bluuebunny/crossref_metadata_2025 huggingface dataset:
Depolarized light scattering from prolate anisotropic particles: The influence of the particle shape on the field autocorrelation function
Authors: Passow Christopher , ten Hagen Borge , Löwen Hartmut , Wagner Joachim
Published: July 2015

We provide a theoretical analysis for the intermediate scattering function typically measured in depolarized dynamic light scattering experiments. We calculate the field autocorrelation function g1V H(Q,t) in dependence on the wave vector Q and the time t explicitly in a vertical-horizontal scattering geometry for differently shaped solids of revolution. The shape of prolate cylinders, spherocylinders, spindles, and double cones with variable aspect ratio is expanded in rotational invariants flm(r). By Fourier transform of these expansion coefficients, a formal multipole expansion of the scattering function is obtained, which is used to calculate the weighting coefficients appearing in the depolarized scattering function. In addition to translational and rotational diffusion, especially the translational-rotational coupling of shape-anisotropic objects is considered. From the short-time behavior of the intermediate scattering function, the first cumulants Γ(Q) are calculated. In a depolarized scattering experiment, they deviate from the simple proportionality to Q2. The coefficients flm(Q) strongly depend on the geometry and aspect ratio of the particles. The time dependence, in addition, is governed by the translational and rotational diffusion tensors, which are calculated by means of bead models for differently shaped particles in dependence on their aspect ratio. Therefore, our analysis shows how details of the particle shape—beyond their aspect ratio—can be determined by a precise scattering experiment. This is of high relevance in understanding smart materials which involve suspensions of anisotropic colloidal particles.
Influence of local magnetization on acceptor-bound complex state in Hg1−xMnxTe single crystals
Authors: Zhu Liangqing , Shao Jun , Zhu Liang , Chen Xiren , Qi Zhen , Lin Tie , Bai Wei , Tang Xiaodong , Chu Junhao
Published: July 2015

We performed temperature-dependent magnetic measurements and infrared photoluminescence (PL) measurements in various geometries on a series of p-type Hg1–xMnxTe single crystals (0.20≤x≤0.26). Evolution of PL features was observed, and zero-field spin splitting was identified for the acceptor-bound magnetic polaron (A0BMP). The results show direct evidence for local spontaneous magnetization of the A0BMP. Comparison with the Ditel–Spałek model indicates that besides the fluctuation and collective regimes, the A0BMP exhibits a new regime at low temperatures owing to the formation of the spin-glass state in Hg1−xMnxTe. The dissociation energy of the exciton bound to the A0BMP ((A0,X)BMP) varied rapidly with temperature, and the ratio of the dissociation energy of the (A0,X)BMP to the binding energy of the A0BMP was larger than the classical value of the A0X and no longer a constant, which breaks the Haynes rule. The free exciton localization process helps enhance the local magnetization of the (A0,X)BMP by transferring energy from the carrier system to the Mn-spin system, and it may lead to a photoinduced configuration of non-interacting ferromagnetic domains or the photoinduced magnetization effect.
Inequalities for operator space numerical radius of 2 × 2 block matrices
Authors: Moslehian Mohammad Sal , Sattari Mostafa
Published: July 2015

In this paper, we study the relationship between operator space norm and operator space numerical radius on the matrix space Mn(X), when X is a numerical radius operator space. Moreover, we establish several inequalities for operator space numerical radius and the maximal numerical radius norm of 2 × 2 operator matrices and their off-diagonal parts. One of our main results states that if (X, (On)) is an operator space, then 12max(Wmax(x1+x2),Wmax(x1−x2))≤Wmax(0x1x20)≤12Wmax(x1+x2)+Wmax(x1−x2) for all x1,x2∈Mn(X).
Assessment of the accuracy of plasma shape reconstruction by the Cauchy condition surface method in JT-60SA
Authors: Miyata Y. , Suzuki T. , Takechi M. , Urano H. , Ide S.
Published: July 2015

For the purpose of stable plasma equilibrium control and detailed analysis, it is essential to reconstruct an accurate plasma boundary on the poloidal cross section in tokamak devices. The Cauchy condition surface (CCS) method is a numerical approach for calculating the spatial distribution of the magnetic flux outside a hypothetical surface and reconstructing the plasma boundary from the magnetic measurements located outside the plasma. The accuracy of the plasma shape reconstruction has been assessed by comparing the CCS method and an equilibrium calculation in JT-60SA with a high elongation and triangularity of plasma shape. The CCS, on which both Dirichlet and Neumann conditions are unknown, is defined as a hypothetical surface located inside the real plasma region. The accuracy of the plasma shape reconstruction is sensitive to the CCS free parameters such as the number of unknown parameters and the shape in JT-60SA. It is found that the optimum number of unknown parameters and the size of the CCS that minimizes errors in the reconstructed plasma shape are in proportion to the plasma size. Furthermore, it is shown that the accuracy of the plasma shape reconstruction is greatly improved using the optimum number of unknown parameters and shape of the CCS, and the reachable reconstruction errors in plasma shape and locations of strike points are within the target ranges in JT-60SA.
Homogeneous averaging operators on simple finite conformal Lie algebras
Authors: Kolesnikov Pavel
Published: July 2015

