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Outbreak prediction

Heidi L Tessmer, Kimihito Ito, Ryosuke Omori
To estimate and predict the transmission dynamics of respiratory viruses, the estimation of the basic reproduction number, R 0 , is essential. Recently, approximate Bayesian computation methods have been used as likelihood free methods to estimate epidemiological model parameters, particularly R 0 . In this paper, we explore various machine learning approaches, the multi-layer perceptron, convolutional neural network, and long-short term memory, to learn and estimate the parameters. Further, we compare the accuracy of the estimates and time requirements for machine learning and the approximate Bayesian computation methods on both simulated and real-world epidemiological data from outbreaks of influenza A(H1N1)pdm09, mumps, and measles...
2018: Frontiers in Microbiology
David Lopez, Sébastien Ribeiro, Philippe Label, Boris Fumanal, Jean-Stéphane Venisse, Annegret Kohler, Ricardo R de Oliveira, Kurt Labutti, Anna Lipzen, Kathleen Lail, Diane Bauer, Robin A Ohm, Kerrie W Barry, Joseph Spatafora, Igor V Grigoriev, Francis M Martin, Valérie Pujade-Renaud
Corynespora cassiicola is an Ascomycetes fungus with a broad host range and diverse life styles. Mostly known as a necrotrophic plant pathogen, it has also been associated with rare cases of human infection. In the rubber tree, this fungus causes the Corynespora leaf fall (CLF) disease, which increasingly affects natural rubber production in Asia and Africa. It has also been found as an endophyte in South American rubber plantations where no CLF outbreak has yet occurred. The C. cassiicola species is genetically highly diverse, but no clear relationship has been evidenced between phylogenetic lineage and pathogenicity...
2018: Frontiers in Microbiology
Noorakmar Jusoh, Hasanuddin Zainal, Azzmer Azzar Abdul Hamid, Noraslinda M Bunnori, Khairul Bariyyah Abd Halim, Shafida Abd Hamid
Recent outbreaks of highly pathogenic influenza strains have highlighted the need to develop new anti-influenza drugs. Here, we report an in silico study of carvone derivatives to analyze their binding modes with neuraminidase (NA) active sites. Two proposed carvone analogues, CV(A) and CV(B), with 36 designed ligands were predicted to inhibit NA (PDB ID: 3TI6) using molecular docking. The design is based on structural resemblance with the commercial inhibitor, oseltamivir (OTV), ligand polarity, and amino acid residues in the NA active sites...
March 15, 2018: Journal of Molecular Modeling
Corneliu Petru Popescu, Simin Aysel Florescu, Ani Ioana Cotar, Daniela Badescu, Cornelia Svetlana Ceianu, Mihaela Zaharia, Gratiela Tardei, Daniel Codreanu, Emanoil Ceausu, Simona Maria Ruta
BACKGROUND: In Romania, after a major outbreak in 1996, West Nile neuroinvasive disease (WNND) was reported only in a limited number of cases annually. During 2016-2017, a significant increase in the number of WNND cases was reported at the national level, associated with high mortality rates. METHODS: A retrospective analysis of all cases confirmed with WNND, hospitalized during 2012-2017 in a single tertiary facility from Bucharest was performed in order to determine the annual prevalence and mortality rate and the risk factors associated with a severe outcome...
March 12, 2018: Travel Medicine and Infectious Disease
Arran Hamlet, Kévin Jean, William Perea, Sergio Yactayo, Joseph Biey, Maria Van Kerkhove, Neil Ferguson, Tini Garske
BACKGROUND: Yellow fever virus (YFV) is a vector-borne flavivirus endemic to Africa and Latin America. Ninety per cent of the global burden occurs in Africa where it is primarily transmitted by Aedes spp, with Aedes aegypti the main vector for urban yellow fever (YF). Mosquito life cycle and viral replication in the mosquito are heavily dependent on climate, particularly temperature and rainfall. We aimed to assess whether seasonal variations in climatic factors are associated with the seasonality of YF reports...
March 2018: PLoS Neglected Tropical Diseases
Nongluk Sriwilaijaroen, Shin-Ichi Nakakita, Sachiko Kondo, Hirokazu Yagi, Koichi Kato, Takeomi Murata, Hiroaki Hiramatsu, Toshio Kawahara, Yohei Watanabe, Yasushi Kanai, Takao Ono, Jun Hirabayashi, Kazuhiko Matsumoto, Yasuo Suzuki
The rapidly evolvable influenza A virus has caused pandemics linked to millions of deaths in the past century. Influenza A viruses are categorized by H (hemagglutinin; HA) and N (neuraminidase; NA) proteins expressed on the viral envelope surface. Analyses of past pandemics suggest that the HA gene segment comes from a nonhuman virus, which is then introduced into an immunologically naïve human population with potentially devastating consequences. As a prerequisite for infection, the nonhuman HA molecules of H1-H16 viruses must be able to bind to specific sialyl receptors on the host cell surface along the human respiratory tract...
