bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monocyte apoptotic bodies are vehicles for influenza A virus propagation
Authors: Atkin-Smith Georgia K. , Duan Mubing , Zanker Damien J. , Loh Liyen , Nguyen Thi H. O. , Koutsakos Marios , Nguyen Tien , Jiang Xiangrui , Carrera Julio , Phan Thanh Kha , Liu Chuanxin , Paone Stephanie , Oveissi Sara , Hodge Amy L. , Baxter Amy A. , Kedzierska Katherine , Mackenzie Jason M. , Hulett Mark D. , Bilsel Pamuk , Chen Weisan , Poon Ivan K. H. 
Published: May 2020

AbstractThe disassembly of apoptotic cells into small membrane-bound vesicles termed apoptotic bodies (ApoBDs) is a hallmark of apoptosis; however, the functional significance of this process is not well defined. We recently discovered a new membrane protrusion (termed beaded apoptopodia) generated by apoptotic monocytes which fragments to release an abundance of ApoBDs. To investigate the function of apoptotic monocyte disassembly, we used influenza A virus (IAV) infection as a proof-of-concept model, as IAV commonly infects monocytes in physiological settings. We show that ApoBDs generated from IAV-infected monocytes contained IAV mRNA, protein and virions and consequently, could facilitate viral propagation in vitro and in vivo, and induce a robust antiviral immune response. We also identified an antipsychotic, Haloperidol, as an unexpected inhibitor of monocyte cell disassembly which could impair ApoBD-mediated viral propagation under in vitro conditions. Together, this study reveals a previously unrecognised function of apoptotic monocyte disassembly in the pathogenesis of IAV infections.
Hyperpolarized water through dissolution dynamic nuclear polarization with UV-generated radicals
Authors: Pinon Arthur C. , Capozzi Andrea , Ardenkjær-Larsen Jan Henrik 
Published: May 2020

AbstractIn recent years, hyperpolarization of water protons via dissolution Dynamic Nuclear Polarization (dDNP) has attracted increasing interest in the magnetic resonance community. Hyperpolarized water may provide an alternative to Gd-based contrast agents for angiographic and perfusion Magnetic Resonance Imaging (MRI) examinations, and it may report on chemical and biochemical reactions and proton exchange while perfoming Nuclear Magnetic Resonance (NMR) investigations. However, hyperpolarizing water protons is challenging. The main reason is the presence of radicals, required to create the hyperpolarized nuclear spin state. Indeed, the radicals will also be the main source of relaxation during the dissolution and transfer to the NMR or MRI system. In this work, we report water magnetizations otherwise requiring a field of 10,000 T at room temperature on a sample of pure water, by employing dDNP via UV-generated, labile radicals. We demonstrate the potential of our methodology by acquiring a 15N spectrum from natural abundance urea with a single scan, after spontaneous magnetization transfer from water protons to nitrogen nuclei.
Mechanistic and microkinetic study of non-oxidative methane coupling on a single-atom iron catalyst
Authors: Kim Seok Ki , Kim Hyun Woo , Han Seung Ju , Lee Sung Woo , Shin Jungho , Kim Yong Tae 
Published: May 2020

AbstractNon-oxidative methane coupling has promising economic potential, but the catalytic and radical reactions become complicated at high temperatures. Here, we investigate the mechanism of non-oxidative methane coupling on an iron single-atom catalyst using density functional theory, and evaluate the catalytic performance under various reaction conditions using microkinetic modelling and experiments. Under typical reaction conditions (1300 K and 1 bar), C–C coupling and subsequent dehydrogenation to produce ethylene shows comparable energetics between the gas-phase and catalytic pathways. However, the microkinetic analysis reveals that the iron single-atom catalyst converted methane to mainly CH3 and H2 at reaction temperatures above 1300 K, and acetylene production is dominant over ethylene production. The sensitivity analysis suggests that increasing the C2 hydrocarbon yield by optimising the reaction conditions is limited. The experimental results obtained at 1293 K are consistent with the theoretical estimation that acetylene is the main C2 product over the iron single-atom catalyst.
Two‐vector based low‐complexity model predictive flux control for current‐source inverter‐fed induction motor drive
Authors: Gao Hang , Wu Bin , Xu Dewei , Zargari Navid R. 
Published: May 2020

