bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of top and bottom interfaces of a Pt/Co/AlOx system in Dzyaloshinskii-Moriya interaction, interface perpendicular magnetic anisotropy, and magneto-optical Kerr effect
Authors: Kim Nam-Hui , Cho Jaehun , Jung Jinyong , Han Dong-Soo , Yin Yuxiang , Kim June-Seo , Swagten Henk J. M. , Lee Kyujoon , Jung Myung-Hwa , You Chun-Yeol
Published: March 2017

We investigate the role of top and bottom interfaces in inversion symmetry-breaking Pt/Co/AlOx systems by inserting ultra-thin Cu layers. Wedge-type ultrathin Cu layers (0-0.5 nm) are introduced between Pt/Co or Co/AlOx interfaces. Interface sensitive physical quantities such as the interfacial Dzyaloshinskii-Moriya interaction (iDMI) energy density, the interfacial perpendicular magnetic anisotropy (iPMA), and the magneto-optical Kerr effects (MOKE) are systematically measured as a function of Cu-insertion layer thickness. We find that the Cu-insertion layer in the bottom interface (Pt/Co) plays a more important role in iDMI, PMA, and MOKE. In contrast, the top interface (Co/AlOx) noticeably contributes to only PMA, while its contributions to iDMI and MOKE enhancement are less significant. Although the PMA mainly comes from the bottom interface (Pt/Co), the Cu-insertion layers of all interfaces (Pt/Co, Co/AlOx) influence PMA. For iDMI, only the Cu-insertion layer in the bottom interface exerts SOC suppression which leads iDMI energy to decrease rapidly.
Optical properties of organic-silicon photonic crystal nanoslot cavity light source
Authors: Yang Ming-Jay , Lin Chun-Chi , Wu Yu-Shu , Wang Likarn , Na Neil
Published: March 2017

We theoretically study a dielectric photonic crystal nanoslot cavity immersed in an organic fluid containing near-infrared dyes by means of a full rate equation model including the complete cavity QED effects. Based on the modeling results, we numerically design an organic-silicon cavity light source in which its mode volume, quality factor, and far-field emission pattern are optimized for energy-efficient, high-speed applications. Dye quantum efficiency improved by two orders of magnitude and 3dB modulation bandwidth of a few hundred GHz can be obtained.
Nearshore Habitat and Fish Assemblages along a Gradient of Shoreline Development
Authors: Dustin Donna L. , Vondracek Bruce
Published: March 2017

Littoral habitat is a critical component of lake ecosystems. Expansion of residential development along lakeshores has led to habitat modification, which may alter lentic fish communities. Previous studies have linked lakeshore development to reductions in abundance of aquatic vegetation and coarse woody structure (CWS), and many have quantified the influence of the density of docks on aquatic habitat structure and individual fish species. However, few studies have quantified fish assemblages relative to the effect of density or pattern of development. Using docks as a proxy for development, we calculated dock density, cumulative dock area, and estimates of the proportion of shoreline that was developed, affected by development, or left in large undeveloped segments for 28 Minnesota lakes. We assessed nearshore structural habitat (aquatic vegetation, CWS, and riparian features), a lake-wide fish index of biotic integrity (IBI), and nearshore components of the fish IBI relative to the development measures derived from docks. The nearshore IBI metrics were community composition metrics based on the proportion of intolerant, small benthic-dwelling, and vegetation-dwelling species caught in nearshore sampling, which we also evaluated individually and summed as a nearshore IBI. All measures of development were correlated and performed similarly in our models. Emergent vegetation and CWS declined with increasing development. Nearshore fish IBI declined with increasing development, but the lake-wide IBI did not change significantly with development. The decline of the nearshore fish IBI appeared to have been driven by a decline in vegetation-dwelling species.

Received June 9, 2016; accepted January 6, 2017 Published online March 15, 2017
Distinguishing Yellowstone Cutthroat Trout, Rainbow Trout, and Hybrids by Use of Field-Based Phenotypic Characteristics
Authors: Meyer Kevin A. , Kennedy Patrick , High Brett , Campbell Matthew R.
Published: March 2017

Native and nonnative salmonids within the same genus sometimes hybridize, and the hybrids are often difficult to visually distinguish from parental species. We compared phenotypic delineations (based on several visual characteristics) and genotypic screening (using seven nuclear DNA loci) for 323 fish collected from an Idaho stream where Yellowstone Cutthroat Trout O. clarkii bouvieri were introgressed with Rainbow Trout O. mykiss to evaluate our ability to visually distinguish Yellowstone Cutthroat Trout from Rainbow Trout and hybrids. Assuming that the genotypes were 100% accurate, correct phenotypic classification was highest for Yellowstone Cutthroat Trout (the genotype confirmed the phenotype 94% of the time), followed by hybrids (79%) and Rainbow Trout (71%). All errors were between pure and hybrid fish. All of the measured phenotypic characteristics were useful for differentiating Yellowstone Cutthroat Trout from hybrids, but the most informative characteristics were the lack of a white leading tip on the anal and dorsal fins, the presence of fewer than five spots on the top of the head, and the presence of a bright red-orange throat slash. Fish size did not influence correct phenotypic identification, although fry were excluded from our study. A logistic regression model predicted that biologists were more than 50% likely to visually detect Rainbow Trout traits in a hybrid when its level of hybridization was greater than 22% (95% confidence interval = 4–30%). For an additional 189 fish in three other Idaho streams, phenotypic differentiation of Yellowstone Cutthroat Trout from Rainbow Trout and hybrids was 91% accurate. These results can be used to screen for introgression in Yellowstone Cutthroat Trout populations or to selectively remove Rainbow Trout and hybrids from Yellowstone Cutthroat Trout populations. However, in most cases, genetic confirmation of purity or introgression would still be valuable for identifying low levels of hybridization in individuals or in the population at large.