We describe all homogeneous averaging operators on finite simple conformal Lie algebras. In the case of current algebras, these operators are closely related to rational solutions of the classical Yang–Baxter equation.
A broadly applicable function for describing luminescence dose response
Authors: Burbidge C. I.
Published: July 2015

The basic form of luminescence dose response is investigated, with the aim of developing a single function to account for the appearance of linear, superlinear, sublinear, and supralinear behaviors and variations in saturation signal level and rate. A function is assembled based on the assumption of first order behavior in different major factors contributing to measured luminescence-dosimetric signals. Different versions of the function are developed for standardized and non-dose-normalized responses. Data generated using a two trap two recombination center model and experimental data for natural quartz are analyzed to compare results obtained using different signals, measurement protocols, pretreatment conditions, and radiation qualities. The function well describes a range of dose dependent behavior, including sublinear, superlinear, supralinear, and non-monotonic responses and relative response to α and β radiation, based on change in relative recombination and trapping probability affecting signals sourced from a single electron trap.
X-ray imaging for studying behavior of liquids at high pressures and high temperatures using Paris-Edinburgh press
Authors: Kono Yoshio , Kenney-Benson Curtis , Shibazaki Yuki , Park Changyong , Wang Yanbin , Shen Guoyin
Published: July 2015

Several X-ray techniques for studying structure, elastic properties, viscosity, and immiscibility of liquids at high pressures have been integrated using a Paris-Edinburgh press at the 16-BM-B beamline of the Advanced Photon Source. Here, we report the development of X-ray imaging techniques suitable for studying behavior of liquids at high pressures and high temperatures. White X-ray radiography allows for imaging phase separation and immiscibility of melts at high pressures, identified not only by density contrast but also by phase contrast imaging in particular for low density contrast liquids such as silicate and carbonate melts. In addition, ultrafast X-ray imaging, at frame rates up to ∼105 frames/second (fps) in air and up to ∼104 fps in Paris-Edinburgh press, enables us to investigate dynamics of liquids at high pressures. Very low viscosities of melts similar to that of water can be reliably measured. These high-pressure X-ray imaging techniques provide useful tools for understanding behavior of liquids or melts at high pressures and high temperatures.
Two dimensional numerical simulations of carrier dynamics during time-resolved photoluminescence decays in two-photon microscopy measurements in semiconductors
Authors: Kanevce Ana , Kuciauskas Darius , Levi Dean H. , Allende Motz Alyssa M. , Johnston Steven W.
Published: July 2015

We use two-dimensional numerical simulations to analyze high spatial resolution time-resolved spectroscopy data. This analysis is applied to two-photon excitation time-resolved photoluminescence (2PE-TRPL) but is broadly applicable to all microscopic time-resolved techniques. By solving time-dependent drift-diffusion equations, we gain insight into carrier dynamics and transport characteristics. Accurate understanding of measurement results establishes the limits and potential of the measurement and enhances its value as a characterization method. Diffusion of carriers outside of the collection volume can have a significant impact on the measured decay but can also provide an estimate of carrier mobility as well as lifetime. In addition to material parameters, the experimental conditions, such as spot size and injection level, can impact the measurement results. Although small spot size provides better resolution, it also increases the impact of diffusion on the decay; if the spot size is much smaller than the diffusion length, it impacts the entire decay. By reproducing experimental 2PE-TRPL decays, the simulations determine the bulk carrier lifetime from the data. The analysis is applied to single-crystal and heteroepitaxial CdTe, material important for solar cells, but it is also applicable to other semiconductors where carrier diffusion from the excitation volume could affect experimental measurements.
Principle of radial transport in low temperature annular plasmas
Authors: Zhang Yunchao , Charles Christine , Boswell Rod
Published: July 2015

Radial transport in low temperature annular plasmas is investigated theoretically in this paper. The electrons are assumed to be in quasi-equilibrium due to their high temperature and light inertial mass. The ions are not in equilibrium and their transport is analyzed in three different situations: a low electric field (LEF) model, an intermediate electric field (IEF) model, and a high electric field (HEF) model. The universal IEF model smoothly connects the LEF and HEF models at their respective electric field strength limits and gives more accurate results of the ion mobility coefficient and effective ion temperature over the entire electric field strength range. Annular modelling is applied to an argon plasma and numerical results of the density peak position, the annular boundary loss coefficient and the electron temperature are given as functions of the annular geometry ratio and Paschen number.
Spin conductances and spin polarization components in a three-terminal ring subject to Rashba coupling
Authors: Wang Yan , Duan Lu-Zhao , Zhai Li-Xue
Published: July 2015

