Connectivity,reproduction number,and mobility interact to determine communities’ epidemiological superspreader potential in a metapopulation network

Disease epidemic outbreaks on human metapopulation networks are often driven by a small number of superspreader nodes, which are primarily responsible for spreading the disease throughout the network. Superspreader nodes typically are characterized either by their locations within the network, by their degree of connectivity and centrality, or by their habitat suitability for the disease, described by their reproduction number (R). Here we introduce a model that considers simultaneously the effects of network properties and R on superspreaders, as opposed to previous research which considered each factor separately. This type of model is applicable to diseases for which habitat suitability varies by climate or land cover, and for direct transmitted diseases for which population density and mitigation practices influences R. We present analytical models that quantify the superspreader capacity of a population node by two measures: probability-dependent superspreader capacity, the expected number of neighboring nodes to which the node in consideration will randomly spread the disease per epidemic generation, and time-dependent superspreader capacity, the rate at which the node spreads the disease to each of its neighbors. We validate our analytical models with a Monte Carlo analysis of repeated stochastic Susceptible-Infected-Recovered (SIR) simulations on randomly generated human population networks, and we use a random forest statistical model to relate superspreader risk to connectivity, R, centrality, clustering, and diffusion. We demonstrate that either degree of connectivity or R above a certain threshold are sufficient conditions for a node to have a moderate superspreader risk factor, but both are necessary for a node to have a high-risk factor. The statistical model presented in this article can be used to predict the location of superspreader events in future epidemics, and to predict the effectiveness of mitigation strategies that seek to reduce the value of R, alter host movements, or both.     

A network control theory approach to modeling and optimal control of zoonoses: case study of brucellosis transmission in sub-Saharan Africa

Background

Developing control policies for zoonotic diseases is challenging, both because of the complex spread dynamics exhibited by these diseases, and because of the need for implementing complex multi-species surveillance and control efforts using limited resources. Mathematical models, and in particular network models, of disease spread are promising as tools for control-policy design, because they can provide comprehensive quantitative representations of disease transmission.

Methodology/Principal Findings

A layered dynamical network model for the transmission and control of zoonotic diseases is introduced as a tool for analyzing disease spread and designing cost-effective surveillance and control. The model development is achieved using brucellosis transmission among wildlife, cattle herds, and human sub-populations in an agricultural system as a case study. Precisely, a model that tracks infection counts in interacting animal herds of multiple species (e.g., cattle herds and groups of wildlife for brucellosis) and in human subpopulations is introduced. The model is then abstracted to a form that permits comprehensive targeted design of multiple control capabilities as well as model identification from data. Next, techniques are developed for such quantitative design of control policies (that are directed to both the animal and human populations), and for model identification from snapshot and time-course data, by drawing on recent results in the network control community.

Conclusions/Significance

The modeling approach is shown to provide quantitative insight into comprehensive control policies for zoonotic diseases, and in turn to permit policy design for mitigation of these diseases. For the brucellosis-transmission example in particular, numerous insights are obtained regarding the optimal distribution of resources among available control capabilities (e.g., vaccination, surveillance and culling, pasteurization of milk) and points in the spread network (e.g., transhumance vs. sedentary herds). In addition, a preliminary identification of the network model for brucellosis is achieved using historical data, and the robustness of the obtained model is demonstrated. As a whole, our results indicate that network modeling can aid in designing control policies for zoonotic diseases.     

