bluuebunny/crossref_metadata_2025 huggingface dataset:
Improvement of energy storage properties with the reduction of depolarization temperature in lead-free (1 – x)Na0.5Bi0.5TiO3-xAgTaO3 ceramics
Authors: Verma Anita , Yadav Arun Kumar , Kumar Sunil , Srihari Velaga , Jangir Ravindra , Poswal Himanshu K. , Liu Shun-Wei , Biring Sajal , Sen Somaditya
Published: February 2019

The effects of electric field and temperature on structural, dielectric, and ferroelectric properties of (1 – x)(Na0.50Bi0.50TiO3)-xAgTaO3 (x = 0, 0.03, 0.05, and 0.10) ceramics prepared via the modified sol-gel method were investigated. Rietveld refinement of synchrotron radiation x-ray diffraction data (SRPXRD) confirmed the rhombohedral (R3c) phase in all the unpoled samples. After poling, the samples remained in the rhombohedral phase for x ≤ 0.03, whereas for x ≥ 0.05, it showed a mixed rhombohedral and tetragonal (P4bm) phase. The anti-phase octahedral tilt angle was found to increase from 8.49° to 9.50° (for x = 0) and from 7.60° to 7.85° (for x = 0.10) with poling due to the long-range ordering phenomenon in the lattice system. The temperature-dependent dielectric study showed that the depolarization temperature decreases with increasing composition. Unpoled x = 0.10 composition exhibited the wide thermal stability dielectric constant in the temperature range 120-450 °C with 1795 ± 15% (tan δ < 0.041). Polarization versus electric field measurement revealed that at room temperature, the presence of anti-ferroelectric ordering increases the energy storage efficiency from 2.6% (for x = 0) to 48.2% (for x = 0.10). With increasing temperature, it increased from 48.2% (30 °C) to 85.5% (140 °C) for x = 0.10 composition. Improvement in the energy storage efficiency was correlated with structural changes probed by temperature dependent SRPXRD measurements; it confirmed the increase in antiferroelectric ordering with increasing temperature. Dielectric and ferroelectric results indicate the usefulness of this material system in the field of wide thermal stability dielectric constant and high-temperature energy storage applications.
Committors, first-passage times, fluxes, Markov states, milestones, and all that
Authors: Berezhkovskii Alexander M. , Szabo Attila
Published: February 2019

Milestoning on a one-dimensional potential starts by choosing a set of points, called milestones, and initiating short trajectories from each milestone, which are terminated when they reach an adjacent milestone for the first time. From the average duration of these trajectories and the probabilities of where they terminate, a rate matrix can be constructed and then used to calculate the mean first-passage time (MFPT) between any two milestones. All these MFPT’s turn out to be exact. Here we adopt a point of view from which this remarkable result is not unexpected. In addition, we clarify the nature of the “states” whose interconversion is described by the rate matrix constructed using information obtained from short trajectories and provide a microscopic expression for the “equilibrium population” of these states in terms of equilibrium averages of the committors.
Enhanced photovoltaic performance of perovskite solar cells by Co-doped spinel nickel cobaltite hole transporting layer
Authors: Ioakeimidis Apostolos , Papadas Ioannis T. , Tsikritzis Dimitris , Armatas Gerasimos S. , Kennou Stella , Choulis Stelios A.
Published: February 2019

A solution combustion synthesized hole transport layer (HTL) of spinel nickel cobaltite (NiCo2O4) incorporating 3% Cu–2% Li was fabricated using the doctor-blading technique for planar inverted perovskite solar cells (PVSCs). PVSCs incorporating 3% Cu–2% Li-doped NiCo2O4 showed an increase in Jsc and Voc device performance parameters compared to unmodified NiCo2O4, leading to power conversion efficiency (PCE) of 16.5%. X-ray photoelectron spectroscopy measurements revealed the tendency of Cu cations to replace preferably the surface Ni atoms by changing the surface stoichiometry of NiCo2O4, inducing a cathodic polarization. Ultraviolet photoelectron spectroscopy measurements unveiled the increase in the ionization potential by 0.1 eV for a co-doped NiCo2O4 film compared to unmodified NiCo2O4-based HTL. We attribute the enhanced PCE of the inverted PVSCs presented to the improved hole extraction properties of 3% Cu–2% Li NiCo2O4 HTL.
Activated micromotor propulsion by enzyme catalysis in a biofluid medium
Authors: Poddar Antarip , Bandopadhyay Aditya , Chakraborty Suman
Published: February 2019

Autonomous biocompatible systems have emerged to be of immense interest to the research community in recent times, owing to their wide gamut of applications ranging from biomimetics and nanomachinery on the one hand to targeted drug delivery on the other hand. While the electric field generated out of enzyme catalysis has been demonstrated to self-propel these active particles, the role of the intervening bio-fluid media in altering their motion remains unresolved. Here, through numerical simulations, we report unique interactions between enzyme-catalysis powered micromotors and complex bio-fluids towards achieving highly efficient electro-catalytic propulsion, surpassing the established limits to a large extent. These results may turn out to be of profound importance in realizing unprecedented control on electro-chemically induced locomotion of microscale or nanoscale objects in physiologically relevant fluidic pathways of in-vivo or in-vitro systems.
A dual electromagnetic array with intrinsic frequency up-conversion for broadband vibrational energy harvesting
Authors: Chen Jingfan , Wang Ya
Published: February 2019