Received September 19, 2016; accepted December 29, 2016 Published online March 15, 2017
Visual versus auditory Simon effect: A behavioural and physiological investigation
Authors: D’Ascenzo Stefania , Lugli Luisa , Baroni Giulia , Guidotti Roberto , Rubichi Sandro , Iani Cristina , Nicoletti Roberto
Published: March 2017

This study investigated whether the visual and auditory Simon effects could be accounted for by the same mechanism. In a single experiment, we performed a detailed comparison of the visual and the auditory Simon effects arising in behavioural responses and in pupil dilation, a psychophysiological measure considered as a marker of the cognitive effort induced by conflict processing. To address our question, we performed sequential and distributional analyses on both reaction times and pupil dilation. Results confirmed that the mechanisms underlying the visual and auditory Simon effects are functionally equivalent in terms of the interaction between unconditional and conditional response processes. The two modalities, however, differ with respect to the strength of their activation and inhibition. Importantly, pupillary data mirrored the pattern observed in behavioural data for both tasks, adding physiological evidence to the current literature on the processing of visual and auditory information in a conflict task.
Information and communication technology in cross-industry glossaries
Authors: Pronichev A N , Polyakov E V , Nikitaev V G , Vasilyev N P , Dmitrieva V V , Ulina I V
Published: March 2017

Interdisciplinary glossary is proposed to ensure mutual understanding of specialists from various fields of science and technology. Glossary is designed with application of information technologies. The field of information technologies is considered. It is necessary for the understanding and cooperation of specialists in various areas. The technological solutions and applications for multi-disciplinary areas, results of testing of the developed techniques are presented.
SeqArray—a storage-efficient high-performance data format for WGS variant calls
Authors: Zheng Xiuwen , Gogarten Stephanie M , Lawrence Michael , Stilp Adrienne , Conomos Matthew P , Weir Bruce S , Laurie Cathy , Levine David
Published: March 2017

Motivation

Whole-genome sequencing (WGS) data are being generated at an unprecedented rate. Analysis of WGS data requires a flexible data format to store the different types of DNA variation. Variant call format (VCF) is a general text-based format developed to store variant genotypes and their annotations. However, VCF files are large and data retrieval is relatively slow. Here we introduce a new WGS variant data format implemented in the R/Bioconductor package ‘SeqArray’ for storing variant calls in an array-oriented manner which provides the same capabilities as VCF, but with multiple high compression options and data access using high-performance parallel computing.

Results

Benchmarks using 1000 Genomes Phase 3 data show file sizes are 14.0 Gb (VCF), 12.3 Gb (BCF, binary VCF), 3.5 Gb (BGT) and 2.6 Gb (SeqArray) respectively. Reading genotypes in the SeqArray package are two to three times faster compared with the htslib C library using BCF files. For the allele frequency calculation, the implementation in the SeqArray package is over 5 times faster than PLINK v1.9 with VCF and BCF files, and over 16 times faster than vcftools. When used in conjunction with R/Bioconductor packages, the SeqArray package provides users a flexible, feature-rich, high-performance programming environment for analysis of WGS variant data.

Availability and Implementation

http://www.bioconductor.org/packages/SeqArray

Supplementary information

Supplementary data are available at Bioinformatics online.
Characterizing Adult Cervical Deformity and Disability Based on Existing Cervical and Adult Deformity Classification Schemes at Presentation and Following Correction
Authors: Passias Peter G , Jalai Cyrus M , Smith Justin S , Lafage Virginie , Diebo Bassel G , Protopsaltis Themistocles , Poorman Gregory , Ramchandran Subaraman , Bess Shay , Shaffrey Christopher I , Ames Christopher P , Schwab Frank ,   on behalf of the International Spine Study Group
Published: March 2017

BACKGROUND

Adult cervical deformity (ACD) classifications have not been implemented in a prospective ACD population and in conjunction with adult spinal deformity (ASD) classifications.

OBJECTIVE

To characterize cervical deformity type and malalignment with 2 classifications (Ames-ACD and Schwab-ASD).

