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Background: Since 1990, the world’s homicide rate has declined by nearly 20%. While prior research has documented parallel homicide declines across many individual countries, the causes of a shared international homicide decline remain unknown. Drawing on a worldwide process of population ageing, and on research linking age to criminal activity, this study investigates the contribution of global demographic shifts to the international homicide decline. Methods: We draw from (1) a High Coverage Sample of 126 countries since 1990, and (2) a Long Series Sample of 26 countries since 1960 and utilize fixed-effect regressions to evaluate the impact of age structure on homicide trends. In addition, we use a quantile regression to explore variations in the relationship between age structure and homicide conditional on homicide levels. Findings: Results using the High Coverage Sample suggest no relationship between age structure and homicide. However, results from the Long Series Sample suggest that changes in the relative size of countries’ youth population is a major predictor of homicide trends since 1960. In exploring this divergence, we find that the influence of age structure on homicide becomes less evident as other risk factors for violence gain prominence. Thus, while high homicide countries had the most to gain from falling homicide rates, the safety benefits of an ageing population have been concentrated among the least violent countries. Interpretation: While the homicide declines of individual countries have often been attributed to domestic policies, the universality of international homicide trends suggests the influence of broader global phenomenon. We find that countries’ homicide trends are strongly associated with changes in the size of their youth populations, particularly where there are few competing criminogenic forces. Based on these results, we propose an explanation for the international homicide decline, while highlighting the importance of demographic patterns in explaining homicide trends. [ABSTRACT FROM AUTHOR]

HIV-1 gene expression is regulated by host and viral factors that interact with viral motifs and is influenced by proviral integration sites. Here, expression variation among integrants was followed for hundreds of individual proviral clones within polyclonal populations throughout successive rounds of virus and cultured cell replication, with limited findings using CD4+ cells from donor blood consistent with observations in immortalized cells. Tracking clonal behavior by proviral “zip codes” indicated that mutational inactivation during reverse transcription was rare, while clonal expansion and proviral expression states varied widely. By sorting for provirus expression using a GFP reporter in the nef open reading frame, distinct clone-specific variation in on/off proportions were observed that spanned three orders of magnitude. Tracking GFP phenotypes over time revealed that as cells divided, their progeny alternated between HIV transcriptional activity and non-activity. Despite these phenotypic oscillations, the overall GFP+ population within each clone was remarkably stable, with clones maintaining clone-specific equilibrium mixtures of GFP+ and GFP- cells. Integration sites were analyzed for correlations between genomic features and the epigenetic phenomena described here. Integrants inserted in the sense orientation of genes were more frequently found to be GFP negative than those in the antisense orientation, and clones with high GFP+ proportions were more distal to repressive H3K9me3 peaks than low GFP+ clones. Clones with low frequencies of GFP positivity appeared to expand more rapidly than clones for which most cells were GFP+, even though the tested proviruses were Vpr-. Thus, much of the increase in the GFP- population in these polyclonal pools over time reflected differential clonal expansion. Together, these results underscore the temporal and quantitative variability in HIV-1 gene expression among proviral clones that are conferred in the absence of metabolic or cell-type dependent variability, and shed light on cell-intrinsic layers of regulation that affect HIV-1 population dynamics. [ABSTRACT FROM AUTHOR]

Introduction: Metabolic risk factors for cardiovascular disease (CVD) warrant significant public health concern globally. This study aims to utilise the regional database of a major laboratory network to describe the geographic distribution pattern of eight different cardiometabolic risk factors (CMRFs), which in turn can potentially generate hypotheses for future research into locality specific preventive approaches. Method: A cross-sectional design utilising de-identified laboratory data on eight CMRFs including fasting blood sugar level (FBSL); glycated haemoglobin (HbA1c); total cholesterol (TC); high density lipoprotein (HDL); albumin creatinine ratio (ACR); estimated glomerular filtration rate (eGFR); body mass index (BMI); and diabetes mellitus (DM) status was used to undertake descriptive and spatial analyses. CMRF test results were dichotomised into ‘higher risk’ and ‘lower risk’ values based on existing risk definitions. Australian Census Statistical Area Level 1 (SA1) were used as the geographic units of analysis, and an Empirical Bayes (EB) approach was used to smooth rates at SA1 level. Choropleth maps demonstrating the distribution of CMRFs rates at SA1 level were produced. Spatial clustering of CMRFs was assessed using Global Moran’s I test and Local Indicators of Spatial Autocorrelation (LISA). Results: A total of 1,132,016 test data derived from 256,525 individuals revealed significant geographic variation in the distribution of ‘higher risk' CMRF findings. The populated eastern seaboard of the study region demonstrated the highest rates of CMRFs. Global Moran’s I values were significant and positive at SA1 level for all CMRFs. The highest spatial autocorrelation strength was found among obesity rates (0.328), and the lowest for albuminuria (0.028). LISA tests identified significant High-High (HH) and Low-Low (LL) spatial clusters of CMRFs, with LL predominantly in the less populated northern, central and southern regions of the study area. Conclusion: The study describes a range of CMRFs with different distributions in the study region. The results allow generation of hypotheses to test in future research concerning location specific population health approaches. [ABSTRACT FROM AUTHOR]

Aphids are major pests of wheat crop in Pakistan inflicting considerable economic losses. A better knowledge of landscape scale spatial distribution of aphids and their natural enemies could be used to improve integrated pest management programs. Therefore, the present study aimed to document spatio-temporal variations in populations of wheat aphids and their natural enemies in Pakistan. The 2-year survey study was carried out at ten experimental farms located in five districts of four contrasted agro-ecological zones of eastern Pakistan (Punjab area) i.e. District Chakwal in arid zone, Gujranwala in rice-cropped zone, Faisalabad in central mixed-cropped zone, and Khanewal and Multan in cotton-cropped zone. The dominant aphid species i.e. Schizaphis graminum, Rhopalosiphum padi, R. maidis and Sitobion avenae varied significantly among the five districts surveyed. The population of S. graminum was observed more abundant in arid, R. padi in rice, S. avenae in aird and rice, and R. maidis in cotton-I zones. Aphids ended their population dynamics on 25th March in central mixed-cropped zone and 12th April in other three zones. Various species of natural enemies, mainly Coccinella septumpunctata, C. undecimpunctata, Menochilus sexmaculata, Chrysoperla carnea, Syrphidae and parasitoid mummies were inconsistently observed in four agro-ecological zones. The population of C. septumpunctata, was observed more abundant in rice zone, C. undecimpunctata and C. carnea in cotton-I and arid zones, M. sexmaculata in cotton-I and II zones, Syrphidae in cotton-I zone and parasitoid mummies in rice and arid zones. There were no clear relationships between aphid and the natural enemy populations. The present study may serve as a baseline regarding distribution of wheat aphids and their natural enemies and the results provided insights for further studies on the potential top-down (natural enemies) versus bottom-up (fertilization and irrigation regimes) forces in management of wheat aphids in eastern Pakistan. [ABSTRACT FROM AUTHOR]

Attempts to assess behavioral responses of prey to predation risk are often confounded by depredation of prey. Moreover, the scale at which the response of prey is assessed has important implications for discovering how predation risk alters prey behavior. Herein, we assessed space use of wild Ring-necked Pheasants (Phasianus colchicus) in response to spatial and temporal variation in recreational hunting. We radio-marked pheasants and monitored space use at two spatial scales: short-term seasonal home range, and nightly resting locations. Additionally, we considered temporal variation in predation risk by monitoring space use prior to and during the pheasant hunting season. Although we found no change in nightly resting location, pheasants subjected to predation risk expanded their home range and shifted home range location even when invulnerable to predation. Home range formation was plastic, with home ranges expanding and contracting as risk fluctuated before and during the hunting season. Depredation reduced the measured response within the population, obscuring the potential importance of perceived predation risk in shaping prey communities, particularly when not measured at the appropriate scale. By assessing space use of a wild prey population at multiple scales, considering spatial and temporal variation in predation risk, we show that not only does predation risk affect space use, but that the effects at the population level may be challenging to assess when not measured at the appropriate ecological scale because of the direct effects of differential mortality on the same behaviors. [ABSTRACT FROM AUTHOR]