This letter proposes a dual electromagnetic array to transform low frequency rectilinear vibrations into electricity with frequency up-conversion. The free of mechanical contact harvester consists of a rectilinear oscillator (RLO) and an array of two identical rotary oscillators (RTO). The RTO includes a rotor and a stator. The rotor has eight cubic magnets distributed centrosymmetrically, and the stator has eight coils. Under rectilinear vibrational excitations, the RLO drives the rotor of the RTO to rotate through magnetic torque acting on the rotors. A slight fluctuation of the rectilinear motion can lead to a great change of torque, which converts the low frequency vibrations into high frequency rotational motions. By adopting the frequency up-conversion mechanism, a high instantaneous output voltage is produced and maintained from 3.0 Hz to 9.5 Hz. Experiments show that with the dual rotor array, the output power is improved and the RLO is able to oscillate at its resonance even if the input frequency is greater than its resonant frequency, which implies a potential solution to suppress and harvest vibration energy during an earthquake if properly arraying multiple rotors. Under the excitation of 0.5 g and 4.0 Hz, the harvester can provide a stable DC power of 3.1 mW after AC-DC conversion.
Heteroepitaxy of MoSe2 on Si(111) substrates: Role of surface passivation
Authors: Ohtake Akihiro , Sakuma Yoshiki
Published: February 2019

We have studied the growth processes of MoSe2 thin films on Si(111) substrates by molecular-beam epitaxy. The surface termination of the Si substrate plays a crucial role in the growth of epitaxial MoSe2 films: when the Si(111) substrate is passivated with a GaSe bilayer, highly oriented MoSe2 films could be grown under optimized growth conditions. On the other hand, the growth on the Si(111)-(7 × 7) substrate results in the preferential formation of the MoSi2 phase, which prevents the formation of epitaxial MoSe2 films. We found that the As termination of the Si(111) surface is less effective in promoting the planar MoSe2 growth, despite its highly passivated nature.
Solutions of the linear and nonlinear differential equations within the generalized fractional derivatives
Authors: Akgül Esra Karatas
Published: February 2019

The main goal of this work is to find the solutions of linear and nonlinear fractional differential equations with the Mittag-Leffler nonsingular kernel. An accurate numerical method to search this problem has been constructed. The theoretical results are proved by utilizing two experiments.
Wideband electromagnetic dynamic acoustic transducers (WEMDATs) for air-coupled ultrasonic applications
Authors: Kang Lei , Feeney Andrew , Dixon Steve
Published: February 2019

Achieving sufficient energy transmission over a wide frequency range is a challenge which has restricted the application of many types of air-coupled ultrasonic transducers. Conventional transducer configurations such as the piezoelectric micromachined or flexural ultrasonic transducers can be considered as narrowband. This study reports a type of ultrasonic transducer, the wideband electromagnetic dynamic acoustic transducer (WEMDAT), which operates through a combination of electromagnetic induction and Lorentz force with dynamic behaviour of a micro-scale-thick conductive film. WEMDAT prototypes have been designed, fabricated, and tested, showing their compatibility with both low and high power inputs, operating efficiently as a wideband transmitter from 46.4 kHz to 144.6 kHz with a good directivity. The WEMDAT has also been shown to operate effectively as a wideband ultrasonic receiver through the measurement in a pitch-catch configuration. The WEMDAT prototypes possess an adjustable drive coil lift-off distance from the active membrane, providing flexibility for optimizing the sensitivity of the transducers for different input levels. The performance of the WEMDATs can be optimized, showing significant potential for air-coupled ultrasonic applications.
Single-pixel phase imaging by Fourier spectrum sampling
Authors: Hu Xinyao , Zhang Hao , Zhao Qian , Yu Panpan , Li Yinmei , Gong Lei
Published: February 2019

We present a single-pixel imaging technique that enables phase extraction from objects by complex Fourier spectrum sampling. The technique exploits a digital micromirror device to scan a wavevector-varying plane wave, which interferes with a stationary reference beam to produce time-varying spatial frequencies on the object. Synchronized intensity measurements are made using a single-pixel detector, and four-step phase-shifting is adopted in spectrum acquisition. Applying inverse Fourier transform to the obtained spectrum yields the desired image. The proposed technique is demonstrated by imaging two digital phase objects. Furthermore, we show that the image can be reconstructed from sub-Nyquist measurements via compressive sensing, considerably accelerating the acquisition process. As a particular application, we use the technique to characterize the orbital angular momentum of vortex beams, which could benefit multiplexing techniques in classical and quantum communications. This technique is readily integrated into commercial microscopes for quantitative phase microscopy.
Suitable junction partners for promising solar absorbers
Authors: Cesare Chris
Published: February 2019

Screening for optimal electronic band offsets and low strain identifies four partner materials that merit future study.
Complex genetic relationships within and among cytotypes in the Lepidosperma costale species complex (Cyperaceae) on rocky outcrops in Western Australia
Authors: Wallace Mark J. , Krauss Siegfried L. , Barrett Matthew D.
Published: February 2019

