bluuebunny/crossref_metadata_2025 huggingface dataset:
Standard map-like models for single and multiple walkers in an annular cavity
Authors: Rahman Aminur
Published: September 2018

Recent experiments on walking droplets in an annular cavity showed the existence of complex dynamics including chaotically changing velocity. This article presents models, influenced by the kicked rotator/standard map, for both single and multiple droplets. The models are shown to achieve both qualitative and quantitative agreement with the experiments, and make predictions about heretofore unobserved behavior. Using dynamical systems techniques and bifurcation theory, the single droplet model is analyzed to prove dynamics suggested by the numerical simulations.
Terahertz radiation generation by beating of two oblique arbitrary laser beam profiles in a collisional plasma
Authors: Hematizadeh Ayoob , Jazayeri Seyed Masud , Ghafary Bijan
Published: September 2018

This paper presents a scheme to achieve THz radiation by the beating of two laser beams in a plasma. Lasers are obliquely incident on an underdense plasma with density ripples. Lasers having different frequencies and wave numbers but the same electric fields exert a ponderomotive force on the plasma electrons at the beating frequency which creates THz waves. The general formulas for the efficiency and THz field amplitude with arbitrary laser beam profiles (such as super-Gaussian and triangular) are derived where the effect of electron-neutral collisions is taken into account. The results show that the efficiency of THz radiation is sensitive to the angle of incidence, beam profile, collision frequency, and beating frequency. The most striking feature of this paper is that with obliquely incident laser beams, higher efficiency can be reached for collisionless and collisional plasma compared to normal incidence.
Ion movement in thin Nafion films under an applied electric field
Authors: Dugger Jason W. , Collins Liam , Welbourn Rebecca J. L. , Skoda Maximilian W. A. , Balke Nina , Lokitz Bradley S. , Browning James F.
Published: September 2018

The electromechanical response of Nafion films with and without an ionic liquid (1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide) ([emim]Tf2N) additive were characterized under an applied electric field in situ using neutron reflectometry (NR) and voltage modulated atomic force microscopy (VM-AFM). NR showed that pure Nafion films exhibited no response under field strengths of ∼0.18 V/μm, while VM-AFM measurements showed a minimal response at higher field strengths (∼200 V/μm), which is ascribed to the residual water presence in the films. The addition of ionic liquid resulted in clear electroresponsiveness seen in both NR and VM-AFM. NR results indicated mass migration away from the cathodic interface driven by the [emim]+ movement in the direction of the electric field. The lack of ionic liquid accumulation at the electrode interfaces contrasts the bulk electromechanical behavior of similar systems reported in the literature. VM-AFM measurements were able to resolve the relative contributions of the [emim]+ cation and Tf2N− anion to film deformation by alternating the direction of the applied field and support the [emim]+ dominant migration seen in the NR results. The findings presented here emphasize the need for the nanoscale analysis of material properties of electroresponsive thin film systems and demonstrate the potential for probing electric field effects using in situ techniques.
Temperature-dependent photoluminescence spectra and decay dynamics of MAPbBr3 and MAPbI3 thin films
Authors: Liu Yiting , Lu Haizhou , Niu Jiaxin , Zhang Huotian , Lou Shitao , Gao Chunlei , Zhan Yiqiang , Zhang Xiaolei , Jin Qingyuan , Zheng Lirong
Published: September 2018

The steady-state spectra and fluorescence lifetimes are investigated under vacuum for methylammonium lead bromide and iodide (CH3NH3PbBr3 or MAPbBr3, and CH3NH3PbI3 or MAPbI3) thin films by stably controlling the sample temperature in the range of 78 K to 320 K. The transformation of spectrum features and lifetime components are proved to be quite sensitive to the temperatures in accordance with the phase transition of structures. Our work demonstrates that the halide anions I- and Br- lead to remarkable differences on optical characteristics. Due to the distinct behaviors of excitons, electron-hole pairs and free carriers in decay channels, MAPbI3 has much longer lifetime and higher low-temperature fluorescence efficiency than those of MAPbBr3. The findings provide possible choices for certain perovskites under various ambient temperature conditions to display photovoltaic or luminescent advantage.
Plasma mass separation
Authors: Zweben S. J. , Gueroult R. , Fisch N. J.
Published: September 2018

This tutorial describes mechanisms for separating ions in a plasma device with respect to their atomic or molecular mass for practical applications. The focus here is not on separating isotopes of a single atomic species but rather on systems with a much lower mass resolution and a higher throughput. These separation mechanisms include ion gyro-orbit separation, drift-orbit separation, vacuum arc centrifugation, steady-state rotating plasmas, and several other geometries. Generic physics issues are discussed such as the ion charge state, neutrals and molecules, collisions, radiation loss, and electric fields and fluctuations. Generic technology issues are also discussed such as plasma sources and ion heating, and suggestions are made for future research.
Vortex structures and configurations in a superconductor under helical magnetic field
Authors: Fukui Saoto , Kato Masaru , Togawa Yoshihiko , Sato Osamu
Published: September 2018

