Modeling epidemics on adaptively evolving networks: A data-mining perspective.

Abstract:

:The exploration of epidemic dynamics on dynamically evolving ("adaptive") networks poses nontrivial challenges to the modeler, such as the determination of a small number of informative statistics of the detailed network state (that is, a few "good observables") that usefully summarize the overall (macroscopic, systems-level) behavior. Obtaining reduced, small size accurate models in terms of these few statistical observables--that is, trying to coarse-grain the full network epidemic model to a small but useful macroscopic one--is even more daunting. Here we describe a data-based approach to solving the first challenge: the detection of a few informative collective observables of the detailed epidemic dynamics. This is accomplished through Diffusion Maps (DMAPS), a recently developed data-mining technique. We illustrate the approach through simulations of a simple mathematical model of epidemics on a network: a model known to exhibit complex temporal dynamics. We discuss potential extensions of the approach, as well as possible shortcomings.

journal_name

Virulence

journal_title

Virulence

authors

Kattis AA,Holiday A,Stoica AA,Kevrekidis IG

doi

10.1080/21505594.2015.1121357

subject

Has Abstract

pub_date

2016-01-01 00:00:00

pages

153-62

issue

2

eissn

2150-5594

issn

2150-5608

journal_volume

7

pub_type

杂志文章
  • The role of inflammasome modulation in virulence.

    abstract::Pathogens frequently exist in an immunological balancing act with their host. Pathogens must not only replicate within a host but also transmit effectively between hosts to perpetuate their species. On the other hand, the host seeks to maintain homeostasis by clearing pathogens. The inflammasome is a multi-protein com...

    journal_title:Virulence

    pub_type: 杂志文章,评审

    doi:10.4161/viru.20266

    authors: Lupfer CR,Kanneganti TD

    更新日期:2012-05-01 00:00:00

  • Passive therapy with humanized anti-staphylococcal enterotoxin B antibodies attenuates systemic inflammatory response and protects from lethal pneumonia caused by staphylococcal enterotoxin B-producing Staphylococcus aureus.

    abstract::Drugs such as linezolid that inhibit bacterial protein synthesis may be beneficial in treating infections caused by toxigenic Staphylococcus aureus. As protein synthesis inhibitors have no effect on preformed toxins, neutralization of pathogenic exotoxins with anti-toxin antibodies may be beneficial in conjunction wit...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2016.1267894

    authors: Karau MJ,Tilahun ME,Krogman A,Osborne BA,Goldsby RA,David CS,Mandrekar JN,Patel R,Rajagopalan G

    更新日期:2017-10-03 00:00:00

  • Typing of Streptococcus pyogenes strains using the phage profiling method.

    abstract::We recently developed a method that allows fast differentiation between Streptococcus pyogenes (GAS) strains. The method named phage profiling (PP) is based on a simple assumption that a regular PCR reaction with Taq polymerase and relatively short elongation time is not able to yield long DNA fragment, such as ~40-50...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.4161/viru.21887

    authors: Borek AL,Obszańska K,Hryniewicz W,Sitkiewicz I

    更新日期:2012-10-01 00:00:00

  • Structural features and mechanism of translocation of non-LTR retrotransposons in Candida albicans.

    abstract::A number of abundant mobile genetic elements called retrotransposons reverse transcribe RNA to generate DNA for insertion into eukaryotic genomes. Non-long-terminal repeat (non-LTR) retrotransposons represent a major class of retrotransposons, and transposons that move by target-primed reverse transcription lack LTRs ...

    journal_title:Virulence

    pub_type: 杂志文章,评审

    doi:10.4161/viru.27278

    authors: Jiang J,Zhao L,Yan L,Zhang L,Cao Y,Wang Y,Jiang Y,Yan T,Cao Y

    更新日期:2014-02-15 00:00:00

  • Galleria mellonella as a host model to study Aspergillus terreus virulence and amphotericin B resistance.

