ALBERT

Description: It has been postulated that the brain operates in a self-organized critical state that brings multiple benefits, such as optimal sensitivity to input. Thus far, self-organized criticality has typically been depicted as a one-dimensional process, where one parameter is tuned to a critical value. However, the number of adjustable parameters in the brain is vast, and hence critical states can be expected to occupy a high-dimensional manifold inside a high-dimensional parameter space. Here, we show that adaptation rules inspired by homeostatic plasticity drive a neuro-inspired network to drift on a critical manifold, where the system is poised between inactivity and persistent activity. During the drift, global network parameters continue to change while the system remains at criticality.

Description: Due to its involvement in numerous feedbacks, sea ice plays a crucial role not only for polar climate but also at global scale. We analyse state-of-the-art observed, reconstructed, and modelled sea-ice concentration (SIC) together with sea surface temperature (SST) to disentangle the influence of different forcing factors on the variability of these coupled fields. Canonical Correlation Analysis provides distinct pairs of coupled Arctic SIC–Atlantic SST variability which are linked to prominent oceanic and atmospheric modes of variability over the period 1854–2017. The first pair captures the behaviour of the Atlantic meridional overturning circulation (AMOC) while the third and can be associated with the North Atlantic Oscillation (NAO) in a physically consistent manner. The dominant global SIC–Atlantic SST coupled mode highlights the contrast between the responses of Arctic and Antarctic sea ice to changes in AMOC over the 1959–2021 period. Model results indicate that coupled SST–SIC patterns can be associated with changes in ocean circulation. We conclude that a correct representation of AMOC-induced coupled SST–SIC variability in climate models is essential to understand the past, present and future sea-ice evolution.

Description: Euphausia superba is a key species of the Southern Ocean, impacted by climate change and human exploitation. Understanding how these changes affect the distribution and abundance of krill is crucial for generating projections of change for Southern Ocean ecosystems. Krill growth is an important indicator of habitat suitability and a series of models have been developed and used to examine krill growth potential at different spatial and temporal scales. The available models have been developed using a range of empirical and mechanistic approaches, providing alternative perspectives and comparative analyses of the key processes influencing krill growth. Here we undertake an intercomparison of a suite of the available models to understand their sensitivities to major driving variables. This illustrates that the results are strongly determined by the model structure and technical characteristics, and the data on which they were developed and validated. Our results emphasize the importance of assessing the constraints and requirements of individual krill growth models to ensure their appropriate application. The study also demonstrates the value of the development of alternative modelling approaches to identify key processes affecting the dynamics of krill. Of critical importance for modelling the growth of krill is appropriately assessing and accounting for differences in estimates of food availability resulting from alternative methods of observation. We suggest that an intercomparison approach is particularly valuable in the development and application of models for the assessment of krill growth potential at circumpolar scales and for future projections. As another result of the intercomparison, the implementations of the models used in this study are now publicly available for future use and analyses.

Description: The superfamily Orthalicoidea comprises approximately 2,000 species of terrestrial gastropods, mostly concentrated in the Neotropics but also present in southern Africa and Oceania. We provide a multi-marker molecular phylogeny of this superfamily, reassessing its \nfamily- and genus-level classification. We exclude two families from the group, Odontostomidae and Vidaliellidae, transferring them to Rhytidoidea based on their phylogenetic relationships as recovered herein. Two new families are recognized herein as members of \nOrthalicoidea, Tomogeridae and Cyclodontinidae fam. nov. The family Megaspiridae and \nthe subfamily Prestonellinae are paraphyletic but are retained herein for taxonomic stability. \nThe subfamily Placostylinae is synonymized with Bothriembryontinae. The new genera \nAlterorhinus gen. nov. and Sanniostracus gen. nov. containing some Brazilian species are \ndescribed here to better reflect the phylogeny. The fossil record and paleobiogeographic \nhistory of the group is explored under the new phylogenetic framework.

Description: Insect population numbers and biodiversity have been rapidly declining with time, and monitoring \nthese trends has become increasingly important for conservation measures to be \neffectively implemented. But monitoring methods are often invasive, time and resource \nintense, and prone to various biases. Many insect species produce characteristic sounds \nthat can easily be detected and recorded without large cost or effort. Using deep learning \nmethods, insect sounds from field recordings could be automatically detected and classified \nto monitor biodiversity and species distribution ranges. We implement this using recently \npublished datasets of insect sounds (up to 66 species of Orthoptera and Cicadidae) and \nmachine learning methods and evaluate their potential for acoustic insect monitoring. We \ncompare the performance of the conventional spectrogram-based audio representation \nagainst LEAF, a new adaptive and waveform-based frontend. LEAF achieved better classification \nperformance than the mel-spectrogram frontend by adapting its feature extraction \nparameters during training. This result is encouraging for future implementations of deep \nlearning technology for automatic insect sound recognition, especially as larger datasets \nbecome available.

Description: Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species’ distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.

Description: Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth.

Description: Current questions in ecology revolve around instabilities in the dynamics on spatial networks and particularly the effect of node heterogeneity. We extend the master stability function formalism to inhomogeneous biregular networks having two types of spatial nodes. Notably, this class of systems also allows the investigation of certain types of dynamics on higher-order networks. Combined with the generalized modeling approach to study the linear stability of steady states, this is a powerful tool to numerically asses the stability of large ensembles of systems. We analyze the stability of ecological metacommunities with two distinct types of habitats analytically and numerically in order to identify several sets of conditions under which the dynamics can become stabilized by dispersal. Our analytical approach allows general insights into stabilizing and destabilizing effects in metapopulations. Specifically, we identify self-regulation and negative feedback loops between source and sink populations as stabilizing mechanisms and we show that maladaptive dispersal may be stable under certain conditions.

Description: While the output of a team is evident, the productivity of each team member is typically not readily identifiable. In this paper we consider the problem of measuring the productivity of team members. We propose a new concept of coworker productivity, which we refer to as eigenvalue productivity (EVP). We demonstrate the existence and uniqueness of our concept and show that it possesses several desirable properties. Also, we suggest a procedure for specifying the required productivity matrix of a team, and illustrate the operational practicability of EVP by means of three examples representing different types of available data.

Description: Since plastics degrade very slowly, they remain in the environment on much longer timescales than most natural organic substrates and provide a novel habitat for colonization by bacterial communities. The spectrum of relationships between plastics and bacteria, however, is little understood. The first objective of this study was to examine plastics as substrates for communities of Bacteria in estuarine surface waters. We used next-generation sequencing of the 16S rRNA gene to characterize communities from plastics collected in the field, and over the course of two colonization experiments, from biofilms that developed on plastic (low-density polyethylene, high-density polyethylene, polypropylene, polycarbonate, polystyrene) and glass substrates placed in the environment. Both field sampling and colonization experiments were conducted in estuarine tributaries of the lower Chesapeake Bay. As a second objective, we concomitantly analyzed biofilms on plastic substrates to ascertain the presence and abundance of Vibrio spp. bacteria, then isolated three human pathogens, V. cholerae, V. parahaemolyticus, and V. vulnificus, and determined their antibiotic-resistant profiles. In both components of this study, we compared our results with analyses conducted on paired samples of estuarine water. This research adds to a nascent literature that suggests environmental factors govern the development of bacterial communities on plastics, more so than the characteristics of the plastic substrates themselves. In addition, this study is the first to culture three pathogenic vibrios from plastics in estuaries, reinforcing and expanding upon earlier reports of plastic pollution as a habitat for Vibrio species. The antibiotic resistance detected among the isolates, coupled with the longevity of plastics in the aqueous environment, suggests biofilms on plastics have potential to persist and serve as focal points of potential pathogens and horizontal gene transfer.

