bluuebunny/crossref_metadata_2025 huggingface dataset:
Biomechanics of aerial righting in wingless nymphal stick insects
Authors: Zeng Yu , Lam Kenrick , Chen Yuexiang , Gong Mengsha , Xu Zheyuan , Dudley Robert
Published: December 2016

Numerous wingless arthropods as well as diverse vertebrates are capable of mid-air righting. We studied the biomechanics of the aerial righting reflex in first-instar nymphs of the stick insectExtatosoma tiaratum. After being released upside-down, insects reoriented dorsoventrally and stabilized body posture via active modulation of limb positions and associated aerodynamic torques. We identified specific reflexes for bilaterally asymmetric leg displacements which elicit body rotation and subsequently stabilize mid-air posture. Coordinated appendicular movements thus improve torsional manoeuvrability in the absence of wings, as may have characterized the initial origins of controlled aerial behaviour in arthropods. Design of small aerial or multimodal robotic vehicles may similarly benefit from use of such strategies for flight control.
Wake analysis of drag components in gliding flight of a jackdaw (Corvus monedula) during moult
Authors: KleinHeerenbrink Marco , Hedenström Anders
Published: December 2016

To maintain the quality of the feathers, birds regularly undergo moult. It is widely accepted that moult affects flight performance, but the specific aerodynamic consequences have received relatively little attention. Here we measured the components of aerodynamic drag from the wake behind a gliding jackdaw (Corvus monedula) at different stages of its natural wing moult. We found that span efficiency was reduced (lift induced drag increased) and the wing profile drag coefficient was increased. Both effects best correlated with the corresponding reduction in spanwise camber. The negative effects are partially mitigated by adjustments of wing posture to minimize gaps in the wing, and by weight loss to reduce wing loading. By studying the aerodynamic consequences of moult, we can refine our understanding of the emergence of various moulting strategies found among birds.
Sleeping on the wing
Authors: Rattenborg Niels C.
Published: December 2016

Wakefulness enables animals to interface adaptively with the environment. Paradoxically, in insects to humans, the efficacy of wakefulness depends on daily sleep, a mysterious, usually quiescent state of reduced environmental awareness. However, several birds fly non-stop for days, weeks or months without landing, questioning whether and how they sleep. It is commonly assumed that such birds sleep with one cerebral hemisphere at a time (i.e. unihemispherically) and with only the corresponding eye closed, as observed in swimming dolphins. However, the discovery that birds on land can perform adaptively despite sleeping very little raised the possibility that birds forgo sleep during long flights. In the first study to measure the brain state of birds during long flights, great frigatebirds (Fregata minor) slept, but only during soaring and gliding flight. Although sleep was more unihemispheric in flight than on land, sleep also occurred with both brain hemispheres, indicating that having at least one hemisphere awake is not required to maintain the aerodynamic control of flight. Nonetheless, soaring frigatebirds appeared to use unihemispheric sleep to watch where they were going while circling in rising air currents. Despite being able to engage in all types of sleep in flight, the birds only slept for 0.7 h d−1during flights lasting up to 10 days. By contrast, once back on land they slept 12.8 h d−1. This suggests that the ecological demands for attention usually exceeded that afforded by sleeping unihemispherically. The ability to interface adaptively with the environment despite sleeping very little challenges commonly held views regarding sleep, and therefore serves as a powerful system for examining the functions of sleep and the consequences of its loss.
The influence of aspect ratio and stroke pattern on force generation of a bat-inspired membrane wing
Authors: Schunk Cosima , Swartz Sharon M. , Breuer Kenneth S.
Published: December 2016

Aspect ratio (AR) is one parameter used to predict the flight performance of a bat species based on wing shape. Bats with high AR wings are thought to have superior lift-to-drag ratios and are therefore predicted to be able to fly faster or to sustain longer flights. By contrast, bats with lower AR wings are usually thought to exhibit higher manoeuvrability. However, the half-span ARs of most bat wings fall into a narrow range of about 2.5–4.5. Furthermore, these predictions do not take into account the wide variation in flapping motion observed in bats. To examine the influence of different stroke patterns, we measured lift and drag of highly compliant membrane wings with different bat-relevant ARs. A two degrees of freedom shoulder joint allowed for independent control of flapping amplitude and wing sweep. We tested five models with the same variations of stroke patterns, flapping frequencies and wind speed velocities. Our results suggest that within the relatively small AR range of bat wings, AR has no clear effect on force generation. Instead, the generation of lift by our simple model mostly depends on wingbeat frequency, flapping amplitude and freestream velocity; drag is mostly affected by the flapping amplitude.
Petiolate wings: effects on the leading-edge vortex in flapping flight
Authors: Phillips Nathan , Knowles Kevin , Bomphrey Richard J.
Published: December 2016

