bluuebunny/crossref_metadata_2025 huggingface dataset:
Languaging when providing and processing peer feedback
Authors: Storch Neomy , Alshuraidah Ali
Published: April 2020

Two commonly used activities in second language
(L2) writing classes are collaborative writing and peer response.
Our study compared the quantity and quality of languaging generated
by these two activities. In this study, conducted in Saudi Arabia,
34 college English language learners worked in the same
self-selected small groups (predominantly pairs) on three successive
activities. They completed a collaborative writing task, provided
written feedback on a text written by another group, and revised
their text in response to the peer feedback received. Analysis of
recorded talk during these three activities found that the
collaborative writing activity generated more languaging episodes
than the other activities. We discuss the implications of these
findings for L2 writing pedagogy and propose research
directions.
Talking about language
Authors: Gánem-Gutiérrez Gabriela Adela , Roehr-Brackin Karen
Published: April 2020

This qualitatively oriented study
investigated the role of second language (L2) metalinguistic
knowledge in languaging during performance on two pedagogic
tasks – a gap-fill and a dictogloss. It involved 14 L1
English university-level learners of L2 Spanish
(N = 8) and L2 German
(N = 6). Drawing on individual
think-aloud protocols and learners’ pair-work interactions,
we investigated the extent to which metalinguistic knowledge
was used during task completion, its purposes, and whether
it was associated with successful task performance. Although
considerable inter-learner variation was in evidence, we
identified a relationship not only between the use of
metalinguistic knowledge and successful task completion but
also between the purpose for which metalinguistic knowledge
was employed during languaging and the balance of expertise
between partners.
The discourse of manners and politeness in Restoration and
eighteenth-century drama
Authors: Jucker Andreas H.
Published: April 2020

The eighteenth century is often referred to as the
age of politeness, and the term politeness has been argued
to be a key term in a variety of settings at this time. This paper sets out
to investigate the discourse of politeness and, more generally, the
discourse of manners during this period and the period leading up to it
(1660 to 1790). It focuses on the vocabulary used in talking about manners
and politeness and on the way this vocabulary is used in actual
interactions. In a first step, it investigates several large corpora and
what they can tell us about the development of the vocabulary of manners and
politeness before it zooms in, in a second step, on a more detailed
investigation of three comedies of the period: Aphra Behn’s The Town-Fop: or Sir Timothy
Tawdrey (1676), Sir Richard Steele’s The Conscious Lovers
(1722), and Oliver Goldsmith’s
She Stoops to Conquer, or The Mistakes of a Night
(1773). A close reading and a careful analysis of the discourse
of manners and politeness, and crucially the discourse of violations of
manners and politeness, in these three plays reveals a significant shift
from a preoccupation with honour and reputation in the Restoration period to
the politeness of a good character in the early eighteenth century and
finally to a concern for polished and somewhat superficial manners in the
late eighteenth century. The three comedies thus mirror in a detailed and
nuanced way what the development of the vocabulary of manners and politeness
suggests in a broad-brush perspective on a much larger scale.
Transgressions as a socialisation strategy in Samuel Richardson’s
The Apprentice’s Vade Mecum (1734)
Authors: Shvanyukova Polina
Published: April 2020

Conduct manuals disseminating norms of behaviour
were popular in Early and Late Modern England. In this contribution I offer
a close reading of an influential eighteenth-century conduct manual for
newly apprenticed boys, Samuel Richardson’s The Apprentice’s Vade
Mecum (Richardson
2012[1734]). In my analysis of its contents I aim to identify the
specific set of norms of conduct young apprentices were impelled to comply
with, in an attempt to shed light on the ways in which representations of
acts of transgressive behaviour in didactic advice literature were
instrumental in the process of indoctrinating social novices about the norms
of the dominant world order. I then examine the distinctive traits of the
author’s instructive language, that is to say, the specific linguistic
strategies Richardson employs in order to deliver his instructions in the
most efficient, unequivocal and accessible way. Finally, I argue that in
Richardson’s in-depth treatment of transgressive acts we find evidence of
the existence of a coherent code of anti-normative behaviour.
Variations from letter-writing manuals
Authors: Calvo Cortés Nuria
Published: April 2020

The present study analyses two sets of 25 petitions
each. They were signed by different women who possibly belonged to lower
social ranks, and they were addressed to the governors of the Foundling
Hospital and the Bank of England. These were most probably men who occupied
high positions in society. The study focuses on the comparison between the
information present in the manuals and the petitions selected for this
study. The petitioners had different needs and their circumstances also
varied. This is reflected in the results, which show differences, and also
similarities, between the two sets of petitions. Furthermore, most display
some features found in the manuals, but not all of them follow the rules or
recommendations faithfully. The writers, who cannot always be identified and
may not have been the same as the signees, seem to have been aware of the
existence of letter-writing manuals, but they may not have had first-hand
contact with them.
Impoliteness in Blunderland
Authors: Ermida Isabel
Published: April 2020

Lewis Carroll’s Alice’s Adventures in
Wonderland (1865)
and Through the Looking-Glass (1871), two linguistic treatises in disguise,
create ingenious fantasy worlds where the rules of language and the
conventions of communication are turned upside down. What is (semantically)
illogical or (pragmatically) inappropriate confounds Alice, who struggles to
make sense of nonsense and to keep the order of a polite, rational world in
place. In her dialogues with anthropomorphic animals and objects, ambiguity
and fallacy coexist with interactive manipulation, while her communicative
expectations crumble and comic misunderstandings arise.

