Programs and Communities
The collection collates collections by schools, centers, programs, and research groups.
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- Creators: School of Human Evolution and Social Change
- Creators: Julie Ann Wrigley Global Institute of Sustainability
Description
The City of Phoenix Street Transportation Department partnered with the Rob and Melani Walton Sustainability Solutions Service at Arizona State University (ASU) and researchers from various ASU schools to evaluate the effectiveness, performance, and community perception of the new pavement coating. The data collection and analysis occurred across multiple neighborhoods and at varying times across days and/or months over the course of one year (July 15, 2020–July 14, 2021), allowing the team to study the impacts of the surface treatment under various weather conditions.
ContributorsMiddel, Ariane (Author) / Vanos, Jennifer K. (Author) / Hondula, David M. (Author) / Kaloush, Kamil (Author) / Sailor, David (Author) / Medina, Jose R. (Jose Roberto) (Author) / Schneider, Florian (Author) / Ortiz, Johny Cordova (Author) / Campbell, Bill (Author) / Epel, Erin (Contributor) / Rice, Brendan (Contributor) / Garcia, Ruth (Contributor) / Phoenix (Ariz.). Street Transportation Department (Contributor) / City of Phoenix (Funder) / Industrial Development Authority of the County of Maricopa (Funder) / Julie Ann Wrigley Global Institute of Sustainability (Funder) / Arizona State University. Healthy Urban Environments Program (Contributor)
Created2021-09
Description
Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tuberculosis complex, MTBC) continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterial-specific single- and multi-copy loci using qPCR. In a trial study in which armadillos were artificially infected with M. leprae, these techniques were specific and sensitive to pathogen detection, while more traditional ELISAs were only specific. These assays were then employed in a case study to detect M. leprae as well as MTBC in wild marmosets. All marmosets were negative for M. leprae DNA, but 14 were positive for the mycobacterial rpoB gene assay. Targeted capture and sequencing of rpoB and other MTBC genes validated the presence of mycobacterial DNA in these samples and revealed that qPCR is useful for identifying mycobacterial-infected animal hosts.
ContributorsHousman, Genevieve (Author) / Malukiewicz, Joanna (Author) / Boere, Vanner (Author) / Grativol, Adriana D. (Author) / Pereira, Luiz Cezar M. (Author) / de Oliveira e Silva, Ita (Author) / Ruiz-Miranda, Carlos R. (Author) / Truman, Richard (Author) / Stone, Anne (Author) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Biodesign Institute (Contributor) / Personalized Diagnostics (Contributor)
Created2015-11-16
Description
Background
In 2015, the Zika arbovirus (ZIKV) began circulating in the Americas, rapidly expanding its global geographic range in explosive outbreaks. Unusual among mosquito-borne diseases, ZIKV has been shown to also be sexually transmitted, although sustained autochthonous transmission due to sexual transmission alone has not been observed, indicating the reproduction number (R0) for sexual transmission alone is less than 1. Critical to the assessment of outbreak risk, estimation of the potential attack rates, and assessment of control measures, are estimates of the basic reproduction number, R0.
Methods
We estimated the R0 of the 2015 ZIKV outbreak in Barranquilla, Colombia, through an analysis of the exponential rise in clinically identified ZIKV cases (n = 359 to the end of November, 2015).
Findings
The rate of exponential rise in cases was ρ = 0.076 days[superscript −1], with 95% CI [0.066,0.087] days[superscript −1]. We used a vector-borne disease model with additional direct transmission to estimate the R0; assuming the R0 of sexual transmission alone is less than 1, we estimated the total R0 = 3.8 [2.4,5.6], and that the fraction of cases due to sexual transmission was 0.23 [0.01,0.47] with 95% confidence.
Interpretation
This is among the first estimates of R0 for a ZIKV outbreak in the Americas, and also among the first quantifications of the relative impact of sexual transmission.
ContributorsTowers, Sherry (Author) / Brauer, Fred (Author) / Castillo-Chavez, Carlos (Author) / Falconar, Andrew K. I. (Author) / Mubayi, Anuj (Author) / Romero-Vivas, Claudia M. E. (Author) / School of Human Evolution and Social Change (Contributor) / Simon M. Levin Mathematical, Computational and Modeling Sciences Center (Contributor) / Mathematical and Theoretical Biology Institute (MTBI) (Contributor)
Created2016-10-17
Description
A two-patch mathematical model of Dengue virus type 2 (DENV-2) that accounts for vectors’ vertical transmission and between patches human dispersal is introduced. Dispersal is modelled via a Lagrangian approach. A host-patch residence-times basic reproduction number is derived and conditions under which the disease dies out or persists are established. Analytical and numerical results highlight the role of hosts’ dispersal in mitigating or exacerbating disease dynamics. The framework is used to explore dengue dynamics using, as a starting point, the 2002 outbreak in the state of Colima, Mexico.
