bluuebunny/crossref_metadata_2025 huggingface dataset:
On complex systems of adaptive frugal products
Authors: Rao Balkrishna C.
Published: July 2020

Frugal
products possess a proper mix of features including minimal consumption of resources, good functionality under nominal conditions and low cost. Therefore, increasing use of
frugal
products, that are designed and also fabricated systematically, is crucial to all-round
sustainable development
. However, their low factor-of-safety rigorous-design makes them inherently prone to failure under conditions of overloading. And multitudes of such coupled-products would create topologies of interconnected complex systems in the foreseeable future whose individual products should be made to adapt against any events of failure to enhance functionality while maintaining low cost. Accordingly, this paper proposes a two-pronged methodology for adaptation of
frugal
products along with ramifications of complex systems of
frugal
products. The adaptation methodology is crucial to the functioning of individual and also networks of
frugal
products and this work accordingly explicates scenarios of ensuing networks. Other than application to various sectors including
electric vehicles
, a basic example of which is covered in this paper, the proposed adaptation-and-networking framework can also be applied to a growing numbers of sustainable products, which are
frugal
according to the terminology of this effort and hence prone to premature failure.
Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts
Authors: Tehel Anja , Streicher Tabea , Tragust Simon , Paxton Robert J.
Published: July 2020

Pathogen spillover represents an important cause of biodiversity decline. For wild bee species such as bumblebees, many of which are in decline, correlational data point towards viral spillover from managed honeybees as a potential cause. Yet, impacts of these viruses on wild bees are rarely evaluated. Here, in a series of highly controlled laboratory infection assays with well-characterized viral inocula, we show that three viral types isolated from honeybees (deformed wing virus genotype A, deformed wing virus genotype B and black queen cell virus) readily replicate within hosts of the bumblebeeBombus terrestris. Impacts of these honeybee-derived viruses - either injected or fed - on the mortality ofB. terrestrisworkers were, however, negligible and probably dependent on host condition. Our results highlight the potential threat of viral spillover from honeybees to novel wild bee species, though they also underscore the importance of additional studies on this and other wild bee species under field-realistic conditions to evaluate whether pathogen spillover has a negative impact on wild bee individuals and population fitness.
Brain microRNAs among social and solitary bees
Authors: Kapheim Karen M. , Jones Beryl M. , Søvik Eirik , Stolle Eckart , Waterhouse Robert M. , Bloch Guy , Ben-Shahar Yehuda
Published: July 2020

Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20–35%) of detected miRNAs had lineage-specific expression in the brain, 24–72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.
Growth, physiological and transcriptomic analysis of the perennial ryegrassLolium perennein response to saline stress
Authors: Xu Hai-Shun , Guo Su-Ming , Zhu Lin , Xing Jin-Cheng
Published: July 2020

Salinization of soil is a global environmental concern. To bioremediate or use saline-alkali lands, most studies focused on screening of halophytes and breeding of saline-tolerant non-halophyte vegetables. Seldom studies investigated effects of salinity on general landscape plants, which are important for landscape construction in urban areas. In the present study, effects of salinity on seed germination and seedling growth of the perennial ryegrassLolium perennewere investigated. The final seed germination rate was not affected at salinity up to 6.4‰. Partial seedlings wilted in all saline treatments and the mortality ofL. perennewas positively correlated with salinity. Treatments with salinity equal to or lower than 1.6‰ did not affect length and dry weight of shoot and root. These results suggested thatL. perennecould be sowed and then grow well in low-salinity areas. To explore the underlying physiological mechanisms, contents of photosynthetic pigments and antioxidant indices were determined. The results showed that contents of chlorophylla,band carotenoid significantly decreased in all saline treatments, in comparison to the control. Similarly, activities of superoxide dismutase and peroxidase decreased and contents of glutathione and malondialdehyde increased in saline treatments. Additionally, transcriptome analysis identified 792 differentially expressed genes (DEGs) inL. perenneshoots between 6.4‰ saline treatment and the control. Compared with the control, genes in relation to iron transportation and amino acid metabolism were downregulated, but genes participating in energy metabolism were upregulated. These changes would inhibit toxicity of ion accumulation and provide more energy for plants to resist saline stress.
Randomized Controlled Trial Effect of Short-Term MIND Diet Intervention on Hunger Hormones, Anthropometric Parameters, and Brain Structures in Middle-Aged Obese Women
Authors: Arjmand Golnaz , Abbas-Zadeh Mojtaba , fardaei Majid , Eftekhari Mohammad Hassan
Published: July 2020

