scholarly journals Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

2021 ◽  
Vol 17 (4) ◽  
pp. e1009499
Author(s):  
Andrew L. Valesano ◽  
Kalee E. Rumfelt ◽  
Derek E. Dimcheff ◽  
Christopher N. Blair ◽  
William J. Fitzsimmons ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Medical Center ◽  
Variant Calling ◽  
Critical Factor ◽  
Global Consensus ◽  
Temporal Aspects ◽  
Host Genetic ◽  
Insight Into ◽  
High Depth ◽  
Variant Identification

Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified viral load as a critical factor in variant identification. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.

scholarly journals Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

2021 ◽  
Author(s):  
Andrew L. Valesano ◽  
Kalee E. Rumfelt ◽  
Derek E. Dimcheff ◽  
Christopher N. Blair ◽  
William J. Fitzsimmons ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Temporal Dynamics ◽  
Medical Center ◽  
Variant Calling ◽  
Global Consensus ◽  
Temporal Aspects ◽  
Host Genetic ◽  
Insight Into ◽  
High Depth ◽  
Shared Variation

AbstractAnalysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.

Permutation Min-Entropy and Statistical Complexity Analysis of Electricity Spot Price

2015 ◽  
Vol 14 (04) ◽  
pp. 1550040 ◽  
Author(s):  
Qingju Fan ◽  
Dan Li
Keyword(s):  
Temporal Dynamics ◽  
Complexity Analysis ◽  
Spot Price ◽  
Temporal Correlations ◽  
Price Series ◽  
Statistical Complexity ◽  
Electricity Spot Price ◽  
Insight Into ◽  
Refined Classification

In this study, we investigate the subtle temporal dynamics of California 1999–2000 spot price series based on permutation min-entropy (PME) and complexity-entropy causality plane. The dynamical transitions of price series are captured and the temporal correlations of price series are also discriminated by the recently introduced PME. Moreover, utilizing the CECP, we provide a refined classification of the monthly price dynamics and obtain an insight into the stochastic nature of price series. The results uncover that the spot price signal presents diverse temporal correlations and exhibits a higher stochastic behavior during the periods of crisis.

scholarly journals Current perspective on production and applications of microbial cellulases: a review

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Nisha Bhardwaj ◽  
Bikash Kumar ◽  
Komal Agrawal ◽  
Pradeep Verma
Keyword(s):  
Critical Factor ◽  
Industrial Sector ◽  
Industrial Applications ◽  
Cellulolytic Enzymes ◽  
Promising Tool ◽  
The Status ◽  
Key Enzyme ◽  
Increasing Demand ◽  
Immobilization Techniques ◽  
Insight Into

AbstractThe potential of cellulolytic enzymes has been widely studied and explored for bioconversion processes and plays a key role in various industrial applications. Cellulase, a key enzyme for cellulose-rich waste feedstock-based biorefinery, has increasing demand in various industries, e.g., paper and pulp, juice clarification, etc. Also, there has been constant progress in developing new strategies to enhance its production, such as the application of waste feedstock as the substrate for the production of individual or enzyme cocktails, process parameters control, and genetic manipulations for enzyme production with enhanced yield, efficiency, and specificity. Further, an insight into immobilization techniques has also been presented for improved reusability of cellulase, a critical factor that controls the cost of the enzyme at an industrial scale. In addition, the review also gives an insight into the status of the significant application of cellulase in the industrial sector, with its techno-economic analysis for future applications. The present review gives a complete overview of current perspectives on the production of microbial cellulases as a promising tool to develop a sustainable and greener concept for industrial applications.

scholarly journals Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference

2019 ◽  
Author(s):  
Katharine S. Walter ◽  
Caroline Colijn ◽  
Ted Cohen ◽  
Barun Mathema ◽  
Qingyun Liu ◽  
...  
Keyword(s):  
Sequence Data ◽  
Variant Calling ◽  
Genomic Variation ◽  
Human Pathogens ◽  
Phylogenetic Structure ◽  
Genomic Epidemiology ◽  
Tuberculosis Transmission ◽  
Epidemiology Studies ◽  
Global And Local ◽  
Variant Identification

AbstractPathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet there is no current consensus on how to measure genomic variation. We investigated the effects of variant identification approaches on transmission inferences for M. tuberculosis by comparing variants identified by five different groups in the same sequence data from a clonal outbreak. We then measured the performance of commonly used variant calling approaches in recovering variation in a simulated tuberculosis outbreak and tested the effect of applying increasingly stringent filters on transmission inferences and phylogenies. We found that variant calling approaches used by different groups do not recover consistent sets of variants, often leading to conflicting transmission inferences. Further, performance in recovering true outbreak variation varied widely across approaches. Finally, stringent filters rapidly eroded the accuracy of transmission inferences and quality of phylogenies reconstructed from outbreak variation. We conclude that measurements of genetic distance and phylogenetic structure are dependent on variant calling approach. Variant calling algorithms trained upon true sequence data outperform other approaches and enable inclusion of repetitive regions typically excluded from genomic epidemiology studies, maximizing the information gleaned from outbreak genomes.