The true spatiotemporal structure of a fish population is often more complex than represented in assessments because movement between spawning components is disregarded and data at the necessary scale are unavailable. This can generate poor advice. We explore the impacts of modelling choices and their associated risks given limited data and lack of biological knowledge on spawning component structure and connectivity. Pseudo-data for an age structured fish population were simulated with two spawning components that experience various levels of connectivity and that might overlap during a certain period but segregate during reproduction. A variety of implicit spatiotemporal and simpler models were fitted to the pseudo-datasets, mimicking different situations of data availability. To reproduce the true stock characteristics, the spatiotemporal models required total catch data disaggregated by spawning component; however, catch-at-age was not as important nor were disaggregated biomass indices to reproduce true dynamics. Even with just 5% connectivity between spawning components, both the spatiotemporal models and simpler alternatives generally overestimated stock biomass. Although bias was smallest when considering one unit population, spawning components might still need to be considered for management and conservation. In such case, the spatiotemporal model was less influenced by ignored connectivity patterns compared to a model focussing on one spawning component only. [ABSTRACT FROM AUTHOR]

Seoul hantavirus (SEOV) has recently raised concern by causing geographic range expansion of hemorrhagic fever with renal syndrome (HFRS). SEOV infections in humans are significantly underestimated worldwide and epidemic dynamics of SEOV-related HFRS are poorly understood because of a lack of field data and empirically validated models. Here, we use mathematical models to examine both intrinsic and extrinsic drivers of disease transmission from animal (the Norway rat) to humans in a SEOV-endemic area in China. We found that rat eradication schemes and vaccination campaigns, but below the local elimination threshold, could diminish the amplitude of the HFRS epidemic but did not modify its seasonality. Models demonstrate population dynamics of the rodent host were insensitive to climate variations in urban settings, while relative humidity had a negative effect on the seasonality in transmission. Our study contributes to a better understanding of the epidemiology of SEOV-related HFRS, demonstrates asynchronies between rodent population dynamics and transmission rate, and identifies potential drivers of the SEOV seasonality. [ABSTRACT FROM AUTHOR]

Amphibians, the most threatened group of vertebrates, are seen as indicators of the sixth mass extinction on earth. Thousands of species are threatened with extinction and many have been affected by an emerging infectious disease, chytridiomycosis, caused by the fungal pathogen, Batrachochytrium dendrobatidis (Bd). However, amphibians exhibit different responses to the pathogen, such as survival and population persistence with infection, or mortality of individuals and complete population collapse after pathogen invasion. Multiple factors can affect host pathogen dynamics, yet few studies have provided a temporal view that encompasses both the epizootic phase (i.e. pathogen invasion and host collapse), and the transition to a more stable co-existence (i.e. recovery of infected host populations). In the Sierra Nevada mountains of California, USA, conspecific populations of frogs currently exhibit dramatically different host/ Bd-pathogen dynamics. To provide a temporal context by which present day dynamics may be better understood, we use a Bd qPCR assay to test 1165 amphibian specimens collected between 1900 and 2005. Our historical analyses reveal a pattern of pathogen invasion and eventual spread across the Sierra Nevada over the last century. Although we found a small number of Bd-infections prior to 1970, these showed no sign of spread or increase in infection prevalence over multiple decades. After the late 1970s, when mass die offs were first noted, our data show Bd as much more prevalent and more spatially spread out, suggesting epizootic spread. However, across the ~400km2 area, we found no evidence of a wave-like pattern, but instead discovered multiple, nearly-simultaneous invasions within regions. We found that Bd invaded and spread in the central Sierra Nevada (Yosemite National Park area) about four decades before it invaded and spread in the southern Sierra Nevada (Sequoia and Kings Canyon National Parks area), and suggest that the temporal pattern of pathogen invasion may help explain divergent contemporary host pathogen dynamics. [ABSTRACT FROM AUTHOR]

One approach to improving antibiotic stewardship in primary care may be to support all General Practitioners (GPs) to have access to point of care C-Reactive Protein tests to guide their prescribing decisions in patients presenting with symptoms of lower respiratory tract infection. However, to date there has been no work to understand how clinical commissioning groups might approach the practicalities of system-wide implementation. We aimed to develop an accessible service delivery modelling tool that, based on open data, could generate a layout of the geographical distribution of point of care facilities that minimised the cost and travel distance for patients across a given region. We considered different implementation models where point of care tests were placed at either GP surgeries, pharmacies or both. We analysed the trade-offs between cost and travel found by running the model under different configurations and analysing the model results in four regions of England (two urban, two rural). Our model suggests that even under assumptions of short travel distances for patients (e.g. under 500m), it is possible to achieve a meaningful reduction in the number of necessary point of care testing facilities to serve a region by referring some patients to be tested at nearby GP surgeries or pharmacies. In our test cases pharmacy-led implementation models resulted in some patients having to travel long distances to obtain a test, beyond the desired travel limits. These results indicate that an efficient implementation strategy for point of care tests over a geographic region, potentially building on primary care networks, might lead to significant cost reduction in equipment and associated personnel training, maintenance and quality control costs; as well as achieving fair access to testing facilities. [ABSTRACT FROM AUTHOR]

Background: Breast cancer is the most prevalent cancer among females worldwide including Sudan. The aim of this study was to determine the spatial distribution of breast cancer in Sudan. Materials and methods: A facility based cross-sectional study was implemented in eighteen histopathology laboratories distributed in the three localities of Khartoum State on a sample of 4630 Breast Cancer cases diagnosed during the period 2010–2016. A master database was developed through Epi InfoTM 7.1.5.2 for computerizing the data collected: the facility name, type (public or private), and its geo-location (latitude and longitude). Personal data on patients were extracted from their respective medical records (name, age, marital status, ethnic group, state, locality, administrative unit, permanent address and phone number, histopathology diagnosis). The data was summarized through SPSS to generate frequency tables for estimating prevalence and the geographical information system (ArcGIS 10.3) was used to generate the epidemiological distribution maps. ArcGIS 10.3 spatial analysis features were used to develop risk maps based on the kriging method. Results: Breast cancer prevalence was 3.9 cases per 100,000 female populations. Of the 4423 cases of breast cancer, invasive breast carcinoma of no special type (NST) was the most frequent (79.5%, 3517/4423) histopathological diagnosis. The spatial analysis indicated as high risk areas for breast cancer in Sudan the States of Nile River, Northern, Red Sea, White Nile, Northern and Southern Kordofan. Conclusions: The attempt to develop a predictive map of breast cancer in Sudan revealed three levels of risk areas (risk, intermediate and high risk areas); regardless the risk level, appropriate preventive and curative health interventions with full support from decision makers are urgently needed. [ABSTRACT FROM AUTHOR]

The South American plains vizcacha, Lagostomus maximus inhabits primarily the Pampean and adjoining Espinal, Monte and Chaquenean regions of Argentina. In order to study the population genetic structure of L. maximus, a fragment of 560 bp of the mitochondrial DNA hypervariable region 1from 90 individuals collected from the 3 subspecies and 8 groups along Argentina was amplified and analyzed. We found 9 haplotypes. The haplotype network did not show an apparent phylogeographical signal. Although low levels of genetic variation were found in all the subspecies and groups analyzed, a radiation of L. maximus would have occurred from the North and Center of the Pampean region toward the rest of its geographic range in Argentina. Low levels of genetic diversity, the existence of a single genetically distinct population in Argentina and changes of its effective size indicate that metapopulation processes and changes in human population dynamics during the late-Holocene were important factors shaping the population genetic structure of L. maximus in Argentina. [ABSTRACT FROM AUTHOR]

Most current methods for detecting natural selection from DNA sequence data are limited in that they are either based on summary statistics or a composite likelihood, and as a consequence, do not make full use of the information available in DNA sequence data. We here present a new importance sampling approach for approximating the full likelihood function for the selection coefficient. Our method treats the ancestral recombination graph (ARG) as a latent variable that is integrated out using previously published Markov Chain Monte Carlo (MCMC) methods. The method can be used for detecting selection, estimating selection coefficients, testing models of changes in the strength of selection, estimating the time of the start of a selective sweep, and for inferring the allele frequency trajectory of a selected or neutral allele. We perform extensive simulations to evaluate the method and show that it uniformly improves power to detect selection compared to current popular methods such as nSL and SDS, and can provide reliable inferences of allele frequency trajectories under many conditions. We also explore the potential of our method to detect extremely recent changes in the strength of selection. We use the method to infer the past allele frequency trajectory for a lactase persistence SNP (MCM6) in Europeans. We also infer the trajectory of a SNP (EDAR) in Han Chinese, finding evidence that this allele’s age is much older than previously claimed. We also study a set of 11 pigmentation-associated variants. Several genes show evidence of strong selection particularly within the last 5,000 years, including ASIP, KITLG, and TYR. However, selection on OCA2/HERC2 seems to be much older and, in contrast to previous claims, we find no evidence of selection on TYRP1. [ABSTRACT FROM AUTHOR]

