bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular nanowires and their properties as electrical conductors
Authors: Kirczenow George
Published: August 2017

This article describes the properties of molecular nanowires as electrical conductors. It begins by defining a molecular nanowire and describing a specific example of a molecular nanowire, along with the concept of molecular nanowire self-assembly. It then considers how molecular nanowires are realized in the laboratory as well as the relationships between these methodologies, the systems that are produced and some experiments being performed on them. It also looks at the different kinds of molecules, electrodes and linkers out of which molecular nanowires are being or may be constructed; the Landauer approach to electrical conduction in molecular nanowires; the principles and limitations of ab-initio and semi-empirical modelling of molecular nanowires in the context of electrical conduction; and four specific experimental systems and the extent to which their observed behavior has been understood theoretically. The article concludes with a summary of key issues for the future development of the field.
Self-organizing atom chains
Authors: van Houselt Arie , Zandvliet Harold J.W.
Published: August 2017

This article examines the intriguing physical properties of nanowires, with particular emphasis on self-organizing atom chains. It begins with an overview of the one-dimensional free electron model and some interesting phenomena of one-dimensional electron systems. It derives an expression for the 1D density of states, which exhibits a singularity at the bottom of the band and extends the free-electron model, taking into consideration a weak periodic potential that is induced by the lattice. It also describes the electrostatic interactions between the electrons and goes on to discuss two interesting features of 1D systems: the quantization of conductance and Peierls instability. Finally, the article presents the experimental results of a nearly ideal one-dimensional system, namely self-organizing platinum atom chains on a Ge(001) surface, focusing on their formation, quantum confinement between the Pt chains and the occurrence of a Peierls transition within the chains.
Optical properties of carbon nanotubes and nanographene
Authors: Saito R. , Jorio A. , Jiang J. , Sasaki K. , Dresselhaus G. , Dresselhaus M.S.
Published: August 2017

This article examines the optical properties of single-wall carbon nanotubes (SWNTs) and nanographene. It begins with an overview of the shape of graphene and nanotubes, along wit the use of Raman spectroscopy to study the structure and exciton physics of SWNTs. It then considers the basic definition of a carbon nanotube and graphene, focusing on the crystal structure of graphene and the electronic structure of SWNTs, before describing the experimental setup for confocal resonance Raman spectroscopy. It also discusses the process of resonance Raman scattering, double-resonance Raman scattering, and the Raman signals of a SWNT as well as the dispersion behavior of second-order Raman modes, the doping effect on the Kohn anomaly of phonons, and the elastic scattering of electrons and photons. The article concludes with an analysis of excitons in SWNTs and outlines future directions for research.
Thermopower of low-dimensional structures: The effect of electron–phonon coupling
Authors: Tsaousidou M.
Published: August 2017

This article examines the effect of electron-phonon coupling on the thermopower of low-dimensional structures. It begins with a review of the theoretical approaches and the basic concepts regarding phonon drag under different transport regimes in two- and one-dimensional systems. It then considers the thermopower of two-dimensional semiconductor structures, focusing on phonon drag in semi-classical two-dimensional electron gases confined in semiconductor nanostructures. It also analyzes the influence of phonon drag on the thermopower of semiconductor quantum wires and describes the phonon-drag thermopower of doped single-wall carbon nanotubes. The article compares theory and experiment in order to demonstrate the role of phonon-drag and electron-phonon coupling in the thermopower in two and one dimensions.
Unusual properties of nanoscale ferroelectrics
Authors: Fu Huaxiang
Published: August 2017

This article describes the unusual properties of nanoscale ferroelectrics (FE), including widely tunable polarization and improved properties in strained ferroelectric thin films; polarization enhancement in superlattices; polarization saturation in ferroelectric thin films under very large inplane strains; occurrence of ferroelectric phase transitions in one-dimensional wires; existence of the toroidal structural phase in ferroelectric nanoparticles; and the symmetry-broken phase-transition path when one transforms a vortex phase into a polarization phase. The article first considers some of the critical questions on low-dimensional ferroelectricity before discussing the theoretical approaches used to determine the properties of ferroelectric nanostructures. It also looks at 2D ferroelectric structures such as surfaces, superlattices and thin films, along with 1D ferroelectric nanowires and ferroelectric nanoparticles.
Scanning transmission electron microscopy of nanostructures
Authors: Pennycook S.J. , Varela M. , Chisholm M.F. , Borisevich A.Y. , Lupini A.R. , van Benthem K. , Oxley M.P. , Luo W. , McBride J.R. , Rosenthal S.J. , Oh S.H. , Sales D.L. , Molina S.I. , Sohlberg K. , Pantelides S.T.
Published: August 2017