There is a growing realisation that cytotype variation within species complexes plays an important role in plant evolution; however, there are relatively few investigations that describe the genetic diversity within and among related cytotypes. In the present study, we analysed patterns of genetic variation in 774 individuals from nine diploid, 14 tetraploid and five mixed ploidy populations of the Lepidosperma costale complex (Cyperaceae) from rocky outcrops in south-west Australia. Application of nuclear (nSSR) and chloroplast (cpSSR) microsatellites suggests that polyploids are of autopolyploid and allopolyploid origin and that polyploidisation is associated with a shift to facultative clonal reproduction, including apomictic reproduction. The newly-discovered putative allopolyploids were commonly associated with disturbed environments, an association commonly reported for allopolyploids. Diploid populations generally contained more genetic diversity than polyploid populations, and there was little genetic differentiation among diploid populations. In contrast, polyploids were characterised by higher heterozygosity and differentiation among populations, but possessed lower within-population diversity. The high differentiation among polyploid populations suggests that polyploids may have formed recurrently and are an important component of morphologically cryptic diversity within the species complex. Ploidy level is a critical factor affecting genetic diversity in this species complex, highlighting the potential contributions of polyploidy to genetic differentiation, and potentially speciation.
A multi-gene phylogeny of Australian Monomorium Mayr (Hymenoptera : Formicidae) results in reinterpretation of the genus and resurrection of Chelaner Emery
Authors: Sparks Kathryn S. , Andersen Alan N. , Austin Andrew D.
Published: February 2019

Monomorium Mayr is a speciose, cosmopolitan genus of myrmicine ants that has had a challenging systematic history, comprising numerous lineages whose relationships are problematic. This study employed an extensive sampling of mostly Australian taxa, along with exemplars of other genera of Solenopsidini, to examine relationships among the continent’s Monomorium fauna. Sequences from elongation factor 1α F2, wingless and cytochrome oxidase subunit 1 (COI) were analysed using Bayesian and maximum likelihood methods. The resultant phylogeny resolved Australian Monomorium into two major clades separated by exemplars from other genera; one comprised predominantly species with 11-segmented antennae (corresponding to Monomorium s. str. in a recent study of Myrmicinae) along with three Paleotropical species. The second clade included Australian species with 12-segmented antennae, two New Zealand species and two from New Caledonia. Two Australian cryptobiotic species were resolved as sister to Clade 2. COI analysis indicated that some species (M. fieldi Forel, M. leave Mayr and M. leae Forel) possibly represent cryptic species complexes. The New Zealand M. antipodum Forel was recovered as a valid species, and is closely related to an eastern Australian population. We resurrect the genus Chelaner Emery for species in the second clade (with 12-segmented antennae) and outline morphological characters to separate Chelaner from Monomorium s. str. Fifty-three species of Chelaner are treated as either stat. nov. or stat. rev.
Revision of the Parasesarma guttatum species complex reveals a new pseudocryptic species in south-east African mangroves
Authors: Fratini Sara , Cannicci Stefano , Porri Francesca , Innocenti Gianna
Published: February 2019

Parasesarma De Man, 1895 is the most speciose genus in the family Sesarmidae (Decapoda: Brachyura: Thoracotremata). In the western Indian Ocean, Parasesarma is represented by five species only, although some genetic evidence suggests that P. guttatum could be a species complex comprising two cryptic species. Accordingly, P. guttatum is here split into two pseudocryptic species, and a new species, Parasesarma capensis, sp. nov., is described. P. capensis, sp. nov. fills the same ecological niche as P. guttatum south of the Mozambique Channel. While variation in mitochondrial DNA and morphological differences clearly distinguish the two species, there is no nuclear genetic variation. This may reflect a short history of reproductive isolation. The distinguishing morphological characters of the new species are the 13–15 rounded tubercles on the movable finger, the upper surface of the palm with three transverse crests (one regularly tuberculate and two pectinated), and the shape of the first gonopod. Phylogenetic inference analyses show a sister-species relationship between P. guttatum and P. capensis, sp. nov., and strongly suggest that at least two East African Parasesarma species need a taxonomic revision. The description of this new sesarmid species from the south-eastern African coast sheds new light on the overall biogeographic patterns and general biodiversity of this taxon within the western Indian Ocean.
Same stimuli, same subjects, different perception
Authors: Sloos Marjoleine , Lei Wang
Published: February 2019

Believed dialect influences speech perception by linguistically naïve speakers. How much accent-induced bias affects perception of linguistically trained speakers is still unclear. This study experimentally investigates the influence of believed dialect on plosive perception by subjects who were phonetically and phonologically trained. Identical syllables were presented twice to each subject. In one session, the subjects were informed that the variety was a Mandarin dialect which has voiceless unaspirated and aspirated voiceless stops; and in the other session that it was a Wu dialect, which has voiceless unaspirated, voiceless aspirated, and breathy stops. More breathy stops were reported if Wu was the believed dialect. Plosive phonation in Wu is related to lexical tone, and we show that lexical tone causes another bias to plosive perception. This suggests that linguistically trained transcribers are susceptible to higher order linguistic knowledge and it demonstrates the difficulty of avoiding biased perception when the coder forms a belief about the variety that he/she transcribes. We also advocate speech perception models which include a component that accounts for the role ofexpectedsounds.
Tribological properties of microarc oxidation coatings on Zirlo alloy
Authors: Wei Kejian , Chen Lin , Qu Yao , Yu Jiahao , Jin Xiaoyue , Du Jiancheng , Xue Wenbin , Zhang Jinlong
Published: February 2019