A key question in ecology is the relative impact of internal nonlinear dynamics and external perturbations on the long-term trajectories of natural systems. Measles has been analyzed extensively as a paradigm for consumer-resource dynamics due to the oscillatory nature of the host-pathogen life cycle, the abundance of rich data to test theory, and public health relevance. The dynamics of measles in London, in particular, has acted as a prototypical test bed for such analysis using incidence data from the pre-vaccination era (1944–1967). However, during this timeframe there were few external large-scale perturbations, limiting an assessment of the relative impact of internal and extra demographic perturbations to the host population. Here, we extended the previous London analyses to include nearly a century of data that also contains four major demographic changes: the First and Second World Wars, the 1918 influenza pandemic, and the start of a measles mass vaccination program. By combining mortality and incidence data using particle filtering methods, we show that a simple stochastic epidemic model, with minimal historical specifications, can capture the nearly 100 years of dynamics including changes caused by each of the major perturbations. We show that the majority of dynamic changes are explainable by the internal nonlinear dynamics of the system, tuned by demographic changes. In addition, the 1918 influenza pandemic and World War II acted as extra perturbations to this basic epidemic oscillator. Our analysis underlines that long-term ecological and epidemiological dynamics can follow very simple rules, even in a non-stationary population subject to significant perturbations and major secular changes. [ABSTRACT FROM AUTHOR]

Land cover change is a key component of anthropogenic global environmental change, contributing to changes in environmental conditions of habitats. Deforestation is globally the most widespread and anthropogenically driven land cover change leading to conversion from closed forest to open non-forest habitat. This study investigates the relative roles of geographic features, characteristics of species climatic niche and species traits in determining the ability of open-habitat plant species to take advantage of recently opened habitats. We use current occurrence records of 18 herbaceous, predominantly open-habitat species of the genus Acaena (Rosaceae) to determine their prevalence in recently opened habitat. We tested correlation of species prevalence in anthropogenically opened habitat with (i) geographic features of the spatial distribution of open habitat, (ii) characteristics of species climatic niche, and (iii) species traits related to dispersal. While primary open habitat (naturally open) was characterised by cold climates, secondary open habitat (naturally closed but anthropogenically opened) is characterised by warmer and wetter conditions. We found high levels of variation in the species prevalence in secondary open habitat indicating species differences in their ability to colonise newly opened habitat. For the species investigated, geographical features of habitat and climatic niche factors showed generally stronger relationships with species prevalence in secondary open habitat than functional traits. Therefore, for small herbaceous species, geographical features of habitat and environmental factors appear to be more important than species functional traits for facilitating expansion into secondary open habitats. Our results suggested that the land cover change might have triggered the shifts of factors controlling open-habitat plant distributions from the competition with forest trees to current environmental constraints. [ABSTRACT FROM AUTHOR]

Seed germination traits are key drivers of population dynamics, yet they are under-represented in community ecology studies, which have predominately focussed on adult plant and seed morphological traits. We studied the seed traits and germination strategy of eight woody plant species to investigate regeneration strategies in the arid zone of eastern Australia. To cope with stochastic and minimal rainfall, we predict that arid seeds will either have rapid germination across a wide range of temperatures, improved germination under cooler temperatures, or dormancy and/or longevity traits to delay or stagger germination across time. To understand how temperature affects germination responses, seeds of eight keystone arid species were germinated under laboratory conditions, and under three diurnal temperatures (30/20°C, 25/15°C and 17/7°C) for 30 days. We also tested for decline in seed viability across 24 months in a dry-aging treatment (~20°C). Six of the eight arid species studied had non-dormant, rapidly germinating seeds, and only two species had physiological dormancy traits. Seed longevity differed widely between species, from one recalcitrant species surviving only months in aging (P50 = <3 months) and one serotinous species surviving for many years (P50 = 84 months). Our results highlight the importance of understanding the reproductive strategies of plant species in arid environments. Rapid germination, the dominant seed trait of species included in this study, allows arid species to capitalise on sporadic rainfall. However, some species also exhibit dormancy and delayed germination; this an alternative strategy which spreads the risk of germination failure over time. [ABSTRACT FROM AUTHOR]

We analyzed data from across five decades of passerine bird banding at Manomet in Plymouth, Massachusetts, USA. This included 172,609 captures during spring migration and 253,265 during fall migration, from 1969 to 2015. Migration counts are prone to large interannual variation and trends are often difficult to interpret, but have the advantage of sampling many breeding populations in a single locale. We employed a Bayesian state-space modeling approach to estimate patterns in abundance over time while accounting for observation error, and a hierarchical clustering method to identify species groups with similar trends over time. Although continent-wide there has been an overall decrease in landbird populations over the past 40 years, we found a variety of patterns in abundance over time. Consistent with other studies, we found an overall decline in numbers of birds in the aggregate, with most species showing significant net declines in migratory cohort size in spring, fall, or both (49/73 species evaluated). Other species, however, exhibited different patterns, including abundance increases (10 species). Even among increasing and declining species, the specific trends varied in shape over time, forming seven distinct clusters in fall and ten in spring. The remaining species followed largely independent and irregular pathways. Overall, life-history traits (dependence on open habitat, nesting on or near the ground, migratory strategy, human commensal, spruce budworm specialists) did a poor job of predicting species groupings of abundance patterns in both spring and fall, but median date of passage was a good predictor of abundance trends during spring (but not fall) migration. This suggests that some species with very similar patterns of abundance were unlikely to be responding to the same environmental forces. Changes in abundance at this banding station were generally consistent with BBS trend data for the same geographic region. [ABSTRACT FROM AUTHOR]

Invasive predators have caused rapid declines in many native prey species across the globe. Predator invasion success may be attributed to prey naïveté, or the absence of anti-predator behavior between native and non-native species. An understanding of the effects of naïveté at different timescales since introduction and across multiple trophic levels is lacking, however, particularly in marine systems. Given the central role of trophic interactions in invasion dynamics, this knowledge gap limits the ability to predict high impact predator invasions. Naïveté was examined across three trophic levels of marine invertebrates: a native basal prey (hard clam), two non-native intermediate predators (the recently-introduced Asian shore crab and the long-established European green crab), a native intermediate predator (juvenile blue crabs), and a native top predator (adult blue crab). We hypothesized that naïveté would be more pronounced in trophic interactions involving the recently-introduced non-native predator in comparison to the long-established non-native and native intermediate predators. We further hypothesized that the recently-introduced intermediate predator would both benefit from naïveté of the native basal prey and be hindered by higher mortality through its own naïveté to the native top predator. To test these hypotheses, three laboratory experiments and a field experiment were used. Consistent with our hypotheses, basal prey naïveté was most pronounced with the recently-introduced intermediate predator, and this increased the predator’s foraging success. This recently-introduced intermediate predator, however, exhibited an ineffective anti-predator response to the native top predator, and was also preyed upon more in the field than its long-established and native counterparts. Therefore, despite direct benefits from basal prey naïveté, the recently-introduced intermediate predator’s naïveté to its own predators may limit its invasion success. These results highlight the importance of a multi-trophic perspective on predator-prey dynamics to more fully understand the consequences of naïveté in invasion biology. [ABSTRACT FROM AUTHOR]

Climate change is amongst the main threats to biodiversity. Considering extant mammals endured Quaternary climate change, we analyzed the extent to which this past change predicts current mammals’ extinction risk at global and biogeographical scales. We accessed range dynamics by modeling the potential distribution of all extant terrestrial mammals in the Last Glacial Maximum (LGM, 21,000 years ago) and in current climate conditions and used extinction risk from IUCN red list. We built General Linear Mixed-Effects Models to test the magnitude with which the variation in geographic range (ΔRange) and a proxy for abundance (ΔSuitability) between the LGM and present-day predicts current mammal’s extinction risk. We found past climate change most strongly reduced the geographical range and climatic suitability of threatened rather than non-threatened mammals. Quaternary range contractions and reduced suitability explain around 40% of species extinction risk, particularly for small-bodied mammals. At global and biogeographical scales, all groups that suffered significant Quaternary range contractions now contain a greater proportion of threatened species when compared to groups whose ranges did not significantly contract. This reinforces the importance of using historical range contractions as a key predictor of extinction risk for species in the present and future climate change scenarios and supports current efforts to fight climate change for biodiversity conservation. [ABSTRACT FROM AUTHOR]

