from the hyperthermophilic archaeon Pyrococcus horikoshii
Authors: Goda Shuichiro , Koga Tomoyuki , Yamashita Kenichiro , Kuriura Ryo , Ueda Toshifumi
Published: April 2018

In Archaea and Bacteria, surface layer (S-layer) proteins form the cell envelope and are involved in cell protection. In the present study, a putative S-layer protein was purified from the crude extract of Pyrococcus horikoshii using affinity chromatography. The S-layer gene was cloned and expressed in Escherichia coli. Isothermal titration calorimetry analyses showed that the S-layer protein bound N-acetylglucosamine and induced agglutination of the gram-positive bacterium Micrococcus lysodeikticus. The protein comprised a 21-mer structure, with a molecular mass of 1,340 kDa, as determined using small-angle X-ray scattering. This protein showed high thermal stability, with a midpoint of thermal denaturation of 79 °C in dynamic light scattering experiments. This is the first description of the carbohydrate-binding archaeal S-layer protein and its characteristics.
Identification of the 7S and 11S globulins as percutaneously sensitizing soybean allergens as demonstrated through epidermal application of crude soybean extract
Authors: Murakami Hiroki , Ogawa Takashi , Takafuta Akiho , Yano Erika , Zaima Nobuhiro , Moriyama Tatsuya
Published: April 2018

Cutaneous exposure to food allergens can predispose individuals to food allergies. Soybean, a major allergenic food, is an ingredient in various cosmetic products. However, the types of soybean proteins that are percutaneously sensitizing in humans or animal models remain unknown. In this study, BALB/c mice were dorsally shaved and epicutaneously exposed to a crude soybean extract including sodium dodecyl sulfate or distilled water alone. Specific IgEs secreted in response to 7S globulin (Gly m 5), 11S globulin (Gly m 6), Gly m 3, and Gly m 4 were measured using enzyme-linked immunosorbent assays or immunoblots. Exposure to soybean extract elicited the secretion of soybean-specific IgEs. Of the soybean proteins, 7S and 11S globulins acted as percutaneous sensitizers in 6/9 mice (67%). Additionally, IgE bound specifically and preferentially to the 7S globulin β subunit. In conclusion, this is the first report to identify percutaneously sensitizing soybean allergens in a mouse model.
Active and inactive β1 integrins segregate into distinct nanoclusters in focal adhesions
Authors: Spiess Matthias , Hernandez-Varas Pablo , Oddone Anna , Olofsson Helene , Blom Hans , Waithe Dominic , Lock John G. , Lakadamyali Melike , Strömblad Staffan
Published: April 2018

Integrins are the core constituents of cell–matrix adhesion complexes such as focal adhesions (FAs) and play key roles in physiology and disease. Integrins fluctuate between active and inactive conformations, yet whether the activity state influences the spatial organization of integrins within FAs has remained unclear. In this study, we address this question and also ask whether integrin activity may be regulated either independently for each integrin molecule or through locally coordinated mechanisms. We used two distinct superresolution microscopy techniques, stochastic optical reconstruction microscopy (STORM) and stimulated emission depletion microscopy (STED), to visualize active versus inactive β1 integrins. We first reveal a spatial hierarchy of integrin organization with integrin molecules arranged in nanoclusters, which align to form linear substructures that in turn build FAs. Remarkably, within FAs, active and inactive β1 integrins segregate into distinct nanoclusters, with active integrin nanoclusters being more organized. This unexpected segregation indicates synchronization of integrin activities within nanoclusters, implying the existence of a coordinate mechanism of integrin activity regulation.
Correction and Prevention of the Pixie Ear Deformity: A Combined Technique
Authors: Kaye Kai O , Casabona Gabriela R , Kästner Sonja , Paprottka Felix J
Published: April 2018

Background

Ear and earlobe deformities after surgical rhytidectomy are common and can significantly diminish the aesthetic outcome. The main causes of ear/earlobe distortion are skin overresection, an imbalance between vertical/horizontal skin-lift vectors, and tractional distortions through superficial muscularaponeurotic system (SMAS) tension.

Objectives

To demonstrate a new method for earlobe suturing and ear fixation that would prevent aesthetics-related complications after facelift surgery.

Methods

A total of 105 primary SMAS facelift surgeries were performed between 2015 and 2016 by the first author. A combination technique consisting of a posterior earlobe rotation flap (PERF) and a concha-mastoid suspension suture (CMSS) was executed bilaterally within each facelift procedure (n = 210). A retrospective data analysis was conducted (preoperatively and one year postoperatively) using our hospital information system and a photometric data analysis to assess auricular displacement, earlobe distortion, and hypertrophic scarring.