Description: Aquatic ecosystems worldwide continue to experience unprecedented warming and ecological change. Warming increases metabolic rates of animals, plants, and microbes, accelerating their use of energy and materials, their population growth, and interaction rates. At a much larger biological scale, warming accelerates ecosystem-level processes, elevating fluxes of carbon and oxygen between biota and the atmosphere. Although these general effects of temperature at finer and broader biological scales are widely observed, they can lead to contradictory predictions for how warming affects the structure and function of ecological communities at the intermediate scale of biological organization. We experimentally tested the hypothesis that the presence of predators and their associated species interactions modify the temperature dependence of net ecosystem oxygen production and respiration. We tracked a series of independent freshwater ecosystems (370 L) over 9 weeks, and we found that at higher temperatures, cascading effects of predators on zooplankton prey and algae were stronger than at lower temperatures. When grazing was weak or absent, standing phytoplankton biomass declined by 85%–95% (〈1-fold) over the temperature gradient (19–30 °C), and by 3-fold when grazers were present and lacked predators. These temperature-dependent species interactions and consequent community biomass shifts occurred without signs of species loss or community collapse, and only modestly affected the temperature dependence of net ecosystem oxygen fluxes. The exponential increases in net ecosystem oxygen production and consumption were relatively insensitive to differences in trophic interactions among ecosystems. Furthermore, monotonic declines in phytoplankton standing stock suggested no threshold effects of warming across systems. We conclude that local changes in community structure, including temperature-dependent trophic cascades, may be compatible with prevailing and predictable effects of temperature on ecosystem functions related to fundamental effects of temperature on metabolism.

Description: Almost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, the metaorganism. Natural selection should favor hosts that shape the community composition of these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal hosts often pose selective environments, which only a subset of the environmentally available microbes are able to colonize. How these microbes assemble after colonization to form the complex microbiota is less clear. Neutral models are based on the assumption that the alternatives in microbiota community composition are selectively equivalent and thus entirely shaped by random population dynamics and dispersal. Here, we use the neutral model as a null hypothesis to assess microbiata composition in host organisms, which does not rely on invoking any adaptive processes underlying microbial community assembly. We show that the overall microbiota community structure from a wide range of host organisms, in particular including previously understudied invertebrates, is in many cases consistent with neutral expectations. Our approach allows to identify individual microbes that are deviating from the neutral expectation and are therefore interesting candidates for further study. Moreover, using simulated communities, we demonstrate that transient community states may play a role in the deviations from the neutral expectation. Our findings highlight that the consideration of neutral processes and temporal changes in community composition are critical for an in-depth understanding of microbiota-host interactions.

Description: Author(s): F. Buccella We assume that the two hidden charm pentaquark states discovered at L H C b are built from three light quarks and a c c ¯ pair. Further assumed is that the three light quarks and the c c ¯ pair are both in colour octet states. Thus, for the final J P = 5 2 + state, the three light quarks and the c c ¯ pair are in... [Phys. Rev. D 98, 114011] Published Thu Dec 13, 2018

Description: Author(s): H. Bahtiyar, K. U. Can, G. Erkol, M. Oka, and T. T. Takahashi We evaluate the spin- 3 / 2 → spin − 1 / 2 electromagnetic transitions of the doubly charmed baryons on 2 + 1 flavor, 3 2 3 × 64 PACS-CS lattices with a pion mass of 156 ( 9 )     MeV / c 2 . A relativistic heavy quark action is employed to minimize the associated systematic errors on charm-quark observables. We extract the... [Phys. Rev. D 98, 114505] Published Thu Dec 13, 2018

Description: Author(s): Dorota M. Grabowska, Tom Melia, and Surjeet Rajendran Current dark matter detection strategies are based on the assumption that the dark matter is a gas of noninteracting particles with a reasonably large number density. This picture is dramatically altered if there are significant self-interactions within the dark sector, potentially resulting in the ... [Phys. Rev. D 98, 115020] Published Thu Dec 13, 2018

Description: Author(s): C. S. Kim, G. López Castro, and Dibyakrupa Sahoo Anomalies in several short-baseline neutrino oscillation experiments suggest the possible existence of sterile neutrinos at about the eV scale that have appreciable mixing with the three known neutrinos. We find that if such a light sterile neutrino exists, through a combined study of the leptonic d... [Phys. Rev. D 98, 115021] Published Thu Dec 13, 2018

Description: by Cedric Alaux, Samuel Soubeyrand, Alberto Prado, Mathilde Peruzzi, Alban Maisonnasse, Julien Vallon, Julie Hernandez, Pascal Jourdan, Yves Le Conte Honeybee colonies are increasingly exposed to environmental stress factors, which can lead to their decline or failure. However, there are major gaps in stressor risk assessment due to the difficulty of assessing the honeybee colony state and detecting abnormal events. Since stress factors usually induce a demographic disturbance in the colony (e.g. loss of foragers, early transition from nurse to forager state), we suggest that disturbances could be revealed indirectly by measuring the age- and task-related physiological state of bees, which can be referred to as biological age (an indicator of the changes in physiological state that occur throughout an individual lifespan). We therefore estimated the biological age of bees from the relationship between age and biomarkers of task specialization (vitellogenin and the adipokinetic hormone receptor). This relationship was determined from a calibrated sample set of known-age bees and mathematically modelled for biological age prediction. Then, we determined throughout the foraging season the evolution of the biological age of bees from colonies with low (conventional apiary) or high Varroa destructor infestation rates (organic apiary). We found that the biological age of bees from the conventional apiary progressively decreased from the spring (17 days) to the fall (6 days). However, in colonies from the organic apiary, the population aged from spring (13 days) to summer (18.5 days) and then rejuvenated in the fall (13 days) after Varroa treatment. Biological age was positively correlated with the amount of brood (open and closed cells) in the apiary with low Varroa pressure, and negatively correlated with Varroa infestation level in the apiary with high Varroa pressure. Altogether, these results show that the estimation of biological age is a useful and effective method for assessing colony demographic state and likely detrimental effects of stress factors.

Description: by Maganizo B. Chagomerana, William C. Miller, Jennifer H. Tang, Irving F. Hoffman, Bryna J. Harrington, Bethany DiPrete, Shaphil Wallie, Allan Jumbe, Laura Limarzi, Mina C. Hosseinipour Background In Malawi’s PMTCT Option B+ program, HIV-infected pregnant women who are already receiving ART are continued on their current therapy regimen without testing for treatment failure at the first antenatal care (ANC) visit. HIV RNA screening at ANC may identify women with treatment failure and ensure that viral suppression is maintained throughout the pregnancy. Methods We conducted a cross-sectional study of HIV-infected pregnant women who had been receiving ART for at least 6 months at the first ANC visit under the PMTCT Option B+ program at Bwaila Hospital in Lilongwe, Malawi from June 2015 to December 2017. Poisson regression models with robust variance were used to investigate the predictors of ART treatment failure defined as viral load ≥1000 copies/ml. Results The median age of 864 women tested for ART failure was 31.1 years (interquartile range: 26.9–34.5). The prevalence of treatment failure was 7.6% (95% confidence interval (CI): 6.0–9.6). CD4 cell count (adjusted prevalence ratio (aPR) = 0.57; 95% CI: 0.50–0.65) was strongly associated with treatment failure. Conclusion The low prevalence of treatment failure among women presenting for their first ANC in urban Malawi demonstrates success of Option B+ in maintaining viral suppression and suggests progress towards the last 90% of the UNAIDS 90-90-90 targets. Women failing on ART should be identified early for adherence counseling and may require switching to an alternative ART regimen.

Description: by Rie Matsushima-Nishiwaki, Noriko Yamada, Kouki Fukuchi, Osamu Kozawa A bioactive lipid, sphingosine 1-phosphate (S1P), acts extracellularly as a potent mediator, and is implicated in the progression of various cancers including hepatocellular carcinoma (HCC). S1P exerts its functions by binding to five types of specific receptors, S1P receptor 1 (S1PR1), S1PR2, S1PR3, S1PR4 and S1PR5 on the plasma membrane. However, the exact roles of S1P and each S1PR in HCC cells remain to be clarified. In the present study, we investigated the effect of S1P on the hepatocyte growth factor (HGF)-induced migration of human HCC-derived HuH7 cells, and the involvement of each S1PR. S1P dose-dependently reduced the HGF-induced migration of HuH7 cells. We found that all S1PRs exist in the HuH7 cells. Among each selective agonist for five S1PRs, CYM5520, a selective S1PR2 agonist, significantly suppressed the HGF-induced HuH7 cell migration whereas selective agonists for S1PR1, S1PR3, S1PR4 or S1PR5 failed to affect the migration. The reduction of the HGF-induced migration by S1P was markedly reversed by treatment of JTE013, a selective antagonist for S1PR2, and S1PR2- siRNA. These results strongly suggest that S1P reduces the HGF-induced HCC cell migration via S1PR2. Our findings may provide a novel potential of S1PR2 to therapeutic strategy for metastasis of HCC.