The ceramic coatings were prepared on Zirlo alloy using Microarc Oxidation (MAO) technology. Their tribological properties were evaluated by a ball-on-disc friction and wear tester in dry sliding against GCr15 steel ball, and their wear mechanism was also discussed. Compared to bare Zirlo alloy, the MAO coatings had good wear resistance. Their lowest wear rate was about 4.59 × 10−6 mm3 N−1 m−1, which was only about 1/60 of bare Zirlo alloy. In addition, the polishing treatment of MAO coatings could reduce the wear rate and improve their wear resistance. Composition and micrograph of worn surface indicated that the wear mechanism of MAO coatings was mainly the adhesive wear while the bare Zirlo alloy showed mainly the abrasive wear.
Enhancing the weldability of CP titanium friction stir welds with elemental foils
Authors: Fonda Richard W. , Knipling Keith E. , Levinson Amanda J. , Feng C. R.
Published: February 2019

Friction stir welding (FSW) has proven to be a viable technique for joining a wide variety of alloys. However, thick section welding of alpha and near-alpha Ti alloys has proven particularly challenging. Previous research at the Naval Research Laboratory using Ni markers in CP Ti friction stir welds indicated that elemental additions of Ni to the joint line can provide substantial benefits for improved weldability of these alloys. The current study surveys the effects of Ni and other elemental additions to CP Ti friction stir welds to determine their influence on the resultant weld microstructure, weld surface finish, and welding machine forces. These results reveal that Ni provides the most benefits for the concentrations examined, but other elements may also provide benefits at lower concentrations. The addition of these elements may improve the weldability and weld quality for FSW of CP Ti, enabling thick section welding of this and similar alloys.
Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP
Authors: Leone Vanessa , Waclawska Izabela , Kossmann Katharina , Koshy Caroline , Sharma Monika , Prisner Thomas F. , Ziegler Christine , Endeward Burkhard , Forrest Lucy R.
Published: February 2019

Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic techniques such as electron spin resonance (ESR) pulsed electron–electron double resonance (PELDOR), also known as double electron–electron resonance (DEER), provide a complement to atomistic structures obtained from x-ray crystallography or cryo-EM, since spectroscopic data reflect an ensemble and can be measured in more native solvents, unperturbed by a crystal lattice. However, attempts to interpret DEER data are frequently stymied by discrepancies with the structural data, which may arise due to differences in conditions, the dynamics of the protein, or the flexibility of the attached paramagnetic spin labels. Recently, molecular simulation techniques such as EBMetaD have been developed that create a conformational ensemble matching an experimental distance distribution while applying the minimal possible bias. Moreover, it has been proposed that the work required during an EBMetaD simulation to match an experimentally determined distribution could be used as a metric with which to assign conformational states to a given measurement. Here, we demonstrate the application of this concept for a sodium-coupled transport protein, BetP. Because the probe, protein, and lipid bilayer are all represented in atomic detail, the different contributions to the work, such as the extent of protein backbone movements, can be separated. This work therefore illustrates how ranking simulations based on EBMetaD can help to bridge the gap between structural and biophysical data and thereby enhance our understanding of membrane protein conformational mechanisms.
The binding interactions that maintain excitation–contraction coupling junctions in skeletal muscle
Authors: Ríos Eduardo , Gillespie Dirk , Franzini-Armstrong Clara
Published: February 2019

Calcium for contraction of skeletal muscles is released via tetrameric ryanodine receptor (RYR1) channels of the sarcoplasmic reticulum (SR), which are assembled in ordered arrays called couplons at junctions where the SR abuts T tubules or plasmalemma. Voltage-gated Ca2+ (CaV1.1) channels, found in tubules or plasmalemma, form symmetric complexes called CaV tetrads that associate with and activate underlying RYR tetramers during membrane depolarization by conveying a conformational change. Intriguingly, CaV tetrads regularly skip every other RYR tetramer within the array; therefore, the RYRs underlying tetrads (named V), but not the voltage sensor–lacking (C) RYRs, should be activated by depolarization. Here we hypothesize that the checkerboard association is maintained solely by reversible binary interactions between CaVs and RYRs and test this hypothesis using a quantitative model of the energies that govern CaV1.1–RYR1 binding, which are assumed to depend on number and location of bound CaVs. A Monte Carlo simulation generates large statistical samples and distributions of state variables that can be compared with quantitative features in freeze-fracture images of couplons from various sources. This analysis reveals two necessary model features: (1) the energy of a tetramer must have wells at low and high occupation by CaVs, so that CaVs positively cooperate in binding RYR (an allosteric effect), and (2) a large energy penalty results when two CaVs bind simultaneously to adjacent RYR protomers in adjacent tetramers (a steric clash). Under the hypothesis, V and C channels will eventually reverse roles. Role reversal justifies the presence of sensor-lacking C channels, as a structural and functional reserve for control of muscle contraction.
Cellular eIF2B subunit localization: implications for the integrated stress response and its control by small molecule drugs
Authors: Hodgson Rachel E. , Varanda Beatriz A. , Ashe Mark P. , Allen K. Elizabeth , Campbell Susan G.
Published: February 2019

