bluuebunny/crossref_metadata_2025 huggingface dataset:
Cobalt-related defects in silicon
Authors: Gibbons T. M. , Backlund D. J. , Estreicher S. K.
Published: January 2017

Transition metals from the 3d series are unavoidable and unwanted contaminants in Si-based devices. Cobalt is one of the most poorly understood impurities with incomplete experimental information and few theoretical studies. In this contribution, the properties of interstitial cobalt (Coi) in Si and its interactions with the vacancy, self-interstitial, hydrogen, and substitutional boron are calculated using the first-principles tools. The stable configurations, gap levels, and binding energies are predicted. The activation energy for diffusing Coi is calculated with the nudged-elastic-band method and found to be slightly lower than that of interstitial copper and nickel. The binding energies and gap levels of the substitutional cobalt (Cos) and of the {Cos,H} and {Cos,H,H} complexes are close to the experimental data. The properties of the cobalt-boron pair are calculated.
Effect of thickness on magnetic and microwave properties of RF-sputtered Zn-ferrite thin films
Authors: Sahu B. N. , Venkataramani N. , Prasad Shiva , Krishnan R.
Published: January 2017

Zinc ferrite thin films of varying thickness were deposited at ambient temperature using RF-magnetron sputtering. The films were annealed at temperatures in the range 250 °C to 650 °C in air for 2 hrs. The magnetization of the film was observed to depend on the average grain size and also on thickness of the film. It was found that thermal annealing reduces the peak to peak ferromagnetic resonance (FMR) line width. A low in-plane line width of 195 Oe and a line width of 170 Oe in perpendicular configuration was observed for a 240 nm thickness film annealed at TA=450 °C.
Polymer nanomechanics: Separating the size effect from the substrate effect in nanoindentation
Authors: Li Le , Encarnacao Lucas M. , Brown Keith A.
Published: January 2017

While the moduli of thin polymer films are known to deviate dramatically from their bulk values, there is not a consensus regarding the nature of this size effect. In particular, indenting experiments appear to contradict results from both buckling experiments and molecular dynamics calculations. In this letter, we present a combined computational and experimental method for measuring the modulus of nanoindented soft films on rigid substrates that reconciles this discrepancy. Through extensive finite element simulation, we determine a correction to the Hertzian contact model that separates the substrate effect from the thickness-dependent modulus of the film. Interestingly, this correction only depends upon a dimensionless film thickness and the Poisson ratio of the film. To experimentally test this approach, we prepared poly(methyl methacrylate), polystyrene, and parylene films with thicknesses ranging from 20 to 300 nm and studied these films using atomic force microscope-based nanoindenting. Strikingly, when experiments were interpreted using the computationally derived substrate correction, sub-70 nm films were found to be softer than bulk, in agreement with buckling experiments and molecular dynamics studies. This correction can serve as a general method for unambiguously determining the size effect of thin polymer films and ultimately lead to the ability to quantitatively image the mechanical properties of heterogeneous materials such as composites.
Development of precise off-diagonal magnetoimpedance gradiometer for magnetocardiography
Authors: Uchiyama Tsuyoshi , Takiya Takashi
Published: January 2017

We have developed a precise off-diagonal magnetoimpedance (MI) gradiometer that can operate in an unshielded environment and at room temperature with 200 pT root-mean-square noise in a 100 Hz bandwidth. The MI sensor probe is compact and easy to handle. The achieved noise level corresponds approximately to the maximum magnetocardiography (MCG) signal reported so far. We have performed MCG measurements using the developed gradiometer system in an unshielded environment, and a real-time signal like MCG can be identified by the MI gradiometer when the distance between the sensor head and chest surface is less than 3 mm. However, the signal seems to be affected by the movement of the chest surface caused by the heartbeat. A peak magnetic signal of 100 pT (corresponding to conventional MCG) was observed when the sensor head was set 10 mm apart from the chest surface to avoid the influence of the chest movement. Under such conditions, the signal needed to be averaged over more than 50 cycles to identify the peak magnetic signal.
Formation of x-ray Newton’s rings from nano-scale spallation shells of metals in laser ablation
Authors: Nishikino Masaharu , Hasegawa Noboru , Tomita Takuro , Minami Yasuo , Eyama Takashi , Kakimoto Naoya , Izutsu Rui , Baba Motoyoshi , Kawachi Tetsuya , Suemoto Tohru
Published: January 2017

The initial stages of the femtosecond (fs) laser ablation process of gold, platinum, and tungsten were observed by single-shot soft x-ray imaging technique. The formation and evolution of soft x-ray Newton’s rings (NRs) were found for the first time. The soft x-ray NRs are caused by the interference between the bulk ablated surface and nanometer-scale thin spallation layer; they originate from the metal surface at pump energy fluence of around 1 J/cm2 and work as a flying soft x-ray beam splitter.
Magnetic field effect on Poiseuille flow and heat transfer of carbon nanotubes along a vertical channel filled with Casson fluid
Authors: Aman Sidra , Khan Ilyas , Ismail Zulkhibri , Salleh Mohd Zuki , Alshomrani Ali Saleh , Alghamdi Metib Said
Published: January 2017