This article looks into the construction of linguistic and pragmatic
transgressions in Carroll’s acclaimed books with a view to unveiling their
contribution to impoliteness. On the one hand, the paper analyses the
structural mechanisms of wordplay vis-à-vis phonetic, morpho-syntactic and
lexical ambiguity. On the other, it examines the pragmatic strategies
whereby speech-act infelicities, conversational maxim violations, and
bald-on-record clashes contribute to reversing the established conventions
of (polite) social interaction. The premise guiding the analysis is that the
pervasive existence of double meaning and incongruity in the Alice books
underlies not only linguistic phenomena such as punning, neologism, and
relexicalisation, but also interactive patterns, in which the expected norms
of courteous conduct in social exchanges do not obtain. The antithetical and
script-oppositional (hence, humorous) nature of this process defrauds
outsider Alice – the victim, but at times the happy recipient, of the
uncooperative challenges of this inverted, refracted, teasingly nonsensical
world.
A note on the minimization of a Tikhonov functional with ℓ1-penalty
Authors: Hinterer Fabian , Hubmer Simon , Ramlau Ronny
Published: April 2020

In this paper, we consider the minimization of a Tikhonov functional with an ℓ
1 penalty for solving linear inverse problems with sparsity constraints. One of the many approaches used to solve this problem uses the Nemskii operator to transform the Tikhonov functional into one with an ℓ
2 penalty term but a nonlinear operator. The transformed problem can then be analyzed and minimized using standard methods. However, by the nature of this transform, the resulting functional is only once continuously differentiable, which prohibits the use of second order methods. Hence, in this paper, we propose a different transformation, which leads to a twice differentiable functional that can now be minimized using efficient second order methods like Newton’s method. We provide a convergence analysis of our proposed scheme, as well as a number of numerical results showing the usefulness of our proposed approach.
Collision of Li2+ with Li(2s) and Li(2p): differential and total ionization; discrete excitations; elastic scattering, and total cross section
Authors: Walters H R J , Whelan Colm T
Published: April 2020

The coupled pseudostate approximation (McGovern et al 2009 Phys. Rev. A
79 042707) has been applied to Li2+ + Li(2s, 2p0,±1) collisions at 16 MeV with emphasis on studying the fully differential ionization measurements of Ghanbari-Adivi et al in the azimuthal plane (2017 J. Phys. B: At. Mol. Opt. Phys.
50 215202). The states of the valence electron in the Li target are calculated using the model potential of Stein (1993 J. Phys. B: At. Mol. Opt. Phys.
26 2087). Altogether 164 states with angular momenta l = 0 to 9 are employed in the scattering calculation. It is assumed that the electron in the Li2+ is frozen in the 1s state and its screening of the Li2+ nucleus is fully taken into account. Previous calculations on this system (3DW-EIS and CDW-EIS) have treated the Li2+ as a bare ion with a nuclear charge of 2 au. Except for normalisation, agreement with the experimental data of Ghanbari-Adivi et al is generally quite good. But, where agreement is best it is found that the cross section is very much first Born. Except in one case, quite good accord is also obtained with the 3DW-EIS calculations of Ghanbari-Adivi et al, particularly on normalisation. Screening by the 1s electron has little effect on the fully differential calculations undertaken here. The double differential cross section d
2
σ/dEdq

t
and the single differential cross section dσ/dE are also calculated. Here 1s screening is found to be important at large (transverse) momentum transfers q

t
and large ejection energies E. In addition, the pseudostate approximation gives cross sections for discrete transitions, total ionization and total scattering.
A deep condition feature learning approach for rotating machinery based on MMSDE and optimized SAEs
Authors: Ge Ming-Feng , Ge Ziyue , Pan Hao , Liu Yiben , Xu Yanhe , Liu Jie
Published: April 2020

The failure of rotating machinery affects the quality of the product and the entire production process. However, it usually suffers the subsequent deficiency that the hyperparameters of the fault diagnosis model require constant debugging. This paper proposes a deep condition feature learning approach for rotating machinery based on modified multi-scale symbolic dynamic entropy (MMSDE) and optimized stacked auto-encoders (SAEs). Firstly, MMSDE has been used to extract fault characteristics of the original vibration signal, because such methods do not rely on prior knowledge and experience. MMSDE conducts multi-scale analysis on the original vibration signal and calculates the entropy of the multi-scale signal. The multi-scale fault characteristics are obtained. Then, Bayesian optimization-based SAEs are applied to select feature samples and classify the fault status in mechanical fault diagnosis without debugging. The effectiveness of the proposed method is verified by using open-source data and experimental data. Multiple working conditions are also considered and investigated.
Using the entropy of the corneal pulse signal to distinguish healthy eyes from eyes affected by primary open-angle glaucoma
Authors: Danielewska Monika E , Placek Michał M , Kicińska Aleksandra K , Rękas Marek
Published: April 2020

