bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of various flow, sediment and geometrical parameters on partially or fully submerged deck scour
Authors: Baduna Koçyiğit Müsteyde , Karakurt Onur , Akay Hüseyin
Published: February 2021

The effect of various parameters of flow, sediment and geometric features of the bridge on the depth and shape of the scour hole occurred underneath a bridge deck model without a pier was investigated by a series of experiments conducted in a flume under partially and fully submerged flow and clear water conditions. The experiments were performed with factors such as approach flow depth, discharge, sediment size, degree of submergence, girder location and depth. A total of 112 experiments were conducted for both partially and fully submerged flow conditions. The experimental data showed that the partially submerged flow increased the maximum depth of scour hole and affected the shape of the scour hole more when compared to the fully submerged flow. It was also noted that parameters that directly affected flow structure in the bridge opening such as girder height might significantly increase the maximum depth of scour hole. Effect of the distance between a single girder and the bridge edge was also tested by using three different girder location and it was found that as the distance increased, the depth of the scour hole decreased and the location of the maximum scour depth moved with the girder to where the contraction in the flow area occurred.
Beyond Classical Definition: The Non-definition of Gamification
Authors: Staller Mario S. , Koerner Swen
Published: February 2021

Gamification is regularly defined as the use of game elements in non-gaming contexts. However, discussions in the context of the pedagogical value of gamification suggest controversies on various levels. While on the one hand, the potential is seen in the design of joyful learning environments, critics point out the pedagogical dangers or the problems related to optimizing working life. It becomes apparent that the assumptions guiding action on the subject matter of gamification in educational contexts differ, which leads to different derivations for pedagogical practice—but also allows for different perspectives on initially controversial positions. Being aware of these assumptions is the claim of a reflexive pedagogy. With regard to the pedagogical use of gamifying elements and their empirical investigation, there are three main anchor points to consider from a reflexive stance: (a) the high context-specificity of the teaching undertaken and (b) the (non-)visibility of the design elements and (c) the (non-)acceptance of the gamified elements by the students. We start by providing a discussion of the definitional discourse on what is understood as gamification leading to our argument for a non-definition of gamification. We describe the potential of this non-definition of gamification and exemplify its use in a gamified concept of teaching police recruits professional reflexivity. The concept features the narrative of a potential crime that has been undertaken and that students decide for themselves if they want to engage with it.
Correction to: Prevention of spinal fusion post-operative wound infections in pediatric patients with scoliosis: a quality improvement initiative
Authors: Partridge Elizabeth , Blumberg Dean , Roberto Rolando F.
Published: February 2021

The original version of this article unfortunately contained a mistake.
Understanding Dialogue
Authors: Pickering Martin J. , Garrod Simon
Published: February 2021

Linguistic interaction between two people is the fundamental form of communication, yet almost all research in language use focuses on isolated speakers and listeners. In this innovative work, Garrod and Pickering extend the scope of psycholinguistics beyond individuals by introducing communication as a social activity. Drawing on psychological, linguistic, philosophical and sociological research, they expand their theory that alignment across individuals is the basis of communication, through the model of a 'shared workspace account'. In this workspace, interlocutors are actors who jointly manipulate and control the interaction and develop similar representations of both language and social context, in order to achieve communicative success. The book also explores dialogue within groups, technologies, as well as the role of culture more generally. Providing a new understanding of cognitive representation, this trailblazing work will be highly influential in the fields of linguistics, psychology and cognitive linguistics.
An investigation into the experiences of school counsellors working with adolescents
Authors: Bettman Cathy G. , Digiacomo Alexander
Published: February 2021

Currently, Australia’s school counsellors are increasingly being called upon to respond to adolescent mental health needs. Through semistructured interviews with seven school counsellors working with adolescents, this qualitative study aimed to capture the lived experiences of this group of practitioners. By adopting a phenomenological approach and using thematic analysis, this study provides insight into their profession: the current ambiguity surrounding their role; the opportunities and obstacles they face; as well as the often-present tension between stakeholders including parents, other school staff and external agencies. The findings of this study indicate that school counsellors are challenged by the need to be advocates not only for their students but also for themselves and their roles within the school context.
Phylogenetic position of Sphincterodiplostomum Dubois, 1936 (Digenea: Diplostomoidea) with description of a second species from Pantanal, Brazil
Authors: Achatz T.J. , Bell J.A. , Melo F.T.V. , Fecchio A. , Tkach V.V.
Published: February 2021

