Papers by Yael Artzy-Randrup
In late March 2020, SARS-CoV-2 arrived in Manaus, Brazil, and rapidly developed into a large-scal... more In late March 2020, SARS-CoV-2 arrived in Manaus, Brazil, and rapidly developed into a large-scale epidemic that collapsed the local health system, and resulted in extreme death rates. Several key studies reported that ~76% of residents of Manaus were infected (attack rate AR≃76%) by October 2020, suggesting protective herd immunity had been reached. Despite this, in November an unexpected second wave of COVID-19 struck again, and proved to be larger than the first creating a catastrophe for the unprepared population. It has been suggested that this could only be possible if the second wave was driven by reinfections. Here we use novel methods to model the epidemic from mortality data, evaluate the impact of interventions, in order to provide an alternative explanation as to why the second wave appeared. The method fits a "flexible" reproductive number R0(t) that changes over the epidemic, and found AR≃30-34% by October 2020, for the first wave, which is far less than requ...
In late March 2020, SARS-CoV-2 arrived in Manaus, Brazil, and rapidly developed into a large-scal... more In late March 2020, SARS-CoV-2 arrived in Manaus, Brazil, and rapidly developed into a large-scale epidemic that collapsed the local health system, and resulted in extreme death rates. Several key studies reported that ∼76% of residents of Manaus were infected (attack rate AR≃76%) by October 2020, suggesting protective herd immunity had been reached. Despite this, in November an unexpected second wave of COVID-19 struck again, and proved to be larger than the first creating a catastrophe for the unprepared population. It has been suggested that this could only be possible if the second wave was driven by reinfections. Here we use novel methods to model the epidemic from mortality data, evaluate the impact of interventions, in order to provide an alternative explanation as to why the second wave appeared. The method fits a “flexible” reproductive number R0(t) that changes over the epidemic, and found AR≃30-34% by October 2020, for the first wave, which is far less than required for h...
Dynamics On and Of Complex Networks, 2009
Proceedings of the National Academy of Sciences, 2008
Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the s... more Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic gene-sharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification. Our results indicate that, on average, at least 81 ± 15% of the genes in each genome studied were involved in lateral gene transfer at some point in their history, even though they can be vertically inherited after acquisition, uncovering a substantial cumulative effect of lateral gene transfer on longer evolutionary time scales.
Physical Review Letters, 2009
Standard techniques for analyzing network models usually break down in the presence of clustering... more Standard techniques for analyzing network models usually break down in the presence of clustering. Here we introduce a new analytic tool, the ''free-excess degree'' distribution, which extends the generating function framework, making it applicable for clustered networks (C > 0). The methodology is general and provides a new expression for the threshold point at which the giant component emerges and shows that it scales as ð1 À CÞ À1 . In addition, the size of the giant component may be predicted even for more complicated scenarios such as the removal of a fixed fraction of nodes at random.
Limnology and Oceanography: Methods, 2008
Size-frequency distributions (SFDs) have been used to assess the ecological status of different p... more Size-frequency distributions (SFDs) have been used to assess the ecological status of different populations in a variety of ecosystems and recently have become widely used to examine reef corals. SFDs may reflect the response of time-varying influences of the environment, including the intensity and frequency of disturbances and the degree of environmental degradation. Here we elucidate the biases that can arise in the application of popular and traditional sampling methods (e.g. quadrat, belt-transect, and line-intercept). We show that these biases on the estimated SFD arise due to boundary effects of the sampling units. Incorrect evaluations of SFDs may lead to biased estimations of the ecological status of coral populations and may result in, among other things, erroneous nature reserve management policies. Our analysis is based on analytical calculations, simulations, and field observations. We have developed simple mathematical corrections, which provide unbiased estimations for previously collected data acquired by these widely used methods. In addition, we offer alternative sampling methods that do not suffer from these shortcomings. Eliminating these types of sampling errors will not only provide better assessments of the status of a given coral reef, but will also make way for more precise comparisons among coral reefs in different regions. Although we discuss the biases of SFDs in regard to reef coral populations, the work is equally relevant in other ecological contexts.