Description: by Mircea Zloteanu, Nigel Harvey, David Tuckett, Giacomo Livan The Sharing Economy (SE) is a growing ecosystem focusing on peer-to-peer enterprise. In the SE the information available to assist individuals (users) in making decisions focuses predominantly on community-generated trust and reputation information. However, how such information impacts user judgement is still being understood. To explore such effects, we constructed an artificial SE accommodation platform where we varied the elements related to hosts’ digital identity, measuring users’ perceptions and decisions to interact. Across three studies, we find that trust and reputation information increases not only the users’ perceived trustworthiness, credibility, and sociability of hosts, but also the propensity to rent a private room in their home. This effect is seen when providing users both with complete profiles and profiles with partial user-selected information. Closer investigations reveal that three elements relating to the host’s digital identity are sufficient to produce such positive perceptions and increased rental decisions, regardless of which three elements are presented. Our findings have relevant implications for human judgment and privacy in the SE, and question its current culture of ever increasing information-sharing.

Description: by Tucker Maxson, Candace D. Blancett, Amanda S. Graham, Christopher P. Stefan, Timothy D. Minogue Development and implementation of rapid antimicrobial susceptibility testing is critical for guiding patient care and improving clinical outcomes, especially in cases of sepsis. One approach to reduce the time-to-answer for antimicrobial susceptibility is monitoring the inhibition of DNA production, as differences in DNA concentrations are more quickly impacted compared to optical density changes in traditional antimicrobial susceptibility testing. Here, we use real-time PCR to rapidly determine antimicrobial susceptibility after short incubations with antibiotic. Application of this assay to a collection of 144 isolates in mock blood culture, covering medically relevant pathogens displaying high rates of resistance, provided susceptibility data in under 4 hours. This assay provided categorical agreement with a reference method in 96.3% of cases across all species. Sequencing of a subset of PCR amplicons showed accurate genus level identification. Overall, implementation of this method could provide accurate susceptibility results with a reduced time-to-answer for a number of medically relevant bacteria commonly isolated from blood culture.

Description: by Ágota Nagy, Levente Kovács, Zoltán Lipinszki, Margit Pál, Péter Deák In most Eukaryotes, ubiquitin either exists as free monoubiquitin or as a molecule that is covalently linked to other proteins. These two forms cycle between each other and due to the concerted antagonistic activity of ubiquitylating and deubiquitylating enzymes, an intracellular ubiquitin equilibrium is maintained that is essential for normal biological function. However, measuring the level and ratio of these forms of ubiquitin has been difficult and time consuming. In this paper, we have adapted a simple immunoblotting technique to monitor ubiquitin content and equilibrium dynamics in different developmental stages and tissues of Drosophila . Our data show that the level of total ubiquitin is distinct in different developmental stages, lowest at the larval-pupal transition and in three days old adult males, and highest in first instar larvae. Interestingly, the ratio of free mono-ubiquitin remains within 30–50% range of the total throughout larval development, but peaks to 70–80% at the larval-pupal and the pupal-adult transitions. It stays within the 70–80% range in adults. In developmentally and physiologically active tissues, the ratio of free ubiquitin is similarly high, most likely reflecting a high demand for ubiquitin availability. We also used this method to demonstrate the disruption of the finely tuned ubiquitin equilibrium by the abolition of proteasome function or the housekeeping deubiquitylase, Usp5. Our data support the notion that the ubiquitin equilibrium is regulated by tissue- and developmental stage-specific mechanisms.

Description: by Huirong Cheng, Pei Hu, Weihua Wen, Ling Liu Three arsenic species in urine are measured using an atomic absorption spectrophotometer. RT-PCR is performed to detect the expression levels of AS3MT, 3 miRNAs, and 17 relative mRNAs in 43 workers producing arsenic trioxide, 36 workers who stopped exposure to arsenic for 85 days, and 24 individuals as the control group. The concentrations of urinary arsenic are very high in workers. A negative correlation between AS3MT and MiR-5 48c-3p is found. There exist significant changes for most selected miRNAs and mRNAs in workers. There are no significant differences between workers who stopped exposure to arsenic and the control group for most miRNAs and mRNAs, but the MiR-5 48c-3p levels show significant changes. Similar positive correlations between the expression of AS3MT and all selected mRNAs are found. Negative correlations between the expression of MiR-5 48c-3p and many relative mRNAs are found as well. AS3MT and MiR-5 48c-3p may regulate arsenic methylation jointly, which when involved in a group of relative mRNAs may play roles in arsenic metabolism and epigenetic changes caused by this metabolism.

Description: Author(s): Pavel A. Volkov and Sergej Moroz We consider the stability of nodal surfaces in fermionic band systems with respect to the Coulomb repulsion. It is shown that nodal surfaces at the Fermi level are gapped out at low temperatures due to emergent particle-hole orders. Energy dispersion of the nodal surface suppresses the instability t... [Phys. Rev. B 98, 241107(R)] Published Thu Dec 13, 2018

Description: Author(s): Tao Liu, James Jun He, and Franco Nori (野理) Conventional n -dimensional topological superconductors (TSCs) have protected gapless ( n − 1 ) -dimensional boundary states. In contrast to this, second-order TSCs are characterized by topologically protected gapless ( n − 2 ) -dimensional states with the usual gapped ( n − 1 ) boundaries. Here, we study a second... [Phys. Rev. B 98, 245413] Published Thu Dec 13, 2018

Description: Author(s): Xiancong Lu and D. Sénéchal We investigate parity-mixing superconductivity in the two-dimensional Hubbard model with Rashba spin-orbit coupling, using cellular dynamical mean-field theory (CDMFT). A superconducting state with mixed singlet d -wave and triplet p -wave character is found in a wide range of doping. The singlet comp... [Phys. Rev. B 98, 245118] Published Thu Dec 13, 2018

Description: Author(s): Binod K. Rai et al. New experiments reveal anomalous metamagnetic transitions in single crystals of YbRh 3 Si 7 , likely arising from competition between the crystal’s highly anisotropic electric field and magnetic exchange interactions. [Phys. Rev. X 8, 041047] Published Thu Dec 13, 2018

Description: Author(s): Rafael D. Schulman and Kari Dalnoki-Veress Researchers can change the shape of a liquid drop by placing it between two stretched elastic films, allowing the drop to be used as a tiny adjustable lens. [Phys. Rev. Lett. 121, 248004] Published Thu Dec 13, 2018

Description: by Stefanie Hoehl, Gabriela Markova Infants’ cognitive development and learning rely profoundly on their interactions with other people. In the first year, infants become increasingly sensitive to others’ gaze and use it to focus their own attention on relevant visual input. However, infants are not passive observers in early social interactions, and these exchanges are characterized by high levels of contingency and reciprocity. Wass and colleagues offer first insights into the neurobehavioral dynamics of caregiver–infant interactions, demonstrating that caregivers’ scalp-recorded theta band activity responds to their infant’s changes in attention, and parental brain activation is associated with infants’ sustenance of attention. This research opens up entirely new ways of exploring caregiver–infant interactions and to understand early social attention as a reciprocal and dynamic process.

