bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies
Authors: Tada Takuya , Dcosta Belinda M. , Samanovic-Golden Marie , Herati Ramin S. , Cornelius Amber , Mulligan Mark J. , Landau Nathaniel R. 
Published: February 2021

AbstractThe increasing prevalence of SARS-CoV-2 variants with mutations in the spike protein has raised concerns that recovered individuals may not be protected from reinfection and that current vaccines will become less effective. The B.1.1.7 isolate identified in the United Kingdom and B.1.351 isolate identified in the Republic of South Africa encode spike proteins with multiple mutations in the S1 and S2 subunits. In addition, variants have been identified in Columbus, Ohio (COH.20G/677H), Europe (20A.EU2) and in domesticated minks. Analysis by antibody neutralization of pseudotyped viruses showed that convalescent sera from patients infected prior to the emergence of the variant viruses neutralized viruses with the B.1.1.7, B.1.351, COH.20G/677H Columbus Ohio, 20A.EU2 Europe and mink cluster 5 spike proteins with only a minor decrease in titer compared to that of the earlier D614G spike protein. Serum specimens from individuals vaccinated with the BNT162b2 mRNA vaccine neutralized D614G virus with titers that were on average 7-fold greater than convalescent sera. Vaccine elicited antibodies neutralized virus with the B.1.1.7 spike protein with titers similar to D614G virus and neutralized virus with the B.1.351 spike with, on average, a 3-fold reduction in titer (1:500), a titer that was still higher than the average titer with which convalescent sera neutralized D614G (1:139). The reduction in titer was attributable to the E484K mutation in the RBD. The B.1.1.7 and B.1.351 viruses were not more infectious than D614G on ACE2.293T cellsin vitrobut N501Y, an ACE2 contacting residue present in the B.1.1.7, B.1.351 and COH.20G/677H spike proteins caused higher affinity binding to ACE2, likely contributing to their increased transmissibility. These findings suggest that antibodies elicited by primary infection and by the BNT162b2 mRNA vaccine are likely to maintain protective efficacy against B.1.1.7 and most other variants but that the partial resistance of virus with the B.1.351 spike protein could render some individuals less well protected, supporting a rationale for the development of modified vaccines containing E484K.
Innovations to expand drone data collection and analysis for rangeland monitoring
Authors: Gillan Jeffrey K. , Ponce-Campos Guillermo E. , Swetnam Tyson L. , Gorlier Alessandra , Heilman Philip , McClaran Mitchel P. 
Published: February 2021

AbstractIn adaptive management of rangelands, monitoring is the vital link that connects management actions with on-the-ground changes. Traditional field monitoring methods can provide detailed information for assessing the health of rangelands, but cost often limits monitoring locations to a few key areas or random plots. Remotely sensed imagery, and drone-based imagery in particular, can observe larger areas than field methods while retaining high enough spatial resolution to estimate many rangeland indicators of interest. However, the geographic extent of drone imagery products is often limited to a few hectares (for resolution ≤ 1 cm) due to image collection and processing constraints. Overcoming these limitations would allow for more extensive observations and more frequent monitoring. We developed a workflow to increase the extent and speed of acquiring, processing, and analyzing drone imagery for repeated monitoring of two common indicators of interest to rangeland managers: vegetation cover and vegetation heights. By incorporating a suite of existing technologies in drones (real-time kinematic GPS), data processing (automation with Python scripts, high performance computing), and cloud-based analysis (Google Earth Engine), we greatly increased the efficiency of collecting, analyzing, and interpreting high volumes of drone imagery for rangeland monitoring. End-to-end, our workflow took 30 days, while a workflow without these innovations was estimated to require 141 days to complete. The technology around drones and image analysis is rapidly advancing which is making high volume workflows easier to implement. Larger quantities of monitoring data will significantly improve our understanding of the impact management actions have on land processes and ecosystem traits.
Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks and plastoglobular functions
Authors: Michel Elena J.S. , Ponnala Lalit , Wijk Klaas J. van 
Published: February 2021