PLoS ONE, 2010
Although the spread of drug resistance and the influence of climate change on malaria are most of... more Although the spread of drug resistance and the influence of climate change on malaria are most often considered separately, these factors have the potential to interact through altered levels of transmission intensity. The influence of transmission intensity on the evolution of drug resistance has been addressed in theoretical studies from a population genetics' perspective; less is known however on how epidemiological dynamics at the population level modulates this influence. We ask from a theoretical perspective, whether population dynamics can explain non-trivial, non-monotonic, patterns of treatment failure with transmission intensity, and, if so, under what conditions. We then address the implications of warmer temperatures in an East African highland, where, as in other similar regions at the altitudinal edge of malaria's distribution, there has been a pronounced increase of cases from the 1970s to the 1990s. Our theoretical analyses, with a transmission model that includes different levels of immunity, demonstrate that an increase in transmission beyond a threshold can lead to a decrease in drug resistance, as previously shown , but that a second threshold may occur and lead to the re-establishment of drug resistance. Estimates of the increase in transmission intensity from the 1970s to the 1990s for the Kenyan time series, obtained by fitting the two-stage version of the model with an explicit representation of vector dynamics, suggest that warmer temperatures are likely to have moved the system towards the first threshold, and in so doing, to have promoted the faster spread of drug resistance. Climate change and drug resistance can interact and need not be considered as alternative explanations for trends in disease incidence in this region. Non-monotonic patterns of treatment failure with transmission intensity similar to those described as the 'valley phenomenon' for Uganda can result from epidemiological dynamics but under poorly understood assumptions.
PLOS Computational Biology, 2015
During foraging processes, animals must optimize their chances of locating food targets by sampli... more During foraging processes, animals must optimize their chances of locating food targets by sampling the territory with different stochastic search strategies. Recent investigations have reinforced the idea that Lévy walks have beneficial statistical properties that enhance encounter rates when randomly sampling space. Using a generational mutation-based evolutionary algorithm, we have evolved stochastic search strategies starting from random populations of Lévy walkers that can perform all possible types of motion, going from Brownian to ballistic. We determined that the optimal Lévy index of μ=2, emerges from this evolutionary process by means of reproduction, mutation, and selection on Lévy indexes based encounter success.
Coral reefs are in global decline, with coral diseases increasing both in prevalence and in space... more Coral reefs are in global decline, with coral diseases increasing both in prevalence and in space, a situation that is expected only to worsen as future thermal stressors increase. Through intense surveillance, we have collected a unique and highly resolved dataset from the coral reef of Eilat (Israel, Red Sea), that documents the spatiotemporal dynamics of a White Plague Disease (WPD) outbreak over the course of a full season. Based on modern statistical methodologies, we develop a novel spatial epidemiological model that uses a maximum-likelihood procedure to fit the data and assess the transmission pattern of WPD. We link the model to sea surface temperature (SST) and test the possible effect of increasing temperatures on disease dynamics. Our results reveal that the likelihood of a susceptible coral to become infected is governed both by SST and by its spatial location relative to nearby infected corals. The model shows that the magnitude of WPD epidemics strongly depends on dem...
Disseminated cancer cells (DCCs) are detected in the circulation and bone marrow of up to 40% of ... more Disseminated cancer cells (DCCs) are detected in the circulation and bone marrow of up to 40% of breast cancer (BC) patients with clinically localized disease. The formation of metastases is governed by eco-evolutionary interactions of DCCs with the tissue during the transition from microscopic populations to macroscopic disease. Here, we view BC adjuvant and neoadjuvant treatments in the context of small population extinction dynamics observed in the Anthropocene era. Specifically, the unique eco-evolutionary dynamics of small asexually reproducing cancer populations render them highly vulnerable to: (1) environmental and demographic fluctuations, (2) Allee effects, (3) genetic drift and (4) population fragmentation. Furthermore, these typically interact, producing self-reinforcing, destructive dynamics—termed the Extinction Vortex—eradicating the population even when none of the perturbations is individually capable of causing extinction. We propose that developing BC adjuvant and...
