scholarly journals Human plague system associated with rodent diversity and other environmental factors

2019 ◽  
Vol 6 (6) ◽  
pp. 190216 ◽  
Author(s):  
Zhe Sun ◽  
Lei Xu ◽  
Boris V. Schmid ◽  
Katharine R. Dean ◽  
Zhibin Zhang ◽  
...  

Plague remains a threat to public health and is considered as a re-emerging infectious disease today. Rodents play an important role as major hosts in plague persistence and driving plague outbreaks in natural foci; however, few studies have tested the association between host diversity in ecosystems and human plague risk. Here we use zero-inflated generalized additive models to examine the association of species richness with human plague presence (where plague outbreaks could occur) and intensity (the average number of annual human cases when they occurred) in China during the Third Pandemic. We also account for transportation network density, annual precipitation levels and human population size. We found rodent species richness, particularly of rodent plague hosts, is positively associated with the presence of human plague. Further investigation shows that species richness of both wild and commensal rodent plague hosts are positively correlated with the presence, but only the latter correlated with the intensity. Our results indicated a positive relationship between rodent diversity and human plague, which may provide suggestions for the plague surveillance system.

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 72
Author(s):  
Maria Lazarina ◽  
Mariana A. Tsianou ◽  
Georgios Boutsis ◽  
Aristi Andrikou-Charitidou ◽  
Elpida Karadimou ◽  
...  

Human activities like urbanization and agriculture affect spatial biodiversity patterns. The presence and activities of humans richly benefit alien species, but native species usually decline in human-impacted areas. Considering that the richness of alien and native species are inter-related, we explored the effect of human population density, human-related land uses (agricultural and urban), and natural land area on avian (alien and native) species richness of Massachusetts for two time periods using Generalized Additive Models. Avian alien species richness increased with native species richness in both time periods. Despite the predominant role of native species richness as a major driver of alien species richness, human activities play an important additional role in shaping species richness patterns of established aliens. Human-related land uses (urban and agricultural) and human population favored alien species richness in both time periods. Counter to expectations, human activities were also positively associated to native avian species richness. Possible explanations of these patterns may include habitat heterogeneity, increased availability of resources, and reduced predation risk.


2021 ◽  
Author(s):  
Patricia Sayuri Silvestre Matsumoto ◽  
Roberto Mitsuyoshi Hiramoto ◽  
Virginia Bodelao Richini Pereira ◽  
Valeria Medina Camprigher ◽  
Helena Hilomi Taniguchi ◽  
...  

When it comes to visceral leishmaniasis (VL) in Brazil, one of the main targets of public health policies of surveillance is the control of domestic canine reservoirs of Leishmania infantum. This paper aims to evaluate the effect of the household environment risk in the maintenance of natural foci and in the transmission to human and animal hosts in an endemic city for VL, Bauru, in Brazil. We collected 6,578 blood samples of dogs living in 3,916 households from Nov.2019 to Mar.2020 and applied geospatial models to predict the disease risk based on the canine population. We used Kernel density estimation, cluster analysis, geostatistics and Generalized Additive Models (GAM). To validate our models, we used cross-validation and created a ROC graph. We found an overall canine VL (CVL) prevalence of 5.6%. Odds ratios (OR) for CVL increased progressively according to the number of canines for >2 dogs (OR 2.70); households that already had CVL in the past increased the chances for CVL currently (OR 2.73); and the cases of CVL increase the chances for human VL cases (OR 1.16). Our models were statistically significant and demonstrated an association between the canine and human disease, mainly in VL foci that remain endemic. Although the Kernel ratio map had the best performance (AUC=82), all the models showed high risk in the city's northwest area. Canine population dynamics must be considered in public policies and geospatial methods may help target priority areas and planning VL surveillance in low and middle-income countries.


Web Ecology ◽  
2009 ◽  
Vol 9 (1) ◽  
pp. 58-67 ◽  
Author(s):  
D. Nogués-Bravo

Abstract. Multivariable regression models have been used extensively as spatial modelling tools. However, other regression approaches are emerging as more efficient techniques. This paper attempts to present a synthesis of Generalised Regression Models (Generalized Linear Models, GLMs, Generalized Additive Models, GAMs), and a Geographically Weighted Regression, GWR, implemented in a GAM, explaining their statistical formulations and assessing improvements in predictive accuracy compared with linear regressions. The problems associated with these approaches are also discussed. A digital database developed with Geographic Information Systems (GIS), including environmental maps and bird species richness distribution in northern Spain, is used for comparison of the techniques. GWR using splines has shown the highest improvement in accounted deviance when compared with traditional linear regression approach, followed by GAM and GLM.


