bluuebunny/crossref_metadata_2025 huggingface dataset:
GaN nanowires as probes for high resolution atomic force and scanning tunneling microscopy
Authors: Yngman S. , Lenrick F. , Liu Y.-P. , Ren Z. , Khalilian M. , Ohlsson B. J. , Hessman D. , Samuelson L. , Timm R. , Mikkelsen A.
Published: October 2019

GaN nanowires are potential candidates for use in scanning probe microscopy due to their well-defined, reproducible, geometric shapes, their hardness, and their light guiding properties. We have developed and investigated probes for high resolution atomic force microscopy and scanning tunneling microscopy utilizing GaN nanowires as probes. The nanowires are n-doped and the morphology of the nanowires has been tailored for scanning probe microscopy by growing them with a sharp tip for measurements and high thickness for robustness. The individual GaN nanowires were removed from their growth substrate and attached onto commercial atomic force microscopy cantilevers or etched tungsten wires for scanning tunneling microscopy. A standard scanning electron microscope equipped with a nanoprobe, a focused ion beam column and a gas injection system was used to locate, transfer, and attach the nanowires. We evaluated the properties of the GaN probes on different substrates including HOPG, Au, SiO2, InAs, and GaAs. We demonstrate both atomic force microscopy and scanning tunneling microscopy measurements with single atomic layer resolution and evaluate the robustness of the tips by monitoring them before and after scanning. Finally, we explore the use of the tips for scanning tunneling spectroscopy demonstrating that reliable results, which can reveal information on the electronic properties of the surface-tip system, are obtainable. The fundamental properties of these probes, which are demonstrated in this work, show promise for future use of the probes in exploring semiconductor-semiconductor tunneling junctions at the nanoscale as well as for other scanning probe techniques where high resolution is required.
A soft-photon theorem for the Maxwell-Lorentz system
Authors: Dybalski Wojciech , Hoang Duc Viet
Published: October 2019

For the coupled system of classical Maxwell-Lorentz equations, we show that F(x̂,t)=lim|x|→∞|x|2F(x,t) and F(k̂,t)=lim|k|→0|k|F^(k,t), where F is the Faraday tensor, F̂ is its Fourier transform in space, and x̂≔x|x|, is independent of t. We combine this observation with the scattering theory for the Maxwell-Lorentz system due to Komech and Spohn, which gives the asymptotic decoupling of F into the scattered radiation Fsc,± and the soliton field Fv±∞ depending on the asymptotic velocity v±∞ of the electron at large positive (+), respectively, negative (−) times. This gives a soft-photon theorem of the form Fsc,+(k̂)−Fsc,−(k̂)=−(Fv+∞(k̂)−Fv−∞(k̂)), and analogously for F, which links the low-frequency part of the scattered radiation to the change of the electron’s velocity. Implications for the infrared problem in QED are discussed in the Conclusions.
Cylindrical implosion experiments used to understand hydrodynamic instability growth
Authors: Gasparini Allison
Published: October 2019

Researchers investigate hydrodynamic instability growth with cylindrical implosions in order to improve inertial confinement fusion.
Review of Scientific Instruments New Products
Authors: Mandelis Andreas
Published: October 2019

In order to supplement manufacturers’ information, this department will welcome the submission by our readers of brief communications reporting measurements on the physical properties of materials which supersede earlier data or suggest new research applications.
Field benchmarking of the critical external phosphorus requirements of pasture legumes for southern Australia
Authors: Sandral Graeme A. , Price Andrew , Hildebrand Shane M. , Fuller Christopher G. , Haling Rebecca E. , Stefanski Adam , Yang Zongjian , Culvenor Richard A. , Ryan Megan H. , Kidd Daniel R. , Diffey Simon , Lambers Hans , Simpson Richard J.
Published: October 2019

In recent decades several pasture legumes have been available in southern Australia as potential alternatives to the most widely used annual pasture legume Trifolium subterraneum. Little is known about their soil phosphorus (P) requirements, but controlled environment experiments indicate that at least some may differ in their P fertiliser requirements. In this study, pasture legume varieties, including T. subterraneum as the reference species, were grown at up to four sites in any one year over a 3-year period (in total, seven site × year experiments) to measure herbage growth responses in spring to increased soil P availability. A critical soil test P concentration (corresponding to 95% maximum yield) was estimated for 15 legumes and two pasture grasses. The critical soil P requirements of most of the legumes did not differ consistently from that of T. subterraneum, indicating their soil fertility management should follow the current soil test P guidelines for temperate Australian pastures. However, the critical P requirement of Medicago sativa was higher than that of T. subterraneum, but remains ill-defined because extractable soil P concentrations in these experiments were often not high enough to permit a critical P estimate. Three forage crop legumes (Trifolium incarnatum, Trifolium purpureum, Trifolium vesiculosum) and two pasture legumes (Ornithopus compressus, Ornithopus sativus) had lower critical soil test P concentrations. It may be feasible to manage pastures based on these species to a lower soil test P benchmark without compromising yield.
Russian verbs of motion and their aspectual partners in Fluid Construction Grammar
Authors: Beuls Katrien , Knight Yana , Spranger Michael
Published: October 2019