The growing prevalence of obesity and its destructive effects on the hormone’s circulation and brain structures has attracted attention to specific dietary patterns. This trial aimed to examine the effect of short-term newly Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) pattern on anthropometric parameters, hunger hormones as well as brain structures in obese women. The study was a randomized restricted controlled trial in which we analyzed 37 healthy obese women with a mean age of 48 ± 5.38 years and mean Body Mass Index (BMI) 32 ± 4.31 kg/m2. Participants were randomly allocated to a hypocaloric modified MIND diet or a hypocaloric waiting list control diet and followed the protocols for three months. Differences in anthropometric and laboratory analysis, as well as brain structures, were determined at baseline and follow up. There was a more significant reduction in weight, BMI, percentage of body fat, waist circumference, and Leptin concentration in the MIND diet group compared to the control group (ps<0.05). Despite a deceased in plasma levels of Ghrelin and GLP-1 in the control group, results have found a significant increase in these hunger hormones in the MIND diet group (ps<0.05). Our results diminished to detect any differences in the whole and regional brain structures between two groups after three months follow up. Our trial for the first time demonstrated that a three-month MIND diet intervention could improve the potentially devastating effect of obesity on metabolic profiles and anthropometric parameters. However, we couldn’t find the MIND diet effect on brain structures.
Risk Factors for Mortality of COVID-19 Patients
Authors: Ouchetto Ouail , Bourhanbour Asmaa Drissi
Published: July 2020

Background

Lethality rates of COVID-19 are so different between countries and continents. This lethality seems to be very low in Africa and Asia, but exceedingly high in western Europe and North America. Many factors could have a role in this disparity such as comorbidities. Advanced age, obesity, cardiovascular disease, diabetes and cancer were the most frequently cited in the reported COVID-19 data. The main objective was to analyze and evaluate the association between the COVID-19 mortality and the mentioned factors in 164 countries.

Methods

The Data of COVID-19 deaths, latitude degrees, population age distribution, cardiovascular diseases, obesity, diabetes and cancer were extracted from different online sources. For the statistical analysis, we used Spearman to measure the correlation coefficient between numbers of deaths and the mentioned factors until June 29, 2020.

Results

The correlation between COVID-19 mortality and latitude, high age, obesity, CVD and number of cancer patients per 100,000 is significant at 0.01 level with r = 0.489, r=0.511, r=0.489, r=0.561 and r=0.536 respectively. The correlation between the number of deaths and diabetes is less strong than the previous ones, and the correlation coefficient is r= 0.154.

Conclusion

The great lethality of COVID-19 in western Europe and North America can be explained in part by the highest of age, cancer and CVD percentage in these regions. It seems also plausible that the increased obesity in the USA and vitamin D deficiency in Europe may contribute to increasing the number of COVID-19 deaths.
Ultraviolet A Radiation and COVID-19 Deaths in the USA with replication studies in England and Italy
Authors: Cherrie Mark , Clemens Tom , Colandrea Claudio , Feng Zhiqiang , Webb David J , Dibben Chris , Weller Richard B
Published: July 2020

Objectives

To determine whether UVA exposure might be associated with COVID-19 deaths

Design

Ecological regression, with replication in two other countries and pooled estimation

Setting

2,474 counties of the contiguous USA, 6,755 municipalities in Italy, 6,274 small areas in England. Only small areas in their ‘Vitamin D winter’ (monthly mean UVvitd of under 165 KJ/m2) from Jan to April 2020.

Participants

The ‘at-risk’ population is the total small area population, with measures to incorporate spatial infection into the model. The model is adjusted for potential confounders including long-term winter temperature and humidity.

Main outcome measures

We derive UVA measures for each area from remote sensed data and estimate their relationship with COVID-19 mortality with a random effect for States, in a multilevel zero-inflated negative binomial model. In the USA and England death certificates had to record COVID-19. In Italy excess deaths in 2020 over expected from 2015-19.

Data sources

Satellite derived mean daily UVA dataset from Japan Aerospace Exploration Agency. Data on deaths compiled by Center for Disease Control (USA), Office for National Statistics (England) and Italian Institute of Statistics.

Results

Daily mean UVA (January-April 2020) varied between 450 to 1,000 KJ/m2 across the three countries. Our fully adjusted model showed an inverse correlation between UVA and COVID-19 mortality with a Mortality Risk Ratio (MRR) of 0.71 (0.60 to 0.85) per 100KJ/m2 increase UVA in the USA, 0.81 (0.71 to 0.93) in Italy and 0.49 (0.38 to 0.64) in England. Pooled MRR was 0.68 (0.52 to 0.88).

Conclusions

Our analysis, replicated in 3 independent national datasets, suggests ambient UVA exposure is associated with lower COVID-19 specific mortality. This effect is independent of vitamin D, as it occurred at irradiances below that likely to induce significant cutaneous vitamin D3 synthesis. Causal interpretations must be made cautiously in observational studies. Nonetheless this study suggests strategies for reduction of COVID-19 mortality.
Advanced imaging to improve remission rates in patients undergoing transsphenoidal surgery for Cushing’s disease
Authors: Koh Chan Hee , Khan Danyal Z. , Horsfall Hugo Layard , Ali Ahmad , Digpal Ronneil , Evanson Jane , Marcus Hani J. , Korbonits Márta
Published: July 2020

INTRODUCTION

Cushing’s disease is a condition of hypercortisolaemia caused by a functional adrenocorti-cotropic hormone secreting pituitary adenoma. Surgical management is the first line of treatment for Cushing’s disease, but remains challenging in some cases. Various imaging modalities have been tried in an attempt to improve surgical remission rates. However, the sizes and certainties of any effect, in comparison to standard preoperative MRI imaging, remain unclear.