March 15, 2018: FEBS Journal
May Anne Mata, Priscilla Greenwood, Rebecca Tyson
We present an analysis of an avian flu model that yields insight into the roles of different transmission routes in the recurrence of avian influenza epidemics. Recent modelling work suggests that the outbreak periodicity of the disease is mainly determined by the environmental transmission rate. This conclusion, however, is based on a modelling study that only considers a weak between-host transmission rate. We develop an approximate model for stochastic avian flu epidemics, which allows us to determine the relative contribution of environmental and direct transmission routes to the periodicity and intensity of outbreaks over the full range of plausible parameter values for transmission...
March 14, 2018: Bulletin of Mathematical Biology
Fabrizio Bernardi Aubry, Francesco Marcello Falcieri, Jacopo Chiggiato, Alfredo Boldrin, Gian Marco Luna, Stefania Finotto, Elisa Camatti, Francesco Acri, Mauro Sclavo, Sandro Carniel, Lucia Bongiorni
Dense waters (DW) formation in shelf areas and their cascading off the shelf break play a major role in ventilating deep waters, thus potentially affecting ecosystem functioning and biogeochemical cycles. However, whether DW flow across shelves may affect the composition and structure of plankton communities down to the seafloor and the particles transport over long distances has not been fully investigated. Following the 2012 north Adriatic Sea cold outbreak, DW masses were intercepted at ca. 460 km south the area of origin and compared to resident ones in term of plankton biomass partitioning (pico to micro size) and phytoplankton species composition...
March 14, 2018: Scientific Reports
Daeho Kim, Sanghyun Hong, Hongjun Na, Jihwan Chun, Robin B Guevarra, You-Tae Kim, Sangryeol Ryu, Hyeun Bum Kim, Ju-Hoon Lee
Bellflower root ( Platycodon grandiflorum ), which belongs to the Campanulaceae family, is a perennial grass that grows naturally in Korea, northeastern China, and Japan. Bellflower is widely consumed as both food and medicine due to its high nutritional value and potential therapeutic effects. Since foodborne disease outbreaks often come from vegetables, understanding the public health risk of microorganisms on fresh vegetables is pivotal to predict and prevent foodborne disease outbreaks.We investigated the microbial communities on the bellflower root (n=10)...
March 15, 2018: Journal of Microbiology and Biotechnology
Mikko Koivu-Jolma, Arto Annila
Mathematical epidemiology is a well-recognized discipline to model infectious diseases. It also provides guidance for public health officials to limit outbreaks. Nevertheless, epidemics take societies by surprise every now and then, for example, when the Ebola virus epidemic raged seemingly unrestrained in Western Africa. We provide insight to this capricious character of nature by describing the epidemic as a natural process, i.e., a phenomenon governed by thermodynamics. Our account, based on statistical mechanics of open systems, clarifies that it is impossible to predict accurately epidemic courses because everything depends on everything else...
March 10, 2018: Mathematical Biosciences
Matthew Graham, Jonathan E Suk, Saki Takahashi, C Jessica Metcalf, Adela Paez Jimenez, Vladimir Prikazsky, Matthew J Ferrari, Justin Lessler
We report on and evaluate the process and findings of a real-time modeling exercise in response to an outbreak of measles in Lola prefecture, Guinea, in early 2015 in the wake of the Ebola crisis. Multiple statistical methods for the estimation of the size of the susceptible (i.e., unvaccinated) population were applied to weekly reported measles case data on seven subprefectures throughout Lola. Stochastic compartmental models were used to project future measles incidence in each subprefecture in both an initial and a follow-up iteration of forecasting...
March 12, 2018: American Journal of Tropical Medicine and Hygiene
T M Giannaros, K Lagouvardos, V Kotroni, A Matzarakis
This paper presents the development of an operational forecasting service focusing on human-biometeorological conditions. The service is based on the coupling of numerical weather prediction models with an advanced human-biometeorological model. Human thermal perception and stress forecasts are issued on a daily basis for Greece, in both point and gridded format. A user-friendly presentation approach is adopted for communicating the forecasts to the public via the worldwide web. The development of the presented service highlights the feasibility of replacing standard meteorological parameters and/or indices used in operational weather forecasting activities for assessing the thermal environment...