Russian boasts a highly complex aspectual system which can appear irregular and
difficult to learn. It has recently been suggested that motion verbs, which are
normally seen as exceptional in their nature, may in fact be at the core of this
system, motivating aspectual behavior based on stem directionality. This
suggests that analyzing motion verbs may help understand the Russian aspectual
system as a whole. The present work demonstrates how Russian motion verbs and
their aspectual partners can be implemented and processed successfully with
Fluid Constructional Grammar. The study presents an example of language
processing in both production and comprehension in operation and highlights the
flexibility and power of this formalism, despite the challenges that this
complex aspectual system poses.
At the crossroads between (semi-)free relatives and indirect
questions in French
Authors: Konrad Ingrid
Published: October 2019

In this paper, we examine in some detail the
syntactic properties of (semi-)free relatives in French and their
ambiguity with indirect questions. Based on the results of an
acceptability judgment task, we argue that object free relatives
with a human referent and a full NP subject are ungrammatical in
French. We then focus on free relatives with an inanimate referent
and their ambiguity, often neglected in the literature: the
ce que structure can be either a ‘semi-free
relative clause’ (Rebuschi
2001) or an indirect question. We propose a reanalysis
from ce que to skə, suggesting that ce
que has undergone an incorporation process, parallel
but not identical to the one which has occurred with o
que in Portuguese.
Compression in French
Authors: Destruel Emilie , Féry Caroline
Published: October 2019

This paper sheds light on the conditions for
post-focal and post-verbal compression in French canonical
sentences. We report on a production experiment, which results
suggest that arguments and adjuncts are phrased differently, and
that length and information structure only exert a significant
influence on the realization of adjuncts. We formalize these results
in terms of phrasing, arguing that French, as
opposed to English for instance, does not allow compression at any
prosodic level, but only in syntactically motivated prosodic
phrases. We motivate the variation in our data via optional
phrasing.
Nominal and verbal events in Romance causative
constructions
Authors: Donazzan Marta
Published: October 2019

Romance syntactic causative constructions have
mixed properties that make it difficult to decide about their
monoclausal or biclausal structure (Rizzi 1976, Guasti 1996, a.o.).The aim
of this study is to contribute to the debate by providing an
analysis of these constructions in Italian against the background of
complex predicate formation. I address the issue of the syntactic
category of the complement of fare in syntactic
causatives by comparing them to complex predicates in Italian. I
show that, contrary to what has been claimed in recent analyses,
syntactic causatives are bieventive constructions where the
causative verb embeds a complex clause, and I offer an account of
their surface differences in terms of Voice alternation.
Non-verbal predication and clitics in Aromanian
Authors: Mavrogiorgos Marios , Ledgeway Adam
Published: October 2019

This paper discusses predicational structures in
some Aromanian varieties which involve PP or AP predicates combining
with the copula be. In these structures the internal
argument and subject of be is cross-referenced by an
accusative clitic, as long as it is 3rd person and a topic. However,
Individual-Level APs typically resist cliticisation. We propose that
the clitic is the spell-out of topic and gender/number features
available in Stage-Level predicates only (a spatio-temporal argument
à la Kratzer 1995), with
which the subject agrees, before agreeing with T. We argue that this
structural property captures the restriction to Stage-Level predicate subject topics, the person restriction, and also the fact
that the clitic behaves like a direct object clitic
morphosyntactically.
The relevance of relevance in linguistic analysis
Authors: de Jonge Bob
Published: October 2019

The Spanish simple past tenses (imperfecto and indefinido) are studied
in a literary text, supporting the claim that a discourse-related hypothesis about the meaning of these forms
allows for a correct structural analysis and, moreover, enables a revealing literary analysis. That is, the
meaning hypothesis not only accounts for the overall distribution of these forms in texts but also allows literary
analysts to gather independent evidence for the hypothesis as well as illuminating the interpretations of messages
on a literary level. The meaning hypothesis presented in this paper is based on De Jonge (2000a), which proposes that the indefinido is used for eventualities
under focus and the imperfecto is used for supportive eventualities. The corpus used for the
study was drawn from two short stories by Gabriel García Márquez.
Re-visitando significados
Authors: Martínez Angelita , Mailhes Verónica N.
Published: October 2019

En este trabajo, a partir de los principios de la Escuela Lingüística de Columbia, nos replanteamos la
sustancia semántica que subyace al paradigma que constituyen los llamados Futuro sintético y Futuro perifrástico
en español. Proponemos que dichas formas categorizan el control del emisor sobre la ocurrencia del
evento, mediante la consideración de que el hablante recurre al Futuro perifrástico para
señalar control, y al Futuro sintético para señalar la ausencia de control. A la luz de este
significado del Futuro sintético, la forma resulta adecuada para expresar mensajes tanto de
posibilidad como de profecía. Por otra parte, la opción por la perífrasis se adecua a los mensajes que intentan
inferir control. Probamos nuestra hipótesis sobre el significado de las variantes en un corpus de discurso
periodístico.
A comparative study of the restrictive markings of mandarin Jiù, Cái, and
Zhǐ
Authors: Xiang Xuehua
Published: October 2019