Applications of carbon nanotubes, single walls carbon nanotubes (SWCNTs) and multiple walls carbon nanotubes (MWCNTs) in thermal engineering have recently attracted significant attention. However, most of the studies on CNTs are either experimental or numerical and the lack of analytical studies limits further developments in CNTs research particularly in channel flows. In this work, an analytical investigation is performed on heat transfer analysis of SWCNTs and MWCNTs for mixed convection Poiseuille flow of a Casson fluid along a vertical channel. These CNTs are suspended in three different types of base fluids (Water, Kerosene and engine Oil). Xue [Phys. B Condens. Matter 368, 302–307 (2005)] model has been used for effective thermal conductivity of CNTs. A uniform magnetic field is applied in a transverse direction to the flow as magnetic field induces enhancement in the thermal conductivity of nanofluid. The problem is modelled by using the constitutive equations of Casson fluid in order to characterize the non-Newtonian fluid behavior. Using appropriate non-dimensional variables, the governing equations are transformed into the non-dimensional form, and the perturbation method is utilized to solve the governing equations with some physical conditions. Velocity and temperature solutions are obtained and discussed graphically. Expressions for skin friction and Nusselt number are also evaluated in tabular form. Effects of different parameters such as Casson parameter, radiation parameter and volume fraction are observed on the velocity and temperature profiles. It is found that velocity is reduced under influence of the exterior magnetic field. The temperature of single wall CNTs is found greater than MWCNTs for all the three base fluids. Increase in volume fraction leads to a decrease in velocity of the fluid as the nanofluid become more viscous by adding CNTs.
The 3-D numerical simulation research of vacuum injector for linear induction accelerator
Authors: Liu Dagang , Xie Mengjun , Tang Xinbing , Liao Shuqing
Published: January 2017

Simulation method for voltage in-feed and electron injection of vacuum injector is given, and verification of the simulated voltage and current is carried out. The numerical simulation for the magnetic field of solenoid is implemented, and a comparative analysis is conducted between the simulation results and experimental results. A semi-implicit difference algorithm is adopted to suppress the numerical noise, and a parallel acceleration algorithm is used for increasing the computation speed. The RMS emittance calculation method of the beam envelope equations is analyzed. In addition, the simulated results of RMS emittance are compared with the experimental data. Finally, influences of the ferromagnetic rings on the radial and axial magnetic fields of solenoid as well as the emittance of beam are studied.
Structural properties of highly conductive ultra-nanocrystalline diamond films grown by hot-filament CVD
Authors: Mertens M. , Lin I.-N. , Manoharan D. , Moeinian A. , Brühne K. , Fecht H. J.
Published: January 2017

In this work we show the correlation of the electrical conductivity of ultra-nanocrystalline (UNCD) diamond films grown by hot filament chemical vapor deposition (HFCVD) with their structural properties. The substrate temperature, the methane to hydrogen ratio and the pressure are the main factor influencing the growth of conductive UNCD films, which extends from electrical resistive diamond films (<10-4 S/cm) to highly conductive diamond films with a specific conductivity of 300 S/cm. High-resolution-transmission-electron-microscopy (HRTEM) and electron-energy-loss-spectroscopy (EELS) have been done on the highly conductive diamond films, to show the origin of the high electrical conductivity. The HRTEM results show random oriented diamond grains and a large amount of nano-graphite between the diamond crystals. EELS investigations are confirming these results. Raman measurements are correlated with the specific conductivity, which shows structural changes of sp2 carbons bonds as function of conductivity. Hall experiments complete the results, which lead to a model of an electron mobility based conductivity, which is influenced by the structural properties of the grain boundary regions in the ultra-nanocrystalline diamond films.
Reproducibility and off-stoichiometry issues in nickelate thin films grown by pulsed laser deposition
Authors: Preziosi Daniele , Sander Anke , Barthélémy Agnès , Bibes Manuel
Published: January 2017

Rare-earth nickelates are strongly correlated oxides displaying a metal-to-insulator transition at a temperature tunable by the rare-earth ionic radius. In PrNiO3 and NdNiO3, the transition is very sharp and shows an hysteretic behavior akin to a first-order transition. Both the temperature at which the transition occurs and the associated resistivity change are extremely sensitive to doping and therefore to off-stoichiometry issues that may arise during thin film growth. Here we report that strong deviations in the transport properties of NdNiO3 films can arise in films grown consecutively under nominally identical conditions by pulsed laser deposition; some samples show a well-developed transition with a resistivity change of up to five orders of magnitude while others are metallic down to low temperatures. Through a detailed analysis of in-situ X-ray photoelectron spectroscopy data, we relate this behavior to large levels of cationic off-stoichoimetry that also translate in changes in the Ni valence and bandwidth. Finally, we demonstrate that this lack of reproducibility can be remarkably alleviated by using single-phase NdNiO3 targets.
Dynamics of grazing rights and their impact on mobile cattle herders in Bhutan
Authors: Namgay Kuenga , Millar Joanne E. , Black Rosemary S.
Published: January 2017

