bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infection with novel coronavirus (SARS-CoV-2) causes pneumonia in Rhesus macaques
Authors: Shan Chao , Yao Yan-Feng , Yang Xing-Lou , Zhou Yi-Wu , Gao Ge , Peng Yun , Yang Lian , Hu Xue , Xiong Jin , Jiang Ren-Di , Zhang Hua-Jun , Gao Xiao-Xiao , Peng Cheng , Min Juan , Chen Ying , Si Hao-Rui , Wu Jia , Zhou Peng , Wang Yan-Yi , Wei Hong-Ping , Pang Wei , Hu Zheng-Fei , Lv Long-Bao , Zheng Yong-Tang , Shi Zheng-Li , Yuan Zhi-Ming 
Published: July 2020

AbstractThe 2019 novel coronavirus (SARS-CoV-2) outbreak is a major challenge for public health. SARS-CoV-2 infection in human has a broad clinical spectrum ranging from mild to severe cases, with a mortality rate of ~6.4% worldwide (based on World Health Organization daily situation report). However, the dynamics of viral infection, replication and shedding are poorly understood. Here, we show that Rhesus macaques are susceptible to the infection by SARS-CoV-2. After intratracheal inoculation, the first peak of viral RNA was observed in oropharyngeal swabs one day post infection (1 d.p.i.), mainly from the input of the inoculation, while the second peak occurred at 5 d.p.i., which reflected on-site replication in the respiratory tract. Histopathological observation shows that SARS-CoV-2 infection can cause interstitial pneumonia in animals, characterized by hyperemia and edema, and infiltration of monocytes and lymphocytes in alveoli. We also identified SARS-CoV-2 RNA in respiratory tract tissues, including trachea, bronchus and lung; and viruses were also re-isolated from oropharyngeal swabs, bronchus and lung, respectively. Furthermore, we demonstrated that neutralizing antibodies generated from the primary infection could protect the Rhesus macaques from a second-round challenge by SARS-CoV-2. The non-human primate model that we established here provides a valuable platform to study SARS-CoV-2 pathogenesis and to evaluate candidate vaccines and therapeutics.
Roads as a contributor to landscape-scale variation in bird communities
Authors: Cooke Sophia C. , Balmford Andrew , Donald Paul F. , Newson Stuart E. , Johnston Alison 
Published: July 2020

AbstractRoads and their traffic can affect wildlife over large areas and, in regions with dense road networks, may influence a high proportion of the ecological landscape. We assess the abundance of 75 bird species in relation to roads across Great Britain. Of these, 77% vary significantly in abundance with increasing road exposure, just over half negatively so. The effect distances of these negative associations average 700 m from a road, covering over 70% of Great Britain and over 40% of the total area of terrestrial protected sites. Species with smaller national populations generally have lower relative abundance with increasing road exposure, whereas the opposite is true for more common species. Smaller-bodied and migratory species are also more negatively associated with road exposure. By creating environmental conditions that benefit generally common species at the expense of others, road networks may echo other anthropogenic disturbances in bringing about large-scale simplification of avian communities.
Nampt-mediated spindle sizing secures a post-anaphase increase in spindle speed required for extreme asymmetry
Authors: Wei Zhe , Greaney Jessica , Loh Wei-Guo Nicholas , Homer Hayden Anthony 
Published: July 2020