This study analyzes Mandarin 就 (jiù),
才(cái), and 只(zhǐ), all of which
communicate messages of restrictiveness and may be translated as ‘just,’ ‘only,’ ‘no more,’ ‘no other,’ and other
such expressions of small quantity and restriction. The study shows that the three particles distinguish distinct
restricted situations vis-à-vis the backdrop of a “spatio-temporal-existential cline” (Tobin, 1995). Jiù’s restrictive meaning centers on the situation
itself, marking it as all there is. Cái evokes a temporal cline on which more entities
may accrue following the situation’s temporal progression. Zhǐ is similar to the English notion
of “only,” affirming one entity while excluding other entities in the same situation. The paper concludes with a
discussion of comparable restrictive markings in English and Mandarin.
Evolutionary phonology as human behavior
Authors: Blevins Juliette
Published: October 2019

In this chapter I compare Columbia School Phonology as first sketched in Diver (1974, 1979) to Evolutionary Phonology
(Blevins, 2004a, 2005a, 2006a, 2008, 2009a, 2015, 2017), highlighting similarities and differences between the two
approaches. Where Columbia School Phonology grazes the surface of phonological typology, Evolutionary Phonology
grounds itself in extensive cross-linguistic surveys of common and rare sound patterns. Where Columbia School
Phonology suggests relatively simplistic intuitive phonetic explanations for sound patterns, Evolutionary
Phonology refers to detailed empirical work in distinct sub-fields of phonetics, including articulatory phonetics,
aerodynamic modeling, and perceptual studies of speech. And where Columbia School Phonology proposes usage-based
explanations for skewed distributions of sounds, Evolutionary Phonology suggests ways in which these are
inadequate, and proposes analyses where non-phonetic factors interact in complex ways with overriding phonetic
factors.
Lexicalization patterns in Slovak color naming
Authors: Dudová Katarina
Published: October 2019

This chapter deals with lexicalization patterns in Slovak
color naming on the basis of empirical data from the EoSS project
(Evolution of Semantic Systems, 2011–2014, Max Planck Institute for
Psycholinguistics, Nijmegen). Due to the developmental
particularities of the Slovak color naming system, we can find
word-formation, and other grammatical (e.g., syntactic) and semantic
(e.g., metonymy) patterns featured in the creation of Slovak color
terms in the structure of the contemporary Slovak language. For all
these patterns, we use the term lexicalization pattern, which is
involved in creating different semantic categories. Not all
lexicalization patterns are equally productive in the division of
the color spectrum. Therefore, we focus on their productivity, as
well as on the dominant and peripheral types of meanings that have
cultural roots.
Complex color denomination in French and Occitan
Authors: Bach Xavier , Kopecka Anetta , Fagard Benjamin
Published: October 2019

In this chapter, we investigate color naming in French and
Occitan. It is well known that French, compared to other Romance
languages, has a tendency to be very analytic. This raises the
following question: do speakers of French and other Romance languages (here,
Occitan) differ in morphological strategies used to express meaning
in the semantic domain of color? To investigate this question, we compare the color
descriptions provided by speakers of French
(N = 20) and speakers of Occitan
(N = 20). The results show some striking
differences between the two languages in lexical and morphosyntactic
strategies used to name colors. Speakers of Occitan employ secondary
color terms using a variety of derivational suffixes, which are
absent from the French data despite their existence in the language.
Lexicalization patterns in color naming in Croatian, Czech, and
Polish
Authors: Raffaelli Ida , Chromý Jan , Kopecka Anetta
Published: October 2019

The goal of this chapter is to identify and describe
strategies speakers of Croatian, Czech, and Polish use in color
naming. The findings are based on the data from the cross-linguistic
project Evolution of Semantic Systems (Max Planck Institute for Psycholinguistics, the Netherlands). Croatian, Czech, and Polish
were among more than 50 Indo-European languages included in the
project. In this study, we present the results of the color naming
task for the three languages. The study identified the main
lexicalization patterns that are productive in the formation of
Croatian, Czech, and Polish color terms. They are the results of
different grammatical mechanisms used in the lexicalization process.
However, the languages differ with respect to the degree of
conventionalization of these mechanisms in the domain of color
terms.
Ossetic color terms system
Authors: Vydrin Arseniy
Published: October 2019

In this chapter, I determine Iron Ossetic1's basic color terms and the
place of the Iron Ossetic2
system in the evolutionary sequence of the development of basic
color terms. I examine the semantics and use of basic and non-basic
color terms, morphological and lexical color modifiers, the main
patterns used to describe color in modern Ossetic as well as
connotations of color terms. I conclude by comparing the
peculiarities of the Ossetic color system with the systems of some
other Iranian languages.