Spin dependent transport in one-dimensional (1D) three-terminal rings is investigated in the presence of the Rashba spin-orbit coupling (RSOC). We focus on the spin dependent conductances and the components of the spin polarization vectors of the currents in the outgoing terminals. For this purpose, the transmission coefficients with respect to the σx, σy and σz basis are obtained, and the three components of the spin polarization vectors are evaluated analytically. The total conductances, the spin dependent conductances and the polarization components are obtained as functions of the incident electron energy, as well as the RSOC strength, for the totally symmetric, partially symmetric and asymmetric cases. It is found that the spin polarizations corresponding to the σy basis are zero, and that there is a symmetry in the total conductances, the spin dependent conductances and the polarization components for symmetric cases, i.e., G1 = G2, g1τ=g2−τ, and P1i=−P2i(i=x,z). This symmetry is attributed to the rotational symmetry in the symmetrically coupled rings. For asymmetric cases, however, it is broken by the asymmetric lead-ring configuration.
Immobilization of BiOBr/BiOI Hierarchical Microspheres on Fly Ash Cenospheres as Visible Light Photocatalysts
Authors: Lin Li , Wang Ya , Huang Manhong , Chen Donghui
Published: July 2015

Three-dimensional (3D) BiOBr/BiOI hierarchical microspheres were successfully fabricated on the surface of fly ash cenospheres (FACs) via a facile one-pot solvothermal method for the first time. The as-prepared samples were characterized by XRD, SEM, energy-dispersive X-ray spectroscopy, UV–visible diffuse reflectance spectroscopy, and high-resolution transmission electron microscopy. The results indicated that the loaded hierarchical microspheres exhibited a uniform distribution, and some aggregation was observed. These well-dispersed hierarchical microspheres were composed of 2D nanosheets, which possess heterojunction structures. Based on the photodegradation tests examining the removal of rhodamine B from water under visible light irradiation (λ > 420 nm), the photocatalytic activity of BiOB/BiOI/FACs was superior to that of BiOBr/FACs and BiOI/FACs. A proposed mechanism for the enhanced photocatalytic activity displayed by BiOB/BiOI/FACs is discussed.
Pearl millet growth and biochemical alterations determined by mycorrhizal inoculation, water availability and atmospheric CO2 concentration
Authors: Fabbrin Eliseu G. , Gogorcena Yolanda , Mogor Átila F. , Garmendia Idoia , Goicoechea Nieves
Published: July 2015

Pearl millet (Pennisetum glaucum L.) is an important fodder and is a potential feedstock for fuel ethanol production in dry areas. Our objectives were to assess the effect of elevated CO2 and/or reduced irrigation on biomass production and levels of sugars and proteins in leaves of pearl millet and to test whether mycorrhizal inoculation could modulate the effects of these abiotic factors on growth and metabolism. Results showed that mycorrhizal inoculation and water regime most influenced biomass of shoots and roots; however, their individual effects were dependent on the atmospheric CO2 concentration. At ambient CO2, mycorrhizal inoculation helped to alleviate effects of water deficit on pearl millet without significant decreases in biomass production, which contrasted with the low biomass of mycorrhizal plants under restricted irrigation and elevated CO2. Mycorrhizal inoculation enhanced water content in shoots, whereas reduced irrigation decreased water content in roots. The triple interaction between CO2, arbuscular mycorrhizal fungi (AMF) and water regime significantly affected the total amount of soluble sugars and determined the predominant soluble sugars in leaves. Under optimal irrigation, elevated CO2 increased the proportion of hexoses in pearl millet that was not inoculated with AMF, thus improving the quality of this plant material for bioethanol production. By contrast, elevated CO2 decreased the levels of proteins in leaves, thus limiting the quality of pearl millet as fodder and primary source for cattle feed.
Beyond neurological structures
Authors: da Cruz Fernanda Miranda
Published: July 2015

Although clinical criteria ultimately determine the pathological diagnosis of Alzheimer’s disease, ‘Alzheimer’s’ is also an ordinary sign, falling within a range of other possible signs, values and beliefs that define and are used to interpret dementia and mental diseases. While looking at talk-in-interaction in which two people diagnosed with Alzheimer’s interact with other people, this article tries to show that the way in which both lay and professional people interpret Alzheimer’s signs allows us to shed some light upon the core of the traditional and controversial dichotomy between normal and pathological. The interactions analyzed in this paper show how people oppose biomedical discourse, suggesting that other forms of interpreting aging and forgetfulness are possible. It has opened multiple cartographies or varied spheres of communicability influenced by the signs of Alzheimer’s.
Enacting knowledge exchange: a context dependent and ‘role-based’ typology for capturing utility from university research
Authors: Perez Vico Eugenia , Hellsmark Hans , Jacob Merle
Published: July 2015

