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Outbreak prediction

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https://www.readbyqxmd.com/read/28100256/transcriptomic-signatures-differentiate-survival-from-fatal-outcomes-in-humans-infected-with-ebola-virus
#1
Xuan Liu, Emily Speranza, César Muñoz-Fontela, Sam Haldenby, Natasha Y Rickett, Isabel Garcia-Dorival, Yongxiang Fang, Yper Hall, Elsa-Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny, Nichola Rockliffe, E Diane Williamson, Thomas R Laws, Magassouba N'Faly, David A Matthews, Stephan Günther, Andrew R Cossins, Armand Sprecher, John H Connor, Miles W Carroll, Julian A Hiscox
BACKGROUND: In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatment strategies. We used transcriptome data for peripheral blood taken from infected and convalescent recovering patients to identify early stage host factors that are associated with acute illness and those that differentiate patient survival from fatality. RESULTS: The data demonstrate that individuals who succumbed to the disease show stronger upregulation of interferon signalling and acute phase responses compared to survivors during the acute phase of infection...
January 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28096975/a-prospective-survey-of-pseudomonas-aeruginosa-colonization-and-infection-in-the-intensive-care-unit
#2
Regev Cohen, Frida Babushkin, Shoshana Cohen, Marina Afraimov, Maurice Shapiro, Martina Uda, Efrat Khabra, Amos Adler, Ronen Ben Ami, Svetlana Paikin
BACKGROUND: Pseudomonas aeruginosa (PA) surveillance may improve empiric antimicrobial therapy, since colonizing strains frequently cause infections. This colonization may be 'endogenous' or 'exogenous', and the source determines infection control measures. We prospectively investigated the sources of PA, the clinical impact of PA colonization upon admission and the dynamics of colonization at different body sites throughout the intensive care unit stay. METHODS: Intensive care patients were screened on admission and weekly from the pharynx, endotracheal aspirate, rectum and urine...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28095468/evaluating-hospital-based-surveillance-for-outbreak-detection-in-bangladesh-analysis-of-healthcare-utilization-data
#3
Birgit Nikolay, Henrik Salje, Katharine Sturm-Ramirez, Eduardo Azziz-Baumgartner, Nusrat Homaira, Makhdum Ahmed, A Danielle Iuliano, Repon C Paul, Mahmudur Rahman, M Jahangir Hossain, Stephen P Luby, Simon Cauchemez, Emily S Gurley
BACKGROUND: The International Health Regulations outline core requirements to ensure the detection of public health threats of international concern. Assessing the capacity of surveillance systems to detect these threats is crucial for evaluating a country's ability to meet these requirements. METHODS AND FINDINGS: We propose a framework to evaluate the sensitivity and representativeness of hospital-based surveillance and apply it to severe neurological infectious diseases and fatal respiratory infectious diseases in Bangladesh...
January 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28095405/defining-the-risk-of-zika-and-chikungunya-virus-transmission-in-human-population-centers-of-the-eastern-united-states
#4
Carrie A Manore, Richard S Ostfeld, Folashade B Agusto, Holly Gaff, Shannon L LaDeau
The recent spread of mosquito-transmitted viruses and associated disease to the Americas motivates a new, data-driven evaluation of risk in temperate population centers. Temperate regions are generally expected to pose low risk for significant mosquito-borne disease; however, the spread of the Asian tiger mosquito (Aedes albopictus) across densely populated urban areas has established a new landscape of risk. We use a model informed by field data to assess the conditions likely to facilitate local transmission of chikungunya and Zika viruses from an infected traveler to Ae...
