bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of microwave absorption properties of tetrapod-needle zinc oxide whisker radar absorbing material without prior knowledge
Authors: Zhao Yu-Chen , Wang Jie , Liu Jiang-Fan , Song Zhong-Guo , Xi Xiao-Li
Published: July 2017

The radar absorbing material (RAM) containing a tetrapod-needle zinc oxide whisker (T-ZnOw) has been proved to have good efficiency of microwave absorption. However, the available theoretical models, which are intended to predict the microwave absorbing properties of such an interesting composite, still cannot work well without some prior knowledge, like the measured effective electromagnetic parameters of the prepared T-ZnOw composite. Hence, we propose a novel predictive method here to calculate the reflectivity of T-ZnOw RAM without prior knowledge. In this method, the absorbing ability of this kind of material is divided into three main aspects: the unstructured background, the conductive network, and the nanostructured particle. Then, the attenuation properties of these three parts are represented, respectively, by three different approaches: the equivalent spherical particle and the static strong fluctuation theory, the equivalent circuit model obtained from the complex impedance spectra technology, and the combination of four different microscopic electromagnetic responses. The operational calculation scheme can be obtained by integrating these three absorption effects into the existing theoretical attenuation model. The reasonable agreement between the theoretical and experimental data of a T-ZnON/SiO2 composite in the range of 8–14 GHz shows that the proposed scheme can predict the microwave absorption properties of the T-ZnOw RAM. Furthermore, a detailed analysis of these three mechanisms indicates that, on the one hand, the background plays a dominant role in determining the real part of the effective permittivity of the T-ZnOw composite while the network and the particle are the decisive factors of its material loss; on the other hand, an zero-phase impedance, i.e., a pure resistance, with appropriate resonance characteristic might be a rational physical description of the attenuation property of the conductive network, but it is difficult to realize such an impedance property by the traditional resistance and capacitance network. As a result, a series resonant circuit with a relatively low quality factor is introduced to approximate the material loss caused by the network. Finally, the different combinations of these three absorbing mechanisms are analyzed to further display their roles in the overall absorbing performance.
Reconstructing neural networks from limited data
Authors: Larter Raima
Published: July 2017

Researchers offer a new technique for finding hidden neurons from incomplete observations.
Defect induced charge trapping in C-doped α-Al2O3
Authors: Ao Lei , Pham Anh , Xiang Xia , Li Sean , Zu Xiaotao
Published: July 2017

The charged defect states of C-doped α-Al2O3 are investigated systematically with the density functional theory to study their thermodynamic stability and possible effects on the crystal structure and electrical conductivity. Our results reveal that under reducing (Al-rich) synthesis conditions, the most stable defect configuration is CO−2 with a deep (-1|-2) thermodynamic transition level. As a result, C defects are expected to act as double acceptors by introducing appreciable deep electron traps in the host band gap of α-Al2O3. These results are consistent with the proposal that a large number of F+-centers are formed as charge compensators to CO−2 ions in α-Al2O3.
Effect of buckling on the thermal response of microelectromechanical beam resonators
Authors: Zhang Y. , Hosono S. , Nagai N. , Hirakawa K.
Published: July 2017

We have investigated the thermal response of the doubly clamped microelectromechanical (MEMS) beam resonators as a function of an input heating power. When a small amount of heat (<1 mW) is applied to the MEMS beam, reduction in resonance frequency is observed. As the heating power is further increased, however, the resonance frequency levels off and starts to increase, which originates from the buckling of the beam. We find that the slope of the frequency increase at large input powers is 2–3 times steeper than that of the frequency decrease at small input powers and that the buckled device can take larger heating powers without degrading the linearity. These observations suggest that both the thermal sensitivity and the dynamic range can be improved by introducing a proper amount of buckling. Using this insight, we have fabricated a buckled MEMS beam resonator by using a strained InxGa1-xAs (x = 0.001) beam structure on a GaAs substrate. We have found that the frequency responsivity of the InxGa1-xAs beam sample is about 3 times higher than that of the GaAs beam sample, demonstrating that the introduction of buckling is useful for achieving higher thermal sensitivity for the MEMS beam resonators.
A
1∑+ State Lifetime and Predissociation of CuH
Authors: Zhang De-ping , Zhang Qiang , Zhu Bo-xing , Chen Yang , Zhao Dong-feng
Published: July 2017

A combined cavity ringdown (CRD) and laser induced fluorescence (LIF) spectroscopic study on the A1∑+−X1∑+ transition of CuH has been presented. The CuH molecule, as well as its deuterated isotopologue CuD, are produced in a supersonic jet expansion by discharging H2 (or D2) and Ar gas mixtures using two copper needles. Different profiles of relative line intensities are observed between the measured LIF and CRD spectra, providing an experimental evidence for the predissociation behavior in the A1∑+ state of CuH. The lifetimes of individual upper rotational levels are measured by LIF, in which the J′-dependent predissociation rates are obtained. Based on the previous theoretical calculations, a predissociation mechanism is concluded due to the strong spin-orbit coupling between the A1∑+ state and the lowest-lying triplet 3∑+ state, and a tunneling effect may also be involved in the predissociation. Similar experiments are also performed for CuD, showing that the A1∑+ state of CuD does not undergo a predissociation process.
Effects of Shape of Crowders on Dynamics of a Polymer Chain Closure
Authors: Xia Bai-cheng , Zhang Dong-hua , Wang Jia-jun , Yu Wan-cheng
Published: July 2017