Magnetic vortex structures in a superconductor under a helical magnetic field are investigated using the Ginzburg-Landau equations and the three-dimensional finite element method. Magnetic-field-amplitude dependence of vortex structure is investigated. Also how superconductivity is destroyed is shown. Also peculiar vortex structures are found under the helical magnetic field.
Structural, magnetic, and electron-transport properties of epitaxial Mn2PtSn films
Authors: Jin Y. , Valloppilly S. , Kharel P. , Waybright J. , Lukashev P. , Li X. Z. , Sellmyer D. J.
Published: September 2018

The growth of new magnetic materials on suitable insulating substrates is an important part of the development of spin-electronics devices for memory or information processing. Epitaxial thin films of Mn2PtSn were grown on a MgO [001] substrate by magnetron co-sputtering of the constituents. Structural, magnetic, and electron-transport properties were investigated. The epitaxial Mn2PtSn film has an inverse tetragonal structure with the c-axis aligned in the plane of the MgO substrate. The lattice constants determined using XRD and TEM analysis are c = 6.124 Å and a = b = 4.505 Å. The orientation of Mn2PtSn c-axis which is 45° away from the a-axis of MgO has resulted in a small lattice mismatch of about 2.8%. The measured saturation magnetization is 5.3 μB/f.u., which is smaller than the first-principles calculated value of 6.4 μB/f.u. for ferromagnetic spin arrangement. Magnetization measurements determined the bulk magnetocrystalline anisotropy constant Kv of about 11.3 Merg/cm3 (1.13 MJ/m3). The electron-transport behavior is similar to that of normal magnetic metals. These results indicate that Mn2PtSn may have promising applications in spintronic devices.
The effect of methane gas flow rate on the streamer propagation in an atmospheric-pressure methane-air plasma jet
Authors: Kang Jinsong , Qian Muyang , Li Gui , Liu Sanqiu , Ren Chunsheng , Zhang Jialiang , Wang Dezhen
Published: September 2018

In this paper, a two-dimensional axisymmetric fluid model is applied to investigate the streamer discharge characteristics in an atmospheric pressure methane-air plasma jet as a function of methane flow velocities (2.5 m/s and 20 m/s, respectively). Although the streamer ignition and propagation in the dielectric tube are not sensitive to the methane gas flow velocity, the concentration field of methane and air in the mixing layer established by a balance between convective methane flow and back-diffusion of air ambient is crucial for streamer propagation in the gap. As the methane flow velocity is 2.5 m/s, the structure of the streamer head transits from ring-shape into solid disk-shape, while the streamer head always maintains a donut-shaped pattern at high flow velocity of 20 m/s until it impinges on the substrate. At lower gas velocity, the back-diffusion of ambient air into the methane jet is even more pronounced, which causes a larger space charge density at the streamer head, and thus the local electric field near streamer head is greater. Therefore, the overall trend in streamer propagation speed versus methane flow velocity is that the larger the flow velocity, the lower plasma bullet speed. Besides, as the gas flow velocity increases from 2.5 to 20 m/s, less oxygen/nitrogen radical species and charged ions are produced in the streamer discharge, while the produced methane-related particles increase slightly. As for different methane flow velocities, the streamer advances within the methane core.
A 30 GW subnanosecond solid-state pulsed power system based on generator with semiconductor opening switch and gyromagnetic nonlinear transmission lines
Authors: Gusev A. I. , Pedos M. S. , Ponomarev A. V. , Rukin S. N. , Timoshenkov S. P. , Tsyranov S. N.
Published: September 2018

This article describes a subnanosecond solid-state pulsed power system in which an input pulse from a generator with a semiconductor opening switch (generator) is amplified in power and is shortened in time by a two-stage magnetic compressor based on gyromagnetic nonlinear transmission lines. In this approach, the line of each stage operates as a magnetic compression line (MCL) which is realized when the duration of the input pulse is close to the period of oscillations generated by the line. The compression system contains two series connected lines MCL1 and MCL2 with a wave impedance of 40 Ω. The input pulse has a duration of 7 ns and an amplitude of 500 kV. After two compression stages, the pulse amplitude increases to 1.1 MV and the peak power increases from 6 to 30 GW, while the pulse duration transits into subnanosecond range (0.65 ns). In the burst mode, the system operates at a pulse repetition frequency up to 1 kHz.
Highly sensitive temperature sensor based on an isopropanol-sealed optical microfiber coupler
Authors: Zhao Li , Zhang Yundong , Wang Jinfang , Chen Yunhao
Published: September 2018

