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Infectious disease dynamics

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https://www.readbyqxmd.com/read/28106223/next-generation-of-network-medicine-interdisciplinary-signaling-approaches
#1
REVIEW
Tamas Korcsmaros, Maria Victoria Schneider, Giulio Superti-Furga
In the last decade, network approaches have transformed our understanding of biological systems. Network analyses and visualizations have allowed us to identify essential molecules and modules in biological systems, and improved our understanding of how changes in cellular processes can lead to complex diseases, such as cancer, infectious and neurodegenerative diseases. "Network medicine" involves unbiased large-scale network-based analyses of diverse data describing interactions between genes, diseases, phenotypes, drug targets, drug transport, drug side-effects, disease trajectories and more...
January 20, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28102319/temporal-topic-modeling-to-assess-associations-between-news-trends-and-infectious-disease-outbreaks
#2
Saurav Ghosh, Prithwish Chakraborty, Elaine O Nsoesie, Emily Cohn, Sumiko R Mekaru, John S Brownstein, Naren Ramakrishnan
In retrospective assessments, internet news reports have been shown to capture early reports of unknown infectious disease transmission prior to official laboratory confirmation. In general, media interest and reporting peaks and wanes during the course of an outbreak. In this study, we quantify the extent to which media interest during infectious disease outbreaks is indicative of trends of reported incidence. We introduce an approach that uses supervised temporal topic models to transform large corpora of news articles into temporal topic trends...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28099479/social-contact-structures-and-time-use-patterns-in-the-manicaland-province-of-zimbabwe
#3
Alessia Melegaro, Emanuele Del Fava, Piero Poletti, Stefano Merler, Constance Nyamukapa, John Williams, Simon Gregson, Piero Manfredi
BACKGROUND: Patterns of person-to-person contacts relevant for infectious diseases transmission are still poorly quantified in Sub-Saharan Africa (SSA), where socio-demographic structures and behavioral attitudes are expected to be different from those of more developed countries. METHODS AND FINDINGS: We conducted a diary-based survey on daily contacts and time-use of individuals of different ages in one rural and one peri-urban site of Manicaland, Zimbabwe. A total of 2,490 diaries were collected and used to derive age-structured contact matrices, to analyze time spent by individuals in different settings, and to identify the key determinants of individuals' mixing patterns...
2017: PloS One
https://www.readbyqxmd.com/read/28098883/developmental-expression-of-toll%C3%A2-like-receptors-in-the-guinea-pig-lung
#4
Lingjie Ma, Jiali Yang, Li Yang, Juan Shi, Jing Xue, Yong Li, Xiaoming Liu
The guinea pig is a useful model for investigating infectious and non‑infectious lung diseases due to the sensitivity of its respiratory system and susceptibility to infectious agents. Toll‑like receptors (TLRs) are important components of the innate immune response and are critical for lung immune function. In the present study, the differentiation of epithelial cells in the guinea pig lung was examined during gestation by studying anatomic morphology and the major epithelial cell types using cell type‑specific markers...
January 17, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28097052/population-dynamics-of-epidemic-and-endemic-states-of-drug-resistance-emergence-in-infectious-diseases
#5
Diána Knipl, Gergely Röst, Seyed M Moghadas
The emergence and spread of drug-resistance during treatment of many infectious diseases continue to degrade our ability to control and mitigate infection outcomes using therapeutic measures. While the coverage and efficacy of treatment remain key factors in the population dynamics of resistance, the timing for the start of the treatment in infectious individuals can significantly influence such dynamics. We developed a between-host disease transmission model to investigate the short-term (epidemic) and long-term (endemic) states of infections caused by two competing pathogen subtypes, namely the wild-type and resistant-type, when the probability of developing resistance is a function of delay in start of the treatment...
2017: PeerJ
https://www.readbyqxmd.com/read/28095513/changes-in-circulating-b-cell-subsets-associated-with-aging-and-acute-siv-infection-in-rhesus-macaques
#6
W L William Chang, Denise F Gonzalez, Hung T Kieu, Luis D Castillo, Ilhem Messaoudi, Xiaoying Shen, Georgia D Tomaras, Barbara L Shacklett, Peter A Barry, Ellen E Sparger
Aging and certain viral infections can negatively impact humoral responses in humans. To further develop the nonhuman primate (NHP) model for investigating B cell dynamics in human aging and infectious disease, a flow cytometric panel was developed to characterize circulating rhesus B cell subsets. Significant differences between human and macaque B cells included the proportions of cells within IgD+ and switched memory populations and a prominent CD21-CD27+ unswitched memory population detected only in macaques...
2017: PloS One
https://www.readbyqxmd.com/read/28094206/hepatocyte-growth-factor-in-physiology-and-infectious-diseases
#7
REVIEW
Ryu Imamura, Kunio Matsumoto
Hepatocyte growth factor (HGF) is a pleiotropic cytokine composed of an α-chain and a β-chain, and these chains contain four kringle domains and a serine protease-like structure, respectively. The receptor for HGF was identified as the c-met proto-oncogene product of transmembrane receptor tyrosine kinase. HGF-induced signaling through the receptor Met provokes dynamic biological responses that support morphogenesis, regeneration, and the survival of various cells and tissues, which includes hepatocytes, renal tubular cells, and neurons...