AbstractPlastoglobules (PGs) are dynamic protein-lipid micro-compartments in plastids enriched for isoprenoid-derived metabolites. Chloroplast PGs support formation, remodeling and controlled dismantling of thylakoids during developmental transitions and environmental responses. However, the specific molecular functions of most PG proteins are still poorly understood. This study harnesses recent co-mRNA expression from ATTED-II using combined microarray and RNAseq information on an updated inventory of 34 PG proteins, as well as proteomics data across 30 Arabidopsis tissue types from ATHENA. Hierarchical clustering based on relative abundance for the PG proteins across non-photosynthetic and photosynthetic tissue types showed their coordinated protein accumulation across Arabidopsis parts, tissue types, development and senescence. We generated multiple mRNA-based networks by applying different coefficient thresholds; functional enrichment was determined for each network and PG gene. Combined analysis of these stringency networks identified a central hub and four peripheral modules. Enrichment of specific nuclear transcription factors (e.g. Golden2-like) and support for cross-talk between PGs and the plastid gene expression was observed, and specific ABC1 kinases seem part of a light signaling network. Examples of other specific findings are that FBN7b is involved with upstream steps of tetrapyrrole biosynthesis and that ABC1K9 is involved in starch metabolism.HighlightThe plastoglobular proteome shows coherent tissue-specific accumulation, whereas combined analysis of transcriptional co-expression networks, at different stringencies and following in-depth functional annotation, associate selected plastoglobular proteins to specific metabolic functions.
The ability ofPseudomonas aeruginosato adopt a Small Colony Variant (SCV) phenotype is conserved, and not restricted to clinical isolates
Authors: Besse Alison , Trottier Mylène , Groleau Marie-Christine , Déziel Eric 
Published: February 2021

ABSTRACTA subpopulation of Small Colony Variants (SCVs) is a frequently observed feature ofPseudomonas aeruginosaisolated from cystic fibrosis (CF) lungs biofilms. SCVs have almost exclusively been reported from infected hosts, essentially CF individuals or, by extension, from laboratory cultivation of strains originated from infected hosts. We previously reported the identification ofP. aeruginosaSCVs emerging from a non-clinical strain and displaying features shared with clinical SCVs. In the present work, we investigated the ability of 22P. aeruginosaisolates from various environmental origins to, under laboratory culture conditions, spontaneously adopt a SCV-like smaller alternative morphotype distinguishable from the ancestral parent strain. Unexpectedly, we found that all theP. aeruginosastrains tested have the ability to adopt a SCV morphotype, regardless of their origin. Based on the phenotypes already described for SCVs, the SCV-like morphotypes obtained were clustered in two groups displaying various phenotypic profiles, including one characteristic of already described SCVs. We conclude that the ability to switch to a SCV phenotype is a conserved feature inPseudomonas aeruginosa.IMPORTANCEP. aeruginosais an opportunistic pathogen that thrives in many environments. It is significant public health concern, notably because it is the most prevalent pathogen found in the lungs of people with cystic fibrosis (CF). In infected hosts, its persistence is believed to be related to the emergence of an alternative small colony variant (SCV) phenotype. By reporting the distribution ofP. aeruginosaSCVs in various non-clinical environments, this work contributes to understanding a conserved adaptation mechanism used byP. aeruginosato rapidly adapt in all environments. Counteraction of this strategy could preventP. aeruginosapersistent infection in the future.
Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
Authors: Washington Nicole L. , Gangavarapu Karthik , Zeller Mark , Bolze Alexandre , Cirulli Elizabeth T. , Barrett Kelly M. Schiabor , Larsen Brendan B. , Anderson Catelyn , White Simon , Cassens Tyler , Jacobs Sharoni , Levan Geraint , Nguyen Jason , Ramirez Jimmy M. , Rivera-Garcia Charlotte , Sandoval Efren , Wang Xueqing , Wong David , Spencer Emily , Robles-Sikisaka Refugio , Kurzban Ezra , Hughes Laura D. , Deng Xianding , Wang Candace , Servellita Venice , Valentine Holly , De Hoff Peter , Seaver Phoebe , Sathe Shashank , Gietzen Kimberly , Sickler Brad , Antico Jay , Hoon Kelly , Liu Jingtao , Harding Aaron , Bakhtar Omid , Basler Tracy , Austin Brett , Isaksson Magnus , Febbo Phillip G. , Becker David , Laurent Marc , McDonald Eric , Yeo Gene W. , Knight Rob , Laurent Louise C. , de Feo Eileen , Worobey Michael , Chiu Charles , Suchard Marc A. , Lu James T. , Lee William , Andersen Kristian G. 
Published: February 2021

SummaryAs of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
Antibody Tests: They Are More Important Than We Thought
Authors: Guimarães Luís 
Published: February 2021