METHODS

Retrospective review of a prospective multicenter ACD database. Inclusion: patients ≥18 yr with pre- and postoperative radiographs. Patients were classified with Ames-ACD and Schwab-ASD schemes. Ames-ACD descriptors (C = cervical, CT = cervicothoracic, T = thoracic, S = coronal, CVJ = craniovertebral) and alignment modifiers (cervical sagittal vertical axis [cSVA], T1 slope minus cervical lordosis [TS-CL], modified Japanese Ortphopaedic Association [mJOA] score, horizontal gaze) were assigned. Schwab-ASD curve type stratification and modifier grades were also designated. Deformity and alignment group distributions were compared with Pearson χ2/ANOVA.

RESULTS

Ames-ACD descriptors in 84 patients: C = 49 (58.3%), CT = 20 (23.8%), T = 9 (10.7%), S = 6 (7.1%). cSVA modifier grades differed in C, CT, and T deformities (P < .019). In C, TS-CL grade prevalence differed (P = .031). Among Ames-ACD modifiers, high (1+2) cSVA grades differed across deformities (C = 47.7%, CT = 89.5%, T = 77.8%, S = 50.0%, P = .013). Schwab-ASD curve type and presence (n = 74, T = 2, L = 6, D = 2) differed significantly in S deformities (P < .001). Higher Schwab-ASD pelvic incidence minus lumbar lordosis grades were less likely in Ames-ACD CT deformities (P = .027). Higher pelvic tilt grades were greater in high (1+2) cSVA (71.4% vs 36.0%, P = .015) and high (2+3) mJOA (24.0% vs 38.1%, P = .021) scores. Postoperatively, C and CT deformities had a trend toward lower cSVA grades, but only C deformities differed in TS-CL grade prevalence (0 = 31.3%, 1 = 12.2%, 2 = 56.1%, P = .007).

CONCLUSION

Cervical deformities displayed higher TS-CL grades and different cSVA grade distributions. Preoperative associations with global alignment modifiers and Ames-ACD descriptors were observed, though only cervical modifiers showed postoperative differences.
Functional membrane separators for next-generation high-energy rechargeable batteries
Authors: Pan Yuede , Chou Shulei , Liu Hua Kun , Dou Shi Xue
Published: March 2017

The membrane separator is a key component in a liquid-electrolyte battery for electrically separating the cathode and the anode, meanwhile ensuring ionic transport between them. Besides these basic requirements, endowing the separator with specific beneficial functions is now being paid great attention because it provides an important alternative approach for the development of batteries, particularly next-generation high-energy rechargeable batteries. Herein, functional separators are overviewed based on four key criteria of next-generation high-energy rechargeable batteries: stable, safe, smart and sustainable (4S). That is, the applied membrane materials and the corresponding functioning mechanisms of the 4S separators are reviewed. Functional separators with selective permeability have been applied to retard unwanted migration of the specific species (e.g. polysulfide anions in Li-S batteries) from one electrode to the other in order to achieve stable cycling operation. The covered battery types are Li-S, room-temperature Na-S, Li-organic, organic redox-flow (RF) and Li-air batteries. Safe, smart and sustainable separators are then described in sequence following the first criterion of stable cycling. In the final section, key challenges and potential opportunities in the development of 4S separators are discussed.
Vaccination coverage levels among children two years of age and selected aspects of vaccination practices in Canada – 1996
Authors: Bentsi-Enchill Adwoa , Duclos Philippe
Published: March 2017

OBJECTIVE:

To obtain population-based estimates of coverage for routine childhood vaccinations at two years of age and information about selected aspects of vaccination practices in Canada.

METHODS:

Data were collected through a mail survey of a sample of households with two-year-olds born between February 1993 and January 1994. To obtain population estimates, survey data were weighted to match known population distributions of geographic region, community size, household income level and single-parent versus two-parent family type.

RESULTS:

Up-to-date vaccination coverage was estimated as 84.8% (95% CI 82.0 to 87.3) for diphtheria-pertussis-tetanus vaccine, 89.9% (95% CI 87.4 to 92.0) for polio vaccine, 93.3% (95% CI 91.2 to 95.0) for measlesmumps-rubella vaccine and 69.3% (95% CI 65.8 to 72.6) for Hae-mophilus influenzae type b vaccine. Less than one per cent of children had not received vaccination of any kind. Ninety-five per cent of parents cited the benefits of vaccination as a reason for having their children vaccinated.

