scholarly journals New Interval-Specific Phylodynamic Models Improve Inference of the Geographic History of Disease Outbreaks

2021 ◽  
Author(s):  
Jiansi Gao ◽  
Michael R. May ◽  
Bruce Rannala ◽  
Brian R. Moore
Keyword(s):  
Temporal Dynamics ◽  
Disease Outbreaks ◽  
Simulated Data ◽  
Study Data ◽  
Parameter Estimates ◽  
Intervention Measures ◽  
History Of ◽  
Specific Variation ◽  
Key Aspects ◽  
Dispersal Events

Phylodynamic methods reveal the spatial and temporal dynamics of viral geographic spread, and have featured prominently in studies of the COVID-19 pandemic. Virtually all previous studies are based on phylodynamic models that assume—despite direct and compelling evidence to the contrary—that rates of viral geographic dispersal are constant through time. Here, we: (1) extend phylodynamic models to allow both the average and relative rates of viral dispersal to vary independently between pre-specified time intervals; (2) implement methods to infer the number and timing of viral dispersal events between areas; and (3) develop statistics to assess the absolute fit of phylodynamic models to empirical datasets. We first validate our new methods using analyses of simulated data, and then apply them to a SARS-CoV-2 dataset from the early phase of the COVID-19 pandemic. We show that: (1) under simulation, failure to accommodate interval-specific variation in the study data will severely bias parameter estimates; (2) in practice, our interval-specific phylodynamic models can significantly improve the relative and absolute fit to empirical data; and (3) the increased realism of our interval-specific phylodynamic models provides qualitatively different inferences regarding key aspects of the COVID-19 pandemic—revealing significant temporal variation in global viral dispersal rates, viral dispersal routes, and number of viral dispersal events between areas—and alters interpretations regarding the efficacy of intervention measures to mitigate the pandemic.

scholarly journals Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data

2020 ◽  
Vol 37 (7) ◽  
pp. 2124-2136
Author(s):  
Paul D Blischak ◽  
Michael S Barker ◽  
Ryan N Gutenkunst
Keyword(s):  
Puma Concolor ◽  
Demographic History ◽  
Random Mating ◽  
Simulated Data ◽  
Conservation Agriculture ◽  
Model Fit ◽  
Parameter Estimates ◽  
History Of ◽  
Demographic Inference ◽  
Inbred Populations

Abstract Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model’s ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.

scholarly journals Inferring the Demographic History of Inbred Species From Genome-Wide SNP Frequency Data

2019 ◽  
Author(s):  
Paul D. Blischak ◽  
Michael S. Barker ◽  
Ryan N. Gutenkunst
Keyword(s):  
Puma Concolor ◽  
Demographic History ◽  
Random Mating ◽  
Simulated Data ◽  
Conservation Agriculture ◽  
Model Fit ◽  
Parameter Estimates ◽  
History Of ◽  
Demographic Inference ◽  
Inbred Populations

AbstractDemographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model’s ability to co-estimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately co-estimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.

scholarly journals Exploring the spatio-temporal dynamics of geographical processes with geographically weighted regression and geovisual analytics

2008 ◽  
Vol 7 (3-4) ◽  
pp. 181-197 ◽  
Author(s):  
Urška Demšar ◽  
A. Stewart Fotheringham ◽  
Martin Charlton
Keyword(s):  
Geographically Weighted Regression ◽  
Temporal Dynamics ◽  
Simulated Data ◽  
Weighted Regression ◽  
Parameter Estimates ◽  
Data Set ◽  
Complex Processes ◽  
Regression Parameters ◽  
Geovisual Analytics ◽  
Spatio Temporal

The paper examines the potential for combining a spatial statistical methodology – Geographically Weighted Regression (GWR) – with geovisual analytical exploration to help understand complex spatio-temporal processes. This is done by applying the combined statistical – exploratory methodology to a simulated data set in which the behaviour of regression parameters was controlled across space and time. A variety of complex spatio-temporal processes was captured through space-time (i.e. as spatio-temporal) varying parameters whose values were known. The task was to see if the proposed methodology could uncover these complex processes from the data alone. The results of the experiment confirm that the combined methodology can successfully identify spatio-temporal patterns in the local GWR parameter estimates that correspond to the controlled behaviour of the original parameters.

scholarly journals Estimating Simultaneous Equation Models through an Entropy-Based Incremental Variational Bayes Learning Algorithm

Entropy ◽  
2021 ◽  
Vol 23 (4) ◽  
pp. 384
Author(s):  
Rocío Hernández-Sanjaime ◽  
Martín González ◽  
Antonio Peñalver ◽  
Jose J. López-Espín
Keyword(s):  
Statistical Theory ◽  
Learning Algorithm ◽  
Real Life ◽  
Simulated Data ◽  
Simultaneous Equation ◽  
Variational Bayes ◽  
Parameter Estimates ◽  
Step Method ◽  
The One ◽  
Simultaneous Equation Models

