scholarly journals Temporal Dynamics of Wheat Blast Epidemics and Disease Measurements Using Multispectral Imagery

2020 ◽  
Vol 110 (2) ◽  
pp. 393-405 ◽  
Author(s):  
C. Gongora-Canul ◽  
J. D. Salgado ◽  
D. Singh ◽  
A. P. Cruz ◽  
L. Cotrozzi ◽  
...  
Keyword(s):  
Field Experiments ◽  
Temporal Dynamics ◽  
Logistic Models ◽  
Correlation Coefficients ◽  
Host Population ◽  
Multispectral Imagery ◽  
Susceptible Host ◽  
Wheat Blast ◽  
Accuracy And Precision ◽  
Over Time

Wheat blast is a devastating disease caused by the Triticum pathotype of Magnaporthe oryzae. M. oryzae Triticum is capable of infecting leaves and spikes of wheat. Although symptoms of wheat spike blast (WSB) are quite distinct in the field, symptoms on leaves (WLB) are rarely reported because they are usually inconspicuos. Two field experiments were conducted in Bolivia to characterize the change in WLB and WSB intensity over time and determine whether multispectral imagery can be used to accurately assess WSB. Disease progress curves (DPCs) were plotted from WLB and WSB data, and regression models were fitted to describe the nature of WSB epidemics. WLB incidence and severity changed over time; however, the mean WLB severity was inconspicuous before wheat began spike emergence. Overall, both Gompertz and logistic models helped to describe WSB intensity DPCs fitting classic sigmoidal shape curves. Lin’s concordance correlation coefficients were estimated to measure agreement between visual estimates and digital measurements of WSB intensity and to estimate accuracy and precision. Our findings suggest that the change of wheat blast intensity in a susceptible host population over time does not follow a pattern of a monocyclic epidemic. We have also demonstrated that WSB severity can be quantified using a digital approach based on nongreen pixels. Quantification was precise (0.96 < r> 0.83) and accurate (0.92 < ρ > 0.69) at moderately low to high visual WSB severity levels. Additional sensor-based methods must be explored to determine their potential for detection of WLB and WSB at earlier stages.

scholarly journals Epidemiological Criteria to Support Breeding Tactics Against the Emerging, High-Consequence Wheat Blast Disease

Plant Disease ◽  
2020 ◽  
Vol 104 (8) ◽  
pp. 2252-2261 ◽  
Author(s):  
M. Fernández-Campos ◽  
C. Góngora-Canul ◽  
S. Das ◽  
M. R. Kabir ◽  
B. Valent ◽  
...  
Keyword(s):  
Field Experiments ◽  
Temporal Dynamics ◽  
Blast Disease ◽  
Disease Progress Curve ◽  
Disease Progress ◽  
Wheat Blast ◽  
Progress Curve ◽  
Cultivar Selection ◽  
Different Levels ◽  
Epidemiological Parameters

Plant disease epidemiology can make a significant contribution for cultivar selection by elucidating the principles of an epidemic under different levels of resistance. For emerging diseases as wheat blast (WB), epidemiological parameters can provide support for better selection of genetic resources. Field experiments were conducted at two locations in Bolivia in 2018–2019 to characterize the temporal dynamics of the disease on 10 cultivars with different levels of reaction to WB. Logistic models best (R2 = 0.70–0.96) fit the disease progress curve in all cultivars followed by Gompertz (R2 = 0.64–0.94), providing additional evidence of a polycyclic disease. Total area under disease progress curve (tAUDPC), final disease severity (Ymax), and logistic apparent infection rates (rL*) were shown to be appropriate epidemiological parameters for describing resistance and cultivar selection. Cultivars that showed a high spike AUDPC (sAUDPC) showed a high leaf AUDPC (lAUDPC). tAUPDC, Ymax, and rL* were positively correlated among them (P < 0.01) and all were negatively correlated with grain weight (P < 0.01). Based on the epidemiological parameters used, cultivars that showed resistance to WB were Urubó, San Pablo, and AN-120, which were previously reported to have effective resistance against the disease under field conditions. The information generated could help breeding programs to make technical decisions about relevant epidemiological parameters to consider prior to cultivar release.

