bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of nitrogen-related defects on optical and electrical behaviour in HfO2−xNx deposited by high-power impulse magnetron sputtering
Authors: Murdoch B. J. , Ganesan R. , McKenzie D. R. , Bilek M. M. M. , McCulloch D. G. , Partridge J. G.
Published: September 2015

HfO2−xNx films have been deposited by high-power impulse magnetron sputtering in an Ar-O2-N2 atmosphere with a series of nitrogen partial pressures. X-ray absorption spectroscopy revealed the optimum deposition conditions required to passivate O vacancies in the HfO2−xNx films by nitrogen. Low-mobility interstitial species prevent crystallisation of nitrogen-incorporated films. These effects combine to remove leakage paths resulting in superior breakdown strengths compared to films deposited without nitrogen. The bandgap was maintained at ∼5.9 eV in the films in which nitrogen passivated the oxygen vacancies. This is essential to provide sufficient band offsets for HfO2−xNx films to be used an effective gate dielectric.
A high-damping magnetorheological elastomer with bi-directional magnetic-control modulus for potential application in seismology
Authors: Yu Miao , Qi Song , Fu Jie , Zhu Mi
Published: September 2015

A high-damping magnetorheological elastomer (MRE) with bi-directional magnetic-control modulus is developed. This MRE was synthesized by filling NdFeB particles into polyurethane (PU)/ epoxy (EP) interpenetrating network (IPN) structure. The anisotropic samples were prepared in a permanent magnetic field and magnetized in an electromagnetic field of 1 T. Dynamic mechanical responses of the MRE to applied magnetic fields are investigated through magneto-rheometer, and morphology of MREs is observed via scanning electron microscope (SEM). Test result indicates that when the test field orientation is parallel to that of the sample's magnetization, the shear modulus of sample increases. On the other hand, when the orientation is opposite to that of the sample's magnetization, shear modulus decreases. In addition, this PU/EP IPN matrix based MRE has a high-damping property, with high loss factor and can be controlled by applying magnetic field. It is expected that the high damping property and the ability of bi-directional magnetic-control modulus of this MRE offer promising advantages in seismologic application.
Nanoselective area growth and characterization of dislocation-free InGaN nanopyramids on AlN buffered Si(111) templates
Authors: Sundaram S. , El Gmili Y. , Puybaret R. , Li X. , Bonanno P. L. , Pantzas K. , Patriarche G. , Voss P. L. , Salvestrini J. P. , Ougazzaden A.
Published: September 2015

We report the metal organic chemical vapor deposition growth of dislocation-free 100 nm thick hexagonal InGaN nanopyramid arrays with up to 33% of indium content by nano-selective area growth on patterned AlN/Si (111) substrates. InGaN grown on SiO2 patterned templates exhibit high selectivity. Their single crystal structure is confirmed by scanning transmission electron microscope combined with an energy dispersive X-ray analysis, which also reveals the absence of threading dislocations in the InGaN nanopyramids due to elastic strain relaxation mechanisms. Cathodoluminescence measurements on a single InGaN nanopyramid clearly show an improvement of the optical properties when compared to planar InGaN grown under the same conditions. The good structural, morphological, and optical quality of the InGaN nanostructures grown on AlN/Si indicates that the nano-selective area growth technology is attractive for the realization of site-controlled indium-rich InGaN nanostructure-based devices and can also be transferred to other highly mismatched substrates.
Fabricating a n+-Ge contact with ultralow specific contact resistivity by introducing a PtGe alloy as a contact metal
Authors: Hsu C. C. , Chou C. H. , Wang S. Y. , Chi W. C. , Chien C. H. , Luo G. L.
Published: September 2015

In this study, we developed an Ohmic contact structure to an in situ n+-Ge film that has an ultralow specific contact resistivity of [(6.8±2.1)×10−8 Ω⋅cm2]. This structure was developed by introducing a PtGe alloy as the contact metal. We observed that Ohmic contact behavior can be achieved with several other metals, and the contact resistance is related to the work function of the metal. A physical model of the band diagram was created for the Schottky tunneling width, which can provide insight into the validation and explanation of work function-dependent specific contact resistivity. Dopant segregation at the interface and increased interface roughness induced by the formation of the alloy are crucial in further reducing the specific contact resistivity. As a result, a stable PtGe alloy and high doping concentration in Ge are critical in pursuing a lower contact resistance for a Ge n-channel device.
Photoelectron emission yield experiments on evolution of sub-gap states in amorphous In-Ga-Zn-O thin films with post deposition hydrogen treatment
Authors: Hayashi Kazushi , Hino Aya , Tao Hiroaki , Ochi Mototaka , Goto Hiroshi , Kugimiya Toshihiro
Published: September 2015