Description: by Xinyi Liu, Diane L. Lister, Zhijun Zhao, Cameron A. Petrie, Xiongsheng Zeng, Penelope J. Jones, Richard A. Staff, Anil K. Pokharia, Jennifer Bates, Ravindra N. Singh, Steven A. Weber, Giedre Motuzaite Matuzeviciute, Guanghui Dong, Haiming Li, Hongliang Lü, Hongen Jiang, Jianxin Wang, Jian Ma, Duo Tian, Guiyun Jin, Liping Zhou, Xiaohong Wu, Martin K. Jones

Description: by Itamar Daniel Landau, Haim Sompolinsky We present a simple model for coherent, spatially correlated chaos in a recurrent neural network. Networks of randomly connected neurons exhibit chaotic fluctuations and have been studied as a model for capturing the temporal variability of cortical activity. The dynamics generated by such networks, however, are spatially uncorrelated and do not generate coherent fluctuations, which are commonly observed across spatial scales of the neocortex. In our model we introduce a structured component of connectivity, in addition to random connections, which effectively embeds a feedforward structure via unidirectional coupling between a pair of orthogonal modes. Local fluctuations driven by the random connectivity are summed by an output mode and drive coherent activity along an input mode. The orthogonality between input and output mode preserves chaotic fluctuations by preventing feedback loops. In the regime of weak structured connectivity we apply a perturbative approach to solve the dynamic mean-field equations, showing that in this regime coherent fluctuations are driven passively by the chaos of local residual fluctuations. When we introduce a row balance constraint on the random connectivity, stronger structured connectivity puts the network in a distinct dynamical regime of self-tuned coherent chaos. In this regime the coherent component of the dynamics self-adjusts intermittently to yield periods of slow, highly coherent chaos. The dynamics display longer time-scales and switching-like activity. We show how in this regime the dynamics depend qualitatively on the particular realization of the connectivity matrix: a complex leading eigenvalue can yield coherent oscillatory chaos while a real leading eigenvalue can yield chaos with broken symmetry. The level of coherence grows with increasing strength of structured connectivity until the dynamics are almost entirely constrained to a single spatial mode. We examine the effects of network-size scaling and show that these results are not finite-size effects. Finally, we show that in the regime of weak structured connectivity, coherent chaos emerges also for a generalized structured connectivity with multiple input-output modes.

Description: by Maria E. Sousa, Michael H. Farkas

Description: by Jonas R. Kunst, Esther N. Phillibert It is well-established that experiences of discrimination influence immigrants’ acculturation. Yet, whereas a large body of research has demonstrated the role of discrimination by members of the dominant societal group, surprisingly little is known about how being discriminated by members of one’s own group relates to the way immigrants acculturate. With a sample of 162 African first- and second-generation immigrants living in Norway, the present research investigated the relationship between both types of discrimination, acculturation and psychological well-being. It did so, focusing on discrimination based on one’s skin tone, a type of discrimination Africans can experience from White as well as African individuals. Results showed that skin-tone discrimination by Whites was associated with a lower host culture orientation. By contrast, skin-tone discrimination by Africans was associated with a lower heritage culture orientation. Mediation analyses showed that the positive relationship of skin-tone discrimination by Whites and Africans with life satisfaction was mediated by a lower host and heritage culture orientation respectively. This indirect relationship did not reach significance with self-esteem as dependent variable. Participants’ actual skin tone was unrelated to experiences of skin-tone discrimination. We discuss our results in light of previous research and highlight potential limitations.

Description: by Christian Agebratt, Edvin Ström, Thobias Romu, Olof Dahlqvist-Leinhard, Magnus Borga, Per Leandersson, Fredrik H. Nystrom

Description: Author(s): Jing Luo and Gia-Wei Chern We present an extensive numerical study of a type of frustrated itinerant magnetism on the pyrochlore lattice. In this theory, the pyrochlore magnet can be viewed as a cross-linking network of Kondo or double-exchange chains. Contrary to models based on Mott insulators, this itinerant magnetism appr... [Phys. Rev. B 98, 214423] Published Thu Dec 13, 2018

Description: Author(s): Jie Wang and Yuxiang Mo The isotope effect and the g − u symmetry in the HD predissociation have been studied by detecting the H ( 2 s ) , H ( 2 p ) , D ( 2 s ) , and D ( 2 p ) fragments. For transitions to the 3 p π D 1 Π u + ( υ = 4 ) , 4 p π D ′ 1 Π u + ( υ = 1 ) , and 4 p σ B ′ ′ 1 Σ u + ( υ = 2 ) states of HD, the branching ratios of the four dissociation channels, H ( 2 s ) + D ( 1 s ) , ... [Phys. Rev. A 98, 062509] Published Thu Dec 13, 2018

Description: Author(s): Stefan Hartung, Felix Sommer, Simeon Völkel, Johannes Schönke, and Ingo Rehberg The magnetic field of a cuboidal cluster of eight magnetic spheres is measured. It decays with the inverse seventh power of the distance. This corresponds formally to a multipole named a dotriacontapole. This strong decay is explained on the basis of dipole-dipole interaction and the symmetry of the... [Phys. Rev. B 98, 214424] Published Thu Dec 13, 2018

Description: Author(s): T. Rząca-Urban, W. Urban, M. Czerwiński, J. Wiśniewski, A. Blanc, H. Faust, M. Jentschel, P. Mutti, U. Köster, T. Soldner, G. de France, G. S. Simpson, and C. A. Ur The main goal of this work is the determination of spins and parities of excited states in Zr 97 , among others the 2264.3-keV level, which had previously been tentatively reported as the 11 / 2 − excitation corresponding to the h 11 / 2 neutron orbital. Low-spin excited states in Zr 97 were populated via th... [Phys. Rev. C 98, 064315] Published Thu Dec 13, 2018

Description: Author(s): Jasmine Brewer, Swagato Mukherjee, Krishna Rajagopal, and Yi Yin Near a critical point in a phase diagram, certain observables show characteristic fluctuations. The authors qualitatively predict how such fluctuations depend on the rapidity in relativistic heavy-ion collisions, and thereby present a distinctive observable to search for the critical endpoint in the QCD phase diagram. This is particularly relevant to the coming low-beam-energy scan at RHIC. [Phys. Rev. C 98, 061901(R)] Published Thu Dec 13, 2018

Description: Author(s): Hai-Yang Cheng and Yan-Liang Shi The lifetimes of doubly charmed hadrons are analyzed within the framework of the heavy quark expansion (HQE). Lifetime differences arise from spectator effects such as W -exchange and Pauli interference. The Ξ c c + + baryon is longest-lived in the doubly charmed baryon system owing to the destructive Pa... [Phys. Rev. D 98, 113005] Published Thu Dec 13, 2018

Description: Author(s): G. Kramer and H. Spiesberger We study inclusive b -hadron production in p p collisions at the LHC at different center-of-mass energies and compare with experimental data from the LHCb and CMS collaborations. Our predictions for cross sections differential in the transverse momentum and (pseudo)rapidity agree with data within unce... [Phys. Rev. D 98, 114010] Published Thu Dec 13, 2018

Description: Author(s): Vanessa Böhm, Blake D. Sherwin, Jia Liu, J. Colin Hill, Marcel Schmittfull, and Toshiya Namikawa We investigate the impact of non-Gaussian lensing deflections on measurements of the CMB lensing power spectrum. We find that the false assumption of their Gaussianity significantly biases these measurements in current and future experiments at the percent level. The bias is detected by comparing CM... [Phys. Rev. D 98, 123510] Published Thu Dec 13, 2018

Description: Author(s): A. Crisanti and H. Sompolinksy In this work we study of the dynamics of large-size random neural networks. Different methods have been developed to analyze their behavior, and most of them rely on heuristic methods based on Gaussian assumptions regarding the fluctuations in the limit of infinite sizes. These approaches, however, ... [Phys. Rev. E 98, 062120] Published Thu Dec 13, 2018

Description: Author(s): Jim Thomas and Ray Yamada A new amplitude equation that captures the effect of arbitrary topography on surface waves is presented. It can be integrated more quickly than the fully nonlinear equations, while accurately capturing the wave dynamics. [Phys. Rev. Fluids 3, 124802] Published Thu Dec 13, 2018

