bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimisation of HEVC motion estimation exploiting SAD and SSD GPU‐based implementation
Authors: Khemiri Randa , Kibeya Hassan , Sayadi Fatma Ezahra , Bahri Nejmeddine , Atri Mohamed , Masmoudi Nouri
Published: September 2017

The new High‐Efficiency Video Coding (HEVC) standard doubles the video compression ratio compared to the previous H.264/AVC at the same video quality and without any degradation. However, this important performance is achieved by increasing the encoder computational complexity. That's why HEVC complexity is a crucial subject. The most time consuming and the most intensive computing part of HEVC is the motion estimation based principally on the sum of absolute differences (SAD) or the sum of square differences (SSD) algorithms. For these reasons, the authors proposed an implementation of these algorithms on a low cost NVIDIA GPU (graphics processing unit) using the Fermi architecture developed with Compute Unified Device Architecture language. The proposed algorithm is based on the parallel‐difference and the parallel‐reduction process. The investigational results show a significant speed‐up in terms of execution time for most 64 × 64 pixel blocks. In fact, the proposed parallel algorithm permits a significant reduction in the execution time that reaches up to 56.17 and 30.4%, compared to the CPU, for SAD and SSD algorithms, respectively. This improvement proves that parallelising the algorithm with the new proposed reduction process for the Fermi‐GPU generation leads to better results. These findings are based on a static study that determines the PU percentage utilisation for each dimension in the HEVC. This study shows that the larger PUs are the most utilised in temporal levels 3 and 4, which attain 84.56% for class E. This improvement is accompanied by an average peak signal‐to‐noise ratio loss of 0.095 dB and a decrease of 0.64% in terms of BitRate.
Experimental validation of the recovery effect in batteries for wearable sensors and healthcare devices discovering the existence of hidden time constants
Authors: Arora Harneet , Sherratt Robert Simon , Janko Balazs , Harwin William
Published: September 2017

Wearable sensors and healthcare devices use small lightweight batteries to power their operations of monitoring and tracking. It becomes absolutely vital to effectively utilise all the available battery charge for device longevity between charges. The electrochemical recovery effect enables the extraction of more power from the battery when implementing idle times in between use cycles, and has been used to develop various power management techniques. However, there is no evidence concerning the actual increase in available power that can be attained using the recovery effect. Also, this property cannot be generalised on all the battery chemistries since it is an innate phenomenon, relying on the anode/cathode material. Indeed recent developments suggest that recovery effect does not exist at all. Experimental results to verify the presence and level of the recovery effect in commonly used battery chemistries in wearable sensors and healthcare devices are presented. The results have revealed that the recovery effect significantly does exist in certain batteries, and importantly the authors show that it is also comprised of two different time constants. This novel finding has important implications for the development of power management techniques that utilise the recovery effect with application in a large range of battery devices.
Photospheric properties and fundamental parameters of M dwarfs
Authors: Rajpurohit A.S. , Allard F. , Teixeira G. D. C. , Homeier D. , Rajpurohit S. , Mousis O.
Published: September 2017

Context. M dwarfs are an important source of information when studying and probing the lower end of the Hertzsprung-Russell (HR) diagram, down to the hydrogen-burning limit. Being the most numerous and oldest stars in the galaxy, they carry fundamental information on its chemical history. The presence of molecules in their atmospheres, along with various condensed species, complicates our understanding of their physical properties and thus makes the determination of their fundamental stellar parameters more challenging and difficult.

Aim. The aim of this study is to perform a detailed spectroscopic analysis of the high-resolution H-band spectra of M dwarfs in order to determine their fundamental stellar parameters and to validate atmospheric models. The present study will also help us to understand various processes, including dust formation and depletion of metals onto dust grains in M dwarf atmospheres. The high spectral resolution also provides a unique opportunity to constrain other chemical and physical processes that occur in a cool atmosphere.

Methods. The high-resolution APOGEE spectra of M dwarfs, covering the entire H-band, provide a unique opportunity to measure their fundamental parameters. We have performed a detailed spectral synthesis by comparing these high-resolution H-band spectra to that of the most recent BT-Settl model and have obtained fundamental parameters such as effective temperature, surface gravity, and metallicity (Teff, log g, and [Fe/H]), respectively.