Sphincterodiplostomum is a monotypic genus of diplostomid digeneans that parasitize fish-eating birds in the neotropics. The type species Sphincterodiplostomum musculosum has a unique, dorsal, tubular invagination in the opisthosoma with a muscular sphincter. Whereas larvae of S. musculosum are relatively commonly reported in Neotropical fish helminth surveys, adult specimens from birds are rarely collected. Prior to our study, no DNA sequence data for S. musculosum were available. Our molecular and morphological study of mature and immature adult Sphincterodiplostomum specimens from three species of birds and one species of crocodilian revealed the presence of at least two species of Sphincterodiplostomum in the neotropics. We provide the first molecular phylogeny of the Diplostomoidea that includes Sphincterodiplostomum. In addition, this is the first record of S. musculosum from caimans, along with the first record of fully mature adult S. musculosum from green kingfisher Chloroceryle americana. The new species of Sphincterodiplostomum (Sphincterodiplostomum joaopinhoi n. sp.) can be morphologically distinguished from S. musculosum based on the anterior extent of vitelline follicles, narrower prosoma, substantially smaller holdfast organ and structure of tegumental spines. Our data revealed 0.7% interspecific divergence in 28S and 10.6–11.7% divergence in cox1 sequences between the two Sphincterodiplostomum species.
Ontogenetic shifts and sexual dimorphism in the brain organization of the small-spotted catshark Scyliorhinus canicula
Authors: Roussos Ioannis , Megalofonou Persefoni
Published: February 2021

In this study, we investigated ontogenetic and sexual changes of the brain scaling as well as the scaling and the relative size of six major brain areas in the small-spotted catshark Scyliorhinus canicula from the Mediterranean Sea. The brain somatic index (0.31–1.25%) did not differ significantly between sexes but was significantly affected by size with smaller specimens exhibiting higher values. Brain growth exhibited negative allometry (allometric coefficient 0.634), not affected by sex or maturity status. The brain growth rate was found to be higher compared with a previous study from the Atlantic Ocean. Regarding the scaling of the brain areas, the olfactory bulbs scaled with positive allometry, the telencephalon and the diencephalon scaled with the same rate of negative allometry, the mesencephalon exhibited even higher negative allometry, while the cerebellum and the medulla oblongata both followed a close-to-isometric growth pattern. Immature S. canicula possessed a larger mesencephalon and diencephalon, highlighting the importance of vision in this life period, while mature specimens had enlarged olfactory bulbs, indicating that olfaction may be more important after the animal attains sexual maturity. In respect of sexual dimorphism, males had a larger cerebellum and medulla oblongata, while females had enlarged telencephalon and olfactory bulbs.
Phonetic discrimination, phonological awareness, and pre-literacy skills in Spanish–English dual language preschoolers
Authors: SMITH Sara A. , LEON GUERRERO Sibylla , SURRAIN Sarah , LUK Gigi
Published: February 2021

The current study explores variation in phonemic representation among Spanish–English dual language learners (DLLs, n = 60) who were dominant in English or in Spanish. Children were given a phonetic discrimination task with speech sounds that: 1) occur in English and Spanish, 2) are exclusive to English, and 3) are exclusive to Russian, during Fall (age m = 57 months) and Spring (age m = 62 months, n = 42). In Fall, English-dominant DLLs discriminated more accurately than Spanish-dominant DLLs between English-Spanish phones and English-exclusive phones. Both groups discriminated Russian phones at or close to chance. In Spring, however, groups no longer differed in discriminating English-exclusive phones and both groups discriminated Russian phones above chance. Additionally, joint English-Spanish and English-exclusive phonetic discrimination predicted children's phonological awareness in both groups. Results demonstrate plasticity in early childhood through diverse language exposure and suggest that phonemic representation begins to emerge driven by lexical restructuring.
THE METRIC PROJECTIONS ONTO CLOSED CONVEX CONES IN A HILBERT SPACE
Authors: Qiu Yanqi , Wang Zipeng
Published: February 2021

We study the metric projection onto the closed convex cone in a real Hilbert space
$\mathscr {H}$
generated by a sequence
$\mathcal {V} = \{v_n\}_{n=0}^\infty $
. The first main result of this article provides a sufficient condition under which the closed convex cone generated by
$\mathcal {V}$
coincides with the following set:
$$ \begin{align*} \mathcal{C}[[\mathcal{V}]]: = \bigg\{\sum_{n=0}^\infty a_n v_n\Big|a_n\geq 0,\text{ the series }\sum_{n=0}^\infty a_n v_n\text{ converges in } \mathscr{H}\bigg\}. \end{align*} $$
Then, by adapting classical results on general convex cones, we give a useful description of the metric projection onto
$\mathcal {C}[[\mathcal {V}]]$
. As an application, we obtain the best approximations of many concrete functions in
$L^2([-1,1])$
by polynomials with nonnegative coefficients.
Der wechselseitige Einfluss von Selbstkonzept und Leistung bei Grundschulkindern im Lichte verschiedener längsschnittlicher Analysemethoden
Authors: Ehm Jan-Henning , Hasselhorn Marcus , Schmiedek Florian
Published: February 2021