Using 3D Langevin dynamics simulations, we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure. The chain closure in spherical crowders is dominated by the increased medium viscosity so that it gets slower with the increasing volume fraction of crowders. By contrast, the dynamics of chain closure becomes very complicated with increasing volume fraction of crowders in spherocylindrical crowders. Notably, the mean closure time is found to have a dramatic decrease at a range of volume fraction of crowders 0.36–0.44. We then elucidate that an isotropic to nematic transition of spherocylindrical crowders at this range of volume fraction of crowders is responsible for the unexpected dramatic decrease in the mean closure time.
FeOx Coating on Pd/C Catalyst by Atomic Layer Deposition Enhances the Catalytic Activity in Dehydrogenation of Formic Acid
Authors: Li Jun-jie , Lu Jun-ling
Published: July 2017

Hydrogen generation from formic acid (FA) has received significant attention. The challenge is to obtain a highly active catalyst under mild conditions for practical applications. Here atomic layer deposition (ALD) of FeOx was performed to deposit an ultrathin oxide coating layer to a Pd/C catalyst, therein the FeOx coverage was precisely controlled by ALD cycles. Transmission electron microscopy and powder X-ray diffraction measurements suggest that the FeOx coating layer improved the thermal stability of Pd nanoparticles (NPs). X-ray photoelectron spectroscopy measurement showed that deposition of FeOx on the Pd NPs caused a positive shift of Pd3d binding energy. In the FA dehydrogenation reaction, the ultrathin FeOx layer on the Pd/C could considerably improve the catalytic activity, and Pd/C coated with 8 cycles of FeOx showed an optimized activity with turnover frequency being about 2 times higher than the uncoated one. The improved activities were in a volcano-shape as a function of the number of FeOx ALD cycles, indicating the coverage of FeOx is critical for the optimized activity. In summary, simultaneous improvements of activity and thermal stability of Pd/C catalyst by ultra-thin FeOx overlayer suggest to be an effective way to design active catalysts for the FA dehydrogenation reaction.
MmpL3 is the flippase for mycolic acids in mycobacteria
Authors: Xu Zhujun , Meshcheryakov Vladimir A. , Poce Giovanna , Chng Shu-Sin
Published: July 2017

Significance

Biological membranes define cellular boundaries, allow compartmentalization, and represent a prerequisite for life; yet, our understanding of membrane biogenesis remains rudimentary. Mycobacteria, including the human pathogen
Mycobacterium tuberculosis
, are surrounded by a double-membrane cell envelope that makes them intrinsically resistant to many antibiotics. Specifically, the outer membrane (OM) contains unique lipids called mycolic acids (MAs), whose transport mechanism across the envelope is unknown. In this study, we established the role of an essential membrane protein as the flippase for MAs and demonstrated that this protein is a direct target of an antimycobacterial compound. Our work provides insights into OM biogenesis and lipid transport in mycobacteria, and the means to evaluate drugs that disrupt MA transport at the inner membrane.
Microscopic dynamics of charge separation at the aqueous electrochemical interface
Authors: Kattirtzi John A. , Limmer David T. , Willard Adam P.
Published: July 2017

Significance

Aqueous electrode interfaces serve as the backdrop for many important chemical processes in nature and technology. These interfaces continually garner much interest due to their ability to facilitate and even catalyze certain electrochemical reactions. Charge separation is a fundamental step in nearly all catalytic processes that occur at metal interfaces. Traditional electrochemical measurements are able to observe the consequences of charge separation but are limited in their ability to reveal direct molecular details. By studying detailed molecular models of charge transfer at water metal interfaces, we have uncovered the microscopic dynamics of this fundamental process. Elucidating the altered thermodynamics and kinetics of charge separation at water–metal interfaces and identifying their molecular underpinnings will inform the interpretation of macroscopic measurements and the design of better catalysts.
Genetic identification of a hindbrain nucleus essential for innate vocalization
Authors: Hernandez-Miranda Luis Rodrigo , Ruffault Pierre-Louis , Bouvier Julien C. , Murray Andrew J. , Morin-Surun Marie-Pierre , Zampieri Niccolò , Cholewa-Waclaw Justyna B. , Ey Elodie , Brunet Jean-Francois , Champagnat Jean , Fortin Gilles , Birchmeier Carmen
Published: July 2017

Significance

Vocalization is a primary method of communication in many species and relies on coordinated muscle activity. Vocalization and breathing must be synchronized, because calls can be evoked only during expiration. How vocalization and breathing are coordinated is not well understood. Here, we show that newborn mice with impaired development of the nucleus tractus solitarius (NTS) are mute and cannot generate the expiratory pressure needed for vocalization. Furthermore, they do not receive appropriate maternal care. We demonstrate that the NTS contains premotor neurons that directly project to and entrain the activity of spinal (L1) and nucleus ambiguus motor neurons known to control expiratory pressure and laryngeal tension, respectively. We conclude that the NTS is an essential component of the vocal circuit.
Structure of the
Arabidopsis
TOPLESS corepressor provides insight into the evolution of transcriptional repression
Authors: Martin-Arevalillo Raquel , Nanao Max H. , Larrieu Antoine , Vinos-Poyo Thomas , Mast David , Galvan-Ampudia Carlos , Brunoud Géraldine , Vernoux Teva , Dumas Renaud , Parcy François
Published: July 2017