Results. We have determined Teff, log g, and [Fe/H] for 45 M dwarfs using high-resolution H-band spectra. The derived Teff for the sample ranges from 3100 to 3900 K, values of log g lie in the range 4.5 ≤ log g ≤ 5.5, and the resulting metallicities lie in the range −0.5 ≤ [Fe/H] ≤ +0.5. We have explored systematic differences between effective temperature and metallicity calibrations with other studies using the same sample of M dwarfs. We have also shown that the stellar parameters determined using the BT-Settl model are more accurate and reliable compared to other comparative studies using alternative models.
High-resolution Imaging of Transiting Extrasolar Planetary systems (HITEP)
Authors: Evans D. F. , Southworth J. , Smalley B. , Jørgensen U. G. , Dominik M. , Andersen M. I. , Bozza V. , Bramich D. M. , Burgdorf M. J. , Ciceri S. , D’Ago G. , Figuera Jaimes R. , Gu S.-H. , Hinse T. C. , Henning Th. , Hundertmark M. , Kains N. , Kerins E. , Korhonen H. , Kokotanekova R. , Kuffmeier M. , Longa-Peña P. , Mancini L. , MacKenzie J. , Popovas A. , Rabus M. , Rahvar S. , Sajadian S. , Snodgrass C. , Skottfelt J. , Surdej J. , Tronsgaard R. , Unda-Sanzana E. , von Essen C. , Wang Yi-Bo , Wertz O.
Published: September 2017

Context. The formation and dynamical history of hot Jupiters is currently debated, with wide stellar binaries having been suggested as a potential formation pathway. Additionally, contaminating light from both binary companions and unassociated stars can significantly bias the results of planet characterisation studies, but can be corrected for if the properties of the contaminating star are known.

Aim. We search for binary companions to known transiting exoplanet host stars, in order to determine the multiplicity properties of hot Jupiter host stars. We also search for and characterise unassociated stars along the line of sight, allowing photometric and spectroscopic observations of the planetary system to be corrected for contaminating light.

Methods. We analyse lucky imaging observations of 97 Southern hemisphere exoplanet host stars, using the Two Colour Instrument on the Danish 1.54 m telescope. For each detected companion star, we determine flux ratios relative to the planet host star in two passbands, and measure the relative position of the companion. The probability of each companion being physically associated was determined using our two-colour photometry.

Results. A catalogue of close companion stars is presented, including flux ratios, position measurements, and estimated companion star temperature. For companions that are potential binary companions, we review archival and catalogue data for further evidence. For WASP-77AB and WASP-85AB, we combine our data with historical measurements to determine the binary orbits, showing them to be moderately eccentric and inclined to the line of sight (and hence planetary orbital axis). Combining our survey with the similar Friends of Hot Jupiters survey, we conclude that known hot Jupiter host stars show a deficit of high mass stellar companions compared to the field star population; however, this may be a result of the biases in detection and target selection by ground-based surveys.
The effect of speech rehabilitation therapy for muscle tension dysphonia on global postural strategy
Authors: Faralli Mario , Lapenna Ruggero , Pagliari Jenny , Longari Fabrizio , D’Ascanio Luca , Ricci Giampietro
Published: September 2017

Purpose:

To examine postural control in muscle tension dysphonia (MTD) before and after a specific speech rehabilitation program.

Methods:

Twenty-six patients diagnosed with MTD underwent posturographic analysis before and after speech rehabilitation. Romberg test was performed with eyes open (EO), eyes closed (EC) and during the head retroflex (ECR) and the occlusal (ECO) tests to investigate the role of cervical and stomatognathic proprioception. The analyzed posturographic parameters were the Sway area (S), length (L) of the center of pressure (CP) oscillations, coordinates of the CP on frontal and sagittal plane, stomatognathic interference index (SSI) and cervical interference index (CSI). Considered parameters of microphone perturbation were the Jitter (JITT), Shimmer (SHIM) and noise to harmonic ratio (NHR).

Results:

Sixteen patients (61.5%) exhibited values above those expected for at least one of the posturographic parameters during one or more of the conditions with eyes closed. There were values outside the normal range in the Sway area under EC and ECR conditions, and in the coordinates of the center of pressure on the sagittal plane posteriorly under EC conditions. Highly destabilizing SSI was recorded in six of the patients (23%), while CSI was recorded in 18 (69.2%).

After rehabilitation, seven patients continued to show posturographic alterations. There was a statistically significant improvement of all previous altered posturographic parameters. Eight patients whose S parameters had returned to the normal range after speech therapy, also showed significant improvement of all microphone signal parameters.

Conclusion:

This study shows that MTD might interfere with global postural strategy through the involvement of all cervical muscles proprioception. The strong correlation between the improvement of vocal and postural control, suggests that a posturographic study may be useful in the planning of the speech therapy, as well as in the evaluation of its effectiveness in terms of muscle relaxation.
Global Regularity for the 2D MHD Equations with Partial Hyper-resistivity
Authors: Dong Bo-Qing , Li Jingna , Wu Jiahong
Published: September 2017

