Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata.

Abstract:

:Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining 'big' data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.

journal_name

R Soc Open Sci

authors

Hill AA,Crotta M,Wall B,Good L,O'Brien SJ,Guitian J

doi

10.1098/rsos.160721

subject

Has Abstract

pub_date

2017-03-29 00:00:00

pages

160721

issue

3

issn

2054-5703

pii

rsos160721

journal_volume

4

pub_type

杂志文章
  • Nitrogen deposition and multi-dimensional plant diversity at the landscape scale.

    abstract::Estimating effects of nitrogen (N) deposition is essential for understanding human impacts on biodiversity. However, studies relating atmospheric N deposition to plant diversity are usually restricted to small plots of high conservation value. Here, we used data on 381 randomly selected 1 km(2) plots covering most hab...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.150017

    authors: Roth T,Kohli L,Rihm B,Amrhein V,Achermann B

    更新日期:2015-04-08 00:00:00

  • The nature of small molecules adsorbed on defective carbon nanotubes.

    abstract::In this work, we perform a comprehensive theoretical study on adsorption of representative 10-electron molecules H2O, CH4 and NH3 onto defective single-walled carbon nanotubes. Results of adsorption energy and charge transfer reveal the existence of both chemical adsorption (CA) and physical adsorption (PA). While PA ...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.190727

    authors: Li D,Wang F,Zhang Z,Jiang W,Zhu Y,Wang Z,Zhang RQ

    更新日期:2019-08-14 00:00:00

  • Persistent homology in graph power filtrations.

    abstract::The persistence of homological features in simplicial complex representations of big datasets in R n resulting from Vietoris-Rips or Čech filtrations is commonly used to probe the topological structure of such datasets. In this paper, the notion of homological pers...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.160228

    authors: Parks AD,Marchette DJ

    更新日期:2016-10-26 00:00:00

  • Gentoo penguins (Pygoscelis papua) react to underwater sounds.

    abstract::Marine mammals and diving birds face several physiological challenges under water, affecting their thermoregulation and locomotion as well as their sensory systems. Therefore, marine mammals have modified ears for improved underwater hearing. Underwater hearing in birds has been studied in a few species, but for the r...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.191988

    authors: Sørensen K,Neumann C,Dähne M,Hansen KA,Wahlberg M

    更新日期:2020-02-26 00:00:00

  • Waptia fieldensis Walcott, a mandibulate arthropod from the middle Cambrian Burgess Shale.

    abstract::Waptia fieldensis Walcott, 1912 is one of the iconic animals from the middle Cambrian Burgess Shale biota that had lacked a formal description since its discovery at the beginning of the twentieth century. This study, based on over 1800 specimens, finds that W. fieldensis shares general characteristics with pancrustac...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.172206

    authors: Vannier J,Aria C,Taylor RS,Caron JB

    更新日期:2018-06-20 00:00:00

  • Nanoindentation analysis of the micromechanical anisotropy in mouse cortical bone.

    abstract::Studies investigating micromechanical properties in mouse cortical bone often solely focus on the mechanical behaviour along the long axis of the bone. Therefore, data on the anisotropy of mouse cortical bone is scarce. The aim of this study is the first-time evaluation of the anisotropy ratio between the longitudinal...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.160971

    authors: Casanova M,Balmelli A,Carnelli D,Courty D,Schneider P,Müller R

    更新日期:2017-02-22 00:00:00

  • Body synchrony in triadic interaction.

    abstract::Humans subtly synchronize body movement during face-to-face conversation. In this context, bodily synchrony has been linked to affiliation and social bonding, task success and comprehension, and potential conflict. Almost all studies of conversational synchrony involve dyads, and relatively less is known about the str...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.200095

    authors: Dale R,Bryant GA,Manson JH,Gervais MM

    更新日期:2020-09-16 00:00:00

  • The dispersal of planet-forming discs: theory confronts observations.

    abstract::Discs of gas and dust around million-year-old stars are a by-product of the star formation process and provide the raw material to form planets. Hence, their evolution and dispersal directly impact what type of planets can form and affect the final architecture of planetary systems. Here, we review empirical constrain...

    journal_title:Royal Society open science

    pub_type: 杂志文章,评审

    doi:10.1098/rsos.170114

    authors: Ercolano B,Pascucci I

    更新日期:2017-04-26 00:00:00

  • Heaps' Law and Heaps functions in tagged texts: evidences of their linguistic relevance.