Seasonal cattle movements have been an important part of the living cultural heritage in Bhutan for centuries. Herders migrate south every winter to graze their cattle on subtropical pastures and to work in orange orchards. They return north to their villages in spring to grow summer crops. However, the practice of transhumant agropastoralism is under increasing pressure on account of changes in land-use policies, climate change and a declining labour force as youth seek alternative livelihoods. This research investigated the impact of changes in land-use policy, with emphasis on the Land Act 2007, on current and future livelihoods of transhumant herders in Bhutan. During in-depth interviews with 24 transhumant herders and nine livestock advisors, and seven focus-group discussions with 64 participants including herders, downstream residents and development agency personnel, perspectives on this issue were gathered. Findings revealed a lack of herder awareness of changes in land-use policies and minimal consultation of herders during policy development. Confusion and uncertainty about the proposed redistribution of grazing rights and restrictions on herd movements have resulted in confusion and resentment and have created conflicts between upstream and downstream communities. Herders with no current alternatives are concerned about their future livelihoods, whereas others are leaving it to their children to decide their future. It is concluded that the motive behind nationalisation of rangeland is noble and timely, but there are flaws in the redistribution plan. Transhumant agropastoralism is already in decline and there is no need to push towards its end through legislation. Transhumant practices could be left to evolve towards what may be their natural end. Sudden stoppage of inter-district transhumance without offering meaningful alternatives to herders could result in negative environmental and socioeconomic impacts. In future, policy development needs to increasingly embrace science and be based on evidence. A genuine participatory process with citizen engagement could avoid the unintended negative impacts likely to be faced by transhumant herders with marginal land holdings, who depend on this production system for their livelihoods.
Pragmatic stylistics and dramatic dialogue
Authors: Mandala Susan
Published: January 2017

In this chapter, I follow Short (1989, 1998) and view dramatic dialogue as a form of exchange that can be read on the page just as legitimately as it can be experienced on stage. Employing a pragmatic stylistic analysis linking the text on the page to my interpretation, I offer a re-reading of Pinter’s The Dumb Waiter. While for Burton (1980) Ben was “the dominating and superior interactant,” and Gus “the dominated and inferior one” (70), I argue here that it is Gus who can be considered the dominating character and show in the concluding discussion why this recalibration of power is significant for our wider understanding of the play.
Dialogue and character in 21st century TV drama
Authors: Richardson Kay P.
Published: January 2017

The successful British-made TV drama series Sherlock (BBC 2011-present) is one of the latest in a long sequence of dramatisations of the Victorian short stories and novels by Sir Arthur Conan Doyle. This chapter discusses some passages of dialogue from the first episode of this series, demonstrating how the character is created and maintained, focusing in particular on Sherlock’s antisocial tendencies, his eccentricity and his remarkable deductive powers. The analysis further seeks to isolate the distinctive contribution of dialogue in this respect from other aspects of audiovisual production, drawing as appropriate on the sociolinguistics of stance, politeness theory and conversational analysis.
Dialogic interactions on radio
Authors: Mildorf Jarmila
Published: January 2017

This paper focuses on a sub-category of journalistic interviews, namely the so-called “literary interview,” where writers are interviewed about their lives and works. More specifically, the paper investigates the dynamics of literary interviews as radio broadcasts and therefore emphasizes their conversational and medial side, paying attention to turn-taking mechanisms and the use of voice quality and prosody in the authors’ multimodal self-presentations. Key linguistic concepts in this regard are interviewees’ “audience design,” and also participants’ speech accommodation and verbal “duetting,” which point to the collaborative nature of these interviews. The case studies are drawn from American radio journalist Studs Terkel’s interviews with Ralph Ellison, Maya Angelou and Toni Morrison.
Dialogue in comics
Authors: Mikkonen Kai
Published: January 2017

This paper focuses on the dialogue form in comics as a key narrative device, and examines the main elements and narrative functions that characterise scenes of talk in comics. The goal is to develop a medium-specific understanding of the dialogue form in comics. The starting point is the multimodal character of conversational exchange in comics. This requires a focus on the interaction between the utterance and the elements of the narrative drawing, that is, the ways in which the dialogue form (as written and drawn speech) interacts with what is shown in the image. Crucial aspects of graphic showing in scenes of talk in comics are facial expressions, gestures, body language and shape, and participant involvement. Equally, the expressive functions of typography and pictorial symbols, onomatopoeia, as well as graphic style, panel framing, and page layout, can play a major role.
Dialogue and interaction in role-playing games
Authors: Mäyrä Frans
Published: January 2017