Zusammenfassung. Der Zusammenhang zwischen dem akademischen Selbstkonzept und der Leistung wird als reziprok angesehen. Während eine große Anzahl von Studienergebnissen im Sinne einer bidirektionalen Beziehung interpretiert wurden, basieren bisherige Analysen zumeist auf Variationen des klassischen Cross-Lagged-Panel-Modells und beziehen oft nur einen Leistungsindikator in die Modelle mit ein. Ergebnisse basierend auf neueren Modellen, wie beispielsweise dem Random-Intercept Cross-Lagged Panel Model liegen bisher kaum vor. Das Ziel der vorliegenden Studie bestand darin, die längsschnittliche Beziehung zwischen Selbstkonzept und Leistung mit unterschiedlichen Modellen zu analysieren, um herauszufinden, ob die Modelle zu vergleichbaren Ergebnissen hinsichtlich der wechselseitigen Effekte kommen. Basierend auf einer Stichprobe von 1952 Grundschulkindern von Klasse eins bis drei, ergaben sich deutliche Unterschiede. Während Effekte von der Leistung auf das Selbstkonzept in allen Modellen nachgewiesen werden konnten, ist die Evidenz für umgekehrte Effekte eher schwach. Die Ergebnisse werden vor dem Hintergrund theoretischer Annahmen und der Angemessenheit methodischer Verfahren zur Analyse von längschnittlichen Daten diskutiert.
Molecular Signatures of Glacial Dissolved Organic Matter From Svalbard and Greenland
Authors: Kellerman Anne M. , Vonk Jorien , McColaugh Stephanie , Podgorski David C. , van Winden Elise , Hawkings Jon R. , Johnston Sarah Ellen , Humayun Munir , Spencer Robert G. M.
Published: February 2021

Glaciers and ice sheets cover over 10 % of Earth's land surface area and store a globally significant amount of dissolved organic matter (DOM), which is highly bioavailable when exported to proglacial environments. Recent rapid glacier mass loss is hypothesized to have increased fluxes of DOM from these environments, yet the molecular composition of glacially derived DOM has only been studied for a handful of glaciers. We determine DOM composition using ultrahigh resolution mass spectrometry from a diverse suite of Arctic glacial environments, including time series sampling from an ice sheet catchment in Greenland (Russell Glacier) and outflow from valley glaciers in catchments with varying degrees of glacial cover in Svalbard. Samples from the Greenland outflow time series exhibited a higher degree of similarity than glacier outflow between glaciers in Svalbard; however, supraglacial meltwater samples from Greenland and Svalbard were more similar to each other than corresponding glacial outflow. Outflow from Russell Glacier was enriched in polyphenolic formulae, potentially reflecting upstream inputs from plants and soils, or inputs from paleosols overridden by the ice sheet, whereas Svalbard rivers exhibited a high level of molecular richness and dissimilarity between sites. When comparing DOM compositional analyses from other aquatic systems, aliphatic, and peptide‐like formulae appear particularly abundant in supraglacial meltwater, suggesting the DOM quickly metabolized in previous incubations of glacial water originates from energy‐rich supraglacial sources. Therefore, as glaciers lose mass across the region, higher‐quality fuel for microbial degradation will increase heterotrophy in coastal systems with ramifications for carbon cycling.
Practical Data‐Driven Flood Forecasting Based on Dynamical Systems Theory
Authors: Okuno Shunya , Ikeuchi Koji , Aihara Kazuyuki
Published: February 2021

Data‐driven flood forecasting methods are useful, especially for rivers that lack information required for building physical models. Although the former methods can forecast river stages using only past water levels and rainfall data, they cannot easily predict unprecedented water levels and require a large amount of data to build accurate models. We focus on phase‐space reconstruction approaches based on dynamical systems theory and develop a practical data‐driven forecasting method to overcome existing problems. The proposed method can predict unprecedented water levels owing to a proposed correction term, and provide forecasts using only a small number of water level increase events. We applied the proposed method to data from actual rivers and it achieved the best forecast performance among existing data‐driven methods, including a multilayer perceptron, and a conventional method based on phase‐space reconstruction. In addition, the proposed method forecasted the exceedance of the evacuation warning level 6 h earlier for small and steep rivers. Given its performance and maintainability, the proposed method can be applied to many gauged rivers to facilitate early evacuation.
Prospective randomized pharmacogenetic study of topiramate for treating alcohol use disorder
Authors: Kranzler Henry R. , Morris Paige E. , Pond Timothy , Crist Richard C. , Kampman Kyle M. , Hartwell Emily E. , Lynch Kevin G.
Published: February 2021

In a prior study, topiramate reduced heavy drinking among individuals who sought to reduce their drinking, with the effect moderated by a single nucleotide polymorphism (SNP; rs2832407) in GRIK1, which encodes the kainate GluK1 receptor subunit (Kranzler et al. 2014). The present study sought to replicate prospectively the effect of topiramate and rs2832407 in patients with DSM-5 alcohol use disorder (AUD) who sought to reduce or stop their drinking. We stratified the randomization on genotype (rs2832407*C-allele homozygotes vs. A-allele carriers) and assigned 170 European-American participants (71.2% male) to receive 12 weeks of treatment with topiramate (N  = 85), at a maximal daily dosage of 200 mg, or matching placebo (N = 85). At each of nine treatment visits participants received brief counseling to reduce drinking and increase abstinent days. We hypothesized that topiramate-treated patients with the rs2832407*CC genotype would reduce heavy drinking days (HDDs) more than the other three groups. The rate of treatment completion was 91.8% in both groups. The mean number of HDDs per week in the placebo group was 1.67 (95% CI = (1.29, 2.16), p = 0.0001) times greater than in the topiramate group, which was confirmed by the topiramate group’s significantly greater reduction in the concentration of the liver enzyme γ-glutamyltransferase and lower alcohol-related problems score. There was no significant difference in topiramate’s effect on HDDs between genotype groups. Although consistent with other studies showing a reduction in heavy drinking with topiramate treatment, the prior finding of a moderating effect of rs2832407 genotype was not replicated in this prospective trial.
Correction to: FAM83B inhibits ovarian cancer cisplatin resistance through inhibiting Wnt pathway
Authors: He Shanyang , Wang Wei , Wan Zhiyong , Shen Hongwei , Zhao Yunhe , You Zeshan , Liu Jun , Zhu Liwen
Published: February 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41389-021-00303-4
Rab22a-NeoF1 fusion protein promotes osteosarcoma lung metastasis through its secretion into exosomes
Authors: Zhong Li , Liao Dan , Li Jingjing , Liu Wenqiang , Wang Jingxuan , Zeng Cuiling , Wang Xin , Cao Zhiliang , Zhang Ruhua , Li Miao , Jiang Kuntai , Zeng Yi-Xin , Sui Jianhua , Kang Tiebang
Published: February 2021