Significance

In most biological processes, genes have to be activated and/or repressed. In plants, the TOPLESS protein is essential for gene repression through its action as a corepressor bridging transcription factor with chromatin remodeling complexes. Here we combine biochemical and structural studies to describe the structure of TOPLESS, how it tetramerizes, and how it interacts with its protein partners. We show that both the tetramerization interface and the binding site for protein partners have been conserved since algae, highlighting the ancestrality of TOPLESS function. Comparison of this plant protein with one of its animal counterparts also shows how corepressors can use a common domain differently to achieve similar properties, illustrating the tinkering of evolution in transcriptional repression.
Deletion of Gas2l3 in mice leads to specific defects in cardiomyocyte cytokinesis during development
Authors: Stopp Sabine , Gründl Marco , Fackler Marc , Malkmus Jonas , Leone Marina , Naumann Ronald , Frantz Stefan , Wolf Elmar , von Eyss Björn , Engel Felix B. , Gaubatz Stefan
Published: July 2017

Significance

Here, we demonstrate that mice lacking GAS2L3, a cytoskeleton-associated protein that interacts with actin filaments and tubulin, develop cardiomyopathy and heart failure after birth. During embryogenesis, cardiomyocytes rapidly divide. In the perinatal and neonatal period, cardiomyocytes withdraw from the cell cycle, binucleate, and the further increase in cardiac mass is achieved by hypertrophy. Germ-line deletion of
Gas2l3
results in decreased cardiomyocyte proliferation and in cardiomyocyte hypertrophy. Embryonal cardiomyocytes from
Gas2l3
-deficient mice exhibit increased expression of the cell cycle inhibitor p21 and display premature binucleation of cardiomyocytes due to defects in cytokinetic abscission. Together these results suggest that GAS2L3 plays a central role in cardiomyocyte proliferation and cytokinesis during development.
BMTP-11 is active in preclinical models of human osteosarcoma and a candidate targeted drug for clinical translation
Authors: Lewis Valerae O. , Devarajan Eswaran , Cardó-Vila Marina , Thomas Dafydd G. , Kleinerman Eugenie S. , Marchiò Serena , Sidman Richard L. , Pasqualini Renata , Arap Wadih
Published: July 2017

Significance

In its metastatic/recurrent presentation, osteosarcoma is a high-risk tumor with poor management, essentially unchanged over the past 25 years. Osteosarcoma is a relatively rare cancer; however, because it affects predominantly teenagers and young adults, it is a leading disease-related cause of death and a major contributor to years of life lost in this age group. Here, we demonstrate the prognostic value of IL-11Rα in osteosarcoma progression and patient survival. We also report preclinical studies with the IL-11Rα–targeted peptidomimetic bone metastasis-targeting peptidomimetic (BMTP-11) as a therapeutic agent, either alone or in combination with gemcitabine, in both primary tumor and metastatic disease models. This study demonstrates successful applications directed against the IL-11Rα:IL-11 molecular axis in preclinical models of osteosarcoma.
Corticogeniculate feedback sharpens the temporal precision and spatial resolution of visual signals in the ferret
Authors: Hasse J. Michael , Briggs Farran
Published: July 2017

Significance

The functional role of corticothalamic circuits, connecting the cortex to the thalamus in the feedback direction, has remained a fundamental mystery in neuroscience. In spite of the fact that corticothalamic inputs are numerous, their influence on thalamic activity is modest. We used an innovative combination of virus-mediated gene delivery and optogenetics to probe the function of corticothalamic feedback in vision. We found that corticothalamic feedback does not alter the visual response properties of thalamic neurons, but instead controls the timing and fidelity of their responses to incoming visual inputs. Thus, our results provide an answer to a long-standing question in neuroscience: A key function of corticothalamic feedback is to control the timing and precision of thalamic responses.
A distinct subpopulation of CD25−T-follicular regulatory cells localizes in the germinal centers
Authors: Wing James Badger , Kitagawa Yohko , Locci Michela , Hume Hannah , Tay Christopher , Morita Takayoshi , Kidani Yujiro , Matsuda Kyoko , Inoue Takeshi , Kurosaki Tomohiro , Crotty Shane , Coban Cevayir , Ohkura Naganari , Sakaguchi Shimon
Published: July 2017

Significance

T-follicular regulatory (Tfr) cells, a subset of Foxp3-expressing regulatory T (Treg) cells, have a critical role in the control of antibody responses. Whereas Treg cells express CD25 and are dependent on IL-2, Tfr cells also express the transcription factor BCL6 that is inhibited by IL-2 in T-follicular helper (Tfh) cells. In this report, we find that mature Tfr cells in the germinal centers or circulating in human blood down-regulate CD25 and gain a transcriptional signature mixed between Tfh cells and Treg cells while retaining their regulatory function. These cells represent an IL-2–independent branch of effector Treg cells losing CD25 expression but gaining increased expression of Tfh-related markers, such as BCL6 and CXCR5, in both mice and humans.
Crystal structure of CO-bound cytochrome
c
oxidase determined by serial femtosecond X-ray crystallography at room temperature
Authors: Ishigami Izumi , Zatsepin Nadia A. , Hikita Masahide , Conrad Chelsie E. , Nelson Garrett , Coe Jesse D. , Basu Shibom , Grant Thomas D. , Seaberg Matthew H. , Sierra Raymond G. , Hunter Mark S. , Fromme Petra , Fromme Raimund , Yeh Syun-Ru , Rousseau Denis L.
Published: July 2017