小兴安岭7种典型林型林分生物量碳密度与固碳能力

森林生物碳储量作为森林生态系统碳库的重要组成部分, 在全球碳循环中发挥着重要作用。以小兴安岭7种典型林型为研究对象, 通过外业样地调查与室内实验分析相结合的方法, 从林分尺度对林分生物量与碳密度进行计量, 分析了林分生物碳储量的空间分配格局, 并对林分年固碳能力与碳汇潜力进行了探讨。结果表明: 小兴安岭不同林型从幼龄林到成熟林的乔木层碳密度增长速率为: 蒙古栎(Quercus mongolica)林>兴安落叶松(Larix gmelinii)林>云冷杉(Picea-Abies)林>樟子松(Pinus sylvestris var. mongolica)林>山杨(Populus davidiana)林>红松(Pinus koraiensis)林>白桦(Betula platyphylla)林。7种典型林型不同龄组(幼龄林、中龄林、近熟林和成熟林)林分生物量碳密度分别为: 红松林31.4、74.7、118.4和130.2 t·hm^-2; 兴安落叶松林28.9、44.3、74.2和113.3 t·hm^-2; 樟子松林22.8、52.0、71.1和92.6 t·hm^-2; 云冷杉林23.1、44.1、77.6和130.3 t·hm^-2; 白桦林18.8、35.3、66.6和88.5 t·hm^-2; 蒙古栎林25.0、20.0、47.5和68.9 t·hm^-2; 山杨林19.8、28.7、43.7和76.6 t·hm^-2。红松林、兴安落叶松林、樟子松林和蒙古栎林在幼龄林时林分年固碳量较高, 其他林型在成熟林时林分年固碳量较高。7种典型林型不同龄组的林分生物量碳密度均随林龄增长而增加, 但不同林型的碳汇功能存在差异, 同一林型不同林龄的生物量碳密度增幅差异也较大。林分年固碳量在0.4-2.8 t·hm^-2之间, 碳汇能力较强、碳汇潜力较大。尤其是小兴安岭目前林分质量较差, 幼龄林和中龄林所占的比重较大, 具有较大的碳汇潜力。研究结果可为森林经营管理及碳汇功能评价提供参考。     

The adoption of the One Health approach to improve surveillance of venomous animal injury,vector-borne and zoonotic diseases in Foz do Iguaçu,Brazil

Public health institutions with sectorized structure and low integration among field teams, old-fashioned practices such as paper-based storage system, and poorly qualified health agents have limited ability to conduct accurate surveillance and design effective timely interventions. Herein, we describe the steps taken by the Zoonosis Control Center of Foz do Iguaçu (CCZ-Foz) in the last 23 years to move from an archaic and sectorized structure to a modern and timely surveillance program embracing zoonotic diseases, venomous animal injuries, and vector-borne diseases epidemiology under the One Health approach. The full implementation of the One Health approach was based on 5 axes: (1) merging sectorized field teams; (2) adoption of digital solutions; (3) health agents empowerment and permanent capacitation; (4) social mobilization; and (5) active surveys. By doing so, notifications related to zoonotic diseases and venomous animals increased 10 and 21 times, respectively, with no impairment on arbovirus surveillance (major concern in the city). Open sources database (PostgreSQL) and software (QGis) are daily updated and create real-time maps to support timely decisions. The adoption of One Health approach increased preparedness for endemic diseases and reemerging and emerging threats such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).     

A novel approach for combining the use of in vitro and in vivo data to measure and detect emerging moxidectin resistance in gastrointestinal nematodes of goats