Total photoyield emission spectroscopy (TPYS) was applied to study the evolution of sub-gap states in hydrogen-treated amorphous In-Ga-Zn-O (a-IGZO) thin films. The a-IGZO thin films were subjected to hydrogen radicals and subsequently annealed in ultra-high vacuum (UHV) conditions. A clear onset of the electron emission was observed at around 4.3 eV from the hydrogen-treated a-IGZO thin films. After successive UHV annealing at 300 °C, the onset in the TPYS spectra was shifted to 4.15 eV, and the photoelectron emission from the sub-gap states was decreased as the annealing temperature was increased. In conjunction with the results of thermal desorption spectrometer, it was deduced that the hydrogen atoms incorporated in the a-IGZO thin films induced metastable sub-gap states at around 4.3 eV from vacuum level just after the hydrogenation. It was also suggested that the defect configuration was changed due to the higher temperature UHV annealing, and that the hydrogen atoms desorbed with the involvement of Zn atoms. These experiments produced direct evidence to show the formation of sub-gap states as a result of hydrogen incorporation into the a-IGZO thin films.
Small-signal theory of subterahertz overmoded surface wave oscillator with distributed wall loss
Authors: Wang Guangqiang , Wang Jianguo , Li Shuang , Wang Xuefeng
Published: September 2015

A small-signal theory of the overmoded surface wave oscillator (SWO) with distributed wall loss is presented in this letter. The wall loss considered here includes the surface resistance and surface roughness. The cold and hot characteristics of 0.14 THz SWO are studied by the small-signal theory. Numerical results show that as the increase of wall loss, the working frequency decreases slightly, the rise time and startup time of oscillation increase significantly, and the output power decreases dramatically. Particle-in-cell (PIC) simulation confirms the prediction by the small-signal theory.
Protecting trapped animals from heat exposure: the influence of shading on temperature within small metal box traps
Authors: Ellis Murray V.
Published: September 2015

Animal research guidelines recognise that trapped animals can potentially be subjected to heat stress, but recommendations are limited to avoiding exposing traps to weather extremes. Intuitively, shading metal box traps should be beneficial in warm to hot climates. Temperatures inside metal box traps were measured within traps located in direct sunlight concurrently with ones covered with artificial shading. Additionally, comparisons were conducted in continuous shade cast by ground-cover vegetation, and in stippled sunlight under an artificial lattice. Deep continuous shade from vegetation was most effective and able to keep traps within 5°C of ambient. Artificial shading using dark shade cloth could actually elevate trap temperatures above that in uncovered traps when exposed to direct sunshine. Reflective foil insulation cover not only provided rain protection for traps but was the most effective shading method trialled for reducing both the rate at which traps heated after sunrise and the maximum temperature reached during the day when exposed to direct sunshine. The use of foil sleeves can provide an extra level of protection from excessive heat exposure to trapped animals, keeping trap temperatures as much as 15°C lower than unprotected traps.
The myokine irisin increases cortical bone mass
Authors: Colaianni Graziana , Cuscito Concetta , Mongelli Teresa , Pignataro Paolo , Buccoliero Cinzia , Liu Peng , Lu Ping , Sartini Loris , Di Comite Mariasevera , Mori Giorgio , Di Benedetto Adriana , Brunetti Giacomina , Yuen Tony , Sun Li , Reseland Janne E. , Colucci Silvia , New Maria I. , Zaidi Mone , Cinti Saverio , Grano Maria
Published: September 2015

Significance

Although exercise is a well known and potent stimulus for new bone formation, and weightlessness or muscle loss characteristically cause bone loss, it has remained unclear how muscle talks to bone, despite their close proximity. Here, we show that a molecule irisin derived from skeletal muscle in response to exercise has profound effects in enhancing mass and improving the geometry and strength specifically of cortical bone, the key function of which is to resist bending and torsion. Trabecular bone, which is a reservoir for bodily calcium, is remarkably spared. Irisin may therefore not only be the molecule responsible for muscle–bone connectivity, but could also become a therapy for sarcopenia and osteoporosis, which occur in tandem in the elderly.
Propagation of Hybrid Devils Hole Pupfish × Ash Meadows Amargosa Pupfish
Authors: Feuerbacher Olin G , Mapula Justin A , Bonar Scott A
Published: September 2015

Recent censuses of Devils Hole Pupfish Cyprinodon diabolis revealed that fewer than 100 individuals currently remain in the wild. Captive propagation is among actions being considered to prevent their extinction, but no pure-strain Devils Hole Pupfish were available for broodstock. To help provide emergency information, we investigated techniques to propagate their most closely related relative, hybrid Devils Hole Pupfish C. diabolis × Ash Meadows Amargosa Pupfish C. nevadensis mionectes. We tested various temperatures and larval feeds with respect to egg production, larval survival, and growth. Larval survival and growth were similar from 24°C to 32°C and egg production peaked at static 28°C; however, reducing water temperatures to 23°C and then raising them to 28°C resulted in even higher production. Larvae fed infusoria, Rio Grande Silvery Minnow Chow (RGSM), or Zeigler larval diet (ZLD) had the highest survival (79.4, 71.6, and 73.4%, respectively), and those fed Otohime (OTO) had the lowest survival (60.8%), although OTO provided greatest (14 mm) 30-d growth. Supplementation of RGSM or ZLD with Artemia nauplii increased growth but decreased survival. Larval production was maximized by placing six spawning mops, constructed of yarn and tile, in each of four 437-L parental aquaria, stocked with 24 adult fish each (1:1 sex ratio) for 3 d, to attract adults and provide spawning substrate. A 30% water change conducted on the same day of mop placement lowered water temperature from 28°C to 23°C. Water temperature was raised back to 28°C over 48 h. After 3 d, mops were transferred to hatching aquaria that were held at 28°C and aerated until larval hatch. Although some differences likely exist in effective propagation techniques for hybrid and pure-strain Devils Hole Pupfish, these data help provide initial recommendations to aid recovery.
Tolerance and Avoidance Behavior towards Gas Supersaturation in Rock Carp Procypris rabaudi with a History of Previous Exposure
Authors: Wang Yuanming , Liang Ruifeng , Tuo Youcai , Li Kefeng , Hodges Ben
Published: September 2015