scholarly journals Testing Whether Suicide Capability Has a Dynamic Propensity: The Role of Affect and Arousal on Momentary Fluctuations in Suicide Capability

2021 ◽  
Vol 12 ◽  
Author(s):  
Keyne C. Law ◽  
Michael D. Anestis
Keyword(s):  
Suicide Risk ◽  
Pain Threshold ◽  
Temporal Dynamics ◽  
Critical Factor ◽  
Pain Tolerance ◽  
Affective States ◽  
Before And After ◽  
Core Components ◽  
Main Effects

To prevent suicidal behaviors, it is crucial to understand the mechanisms and processes that enable an individual to act on suicidal thoughts. Suicide capability, which involves an increased pain tolerance and fearlessness of death, is a critical factor that enables an individual to endure the physical pain necessary to make a lethal suicide attempt. Extant research has largely conceptualized suicide capability as developing linearly in response to painful and provocative experiences, but the emerging literature on the temporal dynamics of suicide has been challenging the notion of linearity in suicide risk. Few studies have directly measured and compared changes in suicide capability in response to rumination on different affective states. We sought to experimentally test if rumination in the context of low vs. high arousal emotions will prompt distinct changes in two core components of suicide capability: pain tolerance and fearlessness of death on two undergraduate student samples. In both studies, participants provided measures of subjective emotional state as well as pain threshold, tolerance, and persistence before and after completing experimental manipulations which included both emotion and rumination induction procedures. In the second study, measures of fearlessness about death and physiological arousal (heart rate) were added to the experimental procedures. We found significant decreases in pain threshold, tolerance, and persistence following the experimental manipulations but found no main effects of rumination or suicide risk. These findings suggest that suicide capability can fluctuate but these changes may occur through a different mechanism and/or differ between individuals at varying levels of suicide risk.

scholarly journals Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing

2021 ◽  
Vol 22 (19) ◽  
pp. 10400
Author(s):  
H. Busra Cagirici ◽  
Bala Ani Akpinar ◽  
Taner Z. Sen ◽  
Hikmet Budak
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Variant Calling ◽  
High Sensitivity ◽  
Whole Exome ◽  
The Impact ◽  
Multiple Reference ◽  
Reference Genomes ◽  
Selection Of ◽  
Variant Identification

The highly challenging hexaploid wheat (Triticum aestivum) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. Although the process of variant calling is relatively straightforward, selection of the best combination of the computational tools for read alignment and variant calling stages of the analysis and efficient filtering of the false variant calls are not always easy tasks. Previous studies have analyzed the impact of methods on the quality metrics in diploid organisms. Given that variant identification in wheat largely relies on accurate mining of exome data, there is a critical need to better understand how different methods affect the analysis of whole exome sequencing (WES) data in polyploid species. This study aims to address this by performing whole exome sequencing of 48 wheat cultivars and assessing the performance of various variant calling pipelines at their suggested settings. The results show that all the pipelines require filtering to eliminate false-positive calls. The high consensus among the reference SNPs called by the best-performing pipelines suggests that filtering provides accurate and reproducible results. This study also provides detailed comparisons for high sensitivity and precision at individual and population levels for the raw and filtered SNP calls.

scholarly journals Exponentially decaying modes and long-term prediction of sea ice concentration using Koopman mode decomposition

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
James Hogg ◽  
Maria Fonoberova ◽  
Igor Mezić
Keyword(s):  
Sea Ice ◽  
Annual Variation ◽  
Temporal Dynamics ◽  
The Arctic ◽  
Sea Ice Concentration ◽  
Mode Decomposition ◽  
Spatial Modes ◽  
Ice Concentration ◽  
The Mean ◽  
Insight Into

Abstract Sea ice cover in the Arctic and Antarctic is an important indicator of changes in the climate, with important environmental, economic and security consequences. The complexity of the spatio-temporal dynamics of sea ice makes it difficult to assess the temporal nature of the changes—e.g. linear or exponential—and their precise geographical loci. In this study, Koopman Mode Decomposition (KMD) is applied to satellite data of sea ice concentration for the Northern and Southern hemispheres to gain insight into the temporal and spatial dynamics of the sea ice behavior and to predict future sea ice behavior. We observe spatial modes corresponding to the mean and annual variation of Arctic and Antarctic sea ice concentration and observe decreases in the mean sea ice concentration from early to later periods, as well as corresponding shifts in the locations that undergo significant annual variation in sea ice concentration. We discover exponentially decaying spatial modes in both hemispheres and discuss their precise spatial extent, and also perform predictions of future sea ice concentration. The Koopman operator-based, data-driven decomposition technique gives insight into spatial and temporal dynamics of sea ice concentration not apparent in traditional approaches.

scholarly journals Nurses' Experiences of Caring for Older Persons in Transition to Receive Homecare: Being Somewhere in between Competing Values