CONCLUSION:

Coverage levels indicate that the national targets set for 1997 for up-to-date vaccination of children at two years of age have been reached for mumps and rubella, and good progress isbeing made towards targets for the remaining vaccines. Special attention from providers and parents is required to prevent vaccination delays, particularly for 18-month booster doses.
Live Cell Imaging Reveals the Relocation of dsRNA Binding Proteins Upon Viral Infection
Authors: Barton Deborah A. , Roovers Elke F. , Gouil Quentin , da Fonseca Guilherme C. , Reis Rodrigo S. , Jackson Craig , Overall Robyn L. , Fusaro Adriana F. , Waterhouse Peter M.
Published: March 2017

Viral infection triggers a range of plant responses such as the activation of the RNA interference (RNAi) pathway. The double-stranded RNA binding (DRB) proteins DRB3 and DRB4 are part of this pathway and aid in defending against DNA and RNA viruses, respectively. Using live cell imaging, we show that DRB2, DRB3, and DRB5 relocate from their uniform cytoplasmic distribution to concentrated accumulation in nascent viral replication complexes (VRC) that develop following cell invasion by viral RNA. Inactivation of the DRB3 gene in Arabidopsis by T-DNA insertion rendered these plants less able to repress RNA viral replication. We propose a model for the early stages of virus defense in which DRB2, DRB3, and DRB5 are invasion sensors that relocate to nascent VRC, where they bind to viral RNA and inhibit virus replication.
Impacts of silicon-based grass defences across trophic levels under both current and future atmospheric CO
2
scenarios
Authors: Ryalls James M. W. , Hartley Susan E. , Johnson Scott N.
Published: March 2017

Silicon (Si) has important functional roles in plants, including resistance against herbivores. Environmental change, such as increasing atmospheric concentrations of CO
2
, may alter allocation to Si defences in grasses, potentially changing the feeding behaviour and performance of herbivores, which may in turn impact on higher trophic groups. Using Si-treated and untreated grasses (
Phalaris aquatica
) maintained under ambient (400 ppm) and elevated (640 and 800 ppm) CO
2
concentrations, we show that Si reduced feeding by crickets (
Acheta domesticus
), resulting in smaller body mass. This, in turn, reduced predatory behaviour by praying mantids (
Tenodera sinensis
), which consequently performed worse. Despite elevated CO
2
decreasing Si concentrations in
P. aquatica
, this reduction was not large enough to affect the feeding behaviour of crickets or their predator. Our results suggest that Si-based defences in plants have adverse impacts on both primary and secondary trophic taxa, and these are not likely to decline under future climate change scenarios.
Between Charcot and Bernheim: The debate on hypnotism in
fin-de-siècle
Italy
Authors: Brancaccio Maria Teresa
Published: March 2017

In the late 1870s, a small group of Italian psychiatrists became interested in hypnotism in the wake of the studies conducted by the French neurologist Jean-Martin Charcot. Eager to engage in hypnotic research, these physicians referred to the scientific authority of French and German scientists in order to overcome the scepticism of the Italian medical community and establish hypnotism as a research subject based on Charcot's neuropathological model. In the following years, French studies on hypnotism continued to exert a strong influence in Italy. In the mid 1880s, studies on hypnotic suggestion by the Salpêtrière and Nancy Schools of hypnotism gave further impetus to research and therapeutic experimentation and inspired the emergence of an interpretative framework that combined theories by both hypnotic schools. By the end of the decade, however, uncertainties had arisen around both hypnotic theory and the therapeutic use of hypnotism. These uncertainties, which were linked to the crisis of the neuropathological paradigm that had to a large extent framed the understanding of hypnotism in Italy and the theoretical disagreements among the psychiatrists engaged in hypnotic research, ultimately led to a decline in interest in hypnotism in Italy.
Microbe biogeography tracks water masses in a dynamic oceanic frontal system
Authors: Djurhuus Anni , Boersch-Supan Philipp H. , Mikalsen Svein-Ole , Rogers Alex D.
Published: March 2017

Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance–decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living microorganisms from five seamounts located along a gradient from subtropical to subantarctic waters and across three depth layers: (i) the sub-surface chlorophyll maximum (approx. 40 m), (ii) the bottom of the euphotic zone (approx. 200 m), and (iii) the benthic boundary layer (300–2000 m). Diversity and abundance of microbial operational taxonomic units (OTUs) were assessed by amplification and sequencing of the 16S rRNA gene on an Illumina MiSeq platform. Multivariate analyses showed that microbial communities were structured more strongly by depth than by latitude, with similar phyla occurring within each depth stratum across seamounts. The deep layer was homogeneous across the entire survey area, corresponding to the spread of Antarctic intermediate water. However, within both the sub-surface layer and the intermediate depth stratum there was evidence for OTU turnover across fronts. The microbiome of these layers appears to be divided into three distinct biological regimes corresponding to the subantarctic surface water, the convergence zone and subtropical. We show that microbial biogeography across depth and latitudinal gradients is linked to the water masses the microbes persist in, resulting in regional patterns of microbial biogeography that correspond to the regional scale physical oceanography.
Analytical results regarding electrostatic resonances of surface phonon/plasmon polaritons: separation of variables with a twist
Authors: Voicu R. C. , Sandu T.
Published: March 2017

