bluuebunny/crossref_metadata_2025 huggingface dataset:
Slow dynamics coupled with cluster formation in ultrasoft-potential glasses
Authors: Miyazaki Ryoji , Kawasaki Takeshi , Miyazaki Kunimasa
Published: February 2019

We numerically investigate the slow dynamics of a binary mixture of ultrasoft particles interacting with the generalized Hertzian potential. If the softness parameter, α, is small, the particles at high densities start penetrating each other, form clusters, and eventually undergo the glass transition. We find multiple cluster-glass phases characterized by a different number of particles per cluster, whose boundary lines are sharply separated by the cluster size. Anomalous logarithmic slow relaxation of the density correlation functions is observed in the vicinity of these glass-glass phase boundaries, which hints the existence of the higher-order dynamical singularities predicted by the mode-coupling theory. Deeply in the cluster glass phases, it is found that the dynamics of a single particle is decoupled from that of the collective fluctuations.
Monte Carlo-based simulation of x-ray phase-contrast imaging for diagnosing cold fuel layer in cryogenic implosions
Authors: Yan Ji , Zheng Jianhua , Chen ZhongJing , Jiang Wei , Zhang Xing , Jiang Shaoen
Published: February 2019

Diagnosing the layered cryogenic DT implosions with traditional absorption based x-ray backlight radiography in inertial confinement fusion is a challenge because of the low opacity of the cold fuel. Refraction enhanced x-ray phase-contrast imaging was proposed for diagnosing optically opaque material. In this paper, A Monte Carlo tool based on Geant4 is employed to model the x-ray phase-contrast imaging for diagnosing cold fuel layer in cryogenic implosions. This model can successfully explain the x-ray phase-contrast imaging experimental results on a micro focus x-ray tube with triple-layer ablator capsules. Furthermore, the radiographs of ignition-scale capsule target is calculated. The fuel layer of DT ice can be observed with the phase contrast imaging and the image is faded using absorption imaging only. Our simulations show that the shape of cold fuel and implosion velocity can be inferred directly with the phase contrast imaging in inertial confinement fusion(ICF).
Changing available energy for extratropical cyclones and associated convection in Northern Hemisphere summer
Authors: Gertler Charles G. , O’Gorman Paul A.
Published: February 2019

Significance

Extratropical cyclones and their associated convection play a central role in the weather of the midlatitudes and are changing with global warming. By analyzing trends in the energy of the mean state of the atmosphere that is available to be converted to kinetic energy, we show how the warming and moistening of the Northern Hemisphere extratropics relates to the observed weakening of extratropical summer cyclones. We also show that the component of this energy that can be released through convection has increased, despite the weakening of extratropical cyclones. Our results provide a unified framework that illustrates how the observed weakening of the extratropical cyclones in summer can occur while at the same time convection becomes more energetic.
Tissue self-organization based on collective cell migration by contact activation of locomotion and chemotaxis
Authors: Fujimori Taihei , Nakajima Akihiko , Shimada Nao , Sawai Satoshi
Published: February 2019

Significance

Migration of cells as a group is pivotal to the making of various tissues in developing embryos; however, their complexity hinders one from identifying the exact rules. We exploited relatively simple and conditional multicellularity of the social amoebaDictyosteliumto analyze tissue patterning from bottom up by identifying the navigation rules at the individual cell level. We uncovered a guidance mechanism directed by cell–cell contact which gives rise to collective migration and competes with diffusive attractant molecules. Competition of the two directional cues forms the basis of how cells position themselves in the multicellular aggregate according to cell type. A similar scheme of collective migration and sorting may underlie patterning of other developing tissues as well as cancer invasion.
Trilobite evolutionary rates constrain the duration of the Cambrian explosion
Authors: Paterson John R. , Edgecombe Gregory D. , Lee Michael S. Y.
Published: February 2019

Trilobites are often considered exemplary for understanding the Cambrian explosion of animal life, due to their unsurpassed diversity and abundance. These biomineralized arthropods appear abruptly in the fossil record with an established diversity, phylogenetic disparity, and provincialism at the beginning of Cambrian Series 2 (∼521 Ma), suggesting a protracted but cryptic earlier history that possibly extends into the Precambrian. However, recent analyses indicate elevated rates of phenotypic and genomic evolution for arthropods during the early Cambrian, thereby shortening the phylogenetic fuse. Furthermore, comparatively little research has been devoted to understanding the duration of the Cambrian explosion, after which normal Phanerozoic evolutionary rates were established. We test these hypotheses by applying Bayesian tip-dating methods to a comprehensive dataset of Cambrian trilobites. We show that trilobites have a Cambrian origin, as supported by the trace fossil record and molecular clocks. Surprisingly, they exhibit constant evolutionary rates across the entire Cambrian, for all aspects of the preserved phenotype: discrete, meristic, and continuous morphological traits. Our data therefore provide robust, quantitative evidence that by the time the typical Cambrian fossil record begins (∼521 Ma), the Cambrian explosion had already largely concluded. This suggests that a modern-style marine biosphere had rapidly emerged during the latest Ediacaran and earliest Cambrian (∼20 million years), followed by broad-scale evolutionary stasis throughout the remainder of the Cambrian.
White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability
Authors: Marra Nicholas J. , Stanhope Michael J. , Jue Nathaniel K. , Wang Minghui , Sun Qi , Pavinski Bitar Paulina , Richards Vincent P. , Komissarov Aleksey , Rayko Mike , Kliver Sergey , Stanhope Bryce J. , Winkler Chuck , O’Brien Stephen J. , Antunes Agostinho , Jorgensen Salvador , Shivji Mahmood S.
Published: February 2019