    abstract::The aim of this study was to investigate if the alternative in vivo model Galleria mellonella can be used (i) to determine differences in pathogenicity of amphotericin B (AMB) resistant and susceptible A. terreus isolates, (ii) to evaluate AMB efficacy in vivo (iii) and to correlate outcome to in vitro susceptibility ...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2015.1045183

    authors: Maurer E,Browne N,Surlis C,Jukic E,Moser P,Kavanagh K,Lass-Flörl C,Binder U

    更新日期:2015-01-01 00:00:00

  • The formation of Staphylococcus aureus enterotoxin in food environments and advances in risk assessment.

    abstract::The recent finding that the formation of staphylococcal enterotoxins in food is very different from that in cultures of pure Staphylococcus aureus sheds new light on, and brings into question, traditional microbial risk assessment methods based on planktonic liquid cultures. In fact, most bacteria in food appear to be...

    journal_title:Virulence

    pub_type: 杂志文章,评审

    doi:10.4161/viru.2.6.18122

    authors: Schelin J,Wallin-Carlquist N,Cohn MT,Lindqvist R,Barker GC,Rådström P

    更新日期:2011-11-01 00:00:00

  • Histone deacetylases inhibitors effects on Cryptococcus neoformans major virulence phenotypes.

    abstract::Cryptococcus neoformans undergoes phenotypical changes during host infection in order to promote persistence and survival. Studies have demonstrated that such adaptations require alterations in gene transcription networks by distinct mechanisms. Drugs such as the histone deacetylases inhibitors (HDACi) Sodium Butyrate...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2015.1038014

    authors: Brandão FA,Derengowski LS,Albuquerque P,Nicola AM,Silva-Pereira I,Poças-Fonseca MJ

    更新日期:2015-01-01 00:00:00

  • Functional characteristics of the malaria parasite's "chloroquine resistance transporter": implications for chemotherapy.

    abstract::Chloroquine (CQ) was the best and most heavily used drug in the fight against malaria. However, the effectiveness of CQ has declined with the emergence and spread of CQ-resistant (CQR) Plasmodium falciparum parasites. The primary determinant of CQ resistance in P. falciparum is mutations in the parasite's 'chloroquine...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.4161/viru.1.4.12012

    authors: Summers RL,Martin RE

    更新日期:2010-07-01 00:00:00

  • A novel intrinsically disordered outer membrane lipoprotein of Aggregatibacter actinomycetemcomitans binds various cytokines and plays a role in biofilm response to interleukin-1β and interleukin-8.

    abstract::Intrinsically disordered proteins (IDPs) do not have a well-defined and stable 3-dimensional fold. Some IDPs can function as either transient or permanent binders of other proteins and may interact with an array of ligands by adopting different conformations. A novel outer membrane lipoprotein, bacterial interleukin r...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2016.1216294

    authors: Ahlstrand T,Tuominen H,Beklen A,Torittu A,Oscarsson J,Sormunen R,Pöllänen MT,Permi P,Ihalin R

    更新日期:2017-02-17 00:00:00

  • The clinical impact of multidrug-resistant gram-negative bacilli in the management of septic shock.

    abstract::Multi-antibiotic drug-resistant (MDR) gram-negative bacilli are becoming a major threat to the standard care of septic patients. Empiric antimicrobial drug regimens to cover likely bacterial pathogens have to be altered in keeping with the spread of MDR pathogens in the health care setting and in the community. Reliab...

    journal_title:Virulence

    pub_type: 杂志文章,评审

    doi:10.4161/viru.26210

    authors: Pop-Vicas A,Opal SM

    更新日期:2014-01-01 00:00:00

  • Risk stratification and immunogenetic risk for infections following stem cell transplantation.

    abstract::Patients undergoing haematopoietic stem cell transplantation (HSCT) are highly exposed to infectious agents. However, it is not known why certain HSCT recipients rapidly develop severe infections while other, despite similar immunosuppressive conditions, do not. Increasing evidence suggests that such differences may b...