One of the key research and policy problems in innovation studies is the development of tools for understanding and measuring the impact of academic research on society. The paper contributes to resolving this problem by providing a typology that helps us to understand and analyse the roles researchers take on in order to make academic knowledge useful. A key finding is that utility creation is context dependent and varies between individual researchers and research groups. Attempts to measure impact ought therefore to allow for diversity with regard to the individual researcher or research group in the context of knowledge creation.
Negation in context: Evidence from the visual world paradigm
Authors: Orenes Isabel , Moxey Linda , Scheepers Christoph , Santamaría Carlos
Published: July 2015

Literature assumes that negation is more difficult to understand than affirmation, but this might depend on the pragmatic context. The goal of this paper is to show that pragmatic knowledge modulates the unfolding processing of negation due to the previous activation of the negated situation. To test this, we used the visual world paradigm. In this task, we presented affirmative (e.g., her dad was rich) and negative sentences (e.g., her dad was not poor) while viewing two images of the affirmed and denied entities. The critical sentence in each item was preceded by one of three types of contexts: an inconsistent context (e.g., She supposed that her dad had little savings) that activates the negated situation (a poor man), a consistent context (e.g., She supposed that her dad had enough savings) that activates the actual situation (a rich man), or a neutral context (e.g., her dad lived on the other side of town) that activates neither of the two models previously suggested. The results corroborated our hypothesis. Pragmatics is implicated in the unfolding processing of negation. We found an increase in fixations on the target compared to the baseline for negative sentences at 800 ms in the neutral context, 600 ms in the inconsistent context, and 1450 ms in the consistent context. Thus, when the negated situation has been previously introduced via an inconsistent context, negation is facilitated.
Visual perspective in remembering and episodic future thought
Authors: McDermott Kathleen B. , Wooldridge Cynthia L. , Rice Heather J. , Berg Jeffrey J. , Szpunar Karl K.
Published: July 2015

According to the constructive episodic simulation hypothesis, remembering and episodic future thinking are supported by a common set of constructive processes. In the present study, we directly addressed this assertion in the context of third-person perspectives that arise during remembering and episodic future thought. Specifically, we examined the frequency with which participants remembered past events or imagined future events from third-person perspectives. We also examined the different viewpoints from which third-person perspective events were remembered or imagined. Although future events were somewhat more likely to be imagined from a third-person perspective, the spatial viewpoint distributions of third-person perspectives characterizing remembered and imagined events were highly similar. These results suggest that a similar constructive mechanism may be at work when people remember events from a perspective that could not have been experienced in the past and when they imagine events from a perspective that could not be experienced in the future. The findings are discussed in terms of their consistency with—and as extensions of—the constructive episodic simulation hypothesis.
Longitudinal and Transverse Right Ventricular Function in Pulmonary Hypertension: Cardiovascular Magnetic Resonance Imaging Study from the ASPIRE Registry
Authors: Swift Andrew J. , Rajaram Smitha , Capener Dave , Elliot Charlie , Condliffe Robin , Wild Jim M. , Kiely David G.
Published: July 2015

Right ventricular (RV) function is a strong predictor of outcome in cardiovascular diseases. Two components of RV function, longitudinal and transverse motion, have been investigated in pulmonary hypertension (PH). However, their individual clinical significance remains uncertain. The aim of this study was to determine the factors associated with transverse and longitudinal RV motion in patients with PH. In 149 treatment‐naive patients with PH and 16 patients with suspected PH found to have mean pulmonary arterial pressure of <20 mmHg, cardiovascular magnetic resonance imaging was performed within 24 hours of right heart catheterization. In patients with PH, fractional longitudinal motion (fractional tricuspid annulus to apex distance [f‐TAAD]) was significantly greater than fractional transverse motion (fractional septum to free wall distance [f‐SFD]; P = 0.002). In patients without PH, no significant difference between f‐SFD and f‐TAAD was identified (P = 0.442). Longitudinal RV motion was singularly associated with RV ejection fraction independent of age, invasive hemodynamics, and cardiac magnetic resonance measurements (P = 0.024). In contrast, transverse RV motion was independently associated with left ventricular eccentricity (P = 0.036) in addition to RV ejection fraction (P = 0.014). In conclusion, RV motion is significantly greater in the longitudinal direction in patients with PH, whereas patients without PH have equal contributions of transverse and longitudinal motion. Longitudinal RV motion is primarily associated with global RV pump function in PH. Transverse RV motion not only reflects global pump function but is independently influenced by ventricular interaction in patients with PH.
Positive and negative regulation by SLP-76/ADAP and Pyk2 of chemokine-stimulated T-lymphocyte adhesion mediated by integrin α4β1
Authors: Dios-Esponera Ana , Isern de Val Soledad , Sevilla-Movilla Silvia , García-Verdugo Rosa , García-Bernal David , Arellano-Sánchez Nohemí , Cabañas Carlos , Teixidó Joaquin
Published: July 2015