AbstractMeiotic divisions in oocytes are extremely asymmetric and require pre- and post-anaphase-onset phases of spindle migration. The latter induces membrane protrusion that is moulded around the spindle thereby reducing cytoplasmic loss. Here, we find that depleting the NAD biosynthetic enzyme, nicotinamide phosphoribosyl-transferase (Nampt), in mouse oocytes results in markedly longer spindles and compromises asymmetry. By analysing spindle speed in live oocytes, we identify a striking and transient acceleration after anaphase-onset that is severely blunted following Nampt-depletion. Slow-moving midzones of elongated spindles induce cortical furrowing deep within the oocyte before protrusions can form, altogether resulting in larger oocyte fragments being cleaved off. Additionally, we find that Nampt-depletion lowers NAD and ATP levels and that reducing NAD using small molecule Nampt inhibitors also compromises asymmetry. These data show that rapid midzone displacement is critical for extreme asymmetry by delaying furrowing to enable protrusions to form and link metabolic status to asymmetric division.
A nanotrap improves survival in severe sepsis by attenuating hyperinflammation
Authors: Shi Changying , Wang Xiaojing , Wang Lili , Meng Qinghe , Guo Dandan , Chen Li , Dai Matthew , Wang Guirong , Cooney Robert , Luo Juntao 
Published: July 2020

AbstractTargeting single mediators has failed to reduce the mortality of sepsis. We developed a telodendrimer (TD) nanotrap (NT) to capture various biomolecules via multivalent, hybrid and synergistic interactions. Here, we report that the immobilization of TD-NTs in size-exclusive hydrogel resins simultaneously adsorbs septic molecules, e.g. lipopolysaccharides (LPS), cytokines and damage- or pathogen-associated molecular patterns (DAMPs/PAMPs) from blood with high efficiency (92–99%). Distinct surface charges displayed on the majority of pro-inflammatory cytokines (negative) and anti-inflammatory cytokines (positive) allow for the selective capture via TD NTs with different charge moieties. The efficacy of NT therapies in murine sepsis is both time-dependent and charge-dependent. The combination of the optimized NT therapy with a moderate antibiotic treatment results in a 100% survival in severe septic mice by controlling both infection and hyperinflammation, whereas survival are only 50–60% with the individual therapies. Cytokine analysis, inflammatory gene activation and tissue histopathology strongly support the survival benefits of treatments.
Interferon-independent STING signaling promotes resistance to HSV-1 in vivo
Authors: Yamashiro Lívia H. , Wilson Stephen C. , Morrison Huntly M. , Karalis Vasiliki , Chung Jing-Yi J. , Chen Katherine J. , Bateup Helen S. , Szpara Moriah L. , Lee Angus Y. , Cox Jeffery S. , Vance Russell E. 
Published: July 2020

AbstractThe Stimulator of Interferon Genes (STING) pathway initiates potent immune responses upon recognition of DNA. To initiate signaling, serine 365 (S365) in the C-terminal tail (CTT) of STING is phosphorylated, leading to induction of type I interferons (IFNs). Additionally, evolutionary conserved responses such as autophagy also occur downstream of STING, but their relative importance during in vivo infections remains unclear. Here we report that mice harboring a serine 365-to-alanine (S365A) mutation in STING are unexpectedly resistant to Herpes Simplex Virus (HSV)-1, despite lacking STING-induced type I IFN responses. By contrast, resistance to HSV-1 is abolished in mice lacking the STING CTT, suggesting that the STING CTT initiates protective responses against HSV-1, independently of type I IFNs. Interestingly, we find that STING-induced autophagy is a CTT- and TBK1-dependent but IRF3-independent process that is conserved in the STING S365A mice. Thus, interferon-independent functions of STING mediate STING-dependent antiviral responses in vivo.
Discovery and population genomics of structural variation in a songbird genus
Authors: Weissensteiner Matthias H. , Bunikis Ignas , Catalán Ana , Francoijs Kees-Jan , Knief Ulrich , Heim Wieland , Peona Valentina , Pophaly Saurabh D. , Sedlazeck Fritz J. , Suh Alexander , Warmuth Vera M. , Wolf Jochen B. W. 
Published: July 2020

AbstractStructural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.
Extracting local nucleation fields in permanent magnets using machine learning
Authors: Gusenbauer Markus , Oezelt Harald , Fischbacher Johann , Kovacs Alexander , Zhao Panpan , Woodcock Thomas George , Schrefl Thomas 
Published: July 2020

