bluuebunny/crossref_metadata_2025 huggingface dataset:
Particle Residence Time in pulsatile post-stenotic flow
Authors: Jeronimo M. D. , Rival D. E.
Published: April 2020

Particle Residence Time (PRT), a measure of a fluid element’s transit time through a region of interest, is a clear indicator of recirculation. The PRT of fluid recirculating downstream of an idealized stenosis geometry is found to vary dramatically under pulsatile flow conditions. Two-dimensional particle tracking velocimetry is used to track particles directly as they exit the stenosis geometry and are entrained into the region of recirculation immediately downstream. A Lagrangian approach permits long pathlines to be drawn, describing each particle’s motion from the instant they enter the domain. PRT along each pathline is compared here for three mean Reynolds numbers; specifically, Rem = 4800, 9600, and 14 400. The pulsatile waveforms are characterized by Strouhal numbers of 0.04, 0.08, and 0.15 and amplitude ratios of 0.50 and 0.95. As the mean Reynolds number is increased, higher fluid velocities are shown to lower PRT. However, the strength of PRT is truly revealed when highlighting the influence pulsatility has on the degree of mixing beyond the stenosis throat. Higher Strouhal numbers correlate with roll-up across the shear layer and increased PRT distribution at all Reynolds numbers in consideration. Similarly, strong temporal velocity gradients generated by a high amplitude ratio carry large volumes of fluid from the jet deep into the recirculation region, contributing to greater PRT.
Construction and electrochemical properties determination of carbon nanotubes/porous-network carbon micron tubes/silk fibroin composite film neural electrode
Authors: Shen Xuefei , Zhao Yu , Li Qian , Chen Tao
Published: April 2020

A novel carbon nanotubes/porous-network carbon micron tubes/silk fibroin (CPS) composite film neural electrode was presented and characterized. This electrode was fabricated through assembling dispersed carbon nanotubes (CNTs) by phytic acid onto the porous silk fibroin film. Afterward, the silk fibroin around the CNTs was carbonized by laser irradiation, producing porous-network carbon microtubes with good conductivity and biological compatibility. The structure of the CPS composite film was characterized by scanning electron microscopy and Raman spectroscopy. Cyclic voltammetry, electrochemical impedance spectroscopy, and safe charge injection limit (Qinj) of the CPS electrode were also measured by the three-electrode system, and the results exhibited outstanding electrochemical properties with the achieved Qinj of 5.7 mC/cm2. This work provides a promising approach for the preparation of a long-term implanted neural electrode with high charge injection ability and good biocompatibility.
Automatically growing global reactive neural network potential energy surfaces: A trajectory-free active learning strategy
Authors: Lin Qidong , Zhang Yaolong , Zhao Bin , Jiang Bin
Published: April 2020

An efficient and trajectory-free active learning method is proposed to automatically sample data points for constructing globally accurate reactive potential energy surfaces (PESs) using neural networks (NNs). Although NNs do not provide the predictive variance as the Gaussian process regression does, we can alternatively minimize the negative of the squared difference surface (NSDS) given by two different NN models to actively locate the point where the PES is least confident. A batch of points in the minima of this NSDS can be iteratively added into the training set to improve the PES. The configuration space is gradually and globally covered without the need to run classical trajectory (or equivalently molecular dynamics) simulations. Through refitting the available analytical PESs of H3 and OH3 reactive systems, we demonstrate the efficiency and robustness of this new strategy, which enables fast convergence of the reactive PESs with respect to the number of points in terms of quantum scattering probabilities.
Quantum ESPRESSO toward the exascale
Authors: Giannozzi Paolo , Baseggio Oscar , Bonfà Pietro , Brunato Davide , Car Roberto , Carnimeo Ivan , Cavazzoni Carlo , de Gironcoli Stefano , Delugas Pietro , Ferrari Ruffino Fabrizio , Ferretti Andrea , Marzari Nicola , Timrov Iurii , Urru Andrea , Baroni Stefano
Published: April 2020

Quantum ESPRESSO is an open-source distribution of computer codes for quantum-mechanical materials modeling, based on density-functional theory, pseudopotentials, and plane waves, and renowned for its performance on a wide range of hardware architectures, from laptops to massively parallel computers, as well as for the breadth of its applications. In this paper, we present a motivation and brief review of the ongoing effort to port Quantum ESPRESSO onto heterogeneous architectures based on hardware accelerators, which will overcome the energy constraints that are currently hindering the way toward exascale computing.
An investigation of aluminum nitride thin films patterned by femtosecond laser
Authors: Dong Fang , Li Rui , Wu Gai , Liang Kang , Li Guoliang , Nie Yangtian , Gan Zhiyin , Cao Qiang , Wang Xuehui , Zhao Quanzhong , Liu Sheng
Published: April 2020

In this study, a femtosecond laser etching method is proposed to pattern an aluminum nitride (AlN) film, grown by metal-organic chemical vapor deposition on sapphire. Via control of typical pulse energies, the designed pattern was precisely written in the AlN film. The morphology of the patterned structures was characterized using a three-dimensional laser scanning confocal microscope and a scanning electron microscope; crystalline quality and film strain were analyzed using a Raman spectrometer and a transmission electron microscope. The results indicate that consistent morphologies were achieved with only slight changes to the crystalline quality. The tensile stress of the AlN film was released, and the film surface was slightly compressed after laser patterning. Thus, femtosecond etching has the potential to be an in situ patterning method during film growth.
Vip1 is a kinase and pyrophosphatase switch that regulates inositol diphosphate signaling
Authors: Dollins D. Eric , Bai Wenli , Fridy Peter C. , Otto James C. , Neubauer Julie L. , Gattis Samuel G. , Mehta Kavi P. M. , York John D.
Published: April 2020