Stimulation by chemokines of integrin α4β1–dependent T-lymphocyte adhesion is a crucial step for lymphocyte trafficking. The adaptor Vav1 is required for chemokine-activated T-cell adhesion mediated by α4β1. Conceivably, proteins associating with Vav1 could potentially modulate this adhesion. Correlating with activation by the chemokine CXCL12 of T-lymphocyte attachment to α4β1 ligands, a transient stimulation in the association of Vav1 with SLP-76, Pyk2, and ADAP was observed. Using T-cells depleted for SLP-76, ADAP, or Pyk2, or expressing Pyk2 kinase–inactive forms, we show that SLP-76 and ADAP stimulate chemokine-activated, α4β1-mediated adhesion, whereas Pyk2 opposes T-cell attachment. While CXCL12-promoted generation of high-affinity α4β1 is independent of SLP-76, ADAP, and Pyk2, the strength of α4β1-VCAM-1 interaction and cell spreading on VCAM-1 are targets of regulation by these three proteins. GTPase assays, expression of activated or dominant-negative Rac1, or combined ADAP and Pyk2 silencing indicated that Rac1 activation by CXCL12 is a common mediator response in SLP-76–, ADAP-, and Pyk2-regulated cell adhesion involving α4β1. Our data strongly suggest that chemokine-stimulated associations between Vav1, SLP-76, and ADAP facilitate Rac1 activation and α4β1-mediated adhesion, whereas Pyk2 opposes this adhesion by limiting Rac1 activation.
Silica particles cause NADPH oxidase–independent ROS generation and transient phagolysosomal leakage
Authors: Joshi Gaurav N. , Goetjen Alexandra M. , Knecht David A.
Published: July 2015

Chronic inhalation of silica particles causes lung fibrosis and silicosis. Silica taken up by alveolar macrophages causes phagolysosomal membrane damage and leakage of lysosomal material into the cytoplasm to initiate apoptosis. We investigated the role of reactive oxygen species (ROS) in this membrane damage by studying the spatiotemporal generation of ROS. In macrophages, ROS generated by NADPH oxidase 2 (NOX2) was detected in phagolysosomes containing either silica particles or nontoxic latex particles. ROS was only detected in the cytoplasm of cells treated with silica and appeared in parallel with an increase in phagosomal ROS, as well as several hours later associated with mitochondrial production of ROS late in apoptosis. Pharmacological inhibition of NOX activity did not prevent silica-induced phagolysosomal leakage but delayed it. In Cos7 cells, which do not express NOX2, ROS was detected in silica-containing phagolysosomes that leaked. ROS was not detected in phagolysosomes containing latex particles. Leakage of silica-containing phagolysosomes in both cell types was transient, and after resealing of the membrane, endolysosomal fusion continued. These results demonstrate that silica particles can generate phagosomal ROS independent of NOX activity, and we propose that this silica-generated ROS can cause phagolysosomal leakage to initiate apoptosis.
Nocturnal Intermittent Hypoxia Is Associated With Left Ventricular
Hypertrophy in Middle-Aged Men With Hypertension and Obstructive Sleep
Apnea
Authors: Yamaguchi Tasuku , Takata Yoshifumi , Usui Yasuhiro , Asanuma Ryoko , Nishihata Yosuke , Kato Kota , Shiina Kazuki , Yamashina Akira
Published: July 2015

BACKGROUND

Obstructive sleep apnea (OSA) and left ventricular (LV) hypertrophy are considered to be closely associated. However, the relationship has not yet been fully demonstrated and is hence still controversial. The purpose of this study was to assess in hypertensive male patients the relationship between OSA and cardiac structure using a new index, namely, integrated area of desaturation (IAD), in addition to the apnea-hypopnea index (AHI) that is currently the most frequently used index of sleep-disordered breathing.

METHODS

In our cross-sectional study, 223 hypertensive men younger than 65 years with sleep apnea and normal cardiac function were enrolled. All subjects were evaluated by fully attended polysomnography. Cardiac structure and function were evaluated by echocardiography.

RESULTS

LV mass index significantly correlated with IAD ( r = 0.203, P < 0.05), but not with AHI. Multivariate linear regression analyses showed that IAD, brain natriuretic peptide (BNP), and age are independent variables affecting the LV mass index ( β = 0.262, 0.237, and 0.173, respectively, P < 0.05). IAD was the one and only determinant among the indices of sleep-disordered breathing.

CONCLUSIONS

Nocturnal intermittent hypoxia defined by IAD may be associated with LV hypertrophy in men with well-controlled hypertension and obstructive sleep apnea.
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets
Authors: Jin Ying , Tam Oliver H. , Paniagua Eric , Hammell Molly
Published: July 2015

Motivation: Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses.

Results: Here, we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets.

Availability and implementation: The source code, associated GTF files for TE annotation, and testing data are freely available at http://hammelllab.labsites.cshl.edu/software.

