bluuebunny/crossref_metadata_2025 huggingface dataset:
Autocorrelation-subtracted Fourier transform holography method for large specimen imaging
Authors: Lee Kyoung Hwan , Yun Hyeok , Sung Jae Hee , Lee Seong Ku , Lee Hwang Woon , Kim Hyung TaeK , Nam Chang Hee
Published: February 2015

We developed a variation of Fourier transform holography (FTH) method to record larger objects than those tolerable in conventional FTH. This method eliminates the separation condition of FTH by removing the autocorrelation signal, thus allowing three-fold larger specimens than those previously used in FTH under the same illumination conditions. We experimentally demonstrated this FTH variation, using a table-top Ag X-ray laser at 13.9 nm, with a sample violating the separation constraint. The portion of the object image hidden behind its autocorrelation in the FTH image was recovered by subtracting an independently measured autocorrelation signal of the object.
Generation of kinetic Alfven waves in the high-latitude near-Earth magnetotail: A global hybrid simulation
Authors: Guo Zhifang , Hong Minghua , Lin Yu , Du Aimin , Wang Xueyi , Wu Mingyu , Lu Quanming
Published: February 2015

In this paper, effects of a fast flow in the tail plasma sheet on the generation of kinetic Alfven waves (KAWs) in the high-latitude of the near-Earth magnetotail are investigated by performing a two-dimensional (2-D) global-scale hybrid simulation, where the plasma flow is initialized by the E×B drift near the equatorial plane due to the existence of the dawn-dusk convection electric field. It is found that firstly, the plasma sheet becomes thinned and the dipolarization of magnetic field appears around (x,z)=(−10.5RE,0.3RE), where RE is the radius of the Earth. Then, shear Alfven waves are excited in the plasma sheet, and the strong earthward flow is braked by the dipole-like magnetic field. These waves propagate along the magnetic field lines toward the polar regions later. Subsequently, KAWs with k⊥≫k∥ are generated in the high-latitude magnetotail due to the existence of the non-uniformity of the magnetic field and density in the polar regions. The ratio of the electric field to the magnetic field in these waves is found to obey the relation (δEz)/(δBy )∼ω/k∥ of KAWs. Our simulation provides a mechanism for the generation of the observed low-frequency shear Alfven waves in the plasma sheet and kinetic Alfven waves in the high-latitude near-Earth magnetotail, whose source is suggested to be the flow braking in the low-latitude plasma sheet.
Mobile ions generated by external direct current electric field influence direct current measurement of giant magnetoresistance current sensors
Authors: Zhao Gen , Hu Jun , Ouyang Yong , He Jinliang , Wang Shan X. , Yuan Zhiyong
Published: February 2015

The application of giant magnetoresistance (GMR) current sensors in power grid and other industrial fields has a great prospect benefitting from their wide bands, high sensitivity, and good linearity. This paper studies the influence of mobile ions on current measurement of GMR sensor under high external electric field. The R-H curves of GMR multilayer sensor were depicted when the external electric and magnetic fields were both changed under three orthogonal electric field orientations. The experiment results indicate slightly varying resistances of GMR sensor when the external electric field was changed, and simulation analysis reveals that the resistance variation is attributed to the movement of surface ions under high external electric field. Therefore, a Faraday box is essential for GMR sensors to avoid interferences under high-strength field conditions, which is especially significant for their application as current sensors of the power grid.
A resonant electromagnetic vibration energy harvester for intelligent wireless sensor systems
Authors: Qiu Jing , Wen Yumei , Li Ping , Liu Xin , Chen Hengjia , Yang Jin
Published: February 2015

Vibration energy harvesting is now receiving more interest as a means for powering intelligent wireless sensor systems. In this paper, a resonant electromagnetic vibration energy harvester (VEH) employing double cantilever to convert low-frequency vibration energy into electrical energy is presented. The VEH is made up of two cantilever beams, a coil, and magnetic circuits. The electric output performances of the proposed electromagnetic VEH have been investigated. With the enhancement of turns number N, the optimum peak power of electromagnetic VEH increases sharply and the resonance frequency deceases gradually. When the vibration acceleration is 0.5 g, we obtain the optimum output voltage and power of 9.04 V and 50.8 mW at frequency of 14.9 Hz, respectively. In a word, the prototype device was successfully developed and the experimental results exhibit a great enhancement in the output power and bandwidth compared with other traditional electromagnetic VEHs. Remarkably, the proposed resonant electromagnetic VEH have great potential for applying in intelligent wireless sensor systems.
Resonant enhancement of damping within the free layer of a microscale magnetic tunnel valve
Authors: Keatley P. S. , Kruglyak V. V. , Neudert A. , Hicken R. J. , Poimanov V. D. , Childress J. R. , Katine J. A.
Published: February 2015