The wings of many insect species including crane flies and damselflies are petiolate (on stalks), with the wing planform beginning some distance away from the wing hinge, rather than at the hinge. The aerodynamic impact of flapping petiolate wings is relatively unknown, particularly on the formation of the lift-augmenting leading-edge vortex (LEV): a key flow structure exploited by many insects, birds and bats to enhance their lift coefficient. We investigated the aerodynamic implications of petiolationPusing particle image velocimetry flow field measurements on an array of rectangular wings of aspect ratio 3 and petiolation values ofP= 1–3. The wings were driven using a mechanical device, the ‘Flapperatus’, to produce highly repeatable insect-like kinematics. The wings maintained a constant Reynolds number of 1400 and dimensionless stroke amplitudeΛ* (number of chords traversed by the wingtip) of 6.5 across all test cases. Our results showed that for more petiolate wings the LEV is generally larger, stronger in circulation, and covers a greater area of the wing surface, particularly at the mid-span and inboard locations early in the wing stroke cycle. In each case, the LEV was initially arch-like in form with its outboard end terminating in a focus-sink on the wing surface, before transitioning to become continuous with the tip vortex thereafter. In the second half of the wing stroke, more petiolate wings exhibit a more detached LEV, with detachment initiating at approximately 70% and 50% span forP= 1 and 3, respectively. As a consequence, lift coefficients based on the LEV are higher in the first half of the wing stroke for petiolate wings, but more comparable in the second half. Time-averaged LEV lift coefficients show a general rise with petiolation over the range tested.
Wind and water tunnel testing of a morphing aquatic micro air vehicle
Authors: Siddall Robert , Ortega Ancel Alejandro , Kovač Mirko
Published: December 2016

Aerial robots capable of locomotion in both air and water would enable novel mission profiles in complex environments, such as water sampling after floods or underwater structural inspections. The design of such a vehicle is challenging because it implies significant propulsive and structural design trade-offs for operation in both fluids. In this paper, we present a unique Aquatic Micro Air Vehicle (AquaMAV), which uses a reconfigurable wing to dive into the water from flight, inspired by the plunge diving strategy of water diving birds in the family
Sulidae
. The vehicle's performance is investigated in wind and water tunnel experiments, from which we develop a planar trajectory model. This model is used to predict the dive behaviour of the AquaMAV, and investigate the efficacy of passive dives initiated by wing folding as a means of water entry. The paper also includes first field tests of the AquaMAV prototype where the folding wings are used to initiate a plunge dive.
Aerodynamic evaluation of wing shape and wing orientation in four butterfly species using numerical simulations and a low-speed wind tunnel, and its implications for the design of flying micro-robots
Authors: Ortega Ancel Alejandro , Eastwood Rodney , Vogt Daniel , Ithier Carter , Smith Michael , Wood Rob , Kovač Mirko
Published: December 2016

Many insects are well adapted to long-distance migration despite the larger energetic costs of flight for small body sizes. To optimize wing design for next-generation flying micro-robots, we analyse butterfly wing shapes and wing orientations at full scale using numerical simulations and in a low-speed wind tunnel at 2, 3.5 and 5 m s−1. The results indicate that wing orientations which maximize wing span lead to the highest glide performance, with lift to drag ratios up to 6.28, while spreading the fore-wings forward can increase the maximum lift produced and thus improve versatility. We discuss the implications for flying micro-robots and how the results assist in understanding the behaviour of the butterfly species tested.
Flow pattern similarities in the near wake of three bird species suggest a common role for unsteady aerodynamic effects in lift generation
Authors: Gurka Roi , Krishnan Krishnamoorthy , Ben-Gida Hadar , Kirchhefer Adam J. , Kopp Gregory A. , Guglielmo Christopher G.
Published: December 2016

Analysis of the aerodynamics of flapping wings has yielded a general understanding of how birds generate lift and thrust during flight. However, the role of unsteady aerodynamics in avian flight due to the flapping motion still holds open questions in respect to performance and efficiency. We studied the flight of three distinctive bird species: western sandpiper (Calidris mauri), European starling (Sturnus vulgaris) and American robin (Turdus migratorius) using long-duration, time-resolved particle image velocimetry, to better characterize and advance our understanding of how birds use unsteady flow features to enhance their aerodynamic performances during flapping flight. We show that during transitions between downstroke and upstroke phases of the wing cycle, the near wake-flow structures vary and generate unique sets of vortices. These structures appear as quadruple layers of concentrated vorticity aligned at an angle with respect to the horizon (named ‘double branch’). They occur where the circulation gradient changes sign, which implies that the forces exerted by the flapping wings of birds are modified during the transition phases. The flow patterns are similar in (non-dimensional) size and magnitude for the different birds suggesting that there are common mechanisms operating during flapping flight across species. These flow patterns occur at the same phase where drag reduction of about 5% per cycle and lift enhancement were observed in our prior studies. We propose that these flow structures should be considered in wake flow models that seek to account for the contribution of unsteady flow to lift and drag.
Rules to fly by: pigeons navigating horizontal obstacles limit steering by selecting gaps most aligned to their flight direction
Authors: Ros Ivo G. , Bhagavatula Partha S. , Lin Huai-Ti , Biewener Andrew A.
Published: December 2016