The boundary integral equation (BIE) method ascertains explicit relations between localized surface phonon and plasmon polariton resonances and the eigenvalues of its associated electrostatic operator. We show that group-theoretical analysis of the Laplace equation can be used to calculate the full set of eigenvalues and eigenfunctions of the electrostatic operator for shapes and shells described by separable coordinate systems. These results not only unify and generalize many existing studies, but also offer us the opportunity to expand the study of phenomena such as cloaking by anomalous localized resonance. Hence, we calculate the eigenvalues and eigenfunctions of elliptic and circular cylinders. We illustrate the benefits of using the BIE method to interpret recent experiments involving localized surface phonon polariton resonances and the size scaling of plasmon resonances in graphene nanodiscs. Finally, symmetry-based operator analysis can be extended from the electrostatic to the full-wave regime. Thus, bound states of light in the continuum can be studied for shapes beyond spherical configurations.
How do cuticular hydrocarbons evolve? Physiological constraints and climatic and biotic selection pressures act on a complex functional trait
Authors: Menzel Florian , Blaimer Bonnie B. , Schmitt Thomas
Published: March 2017

Cuticular hydrocarbons (CHCs) cover the cuticles of virtually all insects, serving as a waterproofing agent and as a communication signal. The causes for the high CHC variation between species, and the factors influencing CHC profiles, are scarcely understood. Here, we compare CHC profiles of ant species from seven biogeographic regions, searching for physiological constraints and for climatic and biotic selection pressures. Molecule length constrained CHC composition: long-chain profiles contained fewer linear alkanes, but more hydrocarbons with disruptive features in the molecule. This is probably owing to selection on the physiology to build a semi-fluid cuticular layer, which is necessary for waterproofing and communication. CHC composition also depended on the precipitation in the ants' habitats. Species from wet climates had more alkenes and fewer dimethyl alkanes than those from drier habitats, which can be explained by different waterproofing capacities of these compounds. By contrast, temperature did not affect CHC composition. Mutualistically associated (parabiotic) species possessed profiles highly distinct from non-associated species. Our study is, to our knowledge, the first to show systematic impacts of physiological, climatic and biotic factors on quantitative CHC composition across a global, multi-species dataset. We demonstrate how they jointly shape CHC profiles, and advance our understanding of the evolution of this complex functional trait in insects.
Network reorganization and breakdown of an ant–plant protection mutualism with elevation
Authors: Plowman Nichola S. , Hood Amelia S. C. , Moses Jimmy , Redmond Conor , Novotny Vojtech , Klimes Petr , Fayle Tom M.
Published: March 2017

Both the abiotic environment and the composition of animal and plant communities change with elevation. For mutualistic species, these changes are expected to result in altered partner availability, and shifts in context-dependent benefits for partners. To test these predictions, we assessed the network structure of terrestrial ant-plant mutualists and how the benefits to plants of ant inhabitation changed with elevation in tropical forest in Papua New Guinea. At higher elevations, ant-plants were rarer, species richness of both ants and plants decreased, and the average ant or plant species interacted with fewer partners. However, networks became increasingly connected and less specialized, more than could be accounted for by reductions in ant-plant abundance. On the most common ant-plant, ants recruited less and spent less time attacking a surrogate herbivore at higher elevations, and herbivory damage increased. These changes were driven by turnover of ant species rather than by within-species shifts in protective behaviour. We speculate that reduced partner availability at higher elevations results in less specialized networks, while lower temperatures mean that even for ant-inhabited plants, benefits are reduced. Under increased abiotic stress, mutualistic networks can break down, owing to a combination of lower population sizes, and a reduction in context-dependent mutualistic benefits.
The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism
Authors: Ward Philip S. , Branstetter Michael G.
Published: March 2017

Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach—ultraconserved element sequence capture—to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants (Pseudomyrmex ferrugineusgroup) and their associatedVachelliahostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupiedVachelliaand evolved plant-protecting behaviour, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the Late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the pre-existing mutualism. Initiation of thePseudomyrmex/Vachelliainteraction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.
The interactions of ants with their biotic environment
Authors: Chomicki Guillaume , Renner Susanne S.
Published: March 2017

This special featureresults from the symposium ‘Ants 2016: ant interactions with their biotic environments’ held in Munich in May 2016 and deals with the interactions between ants and other insects, plants, microbes and fungi, studied at micro- and macroevolutionary levels with a wide range of approaches, from field ecology to next-generation sequencing, chemical ecology and molecular genetics. In this paper, we review key aspects of these biotic interactions to provide background information for the papers of this special feature. After listing the major types of biotic interactions that ants engage in, we present a brief overview of ant/ant communication, ant/plant interactions, ant/fungus symbioses, and recent insights about ants and their endosymbionts. Using a large molecular clock-dated Formicidae phylogeny, we map the evolutionary origins of different ant clades' interactions with plants, fungi and hemiptera. Ants' biotic interactions provide ideal systems to address fundamental ecological and evolutionary questions about mutualism, coevolution, adaptation and animal communication.
Live tracking of Moving samples in confocal microscopy for vertically grown roots tips
Authors: von Wangenheim Daniel , Hauschild Robert , Fendrych Matyáš , Barone Vanessa , Friml Jiří
Published: March 2017