Ivermectin and moxidectin are closely related avermectin/milbemycin anthelmintics and available data suggest that side resistance occurs with these two drugs. However, moxidectin remains effective against many species of ivermectin-resistant worms due to its higher potency. The larval development assay (LDA) is routinely used to diagnose ivermectin resistance in Haemonchus contortus but laboratory diagnosis of moxidectin resistance is hampered by the lack of any validated in vitro tests. The objective of this study was to measure the relative susceptibility/resistance of H. contortus to moxidectin on goat farms in Georgia, and to validate the DrenchRite LDA for detecting resistance to moxidectin. Fecal egg count reduction tests (FECRT) were performed at five different moxidectin dose levels and DrenchRite LDAs were performed in duplicate on nine meat goat farms in Georgia, USA. To improve our ability to make inferences on the relative levels of resistance between farms, FECRT data were first analysed using a linear mixed model, and then Tukey's sequential trend test was used to evaluate the trend in response across dose levels. LDA data were analysed using log-dose logit-response and probit models. Using these statistical results, we were able to rank the nine farms from the least to the most resistant, and to develop a set of criteria for interpreting DrenchRite LDA results so that this assay can be used to diagnose both clinically apparent moxidectin resistance, as well as sub-clinical emerging resistance. These results suggest that our novel approach for examining these types of data provides a method for obtaining an increased amount of information, thus permitting a more sensitive detection of resistance. Based on results of the LDA, moxidectin-resistant farms had resistance ratios, compared with an ivermectin-sensitive farm, ranging from 32 to 128, and had resistance ratios of 6-24 compared with an ivermectin-resistant/moxidectin naive farm. Moxidectin resistance was diagnosed both in Haemonchus and Trichostrongylus on almost half of the farms tested, despite this drug only being used on these farms for 2-3 years.     

A network pharmacology‐based approach to explore the effects of Chaihu Shugan powder on a non‐alcoholic fatty liver rat model through nuclear receptors

The pathogenesis of non‐alcoholic fatty liver disease (NAFLD) is still not fully understood, and currently, no effective pharmacotherapy is available. Nuclear receptors (NRs) are important biological participants in NAFLD that exhibit great therapeutic potential. Chaihu Shugan powder (CSP) is a traditional Chinese medicine (TCM) formula that has a wide therapeutic spectrum including NAFLD, but the effective components and functional mechanisms of CSP are unclear. We adopted a network pharmacology approach using multiple databases for Gene Ontology (GO) enrichment analysis and the molecular complex detection (MCODE) method for a protein‐protein interaction (PPI) analysis, and we used molecular docking method to screen the NR targets and determine the corresponding CSP components. The screening results were validated through a NAFLD rat model that was used to explain the possible relationship between CSP and NAFLD. Finally, we screened PPARγ, FXR, PPARα, RARα and PPARδ as target genes and quercetin, kaempferol, naringenin, isorhamnetin and nobiletin as target compounds. The five components were detected through high‐performance liquid chromatography‐mass spectrometry (HPLC‐MS), the results of which aligned with the docking experiments of PPARγ, PPARα and PPARδ. After CSP intervention, the NAFLD rat model showed ameliorated effects in terms of bodyweight, hepatic histopathology, and serum and liver lipids, and the mRNA levels of PPARγ, FXR, PPARα and RARα were significantly changed. The results from this study indicate that CSP exhibits healing effects in an NAFLD model and that the network pharmacology approach to screening NR targets and determining the corresponding CSP components is a practical strategy for explaining the mechanism by which CSP ameliorates NAFLD.     

A dynamical model for the basal ganglia-thalamo-cortical oscillatory activity and its implications in Parkinson’s disease

We propose to investigate brain electrophysiological alterations associated with Parkinson’s disease through a novel adaptive dynamical model of the network of the basal ganglia, the cortex and the thalamus. The model uniquely unifies the influence of dopamine in the regulation of the activity of all basal ganglia nuclei, the self-organised neuronal interdependent activity of basal ganglia-thalamo-cortical circuits and the generation of subcortical background oscillations. Variations in the amount of dopamine produced in the neurons of the substantia nigra pars compacta are key both in the onset of Parkinson’s disease and in the basal ganglia action selection. We model these dopamine-induced relationships, and Parkinsonian states are interpreted as spontaneous emergent behaviours associated with different rhythms of oscillatory activity patterns of the basal ganglia-thalamo-cortical network. These results are significant because: (1) the neural populations are built upon single-neuron models that have been robustly designed to have eletrophysiologically-realistic responses, and (2) our model distinctively links changes in the oscillatory activity in subcortical structures, dopamine levels in the basal ganglia and pathological synchronisation neuronal patterns compatible with Parkinsonian states, this still remains an open problem and is crucial to better understand the progression of the disease.Electronic supplementary materialThe online version of this article (10.1007/s11571-020-09653-y) contains supplementary material, which is available to authorized users.     