The white shark (
Carcharodon carcharias
; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability in white and whale sharks may reflect the combined selective pressure of large genome sizes, high repeat content, high long-interspersed element retrotransposon representation, large body size, and long lifespans, represented across these two species. Molecular adaptation for wound healing was also evident, with positive selection in key genes involved in the wound-healing process, as well as Gene Ontology enrichments in fundamental wound-healing pathways. Sharks, particularly apex predators such as the white shark, are believed to have an acute sense of smell. However, we found very few olfactory receptor genes, very few trace amine-associated receptors, and extremely low numbers of G protein-coupled receptors. We did however, identify 13 copies of vomeronasal type 2 (V2R) genes in white shark and 10 in whale shark; this, combined with the over 30 V2Rs reported previously for elephant shark, suggests this gene family may underlie the keen odorant reception of chondrichthyans.
Analysis of new direct sampling indicators for far-field measurements
Authors: Harris Isaac , Kleefeld Andreas
Published: February 2019

This article focuses on the analysis of three direct sampling indicators which can be used for recovering scatterers from the far-field pattern of time-harmonic acoustic measurements. These methods fall under the category of sampling methods where an indicator function is constructed using the far-field operator. Motivated by some recent work, we study the standard indicator using the far-field operator and two indicators derived from the factorization method. We show equivalence of two indicators previously studied as well as propose a new indicator based on the Tikhonov regularization applied to the far-field equation for the factorization method. Finally, we give some numerical examples to show how the reconstructions compare to other direct sampling methods.
System based on subject-specific bands to recognize pedaling motor imagery: towards a BCI for lower-limb rehabilitation
Authors: Delisle-Rodriguez Denis , Cardoso Vivianne , Gurve Dharmendra , Loterio Flavia , Alejandra Romero-Laiseca Maria , Krishnan Sridhar , Bastos-Filho Teodiano
Published: February 2019

Objective. The aim of this study is to propose a recognition system of pedaling motor imagery for lower-limb rehabilitation, which uses unsupervised methods to improve the feature extraction, and consequently the class discrimination of EEG patterns. Approach. After applying a spectrogram based on short-time Fourier transform (SSTFT), both sparseness constraints and total power are used on the time-frequency representation to automatically locate the subject-specific bands that pack the highest power during pedaling motor imagery. The output frequency bands are employed in the recognition system to automatically adjust the cut-off frequency of a low-pass filter (Butterworth, 2nd order). Riemannian geometry is also used to extract spatial features, which are further analyzed through a fast version of neighborhood component analysis to increase the class separability. Main results. For ten healthy subjects, our recognition system based on subject-specific bands achieved mean accuracy of

and mean Kappa of

. Significance. Our approach can be used to obtain a low-cost robotic rehabilitation system based on motorized pedal, as pedaling exercises have shown great potential for improving the muscular performance of post-stroke survivors.
Completeness of representation of solutions for stationary homogeneous isotropic elastic/viscoelastic systems
Authors: Eom Junyong , Nakamura Gen
Published: February 2019

The usual Helmholtz decomposition gives a decomposition of any vector valued function into a sum of a gradient of a scalar function and a rotation of a vector valued function under some mild condition. In this paper we show that the vector valued function of the second term i.e., the divergence free part of this decomposition can be further decomposed into a sum of a vector valued function polarized in one component and the rotation of a vector valued function also polarized in the same component. Hence the divergence free part only depends on two scalar functions. We refer to this as a special Helmholtz decomposition. Further we show the so-called completeness of representation associated to this decomposition for the stationary wave field of a homogeneous, isotropic viscoelastic medium. That is, this wave field can be expressed as a special Helmholtz decomposition and each of its scalar functions satisfies a Helmholtz equation. Our completeness of representation is useful for solving boundary value problems in a cylindrical domain for several partial differential equations of systems in mathematical physics such as stationary isotropic homogeneous elastic/viscoelastic equations of a system.
Exponential decay estimates for fundamental solutions of Schrödinger-type operators
Authors: Mayboroda Svitlana , Poggi Bruno
Published: February 2019

In the present paper, we establish sharp exponential decay estimates for operator and integral kernels of the (not necessarily self-adjoint) operators

L
=
−
(
∇
−
i

a

)
T

A
(
∇
−
i

a

)
+
V

L=-(\nabla -i\mathbf {a})^TA(\nabla -i\mathbf {a})+V

. The latter class includes, in particular, the magnetic Schrödinger operator

−

(
∇
−
i

a

)

2

+
V

-\left (\nabla -i\mathbf {a}\right )^2+V

and the generalized electric Schrödinger operator

−

div 

A
∇
+
V

-\textrm {div }A\nabla +V

. Our exponential decay bounds rest on a generalization of the Fefferman–Phong uncertainty principle to the present context and are governed by the Agmon distance associated with the corresponding maximal function. In the presence of a scale-invariant Harnack inequality—for instance, for the generalized electric Schrödinger operator with real coefficients—we establish both lower and upper estimates for fundamental solutions, thus demonstrating the sharpness of our results. The only previously known estimates of this type pertain to the classical Schrödinger operator