Eukaryotic initiation factor 2 (eIF2) is a G protein critical for translation. It is tightly regulated in the integrated stress response (ISR) via phosphorylation of eIF2α and the subsequent control of eukaryotic initiation factor 2B (eIF2B), a multisubunit guanine nucleotide exchange factor. Through studying the localization of eIF2B subunits, we identified cytoplasmic eIF2B bodies in mammalian cells. We highlight a relationship between body size and the eIF2B subunits localizing to them; larger bodies contain all subunits and smaller bodies contain predominantly catalytic subunits. eIF2 localizes to eIF2B bodies and shuttles within these bodies in a manner that correlates with eIF2B activity. On stress, eIF2α-P localizes predominately to larger bodies and results in a decreased shuttling of eIF2. Interestingly, drugs that inhibit the ISR can rescue eIF2 shuttling in a manner correlating to levels of eIF2α-P. In contrast, smaller bodies show increased eIF2 shuttling in response to stress, which is accompanied by the localization of eIF2Bδ to these bodies, suggesting the formation of a novel trimeric complex of eIF2B. This response is mimicked by ISR-inhibiting drugs, providing insight into their potential mechanism of action. This study provides evidence that the composition and function of mammalian eIF2B bodies are regulated by the ISR and the drugs that control it.
Yeast-to-hypha transition ofSchizosaccharomyces japonicusin response to environmental stimuli
Authors: Kinnaer Cassandre , Dudin Omaya , Martin Sophie G.
Published: February 2019

Many fungal species are dimorphic, exhibiting both unicellular yeast-like and filamentous forms. Schizosaccharomyces japonicus, a member of the fission yeast clade, is one such dimorphic fungus. Here, we first identify fruit extracts as natural, stress-free, starvation-independent inducers of filamentation, which we use to describe the properties of the dimorphic switch. During the yeast-to-hypha transition, the cell evolves from a bipolar to a unipolar system with 10-fold accelerated polarized growth but constant width, vacuoles segregated to the nongrowing half of the cell, and hyper-lengthening of the cell. We demonstrate unusual features of S. japonicus hyphae: these cells lack a Spitzenkörper, a vesicle distribution center at the hyphal tip, but display more rapid cytoskeleton-based transport than the yeast form, with actin cables being essential for the transition. S. japonicus hyphae also remain mononuclear and undergo complete cell divisions, which are highly asymmetric: one daughter cell inherits the vacuole, the other the growing tip. We show that these elongated cells scale their nuclear size, spindle length, and elongation rates, but display altered division size controls. This establishes S. japonicus as a unique system that switches between symmetric and asymmetric modes of growth and division.
MAPK modulation of yeast pheromone signaling output and the role of phosphorylation sites in the scaffold protein Ste5
Authors: Winters Matthew J. , Pryciak Peter M.
Published: February 2019

Mitogen-activated protein kinases (MAPKs) mediate numerous eukaryotic signaling responses. They also can modulate their own signaling output via positive or negative feedback loops. In the yeast pheromone response pathway, the MAPK Fus3 triggers negative feedback that dampens its own activity. One target of this feedback is Ste5, a scaffold protein that promotes Fus3 activation. Binding of Fus3 to a docking motif (D motif) in Ste5 causes signal dampening, which was proposed to involve a central cluster of phosphorylation sites in Ste5. Here, we reanalyzed the role of these central sites. Contrary to prior claims, phosphorylation-mimicking mutations at these sites did not impair signaling. Also, the hyperactive signaling previously observed when these sites were mutated to nonphosphorylatable residues arose from their replacement with valine residues and was not observed with other substitutes. Instead, a cluster of N-terminal sites in Ste5, not the central sites, is required for the rapid dampening of initial responses. Further results suggest that the role of the Fus3 D motif is most simply explained by a tethering effect that promotes Ste5 phosphorylation, rather than an allosteric effect proposed to regulate Fus3 activity. These findings substantially revise our understanding of how MAPK feedback attenuates scaffold-mediated signaling in this model pathway.
Personality and social foraging tactic use in free-living Eurasian tree sparrows (Passer montanus)
Authors: Fülöp Attila , Németh Zoltán , Kocsis Bianka , Deák-Molnár Bettina , Bozsoky Tímea , Barta Zoltán
Published: February 2019

Group-foraging individuals often use alternative behavioral tactics to acquire food: some individuals, the producers, actively search for food, whereas others, the scroungers, look for opportunities to exploit the finders’ discoveries. Although the use of social foraging tactics is partly flexible, yet some individuals tend to produce more, whereas others largely prefer to scrounge. This between-individual variation in tactic use closely resembles the phenomenon of animal personality; however, the connection between personality and social foraging tactic use has rarely been investigated in wild animals. Here, we studied this relationship in free-living Eurasian tree sparrows (Passer montanus) during 2 winters. We found that in females, but not in males, social foraging tactic use was predicted by personality: more exploratory (i.e., more active in a novel environment) females scrounged more. Regardless of sex, the probability of scrounging increased with the density of individuals foraging on feeders and the time of feeding within a foraging bout, that is, the later the individual foraged within a foraging bout the higher the probability of scrounging was. Our results demonstrate that consistent individual behavioral differences are linked, in a sex-dependent manner, to group-level processes in the context of social foraging in free-living tree sparrows, suggesting that individual behavioral traits have implications for social evolution.
Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis
Authors: Jeitziner Rachel , Carrière Mathieu , Rougemont Jacques , Oudot Steve , Hess Kathryn , Brisken Cathrin
Published: February 2019