Roots navigate through soil integrating environmental signals to orient their growth. TheArabidopsisroot is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker - a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.
Solution structure of human STARD1 protein and its interaction with fluorescently-labeled cholesterol analogues with different position of the NBD-group
Authors: Tugaeva Kristina V. , Faletrov Yaroslav V. , Allakhverdiev Elvin S. , Maksimov Eugene G. , Sluchanko Nikolai N.
Published: March 2017

Intracellular cholesterol transfer to mitochondria, a bottleneck of adrenal and gonadal steroidogenesis, relies on the functioning of the steroidogenic acute regulatory protein (StAR, STARD1), for which many disease-associated mutations have been described. Despite significant progress in the field, the exact mechanism of cholesterol binding and transfer by STARD1 remains debatable, and the solution conformation of STARD1 is insufficiently characterized, partially due to its poor solubility. Although cholesterol binding to STARD1 was widely studied by commercially available fluorescent NBD-analogues, the effect of the NBD group position on binding remained unexplored. Here, we analyzed in detail the hydrodynamic properties and solution conformation of STARD1 and its interaction with cholesterol-like steroids bearing 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) group in different position, namely 22-NBD-cholesterol (22NC), 25-NBD-cholesterol (25NC), 20-((NBDamino)-pregn-5-en-3-ol (20NP) and 3-(NBDamino)-cholestane (3NC). The small-angle X-ray scattering (SAXS)-based modeling and docking simulations show that, apart from movements of the flexible Ω1-loop, STARD1 unlikely undergoes significant structural rearrangements proposed earlier as a gating mechanism for cholesterol binding. While being able to stoichiometrically bind 22NC and 20NP with high fluorescence yield and quantitative exhaustion of fluorescence of some protein tryptophans, STARD1 binds 25NC and 3NC with much lower affinity and poor fluorescence yield. In contrast to 3NC, binding of 20NP leads to STARD1 stabilization and increases the NBD fluorescence lifetime. Remarkably, in terms of fluorescence response, 20NP outperforms commonly used 22NC and is recommended for future studies. Our study benefits from state-of-the-art techniques and revisits the results of the STARD1 research over the last 20 years, revealing important novel information.
Management of Mendelian Traits in Breeding Programs by Gene Editing: A Simulation Study
Authors: Cole John B.
Published: March 2017

Background

Genotypes based on high-density single nucleotide polymorphisms have recently been used to identify a number of novel recessive mutations that adversely affect fertility in dairy cattle as well as to track conditions such as polledness. The use of sequential mate allocation strategies that account for increases in genomic inbreeding and the economic impact of affected matings may result in faster allele frequency changes than strategies that do not consider inbreeding and monetary losses. However, the effect of gene editing on selection programs also should be considered because gene editing has the potential to dramatically change allele frequencies in livestock populations.

Methods

A simulation program developed to evaluate dairy cattle breeding schemes was extended to include the use of clustered regularly interspaced short palindromic repeat (CRISPR), transcription activator-like effector nuclease (TALEN), and zinc finger nuclease (ZFN) technologies for gene editing. A hypothetical technology with a perfect success rate was used to establish an upper limit on attainable progress, and a scenario with no editing served as a baseline for comparison.

Results

The technologies differed in the rate of success of gene editing as well as the success rate of embryo transfer based on literature estimates. The number of edited alleles was assumed to have no effect on success rate. The two scenarios evaluated considered only the horned locus or 12 recessive alleles that currently are segregating in the U.S. Holstein population. The top 1, 5, or 10% of bulls were edited each generation, and either no cows or the top 1% of cows were edited. Inefficient editing technologies produced less cumulative genetic gain and lower inbreeding than efficient ones. Gene editing was very effective at reducing the frequency of the horned haplotype (increasing the frequency of polled animals in the population), and allele frequencies of the 12 recessives segregating in the U.S. Holstein population decreased faster with editing than without.

Conclusions

Gene editing can be an effective tool for reducing the rate of harmful alleles in a dairy cattle population even if only a small proportion of elite animals are modified.
Why concatenation fails in the anomaly zone
Authors: Mendes Fábio K. , Hahn Matthew W.
Published: March 2017