scholarly journals Acute symptoms of mild to moderate COVID-19 are highly heterogeneous across individuals and over time

2021 ◽  
Author(s):  
Thomas L Rodebaugh ◽  
Madelyn R Frumkin ◽  
Angela M Reiersen ◽  
Eric J Lenze ◽  
Michael S Avidan ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Survey Methods ◽  
Clinical Care ◽  
Clinical Deterioration ◽  
Symptom Profiles ◽  
Fluctuating Course ◽  
The Common ◽  
Symptom Changes ◽  
Over Time

Abstract Background The symptoms of COVID-19 appear to be heterogenous, and the typical course of these symptoms is unknown. Our objectives were to characterize the common trajectories of COVID-19 symptoms and assess how symptom course predicts other symptom changes as well as clinical deterioration. Methods 162 participants with acute COVID-19 responded to surveys up to 31 times for up to 17 days. Several statistical methods were used to characterize the temporal dynamics of these symptoms. Because nine participants showed clinical deterioration, we explored whether these participants showed any differences in symptom profiles. Results Trajectories varied greatly between individuals, with many having persistently severe symptoms or developing new symptoms several days after being diagnosed. A typical trajectory was for a symptom to improve at a decremental rate, with most symptoms still persisting to some degree at the end of the reporting period. The pattern of symptoms over time suggested a fluctuating course for many patients. Participants who showed clinical deterioration were more likely to present with higher reports of severity of cough and diarrhea. Conclusion The course of symptoms during the initial weeks of COVID-19 is highly heterogeneous and is neither predictable nor easily characterized using typical survey methods. This has implications for clinical care and early-treatment clinical trials. Additional research is needed to determine whether the decelerating improvement pattern seen in our data is related to the phenomenon of patients reporting long-term symptoms, and whether higher symptoms of diarrhea in early illness presages deterioration.

scholarly journals Longitudinal Patterns of Ethical Organisational Culture as a Context for Leaders’ Well-Being: Cumulative Effects Over 6 Years

2021 ◽  
Author(s):  
Mari Huhtala ◽  
Muel Kaptein ◽  
Joona Muotka ◽  
Taru Feldt
Keyword(s):  
Latent Profile Analysis ◽  
Temporal Dynamics ◽  
Ethical Dilemmas ◽  
Extended Period ◽  
Well Being ◽  
Organisational Culture ◽  
Cumulative Effects ◽  
Ethical Culture ◽  
Continuous Increase ◽  
Over Time

AbstractThe aim of this longitudinal study was to investigate the temporal dynamics of ethical organisational culture and how it associates with well-being at work when potential changes in ethical culture are measured over an extended period of 6 years. We used a person-centred study design, which allowed us to detect both typical and atypical patterns of ethical culture stability as well as change among a sample of leaders. Based on latent profile analysis and hierarchical linear modelling we found longitudinal, concurrent relations and cumulative gain and loss cycles between different ethical culture patterns and leaders’ well-being. Leaders in the strongest ethical culture pattern experienced the highest level of work engagement and a decreasing level of ethical dilemmas and stress. Leaders who gave the lowest ratings on ethical culture which also decreased over time reported the highest level of ethical dilemmas, stress, and burnout. They also showed a continuous increase in these negative outcomes over time. Thus, ethical culture has significant cumulative effects on well-being, and these longitudinal effects can be both negative and positive, depending on the experienced strength of the culture’s ethicality.

scholarly journals 520. Longitudinal Analysis of SARS-CoV-2 Viruses in Hospitalized Adults

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S325-S326
Author(s):  
Lacy Simons ◽  
Ramon Lorenzo-Redondo ◽  
Hannah Nam ◽  
Scott C Roberts ◽  
Michael G Ison ◽  
...  
Keyword(s):  
Viral Load ◽  
Genome Sequencing ◽  
Viral Genome ◽  
Temporal Dynamics ◽  
Population Level ◽  
Hospital Staff ◽  
Therapeutic Interventions ◽  
Viral Loads ◽  
Qrt Pcr ◽  
Over Time