    abstract::We study the relationship between vocabulary size and text length in a corpus of 75 literary works in English, authored by six writers, distinguishing between the contributions of three grammatical classes (or 'tags,' namely, nouns, verbs and others), and analyse the progressive appearance of new words of each tag alo...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.200008

    authors: Chacoma A,Zanette DH

    更新日期:2020-03-18 00:00:00

  • Nanostructured mesoporous silica: influence of the preparation conditions on the physical-surface properties for efficient organic dye uptake.

    abstract::A series of ordered mesoporous silica such as MCM-41, SBA-3 and SBA-15, in addition to silica micro- (SM) and nano- (SN) mesoporous particles, were prepared. The preparation conditions were found to greatly influence the physical-surface properties including morphological structure, porosity, particle size, aggregate ...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.172021

    authors: Morsi RE,Mohamed RS

    更新日期:2018-03-14 00:00:00

  • Performance improvement of miniaturized ZnO nanowire accelerometer fabricated by refresh hydrothermal synthesis.

    abstract::Miniaturized accelerometers are necessary for evaluating the performance of small devices, such as haptics, robotics and simulators. In this study, we fabricated miniaturized accelerometers using well-aligned ZnO nanowires. The layer of ZnO nanowires is used for active piezoelectric layer of the accelerometer, and cop...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.170557

    authors: Song S,Kim HC,Kim JW,Kim D,Kim J

    更新日期:2017-09-13 00:00:00

  • Janus microdimer swimming in an oscillating magnetic field.

    abstract::Artificial microswimmers powered by magnetic fields have numerous applications, such as drug delivery, biosensing for minimally invasive medicine and environmental remediation. Recently, a Janus microdimer surface walker that can be propelled by an oscillating magnetic field near a surface was reported by Li et al. (A...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.200378

    authors: Yang J

    更新日期:2020-12-09 00:00:00

  • A single migrant enhances the genetic diversity of an inbred puma population.

    abstract::Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west sid...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.170115

    authors: Gustafson KD,Vickers TW,Boyce WM,Ernest HB

    更新日期:2017-05-24 00:00:00

  • Evolution of reduced minimum critical size as a response to selection for rapid pre-adult development in Drosophila melanogaster.

    abstract::Adult body size in holometabolus insects is directly proportional to the time spent during the larval period. The larval duration can be divided into two parts: (i) pre-critical duration-time required to attain a critical size/critical weight that would result in successful completion of development and metamorphosis ...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.191910

    authors: Sharma K,Mishra N,Shakarad MN

    更新日期:2020-06-10 00:00:00

  • A registered report on how implicit pro-rich bias is shaped by the perceiver's gender and socioeconomic status.

    abstract::Although high status is often considered a desirable quality, this may not always be the case. Different factors may moderate the value of high status along a dimension such as wealth (e.g. gender, perceiver income/education). For example, studies suggest men may value wealth and control over resources more than women...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.191232

    authors: Mattan BD,Cloutier J

    更新日期:2020-08-26 00:00:00

  • The multiple roles of β-diversity help untangle community assembly processes affecting recovery of temperate rocky shores.

    abstract::Metacommunity theory highlights the potential of β-diversity as a useful link to empirical research, especially in diverse systems where species exhibit a range of stage-dependent dispersal characteristics. To investigate the importance of different components and scales of β-diversity in community assembly, we conduc...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.171700

    authors: Chiantore M,Thrush SF,Asnaghi V,Hewitt JE

    更新日期:2018-08-08 00:00:00

  • Functional cervicothoracic boundary modified by anatomical shifts in the neck of giraffes.

    abstract::Here we examined the kinematic function of the morpho- logically unique first thoracic vertebra in giraffes. The first thoracic vertebra of the giraffe displayed similar shape to the seventh cervical vertebra in general ruminants. The flexion experiment using giraffe carcasses demonstrated that the first thoracic vert...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.150604

    authors: Gunji M,Endo H

    更新日期:2016-02-03 00:00:00

  • Integrating viscoelastic mass spring dampers into position-based dynamics to simulate soft tissue deformation in real time.

    abstract::We propose a novel method to simulate soft tissue deformation for virtual surgery applications. The method considers the mechanical properties of soft tissue, such as its viscoelasticity, nonlinearity and incompressibility; its speed, stability and accuracy also meet the requirements for a surgery simulator. Modifying...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.171587

    authors: Xu L,Lu Y,Liu Q

    更新