Epstein-Barr Virus Contributes to the Malignant Phenotype and to Apoptosis Resistance in Burkitt’s Lymphoma Cell Line Akata

In the present study, we established an in vitro system representing the Burkitt’s lymphoma (BL)-type Epstein-Barr virus (EBV) infection which is characterized by expression of EBV-determined nuclear antigen 1 (EBNA-1) and absence of EBNA-2 and latent membrane protein 1 (LMP1) expression. EBV-negative cell clones isolated from the EBV-positive BL line Akata were infected with an EBV recombinant carrying a selectable marker, and the following selection culture easily yielded EBV-infected clones. EBV-reinfected clones showed BL-type EBV expression and restored the capacity for growth on soft agar and tumorigenicity in SCID mice that were originally retained in parental EBV-positive Akata cells and lost in EBV-negative subclones. Moreover, it was found that EBV-positive cells were more resistant to apoptosis than were EBV-negative cells. EBV-infected cells expressed the bcl-2 protein, through which cells might become resistant to apoptosis, at a higher level than did uninfected cells. This is the first report that BL-type EBV infection confers apoptosis resistance even in the absence of expression of LMP1 and BHRF1, both of which are known to have an antiapoptotic function. Surprisingly, transfection of the EBNA-1 gene into EBV-negative Akata clones could not restore malignant phenotypes and apoptosis resistance, thus suggesting that EBNA-1 alone was not sufficient for conferring them. Our results suggest that the persistence of EBV in BL cells is required for the cells to be more malignant and apoptosis resistant, which underlines the oncogenic role of EBV in BL genesis.     

A virtual bird’s eye view: Live streaming nest boxes to continue outreach in the era of COVID‐19

COVID‐19 created a host of challenges for science education; in our case, the pandemic halted our in‐person elementary school outreach project on bird biology. This project was designed as a year‐long program to teach fifth‐grade students in Ithaca, New York, USA, about bird ecology and biodiversity using in‐person presentations, games, activities, and outdoor demonstrations. As a central part of this effort, we set up nest boxes on school property and planned to monitor them with students during bird breeding in the spring. Here, we describe our experiences transitioning this program online: we live streamed nest boxes to the students’ virtual classroom and used them as a focal point for virtual lessons on bird breeding and nestling development. In an era of social distancing and isolation, we propose that nest box live streaming and virtual lessons can support communities by providing access to the outdoors and unconventional science learning opportunities for all students. Instituting similar programs at local schools has the potential to increase equitable learning opportunities for students across geographic locations and with varying degrees of physical access to the outdoors and nature.     

Sweetened beverages and risk of frailty among older women in the Nurses’ Health Study: A cohort study