Flying animals must successfully contend with obstacles in their natural environments. Inspired by the robust manoeuvring abilities of flying animals, unmanned aerial systems are being developed and tested to improve flight control through cluttered environments. We previously examined steering strategies that pigeons adopt to fly through an array of vertical obstacles (VOs). Modelling VO flight guidance revealed that pigeons steer towards larger visual gaps when making fast steering decisions. In the present experiments, we recorded three-dimensional flight kinematics of pigeons as they flew through randomized arrays of horizontal obstacles (HOs). We found that pigeons still decelerated upon approach but flew faster through a denser array of HOs compared with the VO array previously tested. Pigeons exhibited limited steering and chose gaps between obstacles most aligned to their immediate flight direction, in contrast to VO navigation that favoured widest gap steering. In addition, pigeons navigated past the HOs with more variable and decreased wing stroke span and adjusted their wing stroke plane to reduce contact with the obstacles. Variability in wing extension, stroke plane and wing stroke path was greater during HO flight. Pigeons also exhibited pronounced head movements when negotiating HOs, which potentially serve a visual function. These head-bobbing-like movements were most pronounced in the horizontal (flight direction) and vertical directions, consistent with engaging motion vision mechanisms for obstacle detection. These results show that pigeons exhibit a keen kinesthetic sense of their body and wings in relation to obstacles. Together with aerodynamic flapping flight mechanics that favours vertical manoeuvring, pigeons are able to navigate HOs using simple rules, with remarkable success.
Touchdown to take-off: at the interface of flight and surface locomotion
Authors: Roderick William R. T. , Cutkosky Mark R. , Lentink David
Published: December 2016

Small aerial robots are limited to short mission times because aerodynamic and energy conversion efficiency diminish with scale. One way to extend mission times is to perch, as biological flyers do. Beyond perching, small robot flyers benefit from manoeuvring on surfaces for a diverse set of tasks, including exploration, inspection and collection of samples. These opportunities have prompted an interest in bimodal aerial and surface locomotion on both engineered and natural surfaces. To accomplish such novel robot behaviours, recent efforts have included advancing our understanding of the aerodynamics of surface approach and take-off, the contact dynamics of perching and attachment and making surface locomotion more efficient and robust. While current aerial robots show promise, flying animals, including insects, bats and birds, far surpass them in versatility, reliability and robustness. The maximal size of both perching animals and robots is limited by scaling laws for both adhesion and claw-based surface attachment. Biomechanists can use the current variety of specialized robots as inspiration for probing unknown aspects of bimodal animal locomotion. Similarly, the pitch-up landing manoeuvres and surface attachment techniques of animals can offer an evolutionary design guide for developing robots that perch on more diverse and complex surfaces.
Mandibular Actinomyces osteomyelitis mimicking osteosarcoma
Authors: Lau Lawrence , Darraj Majid , Keynan Yoav
Published: December 2016

Introduction:

Actinomyces is a relatively uncommon cause of infection of the head and neck. However, its presentation is usually atypical and can be difficult to recognize. In this case report, we present the diagnostic and therapeutic challenges that can arise from cervicofacial actinomycosis.

Case presentation:

A 26-year-old woman from Northern Manitoba in her second trimester of pregnancy presented to the emergency department with a 2-month history of progressive pain and swelling of her right mandible. Imaging revealed lytic lesions involving the angle and ramus of the right mandible with possibility of osteosarcoma, and she was taken for hemimandibulectomy. Intraoperative specimens revealed Actinomyces odontolyticus. She was subsequently started on piperacillin–tazobactam that was later stepped down to amoxicillin–clavulanate with radiographic and clinical improvement of her osteomyelitis.

Conclusion:

Cervicofacial actinomycosis may mimic several neoplastic, granulomatous and infectious conditions, and often require tissue culture for diagnosis. Therapy often necessitates a combination of surgical resection and prolonged medical therapy, which is tailored to the burden of disease in the individual patient.
Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells
Authors: Böttcher Michael , Kouno Tsukasa , Madissoon Elo , Motakis Efthymios , Abugessaisa Imad , Kato Sachi , Suzuki Harukazu , Hayashizaki Yoshihide , Kasukawa Takeya , Carninci Piero , Lassmann Timo , Shin Jay W. , Plessy Charles
Published: December 2016

We used a transgenic HeLa cell line that reports cell cycle phases through fluorescent, ubiquitination-based cell cycle indicators (Fucci), to produce a reference dataset of more than 270 curated single cells. Microscopic images were taken from each cell followed by RNA-sequencing, so that single-cell expression data is associated to the fluorescence intensity of the Fucci probes in the same cell. We developed an open data management and quality control workflow that enables users to replicate the processing of the sequence and microscopic image data that we deposited in public repositories. The workflow outputs a table with metadata, that is the starting point for further studies on these data. Beyond its use for cell cycle studies, We also expect that our workflow can be adapted to other single-cell projects using a similar combination of sequencing data and fluorescence measurements.
Biodiversity of Tropical Forests
Authors: Tovo A. , Suweis S. , Formentin M. , Favretti M. , Banavar Jayanth R. , Azaele S. , Maritan A.
Published: December 2016