Inositol diphosphates (PP-IPs), also known as inositol pyrophosphates, are high-energy cellular signaling codes involved in nutrient and regulatory responses. We report that the evolutionarily conserved gene product, Vip1, possesses autonomous kinase and pyrophosphatase domains capable of synthesis and destruction of D-1 PP-IPs. Our studies provide atomic-resolution structures of the PP-IP products and unequivocally define that the Vip1 gene product is a highly selective 1-kinase and 1-pyrophosphatase enzyme whose activities arise through distinct active sites. Kinetic analyses of kinase and pyrophosphatase parameters are consistent with Vip1 evolving to modulate levels of 1-IP
7
and 1,5-IP
8
. Individual perturbations in kinase and pyrophosphatase activities in cells result in differential effects on vacuolar morphology and osmotic responses. Analogous to the dual-functional key energy metabolism regulator, phosphofructokinase 2, Vip1 is a kinase and pyrophosphatase switch whose 1-PP-IP products play an important role in a cellular adaptation.
Covert sleep-related biological processes are revealed by probabilistic analysis in
Drosophila
Authors: Wiggin Timothy D. , Goodwin Patricia R. , Donelson Nathan C. , Liu Chang , Trinh Kien , Sanyal Subhabrata , Griffith Leslie C.
Published: April 2020

Sleep pressure and sleep depth are key regulators of wake and sleep. Current methods of measuring these parameters in
Drosophila melanogaster
have low temporal resolution and/or require disrupting sleep. Here we report analysis tools for high-resolution, noninvasive measurement of sleep pressure and depth from movement data. Probability of initiating activity, P(Wake), measures sleep depth while probability of ceasing activity, P(Doze), measures sleep pressure. In vivo and computational analyses show that P(Wake) and P(Doze) are largely independent and control the amount of total sleep. We also develop a Hidden Markov Model that allows visualization of distinct sleep/wake substates. These hidden states have a predictable relationship with P(Doze) and P(Wake), suggesting that the methods capture the same behaviors. Importantly, we demonstrate that both the Doze/Wake probabilities and the sleep/wake substates are tied to specific biological processes. These metrics provide greater mechanistic insight into behavior than measuring the amount of sleep alone.
Cryo-EM structure of C9ORF72–SMCR8–WDR41 reveals the role as a GAP for Rab8a and Rab11a
Authors: Tang Dan , Sheng Jingwen , Xu Liangting , Zhan Xiechao , Liu Jiaming , Jiang Hui , Shu Xiaoling , Liu Xiaoyu , Zhang Tizhong , Jiang Lan , Zhou Cuiyan , Li Wenqi , Cheng Wei , Li Zhonghan , Wang Kunjie , Lu Kefeng , Yan Chuangye , Qi Shiqian
Published: April 2020

A massive intronic hexanucleotide repeat (GGGGCC) expansion inC9ORF72is a genetic origin of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recently, C9ORF72, together with SMCR8 and WDR41, has been shown to regulate autophagy and function as Rab GEF. However, the precise function of C9ORF72 remains unclear. Here, we report the cryogenic electron microscopy (cryo-EM) structure of the human C9ORF72–SMCR8–WDR41 complex at a resolution of 3.2 Å. The structure reveals the dimeric assembly of a heterotrimer of C9ORF72–SMCR8–WDR41. Notably, the C-terminal tail of C9ORF72 and the DENN domain of SMCR8 play critical roles in the dimerization of the two protomers of the C9ORF72–SMCR8–WDR41 complex. In the protomer, C9ORF72 and WDR41 are joined by SMCR8 without direct interaction. WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix. Interestingly, the prominent structural feature of C9ORF72–SMCR8 resembles that of the FLNC–FNIP2 complex, the GTPase activating protein (GAP) of RagC/D. Structural comparison and sequence alignment revealed that Arg147 of SMCR8 is conserved and corresponds to the arginine finger of FLCN, and biochemical analysis indicated that the Arg147 of SMCR8 is critical to the stimulatory effect of the C9ORF72–SMCR8 complex on Rab8a and Rab11a. Our study not only illustrates the basis of C9ORF72–SMCR8–WDR41 complex assembly but also reveals the GAP activity of the C9ORF72–SMCR8 complex.
Mood in future-framed adverbials
Authors: Hoff Mark R.
Published: April 2020

In Spanish adverbial clauses containing
cuando ‘when’ and a present-tense verb, it is
assumed that indicative expresses habituality, but subjunctive
futurity. However, in Rioplatense, indicative [I] occurs in
future-framed adverbials, conveying epistemic pragmatic meaning:
Cuando bajás [I] del bondi,
llamame ‘When you get off the bus, call me.’ An online
questionnaire containing 32 contextualized sentences was distributed
to Rioplatense speakers (N = 140), and respondents
assigned acceptability ratings using a Likert scale. Mixed-effects
linear regression modeling shows that indicative is felicitous with
immediate and temporally-delimited actions, and when epistemic
certainty is conveyed; subjunctive is preferred for
distant/unrestricted future actions, or uncertainty. These findings
suggest an alternative criterion for mood choice in Rioplatense,
based on epistemicity rather than differentiation between present
and future events.
The relationship between iconicity and systematicity in Korean
ideophones
Authors: Kwon Nahyun
Published: April 2020