Abstract Background The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of viral mutations, some of which may have distinct virological and clinical consequences. While whole genome sequencing efforts have worked to map this viral diversity at the population level, little is known about how SARS-CoV-2 may diversify within a host over time. This is particularly important for understanding the emergence of viral resistance to therapeutic interventions and immune pressure. The goal of this study was to assess the change in viral load and viral genome sequence within patients over time and determine if these changes correlate with clinical and/or demographic parameters. Methods Hospitalized patients admitted to Northwestern Memorial Hospital with a positive SARS-CoV-2 test were enrolled in a longitudinal study for the serial collection of nasopharyngeal specimens. Swabs were administered to patients by hospital staff every 4 ± 1 days for up to 32 days or until the patients were discharged. RNA was extracted from each specimen and viral loads were calculated by quantitative reverse transcriptase PCR (qRT-PCR). Specimens with qRT-PCR cycle threshold values less than or equal to 30 were subject to whole viral genome sequencing by reverse transcription, multiplex PCR, and deep sequencing. Variant populations sizes were estimated and subject to phylogenetic analysis relative to publicly available SARS-CoV-2 sequences. Sequence and viral load data were subsequently correlated to available demographic and clinical data. Results 60 patients were enrolled from March 26th to June 20th, 2020. We observed an overall decrease in nasopharyngeal viral load over time across all patients. However, the temporal dynamics of viral load differed on a patient-by-patient basis. Several mutations were also observed to have emerged within patients over time. Distribution of SARS-CoV-2 viral loads in serially collected nasopharyngeal swabs in hospitalized adults as determined by qRT-PCR. Samples were collected every 4 ± 1 days (T#1–8) and viral load is displayed by log(copy number). Conclusion These data indicate that SARS-CoV-2 viral loads in the nasopharynx decrease over time and that the virus can accumulate mutations during replication within individual patients. Future studies will examine if some of these mutations may provide fitness advantages in the presence of therapeutic and/or immune selective pressures. Disclosures Michael G. Ison, MD MS, AlloVir (Consultant)

scholarly journals Reliability and Change in Erosion Measurements by High-Resolution peripheral Quantitative Computed Tomography in a Longitudinal Dataset of Rheumatoid Arthritis Patients

2020 ◽  
pp. jrheum.191391 ◽  
Author(s):  
Stephanie Finzel ◽  
Sarah L. Manske ◽  
Cheryl Barnabe ◽  
Andrew J. Burghardt ◽  
Hubert Marotte ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Computed Tomography ◽  
High Resolution ◽  
Intraclass Correlation ◽  
Quantitative Computed Tomography ◽  
Correlation Coefficients ◽  
Peripheral Quantitative Computed Tomography ◽  
Good Reliability ◽  
Change Over Time ◽  
Over Time

Objective The aim of this multi-reader exercise was to assess the reliability and change over time of erosion measurements in rheumatoid arthritis (RA) patients using high-resolution peripheral quantitative computed tomography (HR-pQCT). Methods HR-pQCT scans of 23 patients with RA were assessed at baseline and 12 months. Four experienced readers examined the dorsal, palmar, radial, and ulnar surfaces of the metacarpal head (MH) and phalangeal base (PB) of the 2nd and 3rd digits, blinded to time order. In total, 368 surfaces (23 patients x16 surfaces) were evaluated per time point to characterize cortical breaks as pathological (erosion) or physiological, and to quantify erosion width and depth. Reliability was evaluated by intraclass correlation coefficients (ICC), percentage agreement, and Light’s kappa; change over time was defined by means ± SD of erosion numbers and dimensions. Results ICCs for the mean measurements of width and depth of the pathological breaks ranged between 0.819 - 0.883, and 0.771 - 0.907 respectively. Most physiological cortical breaks were found at the palmar PB, whereas most pathological cortical breaks were located at the radial MH. There was a significant increase in both the numbers and the dimensions of erosions between baseline and follow-up (p=0.0001 for erosion numbers, width, and depth in axial plane, and p=0.001 for depth in perpendicular plane). Conclusion This exercise confirmed good reliability of HR-pQCT erosion measurements and their ability to detect change over time.