Based on an epidemiological survey,1 human TBEV neuroinfections may have an endemic emergent course, and natural foci are in full territorial expansion. Identified risk areas are Tulcea district, Transylvania, at the base of the Carpathian Mountains and the Transylvanian Alps.2,3 TBE has been a notifiable disease since 1996. Surveillance of TBE is not done at the country level, only regionally in some counties (northern/central/western part, close to Hungary). The passive surveillance system was implemented in 2008. However, there is no regular screening and the relative risk of contracting this disease is unknown. In 1999, an outbreak of TBE in humans was recorded with a total of at least 38 human cases.4


Author(s):  
François Freddy Ateba ◽  
Manuel Febrero-Bande ◽  
Issaka Sagara ◽  
Nafomon Sogoba ◽  
Mahamoudou Touré ◽  
...  

Mali aims to reach the pre-elimination stage of malaria by the next decade. This study used functional regression models to predict the incidence of malaria as a function of past meteorological patterns to better prevent and to act proactively against impending malaria outbreaks. All data were collected over a five-year period (2012–2017) from 1400 persons who sought treatment at Dangassa’s community health center. Rainfall, temperature, humidity, and wind speed variables were collected. Functional Generalized Spectral Additive Model (FGSAM), Functional Generalized Linear Model (FGLM), and Functional Generalized Kernel Additive Model (FGKAM) were used to predict malaria incidence as a function of the pattern of meteorological indicators over a continuum of the 18 weeks preceding the week of interest. Their respective outcomes were compared in terms of predictive abilities. The results showed that (1) the highest malaria incidence rate occurred in the village 10 to 12 weeks after we observed a pattern of air humidity levels >65%, combined with two or more consecutive rain episodes and a mean wind speed <1.8 m/s; (2) among the three models, the FGLM obtained the best results in terms of prediction; and (3) FGSAM was shown to be a good compromise between FGLM and FGKAM in terms of flexibility and simplicity. The models showed that some meteorological conditions may provide a basis for detection of future outbreaks of malaria. The models developed in this paper are useful for implementing preventive strategies using past meteorological and past malaria incidence.


Author(s):  
Mark David Walker ◽  
Mihály Sulyok

Abstract Background Restrictions on social interaction and movement were implemented by the German government in March 2020 to reduce the transmission of coronavirus disease 2019 (COVID-19). Apple's “Mobility Trends” (AMT) data details levels of community mobility; it is a novel resource of potential use to epidemiologists. Objective The aim of the study is to use AMT data to examine the relationship between mobility and COVID-19 case occurrence for Germany. Is a change in mobility apparent following COVID-19 and the implementation of social restrictions? Is there a relationship between mobility and COVID-19 occurrence in Germany? Methods AMT data illustrates mobility levels throughout the epidemic, allowing the relationship between mobility and disease to be examined. Generalized additive models (GAMs) were established for Germany, with mobility categories, and date, as explanatory variables, and case numbers as response. Results Clear reductions in mobility occurred following the implementation of movement restrictions. There was a negative correlation between mobility and confirmed case numbers. GAM using all three categories of mobility data accounted for case occurrence as well and was favorable (AIC or Akaike Information Criterion: 2504) to models using categories separately (AIC with “driving,” 2511. “transit,” 2513. “walking,” 2508). Conclusion These results suggest an association between mobility and case occurrence. Further examination of the relationship between movement restrictions and COVID-19 transmission may be pertinent. The study shows how new sources of online data can be used to investigate problems in epidemiology.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Narayan Sharma ◽  
René Schwendimann ◽  
Olga Endrich ◽  
Dietmar Ausserhofer ◽  
Michael Simon

Abstract Background Understanding how comorbidity measures contribute to patient mortality is essential both to describe patient health status and to adjust for risks and potential confounding. The Charlson and Elixhauser comorbidity indices are well-established for risk adjustment and mortality prediction. Still, a different set of comorbidity weights might improve the prediction of in-hospital mortality. The present study, therefore, aimed to derive a set of new Swiss Elixhauser comorbidity weightings, to validate and compare them against those of the Charlson and Elixhauser-based van Walraven weights in an adult in-patient population-based cohort of general hospitals. Methods Retrospective analysis was conducted with routine data of 102 Swiss general hospitals (2012–2017) for 6.09 million inpatient cases. To derive the Swiss weightings for the Elixhauser comorbidity index, we randomly halved the inpatient data and validated the results of part 1 alongside the established weighting systems in part 2, to predict in-hospital mortality. Charlson and van Walraven weights were applied to Charlson and Elixhauser comorbidity indices. Derivation and validation of weightings were conducted with generalized additive models adjusted for age, gender and hospital types. Results Overall, the Elixhauser indices, c-statistic with Swiss weights (0.867, 95% CI, 0.865–0.868) and van Walraven’s weights (0.863, 95% CI, 0.862–0.864) had substantial advantage over Charlson’s weights (0.850, 95% CI, 0.849–0.851) and in the derivation and validation groups. The net reclassification improvement of new Swiss weights improved the predictive performance by 1.6% on the Elixhauser-van Walraven and 4.9% on the Charlson weights. Conclusions All weightings confirmed previous results with the national dataset. The new Swiss weightings model improved slightly the prediction of in-hospital mortality in Swiss hospitals. The newly derive weights support patient population-based analysis of in-hospital mortality and seek country or specific cohort-based weightings.