Dialogue is central to role-playing games (RPGs). It serves multiple purposes, some of which are related to its functional role in mediating in-game clues or actions, some to the role of language in the collaborative construction of shared fantasy. The aim of this chapter is to identity the multiple functions dialogue has in role-playing games, and to provide illustrative examples and analyses of typical and inventive applications of dialogue in role-play. The examples are also chosen to highlight the similarities and differences between such RPG forms as table-top, pen-and-paper RPGs, larp or live-action role-play, as well as single-player and multiplayer, online computer role-playing games.
The social and political dimensions of visitor management: rural home-based accommodations.
Authors: Hassanli N.
Published: January 2017

This chapter explores visitor management (VM) practices employed by home-based accommodation providers in rural Iran. Two groups of guests staying at these accommodations and their motives are presented, and the challenges faced by the hosts in managing guests are addressed in light of possible hard and soft approaches to VM. The chapter demonstrates how the social and political conditions of a host country influence the choice of VM strategies.
Visitor monitoring in the Tapajós National Forest, Brazil.
Authors: Moreira J. C. , Burns R. C.
Published: January 2017

This chapter covers an in-depth discussion of visitor monitoring in a park/protected area (PPA) in the Amazon region of Brazil. It traces the implementation of a systematic 'best practice' approach that applies and tailors a US Forest Service methodology for visitor monitoring to a region in the Brazilian rainforest. As such, the chapter shows how well established management methods can be transferred and adapted to a different context in order to improve visitor (impact) management.
Augmented reality application to museum visitor experiences.
Authors: Hassan A. , Ramkissoon H.
Published: January 2017

This chapter draws attention to the use of innovative technologies in visitor management, specifically in managing visitor experiences. It aims to replicate cited examples of augmented reality (AR) application in museums in developed countries in the context of Bangladesh, an emerging tourist destination. Bangladesh has distinctive features encompassing history and culture, suggesting that AR can assist in the implementation and promotion of cultural tourism through activities in museums. The study's exploratory findings suggest that AR may be applied to museums such as the Bangladesh National Museum given adequate infrastructure.
Theories of learning and their application in interpretation.
Authors: Kuo ILing Kuo ILing
Published: January 2017

This chapter explores how theories of learning and behavioural changes may be applicable in interpretation, with the main focus on outdoor tourism destinations such as protected areas. Nevertheless, these theories of learning are equally applicable to the design and delivery of interpretation in museums and galleries.
Critical reflections on the role of interpretation in visitor management.
Authors: Moscardo G.
Published: January 2017

This chapter begins with a review of definitions of interpretation, noting its relationships with other forms of communication between management and visitors. This is followed by a brief history of interpretation and visitor management (VM) that highlights the evolution of a range of management functions for interpretation. The evidence that interpretation is an effective VM tool is then critically reviewed, highlighting those factors that have been shown to be consistently related to positive outcomes. The chapter also examines recent critiques of interpretation and explores broader issues about the impacts that interpretation can have on destination communities, with the aim of identifying principles for the more effective use of interpretation in VM. It concludes by looking at future opportunities for interpretation and sustainable tourism.
Current knowledge and future research directions in visitor management.
Authors: Albrecht J. N.
Published: January 2017

This chapter provides a summary and conclusion for this book on visitor management, as well as identifying further research needs. Sections discuss: visitor management in context; critical concepts in visitor management; current issues in visitor management; and the state of the art in guiding and interpretation.
Western holy cities and places - an introduction.
Authors: Leppäkari M. , Griffin K.
Published: January 2017

This introduction explains the objectives of this book on pilgrimage and tourism to Western holy cities, as well as the significance of multidisciplinary approaches for generating holistic perspectives on pilgrimage and its management. The structure of the book is described.
Christianity - contemporary Christian pilgrimage and traditional management practices at sacred sites.
Authors: Enongene V. , Griffin K.
Published: January 2017

This chapter explores contemporary Christian pilgrimage experiences, with emphasis on where pilgrimage fits in the life of a contemporary believer. In so doing, it addresses the changing demands of contemporary pilgrims, as well as the factors that are shaping current pilgrimage patterns. The chapter further discusses how the changing needs and expectations of contemporary pilgrims are altering traditional management practices at sacred sites, and provides examples of innovative management approaches adopted in catering to these needs. It further analyses the implications of such pressures on management at sacred sites and the future of contemporary pilgrimage experiences, and questions whether or not traditional pilgrimage practice has really undergone a fundamental change in recent times.
Christianity - Christian pilgrimage to sacred sites in the Holy Land: a Swedish perspective.
Authors: Gunner G.
Published: January 2017

This chapter takes a past and present perspective on Swedish Christian pilgrimage to Jerusalem and the Holy Land. The discussion commences with an exploration of Jerusalem's special place as a sacred connection between heaven and earth. Before the popularization of travel, Christians in Sweden used imagery and maps to develop their conceptualization of this most holy landscape. As early as the 1000s, Nordic pilgrims were travelling to sites such as Jerusalem and Rome. And while their travels are well documented, it would appear from their writings that their motivations were more to do with curiosity and adventure than pilgrimage. The next generation of travellers discussed in the chapter were those who were interested in building upon their Sunday-school learned concepts of the Holy Land. The manner in which they reported and illustrated what they found further perpetuated the dominant imagery. From the beginning of the 20th century, it became apparent that the commercialization and modernization of Bethlehem, Jerusalem and other important Christian sites was challenging travellers' preconceived notions of these historically and spiritually important spaces. Travel writers started to question the established concepts and traditions, and thereby reflected on the importance for their readers of experiencing something new. In more recent times it has become apparent that this 'something new' is heavily influenced by the writer's own viewpoint, and that of the guides who lead them in their own travels. Thus, the chapter concludes with discussions on witnessing radical change in society, and sacred places as political watersheds.
Islam - contemporary perspective.
Authors: Raj R. , Raja I.
Published: January 2017