This chapter investigates the relationship between two
forms of non-arbitrariness in Korean ideophones: relative iconicity,
which is a resemblance-based mapping between relations among
multiple forms and relations among multiple meanings (exemplified by
paradigmatic consonantal symbolism), and systematicity, which is a
statistical regularities-based mapping between form and meaning
(exemplified by ideophonic vowel harmony). Using a written corpus of
Korean ideophones, the present study quantifies the number of
variants in consonantal constellations, where larger constellations
are judged to have a higher degree of relative iconicity than
smaller constellations. The results reveal that larger
constellations are more susceptible to the influence exerted by
vowel harmony. This language-internal finding suggests a tight
correlation between relative iconicity and systematicity, and allows
further investigation into its generalizability from a broad
typological perspective.
Iconicity of Telugu ideophones and full word
reduplications
Authors: Duggirala Vasanta , Murty Lalita
Published: April 2020

This paper offers an account of variation in iconicity
within and between ideophones and Full Word Reduplications (FWRs) in
Telugu texts. Some of this variation is connected to differences in
the grammatical classes to which these structures belong, the types
of constructions in which they participate, and the semantic
functions they encode. Adverbial ideophones, occurring largely as
optional elements in quotative and collocational constructions have
more iconicity than interoceptive ideophones in predicate-verbal
constructions. Fully reduplicated regular and verbal adverbs with an
augmentation function have higher levels of iconicity than
adjectival FWRs serving multiple functions including evaluative
meanings associated with diminution or attenuation. Based on these
observations, a tentative scale of iconicity is proposed for Telugu.
This scale should be elaborated and validated in future research by
making use of multimodal corpora of ideophones and all varieties of
reduplicative structures.
Heart without ‘the’
Authors: Zhao Xinxin
Published: April 2020

As one of the most intensely studied literary works,
Heart of Darkness has been inviting diversified
and conflicting readings for more than one hundred years.
Politically or culturally oriented readings are overwhelmingly
abundant and often contradict each other. In an effort to
incorporate textual evidence as comprehensively and unbiasedly as
possible, this paper will pay more attention to how
the story is told than to what the story tells.
This paper concentrates on the narrative frame. By comparing inner
and outer narrative frames, I show that the eavesdropping scene (the
inner frame) is a diagrammatic icon of the overall story (the outer
frame). A point-by-point resemblance can be constructed between
these two frames, in which a quasi-storytelling is set up in a dark
world full of voices with rare communication between speakers and
listeners. In both frames, Kurtz’s voice, which is embedded within
voices of others, can be heard, but “that man” (p. 37) is not fully
identified formally and the mysteries surrounding Kurtz are never
clearly revealed. The frames are proliferated only to accentuate its
hollow core. The inner meaning is pointed at but cannot be pinned
down.
Multiword expressions in comparable corpora
Authors: Ďurčo Peter
Published: April 2020

On the basis of Aranea Gigaword Web corpora, a family of
comparable corpora intended for use in contrastive linguistic research,
multilingual lexicography, language teaching and translation studies we
discuss the pros and cons of comparable corpora in contrast to monolingual
and parallel corpora for the analysis of multiword entities (MWEs). We
demonstrate that by using large corpora for two or more languages,
consisting of unrelated texts, yet created in a comparable manner, parallel
language structures and phenomena like MWEs can be identified if the
appropriate tools are employed. With the Aranea corpora, the “bilingual
sketch” functionality of the Sketch Engine is one such tool which provides a
new approach for analyses of similarities of (or differences between)
collocation profiles (word sketches) for words and their translation
equivalents.
Statistical significance for measures of collocation strength
Authors: Oakes Michael P.
Published: April 2020

Of the commonly-used measures of lexical association or
collocation strength, only some directly relate to statistical significance:
the t-score, chi-squared, log-likelihood, the z-score and Fisher’s exact
test. We describe each of these tests, and also describe a computer
simulation by which we can derive confidence limits, and hence the
statistical significance, of any measure of lexical association which is
derived from the contingency table. We illustrate this approach using
pointwise mutual information (PMI). We also describe how the Poisson
distribution enables us to find the statistical significance of the raw
frequency with which a collocation is found. We compare all these methods
using collocates of “take”, namely “take up”, “take place”, “take advantage”
and “take stock”.
Multi-word patterns and networks
Authors: Steyer Kathrin
Published: April 2020

This paper discusses a theoretical and empirical approach to
language fixedness that we have developed at the Institut für Deutsche
Sprache (IDS) (‘Institute for German Language’) in Mannheim in the project
Usuelle Worterbindungen (UWV) over the last decade. The analysis described
is based on the Deutsches Referenzkorpus (‘German Reference Corpus’; DeReKo)
which is located at the IDS. The corpus analysis tool used for accessing the
corpus data is COSMAS II (CII)
and – for statistical analysis – the IDS collocation analysis tool (Belica, 1995; CA). For detecting
lexical patterns and describing their semantic and pragmatic nature we use
the tool lexpan (or ‘Lexical Pattern Analyzer’) that was developed in our
project. We discuss a new corpus-driven pattern dictionary that is relevant
not only to the field of phraseology, but also to usage-based linguistics
and lexicography as a whole.
Improving Chinese students’ English reading through graded readers
Authors: Qiang Wang , Zehang Chen , Xianglin Qi
Published: April 2020