Total dissolved gas (TDG) supersaturation on the upper Yangtze River basin is becoming increasingly serious because of the intense construction of high dams, posing a threat to resident fish. The tolerance and behavior characteristics of Rock Carp Procypris rabaudi preexposed to TDG-supersaturated water were evaluated by placing juveniles (weight 6.4 ± 1.67 g, fork length 7.2 ± 0.7 cm; mean ± SD) in 35-cm-deep tanks at 130% supersaturation for 2.33 h as preexposure. Surviving fish were allowed 5 d of recovery in saturated-equilibrium (100% TDG) water and then examined in an acute lethality experiment at TDG supersaturation values of 120, 125, 130, 135, 140, and 145%. The resulting median lethal times were 10.4, 4.6, 3.2, 2.1, 1.4, and 1.4 h, respectively. The preexposed fish showed a poorer tolerance to TDG-supersaturated water than did a control group that were not preexposed for TDG above 120% supersaturation (P < 0.05 in cases where there was a significant difference between individual groups). Experiments on horizontal behavior and vertical behavior used the same preexposure routine, followed by 5 d of recovery in saturated-equilibrium water. For all behavior experiments, both the preexposed and control groups showed significant avoidance responses to TDG-supersaturated water; however, there were no significant differences between the preexposed and control groups.
Impact of Minimum Daily Dissolved Oxygen Concentration on Production Performance of Hybrid Female Channel Catfish × Male Blue Catfish
Authors: Torrans Les , Ott Brian , Bosworth Brian
Published: September 2015

Hybrid catfish (♀ Channel Catfish Ictalurus punctatus × ♂ Blue Catfish I. furcatus) were reared as single-batch crops during the growing season (June–September) of two years under two different dissolved oxygen (DO) regimes each year: (1) a high-DO (control) treatment with minimum daily DO maintained above 3.8 ppm in both years and (2) a low-DO (test) treatment with minimum DO maintained at 1.6 ppm in the first year and 1.3 ppm in the second year. Fish were fed daily to apparent satiation with a 32% protein commercial feed and harvested each year. In both years, dissolved oxygen concentration significantly impacted gross and net production, final fish weight, and mean fish weight gain due to reduced feed intake. Feed intake was reduced in the low-DO treatment by 26.6% in year 1 and 29.2% in year 2. Food conversion ratios averaged 1.83 overall and were not affected by minimum DO. Fish in high-DO treatments gained an average of 44% more weight (1.50 lb/fish) than fish in low-DO treatments (1.04 lb/fish). Initial weight at stocking also had a significant impact on weight gain: fish stocked at a 0.16-lb average weight (year 2) gained 37% more weight than fish stocked at a 0.11-lb average weight (year 1), even though the stocking rate of the larger fish was 50% higher. Hybrid catfish had less reduction in feed intake at reduced DO compared with reported values for Channel Catfish and Blue Catfish.
Ocean acidification bends the mermaid's wineglass
Authors: Newcomb Laura A. , Milazzo Marco , Hall-Spencer Jason M. , Carrington Emily
Published: September 2015

Ocean acidification lowers the saturation state of calcium carbonate, decreasing net calcification and compromising the skeletons of organisms such as corals, molluscs and algae. These calcified structures can protect organisms from predation and improve access to light, nutrients and dispersive currents. While some species (such as urchins, corals and mussels) survive with decreased calcification, they can suffer from inferior mechanical performance. Here, we used cantilever beam theory to test the hypothesis that decreased calcification would impair the mechanical performance of the green alga
Acetabularia acetabulum
along a CO
2
gradient created by volcanic seeps off Vulcano, Italy. Calcification and mechanical properties declined as calcium carbonate saturation fell; algae at 2283 µatm CO
2
were 32% less calcified, 40% less stiff and 40% droopier. Moreover, calcification was not a linear proxy for mechanical performance; stem stiffness decreased exponentially with reduced calcification. Although calcifying organisms can tolerate high CO
2
conditions, even subtle changes in calcification can cause dramatic changes in skeletal performance, which may in turn affect key biotic and abiotic interactions.
Mates but not sexes differ in migratory niche in a monogamous penguin species
Authors: Thiebot Jean-Baptiste , Bost Charles-André , Dehnhard Nina , Demongin Laurent , Eens Marcel , Lepoint Gilles , Cherel Yves , Poisbleau Maud
Published: September 2015