Picosecond magnetization dynamics in the free and pinned layers of a microscale magnetic tunnel valve have been studied using time-resolved scanning Kerr microscopy. A comparison of the observed dynamics with those of individual free and pinned layers allowed the effect of interlayer coupling to be identified. A weak interlayer coupling in the tunnel valve continuous film reference sample was detected in bulk magnetometry measurements, while focused Kerr magnetometry showed that the coupling was well maintained in the patterned structure. In the tunnel valve, the free layer precession was observed to have reduced amplitude and an enhanced relaxation. During magnetization reversal in the pinned layer, its frequency approached that of the low frequency mode associated with the free layer. At the pinned layer switching field, the linewidth of the free layer became similar to that of the pinned layer. The similarity in their frequencies promotes the formation of precessional modes that exhibit strong collective properties such as frequency shifting and enhanced linewidth, while inhomogeneous magnetization of the pinned layer during reversal may also play a role in these observations. The collective character of precessional dynamics associated with mixing of the free and pinned layer magnetization dynamics must be accounted for even in tunnel valves with a small interlayer coupling.
Strain engineering in graphene by laser irradiation
Authors: Papasimakis N. , Mailis S. , Huang C. C. , Al-Saab F. , Hewak D. W. , Luo Z. , Shen Z. X.
Published: February 2015

We demonstrate that the Raman spectrum of graphene on lithium niobate can be controlled locally by continuous exposure to laser irradiation. We interpret our results in terms of changes to doping and mechanical strain and show that our observations are consistent with light-induced gradual strain relaxation in the graphene layer.
Ternary superlattice boosting interface-stabilized magnetic chirality
Authors: Chen Gong , N'Diaye Alpha T. , Wu Yizheng , Schmid Andreas K.
Published: February 2015

In cobalt-nickel multilayers grown on iridium surfaces, magnetic homo-chirality can be stabilized by Dzyaloshinskii-Moriya interactions (DMI) at the interface with the substrate. When thickness of the multilayers is increased beyond threshold values, then non-chiral bulk properties exceed interface contributions and this type of chirality vanishes. Here, we use spin-polarized low energy electron microscopy to measure these thickness thresholds, and we determine estimates of the strength of the DMI from the measurements. Even though the same 5d heavy metal is used as a substrate, a remarkably large variation is found between the two 3d magnets: our results indicate that the strength of the DMI at Co/Ir interfaces is three times larger than at Ni/Ir interfaces. We show how this finding provides ways to extend interfacial-DMI stabilization of domain wall chirality to 3d/5d/3d ternary multilayers such as [Ni/Ir/Co]n. Such strategies may extend chirality-control to larger film thickness and a wider range of substrates, which may be useful for designing new spintronics devices.
Extended interface layer concept for higher stability and improvement of life time in bulk heterojunction solar cells
Authors: Ali Farman , Sharma Abhishek , Tiwari Jai Prakash , Chand Suresh
Published: February 2015

Power conversion efficiency (PCE) of bulk heterojunction (BHJ) organic solar cells has reached above ∼10%. These BHJ cells have potential for flexible thin films at low processing temperatures using roll to roll printing on flexible substrates. Further, the basic materials properties can be tailored through organic synthetic routes. However, the issues related to its durability should be addressed before its commercialization. Hence, a conventional solar cell of the poly (3-hexylthiophene) (P3HT) :(6, 6)-phenyl-C61butyric acid methyl ester (PC61BM) blend on ITO substrates was fabricated, and investigated, which shows improved life time by using a combinational Ca/Al cathode, wherein the deposition of calcium layer is extended beyond the aluminum layer. The extended deposition of calcium layer beyond aluminum prevents the edge degradation by its oxidation and hence protecting the active pixel area of the device, resulting in the improvement of life time of device from ∼80 hours to ∼ 400 hrs.
Giant fifth-order nonlinearity via tunneling induced quantum interference in triple quantum dots
Authors: Tian Si-Cong , Wan Ren-Gang , Tong Cun-Zhu , Ning Yong-Qiang
Published: February 2015

Schemes for giant fifth-order nonlinearity via tunneling in both linear and triangular triple quantum dots are proposed. In both configurations, the real part of the fifth-order nonlinearity can be greatly enhanced, and simultaneously the absorption is suppressed. The analytical expression and the dressed states of the system show that the two tunnelings between the neighboring quantum dots can induce quantum interference, resulting in the giant higher-order nonlinearity. The scheme proposed here may have important applications in quantum information processing at low light level.
Anisotropic surroundings effects on photo absorption of partially embedded Au nanospheroids in silica glass substrate
Authors: Meng Xuan , Shibayama Tamaki , Yu Ruixuan , Ishioka Junya , Watanabe Seiichi
Published: February 2015