Primary English in China has been in practice since 2001. Despite the success of widespread provision, there have
been concerns regarding the quality of students’ learning. To enhance English literacy in schools, a national English reading
project chaired by university teacher educators using graded readers was introduced to accompany mandated coursebooks in 2014
initially among a few schools then quickly expanded to thousands. The participating schools were guided to use English graded
readers in primary classrooms in collaborative projects with university teacher educators. This paper reports a case study based
on a project school in a suburb of Beijing with a cohort of 290 Grade 4 students and their 8 English teachers. The study
investigated changes the reading project has brought to the students and teachers between 2017 to 2019. Data collected include
three reading test results (pre-, mid-, and post-), and a post-project student questionnaire. Data collected concerning the 8
teachers included classroom observations, teachers’ lesson plans and post project narrative reports. Analyses were closely linked
to how students’ literacy developed, including their reading ability, interests, habits, and creative thinking. Changes in the
teachers’ views and their teaching practices were also examined.
Une possible allusion parodique au Compromis de Caspe (1412) dans la Disputa de l’ase (1417–18) d’Anselm Turmeda
Authors: Alemany Ferrer Rafael
Published: April 2020

La Disputa de l’ase d’Anselm Turmeda (1417–18) est un débat sur la supériorité de l’homme sur les animaux, qui met en scène le savant Frère Anselme et un âne apparemment vulgaire. La séquence initiale de cette œuvre qui, symptomatiquement, n’apparaît pas dans la source arabe directe utilisée par l’apologiste, présente une réunion d’animaux qui, après la mort de leur roi sans héritier direct, sont prêts à choisir son successeur. Il y a suffisamment d’indices suggérant que nous sommes confrontés à une probable parodie du compromis de Caspe (1412), décision politique très controversée qui a résolu le problème de la succession dans la Couronne d’Aragon, après la mort sans descendance du roi Martin l’Humain: la désignation, en tant que nouveau monarque, de Ferdinand d’Antequera, membre de la dynastie royale castillane des Trastámara.
Le chat et la sorcière
Authors: Tassone Claudia
Published: April 2020

Si de nos jours l’image du chat est entourée d’ambiguïté, puisque dans l’imaginaire collectif cette bête représente d’un côté le tendre ami de l’homme, de l’autre le fidèle serviteur du diable, cela est probablement dû à l’imaginaire qu’inspire le Moyen Âge. Tel est du moins le cliché qui alimente nos représentations modernes, où le chat est souvent considéré comme le compagnon par excellence de la sorcière. À l’aide de sources du domaine juridique et démonologique, cette étude se propose donc de reparcourir la naissance et le développement du cliché du chat diabolique. On s’arrêtera sur les premières mentions du chat-diable, adoré par les hérétiques de diverses sectes, et sur les premiers procès de sorcellerie qui ont eu lieu en Suisse, dans le canton de Vaud, où le chat occupe une place de prestige parmi les animaux infernaux. On touchera aussi à la question de la métamorphose des sorcières, abordée surtout dans les traités de démonologie plus tardifs, qui a peut-être renforcé le lien déjà fort entre le chat et la sorcière d’une telle façon qu’il a pu traverser les siècles.
Comment l’animal qui avale Jonas devient-il une baleine?
Authors: Traineau-Durozoy Anne-Sophie
Published: April 2020

Le terme de baleine, qui est utilisé pour la première fois au XIe siècle pour nommer l’animal qui avale Jonas, précède l’identification précise de cette bête évoquée dans l’Ancien Testament. Pour comprendre les mécanismes de cette spécialisation progressive, cet article se propose d’analyser d’abord le contexte d’apparition du mot ‘baleine’ dans les langues vernaculaires aux XIe et XIIe siècles, non seulement pour l’animal du livre de Jonas, mais également pour la constellation de la baleine ou pour la créature marine des bestiaires. Dans un deuxième temps, il étudie, pour les XIIIe et XIVe siècles, la diffusion du mot dans l’espace et dans le temps, et sa coexistence avec d’autres expressions ou termes utilisés pour la créature qui engloutit Jonas; il montre également comment cette bête prend alors des caractéristiques corporelles et morales attribuées à la baleine en général. Enfin, il analyse de quelle manière, au XVe siècle, l’animal biblique, en devenant pleinement baleine au sens naturaliste du terme, perd peu à peu sa dimension symbolique et son pouvoir de fascination.
VOSSEN. An expedition in the modern land of Reynard in 2018
Authors: Daele Rik Van
Published: April 2020

The Phoebus Foundation, a Flemish art foundation based on Anglo-Saxon law with philanthropic objectives, founded
by Fernand Huts, the CEO of the Antwerp enterprise Katoen Natie, bought in the spring of 2016 a collection of 350 Reynardian
books, probably the world’s most important collection of Reynard books. In 2018, a huge Reynardian project was created around this
collection, an expedition in which almost 60,000 participants made a cycling trip through the Flemish Waasland, the port of
Antwerp, and Dutch Zeelandic Flanders. Along the route of this experience the visitors explored the medieval Dutch animal story
Van den vos Reynaerde in a creative, playful way, accessible to a large public of families. This paper
aims to detect the success factors of this event as part of the modern experience economy with the help of Alessandro Baricco’s
essay The Barbarians. An Essay On the Mutation of Culture.
The dancing bear from Spain
Authors: Zillén Erik
Published: April 2020