Model predictive control is an effective approach to achieve high performance on electric motor drives. In this study, a two‐vector based low‐complexity model predictive flux control (TVLC‐MPFC) is proposed and introduced for low power current‐source inverter (CSI)‐fed induction motor (IM) drive. In contrast to conventional two‐vector based model predictive flux control (TV‐MPFC), TVLC‐MPFC is a more simplified scheme with a lower calculation burden, which eliminates the requirement on the iteration procedures to obtain the results of the optimal current vector combination with optimal dwell time. Moreover, since TVLC‐MPFC avoids the possibility of selecting the wrong vector combination in some cases, which would happen with conventional TV‐MPFC, it presents better output performance than TV‐MPFC. The robustness of TVLC‐MPFC under parameter uncertainty is discussed as well. Experimental tests are carried out on a low power CSI‐fed IM drive (5 kW/208 V/14.3 A) and verify the effectiveness of the proposed scheme.
Reliability evaluation of distribution transformers considering the negative and positive effects of rooftop photovoltaics
Authors: Hamzeh Mohsen , Vahidi Behrooz 
Published: May 2020

Rooftop photovoltaics (RPVs) have an impact on the ageing failure rate and reliability of transformers. The advantages and disadvantages of different penetrations of rooftop photovoltaic on the reliability of the transformers are studied. For the first time, the adverse effects of high penetration of RPVs on the transformer failure and power system reliability are examined. Regarding the growing interest in the widespread use of renewable energies on account of global warming, studying the negative effects of DG units presence is so important to predict the future of power system conditions. Monte Carlo simulation is used for the probabilistic nature of clearness index and reliability evaluation. Well‐being criteria that show the different operation modes of the power system is used to identify the at‐risk, marginal and healthy mode of the power system in the presence of different penetrations of rooftop photovoltaic. The results show that the maximum penetration of rooftop photovoltaic for improving the reliability of the power system is 5 kW per house in the feeder of Isin in Bandar Abbas, in Iran.
Not in the mood
Authors: Giancaspro David 
Published: May 2020

Abstract
Previous studies (e.g., van Osch & Sleeman 2016; Perez-Cortes 2016) have found that heritage speakers (HSs) of Spanish produce less lexically-selected subjunctive mood morphology than Spanish-dominant speakers. It remains unclear, however, whether the HSs’ tendency to produce less subjunctive mood than Spanish-dominant speakers is attributable to representational differences (e.g., Montrul 2002, 2008), input quality differences (e.g., Pires & Rothman 2009; Pascual y Cabo & Rothman 2012), or as yet unidentified factors. The present study addresses this question by testing the effect of lexical frequency on advanced proficiency HSs’ productive (Experiment 1) and receptive (Experiment 2) knowledge of lexically-selected subjunctive mood in Spanish. Results of Experiments 1 and 2 indicate that advanced proficiency HSs are both (a) highly accurate with subjunctive mood and yet also (b) significantly less accurate with lower frequency verbs. Given these findings, as well as the categorical subjunctive production of the Spanish-dominant bilingual control group, it is argued that HSs’ differences from dominant speakers may be (partially) attributable to gaps in lexical, rather than morphosyntactic knowledge.
How do parental input and socio-economic status account for differences within and between the cohorts?
Authors: Montanari Elke G. , Abel Roman , Tschudinovski Lilia , Graßer Barbara 
Published: May 2020

Abstract
How does vocabulary in the heritage language develop? Does the social environment of the community have an influence? This chapter presents empirical results regarding the development of expressive and receptive vocabulary in the heritage language and analyzes the effects of amount of exposure, use, socio-economic status, dominance, and community on the acquisition of vocabulary in the heritage language. A Russian-German and a Turkish-German speaking sample are compared: 211 children at the age of 6–10 years were tested with a standardized picture naming task in a cross-sectional design. The results show a good receptive mastery and a limited expressive command of vocabulary with large individual differences, and only a slight development in the timespan of four years. Between the communities we find systematic variation, which we attribute to social and pragmatic differences with moderator and mediator effects. Possible limitations of the results are discussed with respect to cross-linguistic test effects.
Heritage and non-heritage bilinguals
Authors: Andreou Maria , Dosi Ifigenia , Papadopoulou Despina , Tsimpli Ianthi Maria 
Published: May 2020