This article investigates nanostructures by means of scanning transmission electron microscopy. The electron microscope is uniquely suited to the study of individual nanostructures, allowing differentiation of different structures and properties that is difficult or impossible to do with techniques that provide a spatial average. The present generation of aberration correctors, which correct all aberrations up to third order, makes it possible to obtain sufficient sensitivity to image and spectroscopically analyze single atoms. This article begins with a brief overview of the correction of lens aberration in electron microscopy, followed by several examples of insights into nanomaterials and the atomic origins of their functionality. In particular, it considers semiconductor nanocrystals, semiconductor quantum wires, and nanocatalysts. It also discusses magnetism in gold and silver nanoclusters as well as charge ordering in manganites.
Holographic laser processing for three-dimensional photonic lattices
Authors: Shoji Satoru , Zaccaria Remo Proietti , Kawata Satoshi
Published: August 2017

This article describes a holographic laser-processing method for independently controlling the lattice symmetry and lattice constant in three-dimensional photonic lattices. With this approach, optical periodicity is created in lower dimensions and three-dimensional periodicity is obtained by a combination of several lower-dimensional periodic structures. The proposed holographic laser-processing method is compared with the standard four-beam technique. Examples of experimental demonstration achieved in photosensitive polymers are given. The article also introduces a multiphoton direct-writing technique for creating defect structures in lattices towards production of defect cavity-functionalized photonic crystal devices. It shows that all Bravais lattices can be produced by choosing proper incident vectors of laser beams. The lattice constant of the structure can be changed without distorting its lattice symmetry and lattice elements.
Templated carbon nanotubes and the use of their cavities for nanomaterial synthesis
Authors: Kyotani T. , Orikasa H.
Published: August 2017

This article focuses on templated carbon nanotubes (CNTs) and how their cavities can be used for the synthesis of nanomaterials. In particular, it demonstrates how effectively the CNTs can be functionalized by the template carbonization technique. The article first describes the method for synthesizing CNTs and carbon nano-test-tubes (CNTTs). It then considers the controlled filling of magnetic materials into CNTTs, taking into account the electrochemical deposition of Ni-Fe alloy and the magnetic properties of NiFe-filled CNTTs. It also examines the synthesis of water-dispersible and magnetically responsive CNTTs, with emphasis on water dispersibility and the effect of magnetic interaction. Finally, it shows how the cavities of templated CNTs can be utilized as a reaction field for the hydrothermal synthesis of one-dimensional nanomaterials.
Modulation design of plasmonics for diagnostic and drug screening
Authors: Lin C.-W. , Chiu N.-F. , Chang C.-C.
Published: August 2017

This article discusses the modulation design of plasmonics for diagnosis and drug screening applications. It begins with an overview of the advances made in terms of theoretical insights, focusing on the origins of surface plasmon wave and manipulation, admittance loci design method, and surface plasmon grating coupled emission. It then considers how prism coupler, Ge-doped silica waveguide, nanograting and active plasmonics can trigger the excitation of surface plasmon resonance (SPR). It also examines the metallic effect of long-range surface plasmon resonance and conducting metal oxide as adhesive layer before describing three SPR waveguide biosensors that were developed for the realization of a hand-held SPR system. In particular, it presents a lateral-flow microfluidic channel based on a nitrocellulose membrane and integrated with a SPR waveguide biosensor to achieve dynamic detection. Finally, the article evaluates the biomolecular layer effect, with emphasis on kinetics analysis of antibody binding.
Few-electron quantum-dot spintronics
Authors: Melnikov D.V. , Kim J. , Zhang L.-X. , Leburton J.-P.
Published: August 2017

This article examines the spin and charge properties of double and triple quantum dots (QDs) populated containing just a few electrons, with particular emphasis on laterally coupled QDs. It first describes the theoretical approach, known as exact diagonalization method, utilized on the example of the two-electron system in coupled QDs that are modelled as two parabolas. The many-body problem is solved via the exact diagonalization method as well as variational Heitler–London and Monte Carlo methods. The article proceeds by considering the general characteristics of the two-electron double-QD structure and limitations of the approximate methods commonly used for its theoretical description. It also discusses the stability diagram for two circular dots and investigates how its features are affected by the QD elliptical deformations. Finally, it assesses the behavior of the two-electron system in the realistic double-dot confinement potentials.
Evaluating the risks associated with nanomaterials
Authors: Thomas K. , Monteiro-Riviere N. , Warheit D. , Savage N.
Published: August 2017

This article discusses the risks associated with nanomaterials. The use of nanomaterials in consumer products and industrial applications is becoming more prevalent owing to their range of benefits. Nanomaterials have found uses in energy production, home appliances, water treatment, novel therapeutic delivery techniques and dietary supplements, consumer electronics, and sports equipment. While considerable attention has been given to the likely commercial advantages associated with nanomaterials, less emphasis has been placed on the development of a systematic approach for characterizing the human health and environmental risks from exposure to nanomaterials. This article first considers the use of nanomaterials in consumer products and the characterization of nanomaterials before describing a systematic evaluation of the hazards associated with nanomaterials. It also examines pulmonary exposure assessment and dermal exposure assessment, along with risk assessment for exposure to nanomaterials. Finally, it outlines research priorities for the development of more refined estimates of nanomaterial risk.
Spintronics with metallic nanowires
Authors: Ansermet J.-Ph.
Published: August 2017