The article depicts the intense and at times unpredictable fable transfer in eighteenth-century Europe by tracing
the source text of one of the most acclaimed works in Swedish fable history, Anna Maria Lenngren’s “Björndansen” [The dance of the
bear]. This verse fable, published in Stockholms Posten in 1799 and bringing questions of literary quality and
literary criticism into focus, was classified by the poet herself as “Original.” Twentieth-century scholars have identified a
prose fable, “Björnen, Apan och Swinet” [The bear, the ape, and the swine], printed in the same daily paper in 1784 and translated
from Spanish, as her probable source text. Eagerness to safeguard the poetical autonomy of Lenngren seems, though, to have
restrained scholars from trying to find the Spanish original of the prose translation or to detect its author. Following the
trails of French and German renderings of the Spanish fable about the dancing bear, the article demonstrates that “Björndansen” is
a skilful Swedish recasting of “El Oso, la Mona y el Cerdo” [The bear, the ape, and the swine], one of the 67 verse fables in
Tomás de Iriarte’s innovative Fábulas literarias (1782), a collection presenting a neoclassical poetics in the
form of fable. Placing “Björndansen” within this larger international fable historical context, the article also manages, by means
of comparative analysis, to throw new light on the literary devices of the Swedish masterpiece.
Mobilizing others
Authors: Betz Emma , Taleghani-Nikazm Carmen , Golato Peter
Published: April 2020

“Mobilizing others” takes a holistic perspective on the
practices that we use to get others to act with, and for, us. This
introduction reviews recent conceptual developments, notably ‘recruitment’
(Section 1), and then opens up
new territory by arguing for a more explicit focus on ‘activity’ in
describing how mobilizing moves are accountably produced and understood.
After summarizing existing research on ‘activity’ (2) we highlight how embodiment and temporality figure
crucially in interactants’ use of grammatical, vocal, and embodied resources
to reflexively organize larger courses of action (3). Focusing on ‘situation design’ captures the
importance of the overall activity for the design, placement, and
understanding of mobilizing turns, and makes visible implicit layers of
organization which relevantly shape local conduct.
Mobilizing for the next relevant action
Authors: Taleghani-Nikazm Carmen , Drake Veronika , Golato Andrea , Betz Emma
Published: April 2020

This chapter discusses three different actions speakers
can employ to move between two concurrently ongoing activities, playing
cards and talking. Specifically, we describe three turn formats that
mobilize another participant to perform the next move in a card game: (1)
turns including the discourse marker so, (2) imperatives,
and (3) second-person declaratives.

So-turns and imperative forms are used
to resume a game put on hold, however, imperatives are only used if speakers
have already shown an orientation to game resumption. In contrast,
second-person declaratives are used in situations when one player is not
oriented to the game but others are. In the discussion, we show that turn
formats are sensitive to the multimodal context and participation framework
of the interaction.
Mobilizing others when you have little (recognizable) language
Authors: Antaki Charles , Finlay W.M.L. , Walton Chris
Published: April 2020

Getting another person to engage with you is, for most
people, most of the time, a merely trivial challenge. Of course, there are
times when our attempts are awkward, or misfire; nevertheless, usually we
bring them off smoothly and successfully. But it is far from easy if you
have an intellectual impairment; and, a fortiori,
dauntingly challenging if the impairment is profound. For someone with
severe cognitive and communicative incapacity, the attempt to get others to
do things is highly, perhaps entirely, dependent on the others’ doubtful
construction of just what it is that they are supposed to do. This chapter
is about those attempts: how they succeed, and how (as they often do) they
fail.
Membrane‐binding peptides for extracellular vesicles on‐chip analysis
Authors: Gori Alessandro , Romanato Alessandro , Bergamaschi Greta , Strada Alessandro , Gagni Paola , Frigerio Roberto , Brambilla Dario , Vago Riccardo , Galbiati Silvia , Picciolini Silvia , Bedoni Marzia , Daaboul George G. , Chiari Marcella , Cretich Marina
Published: April 2020

Small extracellular vesicles (sEVs) present fairly distinctive lipid membrane features in the extracellular environment. These include high curvature, lipid‐packing defects and a relative abundance in lipids such as phosphatidylserine and ceramide. sEV membrane could be then considered as a “universal” marker, alternative or complementary to traditional, characteristic, surface‐associated proteins. Here, we introduce the use of membrane‐sensing peptides as new, highly efficient ligands to directly integrate sEV capturing and analysis on a microarray platform. Samples were analysed by label‐free, single‐particle counting and sizing, and by fluorescence co‐localisation immune staining with fluorescent anti‐CD9/anti‐CD63/anti‐CD81 antibodies. Peptides performed as selective yet general sEV baits and showed a binding capacity higher than anti‐tetraspanins antibodies. Insights into surface chemistry for optimal peptide performances are also discussed, as capturing efficiency is strictly bound to probes surface orientation effects. We anticipate that this new class of ligands, also due to the versatility and limited costs of synthetic peptides, may greatly enrich the molecular toolbox for EV analysis.
Surface acoustic waves as a sensitive probe for photoresponsive polarization memory in SrTiO3
Authors: Uzun Y , Gurbuz I , De Jong M P , Van Der Wiel W G
Published: April 2020