Objective: The purpose of this study was to evaluate whether the complexity of the corneal pulse (CP) signal can be used to differentiate patients with primary open-angle glaucoma (POAG) from healthy subjects. Approach: The study sample consisted of 28 patients with POAG and a control, age-matched group of 30 subjects. After standard ophthalmic examination, the CP signal from a randomly selected eye of each participant was measured using non-contact ultrasonic micro-displacement measurement technology. After pre-processing, the complexity of the CP signal was estimated using refined composite multiscale fuzzy entropy (RCMFE) up to scale factor 50. The average RCMFE values were computed from three repeated measurements of the CP signals for each participant and each scale factor. Main results: The complexity of the CP signal in glaucomatous eyes was higher than that observed in healthy ones. Also, RCMFE of the CP signal was found to differentiate (statistically significantly) between the two groups for scales in the range from 26 to 43. For these scales, the one for which the lowest p-value (t-test, p = 0.017) was obtained when comparing RCMFE between the two groups was selected as the optimal scale. Next, a receiver operating characteristic analysis for the optimal scale showed that the proposed approach of calculating the multiscale entropy of the CP signal has some potential to discriminate between patients with POAG and healthy controls (sensitivity, specificity and accuracy of 0.643, 0.700 and 0.672, respectively). Significance: In conclusion, RCMFE, as a complexity measure, may be considered an auxiliary indicator to support glaucoma diagnostics.
Flexible and wearable sensor based on graphene nanocomposite hydrogels
Authors: Zhang Yan , Liang Bo , Jiang Qifeng , Li Yang , Feng Ying , Zhang Lingqin , Zhao Yiming , Xiong Xingliang
Published: April 2020

Flexible and wearable sensor based on nanocomposite hydrogels has been proposed for monitoring the human large-scale, small-scale movements and several physiological signals. The nanocomposite hydrogel, prepared from graphene oxide (GO), polyvinyl alcohol (PVA) and polydopamine (PDA), exhibits excellent mechanical and electrical properties with tensile stress of 146.5 KPa, fracture strain of 2580%, fracture energy of 2390.86 KJ m−3, and the conductivity of 5 mS cm−1. In addition, it possesses other merits including good self-healing with the electrical self-healing efficiency of 98% of its original resistance within 10 s, and strong self-adhesion onto a variety of surfaces of materials. This self-adhesive, self-healing, graphene-based conductive hydrogel can further assembled as wearable sensors to accurate and real-time detect the signals of human large-scale motions (including bending and stretching fingers joints, wrists joints, elbows joints, neck joints and knees joints) and small-scale motions (including swallowing, breathing and pulsing) through fracturing and recombination of reduced graphene oxide (rGO) electrical pathways in porous structures of hydrogel networks. Furthermore, the hydrogel can also be used as self-adhesive surface electrodes to detect human electrophysiological (ECG) signals. Therefore, the hydrogel-based wearable sensor is expected to be used for long-term and continuous monitoring human body motion and detecting physiological parameters.
Loss characteristics of HTS coated conductors in field windings of electric aircraft propulsion motors
Authors: Kails Kevin , Zhang Hongye , Mueller Markus , Li Quan
Published: April 2020

High-temperature superconducting (HTS) coated conductors (CCs) are widely regarded as a promising candidate to enable very high power density motors. These machines operate at high rotational speeds, with some designs going up to 12 000 rpm. HTS CCs are applied to the field windings of these motors to increase the magnetic loading and hence the power density. Even though the superconducting field windings operate with a DC current, due to the magnetic field environment, losses are present. This paper examines the dynamic and total loss characteristics of YBCO-coated conductors in the frequency range relevant to high-speed motors for electric aircraft propulsion. A multi-layer model was created using the
H
-formulation and the losses for each layer were highlighted. For the first time, it was shown that the DC transport current region in the HTS layer shrinks as the frequency of the applied field increases due to the increased magnetisation current around the edges of the CC, which reduces the dynamic loss per cycle as the frequency increases. To fully understand the loss distribution in the HTS CC, the total loss in the conductor was investigated. For an applied magnetic field of 100 mT and 800 Hz, more than 30% of the total loss occurs in the copper layer due to the decreased penetration depth of the magnetic field and the skin effect. Results show that to accurately model and understand the losses in superconducting field windings, a multi-layer model should be used, since a significant proportion of loss shifts towards the copper stabilizers. Over all, it was shown that both the dynamic loss as well as magnetisation loss play a crucial role in the estimation of the loss in superconducting field windings.
Perturbation-evoked potentials can be classified from single-trial EEG
Authors: Ditz Jonas C , Schwarz Andreas , Müller-Putz Gernot R
Published: April 2020

Objective. Loss of balance control can have serious consequences on interaction between humans and machines as well as the general well-being of humans. Perceived balance perturbations are always accompanied by a specific cortical activation, the so-called perturbation-evoked potential (PEP). In this study, we investigate the possibility to classify PEPs from ongoing EEG. Approach. Fifteen healthy subjects were exposed to seated whole-body perturbations. Each participant performed 120 trials; they were rapidly tilted to the right and left, 60 times respectively. Main results. We achieved classification accuracies of more than 85% between PEPs and rest EEG using a window-based classification approach. Different window lengths and electrode layouts were compared. We were able to achieve excellent classification performance (87.6 ± 8.0% accuracy) by using a short window length of 200 ms and a minimal electrode layout consisting of only the Cz electrode. The peak classification accuracy coincides in time with the strongest component of PEPs, called N1. Significance. We showed that PEPs can be discriminated against ongoing EEG with high accuracy. These findings can contribute to the development of a system that can detect balance perturbations online.
A system identification analysis of optogenetically evoked electrocorticography and cerebral blood flow responses
Authors: Chin-Hao Chen Rex , Atry Farid , Richner Thomas , Brodnick Sarah , Pisaniello Jane , Ness Jared , Suminski Aaron J , Williams Justin , Pashaie Ramin
Published: April 2020

