bluuebunny/crossref_metadata_2025 huggingface dataset:
Homogeneous dielectric barrier discharges in atmospheric air and its influencing factor
Authors: Ran Junxia , Li Caixia , Ma Dong , Luo Haiyun , Li Xiaowei
Published: March 2018

The stable homogeneous dielectric barrier discharge (DBD) is obtained in atmospheric 2–3 mm air gap. It is generated using center frequency 1 kHz high voltage power supply between two plane parallel electrodes with specific alumina ceramic plates as the dielectric barriers. The discharge characteristics are studied by a measurement of its electrical discharge parameters and observation of its light emission phenomena. The results show that a large single current pulse of about 200 μs duration appearing in each voltage pulse, and its light emission is radially homogeneous and covers the entire surface of the two electrodes. The homogeneous discharge generated is a Townsend discharge during discharge. The influences of applied barrier, its thickness, and surface roughness on the transition of discharge modes are studied. The results show that it is difficult to produce a homogeneous discharge using smooth plates or alumina plate surface roughness Ra < 100 nm even at a 1 mm air gap. If the alumina plate is too thin, the discharge also transits to filamentary discharge. If it is too thick, the discharge is too weak to observe. With the increase of air gap distance and applied voltage, the discharge can also transit from a homogeneous mode to a filamentary mode. In order to generate stable and homogeneous DBD at a larger air gap, proper dielectric material, dielectric thickness, and dielectric surface roughness should be used, and proper applied voltage amplitude and frequency should also be used.
Experimental and ab initio study of Mg doping in the intrinsic ferromagnetic semiconductor GdN
Authors: Lee C.-M. , Schacht J. , Warring H. , Trodahl H. J. , Ruck B. J. , Vézian S. , Gaston N. , Natali F.
Published: March 2018

We report persistent photoconductivity in Mg-doped GdN thin films grown by molecular beam epitaxy. Temperature-dependent measurements were carried out in the time and frequency domains to probe the nature of Mg impurities in GdN. The results reveal an initial fast decay followed by a slow persistent photoconductivity. The magnitude of the photoconductivity as well as the characteristic fast- and slow-decay times was found to decrease systematically with increasing the Mg-doping level. Our experimental results suggest that Mg impurities in epitaxial GdN thin films act as acceptor-like centres. Interestingly they also show that the incorporation of Mg result in a significant decrease in the concentration of nitrogen vacancies, as is demonstrated also to be in agreement with an ab initio calculation.
Inertial migration of particles in Taylor-Couette flows
Authors: Majji Madhu V. , Morris Jeffrey F.
Published: March 2018

An experimental study of inertial migration of neutrally buoyant particles in the circular Couette flow (CCF), Taylor vortex flow (TVF) and wavy vortex flow (WVF) is reported. This work considers a concentric cylinder Taylor-Couette device with a stationary outer cylinder and rotating inner cylinder. The device has a radius ratio of η = ri/ro = 0.877, where ri and ro are the inner and outer radii of the flow annulus. The ratio of the annular width between the cylinders (δ = ro − ri) and the particle diameter (dp) is α = δ/dp = 20. For η = 0.877, the flow of a Newtonian fluid undergoes transitions from CCF to TVF and TVF to WVF at Reynolds numbers Re = 120 and 151, respectively, and for the dilute suspensions studied here, these critical Reynolds numbers are almost unchanged. In CCF, particles were observed to migrate, due to the competition between the shear gradient of the flow and the wall interactions, to an equilibrium location near the middle of the annulus with an offset toward the inner cylinder. In TVF, the vortex motion causes the particles to be exposed to the shear gradient and wall interactions in a different manner, resulting in a circular equilibrium region in each vortex. The radius of this circular region grows with increase in Re. In WVF, the azimuthal waviness results in fairly well-distributed particles across the annulus.
Flexural resonance mechanism of thermal transport across graphene-SiO2 interfaces
Authors: Ong Zhun-Yong , Qiu Bo , Xu Shanglong , Ruan Xiulin , Pop Eric
Published: March 2018

Understanding the microscopic mechanism of heat dissipation at the dimensionally mismatched interface between a two-dimensional (2D) crystal and its substrate is crucial for the thermal management of devices based on 2D materials. Here, we study the lattice contribution to thermal (Kapitza) transport at graphene-SiO2 interfaces using molecular dynamics (MD) simulations and non-equilibrium Green's functions (NEGF). We find that 78 percent of the Kapitza conductance is due to sub-20 THz flexural acoustic modes, and that a resonance mechanism dominates the interfacial phonon transport. MD and NEGF estimate the classical Kapitza conductance to be hK ≈ 10 to 16 MW K−1 m−2 at 300 K, respectively, consistent with existing experimental observations. Taking into account quantum mechanical corrections, this value is approximately 28% lower at 300 K. Our calculations also suggest that hK scales as T2 at low temperatures (T < 100 K) due to the linear frequency dependence of phonon transmission across the graphene-SiO2 interface at low frequencies. Our study sheds light on the role of flexural acoustic phonons in heat dissipation from graphene to its substrate.
Dielectric properties of magnetorheological elastomers with different microstructure
Authors: Moucka R. , Sedlacik M. , Cvek M.
Published: March 2018