Transient electric polarization in single crystalline SrTiO3 (STO) substrates was studied by measuring the transmission of surface acoustic waves (SAWs). We applied a large dc electric field (8 × 106 Vm−1) to interdigital transducers (IDTs) on STO substrates in order to induce local piezoelectricity, which is required to generate and transmit SAWs. The resulting electric polarization and the retention thereof were analyzed as a function of time after the applied electric field was removed, by measuring transient SAW signals. The retained polarization turned out to provide strong electromechanical coupling, comparable to that resulting from the dc-field-induced piezoelectricity. SAW signals were observed for more than 30 h (in absence of an external dc electric field), which is evidence for a long-lasting retention of electric polarization. Remarkably, this polarization was found to be rapidly suppressed as the sample was exposed to visible light. By measuring the transient SAW transmission under illumination with light at different wavelengths, we identified photoconductivity and/or acceleration of oxygen vacancy migration by photon-induced splitting of bound vacancy pairs as the main mechanisms behind this photoresponsive memory effect.
Some remarks on the dynamics of the almost Mathieu equation at critical coupling*
Authors: Bjerklöv Kristian
Published: April 2020

We show that the quasi-periodic Schrödinger cocycle with a continuous potential is of parabolic type, with a unique invariant section, at all gap edges where the Lyapunov exponent vanishes. This applies, in particular, to the almost Mathieu equation with critical coupling. It also provides examples of real-analytic cocycles having a unique invariant section which is not smooth.
Erratum: Black holes and gravitational waves in models of minicharged
dark matter
Authors: Vitor Cardoso  , Caio F.B. Macedo  , Paolo Pani  , Valeria Ferrari
Published: April 2020

Please see the PDF file for details.
Quantum to classical transition induced by a classically small influence*
Authors: Zhao Wen-Lei , Jie Quanlin
Published: April 2020

We investigate the quantum to classical transition induced by two-particle interaction via a system of periodically kicked particles. The classical dynamics of particle 1 is almost unaffected in condition that its mass is much larger than that of particle 2. Interestingly, such classically weak influence leads to the quantum to classical transition of the dynamical behavior of particle 1. Namely, the quantum diffusion of this particle undergoes the transition from dynamical localization to the classically chaotic diffusion with the decrease of the effective Planck constant ℏ
eff. The behind physics is due to the growth of entanglement in the system. The classically very weak interaction leads to the exponential decay of purity in condition that the classical dynamics of external degrees freedom is strongly chaotic.
Giant mechanocaloric materials for solid-state cooling*
Authors: Zhang Junran , Xu Yixuan , An Shihai , Sun Ying , Li Xiaodong , Li Yanchun
Published: April 2020

This article reviews the research progress of measurement techniques and materials on the mechanocaloric effect over the past few decades. Mechanocaloric materials can be divided into elastocaloric and barocaloric materials depending on the applied uniaxial stress or hydrostatic pressure. Elastocaloric materials include non-magnetic shape memory alloys, polymers, and rare-earth compounds. Barocaloric materials include magnetic shape memory alloys, ferroelectric ceramics, superionic conductors, and oxyfluorides. The mechanocaloric effects of these classes of materials are systematically compared in terms of the isothermal entropy change and adiabatic temperature change. In addition to the thermal effects, other characteristics closely related to the application of mechanocaloric materials are also summarized. Finally, perspectives for further development of mechanocaloric materials in the solid-state cooling area are discussed.
Mowing alters nitrogen effects on the community-level plant stoichiometry through shifting plant functional groups in a semi-arid grassland
Authors: Li Shijie , Wang Fuwei , Chen Mengfei , Liu Zhengyi , Zhou Luyao , Deng Jun , Dong Changjun , Bao Guocheng , Bai Tongshuo , Li Zhen , Guo Hui , Wang Yi , Qiu Yunpeng , Hu Shuijin
Published: April 2020

Land-use practices such as mowing and nitrogen (N) fertilization can have significant impacts on plant stoichiometry. However, the interactive effects of mowing and N fertilization on the community-level plant stoichiometry and the underlying processes are not well understood. We examined the impacts of mowing (once a year) and N fertilization (12 g N m−2 yr−1) on the community-level plant stoichiometry in a semi-arid grassland on the Loess Plateau. Results obtained showed that mowing alone had no effect on the community-level plant N or phosphorus (P) concentration. N fertilization alone significantly reduced the community-level plant P concentration, but did not affect the community-level plant N concentration, leading to an enhancement of plant N:P ratio. However, mowing altered the effects of N fertilization, leading to a higher plant N (and P) concentration than the fertilization-only plots. Also, mowing significantly reduced soil nitrate (NO3
−), but increased soil temperature, photosynthetic active radiation, plant diversity, richness and gross ecosystem productivity. In addition, mowing and N fertilization significantly affected plant community composition through shifting dominant plant functional groups (PFGs) (e.g. asteraceae, forbs and grass). Further, our structural equation modeling analysis showed that shifts in PFGs played an important role in regulating plant stoichiometry under mowing and N fertilization. Together, these results illustrate that effective management of mowing and N fertilization may induce changes in soil limiting nutrients and shifts in plant community composition, potentially altering plant N:P stoichiometry at the community level.
Decoration of cellulose nanocrystals with iron oxide nanoparticles
Authors: Chen Lyufei , Sharma Shruti , Darienzo Richard E , Tannenbaum Rina
Published: April 2020