The influence of a directly adjacent or an anisotropic surrounding medium alters the plasmonic properties of a nanoparticle because it provides a mechanism for symmetry breaking of the scattering. Given the success of ion irradiation induced embedment of rigid metallic nanospheroids into amorphous substrate, it is possible to examine the effect of the silica glass substrate on the plasmonic properties of these embedded nanospheroids. In this work presented here, discrete dipole approximation (DDA) calculations for the Au nanospheroids’ optical properties were performed based on 3–dimensional (3D) configuration extracted from planar SEM micrographs and cross–sectional TEM micrographs of the Au nanospheroids partially embedded in the silica glass, and the well–matched simulations with respect to the experimental measurements could demonstrate the dielectric constant at the near surface of silica glass decreased after Ar–ion irradiation.
Hyperelastic tension of graphene
Authors: Saavedra Flores E. I. , Ajaj R. M. , Adhikari S. , Dayyani I. , Friswell M. I. , Castro-Triguero Rafael
Published: February 2015

In this paper, we investigate the hyperelastic tensile behaviour of single layer graphene sheets (SLGSs). A one-term incompressible Ogden-type hyperelastic model is chosen to describe the mechanical response of C-C bonds. By establishing equality between the Ogden strain-energy and the variation of the Tersoff-Brenner interatomic potential, three different geometries of SLGSs are studied under tensile loading. We compute the Young's modulus, the finite-deformation Poisson's ratio, ultimate strains, total reactions, and the variation of the potential energy per carbon atom for large strains. Numerical simulations are compared with results obtained by molecular mechanics and molecular dynamics simulations, finite elements, continuum mechanics theory, and experiments. Our predictions are validated, revealing the potential predictive capabilities of the present hyperelastic framework for the analysis of graphene in the context of infinitesimal and large deformations. The good agreement found between our calculations and the published data suggests that graphene may be described as a hyperelastic material.
Effects of ovarian hyperstimulation on mitochondria in oocytes and early embryos
Authors: Shu Jing , Xing Li-Li , Ding Guo-Lian , Liu Xin-Mei , Yan Qing-Feng , Huang He-Feng
Published: February 2015

A mouse model was used to compare the number and function of mitochondria in oocytes and embryos obtained by superovulation and in a natural cycle (control group). The superovulation group had a higher number of total oocytes, MII oocytes, embryos with two pronuclei, 2-cell embryos and blastocysts than the control group (P < 0.05 for all). The superovulation group had high proportion of MII oocytes with low number of mitochondrial (mt) DNA copies. The average number of mtDNA copies, ATP level and mitochondrial membrane potential (△Ψm) in MII oocytes in the superovulation were lower than in the control group (P < 0.05 for all). However, at the blastocyst stage, mean mtDNA copies, ATP level and △Ψm did not differ significantly between the two groups. These results suggest that ovarian hyperstimulation does not cause damage to the mitochondria in eggs but, rather, more eggs with poor mitochondrial quality are recruited, resulting in a decline in average mitochondrial quality.
The effects of English bilingual education in the Netherlands
Authors: Verspoor Marjolijn , de Bot Kees , Xu Xiaoyan
Published: February 2015

This paper reports on the effectiveness of bilingual education in the Netherlands. After a brief history of the rise of bilingual education in the Netherlands, the study traces the development of English proficiency of two cohorts at Dutch high schools during one year: a group of Year 1 students (average age 12) and a group of Year 3 students (average age 14) were tested three times during one academic year. The results suggest a dynamic interplay as proficiency increases between condition and other factors such as initial proficiency, scholastic aptitude, out of school contact, and motivation/attitude factors. In Year 1, scholastic aptitude and initial proficiency were strong predictors for all students. In Year 3, scholastic aptitude no longer played a role, but initial proficiency and motivation/attitude did. The students who received bilingual education outperformed the students from the other two groups (regulars and controls).
Language learning motivation and CLIL
Authors: Sylvén Liss Kerstin , Thompson Amy S.
Published: February 2015

Language learning is multifaceted, and within Second Language Acquisition (SLA) research, motivation is one of the most frequently studied aspects. The impetus of the current study is to further explore second language learning motivation as well as its impact on the language acquisition process within the context of Content and Language Integrated Learning (CLIL). This study uses Dörnyei’s (2009) framework of the L2 Motivational Self System from which the Motivational Factors Questionnaire (MFQ) has been created and validated by Ryan (2009). This study was conducted at the high school level in Sweden and includes students enrolled in CLIL programs (N = 109) and non-CLIL programs (N = 68) at three different schools. In this paper, the subcategories of the MFQ are analyzed using one-way ANOVAs with CLIL/non-CLIL, L1, and gender as the independent variables. The results indicate that there are differences in attitudes and motivation of CLIL vs. non-CLIL students.
Is CLIL instruction beneficial in terms of general proficiency and specific areas of grammar?
Authors: Martínez Adrián María , Gutiérrez Mangado María Junkal
Published: February 2015