This chapter examines various contemporary perspectives of Islam and in particular addresses an under-researched aspect of religious pilgrimage - the motivation to attend mosques on a daily basis. The chapter contextualizes Islam within contemporary societal development in Europe, wherein Western societies have begun to view Islam as incompatible with, and a security threat to, their secular and liberal way of life. In the chapter it is argued that this is mainly because most often sections of the media, polity and conservative writers present a distasteful view of Islam, featuring it as a source of social ills and all sorts of troubles in the world.
Pilgrimage policy management: between shrine strategy and ritual improvisation.
Authors: Coleman S.
Published: January 2017

This chapter challenges conventional models of managing pilgrimage sites in the West, which often see administrators and managers as needing to 'protect' the sacred from tourists who lack the knowledge to engage in appropriate ways with the shrine and its environs. In addition, it is often assumed - at least by many scholars of religion - that the area of primary interest and focus in a shrine is at its religious and liturgical centre, where the core of believers/pilgrims tend to be concentrated and also to act in relatively more predictable ways. Drawing on case studies of pilgrimage shrines and cathedrals in England, as well as on wider literature on pilgrimage sites around Europe, the chapter questions both of these assumptions. An alternative management model is explored - one that emphasizes how sites might encourage flexibility of movement and interpretation, thus responding to shifting understandings and engagements, often in ways unexpected by both hosts and visitors.
The management of pilgrims with malevolent behaviour in a holy space: a study of Jerusalem syndrome.
Authors: Kalian M. , Witztum E.
Published: January 2017

This chapter focuses on pilgrimage and mental health. It discusses findings about the condition called 'Jerusalem Syndrome', as well as general Western perspectives on mental health, meaning-creating processes and personal crises when travelling. The relevance of religious traditions in mental health work among pilgrims and religious travellers is addressed.
Logistics at holy sites.
Authors: Trono A.
Published: January 2017

After briefly analysing the characteristics of visitors to holy places, this chapter explores the identity and role of large and small operators, both secular and religious, in the organization of pilgrimages and the management of certain holy places in the Western world. The chapter analyses how these operators manage tourist flows at their sites, ensuring availability of infrastructure, transport, communication, facilities and private businesses, including tour operators and hotel providers. It also considers the benefits and the limits of the work they do, as well as the risks and opportunities that 'modern' pilgrimage offers the host regions, with reference to some European places of pilgrimage.
The impact of the Islamic State of Iraq and Syria's campaign on Yezidi religious structures and pilgrimage practices.
Authors: Al-Marashi I.
Published: January 2017

This chapter discusses how the Islamic State of Iraq and Syria (ISIS), through the expulsion of Iraqi Christian Chaldean and 'heterodox' Yezidi and Sabean communities, and the destruction of their religious churches, temples and practices, seeks to create a homogenous neo-Salafi space by 'religious cleansing' of persons and physical structures. The chapter considers the ramifications of such a campaign and how it stretches beyond the local. Eliminating these religious sites severs the opportunity for religious pilgrimage for these minority diaspora and destroys the only spiritual link these exiled, refugee communities possess to their ancestral lands.
Four Lessons from Risk Assessment (and Other Forensic Assessment) Meta-Analyses
Authors: Boccaccini Marcus T.
Published: January 2017

I read the Williams, Wormith, Bonta, and Sitarenios (2017) critique of the Singh, Grann, and Fazel ( 2011 ) meta-analysis as someone who has struggled with conceptual and methodological issues when conducting risk assessment meta-analyses. I offer four lessons for risk assessment meta-analysts, based on my experiences as a risk assessment meta-analyst and consumer of risk assessment research. Lesson 1: We should accept the Dodo bird verdict in risk assessment instrument research and then move forward. Lesson 2: If you must compare, compare within samples. Lesson 3: Meta-analyses are often more useful for showing how much we don't know than how much we do know. Lesson 4: There are not enough risk assessment instrument studies examining the predictive validity of commonly used score interpretations.
Transcriptional determinants of tolerogenic and immunogenic states during dendritic cell maturation
Authors: Vander Lugt Bryan , Riddell Jeremy , Khan Aly A. , Hackney Jason A. , Lesch Justin , DeVoss Jason , Weirauch Matthew T. , Singh Harinder , Mellman Ira
Published: January 2017