This article focuses on spintronics with metallic nanowires. It begins with a review of the highlights of spintronics research, paying attention to the very important developments accomplished with tunnel junctions. It then considers the effect of current on magnetization before discussing spin diffusion and especially spin-dependent conductivities, spin-diffusion lengths, and spin accumulation. It also examines models for spin-polarized currents acting on magnetization, current-induced magnetization switching, and current-driven magnetic excitations. It concludes with an overview of resonant-current excitations, with emphasis on spin-valves and tunnel junctions as well as resonant excitation of spin-waves, domain walls and vortices. In addition, the article reflects on the future of spintronics, citing in particular the potential of the spin Hall effect as the method of generating spin accumulation, free of charge accumulation.
Polyelectrolyte Solutions and Gels
Authors: Dobrynin Andrey V.
Published: August 2017

This article examines the physics of polyelectrolytes, with particular emphasis on the properties of individual charged chains in solution, in more dense environments and in crosslinked gels. Polyelectrolyte solutions and gels are multicomponent systems comprised of solvent molecules, charged polymer chains, counterions, and salt ions. The properties of these systems depend on polymer and salt concentrations, the electrostatic interactions between charges, monomer-solvent interactions controlling the solvent affinity for the polymer backbone, and the interactions between charges and solvent molecules determining solvation of the ions by a solvent. This article first considers dilute salt-free polyelectrolyte solutions, focusing on polyelectrolyte chains, the condensation of counterions, and ionization equilibrium. The discussion then turns to a polyelectrolyte chain in salt solutions, semidilute polyelectrolyte solutions, and phase separation in polyelectrolyte solutions. The article concludes with an analysis of swelling in polyelectrolyte gels.
X-ray upper limits of GW151226 with MAXI
Authors: Serino Motoko , Kawai Nobuyuki , Negoro Hitoshi , Mihara Tatehiro , Masumitsu Takahiro , Nakahira Satoshi
Published: August 2017

The error region of the the gravitational-wave (GW) event GW151226 was observed with Monitor of All-sky X-ray Image (MAXI). MAXI was operating at the time of GW151226, and continuously observed up to 4 min after the event. MAXI covered about 84% of the 90% error region of the GW event during the first 92 min orbit after the event. No significant X-ray transient was detected in the GW error region. A typical 3 σ Gas Slit Camera upper limit for a scan is 1.2 × 10−9 erg cm−2 s−1 in the 2–20 keV band. The autodetection (MAXI nova-search) systems detected a short excess event with a low significance (2.85 σ) from 5257 s to 5260 s after the GW trigger. Finally, we discuss the sensitivity of MAXI to long X-ray emissions of short gamma-ray bursts, which are expected to accompany GW events.
Strain-Specific Hypersensitive and Extreme Resistance Phenotypes Elicited by Potato virus Y Among 39 Potato Cultivars Released in Three World Regions Over a 117-Year Period
Authors: Jones Roger A. C. , Vincent Stuart J.
Published: August 2017

Strain-specific hypersensitive (HR) and extreme resistance (ER) phenotypes elicited in potato plants by three Potato virus Y (PVY) isolates in strain groups PVYO (BL and DEL3) and PVYD (KIP1) were studied. PVYO and PVYD isolates elicit HR genes Ny or putative Nd, respectively, and all three isolates elicit ER gene Ry. They were inoculated to 39 Australasian, European, or North American potato cultivars released over a 117-year period and harvested tubers were replanted. Both primary and secondary symptoms were recorded. Two European cultivars always developed ER following sap and graft inoculation and, thus, carried comprehensive PVY resistance gene Ry. One Australasian and two European cultivars always developed susceptible phenotypes and, thus, lacked genes Ry, Ny, and putative Nd. Sap inoculation with isolate KIP1 elicited localized HR (LHR) in 31 cultivars and both LHR and systemic HR (SHR) in three others; thus, all carried putative Nd. Isolates BL and DEL3 both elicited susceptible phenotypes in 11 of these 34 cultivars but LHR alone, SHR alone, or both LHR and SHR in the other 23 which, therefore, all carry Ny. With these two isolates, SHR expression ranged from very severe to very weak, with the greatest numbers of isolate–cultivar combinations occurring in the severe category with BL (n = 11) and moderate category (n = 12) with DEL3. Within the same isolate–cultivar combination, overall, SHR symptom expression was weaker with secondary than primary infection. With both primary and secondary infection, SHR expression was most severe with KIP1 and weakest with DEL3. Genes Ny and putative Nd were present in cultivars released between 1939 and 2010 or 1893 and 2010, respectively, occurring in cultivars from all three world regions. These findings have important implications concerning breeding new PVY-resistant potato cultivars, especially for countries lacking healthy seed potato stocks, or where subsistence farmers cannot afford them. An alternative to including gene Ry is incorporating as many strain-specific PVY resistance genes as possible.
Social seeking declines in young adolescents
Authors: Dubey Indu , Ropar Danielle , Hamilton Antonia F de C.
Published: August 2017