Significance

A fundamental bioenergetics question is how the redox energy from oxygen reduction in cytochrome
c
oxidase (C
c
O) is coupled to proton translocation. Although crystallography has revealed many properties of the enzyme, the coupling mechanism remains elusive, in part due to artifacts caused by X-ray damage from synchrotron radiation. We determined the structure of CO-bound bovine C
c
O by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser, outrunning radiation damage. The SFX structure is compared with the structure obtained with synchrotron radiation in which the Fe–CO bond was cleaved. Our results reveal that ligand binding to heme
a
3
triggers an allosteric structural transition that may play a critical role in proton translocation in the C
c
O family of enzymes.
Bifunctionality of a biofilm matrix protein controlled by redox state
Authors: Arnaouteli Sofia , Ferreira Ana Sofia , Schor Marieke , Morris Ryan J. , Bromley Keith M. , Jo Jeanyoung , Cortez Krista L. , Sukhodub Tetyana , Prescott Alan R. , Dietrich Lars E. P. , MacPhee Cait E. , Stanley-Wall Nicola R.
Published: July 2017

Significance

The biofilm matrix is a critical target in the hunt for novel strategies to destabilize or stabilize biofilms. Knowledge of the processes controlling matrix assembly is therefore an essential prerequisite to exploitation. Here, we highlight that the complexity of the biofilm matrix is even higher than anticipated, with one matrix component making two independent functional contributions to the community. The influence the protein exerts is dependent on the local environmental properties, providing another dimension to consider during analysis. These findings add to the evidence that bacteria can evolve multifunctional uses for the extracellular matrix components.
Structural insights into lipoprotein N-acylation by
Escherichia coli
apolipoprotein N-acyltransferase
Authors: Noland Cameron L. , Kattke Michele D. , Diao Jingyu , Gloor Susan L. , Pantua Homer , Reichelt Mike , Katakam Anand K. , Yan Donghong , Kang Jing , Zilberleyb Inna , Xu Min , Kapadia Sharookh B. , Murray Jeremy M.
Published: July 2017

Significance

Lipoprotein biosynthesis is crucial for Gram-negative bacterial viability and involves the activities of three essential integral membrane proteins embedded in the inner membrane (Lgt, LspA, and Lnt). These enzymes function sequentially to produce mature triacylated lipoproteins, many of which are then transported to the outer membrane. Lnt is responsible for catalyzing the addition of palmitate to the N terminus of diacylated apolipoproteins. Despite a number of studies that have biochemically characterized
Escherichia coli
Lnt, the structural basis for substrate engagement and catalysis remains unclear. Here we present the crystal structures of wild-type
E. coli
Lnt and a C387S active-site mutant. These structures provide insights into the molecular mechanisms of apolipoprotein N-acylation by Lnt and shed further light on the mechanism of lipoprotein biosynthesis by these essential bacterial enzymes.
Are New Zealanders “rhotic”?
Authors: Marsden Sharon
Published: July 2017

Rhoticity is highly variable across English varieties. Traditionally, descriptions of English have distinguished between “rhotic” and “non-rhotic” varieties. However,Harris’s (2013)recent description of three core rhotic systems (R1, R2 and R3) demonstrates that this dichotomy is overly simplistic. The literature describes New Zealand English (NZE) as “non-rhotic”, with partial rhoticity in the lower South Island. This paper reports on data collected in two semi-rural towns in the North Island where young New Zealanders employ a “mixed” distribution of rhoticity. Alongside /r/ use which is traditionally associated with “non-rhotic” varieties (Harris’s R2 and R3), speakers also exhibit /r/ use which is associated with “rhotic” varieties (Harris’s R1). The findings suggest that dynamic rhoticity in NZE, which also persists historically in Englishes world-wide, can be represented more effectively by dispensing with the notions “rhotic” and “non-rhotic”, and by treating rhoticity as a continuum of /r/ use.
“Like getting nibbled to death by a duck”
Authors: Schwarz Sarah
Published: July 2017

This large-scale corpus study explores new parameters which might indicate grammaticalization of theget-passive in recent American English, where the construction has increased in frequency. To this end, large samples of bothbe- andget-passives from the TIME Magazine Corpus were analyzed with regard to tense, aspect, and situation type (Aktionsart). While tense and aspect preferences of the passives were diachronically stable, the results of the situation-type analysis were of interest for two reasons. First, they showed clear differences in the wayget- andbe-passives are used which reflect theget-passive’s inchoative origins. And second, the diachronic analysis of situation-type preferences forget-passives provides a first indication that they may be further grammaticalizing as they begin to behave more like canonicalbe-passives in the most recent data. This finding is tentatively supported by supplementary data from COHA.
Empirical approaches for investigating the origins of structure in speech
Authors: Little Hannah , Rasilo Heikki , van der Ham Sabine , Eryılmaz Kerem
Published: July 2017