Dendritic cells (DCs) promote either tolerogenic or immunogenic T cell responses, the latter upon sensing microbes. Using an in vitro system, we analyzed transcriptional determinants that enable mature DCs to direct these opposing T cell outcomes. In the absence of microbial products, the transcription factor interferon regulatory factor 4 (IRF4) promotes regulatory T cell (Treg) generation by enhancing expression of genes required for antigen presentation along with those for T cell tolerance. IRF4-deficient DCs were impaired for Treg generation in vivo. When exposed to microbial stimuli, DCs activated nuclear factor (NF)-κB, which induced expression of a proinflammatory cytokine module that, along with the antigen presentation module, promoted the generation of effector T cells. NF-κB was, however, dispensable for Treg development. Chromatin profiling revealed transcriptional motifs associated with the divergent DC programs. Thus, DCs modulate their ability to prime tolerogenic or immunogenic T cells by expressing a core antigen presentation module that is overlaid by distinctive regulatory modules to promote either tolerance or immunity.
Fournierella massiliensis gen. nov., sp. nov., a new human-associated member of the family Ruminococcaceae
Authors: Togo Amadou Hamidou , Durand Guillaume , Khelaifia Saber , Armstrong Nicholas , Robert Catherine , Cadoret Frédéric , Di Pinto Fabrizio , Delerce Jérémy , Levasseur Anthony , Raoult Didier , Million Matthieu
Published: January 2017

An anaerobic bacterium, strain AT2T, was isolated from the fresh stool sample of a healthy French man using the culturomics approach. The 16S rRNA gene sequence analysis showed that strain AT2T had 95.2 % nucleotide sequence similarity with

Gemmiger formicilis

ATCC 27749T, the phylogenetically closest species with standing in nomenclature. Cells are Gram-stain-negative, catalase- and oxidase-negative, obligately anaerobic, non-motile, non-spore-forming, rod-shaped, and the bacilli were mesothermophilic. The major fatty acids were C16 : 0 (43.8 %) and C18 : 1n9 (20 %). The DNA G+C content of the strain based on its genome sequence was 56.8 mol%. Based on the phenotypic, biochemical and phylogenetic analysis, we propose the creation of the genus

Fournierella

gen. nov., which contains strain AT2T (=CSUR P2014T=DSM 100451T) as the type strain of the type species Fournierella massiliensis gen. nov., sp. nov.
Inferential Learning of Serial Order of Perceptual Categories by Rhesus Monkeys (Macaca mulatta)
Authors: Tanner Natalie , Jensen Greg , Ferrera Vincent P. , Terrace Herbert S.
Published: January 2017

Category learning in animals is typically trained explicitly, in most instances by varying the exemplars of a single category in a matching-to-sample task. Here, we show that rhesus macaques can learn categories by a transitive inference paradigm in which novel exemplars of five categories were presented throughout each training session. Instead of requiring decisions about a constant set of repetitively presented stimuli, we studied the macaque’s ability to determine the relative order of multiple exemplars of particular stimuli that were rarely repeated. Ordinal decisions generalized both to novel stimuli and, as a consequence, to novel pairings. Thus, we showed that rhesus monkeys could learn to categorize on the basis of implied ordinal position, and that they could then make inferences about category order. Our results challenge the plausibility of association models of category learning and broaden the scope of the transitive inference paradigm.

Significance Statement

The cognitive abilities of non-human animals are of enduring interest to scientists and the general public because they blur the dividing line between human and non-human intelligence. Categorization and sequence learning are highly abstract cognitive abilities each in their own right. This study is the first to provide evidence that visual categories can be ordered serially by macaque monkeys using a behavioral paradigm that provides no explicit feedback about category or serial order. These results strongly challenge accounts of learning based on stimulus-outcome associations.
A Logic-Based Dynamic Modeling Approach to Explicate the Evolution of the Central Dogma of Molecular Biology
Authors: Jafari Mohieddin , Ansari-Pour Naser , Azimzadeh Sadegh , Mirzaie Mehdi
Published: January 2017

It is nearly half a century past the age of the introduction of the Central Dogma (CD) of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.
Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows–Wheeler Transform
Authors: Naseri Ardalan , Liu Xiaoming , Zhang Shaojie , Zhi Degui
Published: January 2017

With the availability of genotyping data of very large samples, there is an increasing need for tools that can efficiently identify genetic relationships among all individuals in the sample. One fundamental measure of genetic relationship of a pair of individuals isidentity by descent(IBD), chromosomal segments that are shared among two individuals due to common ancestry. However, the efficient identification of IBD segments among a large number of genotyped individuals is a challenging computational problem. Most existing methods are not feasible for even thousands of individuals because they are based on pairwise comparisons of all individuals and thus scale up quadratically with sample size. Some methods, such as GERMLINE, use fast dictionary lookup of short seed sequence matches to achieve a near-linear time efficiency. However, the number of short seed matches often scales up super-linearly in real population data.