This study is based on the methodology proposed by A.
Majid, F. Jordan, and M. Dunn
(2011). The Ossetic material is taken from the field data
collected in North Ossetia, Russia, and data from the Ossetic
corpora3.
Intonation in southern Vietnamese interrogative sentences
Authors: Hà Phạm Thị Thu , Brunelle Marc
Published: October 2019

This study looks at the acoustic cues that characterize the intonation of questions in southern Vietnamese. We find a raised f0 height and a rising contour in a third of interrogatives, but – with the exception of alternative (and some open) questions – we argue that these properties cannot distinguish interrogatives from other sentence types. The only cue systematically associated with questions is that they tend to have a faster speech rate. Our findings replicate recent studies conducted on northern Vietnamese showing that there are idiosyncratic differences in the realization of intonation and that intonation may not be as grammaticalized as in Western languages. Vietnamese interrogatives are marked with particles or inferred from context and their intonation plays an ancillary role.
Vietnamese dialects
Authors: Pham Andrea Hoa
Published: October 2019

Among Vietnamese dialects, the southern dialect of Quảng Nam is notable for its rimal peculiarities. These properties have not generally been reported for any other Vietnamese dialects. However, some features – in particular, the vowel [ɑ] and correspondence between [aw] and [o] – have recently been observed in small dialects of the north-central Hà Tĩnh region. The Thanh Hoá dialect, spoken in a province which lies between the northern and north-central regions of Vietnam, bears certain close similarities to Quảng Nam dialect, yet does not share the features in the same way as they are shared between Quảng Nam and the Hà Tĩnh subdialects. The paper argues for the a between these three non-standard varieties, Quảng Nam, Hà Tĩnh and Thanh Hoá dialects, each belonging to a different major dialectal group (and each geographically separated from one another). Through an examination of the similarities and differences between these dialects, focusing on the Hà Tĩnh subdialect, it is argued that historical migration is the cause of sound change in the Quảng Nam dialect. The paper claims that Quảng Nam dialect was based on the speech of migrants from Thanh Hoá province, and has subsequently integrated certain features from the speech of Hà Tĩnh migrants.
Scalar implicatures and the semantics of wh-indefinites in Vietnamese
Authors: Tsai Cheng-Yu Edwin , Quang Kim Ngọc
Published: October 2019

In this chapter we attempt to account for the meaning of wh-indefinites in Vietnamese through a formal system of scalar implicatures and exhaustification (Chierchia, Fox & Spector 2012; Chierchia 2013). While Vietnamese wh-indefinites occur in a variety of licensing contexts, we conclude that the crucial condition is speaker ignorance, which can be derived compositionally from the interaction between a wh-indefinite, an exhaustification operator, and a speaker-oriented epistemic modal. We further discuss the interpretations of morphologically complex wh-indefinites and bare wh-indefinites in negative sentences and non-epistemic modal environments, and demonstrate how to derive their semantics uniformly. Our proposal presents an alternative to the syntactic analysis by Tran & Bruening (2013), which is critically reviewed.
Vietnamese children’s interpretation of definite noun phrases
Authors: Lê Ni-La , Forsythe Hannah , Schmitt Cristina
Published: October 2019

Most work on the acquisition of definiteness examines languages with definite determiners and grammaticalised number, and finds slower acquisition of definiteness compared to number. We replicate an act-out task from Munn et al. (2006) testing comprehension of definites in Vietnamese – a language with neither of these characteristics. In contrast to the results from English and Spanish children, Vietnamese children are found to make few definiteness errors, instead struggling with number, casting doubt on a universal difficulty with definiteness. We argue that this difference stems from the way in which children integrate information from number and definiteness. Given a high level of task difficulty, children acquiring languages with definite determiners and grammatical number, such as English and Spanish, sacrifice definiteness in favour of number, while those acquiring Vietnamese prioritise definiteness, resulting in number errors.
Interpretation of numerals under memory load by Vietnamese speakers
Authors: Haida Andreas , Trinh Tue , Luong Chi Mai
Published: October 2019

Numerals show an ambiguity between a weak, ‘at least’ meaning and a strong, ‘exactly’ meaning. The Gricean approach takes the weak meaning to be basic and derives the strong meaning as implicature, thus assimilates numerals to other scalar items. The Fregean approach, in contrast, takes the strong meaning of numerals to be basic and derives the weak meaning via type shifting operations. This paper gives a brief summary of these two approaches, followed by a report on a dual-task experiment which is designed to test how Vietnamese speakers interpret numerals under different memory loads. The goal of this experiment is to replicate the results of Marty et al. (2013) which can be interpreted as supporting the Fregean approach. It turns out that this goal could not be achieved, and we give some speculations as to why it was not.
Masculinities and environment.
Authors: Paulson S. , Boose W.
Published: October 2019

This review article supports researchers and practitioners to strengthen attention to variously positioned men and masculine identities in order to increase the rigour of empirical research and to enhance outcomes of work addressing environmental issues. Masculinities interact with other factors to shape patterns of environmental management and to influence responses to environmental challenges; at the same time, human-environment dynamics produce differing expressions and experiences of masculinity. Yet, environmental initiatives implemented in many contexts and scales have been hindered by lack of attention to gendered conditions, identities and expectations associated with diversely positioned men. Theoretically, studies gathered here strive to overcome these limitations by applying concepts of plural masculinities, intersectionality and hegemonic masculinity. Methodologically, this body of work challenges universalizing stereotypes about men by situating empirical studies in specific sociocultural, ethnoracial, ecological and geographical contexts around the world. The 160 publications reviewed here illuminate three realms: productive enterprises including logging, mining, petroleum exploitation, ranching and agroindustry; lifeways and attitudes involving care for health, families and nature; and environmental crises, from disasters to refugees and climate change. Evidence in each realm suggests that some masculine-identified behaviours, attitudes and resources are intertwined with environmentally destructive processes, while others support, or can support, moves toward dynamics that are healthier for humans and non-human nature. After considering skills, tools and frameworks for further research and practice, die review ends with a look at challenges of developing more systemic approaches to gender and environment.
Plasma expansion accompanying superthermal electrons in over-picosecond relativistic laser-foil interactions
Authors: Iwata Natsumi , Sentoku Yasuhiko , Sano Takayoshi , Mima Kunioki
Published: October 2019