AbstractMicrostructural features play an important role in the quality of permanent magnets. The coercivity is greatly influenced by crystallographic defects, like twin boundaries, as is well known for MnAl-C. It would be very useful to be able to predict the macroscopic coercivity from microstructure imaging. Although this is not possible now, in the present work we examine a related question, namely the prediction of simulated nucleation fields of a quasi-three-dimensional (rescaled and extruded) system constructed from a two-dimensional image. We extract features of the image and analyze them via machine learning. A large number of extruded systems are constructed from 10 × 10 pixel sub-images of an Electron Backscatter Diffraction (EBSD) image using an automated meshing procedure. A local nucleation field is calculated by micromagnetic simulation of each quasi-three-dimensional system. Decision trees, trained with the simulation results, can predict nucleation fields of these quasi-three-dimensional systems from new images within seconds. As for now we cannot quantitatively predict the macroscopic coercivity, nevertheless we can identify weak spots in the magnet and see trends in the nucleation field distribution.
Ultra-flat twisted superlattices in 2D heterostructures
Authors: Szendrő Márton , Süle Péter , Dobrik Gergely , Tapasztó Levente 
Published: July 2020

AbstractMoiré-superlattices are ubiquitous in 2D heterostructures, strongly influencing their electronic properties. They give rise to new Dirac cones and are also at the origin of the superconductivity observed in magic-angle bilayer graphene. The modulation amplitude (corrugation) is an important yet largely unexplored parameter in defining the properties of 2D superlattices. The generally accepted view is that the corrugation monotonically decreases with increasing twist angle, while its effects on the electronic structure diminish as the layers become progressively decoupled. Here we found by lattice relaxation of around 8000 different Moiré-superstructures using high scale Classical Molecular Simulations combined with analytical calculations, that even a small amount of external strain can substantially change this picture, giving rise to more complex behavior of superlattice corrugation as a function of twist angle. One of the most surprising findings is the emergence of an ultra-flat phase that can be present for arbitrary small twist angle having a much lower corrugation level than the decoupled phase at large angles. Furthermore, Moiré-phase maps evidence that the state with no external strain is located in the close vicinity of a triple Moiré-phase boundary, implying that very small external strain variations can cause drastic changes in the realized superlattice morphology and corrugation. This renders the practical realization of 2D heterostructures with large-area homogeneous superlattice morphology highly challenging.
Liver transcriptome resources of four commercially exploited teleost species
Authors: Machado André M. , Muñoz-Merida Antonio , Fonseca Elza , Veríssimo Ana , Pinto Rui , Felício Mónica , da Fonseca Rute R. , Froufe Elsa , Castro L. Filipe C. 
Published: July 2020

AbstractThe generation of omic resources is central to develop adequate management strategies for species with economic value. Here, we provide high-coverage RNA-seq datasets of liver tissue (containing between 80,2 and 88,4 million of paired-end reads) from four wildtype teleost species with high commercial value: Trachurus trachurus (TTR; Atlantic horse mackerel), Scomber scombrus (SSC; Atlantic mackerel), Trisopterus luscus (TLU; pout), and Micromesistius poutassou (MPO; blue whiting). A comprehensive assembly pipeline, using de novo single and multi-kmer assembly approaches, produced 64 single high-quality liver transcriptomes – 16 per species. The final assemblies, with N50 values ranging from 2,543–3,700 bp and BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness values between 81.8–86.5% of the Actinopterygii gene set, were subjected to open reading frame (ORF) prediction and functional annotation. Our study provides the first transcriptomic resources for these species and offers valuable tools to evaluate both neutral and selected genetic variation among populations, and to identify candidate genes for environmental adaptation assisting in the investigation of the effects of global changes in fisheries.
The actin nucleator Cobl organises the terminal web of enterocytes
Authors: Beer Anne J. , González Delgado Jule , Steiniger Frank , Qualmann Britta , Kessels Michael M. 
Published: July 2020