Objective. The main objective of this research was to study the coupling between neural circuits and the vascular network in the cortex of small rodents from system engineering point of view and generate a mathematical model for the dynamics of neurovascular coupling. The model was adopted to implement closed-loop blood flow control algorithms. Approach. We used a combination of advanced technologies including optogenetics, electrocorticography, and optical coherence tomography to stimulate selected populations of neurons and simultaneously record induced electrocorticography and hemodynamic signals. We adopted system identification methods to analyze the acquired data and investigate the relation between optogenetic neural activation and consequential electrophysiology and blood flow responses. Main results. We showed that the developed model, once trained by the acquired data, could successfully regenerate subtle spatio-temporal features of evoked electrocorticography and cerebral blood flow responses following an onset of optogenetic stimulation. Significance. The long term goal of this research is to open a new line for computational analysis of neurovascular coupling particularly in pathologies where the normal process of blood flow regulation in the central nervous system is disrupted including Alzheimer’s disease.
High throughput direct 3D bioprinting in multiwell plates
Authors: Hwang Henry H , You Shangting , Ma Xuanyi , Kwe Leilani , Victorine Grace , Lawrence Natalie , Wan Xueyi , Shen Haixu , Zhu Wei , Chen Shaochen
Published: April 2020

Advances in three dimensional (3D) bioprinting have enabled the fabrication of sophisticated 3D tissue scaffolds for biological and medical applications, where high speed, high throughput production in well plates is a critical need. Here, we present an integrated 3D bioprinting platform based on microscale continuous optical printing, capable of high throughput in situ rapid fabrication of complex 3D biomedical samples in multiwell plate formats for subsequent culture and analysis. Our high throughput 3D bioprinter (HT-3DP) was used to showcase constructs of varying spatial geometries of biomimetic significance, tunable mechanical properties, as well as reproducibility. Live hepatocellular carcinoma 3D tissue scaffolds were fabricated in situ in multiwell plates, after which a functional drug response assay against the chemotherapy drug doxorubicin was performed. Dual cell-type populations involving both live hepatocellular carcinoma as well as human umbilical vein endothelial cells were also printed to demonstrate dual-tissue fabrication capability. This work demonstrates a significant advancement in that the production rate of 3D bioprinted tissue scaffolds with controllable spatial architectures and mechanical properties can now be done on a high throughput scale, enabling rapid generation of in vitro 3D tissue models within conventional multiwell cell culture plates for high throughput preclinical drug screening and disease modeling.
Step-flow growth of graphene-boron nitride lateral heterostructures by molecular beam epitaxy
Authors: Thomas James , Bradford Jonathan , Cheng Tin S , Summerfield Alex , Wrigley James , Mellor Christopher J , Khlobystov Andrei N , Foxon C Thomas , Eaves Laurence , Novikov Sergei V , Beton Peter H
Published: April 2020

Integration of graphene and hexagonal boron nitride (hBN) into lateral heterostructures has drawn focus due to the ability to broadly engineer the material properties. Hybrid monolayers with tuneable bandgaps have been reported, while the interface itself possesses unique electronic and magnetic qualities. Herein, we demonstrate lateral heteroepitaxial growth of graphene and hBN by sequential growth using high-temperature molecular beam epitaxy (MBE) on highly oriented pyrolytic graphite (HOPG). We find, using scanning probe microscopy, that graphene growth nucleates at hBN step edges and grows across the surface to form nanoribbons with a controlled width that is highly uniform across the surface. The graphene nanoribbons grow conformally from the armchair edges of hexagonal hBN islands forming multiply connected regions with the growth front alternating from armchair to zigzag in regions nucleated close to the vertices of hexagonal hBN islands. Images with lattice resolution confirm a lateral epitaxial alignment between the hBN and graphene nanoribbons, while the presence of a moiré pattern within the ribbons indicates that some strain relief occurs at the lateral heterojunction. These results demonstrate that high temperature MBE is a viable route towards integrating graphene and hBN in lateral heterostructures.
Nanoscale mapping of ZnO–TiO2 up-conversion phosphor containing Yb3+ and Er3+
Authors: Nonaka Toshihiro , Imai Takahito , Ban Takahiko , Yamamoto Shin-Ichi
Published: April 2020

Up-conversion phosphors have attracted considerable attention for their visible-light emission. In this study, a ZnO–TiO2 up-conversion phosphor containing Yb3+ and Er3+ ions was prepared; its emission characteristics and crystal structure were analyzed, and its nanoscale elemental mapping was examined. The metal organic decomposition (MOD) method was used to fabricate the samples. After firing the sample at 1000 °C, the emission intensity showed a maximum when the molar ratio was Ti/Zn/Yb/Er = 1/1/0.06/0.02. Finally, the function of each element was considered from the viewpoint of the crystal structure and nanoscale mapping.
Boron and nitrogen doping in graphene: an experimental and density functional theory (DFT) study
Authors: Kaykılarlı Cantekin , Uzunsoy Deniz , Parmak Ebru Devrim Şam , Fellah Mehmet Ferdi , Çakır Özgen Çolak
Published: April 2020