The desire to engage with others is an important motivational force throughout our lifespan. It is known that social behaviour and preferences change from childhood to adulthood, but whether this change is linked with any changes in social motivation is not known. We evaluated 255 typically developing participants from ages 4–20 years on a behavioural paradigm ‘Choose a Movie’ (CAM). On every trial, participants had a choice between viewing social or non-social movies presented with different levels of effort (key presses/screen touch required). Hence, participants chose not only the movie they would watch but also how much effort they would make. The difference between the effort levels of the chosen and not chosen stimuli helps in quantifying the motivation to seek it. This task could be used with all the age groups with minimal adaptations, allowing comparison between the groups. Results showed that children (4–8 years), older adolescents (12–16 years) and young adults (17–20 years) made more effort to look at social movies. Counterintuitively, this preference was not seen in young adolescents (around 9–12 years), giving a U-shaped developmental trajectory over the population. We present the first evidence for non-monotonic developmental change in social motivation in typical participants.
Chimpanzees recognize their own delayed self-image
Authors: Hirata Satoshi , Fuwa Kohki , Myowa Masako
Published: August 2017

Unlike mirror self-recognition, recognizing one's own image in delayed video footage may indicate the presence of a concept of self that extends across time and space. While humans typically show this ability around 4 years of age, it is unknown whether this capacity is found in non-human animals. In this study, chimpanzees performed a modified version of the mark test to investigate whether chimpanzees could remove stickers placed on the face and head while watching live and delayed video images. The results showed that three of five chimpanzees consistently removed the mark in delayed-viewing conditions, while they removed the stickers much less frequently in control video conditions which lacked a link to their current state. These findings suggest that chimpanzees, like human children at the age of 4 years and more, can comprehend temporal dissociation in their concept of self.
Flame-retardant polyvinyl alcohol membrane with high transparency based on a reactive phosphorus-containing compound
Authors: Peng Sha , Zhou Ming , Liu Feiyan , Zhang Chang , Liu Xueqing , Liu Jiyan , Zou Liyong , Chen Jia
Published: August 2017

Flame-retardant polyvinyl alcohol (PVA) membranes with high transparency and flexibility were prepared by mixing an aqueous solution of a phosphorus-containing acrylic acid (AOPA) with PVA. The reaction between AOPA and PVA, the transparency, the crystallinity and the flexibility of the membrane were investigated with Fourier transform infrared spectrometry (FTIR), UV–vis light transmittance, X-ray diffraction and tensile tests, respectively. The limited oxygen index (LOI) and vertical flame (UL 94 VTM), microscale combustion calorimetry, thermogravimetric analysis (TGA) and TGA-FTIR were employed to evaluate the flame retardancy as well as to reveal the corresponding mechanisms. Results showed that PVA containing 30 wt% of AOPA can reach the UL 94 VTM V0 rating with an LOI of 27.3% and retain 95% of the original transparency of pure PVA. Adding AOPA reduces crystallinity of PVA, while the flexibility is increased. AOPA depresses the thermal degradation of PVA and promotes char formation during combustion. The proposed decomposition mechanism indicates that AOPA acts mainly in the condensed phase.
Temperature profile in a liquid–vapour interface near the critical point
Authors: Gouin Henri , Seppecher Pierre
Published: August 2017

Thanks to an expansion with respect to densities of energy, mass and entropy, we discuss the concept of
thermocapillary fluid
for inhomogeneous fluids. The non-convex state law valid for homogeneous fluids is modified by adding terms taking account of the gradients of these densities. This seems more realistic than Cahn and Hilliard’s model which uses a density expansion in mass-density gradient only. Indeed, through liquid–vapour interfaces, realistic potentials in molecular theories show that entropy density and temperature do not vary with the mass density as it would do in bulk phases. In this paper, we prove using a rescaling process near the critical point, that liquid–vapour interfaces behave essentially in the same way as in Cahn and Hilliard’s model.
Male relatedness and familiarity are required to modulate male-induced harm to females in
Drosophila
Authors: Le Page Sally , Sepil Irem , Flintham Ewan , Pizzari Tommaso , Carazo Pau , Wigby Stuart
Published: August 2017