March 12, 2018: International Journal of Biometeorology
David J Civitello, Brent E Allman, Connor Morozumi, Jason R Rohr
Anthropogenic resource supplementation can shape wildlife disease directly by altering the traits and densities of hosts and parasites or indirectly by stimulating prey, competitor or predator species. We first assess the direct epidemiological consequences of supplementation, highlighting the similarities and differences between food provisioning and two widespread forms of nutrient input: agricultural fertilization and aquatic nutrient enrichment. We then review an aquatic disease system and a general model to assess whether predator and competitor species can enhance or overturn the direct effects of enrichment...
May 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Hiroyasu Kaya, Jun Ozaki, Hirokazu Okumura
Objective This study retrospectively evaluated fungal dissemination due to hospital reconstruction and explored effective methods of predicting an outbreak. Methods Patients suspected of having invasive aspergillosis were tested for Aspergillus galactomannan antigen before and after reconstruction, and the mean values of three months of testing for positive patients were determined. The characteristics of patients with aspergillosis during this period were also assessed. Results Forty-five patients were positive for Aspergillus antigen (>0...
March 9, 2018: Internal Medicine
Chris A Whitehouse, Shenia Young, Cong Li, Chih-Hao Hsu, Gordon Martin, Shaohua Zhao
Whole genome sequencing (WGS) has become a rapid and affordable tool for public health surveillance and outbreak detection. In this study, we used the Illuminia MiSeq® to sequence 589 Campylobacter isolates obtained in 2015 from retail poultry meats as part of the National Antimicrobial Resistance Monitoring System (NARMS). WGS data were used to identify the Campylobacter species and to compare the concordance between resistance genotypes and phenotypes. WGS accurately identified 386 C. jejuni and 203 C. coli using gyrA sequence information...
August 2018: Food Microbiology
John S Berriman, Ryan A Ellingson, Jaymes D Awbrey, Diane M Rico, Ángel A Valdés, Nerida G Wilson, Andres Aguilar, David G Herbert, Yayoi M Hirano, Cynthia D Trowbridge, Patrick J Krug
Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates...
March 7, 2018: Molecular Phylogenetics and Evolution
Serge W Wiltshire
An agent-based computer model that builds representative regional U.S. hog production networks was developed and employed to assess the potential impact of the ongoing trend towards increased producer specialization upon network-level resilience to catastrophic disease outbreaks. Empirical analyses suggest that the spatial distribution and connectivity patterns of contact networks often predict epidemic spreading dynamics. Our model heuristically generates realistic systems composed of hog producer, feed mill, and slaughter plant agents...
2018: PloS One
Preeti Verma, Soma Sarkar, Poonam Singh, Ramesh C Dhiman
Background & objectives: Uncertainty often arises in differentiating seasonal variation from outbreaks of malaria. The present study was aimed to generalize the theoretical structure of sine curve for detecting an outbreak so that a tool for early warning of malaria may be developed. Methods: A 'case/mean-ratio scale' system was devised for labelling the outbreak in respect of two diverse districts of Assam and Rajasthan. A curve-based method of analysis was developed for determining outbreak and using the properties of sine curve...
November 2017: Indian Journal of Medical Research
Rose M Langsjoen, Sherry L Haller, Chad J Roy, Heather Vinet-Oliphant, Nicholas A Bergren, Jesse H Erasmus, Jill A Livengood, Tim D Powell, Scott C Weaver, Shannan L Rossi
Chikungunya virus (CHIKV) is a reemerging arbovirus capable of causing explosive outbreaks of febrile illness, polyarthritis, and polyarthralgia, inflicting severe morbidity on affected populations. CHIKV can be genetically classified into 3 major lineages: West African (WA); East, Central, and South African (ECSA); Indian Ocean (IOL); and Asian. Additionally, the Indian Ocean (IOL) sublineage emerged within the ECSA clade and the Asian/American sublineage emerged within the Asian clade. While differences in epidemiological and pathological characteristics among outbreaks involving different CHIKV lineages and sublineages have been suggested, few targeted investigations comparing lineage virulence levels have been reported...
March 6, 2018: MBio
Stacy Keough, Jonathan Danielson, Jordan M Marshall, Doris Lagos-Kutz, David J Voegtlin, Rajagopalbabu Srinivasan, Punya Nachappa
Thrips-infesting soybeans were considered of minor economic importance, but recent evidence of their ability to transmit a newly identified soybean virus, Soybean vein necrosis virus (SVNV), has raised their profile as pests. Season-long surveys were conducted using suction traps to determine the effects of temperature and precipitation on the spatiotemporal patterns of three vector species of SVNV, Neohydatothrips variabilis (Beach) (Thysanoptera: Thripidae) (soybean thrips), Frankliniella tritici (Fitch) (Thysanoptera: Thripidae) (eastern flower thrips), and Frankliniella fusca (Hinds) (Thysanoptera: Thripidae) (tobacco thrips) in soybean fields in Indiana in 2013 and 2014...
March 1, 2018: Environmental Entomology
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