January 13, 2017: Cytokine
https://www.readbyqxmd.com/read/28091971/mate-limitation-in-fungal-plant-parasites-can-lead-to-cyclic-epidemics-in-perennial-host-populations
#8
Virginie Ravigné, Valérie Lemesle, Alicia Walter, Ludovic Mailleret, Frédéric M Hamelin
Fungal plant parasites represent a growing concern for biodiversity and food security. Most ascomycete species are capable of producing different types of infectious spores both asexually and sexually. Yet the contributions of both types of spores to epidemiological dynamics have still to been fully researched. Here we studied the effect of mate limitation in parasites which perform both sexual and asexual reproduction in the same host. Since mate limitation implies positive density dependence at low population density, we modeled the dynamics of such species with both density-dependent (sexual) and density-independent (asexual) transmission rates...
January 13, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28090783/probing-the-druggability-of-membrane-bound-rab5-by-molecular-dynamics-simulations
#9
Eileen Edler, Matthias Stein
Rab5 is a small GTPase and a key regulator in early endosomal trafficking. Rab5 and its effectors are involved in a large number of infectious diseases and certain types of cancer. We performed µs atomistic molecular dynamics simulations of inactive and active full-length Rab5 anchored to a complex model bilayer with composition of the early endosome membrane. Direct interactions between the Rab5 G domain and the bilayer were observed. We found two dominant nucleotide-dependent orientations characterised by a different accessibility of the switch regions...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28080980/climate-forcing-of-an-emerging-pathogenic-fungus-across-a-montane-multi-host-community
#10
Frances C Clare, Julia B Halder, Olivia Daniel, Jon Bielby, Mikhail A Semenov, Thibaut Jombart, Adeline Loyau, Dirk S Schmeller, Andrew A Cunningham, Marcus Rowcliffe, Trenton W J Garner, Jaime Bosch, Matthew C Fisher
Changes in the timings of seasonality as a result of anthropogenic climate change are predicted to occur over the coming decades. While this is expected to have widespread impacts on the dynamics of infectious disease through environmental forcing, empirical data are lacking. Here, we investigated whether seasonality, specifically the timing of spring ice-thaw, affected susceptibility to infection by the emerging pathogenic fungus Batrachochytrium dendrobatidis (Bd) across a montane community of amphibians that are suffering declines and extirpations as a consequence of this infection...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28059445/computational-de-novo-design-of-antibodies-binding-to-a-peptide-with-high-affinity
#11
Venkata Giridhar Poosarla, Tong Li, Boon Chong Goh, Klaus Schulten, Thomas K Wood, Costas D Maranas
Antibody drugs play a critical role in infectious diseases, cancer, autoimmune diseases, and inflammation. However, experimental methods for the generation of therapeutic antibodies such as using immunized mice or directed evolution remain time consuming and cannot target a specific antigen epitope. Here, we describe the application of a computational framework called OptMAVEn combined with molecular dynamics to de novo design antibodies. Our reference system is antibody 2D10, a single-chain antibody (scFv) that recognizes the dodecapeptide DVFYPYPYASGS, a peptide mimic of mannose-containing carbohydrates...
January 6, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28055822/global-travel-and-hiv-sti-epidemics-among-msm-what-does-the-future-hold
#12
Veronica C Lee, Patrick S Sullivan, Stefan D Baral
Infectious disease epidemics occur within dynamic systems and environments that shape risk and, ultimately, the spread of infectious diseases. Gay men and other men who have sex with men (MSM) are disproportionately impacted by HIV everywhere in the world. Several emerging trends present risks for sustained or increased HIV acquisition and transmission, and the growth of global travel in the context of emerging online platforms for social/sexual networking is discussed here. Four factors associated with travel that could potentiate HIV transmission are highlighted: different patterns of sexual risk behaviours during travel; the growth of online tools to meet sex partners more efficiently; the global heterogeneity of HIV strains; and the potential for diassortative mixing of men from high- and low-HIV prevalence areas...
January 6, 2017: Sexual Health
https://www.readbyqxmd.com/read/28051146/impacts-of-canine-distemper-virus-infection-on-the-giant-panda-population-from-the-perspective-of-gut-microbiota
#13
Na Zhao, Meng Li, Jing Luo, Supen Wang, Shelan Liu, Shan Wang, Wenting Lyu, Lin Chen, Wen Su, Hua Ding, Hongxuan He
The recent increase in infectious disease outbreaks has been directly linked to the global loss of biodiversity and the decline of some endangered species populations. Between December 2014 and March 2015, five captive giant pandas died due to canine distemper virus (CDV) infection in China. CDV has taken a heavy toll on tigers and lions in recent years. Here, we describe the first gut microbiome diversity study of CDV-infected pandas. By investigating the influence of CDV infection on gut bacterial communities in infected and uninfected individuals and throughout the course of infection, we found that CDV infection distorted the gut microbiota composition by reducing the prevalence of the dominant genera, Escherichia and Clostridium, and increasing microbial diversity...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043017/evolution-and-structural-dynamics-of-bacterial-glycan-binding-adhesins
#14
REVIEW
Kristof Moonens, Han Remaut
Infectious disease processes like bacterial adherence or the activity of secreted toxins frequently gain host and tissue specificity by glycan binding interactions with the host glycome. Recent functional and structural studies highlight the high niche specialization of bacterial lectins, but also reveal a remarkable plasticity in their glycan binding sites and mechanisms, to adapt to host glycome dynamics or changing environmental conditions at the site of infection. In this review we put emphasis on new structural insights in host adaptation and dynamics of bacterial carbohydrate binding adhesins and toxins in human pathogens like uropathogenic and enteropathogenic Escherichia coli, Helicobacter pylori, Yersinia pestis or Vibrio cholera...