We study the plasma expansion dynamics in over-picosecond relativistic laser-foil interactions using one-dimensional particle-in-cell (PIC) simulations. A new expansion mode ‘isofield expansion’ appears after the well-known isothermal expansion due to the continuous energy input from the laser light to the plasma. The blowout of the heated plasma at the front surface triggers the transition from the isothermal mode to the new mode. In the new expansion mode, electrons and ions expand quasi-neutrally with a constant sheath electric field, and a large scale low density plasma is formed where superthermal electrons are produced efficiently. A two-dimensional PIC simulation confirms the appearance of the isofield expansion mode after the plasma blowout for a large focal spot laser.
InP quantum dots-based electroluminescent devices*
Authors: Wu Qianqian , Cao Fan , Kong Lingmei , Yang Xuyong
Published: October 2019

Indium phosphide (InP) quantum dots (QDs) have shown great potential to replace the widely applied toxic cadmium-containing and lead perovskite QDs due to their similar emission wavelength range and emission peak width but without intrinsic toxicity. Recently, electrically driven red and green InP-based quantum-dot light-emitting diodes (QLEDs) have achieved great progress in external quantum efficiency (EQE), reaching up to 12.2% and 6.3%, respectively. Despite the relatively poor device performance comparing with cadmium selenide (CdSe)- and perovskite-based QLEDs, these encouraging facts with unique environmental friendliness and solution-processability foreshadow the enormous potential of InP-based QLEDs for energy-efficient, high-color-quality thin-film display and solid-state lighting applications. In this article, recent advances in the research of the InP-based QLEDs have been discussed, with the main focus on device structure selection and interface research, as well as our outlook for on-going strategies of high-efficiency InP-based QLEDs.
Measurement of the Drell –Yan Angular Coefficients with the CMS Experiment at LHC
Authors: Gorbunov Ilya , Shalaev Vladislav , Smatov Sergey
Published: October 2019

Results of the angular coefficients measurement with the Drell-Yan muon pairs at 8 TeV are presented. A
0 through A
4 coefficients were measured in bins of muon pair transverse momentum and rapidity using the Compact Muon Solenoid (CMS) data collected during the first Large Hadron Collider (LHC) run (Run 1) in 2011 and 2012 corresponding to 19.7 fb
−1. No deviations from the Standard Model (SM) predictions observed within uncertainties in the leading and next-to-leading orders.
Understanding spatial variability of methane fluxes in Arctic wetlands through footprint modelling
Authors: Reuss-Schmidt Kassandra , Levy Peter , Oechel Walter , Tweedie Craig , Wilson Cathy , Zona Donatella
Published: October 2019

The Arctic is warming at twice the rate of the global mean. This warming could further stimulate methane (CH4) emissions from northern wetlands and enhance the greenhouse impact of this region. Arctic wetlands are extremely heterogeneous in terms of geochemistry, vegetation, microtopography, and hydrology, and therefore CH4 fluxes can differ dramatically within the metre scale. Eddy covariance (EC) is one of the most useful methods for estimating CH4 fluxes in remote areas over long periods of time. However, when the areas sampled by these EC towers (i.e. tower footprints) are by definition very heterogeneous, due to encompassing a variety of environmental conditions and vegetation types, modelling environmental controls of CH4 emissions becomes even more challenging, confounding efforts to reduce uncertainty in baseline CH4 emissions from these landscapes. In this study, we evaluated the effect of footprint variability on CH4 fluxes from two EC towers located in wetlands on the North Slope of Alaska. The local domain of each of these sites contains well developed polygonal tundra as well as a drained thermokarst lake basin. We found that the spatiotemporal variability of the footprint, has a significant influence on the observed CH4 fluxes, contributing between 3% and 33% of the variance, depending on site, time period, and modelling method. Multiple indices were used to define spatial heterogeneity, and their explanatory power varied depending on site and season. Overall, the normalised difference water index had the most consistent explanatory power on CH4 fluxes, though generally only when used in concert with at least one other spatial index. The spatial bias (defined here as the difference between the mean for the 0.36 km2 domain around the tower and the footprint-weighted mean) was between ∣51∣% and ∣18∣% depending on the index. This study highlights the need for footprint modelling to infer the representativeness of the carbon fluxes measured by EC towers in these highly heterogeneous tundra ecosystems, and the need to evaluate spatial variability when upscaling EC site-level data to a larger domain.
Plant-mSubP: a computational framework for the prediction of single- and multi-target protein subcellular localization using integrated machine-learning approaches
Authors: Sahu Sitanshu S , Loaiza Cristian D , Kaundal Rakesh
Published: October 2019