Recent studies have highlighted the benefits of CLIL instruction regarding general competence in the acquisition of second languages. However, it is not clear whether these benefits extend to specific areas of grammar. Here we compare the general proficiency and specific linguistic features of a group of learners of L3 English in a CLIL programme with two EFL groups: one matching the CLIL group in age and hours of exposure and a second group two grades ahead. The results confirm that the benefits of CLIL in general competence do not extend to the acquisition of specific linguistic features. In this respect, the best results were obtained by the older EFL learners suggesting that CLIL benefits do not extend to the acquisition of English verbal morphology.
Age-related decrease of IF5/BTG4 in oral and respiratory cavities in mice
Authors: Mano Hiroshi , Nakatani Sachie , Kimira Yoshifumi , Mano Mikiko , Sekiguchi Yuusuke , Im Ryang-Hyock , Shimizu Jun , Wada Masahiro
Published: February 2015

An IF5 cDNA was isolated by expression cloning from a mouse oocyte cDNA library. It encoded a protein of 250 amino acids, and the region of it encoding amino acids 1–137 showed 86.8% alignment with the anti-proliferative domain of BTG/TOB family genes. This gene is also termed BTG4 or PC3B. Transiently expressed IF5/BTG4 induced alkaline phosphatase activity in human embryonic kidney (HEK293T) and 2T3 cells. IF5/BTG4 mRNA was detected by reverse transcription polymerase chain reaction in pharynx, larynx, trachea, oviduct, ovary, caput epididymis, and testis, but not in lung, intestine, or liver. Immunohistochemistry showed the IF5/BTG4 protein to be present in epithelial cells of the tongue, palate, pharynx, internal nose, and trachea. Both protein and mRNA levels of IF5/BTG4 were reduced by aging when comparing 4-week-old mice with 48-week-old mice. Our findings suggest that IF5/BTG4 may be an aging-related gene in epithelial cells.
Simultaneous Monitoring of Behavior & Peripheral Clocks in Drosophila Reveals Unstructured Sleep in an Alzheimer's Model
Authors: Khabirova Eleonora , Chen Ko-Fan , O'Neill John S , Crowther Damian C
Published: February 2015

Sleep and circadian rhythms are ancient, related biological phenomena controlled by distinct neuronal circuits, whose appropriate regulation is critical for health. Whereas the regulatory machinery underlying sleep homeostasis is ill-defined, the biological clock mechanism is better understood: from cell-intrinsic feedback loops of ‘clock gene’ expression to circuits that facilitate rhythmic behavior. Age- and neurodegeneration related deterioration in sleep/wake timing was first described in humans decades ago, but has only recently been recapitulated in model organisms. In order to delineate the causal relationships between aging, sleep, neuronal function and the molecular clockwork, we have developed FLYGLOW, a broadly applicable bioluminescence-based system which allows rest/activity cycles, sleep consolidation and molecular clock gene expression to be quantified simultaneously in dozens of individual flies over many days/weeks. We show that FLYGLOW outperforms existing methods, and demonstrate the utility of the multiparameter correlational analyses within and between flies that it enables. We go on to show unambiguously that peripheral cellular rhythms can free-run independently of the central pacemakers that drive behavioural cycles. Finally, using a fly model of Alzheimer’s disease (AD) we observe a profound disorganization of sleep and activity cycles, that phenocopies the human disease.
Diversity ofMycobacterium tuberculosisacross evolutionary scales
Authors: O'Neill Mary B , Mortimer Tatum D , Pepperell Caitlin S
Published: February 2015

Tuberculosis (TB) is a global public health emergency. Increasingly drug resistant strains ofMycobacterium tuberculosis(M.tb) continue to emerge and spread, highlighting adaptability of this pathogen. Most studies ofM.tbevolution have relied on ‘between-host’ samples, in which each person with TB is represented by a singleM.tbisolate. However, individuals with TB commonly harbor populations ofM.tbnumbering in the billions. Here, we use analyses ofM.tbdiversity found within and between hosts to gain insight into influences shaping genetic diversity of this pathogen. We find that the amount ofM.tbgenetic diversity harbored by individuals with TB can vary dramatically, likely as a function of disease severity. Surprisingly, we did not find an appreciable impact of TB treatment onM.tbdiversity. In examining genomic data fromM.tbsamples within and between hosts with TB, we find that genes involved in the regulation, synthesis, and transportation of immunomodulatory cell envelope lipids appear repeatedly in the extremes of various statistical measures of diversity. Many of these genes have been identified as possible targets of selection in other studies employing different methods and data sets. Taken together, these observations suggest thatM.tbcell envelope lipids are targets of selection within hosts. Many of these lipids are specific to pathogenic mycobacteria and, in some cases, human-pathogenic mycobacteria. We speculate that rapid adaptation of cell envelope lipids is facilitated by functional redundancy, flexibility in their metabolism, and their roles mediating interactions with the host.
More than meets the eye: diversity and geographic patterns in sea cucumbers
Authors: Michonneau François , McPherson Sarah , O'Loughlin P. Mark , Paulay Gustav
Published: February 2015