    journal_title:Virulence

    pub_type: 杂志文章,评审

    doi:10.1080/21505594.2016.1234566

    authors: Wójtowicz A,Bochud PY

    更新日期:2016-11-16 00:00:00

  • Prolonged infection by Fonsecaea pedrosoi after antigenic co-stimulation at different sites in experimental murine chromoblastomycosis.

    abstract::In the present study, we examined prolonged infection after antigenic co-stimulation by inoculation of the fungus Fonsecaea pedrosoi at two different sites in three mouse strains (BALB/c, Swiss, and C57BL/6). Using this murine model of infection, we showed that antigen induction of infection at more than one site led ...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.4161/viru.1.1.9920

    authors: Machado AP,Silva MR,Fischman O

    更新日期:2010-01-01 00:00:00

  • Screen of FDA-approved drug library identifies maprotiline, an antibiofilm and antivirulence compound with QseC sensor-kinase dependent activity in Francisella novicida.

    abstract::Development of new therapeutics against Select Agents such as Francisella is critical preparation in the event of bioterrorism. Testing FDA-approved drugs for this purpose may yield new activities unrelated to their intended purpose and may hasten the discovery of new therapeutics. A library of 420 FDA-approved drugs ...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2015.1046029

    authors: Dean SN,van Hoek ML

    更新日期:2015-01-01 00:00:00

  • Eicosanoid biosynthesis influences the virulence of Candida parapsilosis.

    abstract::Lipid mediators, derived from arachidonic acid metabolism, play an important role in immune regulation. The functions of bioactive eicosanoids range from modulating cytokine signaling and inflammasome formation to anti-inflammatory and pro-resolving activities. Human pathogenic fungi such as Candida albicans, Candida ...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2018.1475797

    authors: Chakraborty T,Thuer E,Heijink M,Tóth R,Bodai L,Vágvölgyi C,Giera M,Gabaldón T,Gácser A

    更新日期:2018-01-01 00:00:00

  • In silico and in vitro evaluation of PCR-based assays for the detection of Bacillus anthracis chromosomal signature sequences.

    abstract::Bacillus anthracis, the causative agent of anthrax, is a zoonotic pathogen that is relatively common throughout the world and may cause life threatening diseases in animals and humans. There are many PCR-based assays in use for the detection of B. anthracis. While most of the developed assays rely on unique markers pr...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.4161/viru.26288

    authors: Ågren J,Hamidjaja RA,Hansen T,Ruuls R,Thierry S,Vigre H,Janse I,Sundström A,Segerman B,Koene M,Löfström C,Van Rotterdam B,Derzelle S

    更新日期:2013-11-15 00:00:00

  • Staphylococcus aureus colonization and non-influenza respiratory viruses: Interactions and synergism mechanisms.

    abstract::Viral infections of the respiratory tract can be complicated by bacterial superinfection, resulting in a significantly longer duration of illness and even a fatal outcome. In this review, we focused on interactions between S. aureus and non-influenza viruses. Clinical data evidenced that rhinovirus infection may incre...

    journal_title:Virulence

    pub_type: 杂志文章,评审

    doi:10.1080/21505594.2018.1504561

    authors: Morgene MF,Botelho-Nevers E,Grattard F,Pillet S,Berthelot P,Pozzetto B,Verhoeven PO

    更新日期:2018-01-01 00:00:00

  • A type 6 secretion system (T6SS) encoded gene within Salmonella enterica serovar Enteritidis contributes to virulence.

    abstract::Bacteria interact with their host through protein secretion systems and surface structures. Pathogenic bacteria encode protein secretion systems that promote the invasion of the host's tissue, the evasion of the host's immune response, the thwarting microbial competitors, and ultimately survival within the host. For m...

    journal_title:Virulence

    pub_type: 评论,社论

    doi:10.1080/21505594.2017.1421829

    authors: Troxell B

    更新日期:2018-01-01 00:00:00

  • Luteolin decreases the pathogenicity of Aeromonas hydrophila via inhibiting the activity of aerolysin.