In language evolution research, the use of computational and experimental methods to investigate the emergence of structure in language is exploding. In this review, we look exclusively at work exploring the emergence of structure in speech, on both a categorical level (what drives the emergence of an inventory of individual speech sounds), and a combinatorial level (how these individual speech sounds emerge and are reused as part of larger structures). We show that computational and experimental methods for investigating population-level processes can be effectively used to explore and measure the effects of learning, communication and transmission on the emergence of structure in speech. We also look at work on child language acquisition as a tool for generating and validating hypotheses for the emergence of speech categories. Further, we review the effects of noise, iconicity and production effects.
Conversation, cognition and cultural evolution
Authors: Roberts Seán G. , Levinson Stephen C.
Published: July 2017

This paper outlines a first attempt to model the special constraints that arise in language processing in conversation, and to explore the implications such functional considerations may have on language typology and language change. In particular, we focus on processing pressures imposed by conversational turn-taking and their consequences for the cultural evolution of the structural properties of language. We present an agent-based model of cultural evolution where agents take turns at talk in conversation. When the start of planning for the next turn is constrained by the position of the verb, the stable distribution of dominant word orders across languages evolves to match the actual distribution reasonably well. We suggest that the interface of cognition and interaction should be a more central part of the story of language evolution.
The Many Deaths of Cyrus the Great
Authors: Beckman Daniel
Published: July 2017

This article uses narratives of the death of Cyrus the Great as a test case in order to examine the use of propaganda in the Achaemenid empire. By comparing the accounts found in Herodotus, Ctesias, and Xenophon, it is shown that these Greek historians have captured propagandistic messages created in the courts of contemporary Achaemenid kings. While the Greek works were very much the product of their authors’ literary imagination, nevertheless they preserved substantial evidence about the role of propaganda during the Achaemenid period.
The fractions SNARC revisited: Processing fractions on a consistent mental number line
Authors: Toomarian Elizabeth Y , Hubbard Edward M
Published: July 2017

The ability to understand fractions is key to establishing a solid foundation in mathematics, yet children and adults struggle to comprehend them. Previous studies have suggested that these struggles emerge because people fail to process fraction magnitude holistically on the mental number line (MNL), focusing instead on fraction components. Subsequent studies have produced evidence for default holistic processing but examined only magnitude processing, not spatial representations. We explored the spatial representations of fractions on the MNL in a series of three experiments. Experiment 1 replicated Bonato et al.; 30 naïve undergraduates compared unit fractions (1/1-1/9) to 1/5, resulting in a reverse SNARC (Spatial-Numerical Association of Response Codes) effect. Experiment 2 countered potential strategic biases induced by the limited set of fractions used by Bonato et al. by expanding the stimulus set to include all irreducible, single-digit proper fractions and asked participants to compare them against 1/2. We observed a classic SNARC effect, completely reversing the pattern from Experiment 1. Together, Experiments 1 and 2 demonstrate that stimulus properties dramatically impact spatial representations of fractions. In Experiment 3, we demonstrated within-subjects reliability of the SNARC effect across both a fractions and whole number comparison task. Our results suggest that adults can indeed process fraction magnitudes holistically, and that their spatial representations occur on a consistent MNL for both whole numbers and fractions.
Circulating exosome microRNA associated with heart failure secondary to myxomatous mitral valve disease in a naturally occurring canine model
Authors: Yang Vicky K. , Loughran Kerry A. , Meola Dawn M. , Juhr Christine M. , Thane Kristen E. , Davis Airiel M. , Hoffman Andrew M.
Published: July 2017

Myxomatous mitral valve disease (MMVD) is functionally and histologically identical to mitral valve prolapse (MVP) in humans. Currently, there are no medical treatments that can delay the progression of this valvular disease or associated cardiac remodelling. Therefore, there is a need to understand the molecular pathology associated with MMVD and MVP better, and thus identify potential therapeutic targets. Circulating exosomes contain small RNA, including miRNA, which reflect cell physiology and pathology. This study explored the association between circulating exosomal miRNA (ex‐miRNA) content and MMVD, heart failure due to MMVD (MMVD‐CHF) and ageing, which is strongly associated with MMVD. Ex‐miRNA was isolated from old normal/healthy dogs (n = 6), young normal dogs (n = 7), dogs with MMVD (n = 7) and dogs with MMVD‐CHF (n = 7). Separately, total plasma miRNA was isolated from normal dogs (n = 8), dogs with MMVD (n = 8) and dogs with MMVD‐CHF (n = 11). Using reverse transcription quantitative polymerase chain reaction, exosomal miR‐181c (p = 0.003) and miR‐495 (p = 0.0001) significantly increased in dogs with MMVD‐CHF compared to the other three groups. Exosomal miR‐9 (p = 0.002) increased in dogs with MMVD and MMVD‐CHF compared to age‐matched (old) normal dogs. Exosomal miR‐599 (p = 0.002) decreased in dogs with MMVD compared to old normal dogs. In total plasma, 58 miRNA were deemed significantly different (p < 0.04) between normal dogs, dogs with MMVD and dogs with MMVD‐CHF. However, in contrast to ex‐miRNA, none of the miRNA in total plasma remained statistically significant if the false discovery rate was <15%. Changes in ex‐miRNA are observed in dogs as they age (miR‐9, miR‐495 and miR‐599), develop MMVD (miR‐9 and miR‐599) and progress from MMVD to CHF (miR‐181c and miR‐495). Ex‐miRNA expression‐level changes appear to be more specific to disease states than total plasma miRNA.