Estimates for the number of species in the sea vary by orders of magnitude. Molecular taxonomy can greatly speed up screening for diversity and evaluating species boundaries, while gaining insights into the biology of the species. DNA barcoding with a region of cytochrome oxidase 1 (COI) is now widely used as a first pass for molecular evaluation of diversity, as it has good potential for identifying cryptic species and improving our understanding of marine biodiversity. We present the results of a large scale barcoding effort for holothuroids (sea cucumbers). We sequenced 3048 individuals from numerous localities spanning the diversity of habitats in which the group occurs, with a particular focus in the shallow tropics (Indo-Pacific and Caribbean) and the Antarctic region. The number of cryptic species is much higher than currently recognized. The vast majority of sister species have allopatric distributions, with species showing genetic differentiation between ocean basins, and some are even differentiated among archipelagos. However, many closely related and sympatric forms, that exhibit distinct color patterns and/or ecology, show little differentiation in, and cannot be separated by, COI sequence data. This pattern is much more common among echinoderms than among molluscs or arthropods, and suggests that echinoderms acquire reproductive isolation at a much faster pace than other marine phyla. Understanding the causes behind such patterns will refine our understanding of diversification and biodiversity in the sea.
Genetics of intra-species variation in avoidance behavior induced by a thermal stimulus inC. elegans
Authors: Ghosh Rajarshi , Bloom Joshua S. , Mohammadi Aylia , Schumer Molly E. , Andolfatto Peter , Ryu William , Kruglyak Leonid
Published: February 2015

Individuals within a species vary in their responses to a wide range of stimuli, partly as a result of differences in their genetic makeup. Relatively little is known about the genetic and neuronal mechanisms contributing to diversity of behavior in natural populations. By studying animal-to-animal variation in innate avoidance behavior to thermal stimuli in the nematodeCaenorhabditis elegans, we uncovered genetic principles of how different components of a behavioral response can be altered in nature to generate behavioral diversity. Using a thermal pulse assay, we uncovered heritable variation in responses to a transient temperature increase. Quantitative trait locus mapping revealed that separate components of this response were controlled by distinct genomic loci. The loci we identified contributed to variation in components of thermal pulse avoidance behavior in an additive fashion. Our results show that the escape behavior induced by thermal stimuli is composed of simpler behavioral components that are influenced by at least six distinct genetic loci. The loci that decouple components of the escape behavior reveal a genetic system that allows independent modification of behavioral parameters. Our work sets the foundation for future studies of evolution of innate behaviors at the molecular and neuronal level.
Fleas (Siphonaptera) are Cretaceous, and Evolved with Theria
Authors: Zhu Qiyun , Hastriter Michael W , Whiting Michael F , Dittmar Katharina
Published: February 2015

Fleas (order Siphonaptera) are highly-specialized, diverse blood-feeding ectoparasites of mammals and birds with an enigmatic evolutionary history and obscure origin. We here present a molecular phylogenetic study based on a comprehensive taxon sampling of 259 flea taxa, representing 16 of the 18 extant families of this order. A Bayesian phylogenetic tree with strong nodal support was recovered, consisting of seven sequentially derived lineages with Macropsyllidae as the earliest divergence, followed by Stephanocircidae. Divergence times of flea lineages were estimated based on fossil records and host specific associations to bats (Chiroptera), suggesting that the common ancestor of extant Siphonaptera diversified during the Cretaceous. However, most of the intraordinal divergence into extant lineages took place after the K-Pg boundary. Ancestral states of host association and biogeographical distribution were reconstructed, suggesting with high likelihood that fleas originated in the southern continents (Gondwana) and migrated from South America to their extant distributions in a relatively short time frame. Theria (placental mammals and marsupials) represent the most likely ancestral host group of extant Siphonaptera, with marsupials occupying a more important role than previously assumed. Major extant flea families evolved in connection to post K-Pg diversification of Placentalia. The association of fleas with monotremes and birds is likely due to later secondary host association. These results suggest caution in casually interpreting recently discovered Mesozoic fossil ?dinosaur fleas? of Northeast Asia as part of what we currently consider Siphonaptera.
The biological functions of Naa10 – from amino-terminal acetylation to human disease
Authors: Doerfel Max , Lyon Gholson J.
Published: February 2015

1

Abstract

N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40 % of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
Do Read Errors Matter for Genome Assembly?
Authors: Shomorony Ilan , Courtade Thomas , Tse David
Published: February 2015