Cellulose nanocrystals (CNCs) are excellent candidates for the design and development of multifunctional biomaterials systems to be used in a variety of technologically relevant applications. They may be used as the structural reinforcement phase of polymer matrices, act as catalyst support constituents, as well as drug delivery vectors. Modifying and functionalizing CNCs by introducing specific functional components can impart electronic, magnetic, catalytic, fluorescence and optical properties to the system. In this work we report the successful in situ tethering of iron oxide nanoparticles (IONPs) onto CNCs by the thermal decomposition of Fe(CO)5 in a H2O/DMF suspension. Following this procedure, IONPs consisting of mixtures of Fe3O4 and Fe2O3 with an average diameter of 20 nm were attached to the CNCs. The type of iron oxide species that was generated was determined by selected area electron diffraction (SAED) and energy dispersive spectroscopy (EDS), and the particle size was evaluated by transmission electron microscopy (TEM). Raman spectroscopy was used to characterize the presence and the nature of the molecular interaction between the IONPs and the CNCs.
Factors associated with the adoption of renewable energy amongst botanical garden members
Authors: Drummond Caitlin , States Sarah L , Wong-Parodi Gabrielle
Published: April 2020

We examine the factors related to the adoption of renewable energy amongst members of a botanical garden. We surveyed botanical garden members roughly seven months after the garden began incentivizing visitors to switch their household energy supplier to a renewable energy provider, offering a free year of membership to those who switched to renewable energy on site. We examine two related research questions: what factors are related to a) already having one’s household run on renewable energy at the time the incentive was put into place and b) switching to renewable energy on site? We find that politically liberal participants were more likely to already use renewable energy, and that younger participants and those who had a pleasant on-site interaction with the renewable energy supplier were more likely to switch to renewable energy on site. We discuss the implications of our findings for encouraging uptake of renewables.
Interlocked attosecond pulse trains in slightly bi-elliptical high harmonic generation
Authors: Bordo Eliyahu , Kfir Ofer , Zayko Sergey , Neufeld Ofer , Fleischer Avner , Ropers Claus , Cohen Oren
Published: April 2020

The ellipticity of high harmonics driven by bi-chromatic (e.g.

ω
−
2
ω

) co-propagating fields can be fully tuned by varying the polarization of the pump components. In order to start revealing the underlying mechanism of this control, we explore a relatively simple regime of this scheme that still gives rise to full control over the harmonics ellipticities. In this regime, the pumps are only slightly elliptical and the high harmonic radiation consists of two (different) interlocked attosecond pulse trains (APTs). We formulate a semi-analytic model that maps the high harmonic ellipticity to properties of the APTs harmonic decompositions. Utilizing this model, we reconstruct these APTs variables from measurements of the high harmonics ellipticities. This ellipticity-resolved spectroscopy of interlocked APTs may be useful for ultrafast probing of chiral degrees of freedom.
Critical mass on the Keller-Segel system with signal-dependent motility
Authors: Jin Hai-Yang , Wang Zhi-An
Published: April 2020

This paper is concerned with the global boundedness and blow-up of solutions to the Keller-Segel system with density-dependent motility in a two-dimensional bounded smooth domain with Neumman boundary conditions. We show that if the motility function decays exponentially, then a critical mass phenomenon similar to the minimal Keller-Segel model will arise. That is, there is a number

m
∗

>
0

m_*>0

, such that the solution will globally exist with uniform-in-time bound if the initial cell mass (i.e.,

L
1

L^1

-norm of the initial value of cell density) is less than

m
∗

m_*

, while the solution may blow up if the initial cell mass is greater than

m
∗

m_*

.
Greater Average Meal Planning Frequency Predicts Greater Weight Loss Outcomes in a Worksite-Based Behavioral Weight Loss Program
Authors: Hayes Jacqueline F , Balantekin Katherine N , Fitzsimmons-Craft Ellen E , Jackson Joshua J , Ridolfi Danielle R , Boeger Holley S , Welch R Robinson , Wilfley Denise E
Published: April 2020

Background

Planning in behavioral weight loss (BWL) programs helps participants enact changes in eating and exercise, although the direct impact on weight loss is unclear.

Purpose

To examine how meal and exercise planning frequencies change in a BWL program and their relations to weight loss outcomes.

Methods

Participants (N = 139) in a 40 week worksite-based BWL program completed a questionnaire regarding meal and exercise planning frequency at Weeks 0, 10, 20, 30, and 40 and were weighed weekly. Growth curve models were used to determine trajectories in meal and exercise planning frequency and to assess the role of an individual’s average meal and exercise planning (between-person effect) and individual variation in planning (within-person effect) on body mass index (BMI).

Results

The best-fitting model, a linear random effect with a quadratic fixed-effect model, demonstrated that meal and exercise planning frequency increased over the course of the program with slowing growth rates. Between participants, higher average meal planning frequency (B = −0.029, t = −3.60), but not exercise planning frequency, was associated with greater weight loss. Within participants, exercise planning, but not meal planning, predicted a higher than expected BMI (B = 3.17, t = 4.21).

