Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants

Evaluating the characteristics of emerging SARS-CoV-2 variants of concern is essential to inform pandemic risk assessment. A variant may grow faster if it produces a larger number of secondary infections (transmissibility advantage) or if the timing of secondary infections (generation time) is better. So far, assessments have largely focused on deriving the transmissibility advantage assuming the generation time was unchanged. Yet, knowledge of both is needed to anticipate impact. Here we develop an analytical framework to investigate the contribution of both the transmissibility advantage and generation time to the growth advantage of a variant. We find that the growth advantage depends on the epidemiological context (level of epidemic control). More specifically, variants conferring earlier transmission are more strongly favoured when the historical strains have fast epidemic growth, while variants conferring later transmission are more strongly favoured when historical strains have slow or negative growth. We develop these conceptual insights into a statistical framework to infer both the transmissibility advantage and generation time of a variant. On simulated data, our framework correctly estimates both parameters when it covers time periods characterized by different epidemiological contexts. Applied to data for the Alpha and Delta variants in England and in Europe, we find that Alpha confers a +54% [95% CI, 45-63%] transmissibility advantage compared to previous strains, and Delta +140% [98-182%] compared to Alpha, and mean generation times are similar to historical strains for both variants. This work helps interpret variant frequency and will strengthen risk assessment for future variants of concern.

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Applying the risk principle to optimize accuracy and equity in correctional risk assessment: Results From a Simulation

International Journal of Offender Therapy and Comparative Criminology ◽

10.1177/0306624x20986523 ◽

2021 ◽

pp. 0306624X2098652

Author(s):

Grant Duwe

Keyword(s):

Risk Assessment ◽

Predictive Accuracy ◽

Ethnic Disparities ◽

Simulated Data ◽

Risk Assessments ◽

Risk Level ◽

Risk Levels ◽

Risk Principle ◽

Changes In Risk ◽

The Impact

As the use of risk assessments for correctional populations has grown, so has concern that these instruments exacerbate existing racial and ethnic disparities. While much of the attention arising from this concern has focused on how algorithms are designed, relatively little consideration has been given to how risk assessments are used. To this end, the present study tests whether application of the risk principle would help preserve predictive accuracy while, at the same time, mitigate disparities. Using a sample of 9,529 inmates released from Minnesota prisons who had been assessed multiple times during their confinement on a fully-automated risk assessment, this study relies on both actual and simulated data to examine the impact of program assignment decisions on changes in risk level from intake to release. The findings showed that while the risk principle was used in practice to some extent, the simulated results showed that greater adherence to the risk principle would increase reductions in risk levels and minimize the disparities observed at intake. The simulated data further revealed the most favorable outcomes would be achieved by not only applying the risk principle, but also by expanding program capacity for the higher-risk inmates in order to adequately reduce their risk.

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Behaviour ofStreptococcus lactisin heat treated (80 °C for 30 min) or sterilized cow's and ewe's milk

Journal of Dairy Research ◽

10.1017/s0022029900023190 ◽

1983 ◽

Vol 50 (3) ◽

pp. 357-363 ◽

Cited By ~ 5

Author(s):

Francisco J. Chavarri ◽

Jose A. Nuñez ◽

Manuel Nuñez

Keyword(s):

Acid Production ◽

Generation Time ◽

Buffer Capacity ◽

Cow’S Milk ◽

Cow's Milk ◽

Vitamin Content ◽

Streptococcus Lactis ◽

Generation Times ◽

Heat Treated ◽

Ewe's Milk

SummaryGeneration times and acid production after 6 and 24 h by 20 strains ofStreptococcus lactisof dairy origin were determined in heat treated (80 °C for 30 min) and sterilized cow's and ewe's milk. Ewe's milk enhanced growth of the streptococci, with significantly (P< 0·001) shorter generation times and higher acid production after 6 h incubation than cow's milk, probably due to its higher vitamin content. The stronger buffer capacity of ewe's milk allowed a higher (P< 0·001) acid production after 24 h than cow's milk. A stimulatory effect of sterilization on generation time and acid production after 24 h was observed in cow's milk. However, the heat treated ewe's milk was shown to be a better substrate than sterilized ewe's milk forStr. lactis.

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An enhanced sequential ground motion selection for risk assessment using a Bayesian updating approach

Journal of Building Engineering ◽

10.1016/j.jobe.2021.103745 ◽

2021 ◽

pp. 103745

Author(s):

Shima Taheri ◽

R. Karami Mohammadi

Keyword(s):

Risk Assessment ◽

Ground Motion ◽

Bayesian Updating ◽

Ground Motion Selection ◽

Selection For

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Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels

Statistical Applications in Genetics and Molecular Biology ◽

10.2202/1544-6115.1125 ◽

2005 ◽

Vol 4 (1) ◽

Cited By ~ 6

Author(s):

Ingrid Lönnstedt ◽

Rebecca Rimini ◽

Peter Nilsson

Keyword(s):

Cell Lines ◽

Empirical Bayes ◽

Dna Microarrays ◽

Linear Models ◽

Simulated Data ◽

Probabilistic Methods ◽

Expression Levels ◽

Statistical Framework ◽

Treatment Conditions ◽

One Way Anova

In the exploding field of gene expression techniques such as DNA microarrays, there are still few general probabilistic methods for analysis of variance. Linear models and ANOVA are heavily used tools in many other disciplines of scientific research. The usual F-statistic is unsatisfactory for microarray data, which explore many thousand genes in parallel, with few replicates.We present three potential one-way ANOVA statistics in a parametric statistical framework. The aim is to separate genes that are differently regulated across several treatment conditions from those with equal regulation. The statistics have different features and are evaluated using both real and simulated data. Our statistic B1 generally shows the best performance, and is extended for use in an algorithm that groups cell lines by equal expression levels for each gene. An extension is also outlined for more general ANOVA tests including several factors.The methods presented are implemented in the freely available statistical language R. They are available at http://www.math.uu.se/staff/pages/?uname=ingrid.