RESPONSIBLE EDITOR Elena Aikawa, Harvard Medical School, USA
Self-sorting of nonmuscle myosins IIA and IIB polarizes the cytoskeleton and modulates cell motility
Authors: Shutova Maria S. , Asokan Sreeja B. , Talwar Shefali , Assoian Richard K. , Bear James E. , Svitkina Tatyana M.
Published: July 2017

Nonmuscle myosin II (NMII) is uniquely responsible for cell contractility and thus defines multiple aspects of cell behavior. To generate contraction, NMII molecules polymerize into bipolar minifilaments. Different NMII paralogs are often coexpressed in cells and can copolymerize, suggesting that they may cooperate to facilitate cell motility. However, whether such cooperation exists and how it may work remain unknown. We show that copolymerization of NMIIA and NMIIB followed by their differential turnover leads to self-sorting of NMIIA and NMIIB along the front–rear axis, thus producing a polarized actin–NMII cytoskeleton. Stress fibers newly formed near the leading edge are enriched in NMIIA, but over time, they become progressively enriched with NMIIB because of faster NMIIA turnover. In combination with retrograde flow, this process results in posterior accumulation of more stable NMIIB-rich stress fibers, thus strengthening cell polarity. By copolymerizing with NMIIB, NMIIA accelerates the intrinsically slow NMIIB dynamics, thus increasing cell motility and traction and enabling chemotaxis.
Cross-Unit Causation and the Identity of Groups
Authors: Glymour Bruce
Published: July 2017

In this article I explore some statistical difficulties confronting going conceptions of ‘group’ as understood in accounts of group selection. Most such theories require real groups but define the reality of groups in ways that make it impossible to test for their reality. There are alternatives, but they either require or invite a nominalism about groups that many theorists abjure.
Computer simulations reveal mechanisms that organize nuclear dynein forces to separate centrosomes
Authors: De Simone Alessandro , Gönczy Pierre
Published: July 2017

Centrosome separation along the surface of the nucleus at the onset of mitosis is critical for bipolar spindle assembly. Dynein anchored on the nuclear envelope is known to be important for centrosome separation, but it is unclear how nuclear dynein forces are organized in an anisotropic manner to promote the movement of centrosomes away from each other. Here we use computational simulations of Caenorhabditis elegans embryos to address this fundamental question, testing three potential mechanisms by which nuclear dynein may act. First, our analysis shows that expansion of the nuclear volume per se does not generate nuclear dynein–driven separation forces. Second, we find that steric interactions between microtubules and centrosomes contribute to robust onset of nuclear dynein–mediated centrosome separation. Third, we find that the initial position of centrosomes, between the male pronucleus and cell cortex at the embryo posterior, is a key determinant in organizing microtubule aster asymmetry to power nuclear dynein–dependent separation. Overall our work reveals that accurate initial centrosome position, together with steric interactions, ensures proper anisotropic organization of nuclear dynein forces to separate centrosomes, thus ensuring robust bipolar spindle assembly.
VariantTools: an extensible framework for developing and testing variant callers
Authors: Lawrence Michael , Gentleman Robert
Published: July 2017

Motivation

Variant calling is the complex task of separating real polymorphisms from errors. The appropriate strategy will depend on characteristics of the sample, the sequencing methodology and on the questions of interest.

Results

We present VariantTools, an extensible framework for developing and testing variant callers. There are facilities for reproducibly tallying, filtering, flagging and annotating variants. The tools are extensible, modular and flexible, so that they are tunable to particular use cases, and they interoperate with existing analysis software so that they can be embedded in established work flows.

Availability and implementation

VariantTools is available from http://www.bioconductor.org/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Tomato spotted wilt virus Can Infect Resistant Tomato when Western Flower Thrips Inoculate Blossoms
Authors: Houle J. L. , Kennedy G. G.
Published: July 2017

Tomato spotted wilt is a major disease of crops worldwide. Resistant cultivars carrying the Sw-5 allele for resistance to tomato spotted wilt disease (TSW) provide the most effective control method in tomato (Solanum lycopersicum). However, infections of fruit on Sw-5+ tomato plants suggest the virus resistance may not be fully expressed in blossoms or developing fruit. The objective of this study was to determine if the thrips vector, the western flower thrips (Frankliniella occidentalis), can transmit non-resistance breaking Tomato spotted wilt virus (TSWV) isolates when confined to blossoms on plants with and without the Sw-5 resistance allele. Twenty-one percent of 33 Sw-5+ plants inoculated by adult thrips feeding on blossom clusters or small fruit developed infections in the reproductive tissue, whereas 68% of 25 Sw-5– plants developed infections. Systemic infections also occurred following inoculation of blossoms in host genotypes with and without Sw-5. These results were further supported by field experiments that showed high proportions of infected fruit as well as a limited infection of foliage on the same stem as the infected fruit in Sw-5+ plants when F. occidentalis were abundant in blossoms. These findings help to explain observations of abundant late season infections of Sw-5 cultivars in commercial plantings and suggest that management of F. occidentalis infestations during the bloom period may be important for effective management of TSWV in susceptible tomato cultivars as well as cultivars expressing the Sw-5 allele for TSW resistance.
Development of a Loop-Mediated Isothermal Amplification Assay for the Detection of Dickeya spp.
Authors: Yasuhara-Bell Jarred , Marrero Glorimar , Arif Mohammad , de Silva Asoka , Alvarez Anne M.
Published: July 2017