Contact:  mhammell@cshl.edu.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cervical cancer screening in immigrant women in Italy: a survey on participation, cytology and histology results
Authors: Campari Cinzia , Fedato Chiara , Iossa Anna , Petrelli Alessio , Zorzi Manuel , Anghinoni Emanuela , Bietta Carla , Brachini Angela , Brezzi Silvia , Cogo Carla , Giordano Livia , Giorgi Daniela , Palazzi Mauro , Petrella Marco , Schivardi Maria R. , Visioli Carmen B. , Giorgi Rossi Paolo
Published: July 2015

Cervical cancer screening programmes in Italy actively invite all 25–64-year-old resident women for the Pap test every 3 years irrespective of their citizenship. Immigrant women come from countries where screening is absent or poorly implemented and the prevalence of human papillomavirus is often high. These women therefore have significant risk factors for cervical cancer. The Italian Group for Cervical Cancer Screening promoted a survey of all the screening programmes on the participation and the positivity and detection rates in Italian and foreign women in 2009–2011. Aggregated data for participation, cytology results, compliance with colposcopy and histology results were collected, distinguishing between women born in Italy and abroad. All comparisons were age adjusted. Forty-eight programmes out of 120 participated in the immigrant survey, with 3 147 428 invited and 1 427 412 screened Italian women and 516 291 invited and 205 948 screened foreign women. Foreign women had a slightly lower participation rate compared with Italians (39.9 vs. 45.4%), whereas compliance with colposcopy was similar (90%). Foreigners showed a higher risk of pathological findings than Italians: cytology positivity [relative risk (RR)=1.25, 95% confidence interval (CI) 1.24–1.27] and detection rate for cervical intraepithelial neoplasia grade 2 (CIN2) (RR=1.39, 95% CI 1.31–1.47), CIN3 (RR=2.07, 95% CI 1.96–2.18) and cancer (RR=2.68, 95% CI 2.24–3.22). The ratio between cancer and CIN was higher in immigrants (0.06 vs. 0.04, P<0.01). Foreign women had a higher risk of cervical precancer and cancer. Because of their high risk and because opportunistic screening does not cover this often disadvantaged group, achieving high participation in screening programmes for foreigners is critical to further reducing the cervical cancer burden in Italy.
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
Authors: Miya M. , Sato Y. , Fukunaga T. , Sado T. , Poulsen J. Y. , Sato K. , Minamoto T. , Yamamoto S. , Yamanaka H. , Araki H. , Kondoh M. , Iwasaki W.
Published: July 2015

We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
Nest inundation from sea-level rise threatens sea turtle population viability
Authors: Pike David A. , Roznik Elizabeth A. , Bell Ian
Published: July 2015

Contemporary sea-level rise will inundate coastal habitats with seawater more frequently, disrupting the life cycles of terrestrial fauna well before permanent habitat loss occurs. Sea turtles are reliant on low-lying coastal habitats worldwide for nesting, where eggs buried in the sand remain vulnerable to inundation until hatching. We show that saltwater inundation directly lowers the viability of green turtle eggs (
Chelonia mydas
) collected from the world's largest green turtle nesting rookery at Raine Island, Australia, which is undergoing enigmatic decline. Inundation for 1 or 3 h reduced egg viability by less than 10%, whereas inundation for 6 h reduced viability by approximately 30%. All embryonic developmental stages were vulnerable to mortality from saltwater inundation. Although the hatchlings that emerged from inundated eggs displayed normal physical and behavioural traits, hypoxia during incubation could influence other aspects of the physiology or behaviour of developing embryos, such as learning or spatial orientation. Saltwater inundation can directly lower hatching success, but it does not completely explain the consistently low rates of hatchling production observed on Raine Island. More frequent nest inundation associated with sea-level rise will increase variability in sea turtle hatching success spatially and temporally, due to direct and indirect impacts of saltwater inundation on developing embryos.
The relationship between pond habitat depth and functional tadpole diversity in an agricultural landscape
Authors: de Souza Queiroz Cássia , da Silva Fernando Rodrigues , de Cerqueira Rossa-Feres Denise
Published: July 2015

One of the most important goals of biodiversity studies is to identify which characteristics of local habitats act as filters that determine the diversity of functional traits along environmental gradients. In this study, we investigated the relationship between the environmental variables of ponds and the functional trait diversity distribution of anuran tadpoles in an agricultural area in southeastern Brazil. Our results show that the functional trait diversity of frog tadpoles has a bell-curve-shaped relationship with the depths of ponds inserted in a pasture matrix. Because we are witnessing increasing human pressure on land use, simple acts (e.g. maintaining reproductive habitats with medium depth) can be the first steps towards preserving the diversity of Neotropical frog tadpole traits in agricultural landscapes.
Variation in the link between oxygen consumption and ATP production, and its relevance for animal performance
Authors: Salin Karine , Auer Sonya K. , Rey Benjamin , Selman Colin , Metcalfe Neil B.
Published: July 2015