Composite materials containing magnetic particles organised within the polymer matrix by the means of an external magnetic field during the curing process were prepared, and their dielectric properties were compared with their isotropic analogues of the same filler concentration but homogeneous spatial distribution. A substantial dielectric response observed for anisotropic systems in a form of relaxation processes was explained as charge transport via the mechanism of variable range hopping. The changes in registered relaxations' critical frequency and shape of dielectric spectra with the filler concentration were discussed in terms of decreasing anisotropy of the system. The knowledge of the dielectric response of studied systems is essential for their practical applications such as piezoresistive sensors or radio-absorbing materials.
SKPM study on organic-inorganic perovskite materials
Authors: Song Kena , Wu Yinghui , Chen Xi , He Yi , Liu Liyu , Chen Guo , Liu Ruchuan
Published: March 2018

We report Atomic Force Microscopy (AFM) and Scanning Kelvin Probe Microscopy (SKPM) studies on the surface morphology and surface potential properties of CH3NH3PbI3, CH3NH3PbI3-xClx, CH3NH3PbI3-xBrx and CH3NH3PbBr3-xClx, respectively. For CH3NH3PbI3 rod structure, its surface potential is independent of the precursor concentration, suggesting a robust electronic feature. Surface potential studies of CH3NH3PbI3 particle reveal that the Fermi level within CH3NH3PbI3 is strongly influenced by the substrate. In the case of CH3NH3PbI3-xClx, its surface potential depends on precursor concentrations and we suspect that chlorine concentrated solutions might lead to more chlorine incorporation in the final products, thus lowering its Fermi level. Also, we studied the surface potentials of CH3NH3PbI3-xBrx and CH3NH3PbBr3-xClxwith specified halide ratios. The surface potential differences between different samples are related to their work function variations. These results are helpful to the understanding of the structural and electronic properties of perovskite materials.
Air-stable memory array of bistable rectifying diodes based on ferroelectric-semiconductor polymer blends
Authors: Kumar Manasvi , Sharifi Dehsari Hamed , Anwar Saleem , Asadi Kamal
Published: March 2018

Organic bistable diodes based on phase-separated blends of ferroelectric and semiconducting polymers have emerged as promising candidates for non-volatile information storage for low-cost solution processable electronics. One of the bottlenecks impeding upscaling is stability and reliable operation of the array in air. Here, we present a memory array fabricated with an air-stable amine-based semiconducting polymer. Memory diode fabrication and full electrical characterizations were carried out in atmospheric conditions (23 °C and 45% relative humidity). The memory diodes showed on/off ratios greater than 100 and further exhibited robust and stable performance upon continuous write-read-erase-read cycles. Moreover, we demonstrate a 4-bit memory array that is free from cross-talk with a shelf-life of several months. Demonstration of the stability and reliable air operation further strengthens the feasibility of the resistance switching in ferroelectric memory diodes for low-cost applications.
KH2PO4 single crystals activated with the Ti4+ ions in the form of TiO2−x × nH2O nanoparticles: Structural peculiarities, point defects, and dielectric properties
Authors: Kuz'micheva Galina M. , Timaeva Olesya I. , Kaurova Irina A. , Svetogorov Roman D. , Mühlbauer Martin J.
Published: March 2018

Potassium dihydrogen phosphate KH2PO4 (KDP) single crystals activated with Ti4+ ions in the form of TiO2−x × nH2O nanoparticles in the η-phase, synthesized by the sulfate method using TiOSO4 × хH2SO4 × yH2O, have been first grown by the temperature lowering method and cut from pyramidal (P) and prismatic (Pr) growth sectors. The first-performed neutron powder diffraction investigation of P and Pr samples cut from the KDP:Ti4+ crystal allowed us to reveal vacancies in the K and H sites for both samples, their number being larger in the Pr structure compared to the P one. Taking into account the deficiency of the K and H sites, full occupation of the O site, presence of Ti4+ ions in the structure, and the electroneutrality condition, a partial substitution of (PO4)3− anion by the (SO4)2− one, larger for the Pr sample, was observed. The real compositions of P and Pr samples, correlated with the cation-anion internuclear distances, were refined. The dielectric permittivity of the Pr sample was significantly lower than that of the P one; it decreases with decreasing К–O, P–O, and O···H distances and increasing deficiency of the K and H sites.
Energy partitioning at low temperatures in broiler breeders
Authors: Nonis M. K. , Gous R. M.
Published: March 2018