Abstrct

Genome-scale sequencing has been of great benefit in recovering species trees, but has not provided final answers. Despite the rapid accumulation of molecular sequences, resolving short and deep branches of the tree of life has remained a challenge, and has prompted the development of new strategies that can make the best use of available data. One such strategy – the concatenation of gene alignments – can be successful when coupled with many tree estimation methods, but has also been shown to fail when there are high levels of incomplete lineage sorting. Here, we focus on the failure of likelihood-based methods in retrieving a rooted, asymmetric four-taxon species tree from concatenated data when the species tree is in or near the anomaly zone – a region of parameter space where the most common gene tree does not match the species tree because of incomplete lineage sorting. First, we use coalescent theory to prove that most informative sites will support the species tree in the anomaly zone, and that as a consequence maximum-parsimony succeeds in recovering the species tree from concatenated data. We further show that maximum-likelihood tree estimation from concatenated data fails both inside and outside the anomaly zone, and that this failure is unconnected to the frequency of the most common gene tree. We provide support for a hypothesis that likelihood-based methods fail in and near the anomaly zone because discordant sites on the species tree have a lower likelihood than those that are discordant on alternative topologies. Our results confirm and extend previous reports of the failure and success of likelihood- and parsimony-based methods, and highlight avenues for future work improving the performance of methods aimed at recovering species tree.
Severe infections emerge from the microbiome by adaptive evolution
Authors: Young Bernadette C. , Wu Chieh-Hsi , Claire Gordon N. , Cole Kevin , Price James R. , Liu Elian , Sheppard Anna E. , Perera Sanuki , Charlesworth Jane , Golubchik Tanya , Iqbal Zamin , Bowden Rory , Massey Ruth C. , Paul John , Crook Derrick W. , Peto Timothy E. A. , Sarah Walker A. , Llewelyn Martin J. , Wyllie David H. , Wilson Daniel J.
Published: March 2017

Bacteria responsible for the greatest global mortality colonize the human microbiome far more frequently than they cause severe infections. Whether mutation and selection within the microbiome accompany infection is unknown. We investigatedde novomutation in 1163Staphylococcus aureusgenomes from 105 infected patients with nose-colonization. We report that 72% of infections emerged from the microbiome, with infecting and nose-colonizing bacteria showing parallel adaptive differences. We found 2.8-to-3.6-fold enrichments of protein-altering variants in genes responding torsp, which regulates surface antigens and toxicity;agr, which regulates quorum-sensing, toxicity and abscess formation; and host-derived antimicrobial peptides. Adaptive mutations in pathogenesis-associated genes were 3.1-fold enriched in infecting but not nose-colonizing bacteria. None of these signatures were observed in healthy carriers nor at the species-level, suggesting disease-associated, short-term, within-host selection pressures. Our results show that infection, like a cancer of the microbiome, emerges through spontaneous adaptive evolution, raising new possibilities for diagnosis and treatment.

One Sentence Summary

Life-threateningS. aureusinfections emerge from nose microbiome bacteria in association with repeatable adaptive evolution.
DLPFC Transcriptome Defines Two Molecular Subtypes of Schizophrenia
Authors: Rhodes C. Harker , Bowen Elijah F. W. , Burgess Jack L. , Granger Richard
Published: March 2017

Little is known about the molecular pathogenesis of schizophrenia, possibly because of unrecognized heterogeneity in diagnosed patient populations. We analyzed gene expression data collected from the dorsolateral prefrontal cortex (DLPFC) of post-mortem frozen brains of 189 adult diagnosed schizophrenics and 206 matched controls. Transcripts from 633 genes are differentially expressed in the DLPFC of schizophrenics as compared to controls at Bonferroni-corrected significance levels. Seventeen of those genes are differentially expressed at very high significance levels (< 10−8after Bonferroni correction).

Weighted Gene Co-expression Network Analysis (WGCNA) of the schizophrenic subjects, based on the transcripts differentially expressed in the schizophrenics as compared to controls, divides them into two groups: "Type 1" schizophrenics, have a DLPFC transcriptome similar to that of controls with no expressed genes identified in this subcohort while the "type 2" schizophrenics have a DLPFC transcriptome dramatically different from that of controls, with 3,652 expression array probes to 3,200 genes detecting transcripts that are differentially expressed at very high significance levels. These findings were re-tested and replicated in a separate independent cohort, using the RNAseq data from the DLPFC of an independent set of schizophrenics and control subjects.

We suggest the hypothesis that these striking differences in DLPFC transcriptomes, identified and replicated in two populations, imply a fundamental biologic difference between these two groups of patients who have been diagnosed as schizophrenic.
Postmating sexual selection and the enigmatic jawed genitalia ofCallosobruchus subinnotatus
Authors: van Haren Merel M. , Liljestrand Rönn Johanna , Schilthuizen Menno , Arnqvist Göran
Published: March 2017

Insect genitalia exhibit rapid divergent evolution. Truly extraordinary structures have evolved in some groups, presumably as a result of post-mating sexual selection. To increase our understanding of this phenomenon, we studied the function of one such structure. The male genitalia ofCallosobruchus subinnotatus(Coleoptera: Bruchinae) contain a pair of jaw-like structures with unknown function. Here, we used phenotypic engineering to ablate the teeth on these jaws. We then experimentally assessed the effects of ablation of the genital jaws on mating duration, ejaculate weight, male fertilization success and female fecundity, using a double-mating experimental design. We predicted that copulatory wounding in females should be positively related to male fertilization success. However, we found no significant correlation between genital tract scarring in females and male fertilization success. Male fertilization success was, however, positively related to the amount of ejaculate transferred by males and negatively related to female ejaculate dumping. Ablation of male genital jaws did not affect male relative fertilization success but resulted in a reduction in female egg production. Our results suggest that postmating sexual selection in males indeed favors these genital jaws, but not primarily through an elevated relative success in sperm competition but by increasing female egg production.
Optimal construction of army ant living bridges
Authors: Graham Jason M. , Kao Albert B. , Wilhelm Dylana A. , Garnier Simon
Published: March 2017