Abstract
The present study explores the effects of literacy support in the languages of the bilingual child on the linguistic and cognitive skills of (non-)heritage speakers. 70 children speaking Albanian (L1) and Greek (L2) are divided into three groups according to whether they receive literacy support in their L1, L2 or in both languages. To test the children's proficiency in Greek, we used an expressive vocabulary task, two working memory tasks, a non-verbal intelligence task and a sentence repetition task (SRT). The findings suggest that good levels of biliteracy established through bilingual education positively influence the child’s linguistic and cognitive performance. Furthermore, the lack of working memory effects on the children’s SRT performance emphasizes the importance of biliteracy development and its educational support, which together with vocabulary knowledge contribute to bilingual development.
Safety Assessment of Electromagnetic Exposure in High-Speed Train Carriage with Full Passengers
Authors: Tian Rui , Lu Mai 
Published: May 2020

AbstractThe objective of this work is to evaluate the safety of the electromagnetic environment in the carriage of high-speed trains exposed to power cables when the train is full of passengers. The electromagnetic model of a real carriage, two sets of power cables and the 84 passengers were set up by using COMSOL Multiphysics software based on CRH5. The distributions of induced electric and magnetic fields in the carriage, inside and on the surface of passengers were investigated. The results show that the induced electric and magnetic fields on the windows are greater than on the passengers and the max value of induced magnetic field is 2627.10 µT, and the max value of induced electric field is 2.0 × 105 mV m−1. The maximum values of the induced electric and magnetic fields in 84 passengers’ brain tissues were obtained, and it was found that the maximum values occurred in the third row passengers. The distribution of induced electric and magnetic fields at the cross-section of passengers’ heads in the third row was also obtained, and we found that the passengers at the window side were greater than those of aisle passengers. In the third row, the maximum values of the induced electric and magnetic fields in the head of two passengers near the window were 94.6 mV m−1, 90.9 µT, 96.3 mV m−1, and 90.4 µT, respectively. We also found the all data were below the ICNIRP Reference Levels, which indicates the electromagnetic exposure caused by power cables when the train is full of passengers will not threat passengers’ health.
Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions
Authors: Wang Debby D , Zhu Mengxu , Yan Hong 
Published: May 2020

AbstractAccurately predicting protein–ligand binding affinities can substantially facilitate the drug discovery process, but it remains as a difficult problem. To tackle the challenge, many computational methods have been proposed. Among these methods, free energy-based simulations and machine learning-based scoring functions can potentially provide accurate predictions. In this paper, we review these two classes of methods, following a number of thermodynamic cycles for the free energy-based simulations and a feature-representation taxonomy for the machine learning-based scoring functions. More recent deep learning-based predictions, where a hierarchy of feature representations are generally extracted, are also reviewed. Strengths and weaknesses of the two classes of methods, coupled with future directions for improvements, are comparatively discussed.
Prediction of cancer driver genes through network-based moment propagation of mutation scores
Authors: Gumpinger Anja C , Lage Kasper , Horn Heiko , Borgwardt Karsten 
Published: May 2020

Abstract

Motivation
Gaining a comprehensive understanding of the genetics underlying cancer development and progression is a central goal of biomedical research. Its accomplishment promises key mechanistic, diagnostic and therapeutic insights. One major step in this direction is the identification of genes that drive the emergence of tumors upon mutation. Recent advances in the field of computational biology have shown the potential of combining genetic summary statistics that represent the mutational burden in genes with biological networks, such as protein–protein interaction networks, to identify cancer driver genes. Those approaches superimpose the summary statistics on the nodes in the network, followed by an unsupervised propagation of the node scores through the network. However, this unsupervised setting does not leverage any knowledge on well-established cancer genes, a potentially valuable resource to improve the identification of novel cancer drivers.