Males compete over mating and fertilization, and often harm females in the process. Inclusive fitness theory predicts that increasing relatedness within groups of males may relax competition and discourage male harm of females as males gain indirect benefits. Recent studies in
Drosophila melanogaster
are consistent with these predictions, and have found that within-group male relatedness increases female fitness, though others have found no effects. Importantly, these studies did not fully disentangle male genetic relatedness from larval familiarity, so the extent to which modulation of harm to females is explained by male familiarity remains unclear. Here we performed a fully factorial design, isolating the effects of male relatedness and larval familiarity on female harm. While we found no differences in male courtship or aggression, there was a significant interaction between male genetic relatedness and familiarity on female reproduction and survival. Relatedness among males increased female lifespan, reproductive lifespan and overall reproductive success, but only when males were familiar. By showing that both male relatedness and larval familiarity are required to modulate female harm, these findings reconcile previous studies, shedding light on the potential role of indirect fitness effects on sexual conflict and the mechanisms underpinning kin recognition in fly populations.
Is behavioural plasticity consistent across different environmental gradients and through time?
Authors: Mitchell David J. , Biro Peter A.
Published: August 2017

Despite accumulating evidence for individual variation in behavioural plasticity, there is currently little understanding of the causes and consequences of this variation. An outstanding question is whether individual reaction norm (RN) slopes are consistent across different environmental variables—that is, whether an individual that is highly responsive to one environmental variable will be equally responsive to a second variable. Another important and related question is whether RNs are themselves consistently expressed through time or whether they are simply state dependent. Here, we quantified individual activity rates of zebrafish in response to independent manipulations of temperature and food availability that were repeated in discrete ‘bursts’ of sampling through time. Individuals that were thermally responsive were not more responsive to food deprivation, but they did exhibit greater unexplained variation. Individual RN slopes were consistent (repeatable) over time for both temperature (
R
slope
= 0.92) and food deprivation responses (
R
slope
= 0.4), as were mean activity rates in the standard environment (
R
intercept
= 0.83). Despite the high potential lability of behaviour, we have demonstrated consistency of behavioural RN components and identified potential energetic constraints leading to high consistency of thermal RNs and low consistency of food deprivation RNs.
neoantigenR: An annotation based pipeline for tumor neoantigen identification from sequencing data
Authors: Tang Shaojun , Madhavan Subha
Published: August 2017

Studies indicate that more than 90% of human genes are alternatively spliced, suggesting the complexity of the transcriptome assembly and analysis. The splicing process is often disrupted, resulting in both functional and non-functional end-products (Sveen et al. 2016) in many cancers. Harnessing the immune system to fight against malignant cancers carrying aberrantly mutated or spliced products is becoming a promising approach to cancer therapy. Advances in immune checkpoint blockade have elicited adaptive immune responses with promising clinical responses to treatments against human malignancies (Tumor Neoantigens in Personalized Cancer Immunotherapy 2017). Emerging data suggest that recognition of patient-specific mutation-associated cancer antigens (i.e. from alternative splicing isoforms) may allow scientists to dissect the immune response in the activity of clinical immunotherapies (Schumacher and Schreiber 2015). The advent of high-throughput sequencing technology has provided a comprehensive view of both splicing aberrations and somatic mutations across a range of human malignancies, allowing for a deeper understanding of the interplay of various disease mechanisms.

Meanwhile, studies show that the number of transcript isoforms reported to date may be limited by the short-read sequencing due to the inherit limitation of transcriptome reconstruction algorithms, whereas long-read sequencing is able to significantly improve the detection of alternative splicing variants since there is no need to assemble full-length transcripts from short reads. The analysis of these high-throughput long-read sequencing data may permit a systematic view of tumor specific peptide epitopes (also known as neoantigens) that could serve as targets for immunotherapy (Tumor Neoantigens in Personalized Cancer Immunotherapy 2017).

Currently, there is no software pipeline available that can efficiently produce mutation-associated cancer antigens from raw high-throughput sequencing data on patient tumor DNA (The Problem with Neoantigen Prediction 2017). In addressing this issue, we introduce a R package that allows the discoveries of peptide epitope candidates, which are the tumor-specific peptide fragments containing potential functional neoantigens. These peptide epitopes consist of structure variants including insertion, deletions, alternative sequences, and peptides from nonsynonymous mutations. Analysis of these precursor candidates with widely used tools such as netMHC allows for the accurate in-silico prediction of neoantigens. The pipeline named neoantigeR is currently hosted inhttps://github.com/ICBI/neoantigeR.
MEG-BIDS: an extension to the Brain Imaging Data Structure for magnetoencephalography
Authors: Niso Guiomar , Gorgolewski Krzysztof J. , Bock Elizabeth , Brooks Teon L. , Flandin Guillaume , Gramfort Alexandre , Henson Richard N. , Jas Mainak , Litvak Vladimir , Moreau Jeremy , Oostenveld Robert , Schoffelen Jan-Mathijs , Tadel Francois , Wexler Joseph , Baillet Sylvain
Published: August 2017