This article establishes the global existence and regularity for a system of the two-dimensional (2D) magnetohydrodynamic (MHD) equations with only directional hyper-resistivity. More precisely, the equation of $b_1$ (the horizontal component of the magnetic field) involves only vertical hyperdiffusion (given by $\Lambda_2^{2\beta} b_1$) while the equation of $b_2$ (the vertical component) has only horizontal hyperdiffusion (given by $\Lambda_1^{2\beta} b_2$), where $\Lambda_1$ and $\Lambda_2$ are directional Fourier multiplier operators with the symbols being $|\xi_1|$ and $|\xi_2|$, respectively. We prove that, for $\beta>1$, this system always possesses a unique global-in-time classical solution when the initial data is sufficiently smooth. The model concerned here is rooted in the MHD equations with only magnetic diffusion, which play a significant role in the study of magnetic reconnection and magnetic turbulence. In certain physical regimes and under suitable scaling, the magnetic diffusion becomes partial (given by part of the Laplacian operator). There have been considerable recent developments on the fundamental issue of whether classical solutions of these equations remain smooth for all time. The papers of Cao–Wu–Yuan [8] and of Jiu–Zhao [26] obtained the global regularity when the magnetic diffusion is given by the full fractional Laplacian $(-\Delta)^\beta$ with $\beta>1$. The main result presented in this article requires only directional fractional diffusion and yet we prove the regularization in all directions. The proof makes use of a key observation on the structure of the nonlinearity in the MHD equations and technical tools on Fourier multiplier operators such as the Hörmander–Mikhlin multiplier theorem. The result presented here appears to be the sharpest for the 2D MHD equations with partial magnetic diffusion.
New Type of Sign-Changing Blow-up Solutions for Scalar Curvature Type Equations
Authors: Deng Shengbing , Musso Monica , Wei Juncheng
Published: September 2017

Let $(M, g)$ be a smooth compact $n$-dimension Riemannian manifold. We are concerned with the existence of sign-changing blow-up solutions to the following elliptic problem \begin{eqnarray*} \Delta_g u+h u=|u|^{\frac{4}{n-2}-\varepsilon}u,\ \ \ \ \ in \ \ M, \end{eqnarray*} where $\Delta_g=-{\rm div}_g(\nabla)$ is the Laplace–Beltrami operator on $M$, $h $ is a $\mathcal {C}^1$ function on $M$, $\varepsilon$ is a small real parameter such that $\varepsilon$ goes to 0.
Adsorption-energy-based activity descriptors for electrocatalysts in energy storage applications
Authors: Wang Youwei , Qiu Wujie , Song Erhong , Gu Feng , Zheng Zhihui , Zhao Xiaolin , Zhao Yingqin , Liu Jianjun , Zhang Wenqing
Published: September 2017

Energy storage technologies, such as fuel cells, ammonia production and lithium–air batteries, are important strategies for addressing the global challenge of energy crisis and environmental pollution. Taking overpotential as a direct criterion, we illustrate in theory and experiment that the adsorption energies of charged species such as Li++e− and H++e− are a central parameter to describe catalytic activities related to electricity-in/electricity-out efficiencies. The essence of catalytic activity is revealed to relate with electronic coupling between catalysts and charged species. Based on adsorption energy, some activity descriptors such as d-band center, eg-electron number and charge-transfer capacity are further defined by electronic properties of catalysts that directly affect interaction between catalysts and charged species. The present review is helpful for understanding the catalytic mechanisms of these electrocatalytic reactions and developing accurate catalytic descriptors, which can be employed to screen high-activity catalysts in future high-throughput calculations and experiments.
CHARACTERIZATION OF AN IN-HOUSE DEVELOPED MULTI-CYLINDRICAL MODERATOR NEUTRON SPECTROMETER
Authors: Liamsuwan T , Channuie J , Wonglee S , Kowatari M , Nishino S
Published: September 2017

This article describes the characterization of an in-house developed multi-cylindrical moderator neutron spectrometer, which consists of a cylindrical 3He proportional counter and cylindrical moderator shells of different sizes. The response matrix of the spectrometer was calculated by Monte Carlo simulations for neutron energies from 1 × 10−8 to 10 MeV and verified with measurements in 0.144 MeV, 1.2 MeV and 241AmBe neutron standard fields. Influence of scattered neutrons was properly eliminated from the measured response using the shadow cone technique. The calculated and measured responses were in good agreement in most cases. Differences were <10% for all moderated counter configurations, while larger deviations were observed for the bare counter configuration. The performance of the neutron spectrometer in terms of spectrum unfolding was verified in the 241AmBe neutron standard field, showing reliable neutron spectrum and fluence rate in the energy range up to 10 MeV as investigated in this work.
Compact Standalone Platform for Neural Recording with Real-Time Spike Sorting and Data Logging
Authors: Luan Song , Williams Ian , Maslik Michal , Liu Yan , de Carvalho Felipe , Jackson Andrew , Quian Quiroga Rodrigo , Constandinou Timothy G
Published: September 2017