−
Δ
+
V

-\Delta +V

.
Association of Bacterial Vaginosis and Human Papilloma Virus Infection With Cervical Squamous Intraepithelial Lesions
Authors: Dahoud Wissam , Michael Claire W , Gokozan Hamza , Nakanishi Amelia K , Harbhajanka Aparna
Published: February 2019

Objectives

Human papillomavirus (HPV) is known to be associated with squamous intraepithelial lesions (SILs). However, there is limited and conflicting literature on the relationship between bacterial vaginosis (BV) and SIL. The aim of this study is to determine the prevalence of BV and evaluate the association between BV and SIL.

Methods

A retrospective study was performed on 10,546 cases between 2012 and 2017. HPV results were available in 7,081 cases.

Results

BV was present in 17.6% of cases. There was significant association between BV, positive HPV infection, and high-grade SIL. BV patients with negative HPV infection showed more squamous abnormalities than BV-negative HPV-negative patients.

Conclusions

We found there is a significant association between BV and SIL. BV is more common among patients with HPV infection and is independently associated with squamous abnormalities in cervical smears and surgical follow-up.
Methyl Bromide Fumigation to Eliminate Thousand Cankers Disease Causal Agents from Black Walnut
Authors: Seabright Kendhl W , Myers Scott W , Fraedrich Stephen W , Mayfield Albert E , Warden Melissa L , Taylor Adam
Published: February 2019

Phytosanitary treatments for logs and barked wood products are needed to mitigate the spread of thousand cankers disease through the movement of these commodities. The disease threatens eastern black walnut (Juglans nigra L.) populations in the United States. It is caused by repeated attacks by the walnut twig beetle (Pityophthorus juglandis Blackman) and subsequent canker development caused by the fungal pathogen Geosmithia morbida M. Kolařík et al. Methyl bromide (MB) fumigations were evaluated for efficacy against P. juglandis and G. morbida in J. nigra bolts. Fumigation with 82 mg/L MB for 24 h at 4.5° C eliminated P. juglandis in J. nigra, but was ineffective against G. morbida. Subsequent experiments focused on eliminating G. morbida, but results were inconclusive because of low rates of pathogen recovery from naturally infested control bolts. Final experiments used J. nigra bolts artificially inoculated with G. morbida. Fumigations with 240 and 320 mg/L MB for 72 h at 10° C were effective in eliminating G. morbida from J. nigra bolts. Results confirm that the USDA fumigation treatment schedule for logs with the oak wilt pathogen will also mitigate the risk of spreading the thousand cankers disease vector and pathogen by movement of walnut bolts and wood products.
Monadic NM-algebras
Authors: Wang Juntao , He Pengfei , She Yanhong
Published: February 2019

In this paper, we investigate universal and existential quantifiers on NM-algebras. The resulting class of algebras will be called monadic NM-algebras. First, we show that the variety of monadic NM-algebras is algebraic semantics of the monadic NM-predicate logic. Moreover, we discuss the relationship among monadic NM-algebras, modal NM-algebras and rough approximation spaces. Second, we introduce and investigate monadic filters in monadic NM-algebras. Using them, we prove the subdirect representation theorem of monadic NM-algebras, and characterize simple and subdirectly irreducible monadic NM-algebras. Finally, we present the monadic NM-logic and prove its (chain) completeness with respect to (strong) monadic NM-algebras. These results constitute a crucial first step for providing an algebraic foundation for the monadic NM-predicate logic.
SLIPS-TENG: robust triboelectric nanogenerator with optical and charge transparency using a slippery interface
Authors: Xu Wanghuai , Zhou Xiaofeng , Hao Chonglei , Zheng Huanxi , Liu Yuan , Yan Xiantong , Yang Zhengbao , Leung Michael , Zeng Xiao Cheng , Xu Ronald X , Wang Zuankai
Published: February 2019

Energy harvesting devices that prosper in harsh environments are highly demanded in a wide range of applications ranging from wearable and biomedical devices to self-powered and intelligent systems. Particularly, over the past several years, the innovation of triboelectric nanogenerators (TENGs) that efficiently convert ambient kinetic energy of water droplets or wave power to electricity has received growing attention. One of the main bottlenecks for the practical implications of such devices originates from the fast degradation of the physiochemical properties of interfacial materials under harsh environments. To overcome these challenges, here we report the design of a novel slippery lubricant-impregnated porous surface (SLIPS) based TENG, referred to as SLIPS-TENG, which exhibits many distinctive advantages over conventional design including optical transparency, configurability, self-cleaning, flexibility, and power generation stability, in a wide range of working environments. Unexpectedly, the slippery and configurable lubricant layer not only serves as a unique substrate for liquid/droplet transport and optical transmission, but also for efficient charge transfer. Moreover, we show that there exists a critical thickness in the liquid layer, below which the triboelectric effect is almost identical to that without the presence of such a liquid film. Such an intriguing charge transparency behavior is reminiscent of the wetting transparency and van der Waals potential transparency of graphene previously reported, though the fundamental mechanism remains to be elucidated. We envision that the marriage of these two seemingly totally different arenas (SLIPS and TENG) provides a paradigm shift in the design of robust and versatile energy devices that can be used as a clean and longer-lifetime alternative in various working environments.
Occupational asthma caused by peracetic acid-hydrogen peroxide mixture
Authors: Walters G I , Burge P S , Moore V C , Thomas M O , Robertson A S
Published: February 2019

Background

Healthcare practice in the UK has moved away from using aldehyde disinfectants for the decontamination of endoscopes, in part due to the risk of respiratory sensitization. Peracetic acid (PAA) in combination with hydrogen peroxide (HP) is a commonly used alternative.