AbstractAntibody testing is a non-pharmaceutical intervention – not recognized so far in the literature – to prevent COVID-19 contagion. I show this in a simple economic model of an epidemic in which agents choose social activity under health state uncertainty. In the model, susceptible and asymptomatic agents are more socially active when theythinkthey might be immune. And this increased activity escalates infections, deaths, and welfare losses. Antibody testing, however, prevents this escalation by revealing that those agents are not immune. Through this mechanism, I find that antibody testing prevents about 12% of COVID-19 related deaths within 12 months.
Automated Detection of COVID-19 through Convolutional Neural Network using Chest x-ray images
Authors: Sarki Rubina , Ahmed Khandakar , Wang Hua , Zhang Yanchun , Wang Kate 
Published: February 2021

AbstractThe COVID-19 epidemic appears to have a catastrophic impact on global well-being and public health. More than 10 million confirmed cases have been reported worldwide until now. Due to the growing number of confirmed cases, timely and accurate classification of healthy and infected patients is essential to control and treat COVID-19. To this end, in this paper, we aim to develop a deep learning-based system for the persuasive classification and reliable detection of COVID-19 using chest radiography. Firstly, we evaluate the performance of various state-of-the-art convolutional neural networks (CNNs) proposed over recent years for medical image classification. Secondly, we develop and train CNN from scratch. In both cases, we use a recently published public X-Ray dataset for training and validation purposes. For transfer learning, we obtain 100% accuracy for binary classification (i.e., Normal/COVID-19) and 87.50% accuracy for tertiary classification (Normal/COVID-19/Pneumonia). With the CNN trained from scratch, we achieve 93.75% accuracy for tertiary classification. We observe, in the case of transfer learning, the classification accuracy drops with an increased number of classes. Our comprehensive ROC and confusion metric analysis with 10-fold cross-validation strongly underpin our findings.
Comparative reproductive biology of deep-sea ophiuroids inhabiting polymetallic-nodule fields in the Clarion-Clipperton Fracture Zone
Authors: Laming Sven R , Christodoulou Magdalini , Arbizu Pedro Martinez , Hilário Ana 
Published: February 2021

AbstractDeep-sea mining in the Pacific Clarion-Clipperton Fracture Zone (CCZ), a low-energy sedimentary habitat with polymetallic nodules, is expected to have considerable and long-lasting environmental impact. The CCZ hosts extraordinarily high species diversity across representatives from all Domains of Life. Data on species biology and ecology remain scarce, however. The current study describes the reproductive biology ofOphiosphalma glabrum(Lütken & Mortensen, 1899) (Ophiosphalmidae) andOphiacantha cosmica(Lyman, 1878) (Ophiacanthidae), two ophiuroids frequently found in the CCZ. Specimens collected in Spring 2015 and 2019 in four contract areas were examined morphologically and histologically. Size-class frequencies (disc diameter and oocytes feret diameters), sex ratios, gametogenic status, putative reproductive mode and a simple proxy for fecundity are presented. Habitat use differs in each. WhileOphiosphalma glabrumis epibenthic, occurring as single individuals,Ophiacantha cosmicaoften form size-stratified groups living on stalked sponges, suggesting gregarious settlement or retention of offspring (though no brooding individuals were found). Further molecular analyses are needed to establish whetherO. cosmicagroups are familial. InOphiosphalma glabrum, for which sample sizes were larger, sex ratios approximated a 1:1 ratio with no size-structuring. In both species, individuals were at various stages of gametogenic maturity but no ripe females were identified. Based on this,O. glabrumis most probably gonochoric. Reproductive mode remains inconclusive forOphiacantha cosmica. Both species are presumptively lecithotrophic, with vitellogenic-oocyte feret diameters exceeding 250 µm. Oocyte feret diameters at times exceeded 400 µm inOphiosphalma glabrum, indicating substantial yolk reserves. Estimates of instantaneous fecundity (vitellogenic specimens ofO. glabrumonly) were confounded by interindividual variability in gonad characteristics. The well-furnished lecithotrophic larvae ofO. glabrumwould be capable of dispersing even under food-impoverished conditions. The current study examines ophiuroid reproductive biology over multiple localities in the CCZ concurrently for the first time, at sites characterised by differing productivity regimes. The reproductive biology of each species is thus discussed with reference to past evolutionary (habitat stability), contemporary (food supply) and future environmental drivers (potential impacts of deep-sea mining).
Speciation across the Earth driven by global cooling in terrestrial Orchids
Authors: Thompson Jamie B. , Davis Katie E. , Dodd Harry O. , Wills Matthew A. , Priest Nicholas K. 
Published: February 2021