Background: Stroke is a major public health concern due to the morbidity and mortality associated with it. Identifying geographic areas with high stroke prevalence is important for informing public health interventions. Therefore, the objective of this study was to investigate geographic disparities and identify geographic hotspots of stroke prevalence in Florida. Materials and methods: County-level stroke prevalence data for 2013 were obtained from the Florida Department of Health’s Behavioral Risk Factor Surveillance System (BRFSS). Geographic clusters of stroke prevalence were investigated using the Kulldorff’s circular spatial scan statistics (CSSS) and Tango’s flexible spatial scan statistics (FSSS) under Poisson model assumption. Exact McNemar’s test was used to compare the proportion of cluster counties identified by each of the two methods. Both Cohen’s Kappa and bias adjusted Kappa were computed to assess the level of agreement between CSSS and FSSS methods of cluster detection. Goodness-of-fit of the models were compared using Cluster Information Criterion. Identified clusters and selected stroke risk factors were mapped. Results: Overall, 3.7% of adults in Florida reported that they had been told by a healthcare professional that they had suffered a stroke. Both CSSS and FSSS methods identified significant high prevalence stroke spatial clusters. However, clusters identified using CSSS tended to be larger than those identified using FSSS. The FSSS had a better fit than the CSSS. Most of the identified clusters are explainable by the prevalence distributions of the known risk factors assessed. Conclusions: Geographic disparities of stroke risk exists in Florida with some counties having significant hotspots of high stroke prevalence. This information is important in guiding future research and control efforts to address the problem. Kulldorff’s CSSS and Tango’s FSSS are complementary to each other and should be used together to provide a more complete picture of the distributions of spatial clusters of health outcomes. [ABSTRACT FROM AUTHOR]

The production of anticompetitor toxins is widespread among bacteria. Because production of such toxins is costly, it is typically regulated. In particular, many toxins are produced only when the local cell density is high. It is unclear which selection pressures shaped the evolution of density-dependent regulation of toxin production. Here, we study the evolution of toxin production, resistance and the response to a cell-density cue in a model of an evolving bacterial population with spatial structure. We present results for two growth regimes: (i) an undisturbed, fixed habitat in which only small fluctuations of cell density occur, and (ii) a serial-transfer regime with large fluctuations in cell density. We find that density-dependent toxin production can evolve under both regimes. However, the selection pressures driving the evolution of regulation differ. In the fixed habitat, regulation evolves because it allows cells to produce toxin only when opportunities for reproduction are highly limited (because of a high local cell density), and the effective fitness costs of toxin production are hence low. Under serial transfers, regulation evolves because it allows cells to switch from a fast-growing non-toxic phenotype when colonising a new habitat, to a slower-growing competitive toxic phenotype when the cell density increases. Colonies of such regulating cells rapidly expand into unoccupied space because their edges consist of fast-growing, non-toxin-producing cells, but are also combative because cells at the interfaces with competing colonies do produce toxin. Because under the two growth regimes different types of regulation evolve, our results underscore the importance of growth conditions in the evolution of social behaviour in bacteria. [ABSTRACT FROM AUTHOR]

Visceral leishmaniasis (VL) is a zoonosis caused by the protozoan Leishmania infantum and in Brazil is transmitted mainly by the bite of Lutzomuyia longipalpis sand flies. Data about the presence, distribution, natural infection rate, seasonal and monthly dynamics of the vector population are important for optimizing the measures to control VL in endemic areas. This study aimed to identify sand fly fauna in an endemic area for VL to detect the prevalence of L. infantum infection in the Lu. longipalpis population and to elucidate the influence of bioclimatic factors on the monthly fluctuations of this vector. HP light traps were monthly set in the intradomicile and peridomicile of residences located in the central and beachfront areas of Camaçari, a VL endemic area. The sand fly collection was conducted in two periods: i) period 1—between December 2011 and November 2012 and ii) period 2—August 2014 and July 2015. Sand fly species were identified and detection of L. infantum infection by qPCR was performed in pools of female Lu. longipalpis. For the first time, the parasite load of positive pools was correlated with the number of Lu. longipalpis captured per month in both periods. Correlation analyses between the monthly fluctuation of the sand fly population and bioclimatic indices of the municipality in both collection periods were also performed. In both evaluated periods, more than 98% of the collected sand flies were Lu. longipalpis, confirming the predominance of this species in the region. It was captured mostly in the beachfront area in all months evaluated (99%). For the period 1, Leishmania DNA was detected in 81% of tested pools representing a minimal infection rate of 9.6%. In the period 2, 40% of the pools were positive with a minimal infection rate of 10.2%. Infected sand flies were only detected in the beachfront area in both periods. The parasite load was low and did not vary in the evaluated months despite the number of collected sand flies. No correlation was observed for climatic factors in both areas of Camaçari. These findings emphasize the high risk of Leishmania transmission in Camaçari regardless of the season and that other factors, aside from bioclimatic elements, are influencing the sand fly population monthly fluctuation. [ABSTRACT FROM AUTHOR]

The Arctic is undergoing rapid changes, with anthropogenic shifts in climate having important and well-documented impacts on habitat. Populations of predators and their prey are affected by changing climate and other anthropogenic factors, and these changing trophic interactions could have profound effects on breeding populations of Arctic birds. Variable abundance of lemmings (a primary prey of generalist Arctic predators) and increasing abundance of light geese (Lesser Snow and Ross’ Geese; a secondary prey) could have negative consequences for numerous sympatric shorebirds (an incidental prey). Using 16 years of predator-prey observations and 13-years of shorebird nest survival data at a site near a goose colony we identify relationships among geese, lemmings, and their shared predators and then relate predator indices to shorebird risk of nest predation. During two years, we also placed time-lapse cameras and artificial shorebird nests at increasing distances from a goose colony to document spatial trends in predators and their effect on risk of predation. In the long-term data, yearly indices of light geese positively influenced indices of gulls and jaegers, and shorebird nest predation rate was negatively correlated with jaeger and fox indices. All three predator indices were highest near the goose colony and artificial nest predation probability was negatively correlated with distance from goose colony, but these effects were less apparent during the second year. Combined, these results highlight the variation in predator-mediated interactions between geese and shorebirds and outline one mechanism by which hyperabundant geese may be contributing to local or regional declines in Arctic-nesting shorebird populations. [ABSTRACT FROM AUTHOR]

Background: Natural-focal diseases are serious diseases that endanger human health. They threaten about 100 million people in Shandong Province, and cause illness in thousands of people each year. However, information on the epidemiological characteristics of natural-focal diseases in Shandong Province has been limited. The purpose of the study was to describe and analyze the epidemiological characteristics of natural-focal diseases in Shandong Province, 2009–2017. Methods: We describe the incidence and distribution of four natural-focal diseases in Shandong Province using surveillance data from 2009–2017. Results: From 2009–2017, 11123 cases of four natural-focal diseases including 257 deaths were reported in Shandong Province, China. The four natural-focal diseases were severe fever with thrombocytopenia syndrome (SFTS), human granulocytic anaplasmosis (HGA), typhus, and scrub typhus. The high-risk groups of the four diseases were farmers and the elderly. The incidence rate of scrub typhus was significantly higher in females. However, this difference was not seen in the other three diseases. The four diseases were mainly clustered in the middle-southern part of Shandong Province and the Shandong Peninsula. The annual incidence of SFTS and scrub typhus increased, typhus was relatively stable, and HGA declined. However, the range of SFTS expanded, while HGA shrunk, and typhus and scrub typhus were unchanged. The epidemic period of SFTS and HGA was from May to October, typhus was from October to November, and scrub typhus was from September to November. The fatality rates of SFTS, typhus, scrub typhus, and HGA were 9.19%, 0%, 0.01%, and 2.24%, respectively. Conclusions: Our study described and analyzed the prevalence of natural-focal diseases in Shandong Province, and confirmed that age was closely related to the SFTS fatality rate. This study may help to improve the understanding of the prevalence of natural-focal diseases in Shandong Province in recent years and to better develop accurate prevention and control strategies for natural-focal diseases. [ABSTRACT FROM AUTHOR]