Aim

We describe a case of occupational asthma (OA) diagnosed at our specialist occupational lung disease clinic and caused by occupational exposure to PAA-HP mixture, used as a disinfectant in an endoscope washer-disinfector machine.

Case report

A 48-year-old man employed as a mycologist and environmental microbiologist at a Birmingham city hospital, UK, presented following an acute exposure to PAA-HP mixture causing lacrimation, burning optic pain and headache. He had also experienced symptoms suggestive of OA for the preceding 10 months, and the diagnosis was confirmed through OASYS analysis of serial peak expiratory flow measurements. He had been exposed to PAA-HP mixture whilst working in the endoscopy department for 12 months prior to the acute episode, and a subsequent specific inhalation challenge test was positive with a late asthmatic response to PAA-HP mixture.

Conclusion

This case provides evidence for a sensitization mechanism in OA caused by PAA-HP mixture.
Lodovico Castelvetro’s Heterodox Poetics
Authors: Leo Russ
Published: February 2019

Chapter 2 explores how the heterodox Italian critic Lodovico Castelvetro appropriated Aristotle’s Poetics to religious ends in his influential 1570 commentary, the Poetica D’Aristotele Vulgarizzata, Et Sposta, a work that is seldom recognized as pious or polemical but which revises the ancient text with an eye to its meaning and utility in Reformed contexts. Castelvetro insists, after Aristotle, that tragedy is an exacting philosophical form, and the Poetics enables him to sharpen Reformed arguments concerning faith and authority. Castelvetro also affirms the importance of performance and, against Aristotle, contends that spectacle and stage-playing are integral to tragedy insofar as they accommodate otherwise difficult or forbidding concepts to diverse audiences. Castelvetro’s is a Melanchthonian interpretation of the Poetics, foregrounding accommodation and the edifying effects of performance, distinguishing between edifying, didactic tragedies and the meager capacities of their audiences.
Checkpoint: An Innovative Programme to Navigate People Away from the Cycle of Reoffending: Implementation Phase Evaluation
Authors: Weir Kevin , Routledge Gillian , Kilili Stephanie
Published: February 2019

This study develops an evidence base for the use of deferred prosecution schemes within a police setting. Checkpoint is a voluntary adult offender deferred prosecution scheme operating in Durham Constabulary, UK. Checkpoint targets low-level offenders entering the Criminal Justice System by providing an alternative to a criminal prosecution. It offers a tailored, 4-month programme agreed through a contract. The scheme targets the reasons why offenders commit crime by assessing their individual needs in order to provide interventions. Applying theories of deterrence and desistance, we describe the process of the Checkpoint intervention and the implementation findings of the 519 offenders in the programme. The results indicate that the Checkpoint Implementation phase cohort achieved a lower re-arrest and reoffending rate in comparison to a typical Durham Out Of Court Disposal sample, at reduced harm and cost. The initial conclusions presented here establish the foundations for further research in this policy area.
A Person-Centered Prehabilitation Program Based on Cognitive-Behavioral Physical Therapy for Patients Scheduled for Lumbar Fusion Surgery: A Randomized Controlled Trial
Authors: Lotzke Hanna , Brisby Helena , Gutke Annelie , Hägg Olle , Jakobsson Max , Smeets Rob , Lundberg Mari
Published: February 2019

Background

Prehabilitation programs have led to improved postoperative outcomes in several surgical contexts, but there are presently no guidelines for the prehabilitation phase before lumbar fusion surgery.

Objective

The objective was to investigate whether a person-centered physical therapy prehabilitation program, based on a cognitive-behavioral approach, is more effective than conventional care in reducing disability and improving functioning after lumbar fusion surgery in patients with degenerative disk disease.

Design

This study was a randomized controlled trial.

Setting

The study took place at 2 private spine clinics and 1 university hospital.

Patients

We prospectively enrolled 118 patients scheduled for lumbar fusion surgery.

Intervention

The active intervention used a person-centered perspective and focused on promoting physical activity and targeting psychological risk factors before surgery. The control group received conventional preoperative care.

Measurements

The primary outcome was the Oswestry Disability Index score. Secondary outcomes were back and leg pain intensity, catastrophizing, kinesiophobia, self-efficacy, anxiety, depression, health-related quality of life, and patient-specific functioning, physical activity, and physical capacity. Data were collected on 6 occasions up to 6 months postoperatively. A linear mixed model was used to analyze the change scores of each outcome.