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Sigrun Hvalvik ◽  
Bjørg Dale
Keyword(s):  
Older Persons ◽  
Critical Factor ◽  
Transition Process ◽  
Competing Values ◽  
Life World ◽  
Professional Care ◽  
Excellent Care ◽  
To Receive ◽  
Insight Into ◽  
Independent Individual

Older persons in transition to need professional care in their homes will constitute a large group in municipalities in the future. The aim of this study was to obtain insight into nurses' experiences and perceptions of caring for patients in transition to receive homecare. Eleven home nurses divided into two focus groups were interviewed, and a phenomenological hermeneutical design was used. Four interpretations closely related to each other were revealed: it is essential to have an understanding of the patients' transition history; the nurse' repertoire is challenged in the transition process; care must be adapted to the patients' life world; the excellence of care is threatened by the context. The nurses strived to provide care based upon respect for the independent individual as a living whole. Their ambitions were, however, challenged and threatened by the caring context. The cooperation across organizational levels was pointed out as a critical factor with potential for improvement. This must be taken seriously to support the nurses in their endeavors to provide excellent care.

Strengthening reliability in high hazard industries: reconciling tensions for impact

2014 ◽  
Vol 29 (2) ◽  
pp. 125-145 ◽  
Author(s):  
Evan H. Offstein ◽  
Raymond Kniphuisen ◽  
D. Robin Bichy ◽  
J. Stephen Childers Jr
Keyword(s):  
Phenomenological Study ◽  
High Reliability ◽  
Critical Factor ◽  
High Reliability Organizations ◽  
Content Type ◽  
Significant Damage ◽  
High Hazard ◽  
Complex Phenomena ◽  
Practical Implications ◽  
Insight Into

Purpose – Recent lapses in the management of high hazard organizations, such as the Fukushima event or the Deepwater Horizon blast, add considerable urgency to better understand the complicated and complex phenomena of leading and managing high reliability organizations (HRO). The purpose of this paper is to offer both theoretical and practical insight to further strengthen reliability in high hazard organizations. Design/methodology/approach – Phenomenological study based on over three years of research and thousands of hours of study in HROs conducted through a scholar-practitioner partnership. Findings – The findings indicate that the identification and the management of competing tensions arising from misalignment within and between public policy, organizational strategy, communication, decision-making, organizational learning, and leadership is the critical factor in explaining improved reliability and safety of HROs. Research limitations/implications – Stops short of full-blown grounded theory. Steps were made to ensure validity; however, generalizability may be limited due to sample. Practical implications – Provides insight into reliably operating organizations that are crucial to society where errors would cause significant damage or loss. Originality/value – Extends high reliability research by investigating more fully the competing tensions present in these complex, societally crucial organizations.

scholarly journals Genomic Comparisons of Lactobacillus crispatus and Lactobacillus iners Reveal Potential Ecological Drivers of Community Composition in the Vagina

2016 ◽  
Vol 82 (24) ◽  
pp. 7063-7073 ◽  
Author(s):  
Michael T. France ◽  
Helena Mendes-Soares ◽  
Larry J. Forney
Keyword(s):  
Temporal Dynamics ◽  
Critical Role ◽  
Niche Overlap ◽  
Vaginal Microbiome ◽  
Niche Space ◽  
Healthy Human ◽  
Content Type ◽  
Lactobacillus Crispatus ◽  
Human Vagina ◽  
Insight Into

ABSTRACTLactobacillus crispatusandLactobacillus inersare common inhabitants of the healthy human vagina. These two species are closely related and are thought to perform similar ecological functions in the vaginal environment. Temporal data on the vaginal microbiome have shown that nontransient instances of cooccurrence are uncommon, while transitions from anL. iners-dominated community to one dominated byL. crispatus, and vice versa, occur often. This suggests that there is substantial overlap in the fundamental niches of these species. Given this apparent niche overlap, it is unclear how they have been maintained as common inhabitants of the human vagina. In this study, we characterized and compared the genomes ofL. inersandL. crispatusto gain insight into possible mechanisms driving the maintenance of this species diversity. Our results highlight differences in the genomes of these two species that may facilitate the partitioning of their shared niche space. Many of the identified differences may impact the protective benefits provided to the host by these two species.IMPORTANCEThe microbial communities that inhabit the human vagina play a critical role in the maintenance of vaginal health through the production of lactic acid and lowering the environmental pH. This precludes the growth of nonindigenous organisms and protects against infectious disease. The two most common types of vaginal communities are dominated by eitherLactobacillus inersorLactobacillus crispatus, while some communities alternate between the two over time. We combined ecological theory with state-of-the-art genome analyses to characterize how these two species might partition their shared niche space in the vagina. We show that the genomes ofL. inersandL. crispatusdiffer in many respects, several of which may drive differences in their competitive abilities in the vagina. Our results provide insight into factors that drive the complicated temporal dynamics of the vaginal microbiome and demonstrate how closely related microbial species partition shared fundamental niche space.

Sign in / Sign up

Export Citation Format

Share Document