It is often assumed that an animal's metabolic rate can be estimated through measuring the whole-organism oxygen consumption rate. However, oxygen consumption alone is unlikely to be a sufficient marker of energy metabolism in many situations. This is due to the inherent variability in the link between oxidation and phosphorylation; that is, the amount of adenosine triphosphate (ATP) generated per molecule of oxygen consumed by mitochondria (P/O ratio). In this article, we describe how the P/O ratio can vary within and among individuals, and in response to a number of environmental parameters, including diet and temperature. As the P/O ratio affects the efficiency of cellular energy production, its variability may have significant consequences for animal performance, such as growth rate and reproductive output. We explore the adaptive significance of such variability and hypothesize that while a reduction in the P/O ratio is energetically costly, it may be associated with advantages in terms of somatic maintenance through reduced production of reactive oxygen species. Finally, we discuss how considering variation in mitochondrial efficiency, together with whole-organism oxygen consumption, can permit a better understanding of the relationship between energy metabolism and life history for studies in evolutionary ecology.
Brain size affects the behavioural response to predators in female guppies (Poecilia reticulata)
Authors: van der Bijl Wouter , Thyselius Malin , Kotrschal Alexander , Kolm Niclas
Published: July 2015

Large brains are thought to result from selection for cognitive benefits, but how enhanced cognition leads to increased fitness remains poorly understood. One explanation is that increased cognitive ability results in improved monitoring and assessment of predator threats. Here, we use male and female guppies (Poecilia reticulata), artificially selected for large and small brain size, to provide an experimental evaluation of this hypothesis. We examined their behavioural response as singletons, pairs or shoals of four towards a model predator. Large-brained females, but not males, spent less time performing predator inspections, an inherently risky behaviour. Video analysis revealed that large-brained females were further away from the model predator when in pairs but that they habituated quickly towards the model when in shoals of four. Males stayed further away from the predator model than females but again we found no brain size effect in males. We conclude that differences in brain size affect the female predator response. Large-brained females might be able to assess risk better or need less sensory information to reach an accurate conclusion. Our results provide experimental support for the general idea that predation pressure is likely to be important for the evolution of brain size in prey species.
Predicting microbial relative growth in a mixed culture from growth curve data
Authors: Ram Yoav , Dellus-Gur Eynat , Bibi Maayan , Obolski Uri , Berman Judith , Hadany Lilach
Published: July 2015

Estimates of microbial fitness from growth curves are inaccurate. Rather, competition experiments are necessary for accurate estimation. But competition experiments require unique markers and are difficult to perform with isolates derived from a common ancestor or non-model organisms. Here we describe a new approach for predicting relative growth of microbes in a mixed culture utilizing mono- and mixed culture growth curve data. We validated this approach using growth curve and competition experiments withE. coli. Our approach provides an effective way to predict growth in a mixed culture and infer relative fitness. Furthermore, by integrating several growth phases, it provides an ecological interpretation for microbial fitness.
Assessment of cladistic data availability for living mammals
Authors: Guillerme Thomas , Cooper Natalie
Published: July 2015

Analyses of living and fossil taxa are crucial for understanding changes in biodiversity through time. The Total Evidence method allows living and fossil taxa to be combined in phylogenies, by using molecular data for living taxa and morphological data for both living and fossil taxa. With this method, substantial overlap of morphological data among living and fossil taxa is crucial for accurately inferring topology. However, although molecular data for living species is widely available, scientists using and generating morphological data mainly focus on fossils. Therefore, there is a gap in our knowledge of neontological morphological data even in well-studied groups such as mammals.

We investigated the amount of morphological (cladistic) data available for living mammals and how this data was phylogenetically distributed across orders. 22 of 28 mammalian orders have<25% species with available morphological data; this has implications for the accurate placement of fossil taxa, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available data are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate Total Evidence phylogenies.
Coalescence with background and balancing selection in systems with bi- and uniparental reproduction: contrasting partial asexuality and selfing
Authors: Agrawal Aneil F. , Hartfield Matthew
Published: July 2015

Uniparental reproduction in diploids, via asexual reproduction or selfing, reduces the independence with which separate loci are transmitted across generations. This is expected to increase the extent to which a neutral marker is affected by selection elsewhere in the genome. Such effects have previously been quantified in coalescent models involving selfing. Here we examine the effects of background selection and balancing selection in diploids capable of both sexual and asexual reproduction (i.e., partial asexuality). We find that the effect of background selection on reducing coalescent time (and effective population size) can be orders of magnitude greater when rates of sex are low than when sex is common. This is because asexuality enhances the effects of background selection through both a recombination effect and a segregation effect. We show that there are several reasons that the strength of background selection differs between systems with partial asexuality and those with comparable levels of uniparental reproduction via selfing. Expectations for reductions inNevia background selection have been verified using stochastic simulations. In contrast to background selection, balancing selection increases the coalescent time for a linked neutral site. With partial asexuality, the effect of balancing selection is somewhat dependent upon the mode of selection (e.g., heterozygote advantage vs. negative frequency dependent selection) in a manner that does not apply to selfing. This is because the frequency of heterozygotes, which are required for recombination onto alternative genetic backgrounds, is more dependent on the pattern of selection with partial asexuality than with selfing.
Sulfur Isotope Effects of Dissimilatory Sulfite Reductase
Authors: Leavitt William D. , Bradley Alexander S. , Santos André A. , Pereira Inês A.C. , Johnston David T.
Published: July 2015