Strong pair bonds generally increase fitness in monogamous organisms, but may also underlie the risk of hampering it when re-pairing fails after the winter season. We investigated whether partners would either maintain contact or offset this risk by exploiting sex-specific favourable niches during winter in a migratory monogamous seabird, the southern rockhopper penguin
Eudyptes chrysocome
. Using light-based geolocation, we show that although the spatial distribution of both sexes largely overlapped, pair-wise mates were located on average 595 ± 260 km (and up to 2500 km) apart during winter. Stable isotope data also indicated a marked overlap between sex-specific isotopic niches (
δ
13
C and
δ
15
N values) but a segregation of the feeding habitats (
δ
13
C values) within pairs. Importantly, the tracked females remained longer (12 days) at sea than males, but all re-mated with their previous partners after winter. Our study provides multiple evidence that migratory species may well demonstrate pair-wise segregation even in the absence of sex-specific winter niches (spatial and isotopic). We suggest that dispersive migration patterns with sex-biased timings may be a sufficient proximal cause for generating such a situation in migratory animals.
Type III secretion systems: the bacterial flagellum and the injectisome
Authors: Diepold Andreas , Armitage Judith P.
Published: September 2015

The flagellum and the injectisome are two of the most complex and fascinating bacterial nanomachines. At their core, they share a type III secretion system (T3SS), a transmembrane export complex that forms the extracellular appendages, the flagellar filament and the injectisome needle. Recent advances, combining structural biology, cryo-electron tomography, molecular genetics,
in vivo
imaging, bioinformatics and biophysics, have greatly increased our understanding of the T3SS, especially the structure of its transmembrane and cytosolic components, the transcriptional, post-transcriptional and functional regulation and the remarkable adaptivity of the system. This review aims to integrate these new findings into our current knowledge of the evolution, function, regulation and dynamics of the T3SS, and to highlight commonalities and differences between the two systems, as well as their potential applications.
Type VI secretion system: secretion by a contractile nanomachine
Authors: Basler Marek
Published: September 2015

The type VI secretion systems (T6SS) are present in about a quarter of all Gram-negative bacteria. Several key components of T6SS are evolutionarily related to components of contractile nanomachines such as phages and R-type pyocins. The T6SS assembly is initiated by formation of a membrane complex that binds a phage-like baseplate with a sharp spike, and this is followed by polymerization of a long rigid inner tube and an outer contractile sheath. Effectors are preloaded onto the spike or into the tube during the assembly by various mechanisms. Contraction of the sheath releases an unprecedented amount of energy, which is used to thrust the spike and tube with the associated effectors out of the effector cell and across membranes of both bacterial and eukaryotic target cells. Subunits of the contracted sheath are recycled by T6SS-specific unfoldase to allow for a new round of assembly. Live-cell imaging has shown that the assembly is highly dynamic and its subcellular localization is in certain bacteria regulated with a remarkable precision. Through the action of effectors, T6SS has mainly been shown to contribute to pathogenicity and competition between bacteria. This review summarizes the knowledge that has contributed to our current understanding of T6SS mode of action.
Lipopolysaccharide transport to the cell surface: periplasmic transport and assembly into the outer membrane
Authors: May Janine M. , Sherman David J. , Simpson Brent W. , Ruiz Natividad , Kahne Daniel
Published: September 2015

Gram-negative bacteria possess an outer membrane (OM) containing lipopolysaccharide (LPS). Proper assembly of the OM not only prevents certain antibiotics from entering the cell, but also allows others to be pumped out. To assemble this barrier, the seven-protein lipopolysaccharide transport (Lpt) system extracts LPS from the outer leaflet of the inner membrane (IM), transports it across the periplasm and inserts it selectively into the outer leaflet of the OM. As LPS is important, if not essential, in most Gram-negative bacteria, the LPS biosynthesis and biogenesis pathways are attractive targets in the development of new classes of antibiotics. The accompanying paper (Simpson BW, May JM, Sherman DJ, Kahne D, Ruiz N. 2015
Phil. Trans. R. Soc. B
370
, 20150029. (
doi:10.1098/rstb.2015.0029
)) reviewed the biosynthesis of LPS and its extraction from the IM. This paper will trace its journey across the periplasm and insertion into the OM.
The bacterial divisome: ready for its close-up
Authors: Rowlett Veronica W. , Margolin William
Published: September 2015

Bacterial cells divide by targeting a transmembrane protein machine to the division site and regulating its assembly and disassembly so that cytokinesis occurs at the correct time in the cell cycle. The structure and dynamics of this machine (divisome) in bacterial model systems are coming more clearly into focus, thanks to incisive cell biology methods in combination with biochemical and genetic approaches. The main conserved structural element of the machine is the tubulin homologue FtsZ, which assembles into a circumferential ring at the division site that is stabilized and anchored to the inner surface of the cytoplasmic membrane by FtsZ-binding proteins. Once this ring is in place, it recruits a series of transmembrane proteins that ultimately trigger cytokinesis. This review will survey the methods used to characterize the structure of the bacterial divisome, focusing mainly on theEscherichia colimodel system, as well as the challenges that remain. These methods include recent super-resolution microscopy, cryo-electron tomography and synthetic reconstitution.
Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces
Authors: Shkoporov Andrei N. , Chaplin Andrei V. , Khokhlova Ekaterina V. , Shcherbakova Victoria A. , Motuzova Oksana V. , Bozhenko Vladimir K. , Kafarskaia Lyudmila I. , Efimov Boris A.
Published: September 2015