We present a significant extension of the Brain Imaging Data Structure (BIDS) to support the specific aspects of magnetoencephalography (MEG) data. MEG provides direct measurement of brain activity with millisecond temporal resolution and unique source imaging capabilities. So far, BIDS has provided a solution to structure the organization of magnetic resonance imaging (MRI) data, which nature and acquisition parameters are different. Despite the lack of standard data format for MEG, MEG-BIDS is a principled solution to store, organize and share the typically-large data volumes produced. It builds on BIDS for MRI, and therefore readily yields a multimodal data organization by construction. This is particularly valuable for the anatomical and functional registration of MEG source imaging with MRI. With MEG-BIDS and a growing range of software adopting the standard, the MEG community has a solution to minimize curation overheads, reduce data handling errors and optimize usage of computational resources for analytics. The standard also includes well-defined metadata, to facilitate future data harmonization and sharing efforts.
chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
Authors: Silva Mickael , Machado Miguel , Silva Diogo N. , Rossi Mirko , Moran-Gilad Jacob , Santos Sergio , Ramirez Mario , Carriço João André
Published: August 2017

Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available athttps://github.com/B-UMMI/chewBBACAor as a docker image athttps://hub.docker.com/r/ummidock/chewbbaca/.

DATA SUMMARY

Assembled genomes used for the tutorial were downloaded from NCBI in August 2016 by selecting those submitted asStreptococcus agalactiaetaxon or sub-taxa. All the assemblies have been deposited as a zip file in FigShare (https://figshare.com/s/9cbe1d422805db54cd52), where a file with the original ftp link for each NCBI directory is also available.

Code for the chewBBACA suite is available athttps://github.com/B-UMMI/chewBBACAwhile the tutorial example is found athttps://github.com/B-UMMI/chewBBACA_tutorial.

I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠

IMPACT STATEMENT

The chewBBACA software offers a computational solution for the creation, evaluation and use of whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) schemas. It allows researchers to develop wg/cgMLST schemes for any bacterial species from a set of genomes of interest. The alleles identified by chewBBACA correspond to potential coding sequences, possibly offering insights into the correspondence between the genetic variability identified and phenotypic variability. The software performs allele calling in a matter of seconds to minutes per strain in a laptop but is easily scalable for the analysis of large datasets of hundreds of thousands of strains using multiprocessing options. The chewBBACA software thus provides an efficient and freely available open source solution for gene-by-gene methods. Moreover, the ability to perform these tasks locally is desirable when the submission of raw data to a central repository or web services is hindered by data protection policies or ethical or legal concerns.
Heterogeneities in afferent connectivity dominate local heterogeneities in the emergence of response decorrelation in the dentate gyrus
Authors: Mishra Poonam , Narayanan Rishikesh
Published: August 2017

The ability of a neuronal population to effectuate response decorrelation has been identified as an essential prelude to efficient neural encoding. To what extent are diverse forms of local and afferent heterogeneities essential in accomplishing such response decorrelation in the dentate gyrus (DG)? Here, we incrementally incorporated four distinct forms of biological heterogeneities into conductance-based network models of the DG and systematically delineate their relative contributions to response decorrelation. We incorporated intrinsic heterogeneities by stochastically generating several electrophysiologically-validated basket and granule cell models that exhibited significant parametric variability, and introduced synaptic heterogeneities through randomized local synaptic strengths. In including adult neurogenesis, we subjected the valid model populations to randomized structural plasticity and matched neuronal excitability to electrophysiological data. We assessed networks comprising different combinations of these three local heterogeneities with identical or heterogeneous afferent inputs from the entorhinal cortex. We found that the three forms of local heterogeneities were independently and synergistically capable of mediating significant response decorrelation when the network was driven by identical afferent inputs. Strikingly, however, when we incorporated afferent heterogeneities into the network to account for the unique divergence in DG afferent connectivity, the impact of all three forms of local heterogeneities were significantly suppressed by the dominant role of afferent heterogeneities in mediating response decorrelation. Our results unveil a unique convergence of cellular- and network-scale degeneracy in the emergence of response decorrelation in the DG, and constitute a significant departure from the literature that assigns a critical role for local network heterogeneities in input discriminability.

SIGNIFICANCE STATEMENT

The olfactory bulb and the dentate gyrus (DG) networks assimilate new neurons in adult rodents, with adult neurogenesis postulated to subserve efficacious information transfer by reducing correlations in neuronal responses to afferent inputs. Heterogeneities emerging from the lateral dendro-dendritic synapses, mediated by locally-projecting neurogenic inhibitory granule cells, are known to play critical roles in channel decorrelation in the olfactory bulb. However, the contributions of different heterogeneities in mediating response decorrelation in DG, comprising neurogenic excitatory granule cells projecting beyond DG and endowed with uniquely divergent afferent inputs, have not been delineated. Here, we quantitatively demonstrate the dominance of afferent heterogeneities, over multiple local heterogeneities, in the emergence of response decorrelation in DG, together unveiling cross-region degeneracy in accomplishing response decorrelation.
A structural and kinetic link between membrane association and amyloid fibril formation of α-Synuclein
Authors: Viennet Thibault , Wördehoff Michael M. , Uluca Boran , Poojari Chetan , Shaykhalishahi Hamed , Willbold Dieter , Strodel Birgit , Heise Henrike , Buell Alexander K. , Hoyer Wolfgang , Etzkorn Manuel
Published: August 2017