The precise interpretation of environmental sulfur isotope records requires a quantitative understanding of the biochemical controls on sulfur isotope fractionation by the principle isotope-fractionating process within the S cycle, microbial sulfate reduction (MSR). Here we provide the only direct observation of the major (34S/32S) and minor (33S/32S,36S/32S) sulfur isotope fractionations imparted by a central enzyme in the energy metabolism of sulfate reducers, dissimilatory sulfite reductase (DsrAB). Results from in vitro sulfite reduction experiments allow us to calculate the in vitro DsrAB isotope effect in34S/32S (hereafter,34εDsrAB) to be 15.3±2‰, 2σ.The accompanying minor isotope effect in33S, described as33λDsrAB, is calculated to be 0.5150±0.0012, 2σ. These observations facilitate a rigorous evaluation of the isotopic fractionation associated with the dissimilatory MSR pathway, as well as of the environmental variables that govern the overall magnitude of fractionation by natural communities of sulfate reducers. The isotope effect induced by DsrAB upon sulfite reduction is a factor of 0.3 to 0.6 times prior indirect estimates, which have ranged from 25 to 53‰ in34εDsrAB. The minor isotope fractionation observed from DsrAB is consistent with a kinetic or equilibrium effect. Our in vitro constraints on the magnitude of34εDsrABis similar to the median value of experimental observations compiled from all known published work, where34εr-p= 16.1‰ (r – pindicates reactant versus product, n = 648). This value closely matches those of MSR operating at high sulfate reduction rates in both laboratory chemostat experiments (34εSO4-H2S= 17.3±1.5‰) and in modern marine sediments (34εSO4-H2S= 17.3±3.8‰). Targeting the direct isotopic consequences of a specific enzymatic processes is a fundamental step toward a biochemical foundation for reinterpreting the biogeochemical and geobiological sulfur isotope records in modern and ancient environments.
ASTRID: Accurate Species TRees from Internode Distances
Authors: Vachaspati Pranjal , Warnow Tandy
Published: July 2015

Background

Incomplete lineage sorting (ILS), modelled by the multi-species coalescent (MSC), is known to create discordance between gene trees and species trees, and lead to inaccurate species tree estimations unless appropriate methods are used to estimate the species tree. While many statistically consistent methods have been developed to estimate the species tree in the presence of ILS, only ASTRAL-2 and NJst have been shown to have good accuracy on large datasets. Yet, NJst is generally slower and less accurate than ASTRAL-2, and cannot run on some datasets.

Results

We have redesigned NJst to enable it to run on all datasets, and we have expanded its design space so that it can be used with different distance-based tree estimation methods. The resultant method, ASTRID, is statistically consistent under the MSC model, and has accuracy that is competitive with ASTRAL-2. Furthermore, ASTRID is much faster than ASTRAL-2, completing in minutes on some datasets for which ASTRAL-2 used hours.

Conclusions

ASTRID is a new coalescent-based method for species tree estimation that is competitive with the best current method in terms of accuracy, while being much faster. ASTRID is available in open source form on github.
Adaptation to temporally fluctuating environments by the evolution of maternal effects
Authors: Dey Snigdhadip , Proulx Stephen R. , Teotónio Henrique
Published: July 2015

Most organisms live in ever-challenging temporally fluctuating environments. Theory suggests that the evolution of anticipatory (or deterministic) maternal effects underlies adaptation to environments that regularly fluctuate every other generation because of selection for increased offspring performance. Evolution of maternal bet-hedging reproductive strategies that randomize offspring phenotypes is in turn expected to underlie adaptation to irregularly fluctuating environments. Although maternal effects are ubiquitous their adaptive significance is unknown since they can easily evolve as a correlated response to selection for increased maternal performance. Using the nematodeCaenorhabditis elegans, we show the experimental evolution of maternal provisioning of offspring with glycogen, in populations facing a novel anoxia hatching environment every other generation. As expected with the evolution of deterministic maternal effects, improved embryo hatching survival under anoxia evolved at the expense of fecundity and glycogen provisioning when mothers experienced anoxia early in life. Unexpectedly, populations facing an irregularly fluctuating anoxia hatching environment failed to evolve maternal bet-hedging reproductive strategies. Instead, adaptation in these populations should have occurred through the evolution of balancing trade-offs over multiple generations, since they evolved reduced fitness over successive generations in anoxia but did not go extinct during experimental evolution. Mathematical modelling confirms our conclusion that adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that they are generally much more likely to contribute to adaptation than maternal bet-hedging reproductive strategies.