It remains unknown for decades how some of the therapeutic fusion proteins positive in a small percentage of cancer cells account for patient outcome. Here, we report that osteosarcoma Rab22a-NeoF1 fusion protein, together with its binding partner PYK2, is sorted into exosomes by HSP90 via its KFERQ-like motif (RVLFLN142). The exosomal Rab22a-NeoF1 fusion protein facilitates the pulmonary pre-metastatic niche formation by recruiting bone marrow-derived macrophages. The exosomal PYK2 activates RhoA in its negative recipient osteosarcoma cells and induces signal transducer and activator of transcription 3 activation in its recipient macrophages to increase M2 phenotype. Consequently, lung metastases of its recipient osteosarcoma cells are promoted by this exosomal Rab22a-NeoF1 fusion protein, and this event can be targeted by disrupting its interaction with PYK2 using a designed internalizing RGD peptide.
Effects of tryptophan depletion on anxiety, a systematic review
Authors: Schopman Simone M. E. , Bosman Renske C. , Muntingh Anna D. T. , van Balkom Anton J. L. M. , Batelaan Neeltje M.
Published: February 2021

Vulnerability markers for onset of anxiety disorders are scarce. In depression, patients at risk tend to respond with a negative mood to ‘acute tryptophan depletion’ (ATD), while healthy volunteers and current patients do not. The serotonergic system thus provides indications for vulnerability for depression. It is unknown whether ATD reveals vulnerability in anxiety too. This study systematically reviews the effects of ATD on anxiety and assesses whether challenging anxiety modifies the response. PubMed, Embase and PsychInfo were systematically searched up to April 2019 for studies in which (1) healthy volunteers or patients with a (remitted) anxiety disorder underwent ATD and (2) levels of anxiety were reported. In total, 21 studies were included. Studies conducted in healthy volunteers (n = 13), and patients with a remitted (n = 6) or current (panic, social or generalised) anxiety disorder (n = 4). Studies were mostly of poor quality and heterogeneous regarding population, challenge test used and outcome measures. ATD did not consistently affect anxiety in any of the groups. Moreover, a challenge test after ATD (n = 17 studies) did not consistently provoke anxiety in healthy volunteers or remitted patients. A 35% CO2 challenge did consistently increase anxiety in patients with a current panic disorder (PD). To conclude, this systematic review found no clear indications that ATD provokes anxiety in those at risk for anxiety disorders. Hence, unlike in depression, ATD does not indicate vulnerability to develop an anxiety disorder. Because included studies were heterogeneous and mostly of poor quality, there is an urgent need for high quality research in homogeneous samples.
Silane- and peroxide-free hydrogen atom transfer hydrogenation using ascorbic acid and cobalt-photoredox dual catalysis
Authors: Kamei Yuji , Seino Yusuke , Yamaguchi Yuto , Yoshino Tatsuhiko , Maeda Satoshi , Kojima Masahiro , Matsunaga Shigeki
Published: February 2021

Hydrogen atom transfer (HAT) hydrogenation has recently emerged as an indispensable method for the chemoselective reduction of unactivated alkenes. However, the hitherto reported systems basically require stoichiometric amounts of silanes and peroxides, which prevents wider applications, especially with respect to sustainability and safety concerns. Herein, we report a silane- and peroxide-free HAT hydrogenation using a combined cobalt/photoredox catalysis and ascorbic acid (vitamin C) as a sole stoichiometric reactant. A cobalt salophen complex is identified as the optimal cocatalyst for this environmentally benign HAT hydrogenation in aqueous media, which exhibits high functional-group tolerance. In addition to its applicability in the late-stage hydrogenation of amino-acid derivatives and drug molecules, this method offers unique advantage in direct transformation of unprotected sugar derivatives and allows the HAT hydrogenation of unprotected C-glycoside in higher yield compared to previously reported HAT hydrogenation protocols. The proposed mechanism is supported by experimental and theoretical studies.
Terahertz-field-induced polar charge order in electronic-type dielectrics
Authors: Yamakawa H. , Miyamoto T. , Morimoto T. , Takamura N. , Liang S. , Yoshimochi H. , Terashige T. , Kida N. , Suda M. , Yamamoto H. M. , Mori H. , Miyagawa K. , Kanoda K. , Okamoto H.
Published: February 2021