January 17, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28095403/a-likelihood-approach-for-real-time-calibration-of-stochastic-compartmental-epidemic-models
#5
Christoph Zimmer, Reza Yaesoubi, Ted Cohen
Stochastic transmission dynamic models are especially useful for studying the early emergence of novel pathogens given the importance of chance events when the number of infectious individuals is small. However, methods for parameter estimation and prediction for these types of stochastic models remain limited. In this manuscript, we describe a calibration and prediction framework for stochastic compartmental transmission models of epidemics. The proposed method, Multiple Shooting for Stochastic systems (MSS), applies a linear noise approximation to describe the size of the fluctuations, and uses each new surveillance observation to update the belief about the true epidemic state...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28095328/an-integrated-proteomic-and-transcriptomic-analysis-of-perivitelline-fluid-proteins-in-a-freshwater-gastropod-laying-aerial-eggs
#6
Huawei Mu, Jin Sun, Horacio Heras, Ka Hou Chu, Jian-Wen Qiu
: Proteins of the egg perivitelline fluid (PVF) that surrounds the embryo are critical for embryonic development in many animals, but little is known about their identities. Using an integrated proteomic and transcriptomic approach, we identified 64 proteins from the PVF of Pomacea maculata - a freshwater snail adopting aerial oviposition. Proteins were classified into eight functional groups: major multifunctional perivitellin subunits, immune response, energy metabolism, protein degradation, oxidation-reduction, signaling and binding, transcription and translation, and others...
January 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28092933/estimation-of-the-size-of-the-iatrogenic-creutzfeldt-jakob-disease-outbreak-associated-with-cadaveric-dura-mater-grafts-in-korea
#7
Byoug-Hak Jeon, Jinseob Kim, GangHyun Kim Kim, Soo Chul Park, SangYun Kim, Hae-Kwan Cheong
Purpose: This study estimated the overall magnitude of Creutzfeldt-Jakob disease (iCJD) based on dura graft cases in Korea using a mathematical model. Methods: We estimated the number of annual cases of dura grafts performed between 1980 and 1995 by applying the proportion of dura grafts recorded by the Health Insurance Review Agency claim dataset in Korea to the number of nationwide neurosurgery cases. The distribution of the incubation period was assumed to fall under a Weibull distribution with density function or a log-logistic distribution with density function...
December 19, 2016: Epidemiology and Health
https://www.readbyqxmd.com/read/28086751/quantifying-predictors-for-the-spatial-diffusion-of-avian-influenza-virus-in-china
#8
Lu Lu, Andrew J Leigh Brown, Samantha J Lycett
BACKGROUND: Avian influenza virus (AIV) causes both severe outbreaks and endemic disease among poultry and has caused sporadic human infections in Asia, furthermore the routes of transmission in avian species between geographic regions can be numerous and complex. Using nucleotide sequences from the internal protein coding segments of AIV, we performed a Bayesian phylogeographic study to uncover regional routes of transmission and factors predictive of the rate of viral diffusion within China...
January 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28081120/epidemiology-of-chikungunya-virus-outbreaks-in-guadeloupe-and-martinique-2014-an-observational-study-in-volunteer-blood-donors
#9
Pierre Gallian, Isabelle Leparc-Goffart, Pascale Richard, Françoise Maire, Olivier Flusin, Rachid Djoudi, Jacques Chiaroni, Remi Charrel, Pierre Tiberghien, Xavier de Lamballerie
BACKGROUND: During Dec-2013, a chikungunya virus (CHIKV) outbreak was first detected in the French-West Indies. Subsequently, the virus dispersed to other Caribbean islands, continental America and many islands in the Pacific Ocean. Previous estimates of the attack rate were based on declaration of clinically suspected cases. METHODS/PRINCIPAL FINDINGS: Individual testing for CHIKV RNA of all (n = 16,386) blood donations between Feb-24th 2014 and Jan-31st 2015 identified 0·36% and 0·42% of positives in Guadeloupe and Martinique, respectively...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28080984/modelling-coffee-leaf-rust-risk-in-colombia-with-climate-reanalysis-data
#10
Daniel P Bebber, Ángela Delgado Castillo, Sarah J Gurr