2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1252.2-1253
Author(s):  
R. Garofoli ◽  
M. Resche-Rigon ◽  
M. Dougados ◽  
D. Van der Heijde ◽  
C. Roux ◽  
...  

Background:Axial spondyloarthritis (axSpA) is a chronic rheumatic disease that encompasses various clinical presentations: inflammatory chronic back pain, peripheral manifestations and extra-articular manifestations. The current nomenclature divides axSpA in radiographic (in the presence of radiographic sacroiliitis) and non-radiographic (in the absence of radiographic sacroiliitis, with or without MRI sacroiliitis. Given that the functional burden of the disease appears to be greater in patients with radiographic forms, it seems crucial to be able to predict which patients will be more likely to develop structural damage over time. Predictive factors for radiographic progression in axSpA have been identified through use of traditional statistical models like logistic regression. However, these models present some limitations. In order to overcome these limitations and to improve the predictive performance, machine learning (ML) methods have been developed.Objectives:To compare ML models to traditional models to predict radiographic progression in patients with early axSpA.Methods:Study design: prospective French multicentric cohort study (DESIR cohort) with 5years of follow-up. Patients: all patients included in the cohort, i.e. 708 patients with inflammatory back pain for >3 months but <3 years, highly suggestive of axSpA. Data on the first 5 years of follow-up was used. Statistical analyses: radiographic progression was defined as progression either at the spine (increase of at least 1 point per 2 years of mSASSS scores) or at the sacroiliac joint (worsening of at least one grade of the mNY score between 2 visits). Traditional modelling: we first performed a bivariate analysis between our outcome (radiographic progression) and explanatory variables at baseline to select the variables to be included in our models and then built a logistic regression model (M1). Variable selection for traditional models was performed with 2 different methods: stepwise selection based on Akaike Information Criterion (stepAIC) method (M2), and the Least Absolute Shrinkage and Selection Operator (LASSO) method (M3). We also performed sensitivity analysis on all patients with manual backward method (M4) after multiple imputation of missing data. Machine learning modelling: using the “SuperLearner” package on R, we modelled radiographic progression with stepAIC, LASSO, random forest, Discrete Bayesian Additive Regression Trees Samplers (DBARTS), Generalized Additive Models (GAM), multivariate adaptive polynomial spline regression (polymars), Recursive Partitioning And Regression Trees (RPART) and Super Learner. Finally, the accuracy of traditional and ML models was compared based on their 10-foldcross-validated AUC (cv-AUC).Results:10-fold cv-AUC for traditional models were 0.79 and 0.78 for M2 and M3, respectively. The 3 best models in the ML algorithm were the GAM, the DBARTS and the Super Learner models, with 10-fold cv-AUC of: 0.77, 0.76 and 0.74, respectively (Table 1).Table 1.Comparison of 10-fold cross-validated AUC between best traditional and machine learning models.Best modelsCross-validated AUCTraditional models M2 (step AIC method)0.79 M3 (LASSO method)0.78Machine learning approach SL Discrete Bayesian Additive Regression Trees Samplers (DBARTS)0.76 SL Generalized Additive Models (GAM)0.77 Super Learner0.74AUC: Area Under the Curve; AIC: Akaike Information Criterion; LASSO: Least Absolute Shrinkage and Selection Operator; SL: SuperLearner. N = 295.Conclusion:Traditional models predicted better radiographic progression than ML models in this early axSpA population. Further ML algorithms image-based or with other artificial intelligence methods (e.g. deep learning) might perform better than traditional models in this setting.Acknowledgments:Thanks to the French National Society of Rheumatology and the DESIR cohort.Disclosure of Interests:Romain Garofoli: None declared, Matthieu resche-rigon: None declared, Maxime Dougados Grant/research support from: AbbVie, Eli Lilly, Merck, Novartis, Pfizer and UCB Pharma, Consultant of: AbbVie, Eli Lilly, Merck, Novartis, Pfizer and UCB Pharma, Speakers bureau: AbbVie, Eli Lilly, Merck, Novartis, Pfizer and UCB Pharma, Désirée van der Heijde Consultant of: AbbVie, Amgen, Astellas, AstraZeneca, BMS, Boehringer Ingelheim, Celgene, Cyxone, Daiichi, Eisai, Eli-Lilly, Galapagos, Gilead Sciences, Inc., Glaxo-Smith-Kline, Janssen, Merck, Novartis, Pfizer, Regeneron, Roche, Sanofi, Takeda, UCB Pharma; Director of Imaging Rheumatology BV, Christian Roux: None declared, Anna Moltó Grant/research support from: Pfizer, UCB, Consultant of: Abbvie, BMS, MSD, Novartis, Pfizer, UCB


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