Results

No statistically significant between-group difference was found on the primary outcome (disability) over time (baseline to 6 months). Among secondary outcome measures, a statistically significant interaction effect (“Group × Time”) was seen for the European Quality of Life 5 Dimensions Questionnaire. The largest between-group difference on the European Quality of Life 5 Dimensions Questionnaire index was seen 1 week prior to surgery and favored the active intervention. The largest between-group effect sizes at the 6-month follow-up favored the active intervention, and were seen for physical activity intensity, steps per day, and the One Leg Stand Test. Both groups reached the minimal important change for the primary outcome and, in several secondary outcomes (pain intensity, back and leg; pain catastrophizing; anxiety; health-related quality of life [EQ5D VAS]), already at 8-week follow-up.

Limitations

The participants’ preoperative level of disability was lower than normative values, which suggests selection bias.

Conclusions

Both interventions led to clinically important changes, but it is not clear what kind of prehabilitation program is the most effective.
Ocean acidification affects somatic and otolith growth relationship in fish: evidence from an
in situ
study
Authors: Di Franco Antonio , Calò Antonio , Sdiri Khalil , Cattano Carlo , Milazzo Marco , Guidetti Paolo
Published: February 2019

Ocean acidification (OA) may have varied effects on fish eco-physiological responses. Most OA studies have been carried out in laboratory conditions without considering the
in situ p
CO
2
/pH variability documented for many marine coastal ecosystems. Using a standard otolith ageing technique, we assessed how
in situ
ocean acidification (ambient, versus end-of-century CO
2
levels) can affect somatic and otolith growth, and their relationship in a coastal fish. Somatic and otolith growth rates of juveniles of the ocellated wrasse
Symphodus ocellatus
living off a Mediterranean CO
2
seep increased at the high-
p
CO
2
site. Also, we detected that slower-growing individuals living at ambient
p
CO
2
levels tend to have larger otoliths at the same somatic length (i.e. higher relative size of otoliths to fish body length) than faster-growing conspecifics living under high
p
CO
2
conditions, with this being attributable to the so-called ‘growth effect’. Our findings suggest the possibility of contrasting OA effects on fish fitness, with higher somatic growth rate and possibly higher survival associated with smaller relative size of otoliths that could impair fish auditory and vestibular sensitivity.
Influence of aggregation on benthic coral reef spatio-temporal dynamics
Authors: Brito-Millán Marlene , Werner B. T. , Sandin Stuart A. , McNamara Dylan E.
Published: February 2019

Spatial patterning of coral reef sessile benthic organisms can constrain competitive and demographic rates, with implications for dynamics over a range of time scales. However, techniques for quantifying and analysing reefscape behaviour, particularly at short to intermediate time scales (weeks to decades), are lacking. An analysis of the dynamics of coral reefscapes simulated with a lattice model shows consistent trends that can be categorized into four stages: a repelling stage that moves rapidly away from an unstable initial condition, a transient stage where spatial rearrangements bring key competitors into contact, an attracting stage where the reefscape decays to a steady-state attractor, and an attractor stage. The transient stage exhibits nonlinear dynamics, whereas the other stages are linear. The relative durations of the stages are affected by the initial spatial configuration as characterized by coral aggregation—a measure of spatial clumpiness, which together with coral and macroalgae fractional cover, more completely describe modelled reefscape dynamics. Incorporating diffusional processes results in aggregated patterns persisting in the attractor. Our quantitative characterization of reefscape dynamics has possible applications to other spatio-temporal systems and implications for reef restoration: high initial aggregation patterns slow losses in herbivore-limited systems and low initial aggregation configurations accelerate growth in herbivore-dominated systems.
Seedless gold nanostars with seed-like advantages for biosensing applications
Authors: Phiri Masauso Moses , Mulder Danielle Wingrove , Vorster Barend Christiaan
Published: February 2019

Gold nanostars (AuNSs) are seen as promising building blocks for biosensors with potential for easy readouts based on naked-eye and ultraviolet–visible spectroscopy detection. We present a seedless synthesis strategy for AuNSs that has the advantages of the seeded methods. The method used ascorbic acid as a reducing agent and silver nitrate as an anisotropic growth control assisting agent. AuNSs with multiple branches and a diameter of 59 nm were produced. They showed good stability when capped with PVP and modified with an enzyme in relatively strong ionic conditions. We investigated their application in plasmonic sensing by modifying them with glucose oxidase and detection of glucose. The AuNSs were found to be a good scaffold for the enzyme, proved to be stable and sensitive as transducers. Thus, the AuNSs showed good promise for further applications in plasmonic biosensing for
in vivo
biomedical diagnosis.
The idemetric property: when most distances are (almost) the same
Authors: Barmpalias George , Huang Neng , Lewis-Pye Andrew , Li Angsheng , Li Xuechen , Pan Yicheng , Roughgarden Tim
Published: February 2019