Results

Pseudoptosis of the earlobe was noted in two cases, and auricular displacement was observed in four cases. Bilateral mild hypertrophic scarring was seen in one patient. The postoperative photometric analysis showed a natural ptosis grade I/II in all the patients, with a statistically significantly reduced postoperative earlobe size (P < 0.05). The total rate of aesthetics-related complications was 4% in our cohort (earlobe distortion with pseudoptosis: 1%; auricular displacement: 2%; hypertrophic scarring: 1%).

Conclusions

Our modification of the facial flap anchoring at the ear base in combination with a CMSS stabilizes the natural position of the ear and prevents distortion while allowing better control over the earlobe’s aesthetic shaping. This novel method reduces the incidence of ear/earlobe deformities and hypertrophic scarring at the ear base after rhytidectomy and, therefore, promises to be a valuable advancement.

Level of Evidence: 4
Deep learning of genomic variation and regulatory network data
Authors: Telenti Amalio , Lippert Christoph , Chang Pi-Chuan , DePristo Mark
Published: April 2018

The human genome is now investigated through high-throughput functional assays, and through the generation of population genomic data. These advances support the identification of functional genetic variants and the prediction of traits (e.g. deleterious variants and disease). This review summarizes lessons learned from the large-scale analyses of genome and exome data sets, modeling of population data and machine-learning strategies to solve complex genomic sequence regions. The review also portrays the rapid adoption of artificial intelligence/deep neural networks in genomics; in particular, deep learning approaches are well suited to model the complex dependencies in the regulatory landscape of the genome, and to provide predictors for genetic variant calling and interpretation.
How was the dageš in Biblical Hebrew Pronounced and Why is it There?
Authors: Khan Geoffrey
Published: April 2018

There is no consensus in the scholarly literature as to the pronunciation of the dageš in the Biblical Hebrew plural form ‘houses’. This article examines the evidence for the way the dageš was pronounced in this word in medieval sources that give us direct access to the Tiberian Masoretic reading tradition. It is shown that there was some degree of diversity of pronunciation across different biblical verses and different sub-traditions of the Tiberian Hebrew pronunciation. An explanation for the existence of the dageš in the word is offered on the basis of comparative evidence within Biblical Hebrew reading traditions and other Semitic languages.
MDM4 is an essential disease driver targeted by 1q gain in Burkitt lymphoma
Authors: Hüllein Jennifer , Słabicki Mikołaj , Rosolowski Maciej , Jethwa Alexander , Habringer Stefan , Tomska Katarzyna , Kurilov Roma , Lu Junyan , Scheinost Sebastian , Wagener Rabea , Huang Zhiqin , Lukas Marina , Yavorska Olena , Helferich Hanne , Scholtysik René , Bonneau Kyle , Tedesco Donato , Küppers Ralf , Klapper Wolfram , Pott Christiane , Stilgenbauer Stephan , Burkhardt Birgit , Löffler Markus , Trümper Lorenz , Hummel Michael , Brors Benedikt , Zapatka Marc , Siebert Reiner ,   consortium MMML, Keller Ulrich , Huber Wolfgang , Kreuz Markus , Zenz Thorsten
Published: April 2018

Oncogenic MYC activation promotes cellular proliferation in Burkitt lymphoma (BL), but also induces cell cycle arrest and apoptosis mediated by TP53, a tumor suppressor gene that is mutated in 40% of BL cases. To identify therapeutic targets in BL, we investigated molecular dependencies in BL cell lines using RNAi-based, loss-of-function screening. By integrating genotypic and RNAi data, we identified a number of genotype-specific dependencies including the dependence of TCF3/ID3 mutant cell lines on TCF3 and of MYD88 mutant cell lines on TLR signaling. TP53 wild-type (TP53wt) BL were dependent on MDM4, a negative regulator of TP53. In BL cell lines, MDM4 knockdown induced cell cycle arrest and decreased tumor growth in a xenograft model in a p53-dependent manner, while small molecule inhibition of the MDM4-p53 interaction restored p53 activity resulting in cell cycle arrest. Consistent with the pathogenic effect of MDM4 upregulation in BL, we found that TP53wt BL samples were enriched for gain of chromosome 1q which includes the MDM4 locus. 1q gain was also enriched across non-BL cancer cell lines (n=789) without TP53 mutation (23% in TP53wt and 12% in TP53mut, p<0.001). In a set of 216 cell lines representing 19 cancer entities from the Achilles project, MDM4 was the strongest genetic dependency in TP53wt cell lines (p<0.001).