Boron (B) and Nitrogen (N) doped few layer graphene (BNG) is directly synthesized via electric arc discharge (EAD) method. NH3 and BCl3 gas mixtures are used in the synthesis atmosphere. Raman spectroscopy is used to determine graphene’s purity and number of layers. The investigation of structure and morphology of pristine graphene and BNG are carried out via Transmission Electron Microscopy (TEM). The presence of B and N in the structure of graphene is detected by Energy Dispersive X-ray Spectroscopy (EDS) analysis. Elemental mapping show that N and B are distributed homogeneously in the graphene structure. It is observed that doping process did not affect the positions of the D, G and 2D bands in the Raman spectroscopy. The effect of doping on the number of layers of graphene is found negligible. TEM results exhibit that pristine graphene and BNG have 5 to 6 layers. Besides, the theoretical calculations based on Density Functional Theory (DFT) are employed to support experimental studies. Theoretical results based on DFT showed that bonding of B and N is favorable.
Strain engineering of the electronic and thermoelectric properties of titanium trisulphide monolayers
Authors: Saiz Fernan , Rurali Riccardo
Published: April 2020

The goal of this work is to evaluate the effect of mechanical strain on a number of electronic and thermoelectric properties of TiS3 monolayers. We have used density-functional theory (DFT) calculations at the hybrid HSE06 level to evaluate the response of the electronic band gap and mobilities, as well as the thermopower, the electrical conductivity, the electronic contribution to the thermal conductivity and the power factor. Our calculations indicate that the band gaps can be increased by 44.25%, reaching a value of 1.55 eV from that of the undeformed case of 1.07 eV. The behaviour of HSE06 band gaps agrees well with that calculated at the G0W0 level of theory. We evaluate the variation of electron mobilities with strain and discuss the possible causes of the existent disagreement between experiments and simulations. In addition, our calculations predict small changes in the Seebeck coefficient, whose S

y
component can be enhanced by up to 11% with a compression of 5% along the y-axis. On the other hand, the electrical conductivity experiences higher variations, nearly doubling its value from the undeformed case under the semiconductor regime of doping and mechanical deformation. Finally, our predicted power factors can be enhanced by nearly twice under the same conditions by which the electrical conductivity is also improved, indicating that the latter drives the optimisation of the former.
Dual-Outcome Intention-to-Treat Analyses in the Women’s Health Initiative Randomized Controlled Hormone Therapy Trials
Authors: Prentice Ross L , Aragaki Aaron K , Chlebowski Rowan T , Zhao Shanshan , Anderson Garnet L , Rossouw Jacques E , Wallace Robert , Banack Hailey , Shadyab Aladdin H , Qi Lihong , Snively Beverly M , Gass Margery , Manson JoAnn E
Published: April 2020

Dual-outcome intention-to-treat hazard rate analyses have potential to complement single-outcome analyses for the evaluation of treatments or exposures in relation to multivariate time-to-response outcomes. Here we consider pairs formed from important clinical outcomes to obtain further insight into influences of menopausal hormone therapy on chronic disease. As part of the Women’s Health Initiative, randomized, placebo-controlled hormone therapy trials of conjugated equine estrogens (CEE) among posthysterectomy participants and of these same estrogens plus medroxyprogesterone acetate (MPA) among participants with an intact uterus were carried out at 40 US clinical centers (1993–2016). These data provide the context for analyses covering the trial intervention periods and a nearly 20-year (median) cumulative duration of follow-up. The rates of multiple outcome pairs were significantly influenced by hormone therapy, especially over cumulative follow-up, providing potential clinical and mechanistic insights. For example, among women randomized to either regimen, hazard ratios for pairs defined by fracture during intervention followed by death from any cause were reduced and hazard ratios for pairs defined by gallbladder disease followed by death were increased, though these findings may primarily reflect single-outcome associations. In comparison, hazard ratios for diabetes followed by death were reduced with CEE but not with CEE + MPA, and those for hypertension followed by death were increased with CEE + MPA but not with CEE.
Unravelling change in forest ground floras. A commentary on: ‘Temporal patterns of seed germination in early spring-flowering temperate woodland geophytes are modified by warming’
Authors: Kirby Keith J
Published: April 2020

This article comments on:

Rosemary J Newton, Fiona R Hay, Richard H Ellis, Temporal patterns of seed germination in early spring-flowering temperate woodland geophytes are modified by warming, Annals of Botany, Volume 125, Issue 7, 4 June 2020, Pages 1013–1023, https://doi.org/10.1093/aob/mcaa025
APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms
Authors: Wang Ruijia , Tian Bin
Published: April 2020

Most eukaryotic genes produce alternative polyadenylation (APA) isoforms. APA is dynamically regulated under different growth and differentiation conditions. Here, we present a bioinformatics package, named APAlyzer, for examining 3′UTR APA, intronic APA and gene expression changes using RNA-seq data and annotated polyadenylation sites in the PolyA_DB database. Using APAlyzer and data from the GTEx database, we present APA profiles across human tissues.