scholarly journals Bayesian modeling and prediction of accrual in multi-regional clinical trials

2014 ◽  
Vol 26 (2) ◽  
pp. 752-765 ◽  
Author(s):  
Yi Deng ◽  
Xiaoxi Zhang ◽  
Qi Long
Keyword(s):  
Clinical Trials ◽  
Poisson Process ◽  
Process Model ◽  
Nonhomogeneous Poisson Process ◽  
Modeling And Prediction ◽  
Accuracy And Precision ◽  
Start Up ◽  
Accrual Rate ◽  
Model Region ◽  
Over Time

In multi-regional trials, the underlying overall and region-specific accrual rates often do not hold constant over time and different regions could have different start-up times, which combined with initial jump in accrual within each region often leads to a discontinuous overall accrual rate, and these issues associated with multi-regional trials have not been adequately investigated. In this paper, we clarify the implication of the multi-regional nature on modeling and prediction of accrual in clinical trials and investigate a Bayesian approach for accrual modeling and prediction, which models region-specific accrual using a nonhomogeneous Poisson process and allows the underlying Poisson rate in each region to vary over time. The proposed approach can accommodate staggered start-up times and different initial accrual rates across regions/centers. Our numerical studies show that the proposed method improves accuracy and precision of accrual prediction compared to existing methods including the nonhomogeneous Poisson process model that does not model region-specific accrual.

scholarly journals Using airborne HIAPER Pole-to-Pole Observations (HIPPO) to evaluate model and remote sensing estimates of atmospheric carbon dioxide

2016 ◽  
Author(s):  
C. Frankenberg ◽  
S. S. Kulawik ◽  
S. Wofsy ◽  
F. Chevallier ◽  
B. Daube ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Atmospheric Carbon Dioxide ◽  
Correlation Coefficients ◽  
Added Value ◽  
Total Carbon ◽  
Accuracy And Precision ◽  
Atmospheric Carbon ◽  
Carbon Dioxide Co2 ◽  
Global Carbon ◽  
Comparable Quality

Abstract. In recent years, space-borne observations of atmospheric carbon-dioxide (CO2) have become increasingly used in global carbon-cycle studies. In order to obtain added value from space-borne measurements, they have to suffice stringent accuracy and precision requirements, with the latter being less crucial as it can be reduced by just enhanced sample size. Validation of CO2 column averaged dry air mole fractions (XCO2) heavily relies on measurements of the Total Carbon Column Observing Network TCCON. Owing to the sparseness of the network and the requirements imposed on space-based measurements, independent additional validation is highly valuable. Here, we use observations from the HIAPER Pole-to-Pole Observations (HIPPO) flights from January 2009 through September 2011 to validate CO2 measurements from satellites (GOSAT, TES, AIRS) and atmospheric inversion models (CarbonTracker CT2013B, MACC v13r1). We find that the atmospheric models capture the XCO2 variability observed in HIPPO flights very well, with correlation coefficients (r2) of 0.93 and 0.95 for CT2013B and MACC, respectively. Some larger discrepancies can be observed in profile comparisons at higher latitudes, esp. at 300 hPa during the peaks of either carbon uptake or release. These deviations can be up to 4 ppm and hint at misrepresentation of vertical transport. Comparisons with the GOSAT satellite are of comparable quality, with an r2 of 0.85, a mean bias μ of −0.06 ppm and a standard deviation σ of 0.45 ppm. TES exhibits an r2 of 0.75, μ of 0.34 ppm and σ of 1.13 ppm. For AIRS, we find an r2 of 0.37, μ of 1.11 ppm and σ of 1.46 ppm, with latitude-dependent biases. For these comparisons at least 6, 20 and 50 atmospheric soundings have been averaged for GOSAT, TES and AIRS, respectively. Overall, we find that GOSAT soundings over the remote pacific ocean mostly meet the stringent accuracy requirements of about 0.5 ppm for space-based CO2 observations.