Our findings show that in TP53wt BL, MDM4-mediated inhibition of p53 is a mechanism to evade cell cycle arrest. The data highlight the critical role of p53 as a tumor suppressor in BL, and identifies MDM4 as a key functional target of 1q gain in a wide range of cancers, which is therapeutically targetable.
Recent demographic histories and genetic diversity across pinnipeds are shaped by anthropogenic interactions and mediated by ecology and life-history
Authors: Stoffel M.A. , Humble E. , Acevedo-Whitehouse K. , Chilvers B.L. , Dickerson B. , Galimberti F. , Gemmell N. , Goldsworthy S.D , Nichols H.J. , Krüger O , Negro S. , Osborne A. , Paijmans A.J. , Pastor T. , Robertson B.C. , Sanvito S. , Schultz J. , Shafer A.B.A , Wolf J.B.W. , Hoffman J.I.
Published: April 2018

A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and negatively impact population viability and adaptive potential. In an era of unprecedented biodiversity loss and climate change, understanding both the determinants and consequences of bottlenecks in wild populations is therefore an increasingly important challenge. However, as most studies have focused on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we used a comparative approach by integrating genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to elucidate the consequences of large-scale commercial exploitation by 18thand 19thcentury sealers. We show that around one third of these species exhibit strong genetic signatures of recent population declines, with estimated bottleneck effective population sizes reflecting just a few tens of surviving individuals in the most extreme cases. Bottleneck strength was strongly associated with both breeding habitat and mating system variation, and together with global abundance explained a large proportion of the variation in genetic diversity across species. Overall, there was no relationship between bottleneck intensity and IUCN status, although three of the four most heavily bottlenecked species are currently endangered. Our study reveals an unforeseen interplay between anthropogenic exploitation, ecology, life history and demographic declines, sheds new light on the determinants of genetic diversity, and is consistent with the notion that both genetic and demographic factors influence population viability.
Myosin filaments reversibly generate large forces in cells
Authors: Lohner James , Rupprecht Jean-Francois , Hu Junquiang , Mandriota Nicola , Saxena Mayur , Hone James , Araujo Diego Pitta de , Sahin Ozgur , Prost Jacques , Sheetz Michael P.
Published: April 2018

We present high resolution experiments performed on elementary contractile units in cells that challenge our current understanding of molecular motor force generation. The key features are the development of a force per motor considerably larger than forces measured in single molecule experiments, a force increase followed by relaxation controlled by a characteristic displacement rather than by a characteristic force, the observation of steps at half the actin filament period even though a large number of motors are at work in an elementary contractile unit. We propose a generic two-state model of molecular motor collections with hand-over-hand contractions and we find that these unexpected observations are spontaneously emerging features of a collective motor behavior.
Prospective Motion correction improves the sensitivity of fMRI pattern decoding
Authors: Huang Pei , Carlin Johan D. , Alink Arjen , Kriegeskorte Nikolaus , Henson Richard N. , Correia Marta M.
Published: April 2018

We evaluated the effectiveness of prospective motion correction (PMC) on a simple visual task when no deliberate subject motion was present. The PMC system utilizes an in-bore optical camera to track an external marker attached to the participant via a custom-moulded mouthpiece. The study was conducted at two resolutions (1.5mm vs 3mm) and under three conditions (PMC On and Mouthpiece On vs PMC Off and Mouthpiece On vs PMC Off and Mouthpiece Off). Multiple data analysis methods were conducted, including univariate and multivariate approaches, and we demonstrated that the benefit of PMC is most apparent for multi-voxel pattern decoding at higher resolutions. Additional testing on two participants showed that our inexpensive, commercially available mouthpiece solution produced comparable results to a dentist-moulded mouthpiece. Our results showed that PMC is increasingly important at higher resolutions for analyses that require accurate voxel registration across time.
Creation and multi-omics characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacteriumSinorhizobium meliloti
Authors: Checcucci Alice , diCenzo George C. , Ghini Veronica , Bazzicalupo Marco , Becker Anke , Decorosi Francesca , Döhlemann Johannes , Fagorzi Camilla , Finan Turlough M. , Fondi Marco , Luchinat Claudio , Turano Paola , Vignolini Tiziano , Viti Carlo , Mengoni Alessio
Published: April 2018

Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbour a multipartite genome composed by more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacteriumSinorhizobium meliloti. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donorS. melilotistrain to an acceptor strain. Thecis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extra-cellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modelling were employed forin silicoprediction of metabolic flux reorganization. Phenotypes of thecis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with thecis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.
Combining Deep Learning and Active Contours Opens The Way to Robust, Automated Analysis of Brain Cytoarchitectonics
Authors: Thierbach Konstantin , Bazin Pierre-Louis , Back Walter De , Gavriilidis Filippos , Kirilina Evgeniya , Jäger Carsten , Morawski Markus , Geyer Stefan , Weiskopf Nikolaus , Scherf Nico
Published: April 2018