BackgroundConsumption of sugar-sweetened beverages (SSBs) has been consistently associated with a higher risk of obesity, type 2 diabetes, cardiovascular disease, and premature mortality, whereas evidence for artificially sweetened beverages (ASBs) and fruit juices on health is less solid. The aim of this study was to evaluate the consumption of SSBs, ASBs, and fruit juices in association with frailty risk among older women.Methods and findingsWe analyzed data from 71,935 women aged ≥60 (average baseline age was 63) participating in the Nurses’ Health Study (NHS), an ongoing cohort study initiated in 1976 among female registered nurses in the United States. Consumption of beverages was derived from 6 repeated food frequency questionnaires (FFQs) administered between 1990 and 2010. Frailty was defined as having at least 3 of the following 5 criteria from the FRAIL scale: fatigue, poor strength, reduced aerobic capacity, having ≥5 chronic illnesses, and weight loss ≥5%. The occurrence of frailty was assessed every 4 years from 1992 to 2014. During 22 years of follow-up, we identified 11,559 incident cases of frailty. Consumption of SSBs was associated with higher risk of frailty after adjustment for diet quality, body mass index (BMI), smoking status, and medication use, specifically, the relative risks (RRs) and 95% confidence interval (95% CI) for ≥2 serving/day versus no SSB consumption was 1.32 (1.10, 1.57); p-value <0.001. ASBs were also associated with frailty [RR ≥2 serving/day versus no consumption: 1.28 (1.17, 1.39); p-value <0.001]. Orange juice was associated with lower risk of frailty [RR ≥1 serving/day versus no consumption: 0.82 (0.76, 0.87); p-value <0.001], whereas other juices were associated with a slightly higher risk [RR ≥1 serving/day versus no consumption: 1.15 (1.03, 1.28); p-value <0.001]. A limitation of this study is that, due to self-reporting of diet and frailty, certain misclassification bias cannot be ruled out; also, some residual confounding may persist.ConclusionsIn this study, we observed that consumption of SSBs and ASBs was associated with a higher risk of frailty. However, orange juice intake showed an inverse association with frailty. These results need to be confirmed in further studies using other frailty definitions.

Ellen Struijk and colleagues investigate the association between sweetened beverage consumption and risk of frailty later in life.     

Idiosyncratic responses to climate‐driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co‐distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo‐Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species‐specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainland Guineo‐Congolian forest and that habitats across the exposed land bridge likely enabled dispersal in some species, but not in others. We did not find evidence that rivers are biogeographic barriers across any of the species complexes. Despite marked differences in the geographic extent of stable climates and temporal estimates of divergence among the species complexes, we recovered a shared pattern of intermittent climatic suitability with recent population connectivity and demographic expansion across the Congo Basin. This pattern supports the hypothesis that genetic exchange across the Congo Basin during humid periods, followed by vicariance during arid periods, has shaped regional diversity. Finally, we identified many distinct lineages among our focal taxa, some of which may reflect incipient or unrecognized species.     

Linking forest fires to lake metabolism and carbon dioxide emissions in the boreal region of Northern Québec

Natural fires annually decimate up to 1% of the forested area in the boreal region of Québec, and represent a major structuring force in the region, creating a mosaic of watersheds characterized by large variations in vegetation structure and composition. Here, we investigate the possible connections between this fire‐induced watershed heterogeneity and lake metabolism and CO₂ dynamics. Plankton respiration, and water–air CO₂ fluxes were measured in the epilimnia of 50 lakes, selected to lie within distinct watershed types in terms of postfire terrestrial succession in the boreal region of Northern Québec. Plankton respiration varied widely among lakes (from 21 to 211 μg C L^?1 day^?1), was negatively related to lake area, and positively related to dissolved organic carbon (DOC). All lakes were supersaturated in CO₂ and the resulting carbon (C) flux to the atmosphere (150 to over 3000 mg C m² day^?1) was negatively related to lake area and positively to DOC concentration. CO₂ fluxes were positively related to integrated water column respiration, suggesting a biological component in this flux. Both respiration and CO₂ fluxes were strongly negatively related to years after the last fire in the basin, such that lakes in recently burnt basins had significantly higher C emissions, even after the influence of lake size was removed. No significant differences were found in nutrients, chlorophyll, and DOC between lakes in different basin types, suggesting that the fire‐induced watershed features influence other, more subtle aspects, such as the quality of the organic C reaching lakes. The fire‐induced enhancement of lake organic C mineralization and C emissions represents a long‐term impact that increases the overall C loss from the landscape as the result of fire, but which has never been included in current regional C budgets and future projections. The need to account for this additional fire‐induced C loss becomes critical in the face of predictions of increasing incidence of fire in the circumboreal landscape.     