The protein α-Synuclein (αS) is linked to Parkinson’s disease through its abnormal aggregation, which is thought to involve an interplay between cytosolic and membrane-bound forms of αS. Therefore, better insights into the molecular determinants of membrane association and their implications for protein aggregation may help deciphering the pathogenesis of Parkinson’s disease. Following previous studies using micelles and vesicles, we present a comprehensive study of αS interaction with phospholipid bilayer nanodiscs. Using a combination of NMR - spectroscopic and complementary biophysical as well as computational methods we structurally and kinetically characterize αS interaction with defined stable planar membranes in a quantitative and site-resolved way. We probe the role of αS acetylation as well as membrane charge, plasticity and available surface area in modulating αS membrane binding modes and directly link these findings to their consequences for αS amyloid fibril formation.
Application of “R” principles to enhance the efficiency of water usage in construction sites
Authors: Waidyasekara K.G.A.S. , De Silva Lalith , Rameezdeen Raufdeen
Published: August 2017

Purpose

Water conservationists have been promoting a hierarchy of measures to preserve water resources in the face of decreasing freshwater availability in the world. However, applicability of water hierarchy to the construction industry is yet to be investigated. To fill this knowledge gap, the purpose of this paper is to investigate water usage, water use efficiency, and conservation measures relevant to the construction operations.

Design/methodology/approach

A triangulation-based mixed-methods approach was adopted for the collection and analysis of data. First, four case studies were carried out to explore the current practices and the possibilities of applying the water hierarchy to the construction operations. This was followed by a questionnaire survey, administered among construction professionals to obtain their views and to verify the findings of case studies.

Findings

Strategies such as reuse and recycling were found to be less applicable and least preferred by the construction professionals compared to reduce, replace, and eliminate. Based on the research findings, three enabling measures, namely, regulation, responsibility, and reward, were found to enhance the effectiveness of these conservation strategies.

Practical implications

Knowledge on preferences of different water conservation measures among the construction professionals and their effectiveness on construction site could help the construction companies to device strategies to mitigate water wastage and enhance water use efficiency. It could also help policy-makers to develop guidelines that would have higher probability of acceptance among construction stakeholders.

Originality/value

The study proposes an extended water hierarchy (3R.6R) by integrating three enabling measures discussed above for the construction project sites.
Collapse: the decline and fall of master planned golf course communities
Authors: Mothorpe Chris , Wyman David
Published: August 2017

Purpose

The purpose of this paper is to examine the pricing of vacant lots in master planned golf course communities (GCCs) over the period of 2000-2016. The authors compare the longitudinal pricing behavior of different lot types during this economic cycle and examine the causes of the property bubble and subsequent deterioration of the business model with the arrival of the Financial Economic Crisis (FEC).

Design/methodology/approach

The authors construct spatial hedonic models for three master planned GCCs in Pickens County, South Carolina and use interaction dummies to examine the pricing of different types of vacant lots before and after the FEC.

Findings

The authors find that there is a collapse in value for interior lots in the GCCs compared to interior lots in the county. As interior lots comprise over 50 percent of inventory in a typical master planned GCC, this loss of real estate value threatens the viability of such communities in the aftermath of the FEC.

Practical implications

The research results inform real estate investors, real estate developers, current homebuyers and potential homebuyers of the impacts of the FEC on master planned GCCs and some of the risks associated with such developments.

Originality/value

This is the first paper the authors are aware of that indicates the financial viability of master planned GCCs is associated with the pricing fragility of interior lots during cyclical markets. While demand for premium quality lots suffers, there is a collapse in demand for interior lots during the crisis.
Development of non-leaching and eco-friendly polyhexamethylene guanidine hydrochloride based antimicrobial waterborne polyacrylates
Authors: Ding Wei , Peng Kaimei , Zou Tao , Wang Ruonan , Guo Jinshan , Tu Wei Ping , Liu Chao , Hu Jianqing
Published: August 2017

Purpose

The purpose of this paper is to develop non-leaching and eco-friendly antimicrobial waterborne polyacrylates with excellent antibacterial properties by grafting antibacterial vinyl monomer, glycidyl methacrylate (GMA) modified polyhexamethylene guanidine hydrochloride (PHMG).

Design/methodology/approach

PHMG of different molecular weights were modified by GMA to synthesize antibacterial vinyl monomer, GMA-modified PHMG (GPHMG). Different content and molecular weights of GPHMG were used to synthesize antimicrobial waterborne polyacrylates through emulsion polymerization.