Motivation

Unbiased clustering methods are needed to analyze growing numbers of complex datasets. Currently available clustering methods often depend on parameters that are set by the user, they lack stability, and are not applicable to small datasets. To overcome these shortcomings we used topological data analysis, an emerging field of mathematics that discerns additional feature and discovers hidden insights on datasets and has a wide application range.

Results

We have developed a topology-based clustering method called Two-Tier Mapper (TTMap) for enhanced analysis of global gene expression datasets. First, TTMap discerns divergent features in the control group, adjusts for them, and identifies outliers. Second, the deviation of each test sample from the control group in a high-dimensional space is computed, and the test samples are clustered using a new Mapper-based topological algorithm at two levels: a global tier and local tiers. All parameters are either carefully chosen or data-driven, avoiding any user-induced bias. The method is stable, different datasets can be combined for analysis, and significant subgroups can be identified. It outperforms current clustering methods in sensitivity and stability on synthetic and biological datasets, in particular when sample sizes are small; outcome is not affected by removal of control samples, by choice of normalization, or by subselection of data. TTMap is readily applicable to complex, highly variable biological samples and holds promise for personalized medicine.

Availability and implementation

TTMap is supplied as an R package in Bioconductor.

Supplementary information

Supplementary data are available at Bioinformatics online.
Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers
Authors: Mehdi Tahmid F , Singh Gurdeep , Mitchell Jennifer A , Moses Alan M
Published: February 2019

Motivation

Mammalian genomes can contain thousands of enhancers but only a subset are actively driving gene expression in a given cellular context. Integrated genomic datasets can be harnessed to predict active enhancers. One challenge in integration of large genomic datasets is the increasing heterogeneity: continuous, binary and discrete features may all be relevant. Coupled with the typically small numbers of training examples, semi-supervised approaches for heterogeneous data are needed; however, current enhancer prediction methods are not designed to handle heterogeneous data in the semi-supervised paradigm.

Results

We implemented a Dirichlet Process Heterogeneous Mixture model that infers Gaussian, Bernoulli and Poisson distributions over features. We derived a novel variational inference algorithm to handle semi-supervised learning tasks where certain observations are forced to cluster together. We applied this model to enhancer candidates in mouse heart tissues based on heterogeneous features. We constrained a small number of known active enhancers to appear in the same cluster, and 47 additional regions clustered with them. Many of these are located near heart-specific genes. The model also predicted 1176 active promoters, suggesting that it can discover new enhancers and promoters.

Availability and implementation

We created the ‘dphmix’ Python package: https://pypi.org/project/dphmix/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Circulating inflammation markers and colorectal adenoma risk
Authors: Huang Wen-Yi , Berndt Sonja I , Shiels Meredith S , Katki Hormuzd A , Chaturvedi Anil K , Wentzensen Nicolas , Trabert Britton , Kemp Troy J , Pinto Ligia A , Hildesheim Allan , Rothman Nathaniel , Purdue Mark P
Published: February 2019

Inflammation is a driver of colorectal neoplasia; however, what particular inflammatory processes play a role in early carcinogenesis are unclear. We compared serum levels of 78 inflammation markers between 171 pathologically confirmed colorectal adenoma cases (including 48 incident cases) and 344 controls within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. We used weighted multivariable logistic regression to compute odds ratio (OR) and 95% confidence interval (CI). We found 14 markers associated with risk of adenoma overall; three of these were also associated with incident adenoma: CC-chemokine cysteine motif chemokine ligand 20 (CCL20) [overall adenoma fourth versus first quartile: OR 4.8, 95% CI 2.0–12, Ptrend 0.0007; incident adenoma third versus first tertile: OR 4.6, 95% CI 1.0–22, Ptrend 0.03], growth-related gene oncogene products (GRO) [OR 3.8, 95% CI 1.6–9.3, Ptrend 0.006 and OR 3.6, 95% CI 1.1–12, Ptrend 0.04, respectively] and insulin [OR 2.9, 95% CI 0.8–10, Ptrend 0.05 and OR 7.8, 95% CI 1.3–46, Ptrend 0.03, respectively]. All statistical tests were two-sided. These results provide important new evidence implicating CCL20- and GRO-related pathways in early colorectal carcinogenesis and further support a role for insulin.
Long-term outcome in a case series of Denys–Drash syndrome
Authors: Roca Neus , Muñoz Marina , Cruz Alejandro , Vilalta Ramon , Lara Enrique , Ariceta Gema
Published: February 2019

Background

Denys–Drash syndrome (DDS) is a rare disease caused by mutations in exons 8 and 9 of the WT1 gene. It is characterized by the association of early onset steroid-resistant nephrotic syndrome (SRNS), Wilms’ tumour and, in some patients, intersex disorders, with increasing risk of gonadoblastoma. There are few published data concerning the long-term outcome of patients with DDS. The aim of this study was to report our experience.