Availability and implementation

APAlyzer is freely available at https://bioconductor.org/packages/release/bioc/html/APAlyzer.html as an R/Bioconductor package.

Supplementary information

Supplementary data are available at Bioinformatics online.
Characteristics of Household Transmission of COVID-19
Authors: Li Wei , Zhang Bo , Lu Jianhua , Liu Shihua , Chang Zhiqiang , Peng Cao , Liu Xinghua , Zhang Peng , Ling Yan , Tao Kaixiong , Chen Jianying
Published: April 2020

Background

Since December 2019, SARS-CoV-2 has extended to most parts of China with >80 000 cases and to at least 100 countries with >60 000 international cases as of 15 March 2020. Here we used a household cohort study to determine the features of household transmission of COVID-19.

Methods

A total of 105 index patients and 392 household contacts were enrolled. Both index patients and household members were tested by SARS-CoV-2 RT-PCR. Information on all recruited individuals was extracted from medical records and confirmed or supplemented by telephone interviews. The baseline characteristics of index cases and contact patients were described. Secondary attack rates of SARS-CoV-2 to contact members were computed and the risk factors for transmission within the household were estimated.

Results

Secondary transmission of SARS-CoV-2 developed in 64 of 392 household contacts (16.3%). The secondary attack rate to children was 4% compared with 17.1% for adults. The secondary attack rate to the contacts within the households with index patients quarantined by themselves since onset of symptoms was 0% compared with 16.9% for contacts without quarantined index patients. The secondary attack rate to contacts who were spouses of index cases was 27.8% compared with 17.3% for other adult members in the households.

Conclusions

The secondary attack rate of SARS-CoV-2 in household is 16.3%. Age of household contacts and spousal relationship to the index case are risk factors for transmission of SARS-CoV-2 within a household. Quarantine of index patients at home since onset of symptoms is useful to prevent the transmission of SARS-Co-2 within a household.
Duration of Viral Shedding of Discharged Patients With Severe COVID-19
Authors: Zhou Bo , She Jianqing , Wang Yadan , Ma Xiancang
Published: April 2020

COVID-19 has drawn global intensive attention. We analyzed the duration of viral shedding and the total time from illness onset to discharge in groups. This has important implications for making decisions for isolation of discharged patients and to provide guidance for the duration of hospitalization of patients with severe COVID-19.
Enhanced Performance of DNA Methylation Markers by Simultaneous Measurement of Sense and Antisense DNA Strands after Cytosine Conversion
Authors: Jensen Sarah Ø , Øgaard Nadia , Nielsen Hans Jørgen , Bramsen Jesper B , Andersen Claus L
Published: April 2020

Background

Most existing DNA methylation-based methods for detection of circulating tumor DNA (ctDNA) are based on conversion of unmethylated cytosines to uracil. After conversion, the 2 DNA strands are no longer complementary; therefore, targeting only 1 DNA strand merely utilizes half of the available input DNA. We investigated whether the sensitivity of methylation-based ctDNA detection strategies could be increased by targeting both DNA strands after bisulfite conversion.

Methods

Dual-strand digital PCR assays were designed for the 3 colorectal cancer (CRC)–specific methylation markers KCNQ5, C9orf50, and CLIP4 and compared with previously reported single-strand assays. Performance was tested in tumor and leukocyte DNA, and the ability to detect ctDNA was investigated in plasma from 43 patients with CRC stages I to IV and 42 colonoscopy-confirmed healthy controls.

Results

Dual-strand assays quantified close to 100% of methylated control DNA input, whereas single-strand assays quantified approximately 50%. Furthermore, dual-strand assays showed a 2-fold increase in the number of methylated DNA copies detected when applied to DNA purified from tumor tissue and plasma from CRC patients. When the results of the 3 DNA methylation markers were combined into a ctDNA detection test and applied to plasma, the dual-strand assay format detected 86% of the cancers compared with 74% for the single-strand assay format. The specificity was 100% for both the dual- and single-strand test formats.

Conclusion

Dual-strand assays enabled more sensitive detection of methylated ctDNA than single-strand assays.
Sex differences in aortic valve calcification in severe aortic valve stenosis: association between computer tomography assessed calcification and valvular calcium concentrations
Authors: Linde Louise , Carter-Storch Rasmus , Christensen Nicolaj Lyhne , Øvrehus Kristian Altern , Diederichsen Axel Cosmus Pyndt , Laursen Kristian , Jensen Pia Søndergaard , Rasmussen Lars Melholt , Møller Jacob Eifer , Dahl Jordi Sanchez
Published: April 2020

Aims

The aims of this study were to investigate the correlation and sex differences between total valve calcium, valve calcium concentration, and aortic valve calcification (AVC) in explanted valves from patients with severe aortic valve stenosis undergoing aortic valve replacement (AVR).