The subcellular localization of proteins is very important for characterizing its function in a cell. Accurate prediction of the subcellular locations in computational paradigm has been an active area of interest. Most of the work has been focused on single localization prediction. Only few studies have discussed the multi-target localization, but have not achieved good accuracy so far; in plant sciences, very limited work has been done. Here we report the development of a novel tool Plant-mSubP, which is based on integrated machine learning approaches to efficiently predict the subcellular localizations in plant proteomes. The proposed approach predicts with high accuracy 11 single localizations and three dual locations of plant cell. Several hybrid features based on composition and physicochemical properties of a protein such as amino acid composition, pseudo amino acid composition, auto-correlation descriptors, quasi-sequence-order descriptors and hybrid features are used to represent the protein. The performance of the proposed method has been assessed through a training set as well as an independent test set. Using the hybrid feature of the pseudo amino acid composition, N-Center-C terminal amino acid composition and the dipeptide composition (PseAAC-NCC-DIPEP), an overall accuracy of 81.97 %, 84.75 % and 87.88 % is achieved on the training data set of proteins containing the single-label, single- and dual-label combined, and dual-label proteins, respectively. When tested on the independent data, an accuracy of 64.36 %, 64.84 % and 81.08 % is achieved on the single-label, single- and dual-label, and dual-label proteins, respectively. The prediction models have been implemented on a web server available at http://bioinfo.usu.edu/Plant-mSubP/. The results indicate that the proposed approach is comparable to the existing methods in single localization prediction and outperforms all other existing tools when compared for dual-label proteins. The prediction tool will be a useful resource for better annotation of various plant proteomes.
High-throughput sequencing is revealing genetic associations with avian plumage color
Authors: Funk Erik R , Taylor Scott A
Published: October 2019

Avian evolution has generated an impressive array of patterns and colors in the ~10,000 bird species that exist on Earth. Recently, a number of exciting studies have utilized whole-genome sequencing to reveal new details on the genetics of avian plumage color. These findings provide compelling evidence for genes that underlie plumage variation across a wide variety of bird species (e.g., juncos, warblers, seedeaters, and estrildid finches). While much is known about large, body-wide color changes, these species exhibit discrete color differences across small plumage patches. Many genetic differences appear to be located in regulatory regions of genes rather than in protein-coding regions, suggesting gene expression is playing a large role in the control of these color patches. Taken together, these studies have the potential to broadly facilitate further research of sexual selection and evolution in these charismatic taxa.
Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration
Authors: Pierre-Jean Morgane , Deleuze Jean-François , Le Floch Edith , Mauger Florence
Published: October 2019

Recent advances in NGS sequencing, microarrays and mass spectrometry for omics data production have enabled the generation and collection of different modalities of high-dimensional molecular data. The integration of multiple omics datasets is a statistical challenge, due to the limited number of individuals, the high number of variables and the heterogeneity of the datasets to integrate. Recently, a lot of tools have been developed to solve the problem of integrating omics data including canonical correlation analysis, matrix factorization and SM. These commonly used techniques aim to analyze simultaneously two or more types of omics. In this article, we compare a panel of 13 unsupervised methods based on these different approaches to integrate various types of multi-omics datasets: iClusterPlus, regularized generalized canonical correlation analysis, sparse generalized canonical correlation analysis, multiple co-inertia analysis (MCIA), integrative-NMF (intNMF), SNF, MoCluster, mixKernel, CIMLR, LRAcluster, ConsensusClustering, PINSPlus and multi-omics factor analysis (MOFA). We evaluate the ability of the methods to recover the subgroups and the variables that drive the clustering on eight benchmarks of simulation. MOFA does not provide any results on these benchmarks. For clustering, SNF, MoCluster, CIMLR, LRAcluster, ConsensusClustering and intNMF provide the best results. For variable selection, MoCluster outperforms the others. However, the performance of the methods seems to depend on the heterogeneity of the datasets (especially for MCIA, intNMF and iClusterPlus). Finally, we apply the methods on three real studies with heterogeneous data and various phenotypes. We conclude that MoCluster is the best method to analyze these omics data. Availability: An R package named CrIMMix is available on GitHub at https://github.com/CNRGH/crimmix to reproduce all the results of this article.
Seismic shear wave anisotropy of an anisotropic rock containing aligned cracks: theory and applications to experiment and field data
Authors: Xu Song , Tang Xiaoming , Su Yuanda , Zhuang Chunxi
Published: October 2019

Cracks universally exist in Earth's crustal rocks. Many rocks are intrinsically anisotropic, which, when coupled with crack-induced anisotropy, significantly affect seismic wave propagation through the rocks. Using the method of sphere equivalency of effective scattering, we have developed a technique to model the effective moduli of transversely isotropic (TI) media containing cracks. The modelling results show that the wave characteristics are significantly affected by the interaction of the two anisotropy mechanisms. To validate the validity and accuracy, the theory was applied to a recent experiment made with a vertical transverse isotropy (VTI) medium containing cracks and shows significantly better agreement with the data. For a more realistic situation, the new modelling was applied to interpret the borehole acoustic anisotropy measurement results from a fractured VTI formation, showing that the theory can adequately explain the anisotropic characteristics of the field data. With the validation and testing, the theoretical results advocated in this study can be used with confidence.
A path dependence analysis of hospital dominance in China (1949–2018): lessons for primary care strengthening
Authors: Xu Jin , Gorsky Martin , Mills Anne
Published: October 2019