We introduce theidemetricproperty, which formalizes the idea that most nodes in a graph have similar distances between them, and which turns out to be quite standard amongst small-world network models. Modulo reasonable sparsity assumptions, we are then able to show that a strong form of idemetricity is actually equivalent to a very weak expander condition (PUMP). This provides a direct way of providing short proofs that small-world network models such as the Watts-Strogatz model are strongly idemetric (for a wide range of parameters), and also provides further evidence that being idemetric is a common property. We then consider how satisfaction of the idemetric property is relevant to algorithm design. For idemetric graphs, we observe, for example, that a single breadth-first search provides a solution to the all-pairs shortest paths problem, so long as one is prepared to accept paths which are of stretch close to 2 with high probability. Since we are able to show that Kleinberg's model is idemetric, these results contrast nicely with the well known negative results of Kleinberg concerning efficient decentralized algorithms for finding short paths: for precisely the same model as Kleinberg's negative results hold, we are able to show that very efficient (and decentralized) algorithms exist if one allows for reasonable preprocessing. For deterministic distributed routing algorithms we are also able to obtain results proving that less routing information is required for idemetric graphs than in the worst case in order to achieve stretch less than 3 with high probability: whileΩ(n2) routing information is required in the worst case for stretch strictly less than 3 on almost all pairs, for idemetric graphs the total routing information required isO(nlog(n)).
Forest passerines as a novel dispersal vector of viable bryophyte propagules
Authors: Chmielewski Matthew W. , Eppley Sarah M.
Published: February 2019

Animal dispersal influences the community structure and diversity of a wide variety of plant taxa, yet the potential effects of animal dispersal in bryophytes (hornworts, liverworts, and mosses) is poorly understood. In many communities, birds use bryophyte-abundant niche space for foraging and gathering nest material, suggesting that birds may play a role in bryophyte dispersal. As highly motile animals with long migratory routes, birds potentially provide a means for both local and long-distance bryophyte dispersal in a manner that differs greatly from passive, aerial spore dispersal. To examine this phenomenon, we collected and germinated bryophyte propagules from the legs, feet and tails of 224 birds from 34 species within a temperate forest community. In total we found 1512 spores, and were able to germinate 242 bryophyte propagules. In addition, we provide evidence that topical (externally-carried) spore load varies by bird species and behaviour. Tail feather spore abundance is highest in bark and foliage gleaning species and is positively correlated with tarsal length. Together, these data suggest that a variety of forest birds exhibit the potential to act as dispersal vectors for bryophyte propagules, including an abundance of spores, and that understanding the effects of animal behaviour on bryophyte dispersal will be key to further understanding this interaction.
Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi cichlids
Authors: Hulsey C. Darrin , Alfaro Michael E. , Zheng Jimmy , Meyer Axel , Holzman Roi
Published: February 2019

Complexity in how mechanistic variation translates into ecological novelty could be critical to organismal diversification. For instance, when multiple distinct morphologies can generate the same mechanical or functional phenotype, this could mitigate trade-offs and/or provide alternative ways to meet the same ecological challenge. To investigate how this type of complexity shapes diversity in a classic adaptive radiation, we tested several evolutionary consequences of the anterior jaw four-bar linkage for Lake Malawi cichlid trophic diversification. Using a novel phylogenetic framework, we demonstrated that different mechanical outputs of the same four jaw elements are evolutionarily associated with both jaw protrusion distance and jaw protrusion angle. However, these two functional aspects of jaw protrusion have evolved independently. Additionally, although four-bar morphology showed little evidence for attraction to optima, there was substantial evidence of adaptive peaks for emergent four-bar linkage mechanics and jaw protrusion abilities among Malawi feeding guilds. Finally, we highlighted a clear case of two cichlid species that have ­independently evolved to graze algae in less than 2 Myr and have converged on similar jaw protrusion abilities as well as four-bar linkage mechanics, but have evolved these similarities via non-convergent four-bar morphologies.
Litorihabitans aurantiacus gen. nov., sp. nov., an actinobacterium of the family Beutenbergiaceae isolated from beach sand
Authors: Hamada Moriyuki , Saitou Satomi , Tamura Tomohiko
Published: February 2019

A novel actinobacterium, designated HIsM16-52T, was isolated from beach sand collected from Ishigaki Island in Japan and its taxonomic position was investigated by a polyphasic approach. Strain HIsM16-52T contained both lysine and ornithine as the diagnostic diamino acids of the peptidoglycan. The predominant isoprenoid quinone was MK-8(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and C14 : 0. The detected polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The DNA G+C content was determined to be 73.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparison revealed that strain HIsM16-52T fell within the cluster of the family

Beutenbergiaceae

and formed a reliable cluster with the members of the genus

Serinibacter

. The highest 16S rRNA gene sequence similarities were obtained to species of the genus

Serinibacter

(97.8–97.9 %), followed by the genera

Miniimonas

(97.0 %),

Beutenbergia

(96.4 %) and

Salana

(95.9 %). However, strain HIsM16-52T differed from the members of the genus

Serinibacter

and the other genera within the family

Beutenbergiaceae

in terms of chemotaxonomic characteristics. Therefore, strain HIsM16-52T is concluded to represent a novel genus and species of the family

Beutenbergiaceae

, for which the name Litorihabitans aurantiacus gen. nov., sp. nov. is proposed. The type strain of L. aurantiacus is HIsM16-52T (=NBRC 112290T=TBRC 7759T).
Streptococcus chenjunshii sp. nov. isolated from feces of Tibetan antelopes
Authors: Tian Zhi , Lu Shan , Jin Dong , Yang Jing , Pu Ji , Lai Xin-He , Bai Xiang-Ning , Wu Xiao-Min , Li Junqin , Wang Suping , Xu Jianguo
Published: February 2019

Three Gram-stain-positive, catalase-negative, α-haemolytic, chain-forming and coccus-shaped microorganisms (strains Z15T, Z1 and Z2) were isolated from feces of Tibetan antelopes collected from the Qinghai–Tibet plateau, PR China. The results of 16S rRNA gene sequence studies indicated that Z15T shared 94.5, 93.1 and 92.2 % similarity with