METHODS

This protocol has been developed according to the PRISMA-P 2015 standards. Searches of PubMed and Embase were conducted on 21 May 2020, and abstract screening commenced. The eligibility criteria, items for data extraction, and the analysis plan are laid out in this protocol, and uploaded prior to commencement of formal data extraction.

DISCUSSION

The results of this review will inform decision-making and priority-setting at the clinical, organisational and research levels. The results will be disseminated throughout the international neurosurgical community through presentations and publications.
Near Term Predictions of Covid-19 Cases in West Bengal, Maharashtra, Delhi and Tamil Nadu in India Based on Basu Model
Authors: Basu Santanu
Published: July 2020

Four states in India account for nearly two thirds of the Covid-19 cases and the numbers are growing fast. A mathematical model which has been recently developed and which has been applied to other countries and regions in the world has been used in this paper to anchor the available data to date and to make near term projections. The projections can be compared to actual data to take steps in the near term in controlling the spread of this disease.
Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits
Authors: Pahl Matthew C. , Doege Claudia A. , Hodge Kenyaita M. , Littleton Sheridan H. , Leonard Michelle E. , Lu Sumei , Rausch Rick , Pippin James A. , Bradfield Jonathan P. , Hammond Reza K. , Boehm Keith , Berkowitz Robert I. , Lasconi Chiara , Su Chun , Chesi Alessandra , Johnson Matthew E. , Wells Andrew D. , Voight Benjamin F. , Leibel Rudolph L. , Cousminer Diana L. , Grant Struan F.A.
Published: July 2020

The hypothalamus regulates metabolic homeostasis by influencing behavior, energy utilization and endocrine systems. Given its role governing health-relevant traits, such as body weight and reproductive timing, understanding the genetic regulation of hypothalamic development and function should yield insights into these traits and diseases. However, given its inaccessibility, studying human hypothalamic gene regulation has proven challenging. To address this gap, we generated a chromatin architecture atlas of an established embryonic stem cell (ESC)-derived hypothalamic-like neuron (HN) model across three stages ofin vitrodifferentiation. We profiled accessible chromatin and identified physically interacting contacts between gene promoters and their putative cis-regulatory elements (cREs) to characterize changes in the gene regulatory landscape during hypothalamic differentiation. Next, we integrated these data with GWAS loci for multiple traits and diseases enriched for heritability in these cells, identifying candidate effector genes and cREs impacting transcription factor binding. Our results reveal common target genes for these traits, potentially identifying core hypothalamic developmental pathways. Our atlas will enable future efforts to determine precise mechanisms underlying hypothalamic development with respect to specific disease pathogenesis.
Identification of ligand-specific G-protein coupled receptor states and prediction of downstream efficacy via data-driven modeling
Authors: Fleetwood Oliver , Carlsson Jens , Delemotte Lucie
Published: July 2020

G protein-coupled receptors (GPCRs) shift between inactive states and active signaling states, to which intracellular binding partners can bind. Extracellular binding of ligands stabilizes different receptor states and modulates the intracellular response via a complex allosteric process, which is not completely understood. Despite the recent advances in structure determination and spectroscopy techniques, a comprehensive view of the ligand-protein interplay remains a challenge. We derived free energy landscapes describing activation of the β2adrenergic receptor (β2AR) bound to ligands with different efficacy profiles using enhanced sampling molecular dynamics (MD) simulations. The resulting free energy landscapes reveal clear shifts towards active-like states at the G protein binding site for receptors bound to partial and full agonists compared to antagonists and inverse agonists. Not only do the ligands control the population of states, they also modulate the conformational ensemble of the receptor by tuning allosteric protein microswitches. We find an excellent correlation between the conformation of the microswitches close to the ligand binding site and in the transmembrane region and experimentally reported cAMP signaling responses, highlighting the predictive power of our approach. Using dimensionality reduction techniques, we could further assess the similarity between the unique conformational states induced by different ligands. Two distant hotspots governing agonism on transmembrane helices 5 and 7, including the conserved NPxxY motif, formed the endpoints of an allosteric pathway between the binding sites. Our results demonstrate how molecular dynamics simulations can further provide insights into the mechanism of GPCR regulation by ligands, which may contribute to the design of drugs with specific efficacy profiles.
NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors
Authors: Mahler Bryon P. , Bujalowski Pawel J. , Mao Huzhang , Dill Erik A. , Jardine Paul J. , Choi Kay H. , Morais Marc C.
Published: July 2020