Description: Author(s): Carl M. Bender, Nima Hassanpour, S. P. Klevansky, and Sarben Sarkar P T -symmetric quantum mechanics began with a study of the Hamiltonian H = p 2 + x 2 ( i x ) ϵ . A surprising feature of this non-Hermitian Hamiltonian is that its eigenvalues are discrete, real, and positive when ϵ ≥ 0 . This paper examines the corresponding quantum-field-theoretic Hamiltonian H = 1 2 ( ∇ ϕ ) 2 + 1 2 ϕ 2 ( i ϕ ) ϵ i... [Phys. Rev. D 98, 125003] Published Thu Dec 13, 2018

Description: Author(s): Sushant Saryal, Juliane U. Klamser, Tridib Sadhu, and Deepak Dhar There is a misconception, widely shared among physicists, that the equilibrium free energy of a one-dimensional classical model with strictly finite-ranged interactions, and at nonzero temperatures, cannot show any singularities as a function of the coupling constants. In this Letter, we discuss an ... [Phys. Rev. Lett. 121, 240601] Published Thu Dec 13, 2018

Description: by Heïdi Serra, Kyuha Choi, Xiaohui Zhao, Alexander R. Blackwell, Juhyun Kim, Ian R. Henderson During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the Arabidopsis thaliana RAC1 and RPP13 disease resistance genes, using varying haplotypic combinations. We observed a negative non-linear relationship between interhomolog divergence and crossover frequency within the hotspots, consistent with polymorphism locally suppressing crossover repair of DSBs. The fancm , recq4a recq4b , figl1 and msh2 mutants, or lines with increased HEI10 dosage, are known to show increased crossovers throughout the genome. Surprisingly, RAC1 crossovers were either unchanged or decreased in these genetic backgrounds, showing that chromosome location and local chromatin environment are important for regulation of crossover activity. We employed deep sequencing of crossovers to examine recombination topology within RAC1 , in wild type, fancm , recq4a recq4b and fancm recq4a recq4b backgrounds. The RAC1 recombination landscape was broadly conserved in the anti-crossover mutants and showed a negative relationship with interhomolog divergence. However, crossovers at the RAC1 5'-end were relatively suppressed in recq4a recq4b backgrounds, further indicating that local context may influence recombination outcomes. Our results demonstrate the importance of interhomolog divergence in shaping recombination within plant disease resistance genes and crossover hotspots.

Description: by Enrico Lavezzo, Michele Berselli, Ilaria Frasson, Rosalba Perrone, Giorgio Palù, Alessandra R. Brazzale, Sara N. Richter, Stefano Toppo G-quadruplexes are non-canonical nucleic-acid structures that control transcription, replication, and recombination in organisms. G-quadruplexes are present in eukaryotes, prokaryotes, and viruses. In the latter, mounting evidence indicates their key biological activity. Since data on viruses are scattered, we here present a comprehensive analysis of potential quadruplex-forming sequences (PQS) in the genome of all known viruses that can infect humans. We show that occurrence and location of PQSs are features characteristic of each virus class and family. Our statistical analysis proves that their presence within the viral genome is orderly arranged, as indicated by the possibility to correctly assign up to two-thirds of viruses to their exact class based on the PQS classification. For each virus we provide: i) the list of all PQS present in the genome (positive and negative strands), ii) their position in the viral genome, iii) the degree of conservation among strains of each PQS in its genome context, iv) the statistical significance of PQS abundance. This information is accessible from a database to allow the easy navigation of the results: http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus. The availability of these data will greatly expedite research on G-quadruplex in viruses, with the possibility to accelerate finding therapeutic opportunities to numerous and some fearsome human diseases.

Description: by Motoyasu Honma, Yuri Masaoka, Shinichi Koyama, Takeshi Kuroda, Akinori Futamura, Azusa Shiromaru, Yasuo Terao, Kenjiro Ono, Mitsuru Kawamura Parkinson's disease (PD) is associated with various cognitive impairments. However, the nature of cognitive modification in patients with PD remains to be elucidated. In the present study, we examined whether patients with PD could correct and maintain subjective time duration and line length estimation. After training sessions, in which participants repeatedly memorized either a duration or a length, we compared a learning performance in 20 PD patients with 20 healthy controls. In the case of duration in the PD patients, the learned durations immediately returned to baseline of pre-training within a few minutes. However, the patients’ ability to learn length estimation remained unimpaired. In contrast, healthy controls were able to retain the learned duration and length estimations. Time compression in PD's internal clock may become entrained to their altered duration estimation even after learning of accurate time duration. These deficits may be associated with disrupting cognitive modification in PD.

Description: Author(s): Takemichi Okui and Arash Yunesi We present how to construct a soft collinear effective theory (SCET) for gravity at the leading and next-to-leading powers from the ground up. The soft graviton theorem and decoupling of collinear gravitons at the leading power are manifest from the outset in the effective symmetries of the theory. ... [Phys. Rev. D 97, 066011] Published Mon Mar 12, 2018

Description: Author(s): Justin Vines and Jan Steinhoff We discuss the effects of the black holes’ spin-multipole structure in the orbital dynamics of binary black holes according to general relativity, focusing on the leading-post-Newtonian-order couplings at each order in an expansion in the black holes’ spins. We first review previous widely confirmed... [Phys. Rev. D 97, 064010] Published Mon Mar 12, 2018

Description: Author(s): Anders Andreassen, William Frost, and Matthew D. Schwartz The authors compute the lifetime of the universe in the Standard Model at next to leading order, obtaining 10 139 years. This involves regularization of the dilatation zero mode. [Phys. Rev. D 97, 056006] Published Mon Mar 12, 2018

Description: Author(s): M. V. Chushnyakova and I. I. Gontchar We study the effect of backscattering of the Brownian particles as they escape out of a metastable state overcoming the potential barrier. For this aim, we model this process numerically using the Langevin equations. This modeling is performed for the wide range of the friction constant covering bot... [Phys. Rev. E 97, 032107] Published Mon Mar 12, 2018

Description: Author(s): Itai Pinkoviezky, Iain D. Couzin, and Nir S. Gov Collective decision-making regarding direction of travel is observed during natural motion of animal and cellular groups. This phenomenon is exemplified, in the simplest case, by a group that contains two informed subgroups that hold conflicting preferred directions of motion. Under such circumstanc... [Phys. Rev. E 97, 032304] Published Mon Mar 12, 2018

Description: Author(s): Seth Hopper Gravitational perturbations due to a point particle moving on a static black hole background are naturally described in Regge-Wheeler gauge. The first-order field equations reduce to a single master wave equation for each radiative mode. The master function satisfying this wave equation is a linear ... [Phys. Rev. D 97, 064007] Published Mon Mar 12, 2018

Description: Author(s): Patricia Ternes, Evy Salcedo, and Marcia C. Barbosa The slip of a fluid layer in contact with a solid confining surface is investigated for different temperatures and densities using molecular dynamic simulations. We show that for an anomalous waterlike fluid the slip goes as follows: for low levels of shear, defect slip appears and is related to the... [Phys. Rev. E 97, 033104] Published Mon Mar 12, 2018

Description: Author(s): Bikash Padhi, Apoorv Tiwari, Chandan Setty, and Philip W. Phillips We study a single-channel Kondo effect using a recently developed [1–4] holographic large- N technique. In order to obtain resistivity of this model, we introduce a probe field. The gravity dual of a localized fermionic impurity in 1 + 1 -dimensional host matter is constructed by embedding a localized t... [Phys. Rev. D 97, 066012] Published Mon Mar 12, 2018

Description: Author(s): J. H. Seo, F. Cadieux, R. Mittal, E. Deem, and L. Cattafesta The response of a laminar separation bubble to synthetic jet forcing with various modulation schemes is numerically investigated. The study suggests that the effectiveness of synthetic jet-based flow control could be improved by carefully designing the spectral content of the modulation scheme. [Phys. Rev. Fluids 3, 033901] Published Mon Mar 12, 2018

Description: Author(s): Tianxing Ma, Lufeng Zhang, Chia-Chen Chang, Hsiang-Hsuan Hung, and Richard T. Scalettar Using exact quantum Monte Carlo calculations, we examine the interplay between localization of electronic states driven by many-body correlations and that by randomness in a two-dimensional system featuring linearly vanishing density of states at the Fermi level. A novel disorder-induced nonmagnetic... [Phys. Rev. Lett. 120, 116601] Published Mon Mar 12, 2018