A simple and highly sensitive temperature sensor based on an isopropanol-sealed optical microfiber coupler (OMC) is reported. Due to the high thermo-optic coefficient of isopropanol, the temperature sensitivity of the OMC can be effectively improved by immersing the OMC into isopropanol. The refractive index change of isopropanol is caused by the surrounding temperature variation which in turn allows highly sensitive temperature sensing. Theoretical analysis demonstrates that the temperature sensitivity increases quickly with the decreasing OMC waist diameter. Temperature sensitivities at different waist diameters exhibit high consistency with the theoretical results. When used for temperature sensing, the transmission spectrum blueshifts as the surrounding temperature increases. The highest sensitivity of −5.89 nm/°C is achieved at the waist diameter of 2.2 μm. This is the most sensitive OMC based temperature sensing device reported so far. Such a compact size, low cost, and highly sensitive device may widen the application range of OMC.
Quantum-induced solid-solid transitions and melting in the Lennard-Jones LJ38 cluster
Authors: Mallory Joel D. , Mandelshtam Vladimir A.
Published: September 2018

The solid-solid and melting transitions that occur in Lennard-Jones LJn clusters have been both fascinating and challenging for the computational physics community over the last several decades. A number of attempts to extend these studies to the quantum case have also been made. Particularly interesting is the exploration of the parallel between the thermally induced and quantum-induced transitions. Yet, both numerically accurate and systematic studies of the latter are still lacking. In this paper, we apply the diffusion Monte Carlo method to the especially difficult case of LJ38. Starting with the truncated octahedral global minimum configuration, as the de Boer quantum delocalization parameter Λ increases, the system undergoes two consecutive solid-solid transitions, switching to anti-Mackay configurations. At sufficiently large values of Λ, the cluster is completely “melted,” which is manifested by delocalization of the ground state wavefunction over a very large number of minima that represent several structural motifs.
Novel use of harmonic feedback enables powering of bioelectronic devices
Authors: Agner Mary Alexandra
Published: September 2018

Harmonic feedback produced by nonlinear components of a wireless power transfer system can be used to control transfer to implanted bioelectronic devices.
Genetic divergence and the number of hybridizing species affect the path to homoploid hybrid speciation
Authors: Comeault Aaron A. , Matute Daniel R.
Published: September 2018

Hybridization is often maladaptive and in some instances has led to the loss of biodiversity. However, hybridization can also promote speciation, such as during homoploid hybrid speciation, thereby generating biodiversity. Despite examples of homoploid hybrid species, the importance of hybridization as a speciation mechanism is still widely debated, and we lack a general understanding of the conditions most likely to generate homoploid hybrid species. Here we show that the level of genetic divergence between hybridizing species has a large effect on the probability that their hybrids evolve reproductive isolation. We find that populations of hybrids formed by parental species with intermediate levels of divergence were more likely to mate assortatively, and discriminate against their parental species, than those generated from weakly or strongly diverged parental species. Reproductive isolation was also found between hybrid populations, suggesting differential sorting of parental traits across populations. Finally, hybrid populations derived from three species were more likely to evolve reproductive isolation than those derived from two species, supporting arguments that hybridization-supplied genetic diversity can lead to the evolution of novel “adaptive systems” and promote speciation. Our results illustrate when we expect hybridization and admixture to promote hybrid speciation. Whether homoploid hybrid speciation is a common speciation mechanism in general remains an outstanding empirical question.
The kinetoplastid kinetochore protein KKT4 is an unconventional microtubule tip–coupling protein
Authors: Llauró Aida , Hayashi Hanako , Bailey Megan E. , Wilson Alex , Ludzia Patryk , Asbury Charles L. , Akiyoshi Bungo
Published: September 2018

Kinetochores are multiprotein machines that drive chromosome segregation by maintaining persistent, load-bearing linkages between chromosomes and dynamic microtubule tips. Kinetochores in commonly studied eukaryotes bind microtubules through widely conserved components like the Ndc80 complex. However, in evolutionarily divergent kinetoplastid species such as Trypanosoma brucei, which causes sleeping sickness, the kinetochores assemble from a unique set of proteins lacking homology to any known microtubule-binding domains. Here, we show that the T. brucei kinetochore protein KKT4 binds directly to microtubules and maintains load-bearing attachments to both growing and shortening microtubule tips. The protein localizes both to kinetochores and to spindle microtubules in vivo, and its depletion causes defects in chromosome segregation. We define a microtubule-binding domain within KKT4 and identify several charged residues important for its microtubule-binding activity. Thus, despite its lack of significant similarity to other known microtubule-binding proteins, KKT4 has key functions required for driving chromosome segregation. We propose that it represents a primary element of the kinetochore–microtubule interface in kinetoplastids.
The Potent ITK/BTK Inhibitor Ibrutinib Is Effective for the Treatment of Experimental Visceral Leishmaniasis Caused by Leishmania donovani
Authors: Varikuti Sanjay , Volpedo Greta , Saljoughian Noushin , Hamza Omar M , Halsey Gregory , Ryan Nathan M , Sedmak Bren E , Seidler Gabriella R , Papenfuss Tracey L , Oghumu Steve , Satoskar Abhay R
Published: September 2018

A new paradigm has emerged for treating infections, which focuses on targeting host pathways that are critical for pathogen invasion, survival, and multiplication. We show that ibrutinib, a ITK/BTK inhibitor, could be host-directed drug for treatment of visceral leishmaniasis.
When Busy Is Less Indulging: Impact of Busy Mindset on Self-Control Behaviors
Authors: Kim Jeehye Christine , Wadhwa Monica , Chattopadhyay Amitava
Published: September 2018