scholarly journals Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

2021 ◽  
Vol 11 ◽  
Author(s):  
Janneke Schreuder ◽  
Francisca C. Velkers ◽  
Alex Bossers ◽  
Ruth J. Bouwstra ◽  
Willem F. de Boer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Intestinal Microbiota ◽  
Environmental Changes ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Sudden Change ◽  
Rrna Gene ◽  
Poultry House ◽  
Over Time

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

scholarly journals Genetic variability of rye-xenic-hybrid traits

2014 ◽  
Vol 65 (3-4) ◽  
pp. 329-333 ◽  
Author(s):  
Lechosław Grochowski ◽  
Jan Kaczmarek ◽  
Władysław Kadłubiec ◽  
Henryk Bujak
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Plant Height ◽  
Combining Ability ◽  
Field Experiments ◽  
Correlation Coefficients ◽  
Winter Rye ◽  
Arithmetic Means ◽  
Coefficients Of Variation ◽  
Standard Cultivar

In field experiments performed in two localities (Smolice, Wrocław) 18 xenic hybrids of winter rye, two testers and standard cultivar Dańkowskie Złote, were analysed. The objects of detailed evaluations were 11 traits. For six of them arithmetic means (x), standard deviations (S), coefficients of variation (cv), coefficients of genetic diversity (h<sup>2</sup>), correlation coefficients were calculated. Moreover, analyses of variance were carried out and the effects of general (GCA) and specific (SCA) combining ability were estimated. The existence of quantitative xenia in hybrids was confirmed. It was shown that xenic hybrids, in respect to most of the analysed traits, were insignificantly inferior to the testers and the standard cultivar. However, the decrease of plant height has shown to be significant and a tendency to higher yield was observed.

scholarly journals Quantifying the relationship between lockdowns, mobility, and effective reproduction number (Rt) during the COVID-19 pandemic in the Greater Toronto Area

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Christopher Dainton ◽  
Alexander Hay
Keyword(s):  
Public Health ◽  
Secular Trend ◽  
Reproduction Number ◽  
Time Lag ◽  
Correlation Coefficients ◽  
Greater Toronto Area ◽  
Global Mobility ◽  
The Relationship ◽  
Second Wave ◽  
Over Time

Abstract Background The effectiveness of lockdowns in mitigating the spread of COVID-19 has been the subject of intense debate. Data on the relationship between public health restrictions, mobility, and pandemic growth has so far been conflicting. Objective We assessed the relationship between public health restriction tiers, mobility, and COVID-19 spread in five contiguous public health units (PHUs) in the Greater Toronto Area (GTA) in Ontario, Canada. Methods Weekly effective reproduction number (Rt) was calculated based on daily cases in each of the five GTA public health units between March 1, 2020, and March 19, 2021. A global mobility index (GMI) for each PHU was calculated using Google Mobility data. Segmented regressions were used to assess changes in the behaviour of Rt over time. We calculated Pearson correlation coefficients between GMI and Rt for each PHU and mobility regression coefficients for each mobility variable, accounting for time lag of 0, 7, and 14 days. Results In all PHUs except Toronto, the most rapid decline in Rt occurred in the first 2 weeks of the first province-wide lockdown, and this was followed by a slight trend to increased Rt as restrictions decreased. This trend reversed in all PHUs between September 6th and October 10th after which Rt decreased slightly over time without respect to public health restriction tier. GMI began to increase in the first wave even before restrictions were decreased. This secular trend to increased mobility continued into the summer, driven by increased mobility to recreational spaces. The decline in GMI as restrictions were reintroduced coincides with decreasing mobility to parks after September. During the first wave, the correlation coefficients between global mobility and Rt were significant (p < 0.01) in all PHUs 14 days after lockdown, indicating moderate to high correlation between decreased mobility and decreased viral reproduction rates, and reflecting that the incubation period brings in a time-lag effect of human mobility on Rt. In the second wave, this relationship was attenuated, and was only significant in Toronto and Durham at 14 days after lockdown. Conclusions The association between mobility and COVID-19 spread was stronger in the first wave than the second wave. Public health restriction tiers did not alter the existing secular trend toward decreasing Rt over time.

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