While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read length and error rate in terms of the information needed for the perfect assembly of the genome. Using an adversarial erasure error model, we make progress on this problem by establishing a critical read length, as a function of the genome and the error rate, above which perfect assembly is guaranteed. For several real genomes, including those from the GAGE dataset, we verify that this critical read length is not significantly greater than the read length required for perfect assembly from reads without errors.
Crossmodal integration improves sensory detection thresholds in the ferret
Authors: Hollensteiner Karl J. , Pieper Florian , Engler Gerhard , König Peter , Engel Andreas K.
Published: February 2015

During the last two decades ferrets (Mustela putorius) have been established as a highly efficient animal model in different fields in neuroscience. Here we asked whether ferrets integrate sensory information according to the same principles established for other species. Since only few methods and protocols are available for behaving ferrets we developed a head-free, body-restrained approach allowing a standardized stimulation position and the utilization of the ferret’s natural response behavior. We established a behavioral paradigm to test audiovisual integration in the ferret. Animals had to detect a brief auditory and/or visual stimulus presented either left or right from their midline. We first determined detection thresholds for auditory amplitude and visual contrast. In a second step, we combined both modalities and compared psychometric fits and the reaction times between all conditions. We employed Maximum Likelihood Estimation (MLE) to model bimodal psychometric curves and to investigate whether ferrets integrate modalities in an optimal manner. Furthermore, to test for a redundant signal effect we pooled the reaction times of all animals to calculate a race model. We observed that bimodal detection thresholds were reduced and reaction times were faster in the bimodal compared to unimodal conditions. The race model and MLE modeling showed that ferrets integrate modalities in a statistically optimal fashion. Taken together, the data indicate that principles of multisensory integration previously demonstrated in other species also apply to crossmodal processing in the ferret.
An Atlas of Genetic Correlations across Human Diseases and Traits
Authors: Bulik-Sullivan Brendan , Finucane Hilary K , Anttila Verneri , Gusev Alexander , Day Felix R. , Duncan Laramie , Perry John R. B. , Patterson Nick , Robinson Elise B. , Daly Mark J. , Price Alkes L. , Neale Benjamin M. ,   ReproGen Consortium,   Psychiatric Genomics Consortium,   Genetic Consortium for Anorexia Nervosa of the Wellcome Trust Case Control Consortium 3
Published: February 2015

Identifying genetic correlations between complex traits and diseases can provide useful etiological insights and help prioritize likely causal relationships. The major challenges preventing estimation of genetic correlation from genome-wide association study (GWAS) data with current methods are the lack of availability of individual genotype data and widespread sample overlap among meta-analyses. We circumvent these difficulties by introducing a technique for estimating genetic correlation that requires only GWAS summary statistics and is not biased by sample overlap. We use our method to estimate 300 genetic correlations among 25 traits, totaling more than 1.5 million unique phenotype measurements. Our results include genetic correlations between anorexia nervosa and schizophrenia, anorexia and obesity and associations between educational attainment and several diseases. These results highlight the power of genome-wide analyses, since there currently are no genome-wide significant SNPs for anorexia nervosa and only three for educational attainment.
Harsh Environments and “Fast” Human Life Histories: What Does the Theory Say?
Authors: Baldini Ryan
Published: February 2015

Abstract

A common belief among human life history researchers is that “harsher” environments - i.e., those with higher mortality rates and resource stress - select for “fast” life histories, i.e. earlier reproduction and faster senescence. I show that these “harsh environments, fast life histories” - or HEFLH - hypotheses are poorly supported by evolutionary theory. First, I use a simple model to show that effects of environmental harshness on life history evolution are incredibly diverse. In particular, small changes in basic but poorly understood variables - e.g., whether and how population density affects vital rates - can cause selection to favor very different life histories. Furthermore, I show that almost all life history theory used to justify HEFLH hypotheses is misapplied in the first place. The reason is that HEFLH hypotheses usually treat plastic responses to heterogeneous environmental conditionswithina population, whereas the theory used to justify such hypotheses treat genetic responses to environmental changes across an entire population. Counter-intuitively, the predictions of the former do not generally apply to the latter: the optimal response to a harsh environment within a large heterogeneous environment is not necessarily the optimal strategy of a population uniformly inhabiting the same harsh environment. I discuss these theoretical results in light of the current state of empirical research.
Assembly by Reduced Complexity (ARC): a hybrid approach for targeted assembly of homologous sequences
Authors: Hunter Samuel S. , Lyon Robert T. , Sarver Brice A. J. , Hardwick Kayla , Forney Larry J. , Settles Matthew L.
Published: February 2015