A novel approach to the identification and quantitative elemental analysis of amyloid deposits—Insights into the pathology of Alzheimer’s disease

There is considerable interest in the role of metals such as iron, copper, and zinc in amyloid plaque formation in Alzheimer’s disease. However to convincingly establish their presence in plaques in vivo, a sensitive technique is required that is both quantitatively accurate and avoids isolation of plaques or staining/fixing brain tissue, since these processes introduce contaminants and redistribute elements within the tissue. Combining the three ion beam techniques of scanning transmission ion microscopy, Rutherford back scattering spectrometry and particle induced X-ray emission in conjunction with a high energy (MeV) proton microprobe we have imaged plaques in freeze-dried unstained brain sections from CRND-8 mice, and simultaneously quantified iron, copper, and zinc. Our results show increased metal concentrations within the amyloid plaques compared with the surrounding tissue: iron (85 ppm compared with 42 ppm), copper (16 ppm compared to 6 ppm), and zinc (87 ppm compared to 34 ppm).     

How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara,the World’s Largest Rodent

Gigantism results when one lineage within a clade evolves extremely large body size relative to its small-bodied ancestors, a common phenomenon in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to increased mutational load. Second, gigantism is achieved through generating a higher number of cells along with higher rates of cell proliferation, thus increasing the likelihood of cancer. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we assembled a draft genome of the capybara (Hydrochoerus hydrochaeris), the world’s largest living rodent. We found that the genome-wide ratio of nonsynonymous to synonymous mutations (ω) is elevated in the capybara relative to other rodents, likely caused by a generation-time effect and consistent with a nearly neutral model of molecular evolution. A genome-wide scan for adaptive protein evolution in the capybara highlighted several genes controlling postnatal bone growth regulation and musculoskeletal development, which are relevant to anatomical and developmental modifications for an increase in overall body size. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T-cell-mediated tumor suppression, offering a potential resolution to the increased cancer risk in this lineage. Our comparative genomic results uncovered the signature of an intragenomic conflict where the evolution of gigantism in the capybara involved selection on genes and pathways that are directly linked to cancer.     

Dracula’s ménagerie: A multispecies occupancy analysis of lynx,wildcat, and wolf in the Romanian Carpathians

1. The recovery of terrestrial carnivores in Europe is a conservation success story. Initiatives focused on restoring top predators require information on how resident species may interact with the re‐introduced species as their interactions have the potential to alter food webs, yet such data are scarce for Europe.
2. In this study, we assessed patterns of occupancy and interactions between three carnivore species in the Romanian Carpathians. Romania houses one of the few intact carnivore guilds in Europe, making it an ideal system to assess intraguild interactions and serve as a guide for reintroductions elsewhere.
3. We used camera trap data from two seasons in Transylvanian forests to assess occupancy and co‐occurrence of carnivores using multispecies occupancy models.
4. Mean occupancy in the study area was highest for lynx (Ψ_winter = 0.76 95% CI: 0.42–0.92; Ψ_autumn = 0.71 CI: 0.38–0.84) and wolf (Ψ_winter = 0.60 CI: 0.34–0.78; Ψ_autumn = 0.81 CI: 0.25–0.95) and lowest for wildcat (Ψ_winter = 0.40 CI: 0.19–0.63; Ψ_autumn = 0.52 CI: 0.17–0.78)
5. We found that marginal occupancy predictors for carnivores varied between seasons. We also found differences in predictors of co‐occurrence between seasons for both lynx‐wolf and wildcat‐wolf co‐occurrence. For both seasons, we found that conditional occupancy probabilities of all three species were higher when another species was present.
6. Our results indicate that while there are seasonal differences in predictors of occupancy and co‐occurrence of the three species, co‐occurrence in our study area is high.
7. Terrestrial carnivore recovery efforts are ongoing worldwide. Insights into interspecific relations between carnivore species are critical when considering the depauperate communities they are introduced in. Our work showcases that apex carnivore coexistence is possible, but dependent on protection afforded to forest habitats and their prey base.