Ultrafast electronic-phase change in solids by light, called photoinduced phase transition, is a central issue in the field of non-equilibrium quantum physics, which has been developed very recently. In most of those phenomena, charge or spin orders in an original phase are melted by photocarrier generations, while an ordered state is usually difficult to be created from a non-ordered state by a photoexcitation. Here, we demonstrate that a strong terahertz electric-field pulse changes a Mott insulator of an organic molecular compound in κ-(ET)2Cu[N(CN)2]Cl (ET = bis(ethylenedithio)tetrathiafulvalene), to a macroscopically polarized charge-order state; herein, electronic ferroelectricity is induced by the collective intermolecular charge transfers in each dimer. In contrast, in an isostructural compound, κ-(ET)2Cu2(CN)3, which shows the spin-liquid state at low temperatures, a similar polar charge order is not stabilized by the same terahertz pulse. From the comparative studies of terahertz-field-induced second-harmonic-generation and reflectivity changes in the two compounds, we suggest the possibility that a coupling of charge and spin degrees of freedom would play important roles in the stabilization of polar charge order.
Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions
Authors: Bi Yang , Deng Zhiping , Ni Weimin , Shrestha Ruben , Savage Dasha , Hartwig Thomas , Patil Sunita , Hong Su Hyun , Zhang Zhenzhen , Oses-Prieto Juan A. , Li Kathy H. , Quail Peter H. , Burlingame Alma L. , Xu Shou-Ling , Wang Zhi-Yong
Published: February 2021

O-GlcNAc modification plays important roles in metabolic regulation of cellular status. Two homologs of O-GlcNAc transferase, SECRET AGENT (SEC) and SPINDLY (SPY), which have O-GlcNAc and O-fucosyl transferase activities, respectively, are essential in Arabidopsis but have largely unknown cellular targets. Here we show that AtACINUS is O-GlcNAcylated and O-fucosylated and mediates regulation of transcription, alternative splicing (AS), and developmental transitions. Knocking-out both AtACINUS and its distant paralog AtPININ causes severe growth defects including dwarfism, delayed seed germination and flowering, and abscisic acid (ABA) hypersensitivity. Transcriptomic and protein-DNA/RNA interaction analyses demonstrate that AtACINUS represses transcription of the flowering repressor FLC and mediates AS of ABH1 and HAB1, two negative regulators of ABA signaling. Proteomic analyses show AtACINUS’s O-GlcNAcylation, O-fucosylation, and association with splicing factors, chromatin remodelers, and transcriptional regulators. Some AtACINUS/AtPININ-dependent AS events are altered in the sec and spy mutants, demonstrating a function of O-glycosylation in regulating alternative RNA splicing.
Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase
Authors: Bellin Leo , Del Caño-Ochoa Francisco , Velázquez-Campoy Adrián , Möhlmann Torsten , Ramón-Maiques Santiago
Published: February 2021

Aspartate transcarbamoylase (ATC), an essential enzyme for de novo pyrimidine biosynthesis, is uniquely regulated in plants by feedback inhibition of uridine 5-monophosphate (UMP). Despite its importance in plant growth, the structure of this UMP-controlled ATC and the regulatory mechanism remain unknown. Here, we report the crystal structures of Arabidopsis ATC trimer free and bound to UMP, complexed to a transition-state analog or bearing a mutation that turns the enzyme insensitive to UMP. We found that UMP binds and blocks the ATC active site, directly competing with the binding of the substrates. We also prove that UMP recognition relies on a loop exclusively conserved in plants that is also responsible for the sequential firing of the active sites. In this work, we describe unique regulatory and catalytic properties of plant ATCs that could be exploited to modulate de novo pyrimidine synthesis and plant growth.
Methodological quality of COVID-19 clinical research
Authors: Jung Richard G. , Di Santo Pietro , Clifford Cole , Prosperi-Porta Graeme , Skanes Stephanie , Hung Annie , Parlow Simon , Visintini Sarah , Ramirez F. Daniel , Simard Trevor , Hibbert Benjamin
Published: February 2021

The COVID-19 pandemic began in early 2020 with major health consequences. While a need to disseminate information to the medical community and general public was paramount, concerns have been raised regarding the scientific rigor in published reports. We performed a systematic review to evaluate the methodological quality of currently available COVID-19 studies compared to historical controls. A total of 9895 titles and abstracts were screened and 686 COVID-19 articles were included in the final analysis. Comparative analysis of COVID-19 to historical articles reveals a shorter time to acceptance (13.0[IQR, 5.0–25.0] days vs. 110.0[IQR, 71.0–156.0] days in COVID-19 and control articles, respectively; p < 0.0001). Furthermore, methodological quality scores are lower in COVID-19 articles across all study designs. COVID-19 clinical studies have a shorter time to publication and have lower methodological quality scores than control studies in the same journal. These studies should be revisited with the emergence of stronger evidence.
COPD awareness in the urban slums and rural areas around Pune city in India
Authors: Ghorpade Deesha Deepak , Raghupathy Anchala , Londhe Jyoti Deepak , Madas Sapna Jitendra , Kale Nisha Vijay , Singh Narula Arvinder Pal , Patil Reshma Sudhir , Barne Monica Sumit , Doke Prakash Prabhakar Rao , Salvi Sundeep Santosh
Published: February 2021