Double-stranded DNA viruses use ATP-powered molecular motors to package their genomes. To do so, these motors must efficiently transition between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes dimerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination.
Revisiting the carbon isotope discrimination and water use efficiency relation: the influence of mesophyll conductance
Authors: Ma Wei Ting , Tcherkez Guillaume , Wang Xu Ming , Schäufele Rudi , Schnyder Hans , Yang Yusheng , Gong Xiao Ying
Published: July 2020

The carbon isotope discrimination (Δ) has been used widely to infer intrinsic water-use efficiency (iWUE) of C3plants, a key parameter linking carbon and water fluxes. Despite the essential role of mesophyll conductance (gm) in photosynthesis and Δ, its effect on Δ-based predictions of iWUE has generally been neglected.

Here, we derive a mathematical expression of iWUE as a function of Δ that includesgm(iWUEmes) and exploits thegm-stomatal conductance (gsc) relationship across drought-stress levels and plant functional groups (deciduous or semi-deciduous woody, evergreen woody and herbaceous species) in a global database. iWUEmeswas further validated with an independent dataset of online-Δ and CO2and H2O gas exchange measurements with seven species.

Drought stress reducedgscby 52% andgmby 45% averaged over all plant functional groups, but had no significant effect on thegsc/gmratio, suggesting a well-constrainedgsc/gmratio of 0.79±0.07 (95%CI,n=198) across plant functional groups and drought-stress treatments. Due in part to the synchronous behavior ofgscandgm,gmwas negatively correlated to iWUE. Incorporating thegsc/gmratio in the iWUEmesmodel significantly improved the estimation of iWUE compared to the simple model.

The inclusion ofgmeffects, even using a fixedgsc/gmratio of 0.79 whengmis unknown, proved desirable to eliminate significant bias in estimating iWUE from Δ across various C3vegetation types.
Nutations in plant shoots: endogenous and exogenous factors in the presence of mechanical deformations
Authors: Agostinelli Daniele , DeSimone Antonio , Noselli Giovanni
Published: July 2020

Abstract

We present a three-dimensional morphoelastic rod model capable to describe the morphogenesis of growing plant shoots, as driven by differential growth at the tip. We discuss the evolution laws for endogenous oscillators, straightening mechanisms and reorientations to directional cues, such as phototropic responses to a far light source and gravitropic reactions governed by the statoliths avalanche dynamics. We use this model to investigate the role of elastic deflections due to gravity loading in circumnutating plant shoots. We show that, in the absence of endogenous cues, pendular and circular oscillations arise as a critical length is attained, thus suggesting the occurrence of a Hopf bifurcation reminiscent of flutter instabilities exhibited by structural systems under nonconservative loads. When also oscillations due to endogenous cues are present, their weight relative to those associated with the Hopf instability varies in time as the shoot length and other biomechanical properties change. Thanks to the simultaneous occurrence of these two oscillatory mechanisms, we are able to reproduce a variety of complex behaviors, including trochoid-like patterns, which evolve into circular orbits as the shoot length increases, and the amplitude of the flutter induced oscillations becomes dominant. Our findings suggest that the relative importance of the two mechanisms is an emergent property of the system that is affected by the amplitude of elastic deformations, and highlight the crucial role of elasticity in the analysis of circumnutations.
A Node-based Informed Modularity Strategy to Identify Organizational Modules in Anatomical Networks
Authors: Esteve-Altava Borja
Published: July 2020

The use of anatomical networks to study the modular organization of morphological systems and their evolution is growing in recent years. A common strategy to find the best partition of anatomical networks into modules is to use a community detection algorithm that tries to optimize the modularity Q function. However, this strategy overlooks the fact that Q has a resolution limit for small modules, which is often the case in anatomical networks. This produces two problems. One is that some algorithms find inexplicable different modules when we input slightly different networks. The other is that algorithms find asymmetric modules in otherwise symmetric networks. These problems have discouraged researchers to use anatomical network analysis and boost criticisms to this methodology. Here, I propose aNode-based Informed Modularity Strategy(NIMS) to identify modules in anatomical networks that bypass resolution and sensitivity limitations by using a bottom-up approach. Starting with the local modularity around every individual node, NIMS returns the modular organization of the network by merging non-redundant modules and assessing their intersection statistically using combinatorial theory. Instead of acting as a black box, NIMS allows researcher to make informed decisions about whether to merge non-redundant modules. NIMS returns network modules that are robust to minor variation and does not require to optimize a global modularity function. NIMS may prove useful to identify modules also in small ecological and social networks.
Genome-wide analysis clarifies the population genetic structure of wild Gilthead Sea Bream (Sparus aurata)
Authors: Maroso Francesco , Gkagkavouzis Konstantinos , De Innocentiis Sabina , Hillen Jasmien , do Prado Fernanda , Karaiskou Nikoleta , Taggart John Bernard , Carr Adrian , Nielsen Einar ,   the Aquatrace consortium, Triantafyllidis Alexandros , Bargelloni Luca
Published: July 2020

Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. Its distribution range goes from the Mediterranean to the African and European coasts of the North-East Atlantic. So far, the genetic structure of this species in the wild has been studied with microsatellite DNA, but the pattern of differentiation could not be fully clarified. In this study, almost 1000 wild sea bream from 23 locations in the Mediterranean Sea and Atlantic ocean where genotyped at 1159 SNP markers, of which 18 potentially under selection. Neutral markers suggested the presence of a weak subdivision into three genetic clusters: Atlantic, West and East Mediterranean. This last group could be further subdivided into an Ionian/Adriatic and an Aegean group using outlier markers. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, and this was also supported by preliminary genomic functional analysis. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry.
Genetic diversity and population structure among goat genotypes in Kenya
Authors: Waineina Ruth W. , Ngeno Kiplangat , Otieno Tobias O. , Ilatsia Evans D.
Published: July 2020

Population structure and relationship information among goats is critical for genetic improvement, utilization and conservation. This study explored population structure and level of gene intermixing among four goat genotypes in Kenya: Alpine (n = 30), Toggenburg (n = 28), Saanen (n = 24) and Galla (n = 12). The population structuring and relatedness were estimated using principal component analysis utilizing allele frequencies of the SNP markers. Genotype relationships were evaluated based on the calculated Reynolds genetic distances. A phylogenetic tree was constructed to represent genotype clustering using iTOL software. Population structure was investigated using model-based clustering (ADMIXTURE) Genotypes relationships revealed four distinctive clusters: Alpine, Galla, Saanen and Toggenburg. The ADMIXTURE results revealed some level of gene intermixing among Alpine, Toggenburg and Saanen with Galla. Saanen goats were the most admixed genotype with 84%, 7% and 4% of its genome derived from Galla, Alpine and Toggenburg respectively. Alpine and Toggenburg goats shared some associations with the Galla goat; 10% and 1% respectively. The association of Galla with other genotypes was anticipated since Galla goat was used as the founder population for crossbreeding with Saanen, Alpine and Toggenburg breed. The genetic variations among the goat genotypes observed, will provide a good opportunity for sustainable utilization, conservation and future genetic resource improvement programs in goat genotypes in Kenya.
Enlarged cortical cells and reduced cortical cell file number improve growth under suboptimal nitrogen, phosphorus and potassium availability
Authors: Yang Xiyu , Niemiec Miranda , Lynch Jonathan P.
Published: July 2020

Reduced cortical cell files (CCFN) and enlarged cortical cells (CCS) reduce root maintenance costs. We usedOpenSimRoot, a functional-structural model, to test the hypothesis that larger CCS, reduced CCFN, and their interactions with root cortical aerenchyma (RCA), are useful adaptations to suboptimal soil N, P, and K availability. Interactions of CCS and CCFN with lateral root branching density (LRBD) and increased carbon availability were evaluated under limited N, P and K availability. The combination of larger CCS and reduced CCFN increases the growth of maize up to 105%, 106%, and 144%, respectively, under limited N, P, or K availability. Interactions among larger CCS, reduced CCFN, and greater RCA results in combined growth benefits of up to 135%, 132%, and 161% under limited N, P, and K levels, respectively. Under low phosphorus and potassium availability, increased LRBD approximately doubles the utility of larger CCS and reduced CCFN. The utility of larger CCS and reduced CCFN is reduced by greater C availability as may occur in future climate scenarios. Our results support the hypothesis that larger CCS, reduced CCFN, and their interactions with RCA could increase nutrient acquisition by reducing root respiration and root nutrient demand. Phene synergisms may exist between CCS, CCFN, and LRBD. Natural genetic variation in CCS and CCFN merit consideration for breeding cereal crops with improved nutrient acquisition, which is critical for global food security.

One sentence summary

Functional-structural modeling indicates that enlarged root cortical cells and reduced cortical cell file number decrease root maintenance cost, permitting greater soil exploration, resource capture, and plant growth under suboptimal nitrogen, phosphorus and potassium availability.
i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results
Authors: Ustjanzew Arsenij , Preussner Jens , Bentsen Mette , Kuenne Carsten , Looso Mario
Published: July 2020

Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation and display of such visualizations. However, the combination of automated data processing pipelines handling omics data and dynamically generated, interactive dashboards is poorly solved. Here, we present i2dash, an R package intended to encapsulate functionality for programmatic creation of customized dashboards. It supports interactive and responsive (linked) visualizations across a set of predefined graphical layouts. i2dash addresses the needs of data analysts for a tool that is compatible and attachable to any R-based analysis pipeline, thereby fostering the separation of data visualization on one hand and data analysis tasks on the other hand. In addition, the generic design of i2dash enables data analysts to generate modular extensions for specific needs. As a proof of principle, we provide an extension of i2dash optimized for single-cell RNA-sequencing analysis, supporting the creation of dashboards for the visualization needs of single-cell sequencing experiments. Equipped with these features, i2dash is suitable for extensive use in large scale sequencing/bioinformatics facilities. Along this line, we provide i2dash as a containerized solution, enabling a straightforward large-scale deployment and sharing of dashboards using cloud services.

i2dash is freely available via the R package archive CRAN.
A DNA-based optical nanosensor forin vivoimaging of acetylcholine in the peripheral nervous system
Authors: Xia Junfei , Yang Hongrong , Mu Michelle , Micovic Nicholas , Poskanzer Kira E. , Monaghan James R. , Clark Heather A.
Published: July 2020

The ability to monitor the release of neurotransmitters during synaptic transmission would significantly impact the diagnosis and treatment of neurological disease. Here, we present a DNA-based enzymatic nanosensor for quantitative detection of acetylcholine (ACh) in the peripheral nervous system of living mice. ACh nanosensors consist of DNA as a scaffold, acetylcholinesterase as a recognition component, pH-sensitive fluorophores as signal generators, and α-bungarotoxin as a targeting moiety. We demonstrate the utility of the nanosensors in the submandibular ganglia of living mice to sensitively detect ACh ranging from 0.228 μM to 358 μM. In addition, the sensor response upon electrical stimulation of the efferent nerve is dose-dependent, reversible, and we observe a reduction of ~76% in sensor signal upon pharmacological inhibition of ACh release. Equipped with an advanced imaging processing tool, we further spatially resolve ACh signal propagation on the tissue level. Our platform enables sensitive measurement and mapping of ACh transmission in the peripheral nervous system.
Animal Model Prescreening: Pre-exposure to SARS-CoV-2 impacts responses in the NHP model
Authors: Ricks Keersten M. , Herbert Andrew S. , Koehler Jeffrey W. , Kuehnert Paul A. , Clements Tamara L. , Shoemaker Charles J. , Kuehne Ana I. , O’Brien Cecilia M. , Coyne Susan R. , Delp Korey L. , Akers Kristen S. , Dye John M. , Hooper Jay W. , Smith Jeffrey M. , Kugelman Jeffrey R. , Beitzel Brett F. , Gibson Kathleen M. , Johnston Sara C. , Minogue Timothy D.
Published: July 2020

COVID-19 presents herculean challenges to research and scientific communities for producing diagnostic and treatment solutions. Any return to normalcy requires rapid development of countermeasures, with animal models serving as a critical tool in testing vaccines and therapeutics. Animal disease status and potential COVID-19 exposure prior to study execution may severely bias efficacy testing. We developed a toolbox of immunological and molecular tests to monitor countermeasure impact on disease outcome and evaluate pre-challenge COVID-19 status. Assay application showed critical necessity for animal pre-screening. Specifically, real-time PCR results documented pre-exposure of an African Green Monkey prior to SARS-CoV-2 challenge with sequence confirmation as a community-acquired exposure. Longitudinal monitoring of nasopharyngeal swabs and serum showed pre-exposure impacted both viral disease course and resulting immunological response. This study demonstrates utility in a comprehensive pre-screening strategy for animal models, which captured the first documented case of community-acquired, non-human primate infection.

One Sentence Summary

Pre-exposure to SARS-CoV-2 affects biomarker responses in animal models, highlighting a need for robust pre-screening protocols prior to medical countermeasure studies.
Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells
Authors: Zeng Fuxing , Li Xin , Pires-Alves Melissa , Chen Xin , Hawk Christopher W. , Jin Hong
Published: July 2020

Conserved developmentally-regulated GTP-binding (Drg) proteins and their binding partner Dfrp proteins are known to be important for embryonic development, cellular growth control, differentiation and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog, Rbg1/Tma46, facilitates translational initiation, elongation and termination via suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, Rbg1 reverses the growth defect resulting from translation stalling and stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoEM structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of Tma46 subunit binds to the 40S, establishing an interaction critical for the complex ribosomal association. Our results answer the fundamental question on how a paused ribosome resumes translation and show that Drg1/Dfrp1 proteins play a critical role in ensuring orderly translation.
Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets
Authors: Chan Agnes. P. , Choi Yongwook , Schork Nicholas J.
Published: July 2020