Although China’s community health system helped inspire the 1978 Alma Ata Declaration on Health for All, it currently faces the challenge of strengthening primary care in response to hospital sector dominance. As the world reaffirms its commitment towards primary health services, China’s recent history provides a salient case study of the issues at stake in optimizing the balance of care. In this study, we have used path dependence analysis to explain China’s coevolution of hospital and primary care facilities between 1949 and 2018. We have identified two cycles of path-dependent development (1949–78 and 1978–2018) involving four sets of institutions related to medical professionalization, financing, organization and governance of health facilities. Both cycles started with a critical juncture amid a radically changing societal context, when institutions favouring hospitals were initiated or renewed, leading to a process of self-reinforcement empowering the hospitals. Later in each cycle, events occurred that modified this hospital dominance. However, pro-primary care policies during these conjunctures encountered resilience from the existing institutional environment. The result was continued consolidation of hospital dominance over the long term. These recurrent constraints suggest that primary care strengthening is unlikely to be successful without a comprehensive set of policy reforms driven by a primary care coalition with strong professional, bureaucratic and community stakes, co-ordinated and sustained over a prolonged period. Our findings imply that it is important to understand the history of health systems in China, where the challenges of health systems strengthening go beyond limited resources and include different developmental paths as compared with Western countries.
Functional cross talk between the Fanconi anemia and ATRX/DAXX histone chaperone pathways promotes replication fork recovery
Authors: Raghunandan Maya , Yeo Jung Eun , Walter Ryan , Saito Kai , Harvey Adam J , Ittershagen Stacie , Lee Eun-A , Yang Jihyeon , Hoatlin Maureen E , Bielinsky Anja K , Hendrickson Eric A , Schärer Orlando , Sobeck Alexandra
Published: October 2019

Fanconi anemia (FA) is a chromosome instability syndrome characterized by increased cancer predisposition. Specifically, the FA pathway functions to protect genome stability during DNA replication. The central FA pathway protein, FANCD2, locates to stalled replication forks and recruits homologous recombination (HR) factors such as CtBP interacting protein (CtIP) to promote replication fork restart while suppressing new origin firing. Here, we identify alpha-thalassemia retardation syndrome X-linked (ATRX) as a novel physical and functional interaction partner of FANCD2. ATRX is a chromatin remodeler that forms a complex with Death domain-associated protein 6 (DAXX) to deposit the histone variant H3.3 into specific genomic regions. Intriguingly, ATRX was recently implicated in replication fork recovery; however, the underlying mechanism(s) remained incompletely understood. Our findings demonstrate that ATRX forms a constitutive protein complex with FANCD2 and protects FANCD2 from proteasomal degradation. ATRX and FANCD2 localize to stalled replication forks where they cooperate to recruit CtIP and promote MRE11 exonuclease-dependent fork restart while suppressing the firing of new replication origins. Remarkably, replication restart requires the concerted histone H3 chaperone activities of ATRX/DAXX and FANCD2, demonstrating that coordinated histone H3 variant deposition is a crucial event during the reinitiation of replicative DNA synthesis. Lastly, ATRX also cooperates with FANCD2 to promote the HR-dependent repair of directly induced DNA double-stranded breaks. We propose that ATRX is a novel functional partner of FANCD2 to promote histone deposition-dependent HR mechanisms in S-phase.
Lipopeptide-Based Oral Vaccine Against Hookworm Infection
Authors: Bartlett Stacey , Eichenberger Ramon M , Nevagi Reshma J , Ghaffar Khairunnisa Abdul , Marasini Nirmal , Dai Yang , Loukas Alex , Toth Istvan , Skwarczynski Mariusz
Published: October 2019

Background

The human hookworm, Necator americanus, is a parasite that infects almost half a billion people worldwide. Although treatment is available, vaccination is favorable to combat the spread of this parasite due to its wide distribution and continuous reinfection cycle in endemic communities.

Methods

We have designed a lipopeptide oral delivery system using a B-cell epitope derived from the aspartic protease Na-APR-1 from N americanus, attached to a T-helper epitope. Lipopeptides were self-assembled into nanoparticles or entrapped in liposomes that were electrostatically coated with alginate and trimethyl chitosan polymer shields. The adjuvant-free vaccine candidates were orally administered to mice and generated a humoral immune response against both peptide antigen, and the parent protein in the hookworm gut.

Results

The vaccine candidates were evaluated in a rodent hookworm challenge model, resulting in up to 98% and 99% decreases in mean intestinal worm and egg burdens in immunized mice, respectively.