Description: Author(s): Aleksandra A. Grigoreva, Andrey V. Tyukhtin, Viktor V. Vorobev, Sergey N. Galyamin, and Sergey Antipov We consider the electromagnetic field of a point charged particle moving along the axis of a cylindrical waveguide from a homogeneously filled area to a dielectric loading area having an axially symmetrical channel. We are interested in studying the Cherenkov radiation excited in the bilayer area. T... [Phys. Rev. Accel. Beams 21, 031302] Published Mon Mar 12, 2018

Description: Author(s): N. E. Sujovolsky, P. D. Mininni, and M. P. Rast We develop a model for particle dispersion observed in stably stratified flows, such as in the ocean and the nocturnal atmosphere, where turbulence is very efficient at mixing and diffusing transported quantities. The model opens new efficient paths for statistical prediction of particle dispersion. [Phys. Rev. Fluids 3, 034603] Published Mon Mar 12, 2018

Description: Author(s): Shin-ichiro Nagahiro and Hiizu Nakanishi [Phys. Rev. E 97, 039901] Published Mon Mar 12, 2018

Description: by Anne Keitel, Joachim Gross, Christoph Kayser During online speech processing, our brain tracks the acoustic fluctuations in speech at different timescales. Previous research has focused on generic timescales (for example, delta or theta bands) that are assumed to map onto linguistic features such as prosody or syllables. However, given the high intersubject variability in speaking patterns, such a generic association between the timescales of brain activity and speech properties can be ambiguous. Here, we analyse speech tracking in source-localised magnetoencephalographic data by directly focusing on timescales extracted from statistical regularities in our speech material. This revealed widespread significant tracking at the timescales of phrases (0.6–1.3 Hz), words (1.8–3 Hz), syllables (2.8–4.8 Hz), and phonemes (8–12.4 Hz). Importantly, when examining its perceptual relevance, we found stronger tracking for correctly comprehended trials in the left premotor (PM) cortex at the phrasal scale as well as in left middle temporal cortex at the word scale. Control analyses using generic bands confirmed that these effects were specific to the speech regularities in our stimuli. Furthermore, we found that the phase at the phrasal timescale coupled to power at beta frequency (13–30 Hz) in motor areas. This cross-frequency coupling presumably reflects top-down temporal prediction in ongoing speech perception. Together, our results reveal specific functional and perceptually relevant roles of distinct tracking and cross-frequency processes along the auditory–motor pathway.

Description: Author(s): D. Sarenac, D. A. Pushin, M. G. Huber, D. S. Hussey, H. Miao, M. Arif, D. G. Cory, A. D. Cronin, B. Heacock, D. L. Jacobson, J. M. LaManna, and H. Wen A new and more flexible neutron interferometer design relies on the moiré effect, in which two periodic patterns are combined to give a longer-period pattern. [Phys. Rev. Lett. 120, 113201] Published Mon Mar 12, 2018

Description: Author(s): Juergen Klepp A new and more flexible neutron interferometer design relies on the moiré effect, in which two periodic patterns are combined to give a longer-period pattern. [Physics 11, 26] Published Mon Mar 12, 2018

Description: Author(s): Lorenzo Di Pietro and Emmanuel Stamou We consider theories with fermionic degrees of freedom that have a fixed point of Wilson–Fisher type in noninteger dimension d = 4 − 2 ε . Due to the presence of evanescent operators, i.e., operators that vanish in integer dimensions, these theories contain families of infinitely many operators that can m... [Phys. Rev. D 97, 065007] Published Mon Mar 12, 2018

Description: Author(s): Mojtaba Najafizadeh In this paper, we first propose the bosonic (fermionic) modified Wigner equations for continuous spin particle (CSP). Secondly, starting from the (Fang-)Fronsdal-like equation, we will reach to the modified action of bosonic (fermionic) continuous spin gauge field in flat spacetime, presented recent... [Phys. Rev. D 97, 065009] Published Mon Mar 12, 2018

Description: Author(s): Filip Kiałka, Alexander R. H. Smith, Mehdi Ahmadi, and Andrzej Dragan We show that massive particles created in a relativistically accelerated reference frame, as predicted by the Unruh effect, can only be found in a tiny layer above the Rindler horizon, whose thickness corresponds to a single Compton wavelength. This is beyond the reach of any detector and suggests t... [Phys. Rev. D 97, 065010] Published Mon Mar 12, 2018

Description: Author(s): I-Sheng Yang We derive the time scale for two initially pure subsystems to become entangled with each other through an arbitrary Hamiltonian that couples them. The entanglement timescale is inversely proportional to the “correlated uncertainty” between the two subsystems, a quantity which we will define and anal... [Phys. Rev. D 97, 066008] Published Mon Mar 12, 2018

Description: Author(s): Miguel Campiglia and Leonardo Coito We study asymptotic charges associated with a spin-zero analog of Weinberg’s soft photon and graviton theorems in even dimensions. Simple spacetime expressions for the charges are given, but unlike gravity or electrodynamics, the symmetry interpretation for the charges remains elusive. This work is ... [Phys. Rev. D 97, 066009] Published Mon Mar 12, 2018

Description: by Hao Ge, Pingping Wu, Hong Qian, Sunney Xiaoliang Xie Within an isogenic population, even in the same extracellular environment, individual cells can exhibit various phenotypic states. The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood, especially in the presence of positive feedback. Recent high-precision single-cell measurements showed that, at least in bacteria, switching in gene states is slow relative to the typical rates of active transcription and translation. Hence using the lac operon as an archetype, in such a region of operon-state switching, we present a fluctuating-rate model for this classical gene regulation module, incorporating the more realistic operon-state switching mechanism that was recently elucidated. We found that the positive feedback mechanism induces bistability (referred to as deterministic bistability), and that the parameter range for its occurrence is significantly broadened by stochastic operon-state switching. We further show that in the absence of positive feedback, operon-state switching must be extremely slow to trigger bistability by itself. However, in the presence of positive feedback, which stabilizes the induced state, the relatively slow operon-state switching kinetics within the physiological region are sufficient to stabilize the uninduced state, together generating a broadened parameter region of bistability (referred to as stochastic bistability). We illustrate the opposite phenotype-transition rate dependence upon the operon-state switching rates in the two types of bistability, with the aid of a recently proposed rate formula for fluctuating-rate models. The rate formula also predicts a maximal transition rate in the intermediate region of operon-state switching, which is validated by numerical simulations in our model. Overall, our findings suggest a biological function of transcriptional “variations” among genetically identical cells, for the emergence of bistability and transition between phenotypic states.

Description: by Gerry Q. Tonkin-Hill, Leily Trianty, Rintis Noviyanti, Hanh H. T. Nguyen, Boni F. Sebayang, Daniel A. Lampah, Jutta Marfurt, Simon A. Cobbold, Janavi S. Rambhatla, Malcolm J. McConville, Stephen J. Rogerson, Graham V. Brown, Karen P. Day, Ric N. Price, Nicholas M. Anstey, Anthony T. Papenfuss, Michael F. Duffy Within the human host, the malaria parasite Plasmodium falciparum is exposed to multiple selection pressures. The host environment changes dramatically in severe malaria, but the extent to which the parasite responds to—or is selected by—this environment remains unclear. From previous studies, the parasites that cause severe malaria appear to increase expression of a restricted but poorly defined subset of the PfEMP1 variant, surface antigens. PfEMP1s are major targets of protective immunity. Here, we used RNA sequencing (RNAseq) to analyse gene expression in 44 parasite isolates that caused severe and uncomplicated malaria in Papuan patients. The transcriptomes of 19 parasite isolates associated with severe malaria indicated that these parasites had decreased glycolysis without activation of compensatory pathways; altered chromatin structure and probably transcriptional regulation through decreased histone methylation; reduced surface expression of PfEMP1; and down-regulated expression of multiple chaperone proteins. Our RNAseq also identified novel associations between disease severity and PfEMP1 transcripts, domains, and smaller sequence segments and also confirmed all previously reported associations between expressed PfEMP1 sequences and severe disease. These findings will inform efforts to identify vaccine targets for severe malaria and also indicate how parasites adapt to—or are selected by—the host environment in severe malaria.