The quantification of tropical tree biodiversity worldwide remains an open and challenging problem. In fact, more than two-fifths of the global tree population can be found either in tropical or sub-tropical forests1, but species identities are known only for ≈ 0.000067% of the individuals in all tropical forests2. For practical reasons, biodiversity is typically measured or monitored at fine spatial scales. However, important drivers of ecological change tend to act at large scales. Conservation issues, for example, apply to diversity at global, national or regional scales. Extrapolating species richness from the local to the global scale is not straightforward. Indeed, a vast number of different biodiversity estimators have been developed under different statistical sampling frameworks3–7, but most of them have been designed for local/regional-scale extrapolations, and they tend to be sensitive to the spatial distribution of trees8, sample coverage and sampling methods9. Here, we introduce an analytical framework that provides robust and accurate estimates of species richness and abundances in biodiversity-rich ecosystems, as confirmed by tests performed on variousin silico-generated forests. The new framework quantifies the minimum percentage cover that should be sampled to achieve a given average confidence in the upscaled estimate of biodiversity. Our analysis of 15 empirical forest plots shows that previous methods10,11have systematically overestimated the total number of species and leads to new estimates of hyper-rarity10at the global scale11, known as Fisher’s paradox2. We show that hyper-rarity is a signature of critical-like behavior12in tropical forests13–15, and it provides a buffer against mass extinctions16. When biotic factors or environmental conditions change, some of these rare species are more able than others to maintain the ecosystem’s functions, thus underscoring the importance of rare species.
MECAT: an ultra-fast mapping, error correction andde novoassembly tool for single-molecule sequencing reads
Authors: Xiao Chuan-Le , Chen Ying , Xie Shang-qian , Chen Kai-Ning , Wang Yan , Luo Feng , Xie Zhi
Published: December 2016

The high computational cost of current assembly methods for the long, noisy single molecular sequencing (SMS) reads has prevented them from assembling large genomes. We introduce an ultra-fast alignment method based on a novel global alignment score. For large human SMS data, our method is 7X faster than MHAP for pairwise alignment and 15X faster than BLASR for reference mapping. We develop a Mapping, Error Correction and de novo Assembly Tool (MECAT) by integrating our new alignment and error correction methods, with the Celera Assembler. MECAT is capable of producing high qualityde novoassembly of large genome from SMS reads with low computational cost. MECAT produces reference-quality assemblies ofSaccharomyces cerevisiae,Arabidopsis thaliana,Drosophila melanogasterand reconstructs the human CHM1 genome with 15% longer NG50 in only 7600 CPU core hours using 54X SMS reads and a Chinese Han genome in 19200 CPU core hours using 102X SMS reads.
Shared Nearest Neighbor clustering in a Locality Sensitive Hashing framework
Authors: Kanj Sawsan , Brüls Thomas , Gazut Stéphane
Published: December 2016

We present a new algorithm to cluster high dimensional sequence data, and its application to the field of metagenomics, which aims to reconstruct individual genomes from a mixture of genomes sampled from an environ-mental site, without any prior knowledge of reference data (genomes) or the shape of clusters. Such problems typically cannot be solved directly with classical approaches seeking to estimate the density of clusters, e.g., using the shared nearest neighbors rule, due to the prohibitive size of contemporary sequence datasets. We explore here a new method based on combining the shared nearest neighbor (SNN) rule with the concept of Locality Sensitive Hashing (LSH). The proposed method, called LSH-SNN, works by randomly splitting the input data into smaller-sized subsets (buckets) and, employing the shared nearest neighbor rule on each of these buckets. Links can be created among neighbors sharing a sufficient number of elements, hence allowing clusters to be grown from linked elements. LSH-SNN can scale up to larger datasets consisting of millions of sequences, while achieving high accuracy across a variety of sample sizes and complexities.
Dynamic flexibility in striatal-cortical circuits supports reinforcement learning
Authors: Gerraty Raphael T. , Davidow Juliet Y. , Foerde Karin , Galvan Adriana , Bassett Danielle S. , Shohamy Daphna
Published: December 2016

Complex learned behaviors must involve the integrated action of distributed brain circuits. While the contributions of individual regions to learning have been extensively investigated, understanding how distributed brain networks orchestrate their activity over the course of learning remains elusive. To address this gap, we used fMRI combined with tools from dynamic network neuroscience to obtain time-resolved descriptions of network coordination during reinforcement learning. We found that learning to associate visual cues with reward involves dynamic changes in network coupling between the striatum and distributed brain regions, including visual, orbitofrontal, and ventromedial prefrontal cortex. Moreover, we found that flexibility in striatal network dynamics correlates with participants’ learning rate and inverse temperature, two parameters derived from reinforcement learning models. Finally, we found that not all forms of learning relate to this circuit: episodic memory, measured in the same participants at the same time, was related to dynamic connectivity in distinct brain networks. These results suggest that dynamic changes in striatal-centered networks provide a mechanism for information integration during reinforcement learning.