Objective. Longitudinal observation of single unit neural activity from large numbers of cortical neurons in awake and mobile animals is often a vital step in studying neural network behaviour and towards the prospect of building effective Brain Machine Interfaces (BMIs). These recordings generate enormous amounts of data for transmission & storage, and typically require offline processing to tease out the behaviour of individual neurons. Our aim was to create a compact system capable of: 1) reducing the data bandwidth by circa 3 orders of magnitude (greatly improving battery lifetime and enabling low power wireless transmission); 2) producing real-time, low-latency, spike sorted data; and 3) long term untethered operation. Approach. We have developed a headstage that operates in two phases. In the short training phase a computer is attached and classic spike sorting is performed to generate templates. In the second phase the system is untethered and performs template matching to create an event driven spike output that is logged to a micro-SD card. To enable validation the system is capable of logging the high bandwidth raw data as well as the spike sorted data. Main results. The system can successfully record 32 channels of raw and/or spike sorted data for well over 24 hours at a time and is robust to power dropouts during battery changes as well as SD card replacement. A 24-hour initial recording in a non-human primate M1 showed consistent spike shapes with the expected changes in neural activity during awake behaviour and sleep cycles. Significance The presented platform allows neural activity to be unobtrusively monitored and processed in real-time in freely behaving untethered animals revealing insights that are not attainable through scheduled recording sessions and provides a robust, low-latency, low-bandwidth output suitable for BMIs, closed loop neuromodulation, wireless transmission and long term data logging.
The genomic landscape at a late stage of stickleback speciation: high genomic divergence interspersed by small localized regions of introgression
Authors: Ravinet Mark , Yoshida Kohta , Shigenobu Shuji , Toyoda Atsushi , Fujiyama Asao , Kitano Jun
Published: September 2017

Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Genomic studies on young species pairs have often revealed peaks of divergence and heterogeneous genomic differentiation. Yet it remains unclear how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation with gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little known of the genomic signatures of divergence and introgression in older systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to hybridise at a low rate throughout divergence. Population genomic data revealed that high levels of genomic differentiation are maintained across the majority of the genome when gene flow occurs. However despite this, we identified multiple, small regions of introgression, strongly correlated with recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

Author summary

When species evolve, reproductive isolation leads to a build-up of differentiation in the genome where genes involved in the process occur. Much of our understanding of this comes from early stage speciation, with relatively few examples from more divergent species pairs that still exchange genes. To address this, we focused on Pacific Ocean and Japan Sea sticklebacks, which co-occur in the Japanese islands. We established that they are the oldest and most divergent known stickleback species pair, that they evolved in the face of gene flow and that this gene flow is still on going. We found introgression is confined to small, localised genomic regions where recombination rate is high. Our results show high divergence can be maintained between species, despite extensive gene flow.
Image-based profiling can discriminate the effects of inhibitors on signaling pathways under differential ligand stimulation
Authors: Tanabe Kenji , Henmi Yuji , Satake Masanobu
Published: September 2017

A major advantage of image-based phenotypic profiling of compounds is that numerous image features can be sampled and quantitatively evaluated in an unbiased way. However, since this assay is a discovery-oriented screening, it is difficult to determine the optimal experimental set-up in advance. In this study, we examined whether variable cellular stimulation affects the efficacy of image-based profiling of compounds. Seven different EGF receptor ligands were used, and the expression of EGF receptor signaling molecules was monitored at various time points. Significant quantitative differences in image features were detected among the differentially treated samples. Next, 14 different compounds that affect EGF receptor signaling were profiled. Nearly half of the compounds were classified into distinct clusters, irrespective of differential ligand stimulation. The results suggest that image-based phenotypic profiling is quite robust in its ability to predict compound interaction with its target. Although this method will have to be validated in other experimental systems, the robustness of image-based compound profiling demonstrated in this work provides a valid basis for further study and its extended application.
Modeling Epidemics: A Primer and Numerus Software Implementation
Authors: Getz Wayne M. , Salter Richard , Muellerklein Oliver , Yoon Hyun S. , Tallam Krti
Published: September 2017

Epidemiological models are dominated by SEIR (Susceptible, Exposed, Infected and Removed) dynamical systems formulations and their elaborations. These formulations can be continuous or discrete, deterministic or stochastic, or spatially homogeneous or heterogeneous, the latter often embracing a network formulation. Here we review the continuous and discrete deterministic and discrete stochastic formulations of the SEIR dynamical systems models, and we outline how they can be easily and rapidly constructed using the Numerus Model Builder, a graphically-driven coding platform. We also demonstrate how to extend these models to a metapopulation setting using both the Numerus Model Builder network and geographical mapping tools.
Propagating actomyosin-generated force to intercellular junction
Authors: Tang Vivian W.
Published: September 2017