Culture-based study of the faecal microbiome in two adult female subjects revealed the presence of two obligately anaerobic, non-spore-forming, rod-shaped, non-motile, Gram-negative bacterial strains that represent novel species. The first strain, designated 627T, was a fastidious, slow-growing, indole-positive bacterium with a non-fermentative type of metabolism. The strain was characterized by the production of acetic and succinic acids as metabolic end products, the prevalence of iso-C15 : 0fatty acid and the presence of menaquinones MK-10 and MK-11. The DNA G+C content was found to be 56.6 mol%. The second strain, designated 177T, was capable of fermenting a rich collection of carbohydrate substrates, producing acetic acid as a terminal product. The strain was indole-negative and resistant to bile. The major cellular fatty acids were iso-C15 : 0and anteiso-C15 : 0(in a 1 : 1 ratio) and the predominant menaquinone was MK-11. The DNA G+C content was 37.8 mol%. A phylogenomic analysis of the draft genomes of strains 627Tand 177Tplaced these bacteria in the generaAlistipes(familyRikenellaceae) andCoprobacter(familyPorphyromonadaceae), respectively.

On the basis of the phenotypic and genotypic properties of strains 627Tand 177T, we conclude that these strains from human faeces represent two novel bacterial species, for which the namesAlistipes inopssp. nov. (type strain 627T = DSM 28863T = VKM B-2859T) andCoprobacter secundussp. nov. (type strain 177T = DSM 28864T = VKM B-2857T) are proposed.
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Authors: Zook Justin M. , Catoe David , McDaniel Jennifer , Vang Lindsay , Spies Noah , Sidow Arend , Weng Ziming , Liu Yuling , Mason Chris , Alexander Noah , Henaff Elizabeth , Chen Feng , Jaeger Erich , Moshrefi Ali , Pham Khoa , Stedman William , Liang Tiffany , Saghbini Michael , Dzakula Zeljko , Hastie Alex , Cao Han , Deikus Gintaras , Schadt Eric , Sebra Robert , Bashir Ali , Truty Rebecca M. , Chang Christopher C. , Gulbahce Natali , Zhao Keyan , Ghosh Srinka , Hyland Fiona , Fu Yutao , Chaisson Mark , Xiao Chunlin , Trow Jonathan , Sherry Stephen T. , Zaranek Alexander W. , Ball Madeleine , Bobe Jason , Estep Preston , Church George M. , Marks Patrick , Kyriazopoulou-Panagiotopoulou Sofia , Zheng Grace X.Y. , Schnall-Levin Michael , Ordonez Heather S. , Mudivarti Patrice A. , Giorda Kristina , Sheng Ying , Rypdal Karoline Bjarnesdatter , Salit Marc
Published: September 2015

The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode™ WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.
Identification of Genomic Regions Carrying a Causal Mutation in Unordered Genomes
Authors: Corredor-Moreno Pilar , Chalstrey Ed , Lugo Carlos A. , MacLean Dan
Published: September 2015

Whole genome sequencing using high-throughput sequencing (HTS) technologies offers powerful opportunities to study genetic variation. Mapping the mutations responsible for different phenotypes is generally an involved and time-consuming process so researchers have developed user-friendly tools for mapping-by-sequencing, yet they are not applicable to organisms with non-sequenced genomes. We introduce SDM (SNP Distribution Method), a reference independent method for rapid discovery of mutagen-induced mutations in typical forward genetic screens. SDM aims to order a disordered collection of HTS reads or contigs such that the fragment carrying the causative mutation can be identified. SDM uses typical distributions of homozygous SNPs that are linked to a phenotype-altering SNP in a non-recombinant region as a model to order the fragments. To implement and test SDM, we created model genomes with an idealised SNP density based onArabidopsis thalianachromosome 1 and analysed fragments with size distribution similar to reads or contigs assembled from HTS sequencing experiments. SDM groups the contigs by their normalised SNP density and arranges them to maximise the fit to the expected SNP distribution. We tested the procedure in existing datasets by examining SNP distributions in recent out-cross and back-cross experiments inArabidopsis thalianabackgrounds. In all the examples we analysed, homozygous SNPs were normally distributed around the causal mutation. We used the real SNP densities obtained from these experiments to prove the efficiency and accuracy of SDM. The algorithm was able to successfully identify small sized (10-100 kb) genomic regions containing the causative mutation.
Bayesian Gaussian Process Latent Variable Models for pseudotime inference in single-cell RNA-seq data
Authors: Campbell Kieran , Yau Christopher
Published: September 2015