The presence of unaccounted heterogeneity in simultaneous equation models (SEMs) is frequently problematic in many real-life applications. Under the usual assumption of homogeneity, the model can be seriously misspecified, and it can potentially induce an important bias in the parameter estimates. This paper focuses on SEMs in which data are heterogeneous and tend to form clustering structures in the endogenous-variable dataset. Because the identification of different clusters is not straightforward, a two-step strategy that first forms groups among the endogenous observations and then uses the standard simultaneous equation scheme is provided. Methodologically, the proposed approach is based on a variational Bayes learning algorithm and does not need to be executed for varying numbers of groups in order to identify the one that adequately fits the data. We describe the statistical theory, evaluate the performance of the suggested algorithm by using simulated data, and apply the two-step method to a macroeconomic problem.

scholarly journals Genetic Architecture of a Morphological Shape Difference Between Two Drosophila Species

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 299-310 ◽  
Author(s):  
Zhao-Bang Zeng ◽  
Jianjun Liu ◽  
Lynn F Stam ◽  
Chen-Hung Kao ◽  
John M Mercer ◽  
...  
Keyword(s):  
Interval Mapping ◽  
Additive Effect ◽  
Parameter Estimates ◽  
Effect Estimate ◽  
Interspecific Difference ◽  
Posterior Lobe ◽  
Complete Dominance ◽  
Backcross Populations ◽  
History Of ◽  
Trait Locus

AbstractThe size and shape of the posterior lobe of the male genital arch differs dramatically between Drosophila simulans and D. mauritiana. This difference can be quantified with a morphometric descriptor (PC1) based on elliptical Fourier and principal components analyses. The genetic basis of the interspecific difference in PC1 was investigated by the application of quantitative trait locus (QTL) mapping procedures to segregating backcross populations. The parental difference (35 environmental standard deviations) and the heritability of PC1 in backcross populations (>90%) are both very large. The use of multiple interval mapping gives evidence for 19 different QTL. The greatest additive effect estimate accounts for 11.4% of the parental difference but could represent multiple closely linked QTL. Dominance parameter estimates vary among loci from essentially no dominance to complete dominance, and mauritiana alleles tend to be dominant over simulans alleles. Epistasis appears to be relatively unimportant as a source of variation. All but one of the additive effect estimates have the same sign, which means that one species has nearly all plus alleles and the other nearly all minus alleles. This result is unexpected under many evolutionary scenarios and suggests a history of strong directional selection acting on the posterior lobe.

scholarly journals Evaluation of whole-body modalities for diagnosis of multifocal osteonecrosis—a pilot study

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Shunichi Yokota ◽  
Keita Sakamoto ◽  
Yukie Shimizu ◽  
Tsuyoshi Asano ◽  
Daisuke Takahashi ◽  
...  
Keyword(s):  
Study Data ◽  
Whole Body ◽  
Hematologic Disease ◽  
Hip Joints ◽  
Patient Demographics ◽  
Examination Time ◽  
History Of ◽  
Body Magnetic Resonance Imaging ◽  
The Cost ◽  
Body Bone

Abstract Background This study aimed to investigate the ability of whole-body bone scintigraphy (WB-BS) in the detection of multifocal osteonecrosis (ON) compared to whole-body magnetic resonance imaging (WB-MRI) and to clarify the characteristics of patients with multifocal ON among those with ON of the femoral head (ONFH) using WB-MRI. Methods Forty-six patients who had symptomatic ONFH and underwent surgery in our hospital from April 2019 to October 2020 were included in the study. Data on patient demographics, including age, sex, body mass index (BMI), history of corticosteroid intake, alcohol abuse, smoking, and symptomatic joints, were collected from their medical records. All patients underwent WB-MRI and WB-BS before surgery. Results The agreement in the detection of ON by WB-MRI vs the uptake lesions by WB-BS in the hip joints was moderate (κ = 0.584), while that in other joints was low (κ < 0.40). Among the 152 joints with ON detected by WB-MRI, 92 joints (60.5%) were symptomatic, and 60 joints (39.5%) were asymptomatic. Twelve out of the 46 (26.0%) patients had multifocal (three or more distinct anatomical sites) ON. Nonetheless, while WB-BS detected symptomatic ON detected by WB-MRI as uptake lesions in 82.6% (76/92) of the joints, asymptomatic ON detected by WB-MRI was detected as uptake lesions in 21.7% (13/60) of the joints. All patients with multifocal ON had a history of steroid therapy, which was significantly higher than that in patients with oligofocal ON (P = 0.035). The patients with a hematologic disease had multifocal ON at a higher rate (P = 0.015). Conclusions It might be difficult for WB-BS to detect the asymptomatic ON detected by WB-MRI compared to symptomatic ON. Considering the cost, examination time, and radiation exposure, WB-MRI might be useful for evaluating multifocal ON. Larger longitudinal studies evaluating the benefits of WB-MRI for detecting the risk factors for multifocal ON are required.