ContributorsBichara, Derdei (Author) / Holechek, Susan (Author) / Velazquez-Castro, Jorge (Author) / Murillo, Anarina (Author) / Castillo-Chavez, Carlos (Author) / Simon M. Levin Mathematical, Computational and Modeling Sciences Center (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Biodesign Institute (Contributor) / Infectious Diseases and Vaccinology (Contributor) / School of Life Sciences (Contributor)
Created2016-08-05
Description
For many species, migration evolves to allow organisms to access better resources. However, the proximate factors that trigger these developmental changes, and how and why these vary across species, remain poorly understood. One prominent hypothesis is that poor-quality food promotes development of migratory phenotypes and this has been clearly shown for some polyphenic insects. In other animals, particularly long-distance bird migrants, it is clear that high-quality food is required to prepare animals for a successful migration. We tested the effect of diet quality on the flight behaviour and morphology of the Mongolian locust, Oedaleus asiaticus. Locusts reared at high population density and fed low-N grass (performance-enhancing for this species) had enhanced migratory morphology relative to locusts fed high-N grass. Furthermore, locusts fed synthetic diets with an optimal 1 : 2 protein : carbohydrate ratio flew for longer times than locusts fed diets with lower or higher protein : carbohydrate ratios. In contrast to the hypothesis that performance-degrading food should enhance migration, our results support the more nuanced hypothesis that high-quality diets promote development of migratory characteristics when migration is physiologically challenging.
ContributorsCease, Arianne (Author) / Harrison, Jon (Author) / Hao, Shuguang (Author) / Niren, Danielle (Author) / Zhang, Guangming (Author) / Kang, Le (Author) / Elser, James (Author) / Julie Ann Wrigley Global Institute of Sustainability (Contributor) / School of Sustainability (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2017-06-07
Description
Recent efforts have attempted to describe the population structure of common chimpanzee, focusing on four subspecies: Pan troglodytes verus, P. t. ellioti, P. t. troglodytes, and P. t. schweinfurthii. However, few studies have pursued the effects of natural selection in shaping their response to pathogens and reproduction. Whey acidic protein (WAP) four-disulfide core domain (WFDC) genes and neighboring semenogelin (SEMG) genes encode proteins with combined roles in immunity and fertility. They display a strikingly high rate of amino acid replacement (dN/dS), indicative of adaptive pressures during primate evolution. In human populations, three signals of selection at the WFDC locus were described, possibly influencing the proteolytic profile and antimicrobial activities of the male reproductive tract. To evaluate the patterns of genomic variation and selection at the WFDC locus in chimpanzees, we sequenced 17 WFDC genes and 47 autosomal pseudogenes in 68 chimpanzees (15 P. t. troglodytes, 22 P. t. verus, and 31 P. t. ellioti). We found a clear differentiation of P. t. verus and estimated the divergence of P. t. troglodytes and P. t. ellioti subspecies in 0.173 Myr; further, at the WFDC locus we identified a signature of strong selective constraints common to the three subspecies in WFDC6—a recent paralog of the epididymal protease inhibitor EPPIN. Overall, chimpanzees and humans do not display similar footprints of selection across the WFDC locus, possibly due to different selective pressures between the two species related to immune response and reproductive biology.
ContributorsFerreira, Zelia (Author) / Hurle, Belen (Author) / Andres, Aida M. (Author) / Kretzschmar, Warren W. (Author) / Mullikin, James C. (Author) / Cherukuri, Praveen F. (Author) / Cruz, Pedro (Author) / Gonder, Mary Katherine (Author) / Stone, Anne (Author) / Tishkoff, Sarah (Author) / Swanson, Willie J. (Author) / Green, Eric D. (Author) / Clark, Andrew G. (Author) / Seixas, Susana (Author) / NISC Comparative Sequencing Program (Author) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2013-12-19
Description
The growth rate hypothesis predicts that organisms with higher maximum growth rates will also have higher body percent phosphorus (P) due to the increased demand for ribosomal RNA production needed to sustain rapid growth. However, this hypothesis was formulated for invertebrates growing at the same temperature. Within a biologically relevant temperature range, increased temperatures can lead to more rapid growth, suggesting that organisms in warmer environments might also contain more P per gram of dry mass. However, since higher growth rates at higher temperature can be supported by more rapid protein synthesis per ribosome rather than increased ribosome investment, increasing temperature might not lead to a positive relationship between growth and percent P. We tested the growth rate hypothesis by examining two genera of Neotropical stream grazers, the leptophlebiid mayfly Thraulodes and the bufonid toad tadpole Rhinella. We measured the body percent P of field-collected Thraulodes as well as the stoichiometry of periphyton resources in six Panamanian streams over an elevational gradient spanning approximately 1,100 m and 7°C in mean annual temperature. We also measured Thraulodes growth rates using in situ growth chambers in two of these streams. Finally, we conducted temperature manipulation experiments with both Thraulodes and Rhinella at the highest and lowest elevation sites and measured differences in percent P and growth rates. Thraulodes body percent P increased with temperature across the six streams, and average specific growth rate was higher in the warmer lowland stream. In the temperature manipulation experiments, both taxa exhibited higher growth rate and body percent P in the lowland experiments regardless of experimental temperature, but growth rate and body percent P of individuals were not correlated. Although we found that Thraulodes from warmer streams grew more rapidly and had higher body percent P, our experimental results suggest that the growth rate hypothesis does not apply across temperatures. Instead, our results indicate that factors other than temperature drive variation in organismal percent P among sites.