COPD is the second leading cause of death and disability adjusted life years (DALYs) in India, yet, it remains poorly recognized. We aimed to study the level of awareness of COPD in urban slums of Pune city in India and its neighboring rural areas. All male and female subjects above the age of 30 years residing in 13 randomly selected slums of Pune city (total population of 3000) and 7 randomly selected neighboring rural villages (total population of 3000) were invited to participate in this cross-sectional community survey. After obtaining written informed consent, 13 trained community health workers (CHWs) administered a questionnaire that captured their level of awareness of COPD. Of the 6000 subjects approached, 5420 residents (mean age ± SD = 48.0 ± 13.5 years; 38% males) consented and answered all questions. The number of people who had ever heard the word COPD was 49/5420 [0.9% (0.6–1.1%); 0.7% (0.5–1.3%) of the urban slum dwellers and 1.15% (0.5–1.3%) of rural residents]. Among those who had never heard the word COPD (n = 5371), when asked what was the name of the disease caused by long-term tobacco smoking, 38% said cancer, 16.7% said asthma, and 4.4% said TB. Among those who had heard the word COPD (n = 49), 6.1% said it was a disease of the heart, and 61% attributed COPD to smoke and dust pollution and 20% to tobacco smoking. The level of awareness of COPD in the Indian community is extremely low, highlighting the need to have nationwide mass awareness programs in India.
Author Correction: Non-local effect of impurity states on the exchange coupling mechanism in magnetic topological insulators
Authors: Peixoto Thiago R. F. , Bentmann Hendrik , Rüßmann Philipp , Tcakaev Abdul-Vakhab , Winnerlein Martin , Schreyeck Steffen , Schatz Sonja , Vidal Raphael Crespo , Stier Fabian , Zabolotnyy Volodymyr , Green Robert J. , Min Chul Hee , Fornari Celso I. , Maaß Henriette , Vasili Hari Babu , Gargiani Pierluigi , Valvidares Manuel , Barla Alessandro , Buck Jens , Hoesch Moritz , Diekmann Florian , Rohlf Sebastian , Kalläne Matthias , Rossnagel Kai , Gould Charles , Brunner Karl , Blügel Stefan , Hinkov Vladimir , Molenkamp Laurens W. , Reinert Friedrich
Published: February 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41535-021-00314-9
Promoting versatile vaccine development for emerging pandemics
Authors: Monrad Joshua T. , Sandbrink Jonas B. , Cherian Neil G.
Published: February 2021

The ongoing COVID-19 pandemic has demonstrated the importance of rapid and versatile development of emergency medical countermeasures such as vaccines. We discuss the role of platform vaccines and prototype pathogen research in modern vaccine development, and outline how previous pathogen-specific funding approaches can be improved to adequately promote vaccine R&D for emerging pandemics. We present a more comprehensive approach to financing vaccine R&D, which maximises biomedical pandemic preparedness by promoting flexible vaccine platforms and translatable research into prototype pathogens. As the numerous platform-based SARS-CoV-2 vaccines show, funders can accelerate pandemic vaccine development by proactively investing in versatile platform technologies. For certain emerging infectious diseases, where vaccine research can translate to other related pathogens with pandemic potential, investment decisions should reflect the full social value of increasing overall preparedness, rather than just the value of bringing a vaccine to market for individual pathogens.
Collegiate athlete brain data for white matter mapping and network neuroscience
Authors: Caron Bradley , Stuck Ricardo , McPherson Brent , Bullock Daniel , Kitchell Lindsey , Faskowitz Joshua , Kellar Derek , Cheng Hu , Newman Sharlene , Port Nicholas , Pestilli Franco
Published: February 2021

We describe a dataset of processed data with associated reproducible preprocessing pipeline collected from two collegiate athlete groups and one non-athlete group. The dataset shares minimally processed diffusion-weighted magnetic resonance imaging (dMRI) data, three models of the diffusion signal in the voxel, full-brain tractograms, segmentation of the major white matter tracts as well as structural connectivity matrices. There is currently a paucity of similar datasets openly shared. Furthermore, major challenges are associated with collecting this type of data. The data and derivatives shared here can be used as a reference to study the effects of long-term exposure to collegiate athletics, such as the effects of repetitive head impacts. We use advanced anatomical and dMRI data processing methods publicly available as reproducible web services at brainlife.io.
Computational scanning tunneling microscope image database
Authors: Choudhary Kamal , Garrity Kevin F. , Camp Charles , Kalinin Sergei V. , Vasudevan Rama , Ziatdinov Maxim , Tavazza Francesca
Published: February 2021