The objective of the present study was to investigate how broiler breeder hens partition dietary metabolisable energy (ME) at low temperatures. Performance of caged broiler breeders fed equal quantities of essential nutrients (other than energy) was measured in six environmental chambers, with the temperature in each chamber being kept constant at 10°C, 12.5°C, 15°C (two chambers), 17.5°C or 20°C for two 6-week periods. Throughout these two trial periods, birds were fed 160 g/day of one of four diets containing 12.9, 11.9, 10.5 or 9.7 MJ apparent ME/kg, so that daily energy allocations ranged from 1552 to 2964 kJ/bird. Irrespective of the environmental temperature to which they were subjected, broiler breeders consumed virtually all of the feed allocated to them each day. Mean rate of lay and egg output in the final 3 weeks of each period of hens on the highest apparent ME feed was unaffected by the decrease in temperature from 19.5°C to 9.9°C, but equally depressed on the three lower energy levels. Both weight gain and egg weight increased marginally, but significantly, as the temperature decreased. As a function of body protein weight (BP, kg), egg output (EO, g/day) and growth (ΔW, g/day), the ME consumed (kJ/day) by broiler breeders over all treatments was partitioned as follows: 2423 (±30.3) BP + 7.04 (±0.41) EO + 13.5 (±1.10) ΔW. An ME intake of 1900 kJ/bird.day would appear to be adequate for broiler breeders over the range of temperatures used in the trial.
Nitrogen deposition changes the distribution of key plant species in the meadow steppe in Hulunbeier, China
Authors: Xuan Wang , Ting Wang Xin , Zhu Liang Cun , Mei Niu Yong
Published: March 2018

Improved understanding of how nutrient levels affect the distribution of plants can provide important insights into the potential impacts of increasing global nitrogen (N) deposition. We used point pattern analyses to examine the impact of nutrient addition on heterogeneity in the spatial distribution of the three main plant species of the meadow steppe community of Hulunbeier, Inner Mongolia: Leymus chinensis (Trin.) Tzvel (aka Aneurotepidimu chinense), a rhizamotous grass; Stipa baicalensis Rasher, a bunch grass; and Artemisia tanacetifolia Linn, a rhizamotous forb. The six treatments tested added nitrogen N in three different concentrations, N with phosphorus (P), P alone and a Control. Although the three plant species were randomly distributed at the start of the experiment in 2011, the spatial distribution of some species in some treatments had changed at the end of 3 years of nutrient addition. There was a significant increase in aggregation of L. chinensis at fine scales of analysis from application of N and P in tandem. However, S. baicalensis and A. tanacetifolia distributions remained random under all treatments. Positive associations of L. chinensis with S. baicalensis and with A. tanacetifolia were apparent at the lowest concentration of added N, 2.5 g N m–2 year–1, which represented an approximate doubling of global N deposition. These associations, which represent clustering among individuals of these species were also apparent where only P was applied. Negative associations, representing dispersion, were prevalent with higher N concentrations. The results indicate that increases in global N deposition up to about double current levels may have a positive influence on meadow steppe communities by increasing the niche overlap of different species. However, increases beyond that level may trigger substantial ecological change through increased competition for other, more limited, environmental resources, and disassociation between plants of the different dominant species. Our findings suggest that studies of the spatial patterning of plant communities can contribute to understanding the potential impacts of climate change.
Environmental factors affecting the germination and emergence of white horehound (Marrubium vulgare L.): a weed of arid-zone areas
Authors: Javaid Muhammad M. , Florentine Singarayer K. , Ali Hafiz H. , Chauhan Bhagirath S.
Published: March 2018

White horehound (Marrubium vulgare L.), is a troublesome weed of arid zones, particularly in cropping and grazing areas. Understanding the seed ecology of white horehound is relevant to its management. The present study investigated the effects of temperature, light, osmotic potential, salinity, pH, and seeding depth on seed germination and seedling emergence of white horehound. Seeds germinated over a wide range of temperatures, with highest germination (100%) occurring at 25/20°C in either 12-h alternating light/dark or complete darkness. Germination decreased from 92% to 10% as the osmotic potential decreased from 0 to minus 0.6 MPa and germination was completely inhibited at minus 0.8 MPa. Increasing concentration of sodium chloride (salinity) from 50 to 150 mM reduced germination from 68% to 11% but was completely inhibited at 200 mM. Germination was not limited by variation of pH in solutions of pH 5 to pH 10. Maximum germination (99%) occurred at pH 7, but slightly decreased (90%) in acidic or alkaline media. Surface located seeds were highly germinable (87%) where seedling emergence significantly declined as seeding depth increased from 0.5 to 3 cm. Nil seedling emergence was occurred at 4 cm burial depth. Light significantly affected germination, time to 50% germination, mean germination time and germination index. Increasing osmotic and salinity stress both significantly increased the time to start germination, time to 50% germination, mean germination time, but decreased germination index. Burial depth adversely affected seedling emergence with surface located seedlings emerging earlier (4.2 days) compared with 20 days for seeds buried at 3 cm. Results suggest that effective management of white horehound should consider targeting surface located seeds in combination with tools that induce minimal soil disturbance, particularly in relatively non-saline environments.
Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults
Authors: Perkins Bradley A. , Caskey C. Thomas , Brar Pamila , Dec Eric , Karow David S. , Kahn Andrew M. , Hou Ying-Chen Claire , Shah Naisha , Boeldt Debbie , Coughlin Erin , Hands Gabby , Lavrenko Victor , Yu James , Procko Andrea , Appis Julia , Dale Anders M. , Guo Lining , Jönsson Thomas J. , Wittmann Bryan M. , Bartha Istvan , Ramakrishnan Smriti , Bernal Axel , Brewer James B. , Brewerton Suzanne , Biggs William H. , Turpaz Yaron , Venter J. Craig
Published: March 2018