    abstract::Aeromonas hydrophila (A. hydrophila) can cause a number of diseases in both human and animals. A. hydrophila-related infections in aquaculture cause severe economic losses every year throughout the world. The emergence of antibiotic resistance that is due to the abuse of antibiotics has limited the application of anti...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2020.1867455

    authors: Dong J,Zhang L,Liu Y,Xu N,Zhou S,Yang Y,Yang Q,Ai X

    更新日期:2021-12-01 00:00:00

  • Functional and structural characteristics of bacterial proteins that bind host cytokines.

    abstract::Several human pathogens bind and respond to host cytokines, which can be considered a virulence mechanism that communicates defensive actions of the host to the pathogen. This review summarizes the current knowledge of bacterial cytokine-binding proteins, with a particular focus on their functional and structural char...

    journal_title:Virulence

    pub_type: 杂志文章,评审

    doi:10.1080/21505594.2017.1363140

    authors: Högbom M,Ihalin R

    更新日期:2017-11-17 00:00:00

  • Decreased expression of 14-3-3 in Paracoccidioides brasiliensis confirms its involvement in fungal pathogenesis.

    abstract::The interaction between the fungal pathogen Paracoccidioides brasiliensis and host cells is usually mediated by specific binding events between adhesins on the fungal surface and receptors on the host extracellular matrix or cell surface. One molecule implicated in the P. brasiliensis-host interaction is the 14-3-3 pr...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2015.1122166

    authors: Marcos CM,Silva Jde F,Oliveira HC,Assato PA,Singulani Jde L,Lopez AM,Tamayo DP,Hernandez-Ruiz O,McEwen JG,Mendes-Giannini MJ,Fusco-Almeida AM

    更新日期:2016-01-01 00:00:00

  • An endocytic CARriage tale: Adenoviruses internalization and trafficking in neurons.

    abstract::In immune-competent hosts, adenoviruses (Ads) are mild pathogens that cause mainly infections of the respiratory and ocular tracks. The advent of Ad-based gene transfer vectors made the understanding of their interaction with the host cellular machinery an intensive field of research over the last decade. As studies f...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.4161/viru.1.3.11379

    authors: Henaff D,Salinas S

    更新日期:2010-05-01 00:00:00

  • Identifying components required for OMP biogenesis as novel targets for antiinfective drugs.

    abstract::The emergence of multiresistant Gram-negative bacteria requires new therapies for combating bacterial infections. Targeting the biogenesis of virulence factors could be an alternative strategy instead of killing bacteria with antibiotics. The outer membrane (OM) of Gram-negative bacteria acts as a physical barrier. At...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2016.1278333

    authors: Weirich J,Bräutigam C,Mühlenkamp M,Franz-Wachtel M,Macek B,Meuskens I,Skurnik M,Leskinen K,Bohn E,Autenrieth I,Schütz M

    更新日期:2017-10-03 00:00:00

  • Surface display of Gaussia princeps luciferase allows sensitive fungal pathogen detection during cutaneous aspergillosis.

    abstract::Non-invasive imaging techniques in microbial disease models have delivered valuable insights in the intimate pathogen-host interplay during infection. Here we describe evaluation and validation of a transgenic bioluminescence reporter strain of the human-pathogenic mold Aspergillus fumigatus, one of the main fungal pa...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.4161/viru.3.1.18799

    authors: Donat S,Hasenberg M,Schäfer T,Ohlsen K,Gunzer M,Einsele H,Löffler J,Beilhack A,Krappmann S

    更新日期:2012-01-01 00:00:00

  • Highly specific host-pathogen interactions influence Metarhizium brunneum blastospore virulence against Culex quinquefasciatus larvae.

    abstract::Entomopathogenic fungi are potential biological control agents of mosquitoes. Our group observed that not all mosquitoes were equally susceptible to fungal infection and observed significant differences in virulence of different spore types. Conidiospores and blastospores were tested against Culex quinquefasciatus lar...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2018.1509665

    authors: Alkhaibari AM,Lord AM,Maffeis T,Bull JC,Olivares FL,Samuels RI,Butt TM

    更新日期:2018-01-01 00:00:00

  • Formyl peptide receptor 2 orchestrates mucosal protection against Citrobacter rodentium infection.