Streptococcus pantholopis

DSM 102135T,

Streptococcus ursoris

NUM 1615T and Streptococcus dentapri NUM 1529T, respectively. rpoB and groEL-based sequence analysis of our three novel isolates revealed interspecies divergence of 16.7 and 14.3 % from Streptococcus pantholopis DSM 102135T. The genomic DNA G+C content of Z15T is 42.48 mol%. Z15T has an average nucleotide identity (ANI) value of 81.19 % with

S. pantholopis

DSM 102135T and a DNA–DNA relatedness value of less than 70 % in the in-silico DNA–DNA hybridization (isDDH) with other species of genus

Streptococcus

deposited in the GenBank database. A whole-genome phylogenetic tree based on 246 core genes of 78 genomes of members of the genus

Streptococcus

indicated that Z15T represents a member of genus

Streptococcus

but one well separated from the currently recognized species. Z15T contains C18 : 1ω7c (25.5 %), C18 : 1ω9c (19.6 %), C16 : 0 (17.5 %) and C16 : 1ω9c (13.3 %) as its major cellular fatty acids. According to the morphological, biochemical and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus

Streptococcus

, and

Streptococcus
chenjunshii sp. nov. is thus proposed. The type strain is Z15T (=CGMCC 1.16529=DSM 106182).
Twinkle is not the mitochondrial DNA replicative helicase in C. elegans, but may have alternate mitochondrial functions
Authors: Henderson Hope R. , Euro Liliya , Suomalainen Anu , Dillin Andrew
Published: February 2019

Dysfunction of mitochondrial DNA replication machinery is a common cause of mitochondrial diseases. The minimal mammalian replisome is made up of DNA polymerase gamma, replicative helicase Twinkle, and single-stranded DNA binding protein. The replisome is localized to the inner mitochondrial membrane and serves as the site of mitochondrial DNA replication and mitochondrial fission. Recently, a sequence homolog of Twinkle was uncovered in the nematode Caenorhabditis elegans. Here, we characterized this homolog, twnk-1, and report that twnk-1 does not function as the primary mitochondrial DNA replicative helicase in this species, as loss of twnk-1 does not result in reduce mitochondrial DNA levels, or result in other expected mitochondrial dysfunctions such as reduced oxygen consumption rates, increased sensitivity to metabolic perturbations, or reduced muscle function. Instead, twnk-1 mutants have increased mitochondrial DNA as they age, and exhibit phenotypes associated with mitochondrial stress, including reduced fecundity, an activation of the mitochondrial unfolded protein response, and mitochondrial fragmentation. Our results suggest in Caenorhabditis elegans, twnk-1 does not function as the mitochondrial DNA replicative helicase, but has an alternative function in regulating mitochondrial function.
SURF1 mutations causative of Leigh syndrome impair human neurogenesis
Authors: Inak Gizem , Rybak-Wolf Agnieszka , Lisowski Pawel , Jüttner René , Zink Annika , Mlody Barbara , Glažar Petar , Secker Christopher , Ciptasari Ummi H. , Stenzel Werner , Hahn Tobias , Diecke Sebastian , Priller Josef , Gotthardt Michael , Kühn Ralf , Wanker Erich E. , Rajewsky Nikolaus , Schülke Markus , Prigione Alessandro
Published: February 2019

Mutations in the mitochondrial complex IV assembly factor SURF1 represent a major cause of Leigh syndrome (LS), a rare fatal neurological disorder. SURF1-deficient animals have failed to recapitulate the neuronal pathology of human LS, hindering our understanding of the disease mechanisms. We generated induced pluripotent stem cells from LS patients carrying homozygous SURF1 mutations (SURF1 iPS) and performed biallelic correction via CRISPR/Cas9. In contrast to corrected cells, SURF1 iPS showed impaired neuronal differentiation. Aberrant bioenergetics in SURF1 iPS occurred already in neural progenitor cells (NPCs), disrupting their neurogenic potency. Cerebral organoids from SURF1 iPS were smaller and recapitulated the neurogenesis defects. Our data imply that SURF1 mutations cause a failure in the development of maturing neurons. Using NPC function as an interventional target, we identified SURF1 gene augmentation as a potential strategy for restoring neurogenesis in LS patients carrying SURF1 mutations.
Inbreeding depression causes reduced fecundity in Golden Retrievers
Authors: Chu Erin T. , Simpson Missy J. , Diehl Kelly , Page Rodney L. , Sams Aaron J. , Boyko Adam R.
Published: February 2019

Inbreeding depression has been demonstrated to impact vital rates, productivity, and performance in many domestic species. Many in the field have demonstrated the value of genomic measures of inbreeding compared to pedigree-based estimates of inbreeding; further, standardized, high-quality phenotype data on all individuals is invaluable for longitudinal analyses of a study cohort. We compared measures of reproductive fitness in a small cohort of Golden Retrievers enrolled in the Golden Retriever Lifetime Study (GRLS) to a genomic measurement of inbreeding, FROH. We demonstrate a statistically significant negative correlation between fecundity and FROH.This work sets the stage for larger scale analyses to investigate genomic regions associated with fecundity and other measures of fitness.
An oligarchy of NO-producing interneurons controls basal and evoked blood flow in the cortex
Authors: Echagarruga Christina T. , Gheres Kyle , Drew Patrick J.
Published: February 2019