Actomyosin II contractility in epithelial cells plays an essential role in tension-dependent adhesion strengthening. One key unsettling question is how cellular contraction transmits force to nascent cell-cell adhesion when there is no stable attachment between the nascent adhesion complex and actin filament. Here, we showed that application of intercellular tension induces myosin 1c accumulation at the lateral membrane between epithelial cells. We hypothesized that the accumulation of myosin 1c at the cell-cell interface allows coupling of actomyosin contractility to the generation of intercellular tension, thus is essential for tension-induced junction maturation. We showed that myosin 1c KD compromises a-actinin-4 recruitment to cell-cell adhesion during normal junction maturation driven by endogenous actomyosin contractility. However, application of cyclic tension to intercellular junction from outside of the cells rescued tension-dependent a-actinin-4 accumulation, suggesting that myosin-1c KD did not compromise the tension response or disrupt the overall integrity of the junctional complex. Our study identifies myosin-1c as a novel tension-sensitive protein on the lateral membrane and underscores a non-junctional contribution to adhesion strengthening at the epithelial cell-cell adhesion interface.
Stage-specific ISG expression reveals functional convergence of type I and II IFNs in SIV infection
Authors: Echebli Nadia , Tchitchek Nicolas , Dupuy Stéphanie , Bruel Timothée , Bittencourt Passaes Caroline Peireira , Bosquet Nathalie , Le Grand Roger , Bourgeois Christine , Favier Benoit , Cheynier Rémi , Lambotte Olivier , Vaslin Bruno
Published: September 2017

Abstract

Interferons play a major role in controlling viral infections including HIV/SIV infections. Persistent up-regulation of interferon-stimulated-genes (ISGs) is associated with chronic immune activation and progression in SIV/HIV infections, but the respective contribution of different IFNs is unclear. We analyzed the expression of annotated IFN-induced genes in SIV-infected macaques to decrypt the respective roles of type-I (α,β) and type-II (γ) IFNs. Both IFN types were induced in lymph nodes during early stage of primary infection. Induction of type-II IFN persisted during the chronic phase, in contrast to undetectable induction of type-I IFN. Interferome-based analysis of ISGs revealed that at both acute and chronic infection phases most differentially expressed ISGs were inducible by both type-I and type-II IFNs and displayed the highest increases, indicating strong convergence and synergy between type-I and type-II IFNs. The analysis of functional signatures of ISG expression revealed temporal changes in IFN expression patterns identifying phase-specific ISGs. These results suggest that IFN-γ strongly contribute to shape ISG upregulation in addition to type-I IFN and may contribute to progression.
Promoter architecture determines co-translational regulation of mRNA
Authors: Espinar Lorena , Schikora Tamarit Miquel Àngel , Domingo Júlia , Carey Lucas B.
Published: September 2017

Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of co-translational regulation on mRNA levels is determined by promoter architecture. Using a novel computational-genetic screen of 6402 RNA-seq experiments we identify the RNA helicase Dbp2 as the mechanism by which co-translational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus the ORF sequence is a major regulator of gene expression, and a non-linear interaction between promoters and ORFs determines mRNA levels.
ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy
Authors: Wang Annie , Lim Hansaim , Cheng Shu-Yuan , Xie Lei
Published: September 2017

Existing1drug discovery process follows a reductionist model of “one-drug-one-gene-one-disease,” which is not adequate to tackle complex diseases that involve multiple malfunctioned genes. The availability of big omics data offers new opportunities to transform the drug discovery process into a new paradigm of systems pharmacology that focuses on designing drugs to target molecular interaction networks instead of a single gene. Here, we develop a reliable multi-rank, multi-layered recommender system, ANTENNA, to mine large-scale chemical genomics and disease association data for the prediction of novel drug-gene-disease associations. ANTENNA integrates a novel tri-factorization based dual-regularized weighted and imputed One Class Collaborative Filtering (OCCF) algorithm, tREMAP, with a statistical framework that is based on Random Walk with Restart and can assess the reliability of a specific prediction. In the benchmark study, tREMAP clearly outperforms the single rank OCCF. We apply ANTENNA to a real-world problem: repurposing old drugs for new clinical indications that have yet had an effective treatment. We discover that FDA-approved drug diazoxide can inhibit multiple kinase genes whose malfunction is responsible for many diseases including cancer, and kill triple negative breast cancer (TNBC) cells effectively at a low concentration (IC50= 0.87 μM). The TNBC is a deadly disease that currently does not have effective targeted therapies. Our finding demonstrates the power of big data analytics in drug discovery, and has a great potential toward developing a targeted therapy for the effective treatment of TNBC.
Effects of tDCS Dosage on Working Memory in Healthy Participants
Authors: Nikolin Stevan , Martin Donel , Loo Colleen K. , Boonstra Tjeerd W.
Published: September 2017

Background

Transcranial direct current stimulation (tDCS) has been found to improve working memory (WM) performance in healthy participants following a single session. However, results are mixed and the overall effect size is small. Interpretation of these results is confounded by heterogeneous study designs, including differences in tDCS dose (current intensity) and sham conditions used.

Aims

We systematically investigated the effect of tDCS dose on working memory using behavioural and neurophysiological outcomes.