Many fungal plant diseases are strongly controlled by weather, and global climate change is thus likely to have affected fungal pathogen distributions and impacts. Modelling the response of plant diseases to climate change is hampered by the difficulty of estimating pathogen-relevant microclimatic variables from standard meteorological data. The availability of increasingly sophisticated high-resolution climate reanalyses may help overcome this challenge. We illustrate the use of climate reanalyses by testing the hypothesis that climate change increased the likelihood of the 2008-2011 outbreak of Coffee Leaf Rust (CLR, Hemileia vastatrix) in Colombia...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28080981/phenotypic-interactions-between-tree-hosts-and-invasive-forest-pathogens-in-the-light-of-globalization-and-climate-change
#11
REVIEW
Jan Stenlid, Jonàs Oliva
Invasive pathogens can cause considerable damage to forest ecosystems. Lack of coevolution is generally thought to enable invasive pathogens to bypass the defence and/or recognition systems in the host. Although mostly true, this argument fails to predict intermittent outcomes in space and time, underlining the need to include the roles of the environment and the phenotype in host-pathogen interactions when predicting disease impacts. We emphasize the need to consider host-tree imbalances from a phenotypic perspective, considering the lack of coevolutionary and evolutionary history with the pathogen and the environment, respectively...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28073508/mixotrophic-ability-of-the-phototrophic-dinoflagellates-alexandrium-andersonii-a-affine-and-a-fraterculus
#12
Kyung Ha Lee, Hae Jin Jeong, Ji Eun Kwon, Hee Chang Kang, Ji Hye Kim, Se Hyeon Jang, Jae Yeon Park, Eun Young Yoon, Jae Seong Kim
The dinoflagellate Alexandrium spp. have received much attention due to their harmful effects on diverse marine organisms, including commercially important species. For minimizing loss due to red tides or blooms of Alexandrium spp., it is very important to understand the eco-physiology of each Alexandrium species and to predict its population dynamics. Its trophic mode (i.e., exclusively autotrophic or mixotrophic) is one of the most critical parameters in establishing prediction models. However, among the 35 Alexandrium species so far described, only six Alexandrium species have been revealed to be mixotrophic...
November 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073444/modelling-the-hydrodynamic-conditions-associated-with-dinophysis-blooms-in-galicia-nw-spain
#13
Manuel Ruiz-Villarreal, Luz M García-García, Marcos Cobas, Patricio A Díaz, Beatriz Reguera
The northwestern Iberian coast (Galician Rías and shelf) is frequently affected by toxic harmful algal blooms (HABs) (mainly Dinophysis spp.), leading to lengthy harvesting closures in a region where aquaculture has a strong socioeconomic impact. The project ASIMUTH (http://www.asimuth.eu) aimed to develop forecasting capabilities to warn of impending HABs along the European Atlantic coast. Simulations with the ROMS model (hydrodynamical and ecological simulations complemented with Lagrangian particle tracking simulations) of the Galician coastal circulation have been performed in the framework of the ASIMUTH project to characterize and forecast oceanographic conditions before and during HAB periods...
March 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073442/toward-predicting-dinophysis-blooms-off-nw-iberia-a-decade-of-events
#14
Ma Teresa Moita, Yolanda Pazos, Carlos Rocha, Rita Nolasco, Paulo B Oliveira
Dinophysis acuminata and Dinophysis acuta are recurrent species off NW Iberia but their outbreaks occur under different conditions. A decade (2004-2013) of weekly data for each species at two sentinel stations located at the entrance of Rias de Aveiro-AV (NW Portugal, 40°38.6'N) and Pontevedra-PO (Galicia, Spain, 42°21.5'N), were used to investigate the regional synchronism and mesoscale differences related to species detection, bloom (>200cellsL(-1)) initiation and development. Results highlight the high interannual variability of bloom events and summarize the associated meteorological/oceanographic conditions...
March 2016: Harmful Algae
https://www.readbyqxmd.com/read/28070933/secretome-analysis-of-diarrhea-inducing-strains-of-escherichia-coli
#15
Raja Sekhar Nirujogi, Babylakshmi Muthusamy, Min-Sik Kim, Gajanan J Sathe, P T V Lakshmi, Olga N Kovbasnjuk, T S Keshava Prasad, Mary Wade, Rabih E Jabbour
Secreted proteins constitute a major part of virulence factors that are responsible for pathogenesis caused by gram negative bacteria. Enterohemorrhagic Escherichia coli (E. coli), EHEC O157:H7 is the major pathogen often causing outbreaks. However, studies have reported that the significant outbreaks caused by non O157:H7 E. coli strains, also known as "Big-Six" serogroup strains are increasing. There is no systematic study describing differential secreted proteins from these non-O157:H7 E. coli strains. In this study, we carried out mass spectrometry-based differential secretome analysis using tandem mass tags labeling strategy of non-O157:H7 E...