Significance Statement

Learning from the outcomes of actions–referred to asreinforcement learning–is an essential part of life. The roles of individual brain regions in reinforcement learning have been well characterized in terms of the updating of values for actions or sensory stimuli. Missing from this account, however, is a description of the manner in which different brain areas interact during learning to integrate sensory and value information. Here we characterize flexible striatal-cortical network dynamics that relate to reinforcement learning behavior.
Patterns of temporal and enemy niche use by a community of leaf cone moths (Caloptilia) coexisting on maples (Acer) as revealed by metabarcoding
Authors: Nakadai Ryosuke , Kawakita Atsushi
Published: December 2016

The diversity of herbivorous insects is often considered a function of host plant diversity. However, recent research has uncovered many examples of closely related herbivores using the same host plant(s), suggesting that partitioning of host plants is not the only mechanism generating diversity. Herbivores sharing hosts may utilize different parts of the same plant, but such resource partitioning is often not apparent; hence, the factors that allow closely related herbivores to coexist are still largely undetermined. We examined whether partitioning of phenology or natural enemies may explain the coexistence of leaf cone moths (Caloptilia; Gracillariidae) associated with maples(Acer;Sapindaceae). Larval activity of 10 sympatricCaloptiliaspecies found on nine maple species was monitored every 2–3 weeks for a total of 13 sampling events, and an exhaustive search for internal parasitoid wasps was conducted using high-throughput sequencing. Blocking primers were used to facilitate the detection of wasp larvae inside moth tissue. We found considerable phenological overlap amongCaloptiliaspecies, with two clear peaks in July and September–October. CoexistingCaloptiliaspecies also had largely overlapping parasitoid communities; a total of 13 wasp species belonging to four families attackedCaloptiliain a non-specific fashion at an overall parasitism rate of 46.4%. Although coexistence may be facilitated by factors not accounted for in this study, it appears that niche partitioning is not necessary for closely related herbivores to stably coexist on shared hosts. Co-occurrence without resource partitioning may provide an additional axis along which herbivorous insects attain increased species richness.
A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination
Authors: Pang Tin Yau
Published: December 2016

A frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position of two genomes in a phylogenetic reconstruction in two different ways: (i) one genome can recombine with a DNA stretch that is similar to the other genome, thereby reducing their pairwise sequence divergence; (ii) one genome can recombine with a DNA stretch from an outgroup genome, increasing the pairwise divergence. While several recombination-aware phylogenetic algorithms exist, many of these cannot account for both types of recombination; some algorithms can, but do so inefficiently. Moreover, many existing algorithms require that a substantial portion of each genome has not been affected by recombination, a sometimes unrealistic assumption. Here, we propose a novel coarse-graining approach for phylogenetic reconstruction (CGP), which is recombination-aware, applicable even if all genomic regions have experienced substantial amounts of recombination, and can be used on both nucleotide and amino acid sequences. CGP considers the local density of substitutions along pairwise genome alignments, fitting a model to the empirical distribution of substitution density to infer the pairwise coalescent time. Given all pairwise coalescent times, CGP reconstructs an ultrametric tree representing vertical inheritance. Based on simulations, we show that the proposed approach can reconstruct ultrametric trees with accurate topology, branch lengths, and root positioning. Applied to a set ofE. colistrains, the reconstructed trees are most consistent with gene distributions when inferred from amino acid sequences, a data type that cannot be utilized by many alternative approaches.

AUTHOR SUMMARY

In homologous recombination, segments of foreign DNA overwrite similar segments of a prokaryotic genome. A single recombination event can simultaneously introduce many DNA substitutions. This disturbs phylogenetic signals, making it difficult to reconstruct prokaryotic family trees. While a handful of recombination-aware phylogenetic algorithms have been proposed, most do not take all effects of recombination into account; others rely on the frequently unrealistic assumption that a substantial part of a genome has not been affected by recombination at all. Here, we introduce a novel approach to phylogenetic reconstruction, which estimates the age of the most recent common ancestor of two strains from the density distribution of DNA or amino acid substitutions between their genomes. The proposed phylogenetic tree is the tree most compatible with these age estimates. Based on nucleotide or amino acid sequences, our approach accurately predicts the topology, branch lengths, and root positioning of prokaryotic family trees.
A room-temperature ferrimagnet made of metallo-proteins?
Authors: Winklhofer Michael , Mouritsen Henrik
Published: December 2016

Qin et al. (A magnetic protein compass, Nature Materials 15, 217-226, 2016) claim that "MagR is the first known protein that carries an intrinsic magnetic moment at ambient temperature". We show here that the claim must, unfortunately, be fundamentally wrong.
Vitrification after multiple rounds of sample application and blotting improves particle density on cryo-electron microscopy grids
Authors: Snijder Joost , Borst Andrew J. , Dosey Annie , Walls Alexandra C. , Burrell Anika , Reddy Vijay S. , Kollman Justin M. , Veesler David
Published: December 2016