Methods

In a single-blind parallel group design, 100 participants were randomised across five groups to receive 15 minutes of bifrontal tDCS at different current intensities (2mA, 1mA, and three sham tDCS conditions at 0.034mA, 0.016mA, or 0mA). EEG activity was acquired while participants performed a WM task prior to, during, and following tDCS. Response time, accuracy and an event-related EEG component (P3) were evaluated.

Results

We found no significant differences in response time or performance accuracy between current intensities. The P3 amplitude was significantly lower in the 0mA condition compared to the 0.034mA, 1mA and 2mA tDCS conditions. Changes in WM accuracy were moderately correlated with changes in the P3 amplitude following tDCS compared to baseline levels (r = 0.34).

Conclusions

Working memory was not significantly altered by tDCS, regardless of dose. The P3 amplitude showed that stimulation at 1mA, 2mA and a sham condition (0.034mA) had biological effects, with the largest effect size for 1mA stimulation. These findings indicate higher sensitivity of neurophysiological outcomes to tDCS and suggests that sham stimulation previously considered inactive may alter neuronal function.
R2ucare: An R package to perform goodness-of-fit tests for capture-recapture models
Authors: Gimenez Olivier , Lebreton Jean-Dominique , Choquet Remi , Pradel Roger
Published: September 2017

Assessing the quality of fit of a statistical model to data is a necessary step for conducting safe inference. We introduce R2ucare, an R package to perform goodness-of-fit tests for open single- and multi-state capture-recapture models. R2ucare also has various functions to manipulate capture-recapture data. We remind the basics and provide guidelines to navigate towards testing the fit of capture-recapture models. We demonstrate the functionality of R2ucare through its application to real data.
Drosophila larval brain neoplasms present tumour-type dependent genome instability
Authors: Rossi Fabrizio , Stephan-Otto Attolini Camille , Mosquera Jose Luis , Gonzalez Cayetano
Published: September 2017

Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) are found at different rates in human cancer. To determine if these genetic lesions appear in Drosophila tumours we have sequenced the genomes of 17 malignant neoplasms caused by mutationsin l(3)mbt, brat, aurA, orlgl. We have found CNVs and SNPs in all the tumours. Tumour-linked CNVs range between 11 and 80 per sample, affecting between 92 and 1546 coding sequences. CNVs are in average less frequent inl(3)mbtthan inbratlines. Nearly half of the CNVs fall within the 10 to 100Kb range, all tumour samples contain CNVs larger that 100 Kb and some have CNVs larger than 1Mb. The rates of tumour-linked SNPs change more than 20-fold depending on the tumour type: late stagebrat,l(3)mbt, andaurAand lgl lines present median values of SNPs/Mb of exome of 0.16, 0.48, and 3.6, respectively. Higher SNP rates are mostly accounted for by C>A transversions, which likely reflect enhanced oxidative stress conditions in the affected tumours. Both CNVs and SNPs turn over rapidly. We found no evidence for selection of a gene signature affected by CNVs or SNPs in the cohort. Altogether, our results show that the rates of CNVs and SNPs, as well as the distribution of CNV sizes in this cohort of Drosophila tumours are well within the range of those reported for human cancer. Genome instability is therefore inherent to Drosophila malignant neoplastic growth at a variable extent that is tumour type dependent.

AUTHOR SUMMARY

Drosophila models of malignant growth can help to understand the molecular mechanisms of malignancy. These models are known to exhibit some of the hallmarks of cancer like sustained growth, immortality, metabolic reprogramming, and others. However, it is currently unclear if these fly models are affected by genome instability, which is another hallmark of many human malignant tumours. To address this issue we have sequenced and analysed the genomes of a cohort of seventeen fly tumour samples. We have found that genome instability is a common trait of Drosophila malignant tumours, which occurs at an extent that is tumour-type dependent, at rates that are similar to those of different human cancers.
Molecular basis for the maintenance of lipid asymmetry in the outer membrane ofEscherichia coli
Authors: Yeow Jiang , Tan Kang Wei , Holdbrook Daniel A. , Chong Zhi-Soon , Marzinek Jan K. , Bond Peter J. , Chng Shu-Sin
Published: September 2017