Methods

Data were collected from five children (three boys) with confirmed DDS diagnosed from 1996 to 2017. The mean follow-up of these patients was 16 years.

Results

The patients presented with SRNS and diffuse mesangial sclerosis at renal biopsy. All patients were hypertensive and progressed to end-stage kidney disease, initiating dialysis at a mean age of 28 months. Three patients developed Wilms’ tumour 9 months after the SRNS was identified, which was treated by nephrectomy and chemotherapy. All five patients received kidney transplantation. SRNS did not recur after transplantation in any of the patients and graft survival was similar to that of other kidney transplant recipients in our programme. All three boys had ambiguous genitalia and cryptorchidism but a confirmed male karyotype (46, XY). One girl presented with gonadal agenesis, whereas the other one had normal female ovarian tissue and external genitalia. Both girls had a female karyotype (46, XX). Gonadoblastoma was not observed at any case.

Conclusions

Early DDS recognition in patients with SRNS is crucial due to its low prevalence, the specific treatment approach required and early detection of Wilms’ tumour. Few data are available regarding long-term outcomes.
Personalized medicine in cardio-oncology: the role of induced pluripotent stem cell
Authors: Sayed Nazish , Ameen Mohamed , Wu Joseph C
Published: February 2019

Treatment of cancer has evolved in the last decade with the introduction of new therapies. Despite these successes, the lingering cardiotoxic side-effects from chemotherapy remain a major cause of morbidity and mortality in cancer survivors. These effects can develop acutely during treatment, or even years later. Although many risk factors can be identified prior to beginning therapy, unexpected toxicity still occurs, often with lasting consequences. Specifically, cardiotoxicity results in cardiac cell death, eventually leading to cardiomyopathy and heart failure. Certain risk factors may predispose an individual to experiencing adverse cardiovascular effects, and when unexpected cardiotoxicity occurs, it is generally managed with supportive care. Animal models of chemotherapy-induced cardiotoxicity have provided some mechanistic insights, but the precise mechanisms by which these drugs affect the heart remains unknown. Moreover, the genetic rationale as to why some patients are more susceptible to developing cardiotoxicity has yet to be determined. Many genome-wide association studies have identified genomic variants that could be associated with chemotherapy-induced cardiotoxicity, but the lack of validation has made these studies more speculative rather than definitive. With the advent of human induced pluripotent stem cell (iPSC) technology, researchers not only have the opportunity to model human diseases, but also to screen drugs for their efficacy and toxicity using human cell models. Furthermore, it allows us to conduct validation studies to confirm the role of genomic variants in human diseases. In this review, we discuss the role of iPSCs in modelling chemotherapy-induced cardiotoxicity.
Predator-induced changes of male and female mating preferences: innate and learned components
Authors: Plath Martin , Liu Kai , Umutoni Diane , Gomes-Silva Guilherme , Wei Jie-Fei , Cyubahiro Eric , Chen Bo-Jian , Sommer-Trembo Carolin
Published: February 2019

While many mating preferences have a genetic basis, the question remains as to whether and how learning/experience can modify individual mate choice decisions. We used wild-caught (predator-experienced) and F1 laboratory-reared (predator-naïve) invasive Western mosquitofish Gambusia affinis from China to test whether mating preferences (assessed in a first mate choice test) would change under immediate predation threat. The same individuals were tested in a second mate choice test during which 1 of 3 types of animated predators was presented: 1) a co-occurring predator, 2) a co-evolved but not currently co-occurring predator, and 3) a non-piscivorous species as control. We compared preference scores derived from both mate choice tests to separate innate from experiential effects of predation. We also asked whether predator-induced changes in mating preferences would differ between sexes or depend on the choosing individual’s personality type and/or body size. Wild-caught fish altered their mate choice decisions most when exposed to the co-occurring predator whereas laboratory-reared individuals responded most to the co-evolved predator, suggesting that both innate mechanisms and learning effects are involved. This behavior likely reduces individuals’ risk of falling victim to predation by temporarily moving away from high-quality (i.e., conspicuous) mating partners. Accordingly, effects were stronger in bolder than shyer, large- compared with small-bodied, and female compared with male focal individuals, likely because those phenotypes face an increased predation risk overall. Our study adds to the growing body of literature appreciating the complexity of the mate choice process, where an array of intrinsic and extrinsic factors interacts during decision-making.
Seascape context modifies how fish respond to restored oyster reef structures
Authors: Gilby Ben L , Olds Andrew D , Henderson Christopher J , Ortodossi Nicholas L , Connolly Rod M , Schlacher Thomas A
Published: February 2019