Analysis of High-throughput sequencing (HTS) data is a difficult problem, especially in the context of non-model organisms where comparison of homologous sequences may be hindered by the lack of a close reference genome. Current mapping-based methods rely on the availability of a highly similar reference sequence, whereasde novoassemblies produce anonymous (unannotated) contigs that are not easily compared across samples. Here, we present Assembly by Reduced Complexity (ARC) a hybrid mapping and assembly approach for targeted assembly of homologous sequences. ARC is an open-source project (http://ibest.github.io/ARC/) implemented in the Python language and consists of the following stages: 1) align sequence reads to reference targets, 2) use alignment results to distribute reads into target specific bins, 3) perform assemblies for each bin (target) to produce contigs, and 4) replace previous reference targets with assembled contigs and iterate. We show that ARC is able to assemble high quality, unbiased mitochondrial genomes seeded from 11 progressively divergent references, and is able to assemble full mitochondrial genomes starting from short, poor quality ancient DNA reads. We also show ARC compares favorably tode novoassembly of a large exome capture dataset for CPU and memory requirements; assembling 7,627 individual targets across 55 samples, completing over 1.3 million assemblies in less than 78 hours, while using under 32 Gb of system memory. ARC breaks the assembly problem down into many smaller problems, solving the anonymous contig and poor scaling inherent in somede novoassembly methods and reference bias inherent in traditional read mapping.
Long-term field experiment on the impacts of the neonicotinoid dinotefuran and the organophosphate fenitrothion on a honeybee colony
Authors: Yamada Toshiro , Yamada Yasuhiro , Yamada Kazuko , Nakamura Hiroko
Published: February 2015

Neonicotinoides are persistent and highly toxic pesticides that have become popular instead of organophosphates, being suspected to be a trigger of massive disappearance of bees that raises concern in the world. The evaluation of the long-term influence for a whole colony in the natural environment is, however, not established yet. In this paper, we conducted a long-term field experiment and found different impacts on honeybee colonies(Apis mellifera)in an apiary between the neonicotinoid dinotefuran and the organophosphate fenitrothion even though whose concentrations in sugar syrup provided for bees were adjusted to have nearly equal short-term effects on a honeybee based on the median lethal dose (LD50) as well as the insecticidal activity to exterminate stinkbugs.

The colony with administration of dinotefran (dinotefuran colony) became extinct in 26 days, while the colony with administration of fenitrothion (fenitrothion colony) survived the administration for the same period. Furthermore, the fenitrothion colony succeeded to be alive for more than 293 days after administration, and also succeeded an overwintering, which indicates that colonies exposed to fenitrothion can recover after the exposure.

Meanwhile, the dinotefuran colony became extinct even though the intake of dinotefuran was estimated to be comparable with that of fenitrothion in terms of the LD50of a honeybee. Moreover, the colonies in our previous long-term experiments where dinotefuran with higher concentration were administered only for first few days (Yamada et al., 2012) became extinct in 104 days and 162 days, respectively. From these results, we speculate that colonies exposed to dinotefuran hardly recover from the damage because dinotefuran is much more persistent than fenitrothion and toxic foods stored in cells can affect a colony in a long period.
Histoimmunogenetics Markup Language 1.0: Reporting Next Generation Sequencing-based HLA and KIR Genotyping
Authors: Milius Robert P. , Heuer Michael , Valiga Daniel , Doroschak Kathryn J. , Kennedy Caleb J. , Bolon Yung –Tsi , Schneider Joel , Pollack Jane , Kim Hwa Ran , Cereb Nezih , Hollenbach Jill A. , Mack Steven J. , Maiers Martin
Published: February 2015

We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and sequence based typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS.

Abbreviations

BRIDG

Biomedical Research Integrated Domain Group

CDISC

Clinical Data Interchange Standards Consortium

DaSH

Data Standard Hackathon

EMBL

European Molecular Biology Laboratory

ENA

European Nucleotide Archive

FDA

Food and Drug Administration

GL

Genotype List

HML

Histoimmunogenetics Markup Language

HLA

Human Leucocyte Antigen

IMGT

ImMunoGeneTics

ISO

International Organization for Standardization

LSDAM

Life Sciences Domain Analysis Model

KIR

Killer-cell Immunoglobulin-like Receptor

MHC

Major Histocompatibility Complex

MIRING

Minimum Information for Reporting Immunogenomic NGS Genotyping

NCI

National Cancer Institute

NGS

Next Generation Sequencing

NMDP

National Marrow Donor Program

OID

Object Identifier

SBT

Sequence Based Typing

SSO

Sequence Specific Oligonucleotide

SSP

Sequence Specific Primer

URI

Uniform Resource Identifier

XML

eXtensible Markup Language
Improving access to endogenous DNA in ancient bone and teeth
Authors: Damgaard Peter B. , Margaryan Ashot , Schroeder Hannes , Orlando Ludovic , Willerslev Eske , Allentoft Morten E.
Published: February 2015