An increasing number of consumers, in recent times, have reported feeling busier than ever. The current research examines how the subjective perception of busyness—which is referred to as a busy mindset in the current research —impacts consumers’ decision-making. Building on different streams of research in sociology and self-view, the current research proposes that a busy mindset bolsters people’s sense of self-importance, which, in turn, can increase self-control. Thus, a busy mindset is predicted to facilitate people’s ability to exert self-control. Seven studies, including a field study, provide support for this busy mindset hypothesis across various self-control domains. Findings from these studies provide support for the underlying process related to self-importance in multiple ways, while also addressing alternative accounts related to stress and the desire for productivity. Finally, findings from the current research delineate important managerially relevant boundary conditions for the proposed busy mindset effect.
Latent power of basking sharks revealed by exceptional breaching events
Authors: Johnston Emmett M. , Halsey Lewis G. , Payne Nicholas L. , Kock Alison A. , Iosilevskii Gil , Whelan Bren , Houghton Jonathan D. R.
Published: September 2018

The fast swimming and associated breaching behaviour of endothermic mackerel sharks is well suited to the capture of agile prey. In contrast, the observed but rarely documented breaching capability of basking sharks is incongruous to their famously languid lifestyle as filter-feeding planktivores. Indeed, by analysing video footage and an animal-instrumented data logger, we found that basking sharks exhibit the same vertical velocity (approx. 5 m s−1) during breach events as the famously powerful predatory great white shark. We estimate that an 8-m, 2700-kg basking shark, recorded breaching at 5 m s−1and accelerating at 0.4 m s−2, expended mechanical energy at a rate of 5.5 W kg−1; a mass-specific energetic cost comparable to that of the great white shark. The energy cost of such a breach is equivalent to around 1/17th of the daily standard metabolic cost for a basking shark, while the ratio is about half this for a great white shark. While breaches by basking sharks must serve a different function to white shark breaches, their similar breaching speeds questions our perception of the physiology of large filter-feeding fish.
The minimally anisotropic metric operator in quasi-Hermitian quantum mechanics
Authors: Krejčiřík David , Lotoreichik Vladimir , Znojil Miloslav
Published: September 2018

We propose a unique way to choose a new inner product in a Hilbert space with respect to which an originally non-self-adjoint operator similar to a self-adjoint operator becomes self-adjoint. Our construction is based on minimizing a ‘Hilbert–Schmidt distance’ to the original inner product among the entire class of admissible inner products. We prove that either the minimizer exists and is unique or it does not exist at all. In the former case, we derive a system of Euler–Lagrange equations by which the optimal inner product is determined. A sufficient condition for the existence of the unique minimally anisotropic metric is obtained. The abstract results are supported by examples in which the optimal inner product does not coincide with the most popular choice fixed through a charge-like symmetry.
Multiple input control strategies for robust and adaptive climate engineering in a low-order 3-box model
Authors: Bonetti F. , McInnes C.
Published: September 2018

A low-order 3-box energy balance model for the climate system is employed with a multivariable control scheme for the evaluation of new robust and adaptive climate engineering strategies using solar radiation management. The climate engineering measures are deployed in three boxes thus representing northern, southern and central bands. It is shown that, through heat transport between the boxes, it is possible to effect a degree of latitudinal control through the reduction of insolation. The approach employed consists of a closed-loop system with an adaptive controller, where the required control intervention is estimated under the
RCP
4.5 radiative scenario. Through the online estimation of the controller parameters, adaptive control can overcome key issues related to uncertainties of the climate model, the external radiative forcing and the dynamics of the actuator used. In fact, the use of adaptive control offers a robust means of dealing with unforeseeable abrupt perturbations, as well as the parametrization of the model considered, to counteract the
RCP
4.5 scenario, while still providing bounds on stability and control performance. Moreover, applying multivariable control theory also allows the formal controllability and observability of the system to be investigated in order to identify all feasible control strategies.
Ecological specialization is associated with genetic structure in the ant-associated butterfly family Lycaenidae
Authors: Schär Sämi , Eastwood Rodney , Arnaldi Kimberly G. , Talavera Gerard , Kaliszewska Zofia A. , Boyle John H. , Espeland Marianne , Nash David R. , Vila Roger , Pierce Naomi E.
Published: September 2018

The role of specialization in diversification can be explored along two geological axes in the butterfly family Lycaenidae. In addition to variation in host-plant specialization normally exhibited by butterflies, the caterpillars of most Lycaenidae have symbioses with ants ranging from no interactions through to obligate and specific associations, increasing niche dimensionality in ant-associated taxa. Based on mitochondrial sequences from 8282 specimens from 967 species and 249 genera, we show that the degree of ecological specialization of lycaenid species is positively correlated with genetic divergence, haplotype diversity and an increase in isolation by distance. Nucleotide substitution rate is higher in carnivorous than phytophagous lycaenids. The effects documented here for both micro- and macroevolutionary processes could result from increased spatial segregation as a consequence of reduced connectivity in specialists, niche-based divergence or a combination of both. They could also provide an explanation for the extraordinary diversity of the Lycaenidae and, more generally, for diversity in groups of organisms with similar multi-dimensional ecological specialization.
The effect of liver enzymes on adiposity: a Mendelian randomization study
Authors: Liu Jun Xi , Au Yeung Shiu Lun , Kwok Man Ki , Yan Leung June Yue , Lin Shi Lin , Hui Lai Ling , Leung Gabriel Matthew , Schooling C. Mary
Published: September 2018