Significance

Advances in technology are enabling evaluation for prevention and early detection of age-related chronic diseases associated with premature mortality, such as cancer and cardiovascular diseases. These diseases kill about one-third of men and one-quarter of women between the ages of 50 and 74 years old in the United States. We used whole-genome sequencing, advanced imaging, and other clinical testing to screen 209 active, symptom-free adults. We identified a broad set of complementary age-related chronic disease risks associated with premature mortality.
Directed nucleation and growth by balancing local supersaturation and substrate/nucleus lattice mismatch
Authors: Li L. , Fijneman A. J. , Kaandorp J. A. , Aizenberg J. , Noorduin W. L.
Published: March 2018

Significance

The energy barrier for a classical heterogeneous crystal nucleation can be controlled by the energy contributions from the substrate/nucleus interface and local supersaturation. Exerting control over crystal growth thus requires modifying either one of these terms. We here introduce a strategy to modulate the contributions of both parameters simultaneously using substrates containing different crystal structures of calcium carbonate. Based on a theoretical analysis, we program both the positioning and growth direction of carbonate salts on preselected polymorphs. These findings may hold relevance for understanding, mimicking, and ultimately expanding upon nature’s mineralization strategies and for developing functional microscale materials.
Spatially disaggregated population estimates in the absence of national population and housing census data
Authors: Wardrop N. A. , Jochem W. C. , Bird T. J. , Chamberlain H. R. , Clarke D. , Kerr D. , Bengtsson L. , Juran S. , Seaman V. , Tatem A. J.
Published: March 2018

Population numbers at local levels are fundamental data for many applications, including the delivery and planning of services, election preparation, and response to disasters. In resource-poor settings, recent and reliable demographic data at subnational scales can often be lacking. National population and housing census data can be outdated, inaccurate, or missing key groups or areas, while registry data are generally lacking or incomplete. Moreover, at local scales accurate boundary data are often limited, and high rates of migration and urban growth make existing data quickly outdated. Here we review past and ongoing work aimed at producing spatially disaggregated local-scale population estimates, and discuss how new technologies are now enabling robust and cost-effective solutions. Recent advances in the availability of detailed satellite imagery, geopositioning tools for field surveys, statistical methods, and computational power are enabling the development and application of approaches that can estimate population distributions at fine spatial scales across entire countries in the absence of census data. We outline the potential of such approaches as well as their limitations, emphasizing the political and operational hurdles for acceptance and sustainable implementation of new approaches, and the continued importance of traditional sources of national statistical data.
Flexible egocentric and allocentric representations of heading signals in parietal cortex
Authors: Chen Xiaodong , DeAngelis Gregory C. , Angelaki Dora E.
Published: March 2018

Significance

Body-centered (egocentric) and world-centered (allocentric) spatial reference frames are both important for spatial navigation. We have previously shown that vestibular heading signals, which are initially coded in a head-centered reference frame, are no longer head-centered in the ventral intraparietal (VIP) area, but instead are represented in either a body- or world-centered frame, as the two frames were not dissociated. Here, we report a flexible switching between egocentric and allocentric reference frames in a subpopulation of VIP neurons, depending on gaze strategy. Other VIP neurons continue to represent heading in a body-centered reference frame despite changes in gaze strategy. These findings suggest that the vestibular representation of heading in VIP is dynamic and may be modulated by task demands.
Full superconducting dome of strong Ising protection in gated monolayer WS
2
Authors: Lu Jianming , Zheliuk Oleksandr , Chen Qihong , Leermakers Inge , Hussey Nigel E. , Zeitler Uli , Ye Jianting
Published: March 2018

Significance

Compared with 3D superconductors, atomically thin superconductors are expected to be easier to engineer for electronic applications. Here, we use field effect gating to induce superconductivity in a monolayer semiconducting transition metal dichalcogenide, WS
2
, grown by chemical vapor deposition. The remarkable doping range allows access to a cascade of electronic phases from a band insulator, a superconductor, to a reentrant insulator at high doping. The large spin-orbit coupling of ∼30 meV makes the Ising paring in WS
2
arguably the most strongly protected superconducting state against external magnetic field. The wide tunability revealed by spanning over a complete superconducting dome paves the way for the integration of monolayer superconductors to functional electronic devices exploiting the field effect control of quantum phases.
Ligand channel in pharmacologically stabilized rhodopsin
Authors: Mattle Daniel , Kuhn Bernd , Aebi Johannes , Bedoucha Marc , Kekilli Demet , Grozinger Nathalie , Alker Andre , Rudolph Markus G. , Schmid Georg , Schertler Gebhard F. X. , Hennig Michael , Standfuss Jörg , Dawson Roger J. P.
Published: March 2018