Poor DNA preservation is the most limiting factor in ancient genomic research. In the vast majority of ancient bones and teeth, endogenous DNA molecules only represent a minor fraction of the whole DNA extract, rendering traditional shot-gun sequencing approaches cost-ineffective for whole-genome characterization. Based on ancient human bone samples from temperate and tropical environments, we show that an initial EDTA-based enzymatic ‘pre-digestion’ of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we identify the optimal pre-digestion time and document an average increase of 2.7 times in the endogenous DNA fraction after 1 hour of pre-digestion. With longer pre-digestion times, the increase is asymptotic while molecular complexity decreases. We repeated the experiment with n=21 and t=15-30’, and document a significant increase in endogenous DNA content (one-sided paired t-test: p=0.009). We advocate the implementation of a short pre-digestion step as a standard procedure in ancient DNA extractions from bone material. Finally, we demonstrate on 14 ancient teeth that crushed cementum of the roots contains up to 14 times more endogenous DNA than the dentine. Our presented methodological guidelines considerably advance the ability to characterize ancient genomes.
Venture creation programs: bridging entrepreneurship education and technology transfer
Authors: Lackéus Martin , Williams Middleton Karen
Published: February 2015

Purpose

– The purpose of this paper is to explore how university-based entrepreneurship programs, incorporating real-life venture creation into educational design and delivery, can bridge the gap between entrepreneurship education and technology transfer within the university environment.

Design/methodology/approach

– Based on a literature review and snowball sampling over a two-year period, 18 entrepreneurship education programs were identified as applying a venture creation approach. Ten of these programs were selected for case study, including direct interviews and participatory observation during a two-day workshop. Empirical findings were iteratively related to theory within entrepreneurship education and technology transfer.

Findings

– The paper identifies the bridging capabilities of venture creation programs (VCP) across five core themes, illustrating the potential benefits of closer collaboration between entrepreneurship education and technology transfer in a university environment.

Research limitations/implications

– A definition for “VCP” is tested empirically. These programs are shown to be sophisticated laboratory environments, allowing for clinical research towards the understanding of entrepreneurship and technology transfer processes.

Practical implications

– Findings identify practical benefits of combining entrepreneurship education and technology transfer activities, such as increased value creation through not only new firms, but also an entrepreneurially equipped graduate population. VCPs allow for “spin-through” of innovative ideas in the university environment, while simultaneously contributing to entrepreneurial learning.

Originality/value

– This paper presents findings from the first multiple case study into entrepreneurship education specifically designed to develop real-life venture as part of the core curriculum. Findings provide basis for investigating the value of integrating entrepreneurship education and technology transfer at the university.
The determinants of VET educators’ occupational choice
Authors: Berger Jean-Louis , Girardet Céline
Published: February 2015

Purpose

– Potential teacher shortage and low esteem of vocational education and training (VET) educator profession, together with the importance of attracting individuals best suited for the profession, lead to concerns about the reasons why people become VET educators as a second career. Accordingly, the purpose of this paper is to investigate the determinants of career choice in Swiss VET educators using an adaption of the Factors Influencing Teaching Choice framework (Watt and Richardson, 2007).

Design/methodology/approach

– With a sample of 605 VET educators undergoing initial teacher training, the authors first provide a description of the determinants of career choice at the sample level, based on a motivational model and analyze differences in these determinants between three types of VET educators. Then, the authors contrast it to the conclusions of other studies on teachers’ career choice.

Findings

– There are somewhat different determinants driving this career choice depending on the type of educators. In terms of motivation, intrinsic value is the most important determinant of a career as VET teacher. VET educators value the activity of teaching more than the potential advantages it may offer.

Originality/value

– The findings of the research provide an insight into VET teachers’ career choice and how to promote the attractiveness of the profession.
The role of androgyny in leader prototypes over four decades
Authors: Powell Gary N. , Butterfield D. Anthony
Published: February 2015

Purpose

– The purpose of this paper is to examine the role of psychological androgyny, a construct that represents a combination of masculinity and femininity, in explaining changes in descriptions of a good manager over time.

Design/methodology/approach

– Samples of the same two populations were surveyed at four different points in time spanning four decades (N= 1,818).

Findings

– Good-manager descriptions became increasingly similar in masculinity and femininity over time, or increasingly androgynous according to the balance conceptualization of androgyny. However, both good-manager masculinity and good-manager femininity declined over time, with masculinity declining to a greater extent, which accounted for the greater similarity in these scores. As a result, according to the high masculinity/high femininity conceptualization of androgyny, good-manager descriptions actually became decreasingly androgynous and more “undifferentiated”. Overall, the trend in leader prototypes over time was toward less emphasis on traits associated with members of either sex.

Research limitations/implications

– Limitations of two alternative methods of analyses and the survey instrument are acknowledged. What constituted a good manager may have depended on the context. Further scholarly attention to the concept of an undifferentiated leadership style is recommended.

Practical implications

– People may be moving beyond leader prototypes based on the simple application of gender stereotypes. Changes in leader prototypes over the past four decades may contribute to enhancements in women’s societal status.

Social implications

– Leader prototypes may disadvantage women less than in the past.

Originality/value

– Results suggest that the role of androgyny in leader prototypes is declining according to the high masculinity/high femininity conceptualization.