Results
We develop a novel node embedding that enables classification of cancer driver genes in a supervised setting. The embedding combines a representation of the mutation score distribution in a node’s local neighborhood with network propagation. We leverage the knowledge of well-established cancer driver genes to define a positive class, resulting in a partially labeled dataset, and develop a cross-validation scheme to enable supervised prediction. The proposed node embedding followed by a supervised classification improves the predictive performance compared with baseline methods and yields a set of promising genes that constitute candidates for further biological validation.

Availability and implementation
Code available at https://github.com/BorgwardtLab/MoProEmbeddings.

Supplementary information
Supplementary data are available at Bioinformatics online.
Metaviral
SPAdes: assembly of viruses from metagenomic data
Authors: Antipov Dmitry , Raiko Mikhail , Lapidus Alla , Pevzner Pavel A 
Published: May 2020

Abstract

Motivation
Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth’s virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies.

Results
We describe a MetaviralSPAdes tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked MetaviralSPAdes on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines.

Availability and implementation
Metaviral SPAdes includes ViralAssembly, ViralVerify and ViralComplete modules that are available as standalone packages: https://github.com/ablab/spades/tree/metaviral_publication, https://github.com/ablab/viralVerify/ and https://github.com/ablab/viralComplete/.

Contact
d.antipov@spbu.ru

Supplementary information
Supplementary data are available at Bioinformatics online.
HALPER facilitates the identification of regulatory element orthologs across species
Authors: Zhang Xiaoyu , Kaplow Irene M , Wirthlin Morgan , Park Tae Yoon , Pfenning Andreas R 
Published: May 2020

Abstract

Summary
Diverse traits have evolved through cis-regulatory changes in genome sequence that influence the magnitude, timing and cell type-specificity of gene expression. Advances in high-throughput sequencing and regulatory genomics have led to the identification of regulatory elements in individual species, but these genomic regions remain difficult to align across taxonomic orders due to their lack of sequence conservation relative to protein coding genes. The groundwork for tracing the evolution of regulatory elements is provided by the recent assembly of hundreds of genomes, the generation of reference-free Cactus multiple sequence alignments of these genomes, and the development of the halLiftover tool for mapping regions across these alignments. We present halLiftover Post-processing for the Evolution of Regulatory Elements (HALPER), a tool for constructing contiguous regulatory element orthologs from the outputs of halLiftover. We anticipate that this tool will enable users to efficiently identify orthologs of regulatory elements across hundreds of species, providing novel insights into the evolution of traits that have evolved through gene expression.

Availability and implementation
HALPER is implemented in python and available on github: https://github.com/pfenninglab/halLiftover-postprocessing.

Supplementary information
Supplementary data are available at Bioinformatics online.
Polyadenylation of mRNA as a novel regulatory mechanism of gene expression in temporal lobe epilepsy
Authors: Parras Alberto , de Diego-Garcia Laura , Alves Mariana , Beamer Edward , Conte Giorgia , Jimenez-Mateos Eva M , Morgan James , Ollà Ivana , Hernandez-Santana Yasmina , Delanty Norman , Farrell Michael A , O’Brien Donncha F , Ocampo Alejandro , Henshall David C , Méndez Raúl , Lucas José J , Engel Tobias 
Published: May 2020