Methods and results

Sixty-nine patients with severe aortic stenosis (AS) scheduled for elective AVR underwent echocardiography and cardiac computed tomography (CT) prior to surgery (AVCin vivo) and CT of the explanted aortic valve (AVCex vivo). Explanted valves were prepared in acid solution, sonicated, and analysed with Arsenazo III dye to estimate total valve calcium and valve calcium concentration. Median AVCex vivo was 2082 (1421–2973) AU; mean valve calcium concentration was 1.43 ± 0.42 µmol Ca2+/mg tissue; median total valve calcium 156 (111–255) mg Ca2+, and valve calcium density 52 (35–81) mg/cm2. AVC displayed a strong correlation with total valve calcium (R2 = 0.98, P < 0.001) and a moderate correlation with valve calcium concentration (R2 = 0.62, P < 0.001). Valvular calcium concentration was associated with sex, aortic valve area, and mean gradient. After adjusting for age and estimated glomerular filtration rate, sex and mean gradient remained associated with valve calcium concentrations.

Conclusion

AVC score provides a strong estimate for total valve calcium but to a lesser degree calcium concentration in the valve tissue of patients with severe AS. Females presented lower valvular calcium concentrations than males irrespective of AS severity, adding evidence and providing support to the important point that sex differences in valvular calcium concentration in AS does not reflect valvular size.
The myocardial phenotype of Fabry disease pre-hypertrophy and pre-detectable storage
Authors: Augusto João B , Johner Nicolas , Shah Dipen , Nordin Sabrina , Knott Kristopher D , Rosmini Stefania , Lau Clement , Alfarih Mashael , Hughes Rebecca , Seraphim Andreas , Vijapurapu Ravi , Bhuva Anish , Lin Linda , Ojrzyńska Natalia , Geberhiwot Tarekegn , Captur Gabriella , Ramaswami Uma , Steeds Richard P , Kozor Rebecca , Hughes Derralynn , Moon James C , Namdar Mehdi
Published: April 2020

Aims

Cardiac involvement in Fabry disease (FD) occurs prior to left ventricular hypertrophy (LVH) and is characterized by low myocardial native T1 with sphingolipid storage reflected by cardiovascular magnetic resonance (CMR) and electrocardiogram (ECG) changes. We hypothesize that a pre-storage myocardial phenotype might occur even earlier, prior to T1 lowering.

Methods and results

FD patients and age-, sex-, and heart rate-matched healthy controls underwent same-day ECG with advanced analysis and multiparametric CMR [cines, global longitudinal strain (GLS), T1 and T2 mapping, stress perfusion (myocardial blood flow, MBF), and late gadolinium enhancement (LGE)]. One hundred and fourteen Fabry patients (46 ± 13 years, 61% female) and 76 controls (49 ± 15 years, 50% female) were included. In pre-LVH FD (n = 72, 63%), a low T1 (n = 32/72, 44%) was associated with a constellation of ECG and functional abnormalities compared to normal T1 FD patients and controls. However, pre-LVH FD with normal T1 (n = 40/72, 56%) also had abnormalities compared to controls: reduced GLS (−18 ± 2 vs. −20 ± 2%, P < 0.001), microvascular changes (lower MBF 2.5 ± 0.7 vs. 3.0 ± 0.8 mL/g/min, P = 0.028), subtle T2 elevation (50 ± 4 vs. 48 ± 2 ms, P = 0.027), and limited LGE (%LGE 0.3 ± 1.1 vs. 0%, P = 0.004). ECG abnormalities included shorter P-wave duration (88 ± 12 vs. 94 ± 15 ms, P = 0.010) and T-wave peak time (Tonset – Tpeak; 104 ± 28 vs. 115 ± 20 ms, P = 0.015), resulting in a more symmetric T wave with lower T-wave time ratio (Tonset – Tpeak)/(Tpeak – Tend) (1.5 ± 0.4 vs. 1.8 ± 0.4, P < 0.001) compared to controls.

Conclusion

FD has a measurable myocardial phenotype pre-LVH and pre-detectable myocyte storage with microvascular dysfunction, subtly impaired GLS and altered atrial depolarization and ventricular repolarization intervals.
Auxiliary information resolution effects on small area estimation in plantation forest inventory
Authors: Green P Corey , Burkhart Harold E , Coulston John W , Radtke Philip J , Thomas Valerie A
Published: April 2020

In forest inventory, traditional ground-based resource assessments are often expensive and time-consuming forcing managers to reduce sample sizes to meet budgetary and logistical constraints. Small area estimation (SAE) is a class of statistical estimators that uses a combination of traditional survey data and linearly related auxiliary information to improve estimate precision. These techniques have been shown to improve the precision of stand-level inventory estimates in loblolly pine plantations using lidar height percentiles and thinning status as covariates. In this study, the effects of reduced lidar point-cloud densities and lower digital elevation model (DEM) spatial resolutions were investigated for total planted volume estimates using area-level SAE models. In the managed Piedmont pine plantation conditions evaluated, lower lidar point-cloud densities and DEM spatial resolutions were found to have minimal effects on estimates and precision. The results of this study are promising to those interested in incorporating SAE methods into forest inventory programs.
Outcomes of a single-step endoscopic ultrasound-guided drainage of pancreatic-fluid collections using an electrocautery-enhanced coaxial lumen-apposing, self-expanding metal stent with and without fluoroscopy
Authors: Olaiya Babatunde , Mekaroonkamol Parit , Li Bai-Wen , Massaad Julia , Vachaparambil Cicily T , Xu Jennifer , Lamm Vladamir , Luo Hui , Shen Shan-Shan , Chen Hui-Min , Keilin Steve , Willingham Field F , Cai Qiang
Published: April 2020

Background

Fluoroscopy is often used during the endoscopic drainage of pancreatic-fluid collections (PFCs). An electrocautery-enhanced coaxial lumen-apposing, self-expanding metal stent (ELAMS) facilitates a single-step procedure and may avoid the need for fluoroscopy. This study compares the treatment outcomes using ELAMS with and without fluoroscopy.