Single-cell genomics has revolutionised modern biology while requiring the development of advanced computational and statistical methods. Advances have been made in uncovering gene expression heterogeneity, discovering new cell types and novel identification of genes and transcription factors involved in cellular processes. One such approach to the analysis is to construct pseudotime orderings of cells as they progress through a particular biological process, such as cell-cycle or differentiation. These methods assign a score - known as the pseudotime - to each cell as a surrogate measure of progression. However, all published methods to date are purely algorithmic and lack any way to give uncertainty to the pseudotime assigned to a cell. Here we present a method that combines Gaussian Process Latent Variable Models (GP-LVM) with a recently published electroGP prior to perform Bayesian inference on the pseudotimes. We go on to show that the posterior variability in these pseudotimes leads to nontrivial uncertainty in the pseudo-temporal ordering of the cells and that pseudotimes should not be thought of as point estimates.
Diffantom: whole-brain diffusion MRI phantoms derived from real datasets of the Human Connectome Project
Authors: Esteban Oscar , Caruyer Emmanuel , Daducci Alessandro , Bach-Cuadra Meritxell , Ledesma-Carbayo Maria-J. , Santos Andres
Published: September 2015

Diffantom is a whole-brain digital phantom generated from a dataset from the Human Connectome Project. Diffantom is presented here to be openly and freely distributed along with the diffantomizer workflow to generate new diffantoms. We encourage the neuroimage community to contribute with their own diffantoms and share them openly.
Transient relay function of midline thalamic nuclei during long-term memory consolidation in humans
Authors: Thielen Jan-Willem , Takashima Atsuko , Rutters Femke , Tendolkar Indira , Fernández Guillén
Published: September 2015

To test the hypothesis that thalamic midline nuclei play a transient role in memory consolidation, we reanalyzed a prospective functional MRI study, contrasting recent and progressively more remote memory retrieval. We revealed a transient thalamic connectivity increase with the hippocampus, the medial prefrontal cortex (mPFC), and a parahippocampal area, which decreased with time. In turn, mPFC-parahippocampal connectivity increased progressively. These findings support a model in which thalamic midline nuclei serve as a hub linking hippocampus, mPFC, and posterior representational areas during memory retrieval at an early (2 h) stage of consolidation, extending classical systems consolidation models by attributing a transient role to midline thalamic nuclei.
Norepinephrine triggers metaplasticity of LTP by increasing translation of specific mRNAs
Authors: Maity Sabyasachi , Rah Sean , Sonenberg Nahum , Gkogkas Christos G. , Nguyen Peter V.
Published: September 2015

Norepinephrine (NE) is a key modulator of synaptic plasticity in the hippocampus, a brain structure crucially involved in memory formation. NE boosts synaptic plasticity mostly through initiation of signaling cascades downstream from beta (β)-adrenergic receptors (β-ARs). Previous studies demonstrated that a β-adrenergic receptor agonist, isoproterenol, can modify the threshold for long-term potentiation (LTP), a putative cellular mechanism for learning and memory, in a process known as “metaplasticity.” Metaplasticity is the ability of synaptic plasticity to be modified by prior experience. We asked whether NE itself could engage metaplastic mechanisms in area CA1 of mouse hippocampal slices. Using extracellular field potential recording and stimulation, we show that application of NE (10 µM), which did not alter basal synaptic strength, enhances the future maintenance of LTP elicited by subthreshold, high-frequency stimulation (HFS: 1 × 100 Hz, 1 sec). HFS applied 30 min after NE washout induced long-lasting (>4 h) LTP, which was significantly extended in duration relative to HFS alone. This NE-induced metaplasticity required β1-AR activation, as coapplication of the β1-receptor antagonist CGP-20712A (1 µM) attenuated maintenance of LTP. We also found that NE-mediated metaplasticity was translation- and transcription-dependent. Polysomal profiles of CA1 revealed increased translation rates for specific mRNAs during NE-induced metaplasticity. Thus, activation of β-ARs by NE primes synapses for future long-lasting plasticity on time scales extending beyond fast synaptic transmission; this may facilitate neural information processing and the subsequent formation of lasting memories.
Histone deacetylase inhibition facilitates massed pattern-induced synaptic plasticity and memory
Authors: Pandey Kiran , Sharma Kaushik P. , Sharma Shiv K.
Published: September 2015

Massed training is less effective for long-term memory formation than the spaced training. The role of acetylation in synaptic plasticity and memory is now well established. However, the role of this important protein modification in synaptic plasticity induced by massed pattern of stimulation or memory induced by massed training is not well understood. Here we show that increasing the level of acetylation enhances long-term potentiation induced by massed pattern of high frequency stimulation. Furthermore, enhancing acetylation level facilitates long-term memory by massed training. Thus, increasing acetylation level facilitates synaptic plasticity and memory by massed patterns.
Polarization analysis in neutron small-angle scattering with a novel triplet dynamic nuclear polarization spin filter
Authors: Niketic N. , van den Brandt B. , Wenckebach W. Th. , Kohlbrecher J. , Hautle P.
Published: September 2015