In this paper we describe a new approach for IBD detection. We take advantage of an efficient population genotype index, Positional BWT (PBWT), by Richard Durbin. PBWT achieves linear time query of perfectly identical subsequences among all samples. However, the original PBWT is not tolerant to genotyping errors which often interrupt long IBD segments into short fragments. We introduce a randomized strategy by running PBWTs over random projections of the original sequences. To boost the detection power we run PBWT multiple times and merge the identified IBD segments through interval tree algorithms. Given a target IBD segment length, RaPID adjust parameters to optimize detection power and accuracy.

Simulation results proved that our tool (RaPID) achieves almost linear scaling up to sample size and is orders of magnitude faster than GERMLINE. At the same time, RaPID maintains a detection power and accuracy comparable to existing mainstream algorithms, GERMLINE and IBDseq. Running multiple times with various target detection lengths over the 1000 Genomes Project data, RaPID can detect population events at different time scales. With our tool, it is feasible to identify IBDs among hundreds of thousands to millions of individuals, a sample size that will become reality in a few years.
Unifying Population and Landscape Ecology with Spatial Capture-recapture
Authors: Royle J. Andrew , Fuller Angela K. , Sutherland Christopher
Published: January 2017

Spatial heterogeneity in the environment induces variation in population demographic rates and dispersal patterns, which result in spatio-temporal variation in density and gene flow. Unfortunately, applying theory to learn about the role of spatial structure on populations has been hindered by the lack of mechanistic spatial models and inability to make precise observations of population structure. Spatial capture-recapture (SCR) represents an individual-based analytic framework for overcoming this fundamental obstacle that has limited the utility of ecological theory. SCR methods make explicit use of spatial encounter information on individuals in order to model density and other spatial aspects of animal population structure, and have been widely adopted in the last decade. We review the historical context and emerging developments in SCR models that enable the integration of explicit ecological hypotheses about landscape connectivity, movement, resource selection, and spatial variation in density, directly with individual encounter history data obtained by new technologies (e.g., camera trapping, non-invasive DNA sampling). We describe ways in which SCR methods stand to revolutionize the study of animal population ecology.
Cryo-Electron Microscopy Structure of theMacrobrachium rosenbergiiNodavirus Capsid at 7 Angstroms Resolution
Authors: Ho Kok Lian , Kueh Chare Li , Beh Poay Ling , Tan Wen Siang , Bhella David
Published: January 2017

White tail disease in the giant freshwater prawnMacrobrachium rosenbergiicauses significant economic losses in shrimp farms and hatcheries and poses a threat to food-security in many developing countries. Outbreaks ofMacrobrachium rosenbergiinodavirus (MrNV), the causative agent of white tail disease (WTD) are associated with up to 100% mortality rates. Recombinant expression of the capsid protein ofMrNV in insect cells leads to the production of VLPs closely resembling the native virus. We have investigated the structure ofMrNV VLPs by cryogenic electron microscopy, determining a structure of the viral capsid at 7 angstroms resolution. Our data show thatMrNV VLPs package nucleic acids in a manner reminiscent of other known nodavirus structures. The structure of the capsid however shows striking differences from insect and fish infecting nodaviruses, which have been shown to assemble trimer-clustered T=3 icosahedral virus particles.MrNV particles have pronounceddimericblade-shaped spikes extending up to 6 nm from the outer surface of the capsid shell. Our structural analysis supports the assertion thatMrNV along with the related virus of marine shrimpPenaeus vannameinodavirus (PvNV) may represent a new genus of theNodaviridae.

Author summary

Macrobrachium rosenbergiinodavirus (MrNV) is the causative agent of white tail disease (WTD) which leads to 100% mortality in shrimp-farms growing giant freshwater prawn (M. rosenbergii).MrNV is therefore a significant threat to food security and causes severe economic losses in developing countries such as Malaysia, Indonesia, Pakistan, Thailand and India. Here we have used electron microscopy to study the three-dimensional structure ofMrNV, revealing that the viral capsid – the protein shell that encloses the viral genome, protecting it and transporting it from one host to the next – is differently organised to capsids produced by other viruses in the nodavirus family. The virus was found to have large blade-like spikes on its outer surface that are likely important in the early stages of infection, when the virus attaches to and enters a host cell.
States and traits of neural irregularity in the age-varying human brain
Authors: Waschke Leonhard , Wöestmann Malte , Obleser Jonas
Published: January 2017

Sensory representations of the physical world and thus human percepts are susceptible to fluctuations in brain state or “neural irregularity”. Furthermore, aging brains display altered levels of irregularity. We here show that a single, within-trial information-theoretic measure (weighted permutation entropy) captures neural irregularity in the human electroencephalogram as a proxy for both, trait-like differences between individuals of varying age, and state-like fluctuations that bias perceptual decisions. First, the overall level of neural irregularity increased with participants‘ age, paralleled by a decrease in variability over time, likely indexing age-related disintegration on structural and functional levels of brain activity. Second, states of higher neural irregularity were associated with optimized sensory encoding and a subsequently increased probability of choosing the first of two physically identical stimuli. In sum, neural irregularity not only characterizes behaviorally relevant brain states, but also can identify trait-like changes that come with age.
Remodeling Pathway Control of Oxidative Phosphorylation by Temperature in the Heart
Authors: Lemieux Hélène , Blier Pierre U. , Gnaiger Erich
Published: January 2017