Significance

A substantial number of known genetic disorders have their origin in mutations that cause misfolding or dysfunction of G protein-coupled receptors (GPCRs). Pharmacological chaperones can rescue such mutant receptors from the endoplasmic reticulum by stabilizing protein conformations that support trafficking into the target membrane. Rhodopsin-mediated retinitis pigmentosa is a misfolding disease that might be targeted by PCs. Here we present a structure-based drug design approach to identify nonretinal compounds that bind and stabilize the receptor. Surprisingly, selected hits induce a previously unknown conformation of the seven-transmembrane helix bundle. Our study thus provides a remarkable example for compound class discovery and for the adaptability of GPCRs to chemically diverse ligands.
Ultrastructure of
Shewanella oneidensis
MR-1 nanowires revealed by electron cryotomography
Authors: Subramanian Poorna , Pirbadian Sahand , El-Naggar Mohamed Y. , Jensen Grant J.
Published: March 2018

Significance

Recent findings from in vivo fluorescence and immunolabeling measurements hinted at the possible role of outer membrane (OM) extensions as
Shewanella oneidensis
MR-1 nanowires. However, a detailed understanding of the architecture and electron transport mechanism along OM extensions was lacking. In this work, we report a unique setup for correlative light and electron microscopy of
Shewanella
OM extensions and demonstrate that they are chains of interconnected outer membrane vesicles with densities, consistent with periplasmic and OM cytochromes, distributed along their length. We propose, based on the packing density of cytochromes measured from electron cryotomograms, that the electron transport mechanism involves a combination of direct electron hopping and diffusion of electron carriers.
Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys
Authors: Holland Stephen J. , Berghuis Lesley M. , King Justin J. , Iyer Lakshminarayan M. , Sikora Katarzyna , Fifield Heather , Peter Sarah , Quinlan Emma M. , Sugahara Fumiaki , Shingate Prashant , Trancoso Inês , Iwanami Norimasa , Temereva Elena , Strohmeier Christine , Kuratani Shigeru , Venkatesh Byrappa , Evanno Guillaume , Aravind L. , Schorpp Michael , Larijani Mani , Boehm Thomas
Published: March 2018

Significance

Cytidine deaminases of the AID/APOBEC family mutate the genetic material of pathogens or contribute to the generation and diversification of antibody repertoires in jawed vertebrates. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the somatic diversification of variable lymphocyte receptor (VLR) repertoires. We discovered an unexpected diversity of cytidine deaminase genes within and among lamprey species. The cytidine deaminases with features comparable to jawed vertebrate AID are always present, suggesting that they are involved in essential processes, such as VLR assembly. In contrast, other genes show a remarkable copy number variation, like the APOBEC3 genes in mammals. This suggests an unexpected similarity in functional deployment of AID/APOBEC cytidine deaminases across all vertebrates.
Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity
Authors: Krishnan Arunkumar , Iyer Lakshminarayan M. , Holland Stephen J. , Boehm Thomas , Aravind L.
Published: March 2018

Significance

Mutagenic AID/APOBEC deaminases (AADs) are central to processes such as generation of antibody diversity and antiviral defense in vertebrates. Their presence and role outside vertebrates are poorly characterized. We report the discovery of several AADs, including some that are secreted, across diverse metazoan, dictyosteliid, and algal lineages. They appear to have emerged from an early transfer of an AAD from bacterial toxin systems, followed by extensive diversification into multiple eukaryotic clades, showing dramatic structural innovation, rapid divergence, gene loss, polymorphism, and lineage-specific expansions. We uncover evidence for their divergence in arms-race scenarios with viruses and genomic retroelements and show that AAD-based nucleic acid mutagenesis as a basis of immune defense is widespread across metazoa, slime molds, and algae.
The role of consolidation in learning context-dependent phonotactic patterns in speech and digital sequence production
Authors: Anderson Nathaniel D. , Dell Gary S.
Published: March 2018

Significance

Language is among the most important things humans learn. It has long been debated about the extent to which language learning employs mechanisms that may not apply in nonlinguistic domains. The current work uses a metaanalysis to document an important property of how speakers learn novel simple and complex rules about how consonants and vowels form syllables: The simple rules are learned quickly, but the complex ones require a consolidation period before they influence behavior. It is then demonstrated that similar results are seen in the learning of sequential patterns of responses made with fingers and thumbs. Thus, an important property of language learning was demonstrated in a nonlinguistic domain, suggesting that some relevant learning mechanisms are domain-general.
Glucagon contributes to liver zonation
Authors: Cheng Xiping , Kim Sun Y. , Okamoto Haruka , Xin Yurong , Yancopoulos George D. , Murphy Andrew J. , Gromada Jesper
Published: March 2018