ContributorsMoody, Eric (Author) / Rugenski, Amanda (Author) / Sabo, John (Author) / Turner, Benjamin L. (Author) / Elser, James (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Julie Ann Wrigley Global Institute of Sustainability (Contributor)
Created2017-04-18
Description
Fire is one of the earliest and most common tools used by humans to modify the earth surface. Landscapes in the Yucatán Peninsula are composed of a mosaic of old growth subtropical forest, secondary vegetation, grasslands, and agricultural land that represent a well-documented example of anthropogenic intervention, much of which involves the use of fire. This research characterizes land use systems and land cover changes in the Yucatán during the 2000–2010 time period. We used an active fire remotely sensed data time series from the Moderate Resolution Imaging Spectroradiometer (MODIS), in combination with forest loss, and anthrome map sources to (1) establish the association between fire and land use change in the region; and (2) explore links between the spatial and temporal patterns of fire and specific types of land use practices, including within- and between-anthromes variability. A spatial multinomial logit model was constructed using fire, landscape configuration, and a set of commonly used control variables to estimate forest persistence, non-forest persistence, and change. Cross-tabulations and descriptive statistics were used to explore the relationships between fire occurrence, location, and timing with respect to the geography of land use. We also compared fire frequencies within and between anthrome groups using a negative binomial model and Tukey pairwise comparisons. Results show that fire data broadly reproduce the geography and timing of anthropogenic land change. Findings indicate that fire and landscape configuration is useful in explaining forest change and non-forest persistence, especially in fragmented (mosaicked) landscapes. Absence of fire occurrence is related usefully to the persistence of spatially continuous core areas of older growth forest. Fire has a positive relationship with forest to non-forest change and a negative relationship with forest persistence. Fire is also a good indicator to distinguish between anthrome groups (e.g., croplands and villages). Our study suggests that active fire data series are a reasonable proxy for anthropogenic land persistence/change in the context of the Yucatán and are useful to differentiate quantitatively and qualitatively between and within anthromes.
ContributorsMillones, Marco (Author) / Rogan, John (Author) / Turner II, B. L. (Author) / Parmentier, Benoit (Author) / Clary Harris, Robert (Author) / Griffith, Daniel A. (Author) / College of Liberal Arts and Sciences (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Julie Ann Wrigley Global Institute of Sustainability (Contributor) / School of Sustainability (Contributor)
Created2017-09-12
Description
Background
Several past studies have found that media reports of suicides and homicides appear to subsequently increase the incidence of similar events in the community, apparently due to the coverage planting the seeds of ideation in at-risk individuals to commit similar acts.
Methods
Here we explore whether or not contagion is evident in more high-profile incidents, such as school shootings and mass killings (incidents with four or more people killed). We fit a contagion model to recent data sets related to such incidents in the US, with terms that take into account the fact that a school shooting or mass murder may temporarily increase the probability of a similar event in the immediate future, by assuming an exponential decay in contagiousness after an event.
Conclusions
We find significant evidence that mass killings involving firearms are incented by similar events in the immediate past. On average, this temporary increase in probability lasts 13 days, and each incident incites at least 0.30 new incidents (p = 0.0015). We also find significant evidence of contagion in school shootings, for which an incident is contagious for an average of 13 days, and incites an average of at least 0.22 new incidents (p = 0.0001). All p-values are assessed based on a likelihood ratio test comparing the likelihood of a contagion model to that of a null model with no contagion. On average, mass killings involving firearms occur approximately every two weeks in the US, while school shootings occur on average monthly. We find that state prevalence of firearm ownership is significantly associated with the state incidence of mass killings with firearms, school shootings, and mass shootings.