Findings

The addition of GPHMG gained by modifying PHMG showed little influence on thermal stability of the films, but decreased the glass transition temperature(Tg). Meanwhile, the tensile strength decreased, while the breaking elongation increased. The antibacterial properties of the antibacterial films with different GPHMG contents were studied, when GPHMG content was around 0.9 Wt.%, antibacterial films showed excellent antibacterial activity (antibacterial rate >= 99.99 per cent). When weight content of GPHMG in the films remained constant, antibacterial property of films increased first and then decreased with the increase of molecular weight of GPHMG. The structural antibacterial polymer film had more perdurable antibacterial activity than the blended one.

Research limitations/implications

The grafting efficiency of GPHMG to antimicrobial waterborne polyacrylates could be further improved.

Practical implications

Antimicrobial waterborne polyacrylates with excellent antibacterial properties can be used to antibacterial coating and adhesive.

Originality/value

The antibacterial properties of films with different molecular weight of GPHMG were studied, and the durability and stability of antibacterial properties between structural antimicrobial films and blended antimicrobial films were also investigated by ring-diffusion method.
Incontinentia pigmenti in a male (XY) infant with long‐term follow up over 8 years
Authors: Matsuzaki Yasushi , Rokunohe Akiko , Minakawa Satoko , Nomura Kazuo , Nakano Hajime , Ito Etsuro , Sawamura Daisuke
Published: August 2017

Incontinentia pigmenti (IP) is an X‐linked genodermatosis affecting the skin and other sites, including the teeth, nails, hair, eyes and nervous system defects in female patients. Generally lethal in males, there are only a few known cases of males surviving this condition. Nuclear factor (NF)‐κB essential modulator (NEMO), also known as inhibitor of kappa light polypeptide gene enhancer in B cells, kinase gamma (IKBKG), constitutes an essential activator of NF‐κB. Over 80% of female patients with IP carry a common deletion mutation involving exons 4–10 of the IKBKG/NEMO gene. We present the case of a male infant (XY) with IP with no concomitant complications. Polymerase chain reaction (PCR) assay showed that the exon 4–10 deletion band was significantly stronger in the skin sample than in blood. Subsequently, long‐range PCR was performed periodically to confirm the spontaneous regression of mutant cells from his blood. Over a period of 6 years, the 2.6‐kb mutant band gradually became weaker, but we did not confirm complete regression. Our patient was a healthy, 8‐year‐old male child with no complications despite the presence of a 2.6‐kb mutant band in his blood. Further follow up is necessary to assess for complications that may develop later.
Ants are the major agents of resource removal from tropical rainforests
Authors: Griffiths Hannah M. , Ashton Louise A. , Walker Alice E. , Hasan Fevziye , Evans Theodore A. , Eggleton Paul , Parr Catherine L.
Published: August 2017

Ants are diverse and abundant, especially in tropical ecosystems. They are often cited as the agents of key ecological processes, but their precise contributions compared with other organisms have rarely been quantified. Through the removal of food resources from the forest floor and subsequent transport to nests, ants play an important role in the redistribution of nutrients in rainforests. This is an essential ecosystem process and a key energetic link between higher trophic levels, decomposers and primary producers.

We used the removal of carbohydrate, protein and seed baits as a proxy to quantify the contribution that ants, other invertebrates and vertebrates make to the redistribution of nutrients around the forest floor, and determined to what extent there is functional redundancy across ants, other invertebrate and vertebrate groups.

Using a large‐scale, field‐based manipulation experiment, we suppressed ants from c. 1 ha plots in a lowland tropical rainforest in Sabah, Malaysia. Using a combination of treatment and control plots, and cages to exclude vertebrates, we made food resources available to: (i) the whole foraging community, (ii) only invertebrates and (iii) only non‐ant invertebrates. This allowed us to partition bait removal into that taken by vertebrates, non‐ant invertebrates and ants. Additionally, we examined how the non‐ant invertebrate community responded to ant exclusion.

When the whole foraging community had access to food resources, we found that ants were responsible for 52% of total bait removal whilst vertebrates and non‐ant invertebrates removed the remaining 48%. Where vertebrates were excluded, ants carried out 61% of invertebrate‐mediated bait removal, with all other invertebrates removing the remaining 39%. Vertebrates were responsible for just 24% of bait removal and invertebrates (including ants) collectively removed the remaining 76%. There was no compensation in bait removal rate when ants and vertebrates were excluded, indicating low functional redundancy between these groups.

This study is the first to quantify the contribution of ants to the removal of food resources from rainforest floors and thus nutrient redistribution. We demonstrate that ants are functionally unique in this role because no other organisms compensated to maintain bait removal rate in their absence. As such, we strengthen a growing body of evidence establishing ants as ecosystem engineers, and provide new insights into the role of ants in maintaining key ecosystem processes. In this way, we further our basic understanding of the functioning of tropical rainforest ecosystems.