Significance

The lobules are the functional units of the liver. They consist of 15–25 layers of hepatocytes with specialized metabolic functions and gene expression patterns relative to their position along the lobule, a phenomenon referred to as metabolic zonation. The Wnt/β-catenin pathway regulates hepatocyte function but how the zonation is controlled to meet the metabolic demands of the liver is unclear. Glucagon regulates hepatic function. We now demonstrate that glucagon contributes to liver zonation by interacting and opposing the actions of the Wnt/β-catenin pathway.
Identification of a queen and king recognition pheromone in the subterranean termite
Reticulitermes flavipes
Authors: Funaro Colin F. , Böröczky Katalin , Vargo Edward L. , Schal Coby
Published: March 2018

Significance

Understanding the mechanisms that social insects use to communicate their individual status within the colony is vital to understanding the evolution of sociality. This study accomplishes this goal by identifying a royal-recognition pheromone in termites, as well as a king pheromone. Our behavioral assay defines royal-specific responses for one species of termites, which will foster future studies of termite behavior. This study also dates cuticular hydrocarbons as royal pheromones to the rise of termites ∼150 million years ago, suggesting that termites and social Hymenoptera convergently evolved the use of these ubiquitous compounds for communication. In conclusion, we have expanded our understanding of chemically mediated royal recognition in termites and helped to understand the evolution of insect societies.
mTOR signaling in VIP neurons regulates circadian clock synchrony and olfaction
Authors: Liu Dong , Stowie Adam , de Zavalia Nuria , Leise Tanya , Pathak Salil Saurav , Drewes Lester R. , Davidson Alec J. , Amir Shimon , Sonenberg Nahum , Cao Ruifeng
Published: March 2018

Significance

The mammalian/mechanistic target of rapamycin (mTOR) kinase resides at the crux of an intracellular signaling network that controls fundamental biological processes. Dysregulation of mTOR signaling is linked to neurological and psychiatric diseases. However, the physiological functions of mTOR signaling in the adult brain are not fully understood. In the current study, we discovered that mTOR in vasoactive intestinal peptide (VIP) neurons plays a key role in regulating neurophysiology in the brain circadian clock and the olfactory system. The conditional
mTOR
knockout mouse will be a useful model for future investigations of mTOR and/or VIP.
Monoterpenyl esters in juvenile mountain pine beetle and sex-specific release of the aggregation pheromone
trans
-verbenol
Authors: Chiu Christine C. , Keeling Christopher I. , Bohlmann Joerg
Published: March 2018

Significance

trans
-Verbenol is a critical aggregation pheromone of the female mountain pine beetle. It is derived from a compound of the host defense, the monoterpene α-pinene. We found that beetles accumulate monoterpenyl esters during early life stages. These may serve as a previously unknown reservoir for the sex-specific release of aggregation pheromone when female beetles synchronize the mass colonization of a new host tree. The improved knowledge of the mountain pine beetle pheromone system can inform prediction of bark beetle outbreaks and invasion of new habitats.
Local growth rules can maintain metabolically efficient spatial structure throughout growth
Authors: Guo Yipei , Tikhonov Mikhail , Brenner Michael P.
Published: March 2018

Significance

In many biological systems, efficient implementation of a multistep chemical reaction is achieved by an ordered spatial arrangement of individual reaction units. How can independently acting agents assemble into such a structure, and how much communication between them is required? We consider a model of a metabolically coupled multispecies bacterial colony and show that surprisingly simple threshold-based responses to local environment are sufficient to assemble a wide variety of structures. We also predict when additional signaling mechanisms between cells may be required.
Nation, national remembrance, and education — Polish schools as factories of nationalism and prejudice
Authors: Żuk Piotr
Published: March 2018

This article describes and attempts to explain the reasons for the conservative and nationalist character of Polish schools. The author uses data from surveys, analyzes political programs, postulates concerning education put forward by conservatives, and quotes poems emphasizing national identity from textbooks used at schools to teach reading skills. According to the author, it can be observed that nationalists build an atmosphere of aversion to immigrants, which affects racism in the school hallways. The article also presents the phenomenon of so-called school chambers of national remembrance, which are part of patriotic rituals practiced by Polish society. The author emphasizes that nationalism is the basis for changes in history programs of study, which are part of the educational reform implemented by the Law and Justice (Prawo i Sprawiedliwość — PiS) government. The cultural soft power, which is used to make reality more “national,” complements the administrative and political hard power of the PiS party — both tools are used to create an authoritarian-nationalist vision of social order.
Concrete slab ford crossing – An anthropogenic factor modifying aquatic invertebrate communities
Authors: Bylak Aneta , Kukuła Krzysztof
Published: March 2018