    abstract::Citrobacter rodentium is an attaching and effacing intestinal murine pathogen which shares similar virulence strategies with the human pathogens enteropathogenic- and enterohemorrhagic Escherichia coli to infect their host. C. rodentium is spontaneously cleared by healthy wild-type (WT) mice whereas mice lacking Muc2 ...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2019.1635417

    authors: Sharba S,Venkatakrishnan V,Padra M,Winther M,Gabl M,Sundqvist M,Wang J,Forsman H,Linden SK

    更新日期:2019-12-01 00:00:00

  • Identification of the pXO1 plasmid in attenuated Bacillus anthracis vaccine strains.

    abstract::Anthrax toxins and capsule are the major virulence factors of Bacillus anthracis. They are encoded by genes located on the plasmids pXO1 and pXO2, respectively. The vaccine strain Pasteur II was produced from high temperature subcultures of B. anthracis, which resulted in virulence attenuation through the loss of the ...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2016.1164366

    authors: Liang X,Zhang H,Zhang E,Wei J,Li W,Wang B,Dong S,Zhu J

    更新日期:2016-07-03 00:00:00

  • Attenuation of pathogenic Rift Valley fever virus strain through the chimeric S-segment encoding sandfly fever phlebovirus NSs or a dominant-negative PKR.

    abstract::Rift Valley fever is a mosquito-borne zoonotic disease affecting ruminants and humans. Rift Valley fever virus (RVFV: family Bunyaviridae, genus Phlebovirus) causes abortions and fetal malformations in ruminants, and hemorrhagic fever, encephalitis, or retinitis in humans. The live-attenuated MP-12 vaccine is conditio...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2016.1195528

    authors: Nishiyama S,Slack OA,Lokugamage N,Hill TE,Juelich TL,Zhang L,Smith JK,Perez D,Gong B,Freiberg AN,Ikegami T

    更新日期:2016-11-16 00:00:00

  • pEntYN10 a plasmid of Escherichia coli O169:H41 associated with adherence and toxin production.

    abstract::In this issue of Virulence, Ban E et al. described the complete sequence of the pEntYN10 plasmid of Escherichia coli O169:H41. The plasmid has 182 coding sequences (CDs); among the identified CDs, some were identified as colonization factors (CFs), one was an enterotoxin and others were insertion sequences (IS). In th...

    journal_title:Virulence

    pub_type: 评论,社论

    doi:10.1080/21505594.2015.1104450

    authors: Navarro A

    更新日期:2015-01-01 00:00:00

  • Pharmacodynamic and pharmacokinetic considerations in the treatment of critically Ill patients infected with carbapenem-resistant Enterobacteriaceae.

    abstract::Carbapenem-Resistant Enterobacteriaceae (CRE) are an emerging healthcare crisis. Infections due to CRE are associated with high morbidity and mortality, especially in critically ill patients. Due to the multi-drug resistant nature of these infections only limited treatment options are available. Antimicrobials that ha...

    journal_title:Virulence

    pub_type: 杂志文章,评审

    doi:10.1080/21505594.2016.1221021

    authors: Neuner EA,Gallagher JC

    更新日期:2017-05-19 00:00:00

  • Hypervirulent Klebsiella pneumoniae is emerging as an increasingly prevalent K. pneumoniae pathotype responsible for nosocomial and healthcare-associated infections in Beijing, China.

    abstract:OBJECTIVES:Hypervirulent Klebsiella pneumoniae(hvKp) is an increasingly important pathogen. Tracking its epidemiology and evolving antimicrobial resistance will facilitate care. METHODS:A retrospective study was conducted in two hospitals. We collected the clinical data. Antimicrobial and virulence-associated phenotyp...

    journal_title:Virulence

    pub_type: 杂志文章

    doi:10.1080/21505594.2020.1809322

    authors: Liu C,Du P,Xiao N,Ji F,Russo TA,Guo J

    更新日期:2020-12-01 00:00:00