Integrating the costs and benefits of collective behaviors is a fundamental challenge to understanding the evolution of group living. These costs and benefits can rarely be quantified simultaneously due to the complexity of the interactions within the group, or even compared to each other because of the absence of common metrics between them. The construction of ‘living bridges’ by New World army ants - which they use to shorten their foraging trails - is a unique example of a collective behavior where costs and benefits have been experimentally measured and related to each other. As a result, it is possible to make quantitative predictions about when and how the behavior will be observed. In this paper, we extend a previous mathematical model of these costs and benefits into a general framework for analyzing the optimal formation, and final configuration, of army ant living bridges. We provide experimentally testable predictions of the final bridge position, as well as the optimal formation process for certain cases, for a wide range of scenarios, which more closely resemble common terrain obstacles that ants encounter in nature. As such, our framework offers a rare benchmark for determining the evolutionary pressures governing the evolution of a naturally occurring collective animal behavior.
The Junction Usage Model (JUM): A method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns
Authors: Wang Qingqing , Rio Donald C.
Published: March 2017

Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-seq data rely on pre-annotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated genomes and can further mask unknown AS patterns. To address this critical bioinformatics problem, we developed a method called the Junction Usage Model (JUM) that uses a bottom-up approach to identify, analyze and quantitate global AS profiles without any prior transcriptome annotations. JUM accurately reports global AS changes in terms of the five conventional AS patterns and an additional “Composite” category composed of inseparable combinations of conventional patterns. JUM stringently classifies the difficult and disease-relevant pattern of intron retention, reducing the false positive rate of IR detection commonly seen in other annotation-based methods to near negligible rates. When analyzing AS in RNA-samples derived from Drosophila heads, human tumors and human cell lines bearing cancer-associated splicing factor mutations, JUM consistently identified ~ twice the number of novel AS events missed by other methods. Computational simulations showed JUM exhibits a 1.2-4.8 times higher true positive rate at a fixed cut-off of 5% false discovery rate. In summary, JUM provides a new framework and improved method that removes the necessity for transcriptome annotations and enables the detection, analysis and quantification of AS patterns in complex metazoan transcriptomes with superior accuracy.
A review of diagnostic approaches to medullary thyroid carcinoma
Authors: Borhani Soheila , Hedayati Mehdi
Published: March 2017

Medullary thyroid carcinoma (MTC), occurring sporadically or as an autosomal dominant trait, accounts for 5-10% of all thyroid gland neoplasms. While the sporadic variant originates from somatic rearranged-during-transfection (RET) mutations, the inherited variant is preceded by germ-line mutations of the RET proto-oncogene. Analysis of the transformations of this certain gene is the cornerstone of diagnostic and prognostic approaches in MTC. Additionally, a panel of histopathological evaluations, biochemical markers, and imaging procedures play a pivotal role in the management of MTC. The survival rate of MTC is relatively low compared to differentiated thyroid neoplasia and is highly influenced by the stage of tumors. Improvement in MTC surveillance significantly depends on early diagnosis as well as implementation of proper screening modalities in hereditary subtypes. The present review addresses medullary thyroid carcinoma, and in particular, the current diagnostic approaches to this challenging malignancy.
The self-healing evaluation of microcapsule-based epoxy coatings applied on AA6061 Al alloy in 3.5% NaCl solution
Authors: Shahidi Zandi Mehdi , Hasanzadeh Majdeh
Published: March 2017

Purpose

The aim of this work is to investigate the self-healing performance of epoxy coatings containing microcapsules. The microcapsule-based coatings were applied on AA6061 Al alloy and immersed in 3.5 per cent NaCl solution.

Design/methodology/approach

Microcapsules with urea–formaldehyde as the shell and linseed oil as the healing agent were prepared by in situ polymerization in an oil-in-water emulsion. For the sake of an optimum self-healing system, some coating samples were prepared by using different microcapsule concentrations: 0, 5, 10 and 20 Wt.%. The scratch-filling efficiency as the theoretical estimate of the self-healing performance was calculated for the coating samples with different microcapsule concentrations. The scratch-sealing efficiency (SSE) as a particularly crucial parameter in the self-healing evaluation of coatings was measured by both electrochemical impedance spectroscopy (EIS) and electrochemical noise (EN) techniques.

Findings

According to EIS and EN results, the coating samples containing 5 and 10 per cent microcapsules provided the insignificant self-healing performance, while the coating sample containing 20 per cent microcapsules exhibited the acceptable self-healing performance to AA6061 alloy in the NaCl solution. The measured SSE values confirmed the good agreement of EN data with electrochemical parameters obtained from the EIS technique.

Originality/value

This work is an attempt to evaluate the self-healing performance of microcapsule-based epoxy coatings applied on AA6061 Al alloy in sea water.