AbstractThough climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localised climate or the accumulation of species with time. But, we need focused analyses of highly specious clades to disentangle the consequences of climate change, geography and time. Here, we show that global cooling shapes the biodiversity of terrestrial orchids. Employing a phylogenetic framework of 1,450 species of Orchidoideae, the largest terrestrial orchid subfamily, we find that speciation rate is causally linked with historic global cooling, not time, habitation in the tropics, altitude, variation in chromosome number, or other types of historic climate change. Relative to the gradual accumulation of species with time, models specifying speciation driven by historic global cooling are 328 times more likely. Evidence ratios estimated for 212 other plant and animal groups reveal that the orchidoids represent one of the best-supported cases of temperature-spurred speciation yet reported. Employing >1.4 M georeferenced records, we find that global cooling drove contemporaneous diversification in each of the seven major orchid bioregions of the earth. With current emphasis on understanding and predicting the immediate impacts of global warming, our study provides a clear case study of the longterm impacts of global climate change on biodiversity.Significance statementThe staggering biodiversity of angiosperms has been difficult to reconcile with the gradual Darwinian process thought to create it. Changes in climate through the Earth’s history could have instigated this diversification, but perceived variability across clades and geography has restrained generalisation. In this paper, we reconstruct the evolutionary history of a rich terrestrial orchid subfamily favoured by Darwin (Orchidoideae, ~5,000 species), and use >1.4 million georeferenced records to test how and where those orchid species arose. We find that global cooling between the Oligocene and present day spurred an avalanche of speciation in orchidoid assemblages across the Earth. This work resolves the orchidoid phylogeny and provides a clear example of how historic climate change drives global patterns of biodiversity.
A clonal fresh water plants acquires transgenerational stress resistance under recurring copper excess
Authors: Huber Meret , Gablenz Saskia , Höfer Martin 
Published: February 2021

ABSTRACTAlthough non-genetic inheritance is thought to play an important role in plant ecology and evolution, evidence for adaptive transgenerational plasticity is scarce. Here, we investigated the consequences of copper excess on offspring defences and fitness in the giant duckweed (Spirodela polyrhiza) across multiple asexual generations. We found that exposing large monoclonal populations (>10,000 individuals) for 30 generations to copper excess decreased plant fitness during the first few generations but increased their fitness in consecutive generations under recurring stress when plants were grown for 5 generations under control conditions prior recurring conditions. Similarly, propagating individual plants as single descendants for 5 or 10 generations under copper excess decreased plant fitness when 5 generations and improved plant fitness when 10 generations passed between initial and recurring stress; thus, transgenerational stress responses likely contributed to the observed variations in offspring fitness of long-term copper exposed populations. Fitness benefits under recurring stress were partially associated with avoidance of excessive copper accumulation, which in turn correlated with transgenerationally modified flavonoid concentrations. Taken together, these data demonstrate time-dependent adaptive transgenerational responses under recurring stress, which highlights the importance of non-genetic inheritance for plant ecology and evolution.
Social selection is density dependent but makes little contribution to total selection in New Zealand giraffe weevils
Authors: Fisher David N , LeGrice Rebecca J , Painting Christina J 
Published: February 2021

AbstractSocial selection occurs when traits of interaction partners influence an individual’s fitness and can fundamentally alter total selection strength. Unlike for direct selection, however, we have little idea of what factors influence the strength of social selection. Further, social selection only contributes to overall selection when there is phenotypic assortment, but simultaneous estimates of social selection and phenotypic assortment are rare. Here we estimated social selection on body size in a wild population of New Zealand giraffe weevils (Lasiorhynchus barbicornis). We did this in a range of contexts and measured phenotypic assortment for both sexes. Social selection was mostly absent and not affected by sex ratio or the body size of the focal individual. However, at high densities selection was negative for both sexes, consistent with competitive interactions based on size for access to mates. Phenotypic assortment was also density dependent, flipping from positive at low densities to negative at high densities. However, it was always close to zero, indicating negative social selection at high densities will not greatly impede the evolution of larger body sizes. Despite its predicted importance, social selection may only influence evolutionary change in specific contexts, leaving direct selection as the dominant driver of evolutionary change.