Species and ecosystems usually face more than one threat. The damage caused by these multiple threats can accumulate nonlinearly: either subadditively, when the joint damage of combined threats is less than the damages of both threats individually added together, or superadditively, when the joint damage is greater than the two individual damages added together. These additivity dynamics are commonly attributed to the nature of the threatening processes, but conflicting empirical observations challenge this assumption. Here, we use a theoretical model to demonstrate that the additivity of threats can change with different magnitudes of threat impacts (effect of a threat on the population parameter, like growth rate). We use a harvested single-species population model to integrate the effects of multiple threats on equilibrium abundance. Our results reveal that threats do not always display consistent additive behavior, even in simple systems. Instead, their additivity depends on the magnitudes of the impacts of two threats, and the population parameter that is impacted by each threat. In our model specifically, when multiple threats have a low impact on the growth rate of a population, they display superadditive dynamics. In contrast, threats that impact the species’ carrying capacity are always additive or subadditive. These dynamics can be understood by reference to the curvature of the relationship between a given population parameter (e.g., growth) and equilibrium population size. Our results suggest that management actions can achieve amplified benefits if they target low-amplitude threats that affect the growth rate, since these will be in a superadditive phase. More generally, our results suggest that cumulative impact theory should focus more than previously on the magnitude of the impact on the population parameter, and should be cautious about attributing additive dynamics to particular threat combinations. [ABSTRACT FROM AUTHOR]

Pollen can decrease (via reduced consumption) or increase (via numerical response) an omnivores consumption of animal prey. Although pollen can increase predation pressure through numerical responses of omnivores, pollen may also suppress predation by increasing omnivore interactions with conspecifics. Despite this potential, studies of the impacts of pollen on predation by omnivores often overlook the effect of these tissues on intraspecific interactions between omnivores. We designed three studies to examine how Spartina foliosa pollen and conspecific density impact scale insect prey consumption by ladybeetle (Naemia seriata) omnivores. First, we assessed how pollen impacts scale insect consumption by isolated ladybeetles. Second, we measured how pollen influences ladybeetle prey suppression when numerical responses were possible. Third, because initial experiments suggested the consumption rates of individual ladybeetles depended on conspecific density, we compared per capita consumption rates of ladybeetles across ladybeetle density. Pollen did not influence prey consumption by isolated ladybeetles. When numerical responses were possible, pollen did not influence total predation on prey despite increasing ladybeetle density, suggesting that pollen decreased per capita prey consumption by ladybeetles. The discrepancy between these studies is likely a consequence of differences in ladybeetle density—the presence of only two other conspecifics decreased per capita prey consumption by 76%. Our findings suggest that pollen may not alter the population level effects of omnivores on prey when omnivore numerical responses are offset by reductions in per capita predation rate. [ABSTRACT FROM AUTHOR]

Forage fishes play an important role in marine ecosystems by transferring energy and nutrients through the food web. The population dynamics of forage species can therefore have cascading effects across multiple trophic levels. Here, we analyzed a 19-year dataset on Pinfish (Lagodon rhomboides) across four eastern Gulf of Mexico estuaries to investigate population dynamics, inter- and intra-annual synchrony, metapopulation portfolio effects, growth, and habitat effects. Young-of-year growth rates did not differ among estuaries. The population dynamics of these four systems were stable in the long-term, but highly dynamic inter-annually. Intra-annual dynamics were stable and predictable despite variation in long-term means. Some estuaries exhibited positive inter-annual synchrony, and all four estuaries were synchronous intra-annually. There was evidence for stronger portfolio effects for the entire four-estuary metapopulation, as well as for the two northern estuaries while the southern estuaries appeared to act as a single population. Submerged aquatic vegetation was by far the most important predictor for both presence and abundance of Pinfish. It is important to understand the factors driving forage fish population fluctuations to better predict ecosystem effects, including those to species of economic and ecological importance. These predictors can be useful for the implementation of ecosystem-based management decisions. [ABSTRACT FROM AUTHOR]

The bonnethead shark, Sphyrna tiburo, is a small elasmobranch distributed in the Eastern Pacific from southern California to Ecuador, and along the Western Atlantic, with preferences for continental margins of North, Central and South America, the Gulf of Mexico, and the Caribbean. Recent studies have suggested that it could be under a process of cryptic speciation, with the possibility to find different species in similar geographic locations. Here we assessed the population structure and genetic diversity of this highly philopatric and non-dispersive species in the Bocas del Toro Archipelago, Panama. Fragments of the mitochondrial genes cytochrome oxidase I and control region, were used to test the genetic structure of adult and juvenile S. tiburo in this area, and were compared with other locations of the Western Atlantic and Belize. We found significant genetic differentiation between Caribbean bonnethead sharks from Bocas del Toro and Belize, when compared to bonnetheads from other locations of the Western Atlantic. These results also suggest that Bocas del Toro could constitute a different genetic population unit for this species, whereby bonnethead sharks in this area could belong to a unique stock. The information obtained in this study could improve our understanding of the population dynamics of the bonnethead shark throughout its distribution range, and may be used as a baseline for future conservation initiatives for coastal sharks in Central America, a poorly studied an often overlooked region for shark conservation and research. [ABSTRACT FROM AUTHOR]

In the past 40 years of reform and opening-up, China has developed from an economically closed country to a country that is highly dependent on foreign trade. From the perspective of spatiotemporal evolution, we analyze how port opening promoted China's reform and opening-up process. First, the port development process is divided into four periods. In the start-up period, the pilot open port policy created a platform for foreign cooperation and exchange. During the expansion period, port openings promoted the continuous optimization of the trade structure. In the cooperation period, port openings corresponded with the adjustment of China's overall industrial structure. During the optimization period, port openings provided guarantees for the implementation of a national development strategy. Second, we analyze the distribution of ports and their relationship with cross-border logistics and passenger flow. Based on data of foreign trade and passenger flow, a port openness degree measurement model includes port logistics intensity, passenger flow intensity and port city foreign-trade volume is constructed. There are significant types, geographical differences and grade differences of ports' openness. [ABSTRACT FROM AUTHOR]

From the microscopic to the macroscopic level, biological life exhibits directed migration in response to environmental conditions. Chemotaxis enables microbes to sense and move towards nutrient-rich regions or to avoid toxic ones. Socio-economic factors drive human populations from rural to urban areas. The effect of collective movement is especially significant when triggered in response to the generation of public goods. Microbial communities can, for instance, alter their environment through the secretion of extracellular substances. Some substances provide antibiotic-resistance, others provide access to nutrients or promote motility. However, in all cases the maintenance of public goods requires costly cooperation and is consequently susceptible to exploitation. The threat of exploitation becomes even more acute with motile individuals because defectors can avoid the consequences of their cheating. Here, we propose a model to investigate the effects of targeted migration and analyze the interplay between social conflicts and migration in ecological public goods. In particular, individuals can locate attractive regions by moving towards higher cooperator densities or avoid unattractive regions by moving away from defectors. Both migration patterns not only shape an individual’s immediate environment but also affects the entire population. For example, defectors hunting cooperators have a homogenizing effect on population densities. This limits the production of the public good and hence inhibits the growth of the population. In contrast, aggregating cooperators promote the spontaneous formation of patterns through heterogeneous density distributions. The positive feedback between cooperator aggregation and public goods production, however, poses analytical and numerical challenges due to its tendency to develop discontinuous distributions. Thus, different modes of directed migration bear the potential to enhance or inhibit the emergence of complex and sometimes dynamic spatial arrangements. Interestingly, whenever patterns emerge, cooperation is promoted, on average, population densities rise, and the risk of extinction is reduced. [ABSTRACT FROM AUTHOR]

Seemingly minor details of mathematical and computational models of evolution are known to change the effect of population structure on the outcome of evolutionary processes. For example, birth-death dynamics often result in amplification of selection, while death-birth processes have been associated with suppression. In many biological populations the interaction structure is not static. Instead, members of the population are in motion and can interact with different individuals at different times. In this work we study populations embedded in a flowing medium; the interaction network is then time dependent. We use computer simulations to investigate how this dynamic structure affects the success of invading mutants, and compare these effects for different coupled birth and death processes. Specifically, we show how the speed of the motion impacts the fixation probability of an invading mutant. Flows of different speeds interpolate between evolutionary dynamics on fixed heterogeneous graphs and well-stirred populations; this allows us to systematically compare against known results for static structured populations. We find that motion has an active role in amplifying or suppressing selection by fragmenting and reconnecting the interaction graph. While increasing flow speeds suppress selection for most evolutionary models, we identify characteristic responses to flow for the different update rules we test. In particular we find that selection can be maximally enhanced or suppressed at intermediate flow speeds. [ABSTRACT FROM AUTHOR]