Poorer liver function is positively associated with diabetes in Mendelian randomization (MR) studies. Observationally, adiposity is associated with poorer liver function. To clarify the etiology, we assessed the association of liver function with adiposity observationally and using two sample MR for validation.

In the “Children of 1997” birth cohort, we used multivariable linear regression to assess the associations of ALT and alkaline phosphatase (ALP) (IU/L) at ∼17.5 years with body mass index (BMI) (kg/m2). Using MR, genetic variants predicting ALT, ALP and gamma glutamyltransferase (GGT) (100% change in concentration), were applied to genome-wide association studies of BMI, waist circumference (WC) and waist-hip ratio (WHR) (standard deviations) to obtain unconfounded inverse-variance weighting estimates.

Observationally, ALT was positively associated with BMI (0.10, 95% confidence interval (CI) 0.09 to 0.11). ALP was inversely associated with BMI (−0.018, 95% CI −0.024 to −0.012). Using MR, ALT was inversely associated with BMI (−0.14, 95% CI −0.20 to −0.07), but not WC or WHR. ALP and GGT were unrelated to adiposity.

Poorer liver function might not cause adiposity; instead higher ALT might reduce BMI. Whether ALT contributes to diabetes by reducing muscle mass, given the no association of ALT with WC or WHR, requires investigation.

Abbreviations

ALT

alanine transaminase

ALP

alkaline phosphatase

GGT

gamma glutamyltransferase

NAFLD

nonalcoholic fatty liver disease

BMI

body mass index

WC

waist circumference

WHR

waist-hip ratio

T2DM

type 2 diabetes mellitus

SEP

socioeconomic position

MR

Mendelian randomizatio

SNP

single nucleotide polymorphisms

GWAS

genome-wide association study

GIANT

Genetic Investigation of ANthropometric Traits

GIANTUKB

2018 GIANT and UK Biobank meta-analysis

SD

standard deviation

IVW

inverse variance weighting

WM

weighted median
Statistical structure of locomotion and its modulation by odors
Authors: Tao Liangyu , Ozarkar Siddhi , Beck Jeff , Bhandawat Vikas
Published: September 2018

Most behaviors such as making tea are not stereotypical but have an obvious structure. However, analytical methods to objectively extract structure from non-stereotyped behaviors are immature. In this study, we analyze the locomotion of fruit flies and show that this non-stereotyped behavior is well-described by a Hierarchical Hidden Markov Model (HHMM). HHMM shows that a fly’s locomotion can be decomposed into a small number of locomotor features, and odors modulate locomotion by altering the time a fly spends performing different locomotor features. Importantly, although all flies in our dataset use the same set of locomotor features, individual flies vary considerably in how often they employ a given locomotor feature, and how this usage is modulated by odor. This variation is so large that the behavior of individual flies is best understood as being grouped into at least 3-5 distinct clusters, rather than variations around an average fly.
Context-based facilitation in visual word recognition: Evidence for visual and lexical but not pre-lexical contributions
Authors: Eisenhauer Susanne , Fiebach Christian J. , Gagl Benjamin
Published: September 2018

Word familiarity and predictive context facilitate visual word processing, leading to faster recognition times and reduced neuronal responses. Previously, models with and without top-down connections, including lexical-semantic, pre-lexical (e.g., orthographic/ phonological), and visual processing levels were successful in accounting for these facilitation effects. Here we systematically assessed context-based facilitation with a repetition priming task and explicitly dissociated pre-lexical and lexical processing levels using a pseudoword familiarization procedure. Experiment 1 investigated the temporal dynamics of neuronal facilitation effects with magnetoencephalography (MEG; N=38 human participants) while Experiment 2 assessed behavioral facilitation effects (N=24 human participants). Across all stimulus conditions, MEG demonstrated context-based facilitation across multiple time windows starting at 100 ms, in occipital brain areas. This finding indicates context based-facilitation at an early visual processing level. In both experiments, we furthermore found an interaction of context and lexical familiarity, such that stimuli with associated meaning showed the strongest context-dependent facilitation in brain activation and behavior. Using MEG, this facilitation effect could be localized to the left anterior temporal lobe at around 400 ms, indicating within-level (i.e., exclusively lexical-semantic) facilitation but no top-down effects on earlier processing stages. Increased pre-lexical familiarity (in pseudowords familiarized utilizing training) did not enhance or reduce context effects significantly. We conclude that context based-facilitation is achieved within visual and lexical processing levels. Finally, by testing alternative hypotheses derived from mechanistic accounts of repetition suppression, we suggest that the facilitatory context effects found here are implemented using a predictive coding mechanism.