Dickeya and Pectobacterium spp. are responsible for soft-rotting diseases of several plant species, some with overlapping host range. On potato, symptoms caused by these pathogens cannot be clearly differentiated. Disease results in the downgrading and rejection of potato seed, thus requiring additional phytosanitary restrictions across Northern Europe and other parts of the world. In an effort to provide a more timely and accurate diagnostic to distinguish these two groups of pathogens, a method for detecting Dickeya spp. using loop-mediated isothermal amplification (LAMP) was developed. The LAMP assay can be used to test crude extracts prepared directly from symptomatic lesions. The entire test can be completed in less than 30 min, making it faster than the current diagnostic standard, the pelADE conventional polymerase chain reaction. Additionally, the LAMP assay was able to detect Dickeya DNA in samples spiked with varying amounts of Pectobacterium DNA, thus demonstrating the highly specific and sensitive nature of the assay, which can be applied on survey samples with mixed soft-rotting bacterial populations.
Auditory Brainstem Implant Array Position Varies Widely Among Adult and Pediatric Patients and Is Associated With Perception
Authors: Barber Samuel R. , Kozin Elliott D. , Remenschneider Aaron K. , Puram Sidharth V. , Smith Max , Herrmann Barbara S. , Cunnane Mary E. , Brown M. Christian , Lee Daniel J.
Published: July 2017

Objectives:

The auditory brainstem implant (ABI) provides sound awareness to patients who are ineligible for cochlear implantation. Auditory performance varies widely among similar ABI cohorts. We hypothesize that differences in electrode array position contribute to this variance. Herein, we classify ABI array position based on postoperative imaging and investigate the relationship between position and perception.

Design:

Retrospective review of pediatric and adult ABI users with postoperative computed tomography. To standardize views across subjects, true axial reformatted series of scans were created using the McRae line. Using multiplanar reconstructions, basion and electrode array tip coordinates and array angles from vertical were measured. From a lateral view, array angles (V) were classified into types I to IV, and from posterior view, array angles (T) were classified into types A to D. Array position was further categorized by measuring distance vertical from basion (D1) and lateral from midline (D2). Differences between array classifications were compared with audiometric thresholds, number of active electrodes, and pitch ranking.

Results:

Pediatric (n = 4, 2 with revisions) and adult (n = 7) ABI subjects were included in this study. Subjects had a wide variety of ABI array angles, but most were aimed superiorly and posteriorly (type II, n = 7) from lateral view and upright or medially tilted from posterior view (type A, n = 6). Mean pediatric distances were 8 to 42% smaller than adults for D1 and D2. In subjects with perceptual data, electrical thresholds and the number of active electrodes differed among classification types.

Conclusions:

In this first study to classify ABI electrode array orientation, array position varied widely. This variability may explain differences in auditory performance.
Postinfectious heterotopic ossification of the ilium involving the iliacus muscle
Authors: Muhamad Effendi Ferdhany , Nam Yunjin , Shin Chang Ho , Cho Tae-Joon , Yoo Won Joon , Cheon Jung-Eun , Choi In Ho
Published: July 2017

Heterotopic ossification in soft tissue or muscle is rare in the pediatric and adolescent age group. Most cases are associated with musculoskeletal injury and trauma to the central nervous system. Here, we describe an adolescent patient without a history of trauma or lesions in the central nervous system who presented with a painful limp with limited motion of the left hip. Investigations indicated unusually large heterotopic ossification extending from the inner aspect of the ilium down to the anterior part of the hip, highly likely to have developed after an unrecognized periacetabular pyomyositis primarily involving the iliacus muscle. Surgical excision was performed successfully without perioperative complications. No recurrence was detected at the final follow-up.
Congenital unilateral absence of the upper extremity may give rise to a specific kind of thoracolumbar curve
Authors: Olgun Z. Deniz , Demirkiran Gokhan , Polly David , Yazici Muharrem
Published: July 2017

There is an increased incidence of scoliosis in patients with congenital malformations of the upper extremity even in the absence of overt vertebral abnormalities. In this case series, we summarize the curve characteristics of four patients presenting to two spine surgery clinics with unilateral amelia or phocomelia and a progressive scoliotic curve with the apex on the side of deficiency. All patients required orthopedic intervention for their curves. Amelia and phocomelia are severe congenital malformations of the upper limb affecting trunk balance and, conceivably, causing scoliosis with the absence of counterbalancing weight on the affected side. The combination of upper limb absence and same-sided scoliosis in these patients may provide a clue of the mechanical factors causing scoliosis in other disorders. In this article, we attempt to define this exceptional deformity, theorize on its etiology, and draw attention to this particular combination of problems. Level of Evidence: Case series; Level IV.
Gain of length–loss of strength? Alteration in muscle strength after femoral leg lengthening in young patients: a prospective longitudinal observational study
Authors: Krieg Andreas H. , Gehmert Sebastian , Neeser Olivia L. , Kaelin Xaver , Speth Bernhard M.
Published: July 2017