December 30, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28039030/sexually-transmitted-infections-and-mate-finding-allee-effects
#15
Luděk Berec, Eva Janoušková, Michal Theuer
Infectious diseases can seriously impact dynamics of their host species. In this study, we model and analyze an interaction between a sexually transmitted infection and its animal host population affected by a mate-finding Allee effect. Since mating drives both host reproduction and infection transmission, the Allee effect shapes the transmission rate of the infection which we show takes a saturating form. Our model combining sexually transmitted infections with the mate-finding Allee effect in the host produces quite rich dynamics, including oscillations, several multistability regimes, and infection-induced host extinction...
December 27, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/28038870/real-time-forecasting-of-infectious-disease-dynamics-with-a-stochastic-semi-mechanistic-model
#16
Sebastian Funk, Anton Camacho, Adam J Kucharski, Rosalind M Eggo, W John Edmunds
Real-time forecasts of infectious diseases can help public health planning, especially during outbreaks. If forecasts are generated from mechanistic models, they can be further used to target resources or to compare the impact of possible interventions. However, paremeterising such models is often difficult in real time, when information on behavioural changes, interventions and routes of transmission are not readily available. Here, we present a semi-mechanistic model of infectious disease dynamics that was used in real time during the 2013-2016 West African Ebola epidemic, and show fits to a Ebola Forecasting Challenge conducted in late 2015 with simulated data mimicking the true epidemic...
December 16, 2016: Epidemics
https://www.readbyqxmd.com/read/28030639/limits-to-causal-inference-with-state-space-reconstruction-for-infectious-disease
#17
Sarah Cobey, Edward B Baskerville
Infectious diseases are notorious for their complex dynamics, which make it difficult to fit models to test hypotheses. Methods based on state-space reconstruction have been proposed to infer causal interactions in noisy, nonlinear dynamical systems. These "model-free" methods are collectively known as convergent cross-mapping (CCM). Although CCM has theoretical support, natural systems routinely violate its assumptions. To identify the practical limits of causal inference under CCM, we simulated the dynamics of two pathogen strains with varying interaction strengths...
2016: PloS One
https://www.readbyqxmd.com/read/28029378/urbanization-and-disease-emergence-dynamics-at-the-wildlife-livestock-human-interface
#18
REVIEW
James M Hassell, Michael Begon, Melissa J Ward, Eric M Fèvre
Urbanization is characterized by rapid intensification of agriculture, socioeconomic change, and ecological fragmentation, which can have profound impacts on the epidemiology of infectious disease. Here, we review current scientific evidence for the drivers and epidemiology of emerging wildlife-borne zoonoses in urban landscapes, where anthropogenic pressures can create diverse wildlife-livestock-human interfaces. We argue that these interfaces represent a critical point for cross-species transmission and emergence of pathogens into new host populations, and thus understanding their form and function is necessary to identify suitable interventions to mitigate the risk of disease emergence...
October 28, 2016: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28028486/effects-of-wind-energy-generation-and-white-nose-syndrome-on-the-viability-of-the-indiana-bat
#19
Richard A Erickson, Wayne E Thogmartin, Jay E Diffendorfer, Robin E Russell, Jennifer A Szymanski
Wind energy generation holds the potential to adversely affect wildlife populations. Species-wide effects are difficult to study and few, if any, studies examine effects of wind energy generation on any species across its entire range. One species that may be affected by wind energy generation is the endangered Indiana bat (Myotis sodalis), which is found in the eastern and midwestern United States. In addition to mortality from wind energy generation, the species also faces range-wide threats from the emerging infectious fungal disease, white-nose syndrome (WNS)...
2016: PeerJ
https://www.readbyqxmd.com/read/28013336/hybrid-markov-chain-models-of-s-i-r-disease-dynamics
#20
Nicolas P Rebuli, N G Bean, J V Ross
Deterministic epidemic models are attractive due to their compact nature, allowing substantial complexity with computational efficiency. This partly explains their dominance in epidemic modelling. However, the small numbers of infectious individuals at early and late stages of an epidemic, in combination with the stochastic nature of transmission and recovery events, are critically important to understanding disease dynamics. This motivates the use of a stochastic model, with continuous-time Markov chains being a popular choice...
December 24, 2016: Journal of Mathematical Biology
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