A novel neutron spin filter whose principle is based on the strong spin dependence of the neutron scattering on protons has been developed. The dimensions of this filter are small, and it works very efficiently and is stable even in inhomogeneous fields. The protons in the naphthalene spin filter crystal are polarized by a recently developed method of dynamic nuclear polarization using photoexcited triplet states. This technique allows the design of a very compact apparatus that can be placed at a close distance to the sample under investigation. The application of this filter as a polarization analyzer is demonstrated in a magnetic small-angle neutron scattering experiment with the measurement of the spin-dependent scattering signals of a CuFeNi alloy. This sample has a pronounced textured structure factor of ferromagnetic precipitates in a paramagnetic matrix. The performance of the spin filter as an analyzer is illustrated by the excellent agreement of the experimental data with simulations based on a model of homogeneously magnetized spherical particles which are ordered in a simple cubic paracrystalline lattice.
Health information seeking of low socioeconomic status Hispanic adults using smartphones
Authors: Kim Henna , Zhang Yan
Published: September 2015

Purpose

– Smartphones have great potential to bridge the digital divide that low-socioeconomic status (SES) Hispanics have been experiencing. However, little is known about this group’s use of smartphones for health information. The purpose of this paper is to fill the gap by exploring the context in which smartphones were used for health information.

Design/methodology/approach

– The authors interviewed 20 low-SES Hispanic participants using the semi-structured interview method. Participants had not obtained college degrees and had annual incomes less than $30,000, but had used their smartphones for health information. The interviews were transcribed and analyzed using the qualitative content analysis method.

Findings

– Being economical was an important reason for low-SES Hispanic users to use smartphones for health information. The users relied heavily on public Wi-Fi to access the internet. They searched a wide range of health topics, mostly using the mobile web rather than apps. They lacked knowledge and skills to effectively using apps, evaluating the quality of health information, and comprehend information.

Research limitations/implications

– Having access to smartphones alone does not help bridge the digital gap for low-SES Hispanics. Interventions need to consider improving these users’ smartphone literacy and health literacy, as well as improving their access to Wi-Fi services and to more quality content in Spanish.

Originality/value

– Prior studies speculated that smartphones could be a means to bridge digital divide experienced by the Hispanic ethnic group. This study provided empirical knowledge about how smartphones are used by these users for health information, and shed light on the design of future informational interventions.
Training comprehensiveness: construct development and relation with role behaviour
Authors: Srivastava Anugamini Priya , Dhar Rajib Lochan
Published: September 2015

Purpose

– This study aims to develop the scale for perception of training comprehensiveness and attempts to examine the influence of perception of training comprehensiveness on role behaviour: teachers’ efficacy as a mediator and job autonomy as a moderator.

Design/methodology/approach

– Through the steps for a generation, refinement, purification and validation of the scale, the measures of training comprehensiveness are defined, followed by an exploratory factor analysis. In all, 961 primary school teachers and 323 principals participated in the study. Teachers rated their perception of training comprehensiveness, self-efficacy and job autonomy, while principals rated the role behaviour of teachers, to avoid self-reporting biases.

Findings

– Regression analysis showed that training comprehensiveness affects teachers’ self-efficacy, higher teachers’ efficacy increases the teachers’ role behaviour, training comprehensiveness indirectly influences role behaviour and job autonomy moderated the channel of teachers’ efficacy and role behaviour. These results indicated that in primary schools specifically in rural areas of India, individual perception of training, skill development and human resource development practice induces teachers’ role behaviour via raising their efficacy to combat with adverse situations. Job autonomy on an independent basis moderates the positive relationship between self-efficacy and role behaviour.

Practical implications

– This study also provides various practical and research-based implications.

Originality/value

– The scale for training comprehensiveness has been developed, and its impact on behavioural attributes like efficacy and role behaviour is examined for a sample of teachers.
Two profiles of the Dutch high performing employee
Authors: de Waal A.A. , Oudshoorn Michella
Published: September 2015

Purpose

– The purpose of this study is to explore the profile of an ideal employee, to be more precise the behavioral characteristics of the Dutch high-performing employee (HPE). Organizational performance depends for a large part on the commitment of employees. Employees provide their knowledge, skills, experiences and creativity to the organization, which makes them critical to the success of the organization.

Design/methodology/approach

– The behavioral characteristics of the Dutch HPE were identified on the basis of a literature review and a questionnaire distributed to 420 Dutch managers and employees.

Findings

– Not one but two profiles for the ideal employee were found. First, an HPE profile was compiled based on the perspectives of managers, which can be used for evaluating employees and recruiting new employees. Second, an HPE profile was compiled based on the perspectives of employees themselves, which can be used for setting up development and coaching programs for employees.

Originality/value

– Most organizations work with one profile of the ideal employee. This study shows, however, that two profiles are needed for such an employee, each with a particular application.
Ecologies of housing and underlying assumptions of vulnerability
Authors: Franz Jill , Bitner Grace , Petriwskyj Andrea , Ward Margaret , Adkins Barbara , Rolfe Annie
Published: September 2015

Purpose

– The purpose of this paper is to understand the difficulties in implementing models of housing, and to help address the lack of accessible and affordable private housing for people with disability in Australia. In responding to this aim, the study formulated an ecological map of housing models, which are examined in this paper in terms of their underlying assumptions of vulnerability.

Design/methodology/approach

– The study involved explanation building, using a multiple case study approach, informed theoretically by an ecological framework. It included organisations, families and individuals with disability.