AbstractBrush borders of intestinal epithelial cells are mandatory for nutrient uptake. Yet, which actin nucleators are crucial for forming the F-actin bundles supporting microvilli and the actin filaments of the terminal web, in which microvilli are rooted, is unknown. We show that mice lacking the actin nucleator Cobl surprisingly did not display reduced microvilli densities or changes in microvillar F-actin bundles or microvilli diameter but particularly in the duodenum displayed increased microvillar length. Interestingly, Cobl-deficient mice furthermore showed a significant widening of the terminal web. Quantitative analyses of high-resolution cryo-scanning electron microscopy (EM) of deep-etched duodenum samples revealed that Cobl is specifically important for the formation of fine filaments in the central terminal web that connect the apical structure of the terminal web underlying the plasma membrane, the microvilli rootlets and the basal structure of the terminal web with each other. Thus, the actin nucleator Cobl is critically involved in generating one of the cellular structures of the brush border-decorated apical cortex of enterocytes representing the absorptive intestinal surface.
Living with parents who smoke predicts levels of toxicant exposure in children
Authors: Park Myung-Bae 
Published: July 2020

AbstractThe detrimental effect of secondhand smoke (SHS) on health is well known; due to various factors, efforts to prevent SHS cannot completely eliminate the effect of smoking substances, and SHS has not been sufficiently investigated among children. This study aimed to assess children’s smoke exposure with respect to parents smoking patterns using biomarkers. This study used data from the 2016/2017 Korea National Health and Nutrition Examination Survey. Data pertaining to 486 subjects was extracted. Exposure to smoking among non-smoking children was assessed based on urine levels of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL). The urine NNAL concentration was highest among children with smoking parents and SHS exposure at home (3.829 pg/mg, 95% confidence interval [CI: 1.499–8.330), followed by children with smoking parents and no SHS exposure at home (1.297, 95% CI: 1.080–1.536), and children with nonsmoking parents and no SHS exposure at home (0.996 pg/mg, 95% CI: 1.026–1.427). Living with a smoking parent was associated with exposure to carcinogens, and a critical predictor of tobacco-specific nitrosamine. Prohibition of smoking at home is effective at preventing SHS in children. However, it cannot completely prevent passive smoking, which might be attributable to thirdhand smoking and undetected secondhand smoke.
Demystifying the factors associated with rural–urban gaps in severe acute malnutrition among under-five children in low- and middle-income countries: a decomposition analysis
Authors: Fagbamigbe A. F. , Kandala N. B. , Uthman A. O. 
Published: July 2020

AbstractWhat explains the underlying causes of rural–urban differentials in severe acute malnutrition (SAM) among under-five children is poorly exploited, operationalized, studied and understood in low- and middle-income countries (LMIC). We decomposed the rural–urban inequalities in the associated factors of SAM while controlling for individual, household, and neighbourhood factors using datasets from successive demographic and health survey conducted between 2010 and 2018 in 51 LMIC. The data consisted of 532,680 under-five children nested within 55,823 neighbourhoods across the 51 countries. We applied the Blinder–Oaxaca decomposition technique to quantify the contribution of various associated factors to the observed rural–urban disparities in SAM. In all, 69% of the children lived in rural areas, ranging from 16% in Gabon to 81% in Chad. The overall prevalence of SAM among rural children was 4.8% compared with 4.2% among urban children. SAM prevalence in rural areas was highest in Timor-Leste (11.1%) while the highest urban prevalence was in Honduras (8.5%). Nine countries had statistically significant pro-rural (significantly higher odds of SAM in rural areas) inequality while only Tajikistan and Malawi showed statistically significant pro-urban inequality (p < 0.05). Overall, neighbourhood socioeconomic status, wealth index, toilet types and sources of drinking water were the most significant contributors to pro-rural inequalities. Other contributors to the pro-rural inequalities are birth weight, maternal age and maternal education. Pro-urban inequalities were mostly affected by neighbourhood socioeconomic status and wealth index. Having SAM among under-five children was explained by the individual-, household- and neighbourhood-level factors. However, we found variations in the contributions of these factors. The rural–urban dichotomy in the prevalence of SAM was generally significant with higher odds found in the rural areas. Our findings suggest the need for urgent intervention on child nutrition in the rural areas of most LMIC.
Transversely isotropic elastic-plastic properties in thermal arc sprayed Al–Zn coating: a microporomechanics approach
Authors: Huen Wai Yeong , Lee Hyuk , Vimonsatit Vanissorn , Mendis Priyan , Lee Han-Seung 
Published: July 2020