Methods

Patients with PFCs who had cystogastrostomy from January 2014 to February 2017 were enrolled. Two groups were studied based on fluoroscopy use. Technical success was defined as uneventful insertion of ELAMS at time of procedure. Clinical success was defined as (i) clinical resolution of symptoms after the procedure and (ii) >75% reduction in cyst size on computed tomography 8 weeks after stent placement. Adverse events including bleeding, stent migration, and infection were recorded.

Results

A total of 21 patients (13 males) had PFCs drainage with ELAMS in the study period. The mean age was 51.6 ± 14.2 years. Thirteen patients had walled-off necrosis while eight had a pancreatic pseudocyst. The mean size of the PFCs was 11.3 ± 3.3 cm. Fluoroscopy was used in seven cases (33%) and was associated with a longer procedure time compared to non-fluoroscopy (43.1 ± 10.4 vs 33.3 ± 10.5 min, P = 0.025). This association was independent of the size, location, or type of PFCs. Fluoroscopy had no effect on the technical success rates. In fluoroless procedures, the clinical resolution was 91% as compared to 71% in fluoroscopy procedures (P = 0.52) and the radiologic resolution was 57% as compared to 71% in fluoroscopy procedures (P = 0. 65). Three cases of stent migration/displacement occurred in the fluoroless procedures.

Conclusions

ELAMS may avoid the need for fluoroscopy during cystogastrostomy. Procedures without fluoroscopy were significantly shorter and fluoroscopy use had no impact on the technical or clinical success rates.
Species-level evaluation of the human respiratory microbiome
Authors: Ibironke Olufunmilola , McGuinness Lora R , Lu Shou-En , Wang Yaquan , Hussain Sabiha , Weisel Clifford P , Kerkhof Lee J
Published: April 2020

Background

Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract.

Findings

Bronchoalveolar lavage, throat swab, mouth rinse, and nasal swab samples were collected from 5 participants. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. More than 1.8 million raw operon reads were obtained from the participants with ~600,000 rRNA reads passing quality assurance/quality control (70–95% identify; >1,200 bp alignment) by Discontiguous MegaBLAST against the EZ BioCloud 16S rRNA gene database. Nearly 3,600 bacterial species were detected overall (>750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The relative abundance of bacterial species along the respiratory tract indicated that most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (<5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were Veillonella dispar and Veillonella atypica while the most abundant mouth-associated bacterial species were Streptococcus infantis and Streptococcus mitis.

Conclusions

Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, >100 bacterial species were found to be enriched in bronchoalveolar lavage samples (compared to mouth/nose) and may play a substantial role in lung health.
Building envelope and energy saving case study: a residential building in Al-Riyadh, Saudi Arabia
Authors: Al-Qahtani Laila Amer Hashem , Elgizawi Lamis Saad Eldeen
Published: April 2020

Around the world, most energy is consumed by buildings; residential buildings consume 40% of energy globally. In the Kingdom of Saudi Arabia (KSA), buildings consume 50% of all energy, and 70% of the buildings in the KSA are not insulated well. Creating an envelope is a key to decreasing energy consumption and providing thermal comfort and healthy internal spaces. Thus, the main aim of this study is to test the effect of selected passive cooling strategies by using a simulation program to evaluate a variety of envelope (floor, external and internal walls and roofs) thermal characteristic proposals to create an eco-interior space, to provide the most comfortable conditions for users and to save energy in buildings in hot climates in Riyadh, Saudi Arabia. One residential building case was selected, and some of the passive cooling strategies were tested. Simulation software—Design Builder—was used to calculate the total energy consumption in 1 year and compare the results before and after applying these strategies to the selected residential building.
Robust integrated covariance intersection fusion Kalman estimators for networked mixed uncertain time-varying systems
Authors: Gao Yuan , Deng Zili
Published: April 2020

For the multisensor time-varying networked mixed uncertain systems with random one-step sensor delays and uncertain-variance multiplicative and linearly dependent additive white noises, a new augmented state method with fictitious noises is presented, by which the original system is transformed into a standard system without delays and with uncertain-variance fictitious white noises. According to the minimax robust estimation principle and the Kalman filtering theory, based on the worst-case system with the conservative upper bounds of uncertain noise variances, the local and integrated covariance intersection (ICI) fused robust time-varying Kalman estimators (filter, predictor and smoother) are presented respectively in the sense that their actual estimation error variances are guaranteed to have the corresponding minimal upper bounds for all admissible uncertainties. Their robustness is proved by the extended Lyapunov equation method, and their accuracy relations are compared based on the traces of the variance matrices and the covariance ellipsoids, respectively. Specially, a universal ICI fusion robust Kalman filtering method of integrating the local robust estimators and their conservative cross-covariances is presented. It overcomes the drawbacks of the original covariance intersection (CI) fusion method and improves robust accuracy of the original CI fuser. A simulation example applied to two-mass spring system shows the effectiveness of the proposed methods and results.