Significance Statement

The goal of reading is to derive meaning from script. This highly automatized process benefits from facilitation depending on word familiarity and text context. Facilitation might occur exclusively within each level of word processing (i.e., visual, pre-lexical, and/or lexical-semantic) but could alternatively also propagate in a top-down manner from higher to lower levels. To test the relevance of these two alternative accounts at each processing level, we combined a pseudoword learning approach controlling for letter string familiarity with repetition priming. We found enhanced context-based facilitation at the lexical-semantic but not pre-lexical processing stage, and no evidence of top-down facilitation from lexical-semantic to earlier word recognition processes. We also identified predictive coding as the most likely mechanism underlying within-level context-based facilitation.
Hypothesis: A plastically-produced phenotype predicts host specialization and can precede subsequent mutations in bacteriophage
Authors: Maxwell Colin S.
Published: September 2018

The role of phenotypic plasticity in the evolution of new traits is controversial due to a lack of direct evidence. Phage host-range becomes plastic in the presence of restriction-modification (R-M) systems in their hosts. I modeled the evolution of phage host-range in the presence of R-M systems. The model makes two main predictions. First, that offspring of the first phage to gain a new methylation pattern by infecting a new host make up a disproportionate fraction of the subsequent specialist population, indicating that the plastically-produced phenotype is highly predictive of evolutionary outcome. Second, that the first phage gain this pattern is not always genetically distinct from other phages in the population. Taken together, these results suggest that plasticity could play a causal role on par with mutation during the evolution of phage host range. This uniquely tractable system could enable the first direct test of ‘plasticity first’ evolution.
Cortico-basal-ganglia communication: Temporally structured activity for selective motor control
Authors: Fischer Petra , Lipski Witold , Neumann Wolf-Julian , Turner Robert Sterling , Fries Pascal , Brown Peter , Richardson Robert Mark
Published: September 2018

Despite the hard-wired structural connectivity of neural pathways, neural circuits allow context-dependent reactions to sensory cues by triggering the desired movement. Cortico-basal-ganglia circuits seem particularly important for flexible motor control as this is impaired in Parkinson’s disease (PD). We analysed subthalamic nucleus (STN) spike and cortical ECoG activity from PD patients performing a visually-cued hand grip task. Fast reaction times were preceded by enhanced STN spike-to-cortical gamma phase coupling irrespective of firing rate changes, suggesting a role of gamma coupling in motor preparation. STN spike timing was offset by half a cycle when comparing ipsilateral with contralateral movements. Additionally, cortical high-frequency activity increased more steeply within each gamma cycle at the sites that showed the strongest coupling with STN spikes. Cortico-basal-ganglia gamma coupling may thus help shape neural activity to facilitate selective motor control. The observation that this effect occurs independent of changes in mean firing rate has far-reaching implications.

Highlights

Fast RTs were preceded by enhanced STN spike-to-cortical gamma phase coupling

STN spike probability was significantly modulated relative to the gamma cycle

During ipsilateral movement, spikes were more likely at the opposite part of the cycle

STN output may thus help shape cortical gamma for selective motor control
AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX
Authors: Shieh Kevin R. , Kratschmer Christina , Maier Keith E. , Greally John M. , Levy Matthew , Golden Aaron
Published: September 2018

High-Throughput Sequencing can enhance the analysis of aptamer libraries generated by the Systematic Evolution of Ligands by EXponential enrichment (HTS-SELEX). Robust analysis of the resulting sequenced rounds is best implemented by determining a ranked consensus of reads following the processing by multiple aptamer detection algorithms. Whilst several such approaches have been developed to this end, their installation and implementation is problematic. We developed AptCompare, a cross-platform program that combines six of the most widely used analytical approaches for the identification of RNA aptamer motifs and uses a simple weighted ranking to order the candidate aptamers, all driven within the same GUI- enabled environment. We demonstrate AptCompare’s performance by identifying the top-ranked candidate aptamers from a previously published selection experiment in our laboratory, with follow-up bench assays demonstrating good correspondence between the sequences’ rankings and their binding affinities.

Availability and Implementation:

The source code and pre-built virtual machine images are freely available at https://bitbucket.org/shiehk/aptcompare.
Using eDNA methodologies to identify the presence/absence of S. thermophilus in yogurt products
Authors: Bejdo Vladimir , Gao Claire
Published: September 2018