AbstractThe transversely isotropic behaviour of thermal sprayed aluminium and zinc coating has been investigated based on a combination of nanoindentation experimental data and microporomechanics theory. A recently developed strength homogenisation approach comprises of the solid and porous medium is adopted to investigate the morphology properties of thermal sprayed aluminum and zinc coating. The finding of this paper demonstrates that the individual aluminum and zinc phases in the coating have a characteristic packing density close to the theoretical highest spherical packing ratio for face-centred cubic and hexagonal close packed. Also, the plasticity properties of solid particles in both aluminum and zinc are found to have a significant transversely isotropic condition, while the elasticity properties are close to isotropic. These findings led to the conclusion that the anisotropic condition of the coating is dominantly affected by the plasticity properties, in terms of cohesion and friction coefficient.
Beta 1 integrin signaling mediates pancreatic ductal adenocarcinoma resistance to MEK inhibition
Authors: Brannon Arthur , Drouillard Donovan , Steele Nina , Schoettle Shadae , Abel Ethan V. , Crawford Howard C. , Pasca di Magliano Marina 
Published: July 2020

AbstractPancreatic cancer, one of the deadliest human malignancies, has a dismal 5-year survival rate of 9%. KRAS is the most commonly mutated gene in pancreatic cancer, but clinical agents that directly target mutant KRAS are not available. Several effector pathways are activated downstream of oncogenic Kras, including MAPK signaling. MAPK signaling can be inhibited by targeting MEK1/2; unfortunately, this approach has been largely ineffective in pancreatic cancer. Here, we set out to identify mechanisms of MEK inhibitor resistance in pancreatic cancer. We optimized the culture of pancreatic tumor 3D clusters that utilized Matrigel as a basement membrane mimetic. Pancreatic tumor 3D clusters recapitulated mutant KRAS dependency and recalcitrance to MEK inhibition. Treatment of the clusters with trametinib, a MEK inhibitor, had only a modest effect on these cultures. We observed that cells adjacent to the basement membrane mimetic Matrigel survived MEK inhibition, while the cells in the interior layers underwent apoptosis. Our findings suggested that basement membrane attachment provided survival signals. We thus targeted integrin β1, a mediator of extracellular matrix contact, and found that combined MEK and integrin β1 inhibition bypassed trametinib resistance. Our data support exploring integrin signaling inhibition as a component of combination therapy in pancreatic cancer.
Probing the relationship between late endogenous ERP components with fluid intelligence in healthy older adults
Authors: Teixeira-Santos Ana C. , Pinal Diego , Pereira Diana R. , Leite Jorge , Carvalho Sandra , Sampaio Adriana 
Published: July 2020

AbstractThe world population is rapidly aging, bringing together the necessity to better understand the advancing age. This characterization may be used to aid early diagnosis and to guide individually-tailored interventions. While some event-related potential (ERP) components, such as the P300 and late positive complex (LPC), have been associated with fluid intelligence (Gf) in young population; little is known whether these associations hold for older people. Therefore, the main goal of this study was to assess whether these ERP components are associated with Gf in the elderly. Fifty-seven older adults performed a continuous performance task (CPT) and a visual oddball paradigm while EEG was recorded. Participants were divided into two groups, according to their performance in the Raven’s Advanced Progressive Matrices test: high-performance (HP) and low-performance (LP). Results showed that the HP group, compared to the LP group, had higher LPC amplitudes in the CPT and shorter P300 latencies in the oddball task, highlighting the role of ERP components as a potential electrophysiological proxy of Gf abilities in the elderly.