Description: by Michael Pablo, Samuel A. Ramirez, Timothy C. Elston Polarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and many other cell types, the Rho GTPase Cdc42 is the key molecular player in polarity establishment. During yeast polarization, multiple patches of Cdc42 initially form, then resolve into a single front. Because polarization relies on strong positive feedback, it is likely that the amplification of molecular-level fluctuations underlies the generation of multiple nascent patches. In the absence of spatial cues, these fluctuations may be key to driving polarization. Here we used particle-based simulations to investigate the role of stochastic effects in a Turing-type model of yeast polarity establishment. In the model, reactions take place either between two molecules on the membrane, or between a cytosolic and a membrane-bound molecule. Thus, we developed a computational platform that explicitly simulates molecules at and near the cell membrane, and implicitly handles molecules away from the membrane. To evaluate stochastic effects, we compared particle simulations to deterministic reaction-diffusion equation simulations. Defining macroscopic rate constants that are consistent with the microscopic parameters for this system is challenging, because diffusion occurs in two dimensions and particles exchange between the membrane and cytoplasm. We address this problem by empirically estimating macroscopic rate constants from appropriately designed particle-based simulations. Ultimately, we find that stochastic fluctuations speed polarity establishment and permit polarization in parameter regions predicted to be Turing stable. These effects can operate at Cdc42 abundances expected of yeast cells, and promote polarization on timescales consistent with experimental results. To our knowledge, our work represents the first particle-based simulations of a model for yeast polarization that is based on a Turing mechanism.

Description: by Britta U. Westner, Sarang S. Dalal, Simon Hanslmayr, Tobias Staudigl Single-trial analyses have the potential to uncover meaningful brain dynamics that are obscured when averaging across trials. However, low signal-to-noise ratio (SNR) can impede the use of single-trial analyses and decoding methods. In this study, we investigate the applicability of a single-trial approach to decode stimulus modality from magnetoencephalographic (MEG) high frequency activity. In order to classify the auditory versus visual presentation of words, we combine beamformer source reconstruction with the random forest classification method. To enable group level inference, the classification is embedded in an across-subjects framework. We show that single-trial gamma SNR allows for good classification performance (accuracy across subjects: 66.44%). This implies that the characteristics of high frequency activity have a high consistency across trials and subjects. The random forest classifier assigned informational value to activity in both auditory and visual cortex with high spatial specificity. Across time, gamma power was most informative during stimulus presentation. Among all frequency bands, the 75 Hz 95 Hz band was the most informative frequency band in visual as well as in auditory areas. Especially in visual areas, a broad range of gamma frequencies (55 Hz 125 Hz) contributed to the successful classification. Thus, we demonstrate the feasibility of single-trial approaches for decoding the stimulus modality across subjects from high frequency activity and describe the discriminative gamma activity in time, frequency, and space.

Description: by Moran Brenner, Lior Lobel, Ilya Borovok, Nadejda Sigal, Anat A. Herskovits Listeria monocytogenes ( Lm ) is a saprophyte and intracellular pathogen. Transition to the pathogenic state relies on sensing of host-derived metabolites, yet it remains unclear how these are recognized and how they mediate virulence gene regulation. We previously found that low availability of isoleucine signals Lm to activate the virulent state. This response is dependent on CodY, a global regulator and isoleucine sensor. Isoleucine-bound CodY represses metabolic pathways including branched-chain amino acids (BCAA) biosynthesis, however under BCAA depletion, as occurs during infection, BCAA biosynthesis is upregulated and isoleucine-unbound CodY activates virulence genes. While isoleucine was revealed as an important input signal, it was not identified how internal levels are controlled during infection. Here we show that Lm regulates BCAA biosynthesis via CodY and via a riboregulator located upstream to the BCAA biosynthesis genes, named Rli60. rli60 is transcribed when BCAA levels drop, forming a ribosome-mediated attenuator that cis -regulates the downstream genes according to BCAA supply. Notably, we found that Rli60 restricts BCAA production, essentially starving Lm , a mechanism that is directly linked to virulence, as it controls the internal isoleucine pool and thereby CodY activity. This controlled BCAA auxotrophy likely evolved to enable isoleucine to serve as a host signal and virulence effector.

Description: Author(s): Lennart Bours, Björn Sothmann, Matteo Carrega, Elia Strambini, Ewelina M. Hankiewicz, Laurens W. Molenkamp, and Francesco Giazotto Keen interest has arisen lately in hybrid topological-insulator–superconductor nanostructures, from both the theoretical and experimental points of view. Among recent advances, the proposal for a Doppler-like shift in the energies of the edge states in toplogical-insulator Josephson junctions leads to a peculiar structure of the Andreev bound states along the helical edges. To exploit this effect, the authors propose a structure consisting of a normal-metal probe tunnel-coupled to the center of such a junction, which would function as a sensitive magnetometer. [Phys. Rev. Applied 10, 014027] Published Wed Jul 25, 2018

Description: Author(s): Junhua Luo, Li Jiang, and Long He The ( n , 2 n ) cross sections and their isomeric ratios ( σ m / σ g ) in the 13–15 MeV neutron energy range have been measured for Hg 196 , 198 by an activation and offline γ-ray spectrometric technique using the Pd-300 Neutron Generator at the Chinese Academy of Engineering Physics (CAEP). Natural Hg samples an... [Phys. Rev. C 98, 014619] Published Wed Jul 25, 2018

Description: Author(s): A. J. R. Puckett et al. [Phys. Rev. C 98, 019907] Published Wed Jul 25, 2018

Description: Author(s): Zoltán Nagy and Davison E. Soper We explore jet physics in hadron collisions using the parton shower event generator Deductor . Of particular interest is the one jet inclusive cross section d σ / d P T for jets of very high P T . Compared to the Born level, the cross section decreases substantially because of P T loss from the jet during sh... [Phys. Rev. D 98, 014035] Published Wed Jul 25, 2018

Description: Author(s): W. A. Yahya, B. I. S. van der Ventel, B. C. Kimene Kaya, and R. A. Bark A microscopic study of proton elastic scattering from unstable nuclei at intermediate energies using a relativistic formalism is presented. We have employed both the original relativistic impulse approximation (IA1) and the generalized impulse approximation (IA2) formalisms to calculate the relativi... [Phys. Rev. C 98, 014620] Published Wed Jul 25, 2018

Description: Author(s): Benjamin Guiot We analyze two consequences of the relationship between collinear factorization and k t -factorization. First, we show that the k t -factorization gives a fundamental justification for the choice of the hard scale Q 2 done in the collinear factorization. Second, we show that in the collinear factorizatio... [Phys. Rev. D 98, 014036] Published Wed Jul 25, 2018

Description: Author(s): Zoltán Nagy and Davison E. Soper We consider idealized parton shower event generators that treat parton spin and color exactly, leaving aside the choice of practical approximations for spin and color. We investigate how the structure of such a parton shower generator is related to the structure of QCD. We argue that a parton shower... [Phys. Rev. D 98, 014034] Published Wed Jul 25, 2018

Description: Author(s): Bradley J. Kavanagh, Daniele Gaggero, and Gianfranco Bertone The formation of astrophysical and primordial black holes influences the distribution of dark matter surrounding them. Black holes are thus expected to carry a dark matter “dress” whose properties depend on their formation mechanism and on the properties of the environment. Here we carry out a numer... [Phys. Rev. D 98, 023536] Published Wed Jul 25, 2018

Description: Author(s): Shao-Wen Wei and Yu-Xiao Liu In this paper, we explore the signatures of nonrotating and rotating black hole mergers in the matter-free modified gravity. First, we solve the unstable circular null orbits and the innermost stable circular timelike orbits via the geodesic motion. The characteristic quantities of these orbits are ... [Phys. Rev. D 98, 024042] Published Wed Jul 25, 2018