The advent of low-cost nuclear acid extraction allows for the creation of low-cost assays which can specifically be used to determine the presence or absence of bacteria in a variety of environments. Commercially sold dietary yogurt claims to contain bacteria forming a microbiome which has been previously linked to improved health outcomes in incidence rates of type 2 diabetes in vulnerable populations. The predicted outcome was that a main bacterial culture used in yogurt production (S. thermophilus) would be present and would be detectable using eDNA methodologies since it is fundamental to the making of yogurt. We gathered DNA from yogurt using yogurt dilutions and filter paper; we then extracted the DNA and also sequenced and used PCR to amplify the DNA. We sequenced PCR products to verify their identity through processing with publicly available BLAST tools which reference already accessioned bacterial genomes. Yogurt from four different commercially available brands (in the U.S.) was tested; not all yogurts tested positive for the bacteria, with higher concentrations of the bacteria in imported Greek-style yogurts, lower concentrations in domestically produced Greek-style yogurts, and no bacterial DNA detected in domestically produced ‘regular’ yogurt products. This research suggests that not all yogurts are equal, putting into question the whole-sale claims made on dietary yogurt’s probiotic preventative health effects and calling for a more detailed analysis to determine firm causal links between the microbiota of yogurts and preventative health effects.
A cortical route for face-like pattern processing in human newborns
Authors: Buiatti Marco , Giorgio Elisa Di , Piazza Manuela , Polloni Carlo , Menna Giuseppe , Taddei Fabrizio , Baldo Ermanno , Vallortigara Giorgio
Published: September 2018

Humans are endowed with an exceptional ability for detecting faces, a competence that in adults is supported by a set of face-specific cortical patches. Human newborns already shortly after birth preferentially orient to faces even when they are presented in the form of highly schematic geometrical patterns, over perceptually equivalent non-face-like stimuli. The neural substrates underlying this early preference are still largely unexplored. Is the adult face-specific cortical circuit already active at birth, or does its specialization develop slowly as a function of experience and/or maturation? We measured EEG responses in 1-4 days old awake, attentive human newborns to schematic face-like patterns and non-face-like control stimuli, visually presented with a slow oscillatory “peekaboo” dynamics (0.8 Hz) in a frequency-tagging design. Despite the limited duration of newborns’ attention, reliable frequency-tagged responses could be estimated for each stimulus from the peak of the EEG power spectrum at the stimulation frequency. Upright face-like stimuli elicited a significantly stronger frequency-tagged response than inverted face-like controls in a large set of electrodes. Source reconstruction of the underlying cortical activity revealed the recruitment of a partially right-lateralized network comprising lateral occipito-temporal and medial parietal areas largely overlapping with the adult face-processing circuit. This result suggests that the cortical route specialized in face processing is already functional at birth.

Significance statement

Newborns show a remarkable ability to detect faces even minutes after birth, an ecologically fundamental skill that is instrumental for interacting with their conspecifics. What are the neural bases of this expertise? Using EEG and a slow oscillatory visual stimulation, we identified a reliable response specific to face-like patterns in newborns, which underlying cortical sources largely overlap with the adult face-specific cortical circuit. This suggests that the development of face perception in infants might rely on an early cortical route specialized in face processing already shortly after birth.
artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis
Authors: Javorka Peter , Raxwal Vivek , Najvarek Jan , Riha Karel
Published: September 2018

Mapping-by-sequencing is a rapid method for identifying both natural as well as induced variations in the genome. However, it requires extensive bioinformatics expertise along with the computational infrastructure to analyze the sequencing data and these requirements have limited its widespread adoption. In the current study, we develop an easy to use tool, artMAP, to discover ethyl methanesulfonate (EMS) induced mutations in the Arabidopsis genome. The artMAP pipeline consists of well-established tools including TrimGalore, BWA, BEDTools, SAMtools, and SnpEff which were integrated in a Docker container. artMAP provides a graphical user interface and can be run on a regular laptop and desktop, thereby limiting the bioinformatics expertise required. artMAP can process input sequencing files generated from single or paired-end sequencing. The results of the analysis are presented in interactive graphs which display the annotation details of each mutation. Due to its ease of use, artMAP made the identification of EMS-induced mutations in Arabidopsis possible with only a few mouse click. The source code of artMAP is available on Github (https://github.com/RihaLab/artMAP).
Effects of alternative blood sources on Wolbachia infected Aedes aegypti females within and across generations
Authors: Paris Véronique , Cottingham Ellen , Ross Perran A. , Axford Jason K. , Hoffmann Ary A.
Published: September 2018

Wolbachia bacteria have been identified as a tool for reducing the transmission of arboviruses transmitted by Aedes aegypti. Research groups around the world are now mass rearing Wolbachia infected Ae. aegypti for deliberate release. We investigated the fitness impact of a crucial element of mass rearing: the blood meal required by female Ae. aegypti to lay eggs. Although Ae. aegypti almost exclusively feed on human blood, it is often difficult to use human blood in disease-endemic settings. When females were fed on sheep or pig blood rather than human blood, egg hatch rates decreased in all three lines tested (uninfected, or infected by wMel, or wAlbB Wolbachia). This finding was particularly pronounced when fed on sheep blood, although fecundity was not affected. Some of these effects persisted after an additional generation on human blood. Attempts to keep populations on sheep and pig blood sources only partly succeeded, suggesting that strong adaptation is required to develop a stably infected line on an alternative blood source. There was a decrease in Wolbachia density when Wolbachia Ae. aegypti were fed on non-human blood sources, although density was higher again in lines kept for multiple generations on the alternate sources. These findings suggest that sheep and pig blood will entail a cost when used as alternative blood sources which needs to be taken into account when considering mass release.
Origin and recent expansion of an endogenous gammaretroviral lineage in canids
Authors: Halo Julia V. , Pendleton Amanda L. , Jarosz Abigail S. , Gifford Robert J. , Day Malika L. , Kidd Jeffrey M.
Published: September 2018