Several past studies have found that media reports of suicides and homicides appear to subsequently increase the incidence of similar events in the community, apparently due to the coverage planting the seeds of ideation in at-risk individuals to commit similar acts.
Methods
Here we explore whether or not contagion is evident in more high-profile incidents, such as school shootings and mass killings (incidents with four or more people killed). We fit a contagion model to recent data sets related to such incidents in the US, with terms that take into account the fact that a school shooting or mass murder may temporarily increase the probability of a similar event in the immediate future, by assuming an exponential decay in contagiousness after an event.
Conclusions
We find significant evidence that mass killings involving firearms are incented by similar events in the immediate past. On average, this temporary increase in probability lasts 13 days, and each incident incites at least 0.30 new incidents (p = 0.0015). We also find significant evidence of contagion in school shootings, for which an incident is contagious for an average of 13 days, and incites an average of at least 0.22 new incidents (p = 0.0001). All p-values are assessed based on a likelihood ratio test comparing the likelihood of a contagion model to that of a null model with no contagion. On average, mass killings involving firearms occur approximately every two weeks in the US, while school shootings occur on average monthly. We find that state prevalence of firearm ownership is significantly associated with the state incidence of mass killings with firearms, school shootings, and mass shootings.
ContributorsTowers, Sherry (Author) / Gomez-Lievano, Andres (Author) / Khan, Maryam (Author) / Mubayi, Anuj (Author) / Castillo-Chavez, Carlos (Author) / Simon M. Levin Mathematical, Computational and Modeling Sciences Center (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-07-02
Description
Background
Seroepidemiological studies before and after the epidemic wave of H1N1-2009 are useful for estimating population attack rates with a potential to validate early estimates of the reproduction number, R, in modeling studies.
Methodology/Principal Findings
Since the final epidemic size, the proportion of individuals in a population who become infected during an epidemic, is not the result of a binomial sampling process because infection events are not independent of each other, we propose the use of an asymptotic distribution of the final size to compute approximate 95% confidence intervals of the observed final size. This allows the comparison of the observed final sizes against predictions based on the modeling study (R = 1.15, 1.40 and 1.90), which also yields simple formulae for determining sample sizes for future seroepidemiological studies. We examine a total of eleven published seroepidemiological studies of H1N1-2009 that took place after observing the peak incidence in a number of countries. Observed seropositive proportions in six studies appear to be smaller than that predicted from R = 1.40; four of the six studies sampled serum less than one month after the reported peak incidence. The comparison of the observed final sizes against R = 1.15 and 1.90 reveals that all eleven studies appear not to be significantly deviating from the prediction with R = 1.15, but final sizes in nine studies indicate overestimation if the value R = 1.90 is used.
Conclusions
Sample sizes of published seroepidemiological studies were too small to assess the validity of model predictions except when R = 1.90 was used. We recommend the use of the proposed approach in determining the sample size of post-epidemic seroepidemiological studies, calculating the 95% confidence interval of observed final size, and conducting relevant hypothesis testing instead of the use of methods that rely on a binomial proportion.
Seroepidemiological studies before and after the epidemic wave of H1N1-2009 are useful for estimating population attack rates with a potential to validate early estimates of the reproduction number, R, in modeling studies.
Methodology/Principal Findings
Since the final epidemic size, the proportion of individuals in a population who become infected during an epidemic, is not the result of a binomial sampling process because infection events are not independent of each other, we propose the use of an asymptotic distribution of the final size to compute approximate 95% confidence intervals of the observed final size. This allows the comparison of the observed final sizes against predictions based on the modeling study (R = 1.15, 1.40 and 1.90), which also yields simple formulae for determining sample sizes for future seroepidemiological studies. We examine a total of eleven published seroepidemiological studies of H1N1-2009 that took place after observing the peak incidence in a number of countries. Observed seropositive proportions in six studies appear to be smaller than that predicted from R = 1.40; four of the six studies sampled serum less than one month after the reported peak incidence. The comparison of the observed final sizes against R = 1.15 and 1.90 reveals that all eleven studies appear not to be significantly deviating from the prediction with R = 1.15, but final sizes in nine studies indicate overestimation if the value R = 1.90 is used.
Conclusions
Sample sizes of published seroepidemiological studies were too small to assess the validity of model predictions except when R = 1.90 was used. We recommend the use of the proposed approach in determining the sample size of post-epidemic seroepidemiological studies, calculating the 95% confidence interval of observed final size, and conducting relevant hypothesis testing instead of the use of methods that rely on a binomial proportion.
ContributorsNishiura, Hiroshi (Author) / Chowell-Puente, Gerardo (Author) / Castillo-Chavez, Carlos (Author) / Simon M. Levin Mathematical, Computational and Modeling Sciences Center (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2011-03-24