Dengue virus serotype 4 (DENV 4) has had a relatively low prevalence worldwide for decades; however, likely due to data paucity, no study has investigated the epidemiology and evolutionary dynamics of DENV 4 genotype I (DENV 4-I). This study aims to understand the diversity, epidemiology and dynamics of DENV 4-I. We collected 404 full length DENV4-1 envelope (E) gene sequences from 14 countries using two sources: Yunnan Province in China (15 strains during 2013–2016) and GenBank (489 strains up to 2018-01-11). Conducting phylogenetic and phylogeographical analyses, we estimated the virus spread, population dynamics, and selection pressures using different statistical analysis methods (substitution saturation, likelihood mapping, Bayesian coalescent inference, and maximum likelihood estimation). Our results show that during the last 60 years (1956–2016), DENV 4-I was present in mainland and maritime Southeast Asia, the Indian subcontinent, the southern provinces of China, parts of Brazil and Australia. The recent spread of DENV 4-I likely originated in the Philippines and later spread to Thailand. From Thailand, it spread to adjacent countries and eventually the Indian subcontinent. Apparently diverging around years 1957, 1963, 1976 and 1990, the different Clades (Clade I-V) were defined. The mean overall evolution rate of DENV 4-I was 9.74 (95% HPD: 8.68–10.82) × 10−4 nucleotide substitutions/site/year. The most recent common ancestor for DENV 4-I traces back to 1956. While the demographic history of DENV 4-I fluctuated, peaks appeared around 1982 and 2006. While purifying selection dominated the majority of E-gene evolution of DENV 4-I, positive selection characterized Clade III (Vietnam). DENV 4-I evolved in situ in Southeast Asia and the Indian subcontinent. Thailand and Indian acted as the main and secondary virus distribution hubs globally and regionally. Our phylogenetic analysis highlights the need for strengthened regional cooperation on surveillance and sharing of sample sequences to improve global dengue control and cross-border transmission prevention efforts. [ABSTRACT FROM AUTHOR]

Open access publication rates have been steadily increasing over time. In spite of this growth, academics in low income settings struggle to gain access to the full canon of research literature. While the vast majority of open access repositories and funding organizations with open access policies are based in high income countries, the geographic patterns of open access publication itself are not well characterized. In this study, we developed a computational approach to better understand the topical and geographical landscape of open access publications in the biomedical research literature. Surprisingly, we found a strong negative correlation between country per capita income and the percentage of open access publication. Open access publication rates were particularly high in sub-Saharan Africa, but vastly lower in the Middle East and North Africa, South Asia, and East Asia and the Pacific. These effects persisted when considering papers only bearing authors from within each region and income group. However, papers resulting from international collaborations did have a higher percentage of OA than single-country papers, and inter-regional collaboration increased OA publication for all world regions. There was no clear relationship between the number of open access policies in a region and the percentage of open access publications in that region. To understand the distribution of open access across topics of biomedical research, we examined keywords that were most enriched and depleted in open access papers. Keywords related to genomics, computational biology, animal models, and infectious disease were enriched in open access publications, while keywords related to the environment, nursing, and surgery were depleted in open access publications. This work identifies geographic regions and fields of research that could be priority areas for open access advocacy. The finding that open access publication rates are highest in sub-Saharan Africa and low income countries suggests that factors other than open access policy strongly influence authors’ decisions to make their work openly accessible. The high proportion of OA resulting from international collaborations indicates yet another benefit of collaborative research. Certain applied fields of medical research, notably nursing, surgery, and environmental fields, appear to have a greater proportion of fee-for-access publications, which presumably creates barriers that prevent researchers and practitioners in low income settings from accessing the literature in those fields. [ABSTRACT FROM AUTHOR]

A central issue in the study of the neural generation of respiratory rhythms is the role of the intrinsic pacemaking capabilities that some respiratory neurons exhibit. The debate on this issue has occurred in parallel to investigations of interactions among respiratory network neurons and how these contribute to respiratory behavior. In this computational study, we demonstrate how these two issues are inextricably linked. We use simulations and dynamical systems analysis to show that once a conditional respiratory pacemaker, which can be tuned across oscillatory and non-oscillatory dynamic regimes in isolation, is embedded into a respiratory network, its dynamics become masked: the network exhibits similar dynamical properties regardless of the conditional pacemaker node’s tuning, and that node’s outputs are dominated by network influences. Furthermore, the outputs of the respiratory central pattern generator as a whole are invariant to these changes of dynamical properties, which ensures flexible and robust performance over a wide dynamic range. [ABSTRACT FROM AUTHOR]

Objective: To identity differences between a general access index (Accessibility/ Remoteness Index of Australia; ARIA+) and a specific acute and aftercare cardiac services access index (Cardiac ARIA). Research design and methods: Exploratory descriptive design. ARIA+ (2011) and Cardiac ARIA (2010) were compared using cross-tabulations (chi-square test for independence) and map visualisations. All Australian locations with ARIA+ and Cardiac ARIA values were included in the analysis (n = 20,223). The unit of analysis was Australian locations. Results: Of the 20,223 locations, 2757 (14% of total) had the highest level of acute cardiac access coupled with the highest level of general access. There were 1029 locations with the poorest access (5% of total). Approximately two thirds of locations in Australia were classed as having the highest level of cardiac aftercare. Locations in Major Cities, Inner Regional Australia, and Outer Regional Australia accounted for approximately 98% of this category. There were significant associations between ARIA+ and Cardiac ARIA acute (χ2 = 25250.73, df = 28, p<0.001, Cramer’s V = 0.559, p<0.001) and Cardiac ARIA aftercare (χ2 = 17204.38, df = 16, Cramer’s V = 0.461, p<0.001). Conclusions: Although there were significant associations between the indices, ARIA+ and Cardiac ARIA are not interchangeable. Systematic differences were apparent which can be attributed largely to the underlying specificity of the Cardiac ARIA (a time critical index that uses distance to the service of interest) compared to general accessibility quantified by the ARIA+ model (an index that uses distance to population centre). It is where the differences are located geographically that have a tangible impact upon the communities in these locations–i.e. peri-urban areas of the major capital cities, and around the more remote regional centres. There is a strong case for specific access models to be developed and updated to assist with efficient deployment of resources and targeted service provision. The reasoning behind the differences highlighted will be generalisable to any comparison between general and service-specific access models. [ABSTRACT FROM AUTHOR]

Residential segregation into spatial neighborhoods and boroughs is a well-known spatial dynamic process that characterise complex urban environments. Existing models of segregation, including the pioneering Schelling ones, often do not consider all the factors that can contribute to this process. Segregation as well as aggregation emerges from local interactions among individuals, and is rooted in the complexity of social, economic and environmental interactions. The main objective of this study is to develop and implement a geospatial agent-based model to simulate the decision-making process of location of new household for incoming immigrant populations. Particularly this study aims to simulate and analyse the dynamics of the new immigrant populations arriving in the bilingual cities and boroughs of the island of Montreal. The model was implemented in NetLogo software, using real geospatial datasets. The obtained simulation results indicate realistic spatial patterns of spatial composition of the ethnographic fabric on the island of Montreal. The proposed model has the potential to be used as part of the city planning purposes. [ABSTRACT FROM AUTHOR]

Coffee is a crop of significant importance for Brazilian agrobusiness. There is evidence that both the geographic distribution of coffee production, and the varieties of coffee produced, have changed throughout Brazil over the course of time. Furthermore, it appears that these developments are associated with structural changes resulting from reductions in government intervention and its effects on prices in the coffee market, which has established a new dynamic of coffee production in the country. In this context, this study’s objective is to analyze the dynamics of coffee production in Brazil, to identify the Brazilian micro-regions specializing in coffee activities, and to track how the spatial distribution of these micro-regions has varied over time. In so doing, the study aims to identify defining economic characteristics of primary coffee-producing regions. Drawing primarily on data from the Brazilian Institute of Geography and Statistics, the study proceeds by applying Pearson correlation, Granger causality test, location quotient, principal components, and clustering analyses to explore how, during the 1984–2015 period, significant changes occurred in the distribution of regions specializing in coffee production. States such as Paraná and São Paulo, historically important coffee producers, declined in importance, leaving only a few micro-regions in these states specialized in coffee production. During the 2014/15 biennium, 80% of the coffee-specialized micro-regions were concentrated in the states of Minas Gerais, Bahia, Rondônia, and Espírito Santo. Minas Gerais and Bahia primarily produced arabica coffee, while Rondônia specialized in conilon (robusta) coffee. Overall, coffee produced in Brazil improved in quality and value-added over this period. [ABSTRACT FROM AUTHOR]