To identify features in the genome of the SARS-CoV-2 pathogen responsible for the COVID-19 pandemic that may contribute to its viral replication, host pathogenicity, and vulnerabilities, we investigated how and to what extent the SARS-CoV-2 genome sequence differs from other well-characterized human and animal coronavirus genomes. Our analyses suggest the presence of unique sequence signatures in the 3’-untranslated region (UTR) of betacoronavirus lineage B, which phylogenetically encompasses SARS-CoV-2, SARS-CoV, as well as multiple groups of bat and animal coronaviruses. In addition, we identified genome-wide patterns of variation across different SARS-CoV-2 strains that likely reflect the effects of selection. Finally, we provide evidence for a possible host microRNA-mediated interaction between the 3’-UTR and human microRNA hsa-miR-1307-3p based on predicted, yet extensive, complementary base-pairings and similar interactions involving the Influenza A H1N1 virus. This interaction also suggests a possible survival mechanism, whereby a mutation in the SARS-CoV-2 3’-UTR leads to a weakened host immune response. The potential roles of host microRNAs in SARS-CoV-2 replication and infection, and the exploitation of conserved features in the 3’-UTR as therapeutic targets warrant further investigation.
Differential spatial computations in ventral and lateral face-selective regions are scaffolded by structural connections
Authors: Finzi Dawn , Gomez Jesse , Nordt Marisa , Rezai Alex A. , Poltoratski Sonia , Grill-Spector Kalanit
Published: July 2020

Face-processing occurs across ventral and lateral visual streams, which are involved in static and dynamic face perception, respectively. However, the nature of spatial computations across streams is unknown. Using functional MRI and novel population receptive field (pRF) mapping, we measured pRFs in face-selective regions. Results reveal that spatial computations by pRFs in ventral face-selective regions are concentrated around the center of gaze (fovea), but spatial computations in lateral face-selective regions extend peripherally. Diffusion MRI reveals that these differences are mirrored by a preponderance of white matter connections between ventral face-selective regions and foveal early visual cortex (EVC), while connections with lateral regions are distributed more uniformly across EVC eccentricities. These findings suggest a rethinking of spatial computations in face-selective regions, showing that they vary across ventral and lateral streams, and further propose that spatial computations in high-level regions are scaffolded by the fine-grain pattern of white matter connections from EVC.
Bi-directional Impacts of Heterotypic Interactions in Engineered 3D Human Cardiac Microtissues Revealed by Single-Cell RNA-Sequencing and Functional Analysis
Authors: Hookway Tracy A. , Matthys Oriane B. , Joy David A. , Sepulveda Jessica E. , Thomas Reuben , McDevitt Todd C.
Published: July 2020

Technological advancements have enabled the design of increasingly complex engineered tissue constructs, which better mimic native tissue cellularity. Therefore, dissecting the bi-directional interactions between distinct cell types in 3D is necessary to understand how heterotypic interactions at the single-cell level impact tissue-level properties. We systematically interrogated the interactions between cardiomyocytes (CMs) and cardiac non-myocytes in 3D self-assembled tissue constructs in an effort to determine the phenotypic and functional contributions of cardiac fibroblasts (CFs) and endothelial cells (ECs) to cardiac tissue properties. One week after tissue formation, cardiac microtissues containing CFs exhibited improved calcium handling function compared to microtissues comprised of CMs alone or CMs mixed with ECs, and CMs cultured with CFs exhibited distinct transcriptional profiles, with increased expression of cytoskeletal and ECM-associated genes. However, one month after tissue formation, functional and phenotypic differences between heterotypic tissues were mitigated, indicating diminishing impacts of non-myocytes on CM phenotype and function over time. The combination of single-cell RNA-sequencing and calcium imaging enabled the determination of reciprocal transcriptomic changes accompanying tissue-level functional properties in engineered heterotypic cardiac microtissues.
Multi-omic profiling of primary mouse neutrophils reveals a pattern of sex and age-related functional regulation
Authors: Lu Ryan , Taylor Shalina , Contrepois Kévin , Ellenberger Mathew , Sampathkumar Nirmal K. , Benayoun Bérénice A.
Published: July 2020

Neutrophils are the most abundant white blood cells in humans and constitute one of the first lines of defense in the innate immune response. Neutrophils are extremely short-lived cells, which survive less than a day after reaching terminal differentiation. Thus, little is known about how organismal aging, rather than the daily cellular aging process, may impact neutrophil biology. In addition, accumulating evidence suggests that both immunity and organismal aging are sex-dimorphic. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male mice, at the transcriptomic, metabolomic and lipidomic levels. Importantly, we identify widespread age-related and sex-dimorphic regulation of ‘omics’ in neutrophils, specifically regulation of chromatin. Using machine-learning, we identify candidate molecular drivers of age-related and sex-dimorphic transcriptional regulation of neutrophils. We leverage our resource to predict increased levels/release of neutrophil elastase in male mice. To date, this dataset represents the largest multi-omics resource for the study of neutrophils across biological sex and ages. This resource identifies molecular states linked to neutrophil characteristics linked to organismal age or sex, which could be targeted to improve immune responses across individuals.
Community factors associated with local RSV epidemic patterns: a spatiotemporal modeling study
Authors: Zheng Zhe , Pitzer Virginia E. , Warren Joshua L. , Weinberger Daniel M.
Published: July 2020

Background

Respiratory syncytial virus (RSV) causes a large burden of morbidity in infants, young children, and the elderly. The timing of RSV seasonal epidemics exhibits strong spatial patterns within the United States. Spatial variability in the timing of RSV epidemics provides an opportunity to probe the factors driving transmission of the virus.