We introduce the systematic database of scanning tunneling microscope (STM) images obtained using density functional theory (DFT) for two-dimensional (2D) materials, calculated using the Tersoff-Hamann method. It currently contains data for 716 exfoliable 2D materials. Examples of the five possible Bravais lattice types for 2D materials and their Fourier-transforms are discussed. All the computational STM images generated in this work are made available on the JARVIS-STM website (https://jarvis.nist.gov/jarvisstm). We find excellent qualitative agreement between the computational and experimental STM images for selected materials. As a first example application of this database, we train a convolution neural network model to identify the Bravais lattice from the STM images. We believe the model can aid high-throughput experimental data analysis. These computational STM images can directly aid the identification of phases, analyzing defects and lattice-distortions in experimental STM images, as well as be incorporated in the autonomous experiment workflows.
Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
Authors: Syuhada Ibnu , Hauwali Nikodemus Umbu Janga , Rosikhin Ahmad , Sustini Euis , Noor Fatimah Arofiati , Winata Toto
Published: February 2021

In this work, we present the bond order redefinition needed to reduce the inherent noise in order to enhance the accuracy of molecular dynamics simulations. We propose defining the bond order as a fraction of energy distribution. It happens due to the character of the material in nature, which tries to maintain its environment. To show the necessity, we developed a factory empirical interatomic potential (FEIP) for carbon that implements the redefinition with a short-range interaction approach. FEIP has been shown to enhance the accuracy of the calculation of lattice constants, cohesive energy, elastic properties, and phonons compared to experimental data, and can even be compared to other potentials with the long-range interaction approach. The enhancements due to FEIP can reduce the inherent noise, then provide a better prediction of the energy based on the behaviour of the atomic environment. FEIP can also transform simple two-body interactions into many-body interactions, which is useful for enhancing accuracy. Due to implementing the bond order redefinition, FEIP offers faster calculations than other complex interatomic potentials.
Long-QT founder variant T309I-Kv7.1 with dominant negative pattern may predispose delayed afterdepolarizations under β-adrenergic stimulation
Authors: Synková Iva , Bébarová Markéta , Andršová Irena , Chmelikova Larisa , Švecová Olga , Hošek Jan , Pásek Michal , Vít Pavel , Valášková Iveta , Gaillyová Renata , Navrátil Rostislav , Novotný Tomáš
Published: February 2021

The variant c.926C > T (p.T309I) in KCNQ1 gene was identified in 10 putatively unrelated Czech families with long QT syndrome (LQTS). Mutation carriers (24 heterozygous individuals) were more symptomatic compared to their non-affected relatives (17 individuals). The carriers showed a mild LQTS phenotype including a longer QTc interval at rest (466 ± 24 ms vs. 418 ± 20 ms) and after exercise (508 ± 32 ms vs. 417 ± 24 ms), 4 syncopes and 2 aborted cardiac arrests. The same haplotype associated with the c.926C > T variant was identified in all probands. Using the whole cell patch clamp technique and confocal microscopy, a complete loss of channel function was revealed in the homozygous setting, caused by an impaired channel trafficking. Dominant negativity with preserved reactivity to β-adrenergic stimulation was apparent in the heterozygous setting. In simulations on a human ventricular cell model, the dysfunction resulted in delayed afterdepolarizations (DADs) and premature action potentials under β-adrenergic stimulation that could be prevented by a slight inhibition of calcium current. We conclude that the KCNQ1 variant c.926C > T is the first identified LQTS-related founder mutation in Central Europe. The dominant negative channel dysfunction may lead to DADs under β-adrenergic stimulation. Inhibition of calcium current could be possible therapeutic strategy in LQTS1 patients refractory to β-blocker therapy.
Optimizing proton minibeam radiotherapy by interlacing and heterogeneous tumor dose on the basis of calculated clonogenic cell survival
Authors: Sammer Matthias , Girst Stefanie , Dollinger Günther
Published: February 2021

Proton minibeam radiotherapy (pMBRT) is a spatial fractionation method using sub-millimeter beams at center-to-center (ctc) distances of a few millimeters to widen the therapeutic index by reduction of side effects in normal tissues. Interlaced minibeams from two opposing or four orthogonal directions are calculated to minimize side effects. In particular, heterogeneous dose distributions applied to the tumor are investigated to evaluate optimized sparing capabilities of normal tissues at the close tumor surrounding. A 5 cm thick tumor is considered at 10 cm depth within a 25 cm thick water phantom. Pencil and planar minibeams are interlaced from two (opposing) directions as well as planar beams from four directions. An initial beam size of σ0 = 0.2 mm (standard deviation) is assumed in all cases. Tissue sparing potential is evaluated by calculating mean clonogenic cell survival using a linear-quadratic model on the calculated dose distributions. Interlacing proton minibeams for homogeneous irradiation of the tumor has only minor benefits for the mean clonogenic cell survival compared to unidirectional minibeam irradiation modes. Enhanced mean cell survival, however, is obtained when a heterogeneous dose distribution within the tumor is permitted. The benefits hold true even for an elevated mean tumor dose, which is necessary to avoid cold spots within the tumor in concerns of a prescribed dose. The heterogeneous irradiation of the tumor allows for larger ctc distances. Thus, a high mean cell survival of up to 47% is maintained even close to the tumor edges for single fraction doses in the tumor of at least 10 Gy. Similar benefits would result for heavy ion minibeams with the advantage of smaller minibeams in deep tissue potentially offering even increased tissue sparing. The enhanced mean clonogenic cell survival through large ctc distances for interlaced pMBRT with heterogeneous tumor dose distribution results in optimum tissue sparing potential. The calculations show the largest enhancement of the mean cell survival in normal tissue for high-dose fractions. Thus, hypo-fractionation or even single dose fractions become possible for tumor irradiation. A widened therapeutic index at big cost reductions is offered by interlaced proton or heavy ion minibeam therapy.
RNAseq shows an all-pervasive day-night rhythm in the transcriptome of the pacemaker of the heart
Authors: Wang Yanwen , Anderson Cali , Dobrzynski Halina , Hart George , D’Souza Alicia , Boyett Mark R.
Published: February 2021