The capacity of mitochondrial oxidative phosphorylation (OXPHOS) and fuel substrate supply are key determinants of cardiac muscle performance. Although temperature exerts a strong effect on energy metabolism, until recently numerous respiratory studies of mammalian mitochondria have been carried out below physiological temperature, with substrates supporting submaximal respiratory capacity. We measured mitochondrial respiration as a function of temperature in permeabilized fibers from the left ventricle of the mouse heart. At 37 °C, OXPHOS capacity with electron entry through either Complex I or Complex II into the Q-junction was about half of respiratory capacity with the corresponding physiological substrate combination reconstituting tricarboxylic acid cycle function with convergent electron flow through the NADH&succinate (NS) pathway. When separating the component core mitochondrial pathways, the relative contribution of the NADH pathway increased with a decrease of temperature from 37 to 25 ºC. The additive effect of convergent electron flow has profound consequences for optimization of mitochondrial respiratory control. The apparent excess capacity of cytochromecoxidase (CIV) was 0.7 above convergent NS-pathway capacity, but would be overestimated nearly 2-fold with respect to respiration restricted by provision of NADH-linked substrates only. The apparent excess capacity of CIV increased sharply at 4 °C, caused by a strong temperature dependence of and OXPHOS limitation by NADH-linked dehydrogenases. This mechanism of mitochondrial respiratory control in the hypothermic mammalian heart is comparable to the pattern in ectotherm species, pointing towards NADH-linked mt-matrix dehydrogenases and the phosphorylation system rather than electron transfer complexes as the primary drivers of thermal sensitivity at low temperature and likely modulators of temperature adaptation and acclimatization. Delineating the link between stress and remodeling of OXPHOS is critically important for improving our understanding of metabolic perturbations in disease evolution and cardiac protection. Temperature is not a trivial experimental parameter to consider when addressing these questions.
LRSim: a Linked Reads Simulator generating insights for better genome partitioning
Authors: Luo Ruibang , Sedlazeck Fritz J. , Darby Charlotte A. , Kelly Stephen M. , Schatz Michael C.
Published: January 2017

Motivation

Linked reads are a form of DNA sequencing commercialized by 10X Genomics that uses highly multiplexed barcoding within microdroplets to tag short reads to progenitor molecules. The linked reads, spanning tens to hundreds of kilobases, offer an alternative to long-read sequencing forde novoassembly, haplotype phasing and other applications. However, there is no available simulator, making it difficult to measure their capability or develop new informatics tools.

Results

Our analysis of 13 real linked read datasets revealed their characteristics of barcodes, molecules and partitions. Based on this, we introduce LRSim that simulates linked reads by emulating the library preparation and sequencing process with fine control of 1) the number of simulated variants; 2) the linked-read characteristics; and 3) the Illumina reads profile. We conclude from the phasing and genome assembly of multiple datasets, recommendations on coverage, fragment length, and partitioning when sequencing human and non-human genome.

Availability

LRSIM is under MIT license and is freely available athttps://github.com/aquaskyline/LRSIM

Contact

rluo5@jhu.edu
Mapping load-bearing in the mammalian spindle reveals local kinetochore-fiber anchorage that provides mechanical isolation and redundancy
Authors: Williard Elting Mary , Prakash Manu , Udy Dylan B. , Dumont Sophie
Published: January 2017

Active forces generated at kinetochores move chromosomes, and the dynamic spindle must robustly anchor kinetochore-fibers (k-fibers) to bear this load. We know that the mammalian spindle body can bear the load of chromosome movement far from poles, but do not know where and how – physically and molecularly – this load is distributed across the spindle. In part, this is because perturbing and reading out spindle mechanics in live cells is difficult. Yet, answering this question is key to understanding how the spindle generates and responds to force, and performs its diverse mechanical functions. Here, we map load-bearing across the mammalian spindle in space-time, and dissect local anchorage mechanics and mechanism. To do so, we laser ablate single k-fibers at different spindle locations, and in different molecular backgrounds, and quantify at high time resolution the immediate relaxation of chromosomes, k-fibers, and microtubule speckles. We find that load redistribution is locally confined in all directions: along the first 3-4 μm from kinetochores, scaling with k-fiber length, and laterally within ~2 μm of k-fiber sides, without neighboring k-fibers sharing load. A phenomenological model constrains the mechanistic underpinnings of these data: it suggests that dense, transient crosslinks to the spindle along k-fibers bear the load of chromosome movement, but that these connections do not limit the timescale of spindle reorganization. The microtubule crosslinker NuMA is needed for the local load-bearing observed, while Eg5 and PRC1 are not, suggesting specialization in mechanical function and a novel function for NuMA throughout the spindle body. Together, the data and model suggest that widespread NuMA-mediated crosslinks locally bear load, providing mechanical isolation and redundancy while allowing spindle fluidity. These features are well-suited to support robust chromosome segregation.