Toxoplasma gondii is a zoonotic protozoan with a worldwide occurrence, but the determinants of the current pattern in the geographical distribution of T. gondii lineages and strains remain poorly understood. To test the influence of human trade on T. gondii populations, we conducted a population genetic study of 72 T. gondii animal isolates from Senegal, a West African country in which the ongoing inland progress of invasive murine hosts (introduced in port cities of Senegal since the 16th century by European sailors) is well described. Isolates were mainly collected on free-range poultry, which are considered as relevant bioindicators of T. gondii strain diversity in the domestic environment. Sampling was conducted in two port cities of Senegal (Dakar and Saint-Louis) and in one inland region (Kedougou). Population genetic analyses using 15 microsatellite markers revealed different patterns between port cities where lineages non-virulent for mice (type II, type III, and Africa 4) were predominant, and Kedougou where the mouse-virulent Africa 1 lineage was the most common. By considering the current spatial pattern in the inland progress of invasive rodents in Senegal, our results suggest that the invasive house mouse Mus musculus domesticus counter-selects the Africa 1 lineage in the invaded areas. The comparison of the microsatellite alleles of type II strains from Senegal to type II strains from other areas in Africa and Western Europe, using discriminant analysis of principal components and Network analysis, point to a mainly Western European origin of the type II lineage in Senegal. Collectively, these findings suggest that human-mediated intercontinental migrations of murine hosts are important vectors of T. gondii strains. Differential susceptibility of endemic and introduced murine hosts to various T. gondii strains probably determines the persistence of these strains in the environment, and therefore their availability for human and animal infection. [ABSTRACT FROM AUTHOR]

The East African Indian (EAI) and Central Asian (CAS) lineages of Mycobacterium tuberculosis complex (MTBC) mainly infect tuberculosis (TB) patients in the eastern hemisphere which contains many of the 22 high TB burden countries including China and India. We investigated if phylogeographical, epidemiological and demographical characteristics for these 2 lineages differed in SITVIT2 database. Genotyping results and associated data (age, sex, HIV serology, drug resistance) on EAI and CAS lineages (n = 10,974 strains) were extracted. Phylogenetic and Bayesian, and other statistical analyses were used to compare isolates. The male/female sex ratio was 907/433 (2.09) for the EAI group vs. 881/544 (1.62) for CAS (p-value<0.002). The proportion of younger patients aged 0–20 yrs. with CAS lineage was significantly higher than for EAI lineage (18.07% vs. 10.85%, p-value<0.0001). The proportion of multidrug resistant and extensively drug resistant TB among CAS group (30.63% and 1.03%, respectively) was significantly higher than in the EAI group (12.14% and 0.29%, respectively; p-value<0.0001). Lastly, the proportion of HIV+ patients was 20.34% among the EAI group vs. 3.46% in the CAS group (p-value<0.0001). This remarkable split observed between various parameters for these 2 lineages was further corroborated by their geographic distribution profile (EAI being predominantly found in Eastern-Coast of Africa, South-India and Southeast Asia, while CAS was predominantly found in Afghanistan, Pakistan, North India, Nepal, Middle-east, Libya, Sudan, Ethiopia, Kenya and Tanzania). Some geo-specificities were highlighted. This study demonstrated a remarkable cleavage for aforementioned characteristics of EAI and CAS lineages, showing a North-South divide along the tropic of cancer in Eastern hemisphere–mainly in Asia, and partly prolonged along the horn of Africa. Such studies would be helpful to better comprehend prevailing TB epidemic in context of its historical spread and evolutionary features, and provide clues to better treatment and patient-care in countries and regions concerned by these lineages. [ABSTRACT FROM AUTHOR]

Taking inspiration from the archaeology of the Texas Coastal Plain (TCP), we develop an ecological theory of population distribution among mobile hunter-gatherers. This theory proposes that, due to the heterogeneity of resources in space and time, foragers create networks of habitats that they access through residential cycling and shared knowledge. The degree of cycling that individuals exhibit in creating networks of habitats, encoded through social relationships, depends on the relative scarcity of resources and fluctuations in those resources. Using a dynamic model of hunter-gatherer population distribution, we illustrate that increases in population density, coupled with shocks to a biophysical or social system, creates a selective environment that favors habitat partitioning and investments in social mechanisms that control the residential cycling of foragers on a landscape. Our work adds a layer of realism to Ideal Distribution Models by adding a time allocation decision process in a variable environment and illustrates a general variance reduction, safe-operating space tradeoff among mobile human foragers that drives social change. [ABSTRACT FROM AUTHOR]

In this work we analyze potential environmental drivers of malaria cases in Northwestern Argentina. We inspect causal links between malaria and climatic variables by means of the convergent cross mapping technique, which provides a causality criterion from the theory of dynamic systems. Analysis is based on 12 years of weekly malaria P. vivax cases in Tartagal, Salta, Argentina—at the southern fringe of malaria incidence in the Americas—together with humidity and temperature time-series spanning the same period. Our results show that there are causal links between malaria cases and both maximum temperature, with a delay of five weeks, and minimum temperature, with delays of zero and twenty two weeks. Humidity is also a driver of malaria cases, with thirteen weeks delay between cause and effect. Furthermore we also determined the sign and strength of the effects. Temperature has always a positive non-linear effect on cases, with maximum temperature effects more pronounced above 25°C and minimum above 17°C, while effects of humidity are more intricate: maximum humidity above 85% has a negative effect, whereas minimum humidity has a positive effect on cases. These results might be signaling processes operating at short (below 5 weeks) and long (over 12 weeks) time delays, corresponding to effects related to parasite cycle and mosquito population dynamics respectively. The non-linearities found for the strength of the effect of temperature on malaria cases make warmer areas more prone to higher increases in the disease incidence. Moreover, our results indicate that an increase of extreme weather events could enhance the risks of malaria spreading and re-emergence beyond the current distribution. Both situations, warmer climate and increase of extreme events, will be remarkably increased by the end of the century in this hot spot of climate change. [ABSTRACT FROM AUTHOR]

Respiratory Syncytial Virus (RSV) is the most common cause of respiratory tract infection in infants and children and shows increasing trend among elderly people worldwide. In many developing country settings, population and household structures have gone through some significant changes in the past decades, namely fewer births, more elderly population, and smaller household size but more RSV high-risk individuals. These dynamics have been captured in a mathematical model with RSV transmission dynamics to predict the disease burden on the detailed population for future targeted interventions. The population and disease dynamics model was constructed and tested against the hospitalization data for Acute Lower Respiratory Tract Infection due to RSV in rural Thai settings between 2005 and 2011. The proportion of extended families is predicted to increase by about 10% from 2005 to 2020, especially for those with elderly population, while the classic nuclear family type (with adults and children) will decline by about 10%. For RSV, infections from extended family type (approximately 60% of all household types) have majorly contributed to the force of infection (FOI). While the model predicted the increase of FOI from the extended family by 15% from 2005 to 2020, the FOI contributed by other household types would be either stable or decrease in the same time period. RSV incidence rate is predominantly high among babies (92.2%) and has been predicted to decrease slightly over time (from 940 to 864 cases per 100,000 population by 2020), while the incidence rates among children and elderly people may remain steadily low over the same period. However, the estimated incidence rates among elderly people were twice than those in children. The model predicts that approximately 60% of FOI for RSV will come from members of the extended family type. The incidence rate of RSV among children and elderly in extended families was about 20 times lower than that in infants and the trend is steady. Targeted intervention strategies, such as health education in some specific groups and targeted vaccination, may be considered, with the focus on extended family type. Target interventions on babies can lessen the transmission to children and elderly especially when transmission within households of extended family type is high. [ABSTRACT FROM AUTHOR]

Extreme weather events affect the development and survival of disease pathogens and vectors. Our aim was to investigate the potential effects of heat waves on the population dynamics of Asian tiger mosquito (Aedes albopictus), which is a major vector of dengue and Zika viruses. We modeled the population abundance of blood-fed mosquito adults based on a mechanistic population model of Ae. albopictus with the consideration of diapause. Using simulated heat wave events derived from a 35-year historical dataset, we assessed how the mosquito population responded to different heat wave characteristics, including the onset day, duration, and the average temperature. Two important observations are made: (1) a heat wave event facilitates the population growth in the early development phase but tends to have an overall inhibitive effect; and (2) two primary factors affecting the development are the unusual onset time of a heat wave and a relatively high temperature over an extended period. We also performed a sensitivity analysis using different heat wave definitions, justifying the robustness of the findings. The study suggests that particular attention should be paid to future heat wave events with an abnormal onset time or a lasting high temperature in order to develop effective strategies to prevent and control Ae. albopictus-borne diseases. [ABSTRACT FROM AUTHOR]