Fear, history, stigma, and bias in the COVID-19 pandemic

2020 ◽  
Vol 18 (7) ◽  
pp. 177-182
Author(s):  
Kevin Kupietz, PhD ◽  
Lesley Gray, MPH
Keyword(s):  
Emergency Management ◽  
Disease Outbreaks ◽  
Social Effects ◽  
Evidence Based ◽  
Stigma And Discrimination ◽  
Emergency Managers ◽  
Global Pandemic ◽  
New Concepts ◽  
History Of ◽  
The Relationship

Introduction: The greatest enemy of a global pandemic is not the virus itself, but the fear, rumor, and stigma that envelopes people. This article explores the context and history of fear and stigma relating to pandemic, summarizing key actions to mitigate the harms during an active pandemic.Method: Our article draws from accounts in literature and journalist accounts documenting the relationship between infectious diseases and major disease outbreaks that have garnered fear and stigmatization. Results: Fear, stigma, and discrimination are not new concepts for pandemics. These social effects run the risk of diverting attention from the presenting disease and government responses. Reactions to fear, stigma, and discrimination risk sabotaging effective efforts to contain, manage, and eradicate the disease.Conclusion: Emergency managers have an important role in dispelling myths, disseminating appropriate and evidence-based information without exacerbating fears. Knowledge about the roots of fear and bias along with a good understanding of historical plagues and pandemics is vital to ensure those in the field of emergency management can effectively manage irrational fears.

HISTORIOGRAPHY OF HISTORY OF THE STAVROPOL COSSACKS: KEY ASPECTS OF STUDYING THE REGIONAL COSSACK GROUP’S PAST

2021 ◽  
pp. 50-62
Author(s):  
K.A. Ushmaeva ◽  
◽  
A.S. Goncharov
Keyword(s):  
Comparative Method ◽  
Educational Institution ◽  
Practical Significance ◽  
Pedagogical Tools ◽  
Ideal Types ◽  
History Of ◽  
Historical Comparative ◽  
State Archives ◽  
Key Aspects ◽  
Economic Ties

This study is devoted to the study of relevant works on the history of the Stavropol Cossacks, works in the field of education of the Stavropol Cossacks as an independent Cossack group, trade, cultural and economic ties in the Stavropol Territory, spiritual life, language, culture, traditions and customs of the Stavropol Cossacks. Among modern studies in the history of the Stavropol Cossacks, the following topics stand out: military life and everyday life, folklore and song traditions, the movement for the revival of the Cossacks, as well as the current state and prospects for the development of Cossack organizations. The prospect of the development of pedagogical technologies based on the Cossack traditions of educating young people in Stavropol is highlighted as a separate topical topic. The relevance of the study lies in the need for a private study of the historiography of the regional Cossack group of Stavropol Cossacks in order to expand the scientific and pedagogical tools in the field of «Cossack studies». The practical significance of the study is expressed in the possibility of using the data of the article in the search for supporting material for teaching the "History of the Cossacks" in a higher educational institution (taking into account the regional specifics). The scientific novelty of the research is expressed in a new view of the Stavropol Cossacks as an independent Cossack group formed at the end of the XVIII century. The source base is represented mainly by archival data from the State Archives of the Stavropol Territory, data banks on archaeological, cultural and linguistic expeditions, sources of personal origin, the works of contemporary historians and directly the works of historians, whose studies formed the basis of the historiography of the history of the Stavropol Cossacks. The research methodology is based on the principles of historiographic comparative studies and comparative analysis of sources. Within the framework of the sociocultural approach, we rely on the following methods. Special-historical: the narrative method, the historical-comparative method, the historical-systemic method, the retrospective method. Sociological: document analysis, method of generalizing characteristics, method of ideal types. Culturological: comparative method, cultural-systemic method. Pedagogical: pedagogical interviewing, a method of studying and generalizing pedagogical experience.