Buss et al. (2021) and Faria et al. (2021) reported that ~76% of the residents of the capital cit... more Buss et al. (2021) and Faria et al. (2021) reported that ~76% of the residents of the capital city of Manaus, had been infected by SARS-CoV-2 by October 2020 suggesting that herd immunity had been achieved by the end of the first wave. But the announcement of herd immunity, which would imply reasonable protection from future outbreaks, only provided the Manaus population with a false sense of security. Within two months later, a second wave of COVID-19 was initiated with death rates much larger than the first attributed to the appearance of the new P.1 Variant of Concern. Faria et al. (2021) suggest that large scale reinfections played an important role in enabling the huge second epidemic wave. In this Technical Comment we challenge such interpretations, and provide quantitative arguments that suggest the attack rate of the first wave was well below 76%. We then present alternative interpretations of the data. <br><br>
&amp;amp;amp;lt;p&amp;amp;amp;gt;Redistribution of evapotranspiration from land via atmos... more &amp;amp;amp;lt;p&amp;amp;amp;gt;Redistribution of evapotranspiration from land via atmospheric circulation is an important Earth system process. Globally, evapotranspiration contributes significantly to terrestrial rainfall, on both regional and more remote scales. In wet, tropical regions (e.g. the Congo basin), transpiration and interception loss from the dense forest cover are the primary drivers of moisture recycling, which plays a crucial role in preserving regional ecosystem functioning. However, for semi-arid and arid regions, our knowledge on the extent and significance of evapotranspiration for moisture recycling is still very limited, despite the significance this may have for addressing challenges of desertification in times of rapid environmental change. Considering this, we are taking the Sahel region as a case study and investigate its contribution to precipitation in the African continent. In addition, we specifically study what fraction of the precipitation originates from vegetation in the Sahel through transpiration and interception loss. Our study is based on simulated atmospheric moisture trajectories derived from the Lagrangian model FLEXPART with a 1-degree resolution, driven by ECMWF reanalysis data over 1980&amp;amp;amp;amp;#8211;2016. Preliminary results show (1) the temporal variability in the contribution of the region to precipitation in African drylands, and (2) a significant contribution of local precipitation recycling. We conclude that consideration of the naturally and anthropogenically-driven greening of the Sahel, as well as land use and land cover changes in the region, may have both local and far-reaching impacts via the transport of moisture through the atmosphere.&amp;amp;amp;lt;/p&amp;amp;amp;gt;
Science Advances
The highly dependent interplay of disease, famine, war, and society is examined based on an extre... more The highly dependent interplay of disease, famine, war, and society is examined based on an extreme period during World War II. Using mathematical modeling, we reassess events during the Holocaust that led to the liquidation of the Warsaw Ghetto (1941–1942), with the eventual goal of deliberately killing ~450,000, mostly Jewish residents, many through widespread starvation and a large-scale typhus epidemic. The Nazis justified genocide supposedly to control the spread of disease. This exemplifies humanity’s ability to turn upon itself, based on racially guided epidemiological principles, merely because of the appearance of a bacterium. Deadly disease and starvation dynamics are explored using modeling and the maths of food ration cards. Strangely, the epidemic was curtailed and was brought to a sudden halt before winter, when typhus normally accelerates. A far more massive epidemic outbreak was prevented through the antiepidemic efforts by the often considered incompetent and corrup...
Cancer Research
Curative therapy for metastatic cancers is equivalent to causing extinction of a large, heterogen... more Curative therapy for metastatic cancers is equivalent to causing extinction of a large, heterogeneous, and geographically dispersed population. Although eradication of dinosaurs is a dramatic example of extinction dynamics, similar application of massive ecoevolutionary force in cancer treatment is typically limited by host toxicity. Here, we investigate the evolutionary dynamics of Anthropocene species extinctions as an alternative model for curative cancer therapy. Human activities can produce extinctions of large, diverse, and geographically distributed populations. The extinction of a species typically follows a pattern in which initial demographic and ecological insults reduce the size and heterogeneity of the population. The surviving individuals, with decreased genetic diversity and often fragmented ecology, are then vulnerable to small stochastic perturbations that further reduce the population until extinction is inevitable. We hypothesize large, diverse, and disseminated cancer populations can be eradicated using similar evolutionary dynamics. Initial therapy is applied to reduce population size and diversity and followed by new treatments to exploit the eco-evolutionary vulnerability of small and/or declining populations. Mathematical models and computer simulations demonstrate initial reductive treatment followed immediately by demographic and ecological perturbations, similar to the empirically derived treatment of pediatric acute lymphocytic leukemia, can consistently achieve curative outcomes in nonpediatric cancers. Significance: Anthropocene extinctions suggest a strategy for eradicating metastatic cancers in which initial therapy, by reducing the size and diversity of the population, renders it vulnerable to extinction by rapidly applied additional perturbations.
WIREs Water
A review of the literature on water governance reveals that most studies focus on blue water gove... more A review of the literature on water governance reveals that most studies focus on blue water governance; while there is some literature on green and atmospheric water, explicit literature on how to govern green and atmospheric water is lacking. Hence, this paper addresses the question: What are the arguments for governing green and atmospheric water? In order to address this question, we have undertaken a scoping analysis of the literature on green and atmospheric water. We conclude that water governance must proactively address green and atmospheric water since: (a) blue water represents only a part of the available fresh water; (b) blue river basins represent only a subset of the wider systemic nature of water; (c) land use change has significant impacts on various water flows, which all may need to be governed; (d) climate variability and change influences blue, green, and atmospheric water availability; (e) an understanding of the socio-ecological uses of the different colors of water is critical for a more optimal and legitimate governance of water; (f) new water technologies make it increasingly possible to modify the use of green and atmospheric water; and (g) global trade infrastructures pressurize local green water resources. Neglecting the need for explicit governance of green and atmospheric water could create new forms of "water grabbing" that would impact water availability beyond the basin scale.
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Papers by Yael Artzy-Randrup