A distinctive feature of the Gram-negative bacterial cell envelope is the asymmetric outer membrane (OM), where lipopolysaccharides (LPS) and phospholipids (PLs) reside in the outer and inner leaflets, respectively. This unique lipid asymmetry renders the OM impermeable to external insults. InEscherichia coli, the OmpC-MlaA complex is believed to maintain lipid asymmetry by removing mislocalized PLs from the outer leaflet of the OM. How it performs this function is unknown. Here, we define the molecular architecture of the OmpC-MlaA complex to gain insights into its role in PL transport. We establish that MlaA sits entirely within the bilayer in complex with OmpC and provides a hydrophilic channel possibly for PL translocation across the OM. Furthermore, we show that flexibility in a hairpin loop adjacent to the channel modulates MlaA activity. Finally, we demonstrate that OmpC plays an active role in maintaining OM lipid asymmetry together with MlaA. Our work offers glimpses into how the OmpC-MlaA complex transports PLs across the OM and has important implications for future antimicrobial drug development.
Deep transfer learning-based hologram classification for molecular diagnostics
Authors: Kim Sung-Jin , Wang Chuangqi , Zhao Bing , Im Hyungsoon , Min Jouha , Choi Hee June , Tadros Joseph , Choi Nu Ri , Castro Cesar M. , Weissleder Ralph , Lee Hakho , Lee Kwonmoo
Published: September 2017

Lens-free digital in-line holography (LDIH) is a promising microscopic tool that overcomes several drawbacks (e.g., limited field of view) of traditional lens-based microcopy. However, extensive computation is required to reconstruct object images from the complex diffraction patterns produced by LDIH, which limits LDIH utility for point-of-care applications, particularly in resource limited settings. Here, we describe a deep transfer learning (DTL) based approach to process LDIH images in the context of cellular analyses. Specifically, we captured holograms of cells labeled with molecular-specific microbeads and trained neural networks to classify these holograms without reconstruction. Using raw holograms as input, the trained networks were able to classify individual cells according to the number of cell-bound microbeads. The DTL-based approach including a VGG19 pretrained network showed robust performance with experimental data. Combined with the developed DTL approach, LDIH could be realized as a low-cost, portable tool for point-of-care diagnostics.
The Asian tiger mosquito,Aedes albopictus(Skuse, 1894), a vector of dengue, chikungunya and zika, reaches Portugal
Authors: Marabuto Eduardo , Rebelo Maria Teresa
Published: September 2017

The mosquitoAedes albopictusis here reported for the first time in Portugal, from the south of the country, at least 240km west of the nearest known observation in Spain. A population of more than fifty specimens was spotted within a suburban garden over seven days of survey. As an important vector of Human affecting zoonoses such as dengue, chikungunya and yellow-fever, the presence of this mosquito in Portugal now enhances the outbreak chances for such diseases.
A model species for agricultural pest genomics: the genome of the Colorado potato beetle,Leptinotarsa decemlineata(Coleoptera: Chrysomelidae)
Authors: Schoville Sean D. , Chen Yolanda H. , Andersson Martin N. , Benoit Joshua B. , Bhandari Anita , Bowsher Julia H. , Brevik Kristian , Cappelle Kaat , Chen Mei-Ju M. , Childers Anna K. , Childers Christopher , Christiaens Olivier , Clements Justin , Didion Elise M. , Elpidina Elena N. , Engsontia Patamarerk , Friedrich Markus , García-Robles Inmaculada , Gibbs Richard A. , Goswami Chandan , Grapputo Alessandro , Gruden Kristina , Grynberg Marcin , Henrissat Bernard , Jennings Emily C. , Jones Jeffery W. , Kalsi Megha , Khan Sher A. , Kumar Abhishek , Li Fei , Lombard Vincent , Ma Xingzhou , Martynov Alexander , Miller Nicholas J. , Mitchell Robert F. , Munoz-Torres Monica , Muszewska Anna , Oppert Brenda , Palli Subba Reddy , Panfilio Kristen A. , Pauchet Yannick , Perkin Lindsey C. , Petek Marko , Poelchau Monica F. , Record Éric , Rinehart Joseph P. , Robertson Hugh M. , Rosendale Andrew J. , Ruiz-Arroyo Victor M. , Smagghe Guy , Szendrei Zsofia , Thomas Gregg W. C. , Torson Alex S. , Vargas Jentzsch Iris M. , Weirauch Matthew T. , Yates Ashley D. , Yocum George D. , Yoon June-Sun , Richards Stephen
Published: September 2017

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain whyLeptinotarsa decemlineatahas high sensitivity to dsRNA. TheL. decemlineatagenome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.
A high throughput screen for active human transposable elements
Authors: Kvikstad Erika M. , Piazza Paolo , Taylor Jenny C. , Lunter Gerton
Published: September 2017