Conclusions

Lipopeptide survived the gastrointestinal conditions, induced humoral immune responses and drived protection against parasite challenge infection.
Zika Virus Causes Acute and Chronic Prostatitis in Mice and Macaques
Authors: Halabi Jacques , Jagger Brett W , Salazar Vanessa , Winkler Emma S , White James P , Humphrey Peter A , Hirsch Alec J , Streblow Daniel N , Diamond Michael S , Moley Kelle
Published: October 2019

Background

Sexual transmission and persistence of Zika virus (ZIKV) in the male reproductive tract has raised concerned for potential damaging effects on function. Animal studies have demonstrated that ZIKV virus can infect and damage the testis and epididymis, and these results has been correlated to lower sperm counts in ZIKV-infected humans. The prostate plays a vital role in the male reproductive tract, with acute and chronic prostatitis linked to male infertility.

Methods

In this study, we evaluated the effects of ZIKV virus on the prostate in mice and nonhuman primates.

Results

In mice, ZIKV infected the prostate and triggered inflammation that persisted even after virus clearance. Evidence of chronic prostatitis associated with ZIKV infection remained for several months. Similar histological findings were observed in the prostate of ZIKV-infected rhesus macaques.

Conclusions

These studies establish that ZIKV replicates in the prostate and can cause acute and chronic inflammatory and proliferative changes in mouse and nonhuman primate models.
Intuitions about Objects: From Teleology to Elimination
Authors: Kovacs David Mark
Published: October 2019

In a series of recent papers, David Rose and Jonathan Schaffer use a number of experiments to show that folk intuitions about composition and persistence are driven by pre-scientific teleological tendencies. They argue that these intuitions are fit for debunking and that the playing field for competing accounts of composition and persistence should therefore be considered even: no view draws more support from folk intuitions than its rivals, and the choice between them should be made exclusively on the basis of theoretical considerations. In this paper I argue that Rose and Schaffer draw the wrong conclusion from their own findings, which should instead push us toward sparse views about composition and persistence. Most metaphysicians (including Schaffer himself, and arguably Rose too) should be worried by this result, since they hold views that are flatly incompatible with it.
On the measurements of assembly bias and splashback radius using optically selected galaxy clusters
Authors: Sunayama Tomomi , More Surhud
Published: October 2019

We critically examine the methodology behind the claimed observational detection of halo assembly bias using optically selected galaxy clusters by Miyatake et al. and More et al. We mimic the optical cluster detection algorithm and apply it to two different mock catalogues generated from the Millennium simulation galaxy catalogue, one in which halo assembly bias signal is present, while the other in which the assembly bias signal has been expressly erased. We split each of these cluster samples into two using the average cluster-centric distance of the member galaxies to measure the difference in the clustering strength of the subsamples with respect to each other. We observe that the subsamples split by cluster-centric radii show differences in clustering strength, even in the catalogue where the true assembly bias signal was erased. We show that this is a result of contamination of the member galaxy sample from interlopers along the line of sight. This undoubtedly shows that the particular methodology adopted in the previous studies cannot be used to claim a detection of the assembly bias signal. We figure out the tell-tale signatures of such contamination, and show that the observational data also show similar signatures. Furthermore, we also show that projection effects in optical galaxy clusters can bias the inference of the 3D edges of galaxy clusters (splashback radius), so appropriate care should be taken while interpreting the splashback radius of optical clusters.
A SCUBA-2 selected Herschel-SPIRE dropout and the nature of this population
Authors: Greenslade J , Aguilar E , Clements D L , Dannerbauer H , Cheng T , Petitpas G , Yang C , Messias H , Oteo I , Farrah D , Michałowski M J , Pérez Fournon I , Aretxaga I , Yun M S , Eales S , Dunne L , Cooray A , Andreani P , Hughes D H , Velázquez M , Sánchez-Argüelles D , Ponthieu N
Published: October 2019

Dusty star-forming galaxies (DSFGs) detected at z > 4 provide important examples of the first generations of massive galaxies. However, few examples with spectroscopic confirmation are currently known, with Hershel struggling to detect significant numbers of z > 6 DSFGs. NGP6_D1 is a bright 850 $\mathrm{ \mu}$m source (12.3 ± 2.5 mJy) with no counterparts at shorter wavelengths (a SPIRE dropout). Interferometric observations confirm it is a single source, with no evidence for any optical or NIR emission, or nearby likely foreground lensing sources. No >3σ detected lines are seen in both LMT Redshift Search Receiver and IRAM 30 m EMIR spectra of NGP6_D1 across 32 GHz of bandwidth despite reaching detection limits of $\sim 1\, \mathrm{mJy}/500 \, \mathrm{km~s}^{-1}$, so the redshift remains unknown. Template fitting suggests that NGP6_D1 is most likely between z = 5.8 and 8.3. SED analysis finds that NGP6_D1 is a ULIRG, with a dust mass ∼108–109 M⊙ and a star-formation rate of ∼500 M⊙ yr−1. We place upper limits on the gas mass of NGP6_D1 of MH2 <(1.1 ± 3.5) × 1011 M⊙, consistent with a gas-to-dust ratio of ∼100–1000. We discuss the nature of NGP6_D1 in the context of the broader sub-mm population, and find that comparable SPIRE dropouts account for ∼20 per cent of all SCUBA-2 detected sources, but with a similar flux density distribution to the general population.