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Inter-observer variation in pathological review and its impact on clinicopathological risk assessment and patient selection for adjuvant systemic treatment in node-negative breast cancer patients

European Journal of Cancer Supplements ◽

10.1016/s1359-6349(08)70790-0 ◽

2008 ◽

Vol 6 (7) ◽

pp. 191

Author(s):

J.M. Bueno-de-Mesquita ◽

D.S.A. Nuyten ◽

J. Wesseling ◽

H. Van Tinteren ◽

S.C. Linn ◽

...

Keyword(s):

Breast Cancer ◽

Risk Assessment ◽

Systemic Treatment ◽

Observer Variation ◽

Breast Cancer Patients ◽

Node Negative ◽

Adjuvant Systemic Treatment ◽

Node Negative Breast Cancer ◽

Pathological Review ◽

Selection For

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Site selection for floating offshore wind turbines in Japanese coasts by quantitative risk assessment

Journal of Marine Science and Technology ◽

10.1007/s00773-018-0613-8 ◽

2018 ◽

Vol 24 (4) ◽

pp. 997-1014

Author(s):

Megumi Shiokari ◽

Shigeru Tabeta ◽

Shigesuke Ishida

Keyword(s):

Risk Assessment ◽

Wind Turbines ◽

Site Selection ◽

Offshore Wind ◽

Quantitative Risk Assessment ◽

Offshore Wind Turbines ◽

Floating Offshore Wind Turbines ◽

Selection For

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A review of the life cycles and life-history adaptations of pelagic tunicates to environmental conditions

ICES Journal of Marine Science ◽

10.1093/icesjms/fsr159 ◽

2011 ◽

Vol 69 (3) ◽

pp. 358-369 ◽

Cited By ~ 33

Author(s):

Don Deibel ◽

Ben Lowen

Keyword(s):

Life History ◽

Environmental Conditions ◽

Generation Time ◽

Egg Production ◽

Food Concentration ◽

Life Cycles ◽

Population Doubling ◽

Event Scale ◽

Generation Times ◽

Doubling Times

Abstract Deibel, D., and Lowen, B. 2012. A review of the life cycles and life-history adaptations of pelagic tunicates to environmental conditions. – ICES Journal of Marine Science, 69: 358–369. Phylogeny, life cycles, and life-history adaptations of pelagic tunicates to temperature and food concentration are reviewed. Using literature data on lifetime egg production and generation time of appendicularians, salps, and doliolids, rmax, the maximum rate of lifetime reproductive fitness, is calculated as a common metric of adaptation to environmental conditions. The rmax values are high for all three groups, ranging from ∼0.1 to 1.9 d−1, so population doubling times range from ∼8 h to 1 week. These high values of rmax are attributable primarily to short generation times, ranging from 2 to 50 d. Clearly, pelagic tunicates are adapted to event-scale (i.e. days to weeks) rather than seasonal-scale changes in environmental conditions. Although they are not closely related phylogenetically, all three groups have a unique life-history adaptation promoting high lifetime fitness. Appendicularians have late oocyte selection, salps are viviparous, and doliolids possess a polymorphic asexual phase. There has been little research on hermaphroditic appendicularians, on large oceanic salps, and on doliolids generally. Research is needed on factors regulating generation time, on the heritability of life-history traits, and on age- and size-specific rates of mortality.

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Rapid juvenile development in old forest lichens

Botany ◽

10.1139/b10-086 ◽

2011 ◽

Vol 89 (1) ◽

pp. 65-72 ◽

Cited By ~ 39

Author(s):

Per Larsson ◽

Yngvar Gauslaa

Keyword(s):

Growth Rates ◽

Generation Time ◽

Population Biology ◽

Limiting Factors ◽

Noninvasive Method ◽

Relative Growth ◽

Relative Growth Rates ◽

Generation Times ◽

Young Forests ◽

Juvenile Development

Generation time and juvenile growth rates are important but poorly known parameters in lichen population biology. By using a noninvasive method, we aimed to quantify these variables in juvenile thalli of Lobaria pulmonaria (L.) Hoffm., L. scrobiculata (Scop.) D.C., and Pseudocyphellaria crocata (L.) Vain., in situ, on twigs of Picea abies (L.) H. Karst in boreal rainforests. Growth was monitored during the summer months (May–August, 106 d), as well as in the remaining part of the year (259 d), for each of two sequential years, by means of repeated photography and imaging analysis. The mean relative thallus-area growth rates were 0.53 ± 0.02, 0.41 ± 0.02, and 0.57 ± 0.04 mm2·mm–2·year–1 (mean ±SE), respectively, in the three species, equivalent to a yearly growth of 101 ± 5%, 70 ± 6%, and 121 ± 12%. Growth was much slower during the winter (0.09–0.12 mm2·cm–2·d–1) than in summer (0.19–0.27 mm2·cm–2·d–1). Relative growth rates significantly declined with increasing thallus size. Estimated generation times in L. scrobiculata and P. crocata, based upon the first observed formation of reproductive structures, were 15–22 and 9–13 years, respectively. Studied L. pulmonaria thalli produced no diaspores during the experiment, consistent with a generation time >17 years. The relative growth rates we measured and our estimated generation times are faster than those earlier recorded. Thus, our noninvasive method can estimate parameters needed to model population growth within a reasonable period of time. The rapid juvenile development implies that the growth rates and generation times are unlikely to be the limiting factors that exclude these lichens from young forests.

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