January 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28070333/corticosterone-inflammation-immune-status-and-telomere-length-in-frigatebird-nestlings-facing-a-severe-herpesvirus-infection
#16
Manrico Sebastiano, Marcel Eens, Frederic Angelier, Kévin Pineau, Olivier Chastel, David Costantini
Herpesvirus outbreaks are common in natural animal populations, but little is known about factors that favour the infection and its consequences for the organism. In this study, we examined the pathophysiological consequences of a disease probably attributable to herpesvirus infection for several markers of immune function, corticosterone, telomere length and inflammation. In addition, we assessed whether any markers used in this study might be associated with the occurrence of visible clinical signs of the disease and its impact on short-term survival perspectives...
2017: Conservation Physiology
https://www.readbyqxmd.com/read/28068339/effect-of-climatic-factors-and-population-density-on-the-distribution-of-dengue-in-sri-lanka-a-gis-based-evaluation-for-prediction-of-outbreaks
#17
Pdnn Sirisena, Faseeha Noordeen, Harithra Kurukulasuriya, Thanuja Alar Romesh, LakKumar Fernando
Dengue is one of the major hurdles to the public health in Sri Lanka, causing high morbidity and mortality. The present study focuses on the use of geographical information systems (GIS) to map and evaluate the spatial and temporal distribution of dengue in Sri Lanka from 2009 to 2014 and to elucidate the association of climatic factors with dengue incidence. Epidemiological, population and meteorological data were collected from the Epidemiology Unit, Department of Census and Statistics and the Department of Meteorology of Sri Lanka...
2017: PloS One
https://www.readbyqxmd.com/read/28067258/a-new-method-for-assessing-the-risk-of-infectious-disease-outbreak
#18
Yilan Liao, Bing Xu, Jinfeng Wang, Xiaochi Liu
Over the past few years, emergent threats posed by infectious diseases and bioterrorism have become public health concerns that have increased the need for prompt disease outbreak warnings. In most of the existing disease surveillance systems, disease outbreak risk is assessed by the detection of disease outbreaks. However, this is a retrospective approach that impacts the timeliness of the warning. Some disease surveillance systems can predict the probabilities of infectious disease outbreaks in advance by determining the relationship between a disease outbreak and the risk factors...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28060934/a-cohort-study-of-adult-patients-with-severe-dengue-in-taiwanese-intensive-care-units-the-elderly-and-aptt-prolongation-matter-for-prognosis
#19
Chih-Cheng Hsieh, Cong-Tat Cia, Jen-Chieh Lee, Junne-Ming Sung, Nan-Yao Lee, Po-Lin Chen, Te-Hui Kuo, Jo-Yen Chao, Wen-Chien Ko
BACKGROUND: There was a large dengue outbreak in Taiwan in 2015, in which the ages of the affected individuals were higher than those in other countries. The aim of this study was to explore the characteristics and prognostic factors for adults with severe dengue in intensive care units (ICUs). METHODS: All adults admitted to ICUs with dengue virus infection (DENV) at a medical center from July 1, 2015 to December 31, 2015 were enrolled. DENV was diagnosed by the presence of serum NS1 antigen, IgM antibodies to dengue virus, or dengue virus RNA by real-time reverse transcriptase polymerase chain reaction...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28060809/dynamic-forecasting-of-zika-epidemics-using-google-trends
#20
Yue Teng, Dehua Bi, Guigang Xie, Yuan Jin, Yong Huang, Baihan Lin, Xiaoping An, Dan Feng, Yigang Tong
We developed a dynamic forecasting model for Zika virus (ZIKV), based on real-time online search data from Google Trends (GTs). It was designed to provide Zika virus disease (ZVD) surveillance and detection for Health Departments, and predictive numbers of infection cases, which would allow them sufficient time to implement interventions. In this study, we found a strong correlation between Zika-related GTs and the cumulative numbers of reported cases (confirmed, suspected and total cases; p<0.001). Then, we used the correlation data from Zika-related online search in GTs and ZIKV epidemics between 12 February and 20 October 2016 to construct an autoregressive integrated moving average (ARIMA) model (0, 1, 3) for the dynamic estimation of ZIKV outbreaks...
2017: PloS One
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