This study aimed to determine the alteration in maximum isokinetic torque in patients after intramedullary femoral leg lengthening. Thirty patients with a median leg-length discrepancy of 3.0 cm underwent femoral limb lengthening with an intramedullary motorized device. Maximum isokinetic, concentric torque of the extensors, and flexors of the knee was measured before (n=30) and 2 years after surgery (n=21). Postoperatively, a significant difference remained for the maximum isokinetic torque of the extensors (22%) between the lengthened and the normal leg, which might have been caused by muscle response to the distraction procedure itself in the form of higher stiffness, less immediate displacement, and inconsistent force relaxation properties. However, we provide evidence that physiotherapy after limb lengthening should focus on extensors to prevent loss of strength.
Botulinum-A intramuscular injection in an orthopaedic paediatric patient cohort: service restructure analysis
Authors: Lee Matthew , Kelly Enda , Kelly Paula
Published: July 2017

Botulinum intramuscular injections are increasingly being used in the management of hypertonic musculature. Historically, injections were administered under general anaesthesia (GA), which has service and economic implications. Our delivery changed to outpatient conscious injections to improve service efficiency. A retrospective analysis of all patient injections from January 2010 to December 2015 analysed cost–benefit and efficiency of service remodelling. 472 patients were administered injections, 298 in theatre under GA and 174 without GA. In 2010, 97 of 102 cases were performed under GA (45 theatre-hours), decreasing to 18 of 68 cases in 2015 (8.4 theatre-hours). The mean hospital stay decreased from 410 to 135 min. The reduction in theatre use and the requirement for a postanaesthetic bed led to significant savings per case. Service remodelling showed successful cost saving and reduced in-hospital stay.
Menstrual pad, a cervical cancer screening tool, a population-based study in rural India
Authors: Budukh Atul , Palayekar Vrushali , Maheshwari Amita , Deodhar Kedar , Purwar Pallavi , Bagal Sonali , Vadigoppula Ashok , Lokhande Manoj , Panse Nandkumar , Dikshit Rajesh , Badwe Rajendra
Published: July 2017

In the rural areas of India, women generally use a piece of old cloth as a menstrual device. The aim of this study was to detect human papilloma virus (HPV) from menstrual blood on the menstrual pad and assess whether this could be a useful screening tool for cervical cancer. In Jamkhed area of rural Maharashtra, (population A), we collected menstrual pads from women who provided consent in the 30–50 year age group. The women who had provided menstrual pads underwent HC2 testing. We standardized the method for extracting DNA by PCR from the menstrual pad. The women who tested HPV positive, on the basis of HC2/PCR testing, underwent colposcopy. In the rural population of Pune area of Maharashtra state (population B), menstrual pads were collected. HPV was tested using the PCR method. HPV-positive women and a few HPV-negative women, selected randomly, underwent colposcopy and HC2 testing. In population A, 164 women provided their used menstrual pads and also underwent an HC2 screening test. Of these, six (3.2%) cases were reported as HPV positive. In population B, 365 women provided their used menstrual pads for HPV testing, of which 18 (4.9%) cases were diagnosed as HPV positive. The women who tested HPV positive, on the basis of PCR testing, and 10% randomly selected HPV-negative cases (37) and 18 women who voluntary requested testing underwent colposcopy and HC2 testing. The sensitivity of menstrual pad HPV testing compared with gold standard HC2 testing was 83% [95% confidence interval (CI): 0.47–0.97], 67% (95% CI: 0.30–0.91) and specificity was 99% (95% CI: 0.96–0.99), 88% (95% CI: 0.77–0.94) in population A and population B, respectively. The sensitivity of diagnosing CIN lesion was 83% (95% CI: 0.44–0.97) and specificity was 95% (95% CI: 0.91–0.97). On the basis of the sensitivity and specificity results, and the completely noninvasive, simple and convenient method of detecting HPV, menstrual pad might be considered a cervical cancer screening tool in rural Indian women.
Mitigation of adverse behavioral impact from predator exposure by the nociceptin/orphanin FQ peptide antagonist J-113397 in rats
Authors: Genovese Raymond F. , Dobre Stefania
Published: July 2017

The nociceptin/orphanin FQ peptide (NOP) receptor is believed to have an integral modulatory function in the stress response system. We evaluated the highly selective NOP antagonist J-113397 (7.5 and 20.0 mg/kg), using a predator exposure in which rats were exposed to predator cats as a stressor. A single dose of J-113397 or vehicle was administered (intraperitoneally) shortly before exposure to the predators or a sham exposure. Behavioral impact was measured using elevated plus maze (EPM), open field activity (OFA), and an olfactory discrimination (OD). The predator exposure produced a relatively long-lasting deficit (decreased time in open arms, decreased basic activity) on the EPM while having little effect on performance on the OFA or OD. J-113397 mitigated the performance deficits on the EPM in a dose-dependent manner while having little effect on performance on the OFA or OD. The largest dose of J-113397, administered with a sham exposure, was essentially devoid of effects on the EPM, OFA, and OD. These results demonstrate that J-113397 can significantly and selectively mitigate the effects of a stressor typically used in a preclinical model of post-traumatic stress disorder. Furthermore, these results are consistent with and extend previous results showing that the NOP receptor has an important role in the response to stress and that NOP antagonism may, potentially, have therapeutic benefit in stress disorders.