Description: Author(s): J. Ricardo G. Mendonça and Rolf E. O. Simões Almost four decades ago, Gacs, Kurdyumov, and Levin introduced three different cellular automata to investigate whether one-dimensional nonequilibrium interacting particle systems are capable of displaying phase transitions, and, as a byproduct, they introduced the density classification problem (th... [Phys. Rev. E 98, 012135] Published Wed Jul 25, 2018

Description: Author(s): A. R. Harikrishnan, Purbarun Dhar, Sateesh Gedupudi, and Sarit K. Das Evaporation kinetics of surfactant-infused nanocolloidal droplets are studied using the pendant mode to understand the pure physics of evaporation in such complex fluids. Oscillatory solute-thermal convective currents are found to be responsible for evaporation rate enhancement in these complex fluids. [Phys. Rev. Fluids 3, 073604] Published Wed Jul 25, 2018

Description: Author(s): Evert van Nieuwenburg and Oded Zilberberg Entanglement plays an important role in our ability to understand, simulate, and harness quantum many-body phenomena. In this work, we investigate the entanglement spectrum for open one-dimensional (1D) systems and propose a natural quantifier for how much a 1D quantum state is entangled while being... [Phys. Rev. A 98, 012327] Published Wed Jul 25, 2018

Description: Author(s): Mattias Palsgaard, Troels Markussen, Tue Gunst, Mads Brandbyge, and Kurt Stokbro Modeling a full photovoltaic device with first-principles simulations is such a tremendous computational task that it has remained out of reach—until now. This joint work between academia and industry combines multiple state-of-the-art methods to enable the simulation of phonon-assisted photocurrent in a realistic device under operating conditions. The fully atomistic calculations include the combined effects of electron-phonon and electron-photon coupling, as well as finite bias and temperature. Excellent agreement with experiment shows that this method could be widely useful for physicists and engineers alike to benchmark tomorrow’s optoelectronic devices. [Phys. Rev. Applied 10, 014026] Published Wed Jul 25, 2018

Description: Author(s): J. Forneris, S. Ditalia Tchernij, P. Traina, E. Moreva, N. Skukan, M. Jakšić, V. Grilj, F. Bosia, E. Enrico, G. Amato, I.P. Degiovanni, B. Naydenov, F. Jelezko, M. Genovese, and P. Olivero Diamond is a promising material for innovative electronic devices, radiation detectors, and integrated platforms for quantum technologies, but with a major hurdle: Deep levels in diamond’s band gap act as charge-carrier traps, causing electric-field inhomogeneities and memory effects. Conventional techniques cannot provide a direct, unambiguous picture of the local field distribution in the defective material. This study use the sensitivity of the native nitrogen-vacancy defect itself to measure the local internal electric field, for a clear view of the inner workings of diamond devices. [Phys. Rev. Applied 10, 014024] Published Wed Jul 25, 2018

Description: Author(s): Amel Derras-Chouk, Eugene M. Chudnovsky, and Dmitry A. Garanin Large thermal fluctuations can destroy skyrmions - tiny speckles of rotated magnetization in two-dimensional films. Yet at low temperatures skyrmions are believed to be topologically stable, which makes them good candidates for data storage and processing. However, as the authors demonstrate here, even at zero temperature a nanoscale skyrmion is not protected against quantum decay. The theory is based on the imaginary-time dynamics of the skyrmion. Due to the fact that even the smallest skyrmion is still formed by many atomic spins, its quantum decay provides an example of a nanoscale Schrödinger’s cat that one can study with modern measuring techniques. [Phys. Rev. B 98, 024423] Published Wed Jul 25, 2018

Description: Author(s): Julien Garaud, Alberto Corticelli, Mihail Silaev, and Egor Babaev Disorder in two-band superconductors with repulsive interband interaction induces a frustrated competition between the phase-locking preferences of the various potential and kinetic terms. This frustrated interaction can result in the formation of an s + i s superconducting state that breaks the time-r... [Phys. Rev. B 98, 014520] Published Wed Jul 25, 2018

Description: Author(s): Hui Hu, Brendan C. Mulkerin, Jia Wang, and Xia-Ji Liu We theoretically investigate how quasiparticle properties of an attractive Fermi polaron are affected by nonzero temperature and finite impurity concentration in three dimensions and in free space. By applying both non-self-consistent and self-consistent many-body T -matrix theories, we calculate the... [Phys. Rev. A 98, 013626] Published Wed Jul 25, 2018

Description: Author(s): Tonmoy K. Bhowmick, Amrit De, and Roger K. Lake In the Kerr rotation geometry, magneto-optic memory devices typically suffer from low figure-of-merit (FOM) and long write times. We show that skyrmions formed at the interface of a thin-film multiferroic and a topological insulator can give rise to high FOM magneto-optic Kerr effects (MOKEs). Huge ... [Phys. Rev. B 98, 024424] Published Wed Jul 25, 2018

Description: Author(s): Haowen Wang, Wei Wang, Ni Hu, Tianci Duan, Songliu Yuan, Shuai Dong, Chengliang Lu, and Jun-Ming Liu Spintronics based on antiferromagnets (rather than ferromagnets) continues to garner intense interest, as antiferromagnets offer no stray fields and ultrafast spin dynamics. However, there is a significant performance gap between antiferromagnetic (AFM) insulators and metals. This study reports the remarkable electronic properties of a series of AFM doped iridates—findings that close the aforementioned performance gap, and furthermore unveil the physics of the coupling between magnetic and charge degrees of freedom in this family of transition-metal oxides. [Phys. Rev. Applied 10, 014025] Published Wed Jul 25, 2018

Description: Author(s): H. Dai et al. (Jefferson Lab Hall A Collaboration) To probe CP violation in the leptonic sector using GeV energy neutrino beams in current and future experiments using argon detectors, precise models of the complex underlying neutrino and antineutrino interactions are needed. The E12-14-012 experiment at Jefferson Lab Hall A was designed to perform ... [Phys. Rev. C 98, 014617] Published Wed Jul 25, 2018

Description: Author(s): Kai Wang, Haizhen Wu, Mengke Ge, Xingang Hou, Ning Liu, Jia He, Wei Xi, and Jun Luo It is well known that surface melting of metal materials is caused by vacancies, and melting proceeds layer by layer in theoretical predictions. However, the melting process has rarely been directly investigated in real time at atomic resolution. Herein, the (200) surface-melting process of Cu nanop... [Phys. Rev. B 98, 045425] Published Wed Jul 25, 2018

Description: Author(s): Neng Wang, Shubo Wang, Zhao-Qing Zhang, and C. T. Chan Using a multiple scattering technique, we derived closed-form expressions for effective constitutive parameters and electro/magneto-strictive tensor components for 2D bianisotropic metamaterials. Using the principle of virtual work, we obtained the electromagnetic stress tensor that can be used to c... [Phys. Rev. B 98, 045426] Published Wed Jul 25, 2018

Description: Author(s): M. Catillo and L. Ya. Glozman The chirally symmetric baryon parity-doublet model can be used as an effective description of the baryon-like objects in the chirally symmetric phase of QCD. Recently it has been found that above the critical temperature, higher chiral spin symmetries emerge in QCD. It is demonstrated here that the ... [Phys. Rev. D 98, 014030] Published Wed Jul 25, 2018

Description: Author(s): David Camarena and Valerio Marra The current 3.8 σ tension between local [A. G. Riess et al. , arXiv:1804.10655 .] and global [N. Aghanim et al. (Planck Collaboration), Astron. Astrophys. 596 , A107 (2016) .] measurements of H 0 cannot be fully explained by the concordance Λ CDM model. It could be produced by unknown systematics or by p... [Phys. Rev. D 98, 023537] Published Wed Jul 25, 2018

Description: Author(s): Rajibul Shaikh We study shadows cast by a certain class of rotating wormholes and point out the crucial role of a rotating wormhole throat in the formation of a shadow. Overlooking this crucial role of a wormhole throat has resulted in incomplete results in the previous studies on shadows of the same class of rota... [Phys. Rev. D 98, 024044] Published Wed Jul 25, 2018