Transposable elements (TEs) are mobile genetic sequences that randomly propagate within their host’s genome. This mobility has the potential to affect gene transcription and cause disease. However, TEs are technically challenging to identify, which complicates efforts to assess the impact of TE insertions on disease. Here we present a targeted sequencing protocol and computational pipeline to identify polymorphic and novel TE insertions using next-generation sequencing: TE-NGS. The method simultaneously targets the three subfamilies that are responsible for the majority of recent TE activity (L1HS,AluYa5/8, andAluYb8/9) thereby obviating the need for multiple experiments and reducing the amount of input material required. Here we describe the laboratory protocol and detection algorithm, and a benchmark experiment for the reference genome NA12878. We demonstrate a substantial enrichment for on-target fragments, and high sensitivity and precision to both reference and NA12878-specific insertions. We report 17 previously unreported loci for this individual which are supported by orthogonal long-read evidence, and we identify 1,471 polymorphic and novel TEs in 12 additional samples that were previously undocumented in databases of insertion polymorphisms. We anticipate that future applications of TE-NGS alongside exome sequencing of patients with sporadic disease will reduce the number of unresolved cases, and improve estimates of the contribution of TEs to human genetic disease.
Paternal-age-related de novo mutations and risk for five disorders
Authors: Taylor Jacob L. , Debost Jean-Christophe P.G. , Morton Sarah U. , Wigdor Emilie M. , Heyne Henrike O. , Lal Dennis , Howrigan Daniel P. , Bloemendal Alex , Larsen Janne T. , Kosmicki Jack A. , Weiner Daniel J. ,   Pediatric Cardiac Genomics Consortium, Homsy Jason , Seidman Jonathan G. , Seidman Christine E. , Agerbo Esben , McGrath John J. , Mortensen Preben Bo , Petersen Liselotte , Daly Mark J. , Robinson Elise B.
Published: September 2017

Background

There are well-established epidemiologic associations between advanced paternal age and increased offspring risk for several psychiatric and developmental disorders. These associations are commonly attributed to age-relatedde novomutations. However, the actual magnitude of risk conferred by age-relatedde novomutations in the male germline is unknown. Quantifying this risk would clarify the clinical and public health significance of delayed paternity.

Methods

Using results from large, parent-child trio whole-exome-sequencing studies, we estimated the relationship between paternal-age-relatedde novosingle nucleotide variants (dnSNVs) and offspring risk for five disorders: autism spectrum disorders (ASD), congenital heart disease (CHD), neurodevelopmental disorders with epilepsy (EPI), intellectual disability (ID), and schizophrenia (SCZ). Using Danish national registry data, we then investigated the degree to which the epidemiologic association between each disorder and advanced paternal age was consistent with the estimated role ofde novomutations.

Results

Incidence rate ratios comparing dnSNV-based risk to offspring of 45 versus 25-year-old fathers ranged from 1.05 (95% confidence interval 1.01–1.13) for SCZ to 1.29 (95% CI 1.13-1.68) for ID. Epidemiologic estimates of paternal age risk for CHD, ID and EPI were consistent with the dnSNV effect. However, epidemiologic effects for ASDs and SCZ significantly exceeded the risk that could be explained by dnSNVs alone (p<2e-4 for both comparisons).

Conclusion

Increasing dnSNVs due to advanced paternal age confer a small amount of offspring risk for psychiatric and developmental disorders. For ASD and SCZ, epidemiologic associations with delayed paternity largely reflect factors that cannot be assumed to increase with age.
Eco-evolutionary dynamics and collective dispersal: implications for salmon metapopulation robustness
Authors: Yeakel Justin D. , Gibert Jean P. , Westley Peter A. H. , Moore Jonathan W.
Published: September 2017

The spatial dispersal of individuals is known to play an important role in the dynamics of populations, and is central to metapopulation theory. At the same time, local adaptation to environmental conditions creates a geographic mosaic of evolutionary forces, where the combined drivers of selection and gene flow interact. Although the dispersal of individuals from donor to recipient populations provides connections within the metapopulation, promoting demographic and evolutionary rescue, it may also introduce maladapted individuals into habitats host to different environmental conditions, potentially lowering the fitness of the recipient population. Thus, dispersal plays a dual role in both promoting and inhibiting local adaptation. Here we explore a model of the eco-evolutionary dynamics between two populations connected by dispersal, where the productivity of each is defined by a trait complex that is subject to local selection. Although general in nature, our model is inspired by salmon metapopulations, where dispersal between populations is defined in terms of the straying rate, which has been shown to be density-dependent, and recently proposed to be shaped by social interactions consistent with collective movement. The results of our model reveal that increased straying between evolving populations leads to alternative stable states, which has large and nonlinear effects on two measures of metapopulation robustness: the portfolio effect and the time to recovery following an induced disturbance. We show that intermediate levels of straying result in large gains in robustness, and that increased habitat heterogeneity promotes robustness when straying rates are low, and erodes robustness when straying rates are high. Finally, we show that density-dependent straying promotes robustness, particularly when the aggregate biomass is low and straying is correspondingly high, which has important ramifications for the conservation of salmon metapopulations facing both natural and anthropogenic disturbances.

Media Summary

Many migratory species, such as salmon, are remarkable in finding their way home. This homing has allowed fine-scale adaptations to the environments in which they evolve. But some individuals do not find their way home and instead stray to other locations, especially when there are fewer individuals to help with collective decision-making. With an eco-evolutionary model, we discovered that an intermediate and density-dependent straying rate allows linked populations to be robust to disturbance but maintain local adaptations.