Deep learning has thoroughly changed the field of image analysis yielding impressive results whenever enough annotated data can be gathered. While partial annotation can be very fast, manual segmentation of 3D biological structures is tedious and error-prone. Additionally, high-level shape concepts such as topology or boundary smoothness are hard if not impossible to encode in Feedforward Neural Networks. Here we present a modular strategy for the accurate segmentation of neural cell bodies from light-sheet microscopy combining mixed-scale convolutional neural networks and topology-preserving geometric deformable models. We show that the network can be trained efficiently from simple cell centroid annotations, and that the final segmentation provides accurate cell detection and smooth segmentations that do not introduce further cell splitting or merging.
Applying generalised allometric regressions to predict live body mass of tropical and temperate arthropods
Authors: Sohlström Esra H. , Marian Lucas , Barnes Andrew D. , Haneda Noor F. , Scheu Stefan , Rall Björn C. , Brose Ulrich , Jochum Malte
Published: April 2018

1. The ecological implications of body size extend from the biology of individual organisms to ecosystem–level processes. Measuring body mass for high numbers of invertebrates can be logistically challenging, making length-mass regressions useful for predicting body mass with minimal effort. However, standardised sets of scaling relationships covering a large range in body length, taxonomic groups, and multiple geographical regions are scarce.

2. We collected 6293 arthropods from 19 higher-level taxa in both temperate and tropical locations to compile a comprehensive set of linear models relating live body mass to a range of predictor variables. For each individual, we measured live weight (hereafter, body mass), body length and width, and conducted linear regressions to predict body mass using body length, body width, taxonomic group and geographic region. Additionally, we quantified prediction error when using parameters from arthropods of a different geographic region.

3. Incorporating body width into taxon- and region-specific length-mass regressions yielded the highest prediction accuracy for body mass. Using regression parameters from a different geographic location increased prediction error, causing over- or underestimation of body mass depending on geographical origin and whether body width was included.

4. We present a comprehensive range of parameters for predicting arthropod body mass and provide guidance for selecting optimal scaling relationships. Given the importance of body mass for functional invertebrate ecology and a paucity of adequate regressions to predict arthropod body mass from different geographical regions, our study provides a long-needed resource for quantifying live body mass in invertebrate ecology research.
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA
Authors: Brandani Giovanni B. , Takada Shoji
Published: April 2018

ATP-dependent chromatin remodelers are molecular machines that control genome organization by repositioning, ejecting, or editing nucleosomes, activities that confer them essential regulatory roles on gene expression and DNA replication. Here, we investigate the molecular mechanism of active nucleosome sliding by means of molecular dynamics simulations of the Snf2 remodeler in complex with a nucleosome. During its inchworm motion driven by ATP consumption, the remodeler overwrites the original nucleosome energy landscape via steric and electrostatic interactions to induce sliding of nucleosomal DNA unidirectionally. The sliding is initiated at the remodeler binding location via the generation of twist defects, which then spontaneously propagate to complete sliding throughout the entire nucleosome. We also reveal how remodeler mutations and DNA sequence control active nucleosome repositioning, explaining several past experimental observations. These results offer a detailed mechanistic picture of remodeling important for the complete understanding of these important biological processes.
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
Authors: Bliven Spencer E , Lafita Aleixa , Rose Peter W , Capitani Guido , Prlić Andreas , Bourne Philip E
Published: April 2018

Many proteins fold into highly regular and repetitive three dimensional structures. The analysis of structural patterns and repeated elements is fundamental to understand protein function and evolution. We present recent improvements to the CE-Symm tool for systematically detecting and analyzing the internal symmetry and structural repeats in proteins. In addition to the accurate detection of internal symmetry, the tool is now capable of i) reporting the type of symmetry, ii) identifying the smallest repeating unit, iii) describing the arrangement of repeats with transformation operations and symmetry axes, and iv) comparing the similarity of all the internal repeats at the residue level. CE-Symm 2.0 helps the user investigate proteins with a robust and intuitive sequence-to-structure analysis, with many applications in protein classification, functional annotation and evolutionary studies. We describe the algorithmic extensions of the method and demonstrate its applications to the study of interesting cases of protein evolution.

Availabilit: CE-Symm is an open source tool integrated into the BioJava library(www.biojava.org)and freely available at https://github.com/rcsb/symmetry.