Single particle cryo-electron microscopy (cryoEM) is becoming widely adopted as a tool for structural characterization of biomolecules at near-atomic resolution. Vitrification of the sample to obtain a dense distribution of particles within a single field of view remains a major bottleneck for the success of such experiments. Here, we describe a simple and cost-effective method to increase the density of frozen-hydrated particles on grids with holey carbon support films. It relies on performing multiple rounds of sample application and blotting prior to plunge freezing in liquid ethane. We show that this approach is generally applicable and significantly increases particle density for a range of samples, such as small protein complexes, viruses and filamentous assemblies. The method is versatile, easy to implement, minimizes sample requirements and can enable characterization of samples that would otherwise resist structural studies using single particle cryoEM.
Co-occurring eQTLs and mQTLs: detecting shared causal variants and shared biological mechanisms
Authors: Pierce Brandon L. , Tong Lin , Argos Maria , Jasmine Farzana , Rakibuz-Zaman Muhammad , Sarwar Golam , Islam Md. Tariqul , Shahriar Hasan , Islam Tariqul , Rahman Mahfuzar , Yunus Md. , Kibriya Muhammad G. , Chen Lin S. , Ahsan Habibul
Published: December 2016

Inherited genetic variation impacts local gene expression and DNA methylation in humans. Expression and methylation quantitative trait loci (cis-eQTLs and cis-mQTLs) often occur at the same genomic location, suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, we use “co-localization” methods to identify 3,695 eQTL-mQTL pairs that are likely to share a causal variant. Using partial correlation analysis and mediation analysis, we identify >500 pairs with evidence of a causal relationships between expression and methylation (i.e., shared mechanism) with many additional pairs that we are underpowered to detect. These co-localized pairs are enriched for SNPs showing opposite effects on expression and methylation, although a many affect multiple CpGs in opposite directions. Evidence of shared SNP-age interaction also supports shared mechanisms for two eQTL-mQTL pairs. This work demonstrates the pervasiveness of co-regulated expression and methylation traits in the human genome. This approach can be applied to other types of molecular QTLs to enhance our understanding of regulatory mechanisms.
X-ray grating interferometer for in situ and at-wavelength wavefront metrology
Authors: Kayser Yves , David Christian , Flechsig Uwe , Krempasky Juraj , Schlott Volker , Abela Rafael
Published: December 2016

A wavefront metrology setup based on the X-ray grating interferometry technique for spatially resolved, quantitative, in situ and at-wavelength measurements of the wavefront at synchrotron radiation and hard X-ray free-electron laser beamlines is reported. Indeed, the ever-increasing demands on the optical components to preserve the wavefront shape and the coherence of the delivered X-ray beam call for more and more sensitive diagnostic instruments. Thanks to its angular sensitivity, X-ray grating interferometry has been established in recent years as an adequate wavefront-sensing technique for quantitatively assessing the quality of the X-ray wavefront under working conditions and hence for the in situ investigation of X-ray optical elements. In order to characterize the optical elements at any given beamline by measuring the aberrations introduced in the wavefront, a transportable X-ray grating interferometry setup was realised at the Swiss Light Source (SLS). The instrument, which is expected to be a valuable tool for investigating the quality of the X-ray beam delivered at an endstation, will be described hereafter in terms of the hardware setup and the related data analysis procedure. Several exemplary experiments performed at the X05DA Optics beamline of the SLS will be presented.
Crystal structure ofcatena-poly[[bis(N-acethylthiomorpholine-κS)copper(I)]-μ-iodido]
Authors: Chiang Hojae , Kim Tae Ho , Park Hyunjin , Kim Jineun
Published: December 2016

The reaction of copper(I) iodide withN-acetylthiomorpholine (L, C6H11NOS) in acetonitrile results in a coordination polymer with composition [CuI(L)2]n. The CuIatom is coordinated by two S atoms and two I atoms, adopting a distorted tetrahedral environment. The μ2-bridging mode of the I atoms gives rise to chains extending parallel to [010]. C—H...O hydrogen-bonding interactions between the chains lead to a three-dimensional network.
Extraction of the characteristics of current-limiting elements from field emission measurement data
Authors: Bachmann Michael , Dams Florian , Düsberg Felix , Hofmann Martin , Pahlke Andreas , Langer Christoph , Ławrowski Robert , Prommesberger Christian , Schreiner Rupert , Serbun Pavel , Lützenkirchen-Hecht Dirk , Müller Günter
Published: December 2016

In this contribution, the authors will present an algorithm to extract the characteristics of nonideal field emission circuit elements from saturation-limited field emission measurement data. The method for calculating the voltage drop on current-limiting circuit elements is based on circuit theory as well as Newton's method. Since the only assumption the authors make on the current-limiting circuit is a connection in series, this method is applicable to most field emission data showing saturation. To be able to determine the significance of any parameter output, the uncertainties of data and extracted parameters as well as the parameter correlations are fully taken into account throughout the algorithm. N-type silicon samples with varying external serial resistors are analyzed. All results show a good agreement to the nominal resistor values. Additionally, several p-type samples are analyzed, showing a diodelike behavior. The extracted current-limiting characteristics of the p-type samples are in good agreement with a pn-junction model. The stability of the emission current of the p-type samples is measured by constant voltage measurements and compared to the extracted current-limiting characteristics. The application of the algorithm to measurement data shows that the given algorithm is a valuable tool to analyze field emission measurement data influenced by nonemissive processes.
Comparison of scanning laser annealing and microwave annealing for As+ implanted Si
Authors: Zhao Zhao , Hilman Joe , Oropeza Manny , Nian Qiong , Alford Terry L.
Published: December 2016