Abstract
Temporal lobe epilepsy is the most common and refractory form of epilepsy in adults. Gene expression within affected structures such as the hippocampus displays extensive dysregulation and is implicated as a central pathomechanism. Post-transcriptional mechanisms are increasingly recognized as determinants of the gene expression landscape, but key mechanisms remain unexplored. Here we show, for first time, that cytoplasmic mRNA polyadenylation, one of the post-transcriptional mechanisms regulating gene expression, undergoes widespread reorganization in temporal lobe epilepsy. In the hippocampus of mice subjected to status epilepticus and epilepsy, we report &gt;25% of the transcriptome displays changes in their poly(A) tail length, with deadenylation disproportionately affecting genes previously associated with epilepsy. Suggesting cytoplasmic polyadenylation element binding proteins (CPEBs) being one of the main contributors to mRNA polyadenylation changes, transcripts targeted by CPEBs were particularly enriched among the gene pool undergoing poly(A) tail alterations during epilepsy. Transcripts bound by CPEB4 were over-represented among transcripts with poly(A) tail alterations and epilepsy-related genes and CPEB4 expression was found to be increased in mouse models of seizures and resected hippocampi from patients with drug-refractory temporal lobe epilepsy. Finally, supporting an adaptive function for CPEB4, deletion of Cpeb4 exacerbated seizure severity and neurodegeneration during status epilepticus and the development of epilepsy in mice. Together, these findings reveal an additional layer of gene expression regulation during epilepsy and point to novel targets for seizure control and disease-modification in epilepsy.
Coronavirus Disease 2019 (COVID-19) Clinical Trial Oversight at a Major Academic Medical Center: Approach of Michigan Medicine
Authors: Spector-Bagdady Kayte , Higgins Peter D R , Aaronson Keith D , Birk Judy , Flaherty Kevin R , Gregg Kevin S , Hyzy Robert C , Kaul Daniel R , Lauring Adam S , Magee John C , Meurer William J , Park Pauline K , Scott Phillip , Lok Anna S 
Published: May 2020

Abstract
Clinicians, eager to offer the best care in the absence of guiding data, have provided patients with coronavirus disease 2019 (COVID-19) diverse clinical interventions. This usage has led to perceptions of efficacy of some interventions that, while receiving media coverage, lack robust evidence. Moving forward, randomized controlled clinical trials are necessary to ensure that clinicians can treat patients effectively during this outbreak and the next. To do so, academic medical centers must address 2 key research issues: (1) how to effectively and efficiently determine which trials have the best chance of benefiting current and future patients and (2) how to establish a transparent and ethical process for subject recruitment while maintaining research integrity and without overburdening patients or staff. We share here the current methods used by Michigan Medicine to address these issues.
Is the propensity to emit alarm calls associated with health status?
Authors: Nash Austin L , Jebb Alexandra H M , Blumstein Daniel T 
Published: May 2020

AbstractThe production and structure of animal signals may depend on an individual’s health status and may provide more than one type of information to receivers. While alarm calls are not typically viewed as health condition dependent, recent studies have suggested that their structure, and possibly their propensity to be emitted, depends on an individual’s health condition and state. We asked whether the propensity of yellow-bellied marmots (Marmota flaviventer) to emit calls is influenced by their immunological or parasite status, by quantifying both trap-elicited and natural calling rates as a function of their neutrophil-to-lymphocyte (NL) ratio, the presence of a blood borne trypanosome, and the presence of several intestinal parasites (Eimeria sp., Entamoeba sp., and Ascaris sp.). We fitted mixed effects models to determine if the health measures we collected were associated with the probability of calling in a trap and with annual rates of natural alarm calling. Marmots infected with a blood-borne trypanosome were marginally more likely to call naturally and when trapped, while those infected with the intestinal parasite Ascaris were less likely to call when trapped. NL ratio was not directly associated with in-trap calling probability, but males were more likely to call when they had higher NL ratios. Thus, health conditions, such as parasite infection and immune system activation, can modulate the production of alarm signals and potentially provide information to both predators and prey about the caller’s condition. Playback experiments are required to confirm if receivers use such information.
Fool Me Once: An Experiment on Credibility and Leadership
Authors: Cooper David J , Hamman John R , Weber Roberto A 
Published: May 2020

Abstract
We investigate ‘social credibility’, a leader’s ability to convince followers that conditions are favourable and that others will follow the leader's advice. To do so, we study an experimental joint venture with three key properties: returns are uncertain, investments are complements, and investment is often more beneficial for the leader than the followers. The leader has private information about investment returns and can facilitate coordination through cheap-talk recommendations. We find that leaders manage social credibility by forgoing potentially profitable advice to invest, increasing the likelihood that subsequent recommendations are followed. We identify factors that affect the persistence of social credibility.