Changes in cortical neural activity are coupled to changes in local arterial diameter and blood flow. However, the neuronal types and the signaling mechanisms that control the basal diameter of cerebral arteries or their evoked dilations are not well understood. Using chronic two-photon microscopy, electrophysiology, chemogenetics, and pharmacology in awake, head-fixed mice, we dissected the cellular mechanisms controlling the basal diameter and evoked dilation in cortical arteries. We found that modulation of overall neural activity up or down caused corresponding increases or decreases in basal arterial diameter. Surprisingly, modulation of pyramidal neuron activity had minimal effects on basal or evoked arterial dilation. Instead, the neurally-mediated component of arterial dilation was largely regulated through nitric oxide released by neuronal nitric oxide synthase (nNOS)-expressing neurons, whose activity was not reflected in electrophysiological measures of population activity. Our results show that cortical hemodynamic signals are not controlled by the average activity of the neural population, but rather the activity of a small ‘oligarchy’ of neurons.
Exact p-values for large-scale single step genome-wide association, with an application for birth weight in American Angus
Authors: Aguilar Ignacio , Legarra Andres , Cardoso Fernando , Masuda Yutaka , Lourenco Daniela , Misztal Ignacy
Published: February 2019

BACKGROUND

Single Step GBLUP (SSGBLUP) is the most comprehensive method for genomic prediction. Point estimates of marker effects from SSGBLUP are often used for Genome Wide Association Studies (GWAS) without a formal framework of hypothesis testing. Our objective was to implement p-values for GWAS studies in the ssGBLUP framework, showing algorithms, computational procedures, and an application to a large beef cattle population.

METHODS

P-values were obtained based on the prediction error (co)variance for SNP, which uses the inverse of the coefficient matrix and formulas to compute SNP effects.

RESULTS

Computation of p-values took a negligible time for a dataset with almost 2 million animals in the pedigree and 1424 genotyped sires, and no inflation was observed. The SNP passing the Bonferroni threshold of 5.9 in the −log10 scale were the same as those that explained the highest proportion of additive genetic variance, but the latter was penalized (as GWAS signal) by low allele frequency.

CONCLUSION

The exact p-value for SSGWAS is a very general and efficient strategy for QTL detection and testing. It can be used in complex data sets such as used in animal breeding, where only a proportion of pedigreed animals are genotyped.
Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy
Authors: Bertero Alessandro , Fields Paul A. , Smith Alec S. T. , Leonard Andrea , Beussman Kevin , Sniadecki Nathan J. , Kim Deok-Ho , Tse Hung-Fat , Pabon Lil , Shendure Jay , Noble William S. , Murry Charles E.
Published: February 2019

Pathogenic mutations in A-type nuclear lamins cause dilated cardiomyopathy, which is postulated to result from dysregulated gene expression due to changes in chromatin organization into active and inactive compartments. To test this, we performed genome-wide chromosome conformation analyses (Hi-C) in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) with a haploinsufficient mutation for lamin A/C. Compared to gene-corrected cells, mutant hiPSC-CMs have marked electrophysiological and contractile alterations, with modest gene expression changes. While large-scale changes in chromosomal topology are evident, differences in chromatin compartmentalization are limited to a few hotspots that escape inactivation during cardiogenesis. These regions exhibit upregulation of multiple non-cardiac genes includingCACNA1A, encoding for neuronal P/Q-type calcium channels. Pharmacological inhibition of the resulting current partially mitigates the electrical alterations. On the other hand, A/B compartment changes do not explain most gene expression alterations in mutant hiPSC-CMs. We conclude that global errors in chromosomal compartmentation are not the primary pathogenic mechanism in heart failure due to lamin A/C haploinsufficiency.

Bertero et al. observe that lamin A/C haploinsufficiency in human cardiomyocytes markedly alters electrophysiology, contractility, gene expression, and chromosomal topology. Contrary to expectations, however, changes in chromatin compartments involve just few regions, and most dysregulated genes lie outside these hotspots.

Condensed title

Genomic effects of lamin A/C haploinsufficiency
Dynamically Linking Influenza Virus Infection Kinetics, Lung Injury, Inflammation, and Disease Severity
Authors: Myers Margaret A. , Smith Amanda P. , Lane Lindey C. , Moquin David J. , Aogo Rosemary , Woolard Stacie , Thomas Paul G. , Vogel Peter , Smith Amber M.
Published: February 2019

Influenza viruses cause a significant amount of morbidity and mortality. Understanding host immune control efficacy and how different factors influence lung injury and disease severity are critical. Here, we established dynamical connections between viral loads, infected cells, CD8+T cell-mediated clearance, lung injury, inflammation, and disease severity using an integrative model-experiment exchange. The model was validated through CD8 depletion and whole lung histomorphometry, which showed that the infected area matched the model-predicted infected cell dynamics and that the resolved area paralleled the relative CD8 dynamics. Inflammation could further be predicted by the infected cell dynamics, and additional analyses revealed nonlinear relations between lung injury, inflammation, and disease severity. These links between important pathogen kinetics and host pathology enhance our ability to forecast disease progression, potential complications, and therapeutic efficacy.