Laser annealing and microwave (MW) annealing are rapid annealing techniques that can be used for postannealing of ion implanted semiconductors. In this study, laser annealing and MW annealing of As+ implanted Si are compared in terms of dopant activation, energy absorption, recrystallization, and dopant diffusion. Laser annealing caused similar recrystallization and a slightly higher dopant activation than MW annealing did, at the same time, the energy density absorbed during laser annealing is ∼1/7 lower than during MW annealing, due to surface heating. Rapid dopant activation and negligible dopant diffusion were achieved in the MW annealed sample. This indicates that MW annealing is a promising method for annealing ion implanted source, drain, and channel regions for shallow-junction transistor fabrication. On the other hand, laser annealing results in significant but uniform dopant diffusion, and therefore, laser annealing appears to be beneficial for quickly forming deep wells with uniform dopant concentrations for small scale wafer.
Consistent sound change between stops and affricates in Seoul Korean within and across individuals: A diachronic investigation
Authors: Lee Hyunjung
Published: December 2016

This study investigated whether sound change that Korean stops currently undergo occurred consistently for affricates at both the group and individual levels. This study compared the duration and F0 properties of Seoul Korean stops to those of the affricates produced by older and younger speakers. Group results showed consistent sound change between the two consonant manner types. In addition, individual examination indicated stability in use of duration and F0 within an individual, and enabled further understanding of the group pattern. The findings provided phonetic evidence to generalize the sound change of the stops to other Korean obstruents.
Near field acoustic holography measurements of carbon nanotube thin film speakers
Authors: Asgarisabet Mahsa , Barnard Andrew R. , Bouman Troy M.
Published: December 2016

Carbon nanotube (CNT) thin film speakers produce sound with the thermoacoustic effect. Better understanding of the physical acoustic properties of these speakers will drive future design improvements. Measuring acoustic properties at the surface of the CNT thin film is difficult because the films, themselves, do not vibrate, are fragile and have a high surface temperature. In order to measure the surface particle velocity and sound pressure level (SPL), near field acoustic holography (NAH) has been used by employing probe microphones. NAH images the acoustic quantities of the source system using the set of acoustic pressure measurements on a hologram parallel to the source surface. It is shown that the particle velocity at the surface of an open-air, double-sided speaker is nominally zero, as expected. However, the SPL distribution is not uniform on the source surface, contrary to common lumped parameter model assumptions. Also, particle velocity and sound intensity distributions on the hologram have been obtained in this study. Finally, measured directivity patterns of the planar CNT speaker are reported.
Time domain characteristics of wave motion in dispersive and anisotropic continuum acoustic metamaterials
Authors: Wang Zhaojun , Zhou Xiaoming
Published: December 2016

The authors study the wave propagation in continuum acoustic metamaterials whose all or not all of the principal elements of the mass tensor or the scalar compressibility can be negative due to wave dispersion. Their time-domain wave characteristics are particularly investigated by the finite-difference time-domain (FDTD) method, in which algorithms for the Drude and Lorentz dispersion pertinent to acoustic metamaterials are provided necessarily. Wave propagation nature of anisotropic acoustic metamaterials with all admissible material parameters are analyzed in a general manner. It is found that anomalous negative refraction phenomena can appear in several dispersion regimes, and their unique time-domain signatures have been discovered by the FDTD modeling. It is further proposed that two different metamaterial layers with specially assigned dispersions could comprise a conjugate pair that permits wave propagation only at specific points in the wave vector space. The time-domain pulse simulation verifies that acoustic directive radiation capable of modulating radiation angle with the wave frequency can be realized with this conjugate pair. The study provides the detailed analysis of wave propagation in anisotropic and dispersive acoustic mediums, which makes a further step toward dispersion engineering and transient wave control through acoustic metamaterials.
The differences in transmission properties of two bird calls show relation to their specific functions
Authors: Piza Paola , Sandoval Luis
Published: December 2016

When vocalizations transmit throughout the environment, attenuation and degradation may change the information of the signal; the loss of information is related to changes in both frequency and duration of vocalizations. The variation in frequency and duration of bird calls is related to the functions of each call type. Using a sound transmission experiment, the authors tested the transmission properties of two call types both produced by white-eared ground-sparrows Melozone leucotis; these calls vary in frequency and duration, suggesting that they may transmit at different distances. The authors broadcasted and re-recorded each call type at four different distances (4, 8, 16, and 32 m) inside ground-sparrow territories. The authors found that calls with a narrow bandwidth and longer duration transmitted at longer distances, and showed a lower attenuation and degradation than the calls with a broad bandwidth and shorter duration. These results support the relationship between the transmission properties of a call and the different functions (short and long distance communication) also evidence how the selection of these calls facilitates the communication over different distances.
ATP-driven calcium transport in membrane vesicles of Streptococcus sanguis
Authors: Houng H S , Lynn A R , Rosen B P
Published: December 2016