Conclusions

Frequent meal planning should be emphasized as a continued, as opposed to intermittent, goal in BWL programs to enhance weight loss. Average exercise planning frequency does not impact weight loss in BWL programs; however, acute increases in exercise planning frequency may be a popular coping strategy during a weight loss setback or, alternatively, may lead to increased calorie consumption and weight gain.
Therapeutic targets and signaling mechanisms of vitamin C activity against sepsis: a bioinformatics study
Authors: Li Rong , Guo Chao , Li Yu , Qin Zuqian , Huang Wenjun
Published: April 2020

Sepsis is a life-threatening complication of pneumonia, including coronavirus disease-2019 (COVID-19)-induced pneumonia. Evidence of the benefits of vitamin C (VC) for the treatment of sepsis is accumulating. However, data revealing the targets and molecular mechanisms of VC action against sepsis are limited. In this report, a bioinformatics analysis of network pharmacology was conducted to demonstrate screening targets, biological functions, and the signaling pathways of VC action against sepsis. As shown in network assays, 63 primary causal targets for the VC action against sepsis were identified from the data, and four optimal core targets for the VC action against sepsis were identified. These core targets were epidermal growth factor receptor (EGFR), mitogen-activated protein kinase-1 (MAPK1), proto-oncogene c (JUN), and signal transducer and activator of transcription-3 (STAT3). In addition, all biological processes (including a top 20) and signaling pathways (including a top 20) potentially involved in the VC action against sepsis were identified. The hub genes potentially involved in the VC action against sepsis and interlaced networks from the Kyoto Encyclopedia of Genes and Genomes Mapper assays were highlighted. Considering all the bioinformatic findings, we conclude that VC antisepsis effects are mechanistically and pharmacologically implicated with suppression of immune dysfunction-related and inflammation-associated functional processes and other signaling pathways. These primary predictive biotargets may potentially be used to treat sepsis in future clinical practice.
dv-trio: a family-based variant calling pipeline using DeepVariant
Authors: Ip Eddie K K , Hadinata Clinton , Ho Joshua W K , Giannoulatou Eleni
Published: April 2020

Motivation

In 2018, Google published an innovative variant caller, DeepVariant, which converts pileups of sequence reads into images and uses a deep neural network to identify single-nucleotide variants and small insertion/deletions from next-generation sequencing data. This approach outperforms existing state-of-the-art tools. However, DeepVariant was designed to call variants within a single sample. In disease sequencing studies, the ability to examine a family trio (father-mother-affected child) provides greater power for disease mutation discovery.

Results

To further improve DeepVariant’s variant calling accuracy in family-based sequencing studies, we have developed a family-based variant calling pipeline, dv-trio, which incorporates the trio information from the Mendelian genetic model into variant calling based on DeepVariant.

Availability and implementation

dv-trio is available via an open source BSD3 license at GitHub (https://github.com/VCCRI/dv-trio/).

Contact

e.giannoulatou@victorchang.edu.au

Supplementary information

Supplementary data are available at Bioinformatics online.
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A
Authors: David Laurent , Vicedomini Riccardo , Richard Hugues , Carbone Alessandra
Published: April 2020

Motivation

The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly ‘explore’ the content of multiple and/or large metagenomic datasets with respect to specific domain targets, avoiding full domain annotation and full assembly.

Results

S3A is a fast and accurate domain-targeted assembler designed for a rapid functional profiling. It is based on a novel construction and a fast traversal of the Overlap-Layout-Consensus graph, designed to reconstruct coding regions from domain annotated metagenomic sequence reads. S3A relies on high-quality domain annotation to efficiently assemble metagenomic sequences and on the design of a new confidence measure for a fast evaluation of overlapping reads. Its implementation is highly generic and can be applied to any arbitrary type of annotation. On simulated data, S3A achieves a level of accuracy similar to that of classical metagenomics assembly tools while permitting to conduct a faster and sensitive profiling on domains of interest. When studying a few dozens of functional domains—a typical scenario—S3A is up to an order of magnitude faster than general purpose metagenomic assemblers, thus enabling the analysis of a larger number of datasets in the same amount of time. S3A opens new avenues to the fast exploration of the rapidly increasing number of metagenomic datasets displaying an ever-increasing size.

Availability and implementation

S3A is available at http://www.lcqb.upmc.fr/S3A_ASSEMBLER/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Knockout of serine-rich single-pass membrane protein 1 (Ssmem1) causes globozoospermia and sterility in male mice†
Authors: Nozawa Kaori , Zhang Qian , Miyata Haruhiko , Devlin Darius J , Yu Zhifeng , Oura Seiya , Koyano Takayuki , Matsuyama Makoto , Ikawa Masahito , Matzuk Martin M
Published: April 2020

Globozoospermia (sperm with an abnormally round head shape) and asthenozoospermia (defective sperm motility) are known causes of male infertility in human patients. Despite many studies, the molecular details of the globozoospermia etiology are still poorly understood. Serine-rich single-pass membrane protein 1 (Ssmem1) is a conserved testis-specific gene in mammals. In this study, we generated Ssmem1 knockout (KO) mice using the CRISPR/Cas9 system, demonstrated that Ssmem1 is essential for male fertility in mice, and found that SSMEM1 protein is expressed during spermatogenesis but not in mature sperm. The sterility of the Ssmem1 KO (null) mice is associated with globozoospermia and loss of sperm motility. To decipher the mechanism causing the phenotype, we analyzed testes with transmission electron microscopy and discovered that Ssmem1-disrupted spermatids have abnormal localization of Golgi at steps eight and nine of spermatid development. Immunofluorescence analysis with anti-Golgin-97 to label the trans-Golgi network, also showed delayed movement of the Golgi to the spermatid posterior region, which causes failure of sperm head shaping, disorganization of the cell organelles, and entrapped tails in the cytoplasmic droplet. In summary, SSMEM1 is crucial for intracellular Golgi movement to ensure proper spatiotemporal formation of the sperm head that is required for fertilization. These studies and the pathway in which SSMEM1 functions have implications for human male infertility and identifying potential targets for nonhormonal contraception.