Unimproved fords provide an easy and inexpensive method of stream crossing. However, vehicles compact the stream bottom and flatten the banks. One simple and relatively permanent solution to this problem is the use of concrete slabs, which can hinder the movement of fish and invertebrates, especially in the presence of low water levels. Although the impact of fords on the stream invertebrate fauna seems clear, there is little available data on this topic, as most reports instead focus on water quality. The impact of a concrete slab ford on the invertebrate fauna of a foothill stream was examined which led to the hypothesis that the benthic invertebrates inhabiting the ford and stream sections immediately upstream and downstream of the crossing would differ significantly from those at a non-transformed natural site. Results revealed that the invertebrate fauna in the vicinity of the ford was altered over relatively long stream sections. The ford disrupted the natural balance between deposition and erosion, with the former dominating above the ford and the latter dominating below the crossing. In small streams, where there are often several similar crossings, this effect would likely be multiplied. The ford's interference in the stream's natural balance between deposition and erosion caused a change in the grain size of the substrate and altered the available organic matter, which directly affected the qualitative and quantitative composition of the macrozoobenthos. As the habitat becomes more homogeneous, the community of invertebrates becomes less diverse. Our results can support management decisions for erosion control.
Endocytosis sustains release at photoreceptor ribbon synapses by restoring fusion competence
Authors: Wen Xiangyi , Van Hook Matthew J. , Grassmeyer Justin J. , Wiesman Alex I. , Rich Grace M. , Cork Karlene M. , Thoreson Wallace B.
Published: March 2018

Endocytosis is an essential process at sites of synaptic release. Not only are synaptic vesicles recycled by endocytosis, but the removal of proteins and lipids by endocytosis is needed to restore release site function at active zones after vesicle fusion. Synaptic exocytosis from vertebrate photoreceptors involves synaptic ribbons that serve to cluster vesicles near the presynaptic membrane. In this study, we hypothesize that this clustering increases the likelihood that exocytosis at one ribbon release site may disrupt release at an adjacent site and therefore that endocytosis may be particularly important for restoring release site competence at photoreceptor ribbon synapses. To test this, we combined optical and electrophysiological techniques in salamander rods. Pharmacological inhibition of dynamin-dependent endocytosis rapidly inhibits release from synaptic ribbons and slows recovery of ribbon-mediated release from paired pulse synaptic depression. Inhibiting endocytosis impairs the ability of second-order horizontal cells to follow rod light responses at frequencies as low as 2 Hz. Inhibition of endocytosis also increases lateral membrane mobility of individual Ca2+ channels, showing that it changes release site structure. Visualization of single synaptic vesicles by total internal reflection fluorescence microscopy reveals that inhibition of endocytosis reduces the likelihood of fusion among vesicles docked near ribbons and increases the likelihood that they will retreat from the membrane without fusion. Vesicle advance toward the membrane is also reduced, but the number of membrane-associated vesicles is not. Endocytosis therefore appears to be more important for restoring later steps in vesicle fusion than for restoring docking. Unlike conventional synapses in which endocytic restoration of release sites is evident only at high frequencies, endocytosis is needed to maintain release from rod ribbon synapses even at modest frequencies.
Synthesis of reference compounds related to Chemical Weapons Convention for verification and drug development purposes – a Brazilian endeavour
Authors: Cavalcante S F A , de Paula R L , Kitagawa D A S , Barcellos M C , Simas A B C , Granjeiro J M
Published: March 2018

This paper deals with challenges that Brazilian Army Organic Synthesis Laboratory has been going through to access reference compounds related to the Chemical Weapons Convention in order to support verification analysis and for research of novel antidotes. Some synthetic procedures to produce the chemicals, as well as Quality Assurance issues and a brief introduction of international agreements banning chemical weapons are also presented.
Schistosomiasis Presenting as Recurring Sigmoid Volvulus in a Danish Man With an Inconspicuous Travel History—A Case Report
Authors: Krog Asger D , Axelsson Johanna M , Bondgaard Anna-Louise R , Kurtzhals Jørgen A
Published: March 2018

A healthy 72-year-old Danish male presenting with recurring sigmoid volvulus was found to be infested with Schistosoma mansoni. No other explanation for recurring volvulus was found. A travel history 12 years ago, which included bathing in the Botswana Okavango delta for 10 minutes, revealed the likely time and place of infection. To our knowledge, this is the first reported case of recurrent sigmoid volvulus and chronic intestinal schistosomiasis in a patient from a nonendemic area.
Evidence for sex microchromosomes in a species with temperature-influenced sex determination (Crotaphytus collaris)
Authors: Wiggins Jodie M. , Santoyo-Brito Enrique , Scales Jon B. , Fox Stanley F.
Published: March 2018