Calcium transport was investigated in membrane vesicles prepared from the oral bacterium Streptococcus sanguis. Procedures were devised for the preparation of membrane vesicles capable of accumulating 45Ca2+. Uptake was ATP dependent and did not require a proton motive force. Calcium transport in these vesicles was compared with 45Ca2+ accumulation in membrane vesicles from Streptococcus faecalis and Escherichia coli. The data support the existence of an ATP-driven calcium pump in S. sanguis similar to that in S. faecalis. This pump, which catalyzes uptake into membrane vesicles, would be responsible for extrusion of calcium from intact cells.
Complete nucleotide sequence and transcription of ermF, a macrolide-lincosamide-streptogramin B resistance determinant from Bacteroides fragilis
Authors: Rasmussen J L , Odelson D A , Macrina F L
Published: December 2016

DNA sequence analysis of a portion of an EcoRI fragment of the Bacteroides fragilis R plasmid pBF4 has allowed us to identify the macrolide-lincosamide-streptogramin B resistance (MLSr) gene, ermF. ermF had a relative moles percent G + C of 32, was 798 base pairs in length, and encoded a protein of approximately 30,360 daltons. Comparison between the deduced amino acid sequence of ermF and six other erm genes from gram-positive bacteria revealed striking homologies among all of these determinants, suggesting a common origin. Based on these and other data, we believe that ermF codes for an rRNA methylase. Analysis of the nucleotide sequences upstream and downstream from the ermF gene revealed the presence of directly repeated sequences, now identified as two copies of the insertion element IS4351. One of these insertion elements was only 26 base pairs from the start codon of ermF and contained the transcriptional start signal for this gene as judged by S1 nuclease mapping experiments. Additional sequence analysis of the 26 base pairs separating ermF and IS4351 disclosed strong similarities between this region and the upstream regulatory control sequences of ermC and ermA (determinants of staphylococcal origin). These results suggested that ermF was not of Bacteroides origin and are discussed in terms of the evolution of ermF and the expression of drug resistance in heterologous hosts.
Molecular cloning of structural and regulatory hydrogenase (hox) genes of Alcaligenes eutrophus H16
Authors: Eberz G , Hogrefe C , Kortlüke C , Kamienski A , Friedrich B
Published: December 2016

A gene bank of the 450-kilobase (kb) megaplasmid pHG1 from the hydrogen-oxidizing bacterium Alcaligenes eutrophus H16 was constructed in the broad-host-range mobilizable vector pSUP202 and maintained in Escherichia coli. hox DNA was identified by screening the E. coli gene bank for restoration of hydrogenase activity in A. eutrophus Hox mutants. Hybrid plasmids that contained an 11.6-kb EcoRI fragment restored soluble NAD-dependent hydrogenase activity when transferred by conjugation into one class of Hos- mutants. An insertion mutant impaired in particulate hydrogenase was partially restored in Hop activity by an 11-kb EcoRI fragment. A contiguous sequence of two EcoRI fragments of 8.6 and 2.0 kb generated Hox+ recombinants from mutants that were devoid of both hydrogenase proteins. hox DNA was subcloned into the vector pVK101. The resulting recombinant plasmids were used in complementation studies. The results indicate that we have cloned parts of the structural genes coding for Hos and Hop activity and a complete regulatory hox DNA sequence which encodes the thermosensitive, energy-dependent derepression signal of hydrogenase synthesis in A. eutrophus H16.
Control of bacteriochlorophyll accumulation by light in Rhodobacter capsulatus
Authors: Biel A J
Published: December 2016

The accumulation of bacteriochlorophyll in Rhodobacter capsulatus grown either anaerobically or under low aeration is repressed by bright light. It has been proposed that an intact photosynthetic membrane system is required for light-mediated regulation. This was tested by measuring bacteriochlorophyll accumulation in various mutant strains grown under 3% oxygen. Mutants lacking either the reaction center and B875 complexes or the B800-850 complex exhibited normal regulation of bacteriochlorophyll accumulation by light, suggesting that neither photosynthesis nor the photosynthetic membrane system is involved in light-mediated regulation. Bright light did not reduce transcription from the bchA, bchC, bchE, or bchF gene. Neither a bch+ strain nor bchG or bchH mutants accumulated greater than normal amounts of any bacteriochlorophyll precursor when grown in bright light, indicating that carbon flow over the bacteriochlorophyll biosynthetic pathway was not being regulated by light intensity. When exposed to bright light, R. capsulatus converted aminolevulinate into a colorless compound with Rf values very similar to those of bacteriochlorophyll. These results suggest that in strains grown under low aeration, light intensity controls bacteriochlorophyll accumulation, but does not control bacteriochlorophyll synthesis.
Plasmid establishment in competent Haemophilus influenzae occurs by illegitimate transformation
Authors: Pifer M L
Published: December 2016

Establishment of plasmids in naturally competent Haemophilus influenzae is incompatible with transformation via the normal DNA translocation pathways. Instead, establishing plasmids appear to evade the degradation which ordinarily accompanies translocation, arriving as intact double-stranded molecules in the cytoplasm. Evidence is presented that plasmid establishment is a rare illegitimate transformation event which resembles artificial transformation. This process is compared with plasmid marker rescue transformation, and a method for greatly increasing establishment frequency is described.