The seascape context of coastal ecosystems plays a pivotal role in shaping patterns in fish recruitment, abundance, and diversity. It might also be a principal determinant in structuring the recruitment of fish assemblages to restored habitats, but the trajectories of these relationships require further testing. In this study, we surveyed fish assemblages from 14 restored oyster reefs and 14 control sites in the Noosa River, Queensland, Australia, that differed in the presence or absence of seagrass within 500 m, over four periods using baited cameras. Fish assemblages at oyster reefs differed from those at control sites, with higher species richness (1.4 times) and more individuals of taxa that are harvested by fishers (1.8 times). The presence or absence of seagrass nearby affected the abundance of a key harvestable fish species (yellowfin bream Acanthopagrus australis) on oyster reefs, but not the overall composition of fish assemblages, species richness, or the total abundance of harvestable fishes overall. These findings highlight the importance of considering species-specific patterns in seascape utilization when selecting restoration sites and setting restoration goals, and suggest that the effects of restoration on fish assemblages might be optimized by focusing efforts in prime positions in coastal seascapes.
Expanding School Resources and Increasing Time on Task: Effects on Students’ Academic and Noncognitive Outcomes
Authors: Lavy Victor
Published: February 2019

This paper uses a natural experiment in Israel to assess the impact of school teaching resources and how it is used, “time-on-task”, on academic achievements and noncognitive outcomes. It exploits variation induced by a change in the funding formula that reduced instructional resources funding for some schools and increased them for others. The results suggest that increased school resources and students’ spending more time at school and on key tasks all lead to increased academic achievements with no behavioral costs. Separate estimations of the effect of increasing subject-specific instructional time per week also show positive and significant effects on math, science, and English test scores and small and nonsignificant effects on Hebrew test scores. However, there are no cross effects of additional instructional time across subjects. This evidence is robust to using different identification strategies. The evidence also shows that a longer school week increases the time that students spend on homework without reducing social and school satisfaction and without increasing school violence.
Long-Term Risk of Hospitalization Among Five-Year Survivors of Childhood Leukemia in the Nordic Countries
Authors: Sørensen Gitte Vrelits , Winther Jeanette Falck , de Fine Licht Sofie , Andersen Klaus Kaa , Holmqvist Anna Sällfors , Madanat-Harjuoja Laura , Tryggvadottir Laufey , Bautz Andrea , Lash Timothy L , Hasle Henrik
Published: February 2019

Background

Adverse effects from childhood leukemia treatment may persist or present years after cure from cancer. We provide a comprehensive evaluation of subsequent hospitalization in five-year survivors of childhood acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), and chronic myeloid leukemia (CML).

Methods

In the Adult Life after Childhood Cancer in Scandinavia Study, we identified 4003 five-year survivors diagnosed with childhood leukemia 1970–2008 in Denmark, Sweden, Iceland, and Finland. Survivors and 129 828 population comparisons were followed for first-time nonpsychiatric hospitalizations for 120 disease categories in the hospital registries. Standardized hospitalization rate ratios and absolute excess rates were calculated. All statistical tests were two-sided.

Results

Survivors of ALL (n = 3391), AML (n = 389), and CML (n = 92) had an increased overall hospitalization rate compared with population comparisons. The rate ratio for any hospitalization was 1.95 (95% confidence interval [CI] = 1.83 to 2.07) in ALL, 3.09 (95% CI = 2.53 to 3.65) in AML, and 4.51 (95% CI = 3.03 to 6.00) in CML survivors and remained increased even 20 years from leukemia diagnosis. Corresponding absolute excess rates per 1000 person-years were 28.48 (95% CI = 24.96 to 32.00), 62.75 (95% CI = 46.00 to 79.50), and 105.31 (95% CI = 60.90 to 149.72).

Conclusion

Leukemia survivors have an increased rate of hospitalization for medical conditions. We provide novel insight into the relative and absolute rate of hospitalization for 120 disease categories in survivors of ALL, AML, and CML, which are likely to be informative for both survivors and healthcare providers.
Cognitive outcomes in meningioma patients undergoing surgery: individual changes over time and predictors of late cognitive functioning
Authors: Rijnen Sophie J M , Meskal Ikram , Bakker Marjan , De Baene Wouter , Rutten Geert-Jan M , Gehring Karin , Sitskoorn Margriet M
Published: February 2019

Background

Meningioma patients are known to face cognitive deficits before and after surgery. We examined individual changes in cognitive performance over time and identified preoperative predictors of cognitive functioning 12 months after surgery in a large sample of meningioma patients.

Methods

Patients underwent neuropsychological assessment (NPA) using CNS Vital Signs 1 day before (T0) and 3 (T3) and 12 (T12) months after surgery. Patients’ sociodemographically corrected scores on 7 cognitive domains were compared with performance of a normative sample using one-sample z tests and chi-square tests of independence. Reliable change indices with correction for practice effects were calculated for individual patients. Linear mixed effects models were used to identify preoperative predictors of performance at T12.

Results

At T0, 261 patients were assessed, and 229 and 82 patients were retested at T3 and T12, respectively. Patients showed impaired cognitive performance before and after surgery, and although performance improved on the group level, cognitive scores remained significantly lower than in the normative sample up to T12. On the individual level, performance remained stable in the majority of patients. Better preoperative performance, younger age, male sex, and higher educational level predicted better late cognitive performance.

Conclusions

Meningioma patients face serious and persistent pre- and postsurgical cognitive deficits. A preoperative NPA together with sociodemographic characteristics may provide valuable information on the late cognitive outcome of individual meningioma patients. These results can help to inform patients and clinicians on late cognitive outcomes at an early stage, and emphasizes the importance of presurgical NPA and timely cognitive rehabilitation.