The characteristics of a species’ evolution can be powerfully influenced by its mode of sex determination and, indeed, sex determination mechanisms vary widely among eukaryotes. In non-avian reptiles, sex was long thought to be determined bimodally, either by temperature or genetics. Here we add to the growing evidence that sex determining mechanisms in reptiles fall along a continuum rather than existing as a mutually exclusive dichotomy. Using qPCR, we demonstrate that the lizard Crotaphytus collaris possesses sex-based gene dosage consistent with the presence of sex michrochromosomes, despite that extreme incubation temperatures can influence hatchling sex ratio. Our results suggest a temperature override that switches genotypic females to phenotypic males at high and low temperatures.
Multisensory expectations shape olfactory input to the brain
Authors: Czarnecki Lindsey A. , Moberly Andrew H. , Fast Cynthia D. , Turkel Daniel J. , McGann John P.
Published: March 2018

The mammalian brain interprets sensory input based on prior multisensory knowledge of the external world, but it is unknown how this knowledge influences neural processing in individual sensory modalities. We found that GABAergic periglomerular interneuron populations in the olfactory bulb endogenously respond not only to odors but also to visual, auditory, and somatosensory stimuli in waking (but not anesthetized) mice. When these stimuli predict future odors, they evoke enhanced interneuron activity during the time odor normally occurs. When expectations are violated by omitting an expected “warning tone” before an odor, odor presentation evokes a burst of interneuron activity. The resulting GABA release presynaptically suppresses neurotransmitter release from the axon terminals of olfactory sensory neurons, the cells that transduce odor in the nasal epithelium and communicate this information to the brain. Expectations, even those evoked by cues in other sensory modalities, can thus affect the very first neurons in the olfactory system.
Diverse RNA interference strategies in early-branching metazoans
Authors: Calcino Andrew D. , Fernandez-Valverde Selene L. , Taft Ryan J. , Degnan Bernard M.
Published: March 2018

Background

Micro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians – sponges, ctenophores, placozoans and cnidarians - appears to be more diverse than that of bilaterians, and includes structurally variable miR-NAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans.

Results

Here we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queens-landica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. In the ctenophore, the absence of miRNAs is confirmed and an abundance of endo-siRNAs is revealed. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs.

Conclusion

Together, these findings suggest that the last common ancestor of animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs.
Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling
Authors: Karabacak Calviello Aslihan , Hirsekorn Antje , Wurmus Ricardo , Yusuf Dilmurat , Ohler Uwe
Published: March 2018

DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBS) in regulatory regions via footprinting. Recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. However, footprinting and the impact of sequence bias have not been extensively studied for ATAC-seq. Here, we undertake a systematic comparison of the two methods and show that a modification to the ATAC-seq protocol increases its yield and its agreement with DNase-seq data from the same cell line. We demonstrate that the two methods have distinct sequence biases and correct for these protocol-specific biases when performing footprinting. Despite differences in footprint shapes, the locations of the inferred footprints in ATAC-seq and DNase-seq are largely concordant. However, the protocol-specific sequence biases in conjunction with the sequence content of TFBSs impacts the discrimination of footprint from background, which leads to one method outperforming the other for some TFs. Finally, we address the depth required for reproducible identification of open chromatin regions and TF footprints.
Growth arrest in the active rare biosphere
Authors: Hausmann Bela , Pelikan Claus , Rattei Thomas , Loy Alexander , Pester Michael
Published: March 2018

Microbial diversity in the environment is mainly concealed within the rare biosphere, which is arbitrarily defined as all species with <0.1% relative abundance. While dormancy explains a low-abundance state very well, the cellular mechanisms leading to rare but active microorganisms are not clear. We used environmental systems biology to genomically and metabolically characterize a cosmopolitan sulfate reducer that is of low abundance but highly active in peat soil, where it contributes to counterbalance methane emissions. We obtained a 98%-complete genome of this low-abundance species, Candidatus Desulfosporosinus infrequens, by metagenomics. To test for environmentally relevant metabolic activity of Ca. D. infrequens, anoxic peat soil microcosms were incubated under diverse in situ-like conditions for 36 days and analyzed by metatranscriptomics. Compared to the no-substrate control, transcriptional activity of Ca. D. infrequens increased 56- to 188-fold in incubations with sulfate and acetate, propionate, lactate, or butyrate, revealing a versatile substrate use. Cellular activation was due to a significant overexpression of genes encoding ribosomal proteins, dissimilatory sulfate reduction, and carbon-degradation pathways, but not of genes encoding DNA or cell replication. We show for the first time that a rare biosphere member transcribes metabolic pathways relevant for carbon and sulfur cycling over prolonged time periods while being growth-arrested in its lag phase.

Significance

The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat’s biomass. Dormancy or starvation are typically used to explain a low-abundance state. We show that low-abundance microorganisms can be highly metabolically active while being growth-arrested over prolonged time periods. We show that this is true for microbial keystone species, such as a cosmopolitan but low-abundance sulfate reducer in wetlands that is involved in counterbalancing greenhouse gas emission. Our results challenge the central dogmas “metabolic activity translates directly into growth” as well as “low abundance equals little ecosystem impact” and provide an important step forward in understanding rare biosphere members relevant for ecosystem functions.