Seahorses are considered one of the most iconic examples of a monogamous species in the animal kingdom. This study investigates the relationship between stocking density and mating and competitive behavior from the context of the field biology of the dwarf seahorse, Hippocampus zosterae (Jordan & Gilbert). Animals were housed in 38 liter tanks at a range of densities and sex ratios (from 2–8 animals per tank), and their reproductive and other social behaviors were monitored from tank introduction through copulation. At low tank densities and even sex ratios but comparatively high field densities, frequency of both mating and competitive behaviors was low in trials. A higher level of males in tanks across all densities increased competition, activity levels, and aggression leading to egg transfer errors and brood expulsion, resulting in lower reproductive success. Across seahorse species, mean and maximum wild densities were consistently lower than those used in ex situ breeding, with adult sex ratios that were significantly female biased. However, significant variation exists in wild seahorse densities across species, with higher densities detected in focal/mark recapture studies and on artificial habitat structures than reported with belt transect sampling techniques. Interchange of knowledge gained in both aquarium and wild contexts will allow us to better understand the biology of this genus, and improve reproduction in captivity. Interpreting ex situ reproductive behaviors of seahorses within various densities reported from natural populations will help us predict the impact of conservation efforts and increase the likelihood of long-term persistence of populations for this threatened genus. [ABSTRACT FROM AUTHOR]

Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems. [ABSTRACT FROM AUTHOR]

In their competition for hosts, parasites with antigens that are novel to the host immune system will be at a competitive advantage. The resulting frequency-dependent selection can structure parasite populations into strains of limited genetic overlap. For the causative agent of malaria, Plasmodium falciparum, the high recombination rates and associated vast diversity of its highly antigenic and multicopy var genes preclude such clear clustering in endemic regions. This undermines the definition of strains as specific, temporally persisting gene variant combinations. We use temporal multilayer networks to analyze the genetic similarity of parasites in both simulated data and in an extensively and longitudinally sampled population in Ghana. When viewed over time, populations are structured into modules (i.e., groups) of parasite genomes whose var gene combinations are more similar within than between the modules and whose persistence is much longer than that of the individual genomes that compose them. Comparison to neutral models that retain parasite population dynamics but lack competition reveals that the selection imposed by host immunity promotes the persistence of these modules. The modular structure is, in turn, associated with a slower acquisition of immunity by individual hosts. Modules thus represent dynamically generated niches in host immune space, which can be interpreted as strains. Negative frequency-dependent selection therefore shapes the organization of the var diversity into parasite genomes, leaving a persistence signature over ecological time scales. Multilayer networks extend the scope of phylodynamics analyses by allowing quantification of temporal genetic structure in organisms that generate variation via recombination or other non-bifurcating processes. A strain structure similar to the one described here should apply to other pathogens with large antigenic spaces that evolve via recombination. For malaria, the temporal modular structure should enable the formulation of tractable epidemiological models that account for parasite antigenic diversity and its influence on intervention outcomes. [ABSTRACT FROM AUTHOR]

The adoption of the shared prosperity goal by the World Bank in 2013 and Sustainable Development Goal 10, on inequality, by the United Nations in 2015 should strengthen the focus of development interventions and cooperation on the income growth of the bottom 40 percent of the income distribution. This paper contributes to the incipient literature on within-country allocations of development institutions and assesses the geographic targeting of World Bank projects to the bottom 40 percent. Bivariate correlations between the allocation of project funding approved over 2005–14 and the geographical distribution of the bottom 40 as measured by survey income or consumption data are complemented by regressions with population and other potential factors affecting the within-country allocations as controls. The correlation analysis shows that, of the 58 countries in the sample, 41 exhibit a positive correlation between the shares of the bottom 40 and World Bank funding, and, in almost half of these, the correlation is above 0.5. Slightly more than a quarter of the countries, mostly in Sub-Saharan Africa, exhibit a negative correlation. The regression analysis shows that, once one controls for population, the correlation between the bottom 40 and World Bank funding switches sign and becomes significant and negative on average. This is entirely driven by Sub-Saharan Africa and not observed in the other regions. Hence, the significant and positive correlation in the estimations without controlling for population suggests that World Bank project funding is concentrated in administrative areas in which more people live (including the bottom 40) rather than in poorer administrative areas. Furthermore, capital cities receive disproportionally high shares of World Bank funding on average. [ABSTRACT FROM AUTHOR]

Background: From a biological and clinical perspective, it is imperative to establish primate spermatogonial cultures. Due to limited availability of human testicular tissues, the macaque (Macaca fascicularis) was employed as non-human primate model. The aim of this study was to characterize the expression of somatic as well as germ cell markers in testicular tissues and to establish macaque testicular primary cell cultures. Materials and methods: Characterization of macaque testicular cell population was performed by immunohistochemical analyses for somatic cell markers (SOX9, VIM, SMA) as well as for germ cell markers (UTF1, MAGEA4, VASA). Testicular cells from adult macaque testes (n = 4) were isolated and cultured for 21 days using three stem cell culture media (SSC, PS and SM). An extended marker gene panel (SOX9, VIM, ACTA2; UTF1, FGFR3, MAGEA4, BOLL, DDX4) was then employed to assess the changes in gene expression levels and throughout the in vitro culture period. Dynamics of the spermatogonial population was further investigated by quantitative analysis of immunofluorescence-labeled MAGEA4-positive cells (n = 3). Results: RNA expression analyses of cell cultures revealed that parallel to decreasing SOX9-expressing Sertoli cells, maintenance of VIM and ACTA2-expressing somatic cells was observed. Expression levels of germ cell marker genes UTF1, FGFR3 and MAGEA4 were maintained until day 14 in SSC and SM media. Findings from MAGEA4 immunofluorescence staining corroborate mRNA expression profiling and substantiate the overall maintenance of MAGEA4-positive pre- and early meiotic germ cells until day 14. Conclusions: Our findings demonstrate maintenance of macaque germ cell subpopulations in vitro. This study provides novel perspective and proof that macaques could be used as a research model for establishing in vitro germ cell-somatic cell cultures, to identify ideal culture conditions for long-term maintenance of primate germ cell subpopulation in vitro. [ABSTRACT FROM AUTHOR]

Almost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, the metaorganism. Natural selection should favor hosts that shape the community composition of these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal hosts often pose selective environments, which only a subset of the environmentally available microbes are able to colonize. How these microbes assemble after colonization to form the complex microbiota is less clear. Neutral models are based on the assumption that the alternatives in microbiota community composition are selectively equivalent and thus entirely shaped by random population dynamics and dispersal. Here, we use the neutral model as a null hypothesis to assess microbiata composition in host organisms, which does not rely on invoking any adaptive processes underlying microbial community assembly. We show that the overall microbiota community structure from a wide range of host organisms, in particular including previously understudied invertebrates, is in many cases consistent with neutral expectations. Our approach allows to identify individual microbes that are deviating from the neutral expectation and are therefore interesting candidates for further study. Moreover, using simulated communities, we demonstrate that transient community states may play a role in the deviations from the neutral expectation. Our findings highlight that the consideration of neutral processes and temporal changes in community composition are critical for an in-depth understanding of microbiota-host interactions. [ABSTRACT FROM AUTHOR]

We introduce a minimal agent-based model to understand the effects of the interplay between dispersal and geometric constraints in metapopulation dynamics under the Allee Effect. The model, which does not impose nonlinear birth and death rates, is studied both analytically and numerically. Our results indicate the existence of a survival-extinction boundary with monotonic behavior for weak spatial constraints and a nonmonotonic behavior for strong spatial constraints so that there is an optimal dispersal that maximizes the survival probability. Such optimal dispersal has empirical support from recent experiments with engineered bacteria. [ABSTRACT FROM AUTHOR]

The family Sciaenidae comprises about 300 species. The black drum Pogonias cromis was the only valid species of the genus. Herein, Pogonias courbina Lacepède 1803 is redescribed based on morphological and molecular evidence and a neotype is designated. Pogonias courbina is distinguished by the following characters: the occurrence of characteristic thickening of the dorsal spines VII to XI in all specimens larger than 250 mm SL; all pterygiophores in the dorsal-fin laminar, thin; anal-fin pterygiophores slender excluded those of spines; lateral projections of gas bladder with few finger-like projections; genetic distance between both species 1%; exclusive occurrence of characters in six informative sites of COI (58 G; 214 G; 328 A; 331 A; 553C; 580 G). The method Automatic Barcode gap Discovery detected gaps in nucleotid distance congruent with the NJ, MP, and ML tree analysis. Also, advertisement calls are three times shorter in duration in P. courbina than in P. cromis. In addition, two monophyletic groups for P. cromis and P. courbina appear in trees obtained with different methodologies, emphasizing the absence of shared haplotypes. A gap of about 8000 km occurs in the distribution of both species along coastal areas of the Atlantic Ocean. [ABSTRACT FROM AUTHOR]