Mammalian genomes contain a fossilized record of ancient retroviral infections in the form of endogenous retroviruses (ERVs). We used whole genome sequence data to assess the origin and evolution of the recently active ERV-Fc gammaretroviral lineage based on the record of past infections retained in the genome of the domestic dog,Canis lupus familiaris.We identified 165 loci, including 58 insertions absent from the dog reference assembly, and characterized element polymorphism across 332 canids from nine species. Insertions were found throughout the dog genome including within and near gene models. Analysis of 19 proviral sequences identified shared disruptive mutations indicating defective proviruses were spread via complementation. The patterns of ERV polymorphism and sequence variation indicate multiple circulating viruses infected canid ancestors within the last 20 million to within 1.6 million years with a recent bust of germline invasion in the lineage leading to wolves and dogs.
R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations
Authors: Broman Karl W. , Gatti Daniel M. , Simecek Petr , Furlotte Nicholas A. , Prins Pjotr , Sen Śaunak , Yandell Brian S. , Churchill Gary A.
Published: September 2018

R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely-used R/qtl software package to include multi-parent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2 comes with a test framework and is free and open source software written in the R and C++ programming languages.
Cul4-Ddb1 ubiquitin ligases facilitate DNA replication-coupled sister chromatid cohesion through regulation of cohesin acetyltransferase Esco2
Authors: Sun Haitao , Zhang Jiaxin , Zhang Jingjing , Li Zhen , Cao Qinhong , Lou Huiqiang
Published: September 2018

Cohesin acetyltransferases Esco1 and Esco2 play a vital role in establishing sister chromatid cohesion. How Esco1 and Esco2 are controlled to achieve this in a DNA replication-coupled manner remains unclear in higher eukaryotes. Here we show that Cul4-RING ligases (CRL4s) play a critical role in sister chromatid cohesion in human cells. Depletion of Cul4A, Cul4B or Ddb1 subunits substantially reduces normal cohesion efficiency. We also show that Mms22L, a vertebrate ortholog of yeast Mms22, is one of Ddb1 and Cul4-associated factors (DCAFs) involved in cohesion. Several lines of evidence suggest a selective interaction of CRL4s with Esco2, but not Esco1. Depletion of either CRL4s or Esco2 causes a defect in Smc3 acetylation which can be rescued by HDAC8 inhibition. More importantly, both CRL4s and PCNA act as mediators for efficiently stabilizing Esco2 on chromatin and catalyzing Smc3 acetylation. Taken together, we propose an evolutionarily conserved mechanism in which CRL4s and PCNA regulate Esco2-dependent establishment of sister chromatid cohesion.

Author summary

We identified human Mms22L as a substrate specific adaptor of Cul4-Ddb1 E3 ubiquitin ligase. Downregulation of Cul4A, Cul4B or Ddb1 subunit causes reduction of acetylated Smc3, via interaction with Esco2 acetyltransferase, and then impairs sister chromatid cohesion in 293T cells. We found functional complementation between Cul4-Ddb1-Mms22L E3 ligase and Esco2 in Smc3 acetylation and sister chromatid cohesion. Interestingly, both Cul4-Ddb1 E3 ubiquitin ligase and PCNA contribute to Esco2 mediated Smc3 acetylation. To summarise, we demonstrated an evolutionarily conserved mechanism in which Cul4-Ddb1 E3 ubiquitin ligases and PCNA regulate Esco2-dependent establishment of sister chromatid cohesion.
Diagnostic Whole Exome Sequencing in Patients with Short Stature
Authors: Zhu Huijuan , Yang Ziying , Sun Jun , Li Wei , Yang Hongbo , Wang Linjie , Gong Fengying , Chen Shi , Lu Lin , Miao Hui , Yuan Xianxian , Liang Hanting , Li Ran , Huang Hui , Peng Zhiyu , Asan  , Pan Hui
Published: September 2018

Short stature is among the most common reasons for children being referred to the pediatric endocrinology clinics. The cause of short stature is broad, in which genetic factors play a substantial role, especially in primary growth disorders. However, identifying the molecular causes for short stature remains as a challenge because of the high heterogeneity of the phenotypes. Here, whole exome sequencing (WES) was used to identify the genetic causes of short stature with unknown etiology for 20 patients aged from 1 to 16 years old. The genetic causes of short stature were identified in 9 of the 20 patients, corresponding to a molecular diagnostic rate of 45%. Notably, in 2 of the 9 patients identified with genetic causes, the diagnosed diseases based on WES are different from the original clinical diagnosis. Our results highlight the clinical utility of WES in the diagnosis of rare, high heterogeneity disorders.