The factors associated with the length of the third stage of labour: A descriptive-analytical study

2021 ◽  
Vol 17 ◽  
Author(s):  
Mansoureh Refaei ◽  
Soodabeh Aghababaei ◽  
Mansoureh Yazdkhasti ◽  
Farideh Kazemi ◽  
Fatemeh Farahmandpour
Keyword(s):  
Cross Sectional Study ◽  
Study Data ◽  
Cross Sectional ◽  
Factors Associated ◽  
The Third ◽  
Third Stage ◽  
History Of ◽  
Mother’S Age ◽  
And Gender ◽  
The Relationship

Background: Several risk factors have been identified for postpartum hemorrhage, one of which being the duration of the third stage of labour. This stage refers to the interval between the expulsion of the fetus to the expulsion of the placenta. Some bleeding occurs in this stage due to the separation of the placenta Objective: This study aimed to identify the factors associated with the length of the third stage of labour. Methods: In this cross-sectional study, 300 women hospitalized for vaginal birth were selected via convenience sampling. The study data were collected using a researcher-made questionnaire. Then, the data were analyzed using univariate and multivariate linear regression analyses. Results: The mean (SD) age of the participants was 26.41 (6.26) years. Investigation of the relationship between the study variables and the time of placental separation indicated that a minute increase in the length of membranes rupture caused a 0.003minute decrease in the time of placental separation. However, this time increased by 2.75, 6.68, and 2.86 minutes in the individuals without the history of abortion, those with the history of stillbirth, and those who had not received hyoscine, respectively. The results of multivariate analysis indicated that suffering from preeclampsia or hypertension, history of stillbirth, not receiving hyoscine, and not receiving misoprostol increased the length of the third stage by 4.40, 8.55, 2.38, and 6.04 minutes, respectively. Conclusion: Suffering from preeclampsia and having the history of stillbirth increased and using hyoscine and misoprostol decreased the length of the third stage of labour. However, no significant relationship was found between the length of the third stage of labour and mother’s age, gestational age, parity, mother’s body mass index, mother’s chronic disorders, history of manual placenta removal, length of the first and second stages, membranes rupture, induction, amount of oxytocin after delivery, and infant’s weight and gender.

Evaluation of Global Forecast System (GFS) Medium-Range Precipitation Forecasts in the Nile River Basin

2021 ◽  
Author(s):  
Haowen Yue ◽  
Mekonnen Gebremichael ◽  
Vahid Nourani
Keyword(s):  
Temporal Dynamics ◽  
Disease Outbreaks ◽  
Rain Gauge ◽  
Global Forecast System ◽  
Forecast System ◽  
Forecast Performance ◽  
Weather Forecasts ◽  
Rain Gauges ◽  
Basin Scale ◽  
Medium Range

Abstract Reliable weather forecasts are valuable in a number of applications, such as, agriculture, hydropower, and weather-related disease outbreaks. Global weather forecasts are widely used, but detailed evaluation over specific regions is paramount for users and operational centers to enhance the usability of forecasts and improve their accuracy. This study presents evaluation of the Global Forecast System (GFS) medium-range (1 day – 15 day) precipitation forecasts in the nine sub-basins of the Nile basin using NASA’s Integrated Multi-satellitE Retrievals (IMERG) “Final Run” satellite-gauge merged rainfall observations. The GFS products are available at a temporal resolution of 3-6 hours, spatial resolution of 0.25°, and its version-15 products are available since 12 June 2019. GFS forecasts are evaluated at a temporal scale of 1-15 days, spatial scale of 0.25° to all the way to the sub-basin scale, and for a period of one year (15 June 2019 – 15 June 2020). The results show that performance of the 1-day lead daily basin-averaged GFS forecast performance, as measured through the modified Kling-Gupta Efficiency (KGE), is poor (0 < KGE < 0.5) for most of the sub-basins. The factors contributing to the low performance are: (1) large overestimation bias in watersheds located in wet climate regimes in the northern hemispheres (Millennium watershed, Upper Atbara & Setit watershed, and Khashm El Gibra watershed), and (2) lower ability in capturing the temporal dynamics of watershed-averaged rainfall that have smaller watershed areas (Roseires at 14,110 sq. km and Sennar at 13,895 sq. km). GFS has better bias for watersheds located in the dry parts of the northern hemisphere or wet parts of the southern hemisphere, and better ability in capturing the temporal dynamics of watershed-average rainfall for large watershed areas. IMERG Early has better bias than GFS forecast for the Millennium watershed but still comparable and worse bias for the Upper Atbara & Setit, and Khashm El Gibra watersheds. The variation in the performance of the IMERG Early could be partly explained by the number of rain gauges used in the reference IMERG Final product, as 16 rain gauges were used for the Millennium watershed but only one rain gauge over each Upper Atbara & Setit, and Khashm El Gibra watershed. A simple climatological bias-correction of IMERG Early reduces in the bias in IMERG Early over most watersheds, but not all watersheds. We recommend exploring methods to increase the performance of GFS forecasts, including post-processing techniques through the use of both near-real-time and research-version satellite rainfall products.

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