Methods

We evaluated competing hypotheses about the associations between RSV epidemic timing at the ZIP-code level and household size, population density, school district boundaries, commuting patterns, and geographic proximity. We used hierarchical Bayesian models with monthly ZIP-code level hospitalization data from New York, New Jersey, and Connecticut between July 1997 and June 2014 to investigate these hypotheses.

Results

Early epidemic timing across ZIP codes was associated with large household sizes and high population density, and nearby ZIP codes shared similar epidemic timing. Variations in epidemic timing attributed to commuting patterns or school district boundaries are negligible.

Conclusion

Our results suggest RSV epidemics take off faster in areas with more household crowding and higher population density, and that epidemic spread follows a spatial diffusion process based on geographic proximity. With several vaccines against RSV under development, it is important to understand the drivers of RSV transmission and disease in order to maximize population protection of a vaccine program. Our findings can inform more effective control measures against RSV, such as vaccine programs and household infection control, and guide future studies on the transmission dynamics of RSV.
Association between consumption of fermented vegetables and COVID-19 mortality at a country level in Europe
Authors: Fonseca Susana C , Rivas Ioar , Romaguera Dora , Quijal Marcos , Czarlewski Wienczyslawa , Vidal Alain , Fonseca Joao A , Ballester Joan , Anto Josep M , Basagana Xavier , Cunha Luis M , Bousquet Jean
Published: July 2020

Background

Many foods have an antioxidant activity and nutrition may mitigate COVID-19. Some of the countries with a low COVID-19 mortality are those with a relatively high consumption of traditional fermented foods. To test the potential role of fermented foods in COVID-19 mortality in Europe, we performed an ecological study.

Methods

The European Food Safety Authority (EFSA) Comprehensive European Food Consumption Database was used to study the country consumption of fermented vegetables, pickled/marinated vegetables, fermented milk, yoghurt and fermented sour milk. We obtained the COVID-19 mortality per number of inhabitants from the Johns Hopkins Coronavirus Resource Center. EuroStat data were used for data on potential confounders at the country level including Gross Domestic Product (GDP) (2019), population density (2018), percentage of people older than 64 years (2019), unemployment rate (2019) and percentage obesity (2014, to avoid missing values). Mortality counts were analyzed with quasi-Poisson regression models - with log of population as an offset - to model the death rate while accounting for over-dispersion.

Results

Of all the variables considered, including confounders, only fermented vegetables reached statistical significance with the COVID-19 death rate per country. For each g/day increase in the average national consumption of fermented vegetables, the mortality risk for COVID-19 decreased by 35.4% (95% CI: 11.4%, 35.5%). Adjustment did not change the point estimate and results were still significant.

Discussion

The negative ecological association between COVID-19 mortality and consumption of fermented vegetables supports the a priory hypothesis previously reported. The hypothesis needs to be tested in individual studies performed in countries where the consumption of fermented vegetables is common.
The relative power of individual distancing efforts and public policies to curb the COVID-19 epidemics*
Authors: Aubert Cécile , Augeraud-Véron Emmanuelle
Published: July 2020

Lockdown curbs the COVID-19 epidemics but at huge costs. Public debates question its impact compared with reliance on individual responsibility. We aim at understanding how rationally chosen self-protective behavior impacts the spread of the epidemics. We want to, first, assess the value of lockdown compared to a counterfactual that incorporates self-protection efforts under unknown disease prevalence; and second, assess how individual behavior modify the epidemic dynamics when mandatory policies are relaxed. We couple an SLIAR model, that includes asymptomatic transmission, with utility maximization: Individuals trade off economic and wellbeing costs from physical distancing with a lower infection risk. Effort depends on risk aversion, perceptions, and the value of contacts. In a Nash equilibrium, individual uncoordinated efforts yield average contact intensity, which drives epidemic transmission. Equilibrium effort differs markedly from constant, stochastic or proportional contacts reduction. It adjusts to reported cases in a way that creates a slightly decreasing plateau in epidemic prevalence. Calibration on French data shows that the number of deaths with no lockdown but equilibrium efforts is only 1/6 to 1/10 of the number predicted with business-as-usual. However, lockdown saves at least 50% more lives than individual efforts alone. Prolonged weaker restrictions prevent an exponential rebound. Public policies post-lockdown have a limited impact as they partly crowd out individual efforts. Compulsory mask wearing helps resume activity but has no impact on the epidemic. Communication that increases risk salience is more effective.