Physiological systems vary in a day-night manner anticipating increased demand at a particular time. Heart is no exception. Cardiac output is primarily determined by heart rate and unsurprisingly this varies in a day-night manner and is higher during the day in the human (anticipating increased day-time demand). Although this is attributed to a day-night rhythm in post-translational ion channel regulation in the heart’s pacemaker, the sinus node, by the autonomic nervous system, we investigated whether there is a day-night rhythm in transcription. RNAseq revealed that ~ 44% of the sinus node transcriptome (7134 of 16,387 transcripts) has a significant day-night rhythm. The data revealed the oscillating components of an intrinsic circadian clock. Presumably this clock (or perhaps the master circadian clock in the suprachiasmatic nucleus) is responsible for the rhythm observed in the transcriptional machinery, which in turn is responsible for the rhythm observed in the transcriptome. For example, there is a rhythm in transcripts responsible for the two principal pacemaker mechanisms (membrane and Ca2+clocks), transcripts responsible for receptors and signalling pathways known to control pacemaking, transcripts from genes identified by GWAS as determinants of resting heart rate, and transcripts from genes responsible for familial and acquired sick sinus syndrome.
Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex
Authors: Ajjugal Yogeeshwar , Tomar Kripi , Rao D. Krishna , Rathinavelan Thenmalarchelvi
Published: February 2021

Base pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.
Role of warm ocean conditions and the MJO in the genesis and intensification of extremely severe cyclone Fani
Authors: Singh Vineet Kumar , Roxy M. K. , Deshpande Medha
Published: February 2021

Cyclone Fani, in April 2019, was the strongest pre-monsoon cyclone to form in the Bay of Bengal after 1994. It underwent rapid intensification and intensified quickly to an extremely severe cyclone. It maintained a wind speed of ≥ 51 m s−1 (≥ 100 knots) for a record time period of 36 h. The total lifespan of the cyclone was double than the climatological lifespan. Also, the duration of the cyclone in its extremely severe phase and the accumulated cyclone energy were significantly larger than the climatological records for the pre-monsoon season. In the current study, we investigate the ocean-atmospheric conditions that led to its genesis, rapid intensification and long lifespan. Our analysis shows that the Madden Julian Oscillation and anomalous high sea surface temperatures provided conducive dynamic and thermodynamic conditions for the genesis of cyclone Fani, despite forming very close to the equator where cyclogenesis is generally unlikely. Further, favourable ocean subsurface conditions and the presence of a warm core eddy in the region led to its rapid intensification to an extremely severe cyclone. A large area of warm ocean surface and subsurface temperatures aided the cyclone to maintain very high wind speed for a record time period. The vital role of the ocean surface and the subsurface in the genesis and the intensification highlights the need to efficiently incorporate ocean initial conditions (surface and sub-surface) and ocean–atmosphere coupling in the operational cyclone forecasting framework.
Arrays of Si vacancies in 4H-SiC produced by focused Li ion beam implantation
Authors: Pavunny Shojan P. , Yeats Andrew L. , Banks Hunter B. , Bielejec Edward , Myers-Ward Rachael L. , DeJarld Matthew T. , Bracker Allan S. , Gaskill D. Kurt , Carter Samuel G.
Published: February 2021

Point defects in SiC are an attractive platform for quantum information and sensing applications because they provide relatively long spin coherence times, optical spin initialization, and spin-dependent fluorescence readout in a fabrication-friendly semiconductor. The ability to precisely place these defects at the optimal location in a host material with nano-scale accuracy is desirable for integration of these quantum systems with traditional electronic and photonic structures. Here, we demonstrate the precise spatial patterning of arrays of silicon vacancy ($${V}_{Si}$$

V

Si

) emitters in an epitaxial 4H-SiC (0001) layer through mask-less focused ion beam implantation of Li+. We characterize these arrays with high-resolution scanning confocal fluorescence microscopy on the Si-face, observing sharp emission lines primarily coming from the $${V1}^{{\prime}}$$

V
1

′

zero-phonon line (ZPL). The implantation dose is varied over 3 orders of magnitude, leading to $${V}_{Si}$$

V

Si

densities from a few per implantation spot to thousands per spot, with a linear dependence between ZPL emission and implantation dose. Optically-detected magnetic resonance (ODMR) is also performed, confirming the presence of V2 $${V}_{Si}$$

V

Si

. Our investigation reveals scalable and reproducible defect generation.