Findings

– For the purpose of this paper, the study revealed a direct relationship between the nature of the housing models proposed, and assumptions of vulnerability. In the context of the study findings, the paper suggests that attempts to address individual housing needs are more likely to achieve a positive outcome when they are person driven, from a premise of ability rather than disability. Overall, it invites a “universalistic” way of conceptualising housing issues for people with disability that has international relevance.

Practical implications

– This paper highlights how assumptions of vulnerability shape environmental responses, such as housing, for people with disability.

Originality/value

– This paper is based on a study that reconciled a person-centred philosophy with an ecological appreciation of the external and internal factors impacting housing choice for people with disability.
The role of housing in adult safeguarding
Authors: Cass Elaine
Published: September 2015

Purpose

– The purpose of this paper is to highlight the role of housing in adult safeguarding under the Care Act (2014) in England.

Design/methodology/approach

– The paper provides a summary of the implications for housing organisations and their staff of adult safeguarding under the Care Act. The implications, underpinned by the six safeguarding principles, are explained within a summary of the legal and practice framework for safeguarding in England.

Findings

– The paper draws upon research by Imogen Parry (2014). It argues that past failings in adult safeguarding in England have placed it high on the housing agenda and that housing has a key role to play in adult safeguarding.

Practical implications

– Housing organisations need to be proactive partners in local multi-agency arrangements for adult safeguarding. Staff and contractors need to receive training in line with their role to raise awareness of their safeguarding responsibilities.

Originality/value

– The value of the paper is to increase and maintain awareness of the need for housing engagement in the adult safeguarding agenda.
Design implications for multi-owned properties from a household survey
Authors: Sajan Jeeva
Published: September 2015

Purpose

– This paper aims to highlight the pertinent design issues that could impact upon satisfaction with apartment living. Till date, the literature review identifies “design inadequacies”, along with a range of other factors, in embracing apartments as a permanent housing option.

Design/methodology/approach

– This paper presents findings from a face-to-face household survey undertaken in a medium-density apartment housing in Fairfield, Sydney, using a mixed method.

Findings

– First, the paper states the four predictors of overall living satisfaction derived through a logistic regression analysis. Second, the top five variables that commanded high dissatisfaction and the two most negative aspects of apartment living for the open-response question are identified. Further, it discusses the possible influence of dwelling floor on residential satisfaction. The coherent narratives of the residents substantiate the design inadequacies from the aforementioned empirical analysis.

Originality/value

– The paper reflects upon ideal design suggestions from a face-to-face household survey, the first of its kind in more than 30 years in Sydney.
Refugees’ resettlement in a Canadian mid-sized Prairie city: examining experiences of multiple forced migrations
Authors: Racine Louise , Lu Yixi
Published: September 2015

Purpose

– The purpose of this paper is to discuss the experiences of multiple forced migrations and resettlement among two refugee families in a mid-sized Canadian city.

Design/methodology/approach

– Case studies are located within the contingencies of the participants’ lives and the meanings they provide to the events. A postcolonial feminist perspective guided the data analysis to explore the micro-level of individual experiences that unfold within a raced, gendered, and classed reality. Open-ended interviews, participant observation, and field notes were used to collect participants’ perspectives. Data were collected until saturation occurred.

Findings

– An in-depth analysis of these two case studies revealed that lack of choice and lack of access to health and social services affect health through constant revival of traumatic past experiences prior to arrival to Canada. Three themes emerged from the data analysis: first, shared experiences of forced migrations; second, the past and present: construction of new identities; and third, resettlement challenges and opportunities. These themes overlap and intersect to shape the experiences of double forced migration.

Research limitations/implications

– This research has limitations related to the sample size but provides data on a topic that deserves more attention in the field of immigrant and health studies. The authors argue that health and social professionals must resist “finalizing” refugees into disempowered identities that undermine human agency.

Originality/value

– Research on resettlement experiences after forced migration is a burgeoning field in refugee studies. The originality lies in drawing on Bahktin to develop practical implications to guide health and social practice in this area marked by racialization and fundamentalism.
Intellectual capital through the eyes of the consumer
Authors: Nguyen Thuy D. , Dadzie Charlene , Davari Arezoo , Guzman Francisco
Published: September 2015

Purpose

– The purpose of this study is to measure intellectual capital of the firm through the eyes of the consumer by investigating the relationships between financial-based brand equity (FBBE) and consumer-based brand equity (CBBE) and their related constructs.

Design/methodology/approach

– Fifteen consumer brands were evaluated based on three different perspectives of CBBE, and were then regressed on FBBE. Prior to the regression analysis, the FBBEs of 15 consumer brands were standardized using the total assets and three-year weighted average of their brand equity values.

Findings

– Findings show that existing CBBE scales and related brand dimensions partially explain FBBE, namely, sustainability and brand experience, and that the product category contributes significantly in explaining FBBE. In addition, brand experience is positively associated with FBBE.

Research limitations/implications

– The study only includes brands from the food, electronics and clothing industries.

Practical implications

– The study provides guidance to brand managers regarding which brand dimensions directly influence brands’ financial values.

Originality/value

– The paper empirically measures consumers’ perceptions of the firm’s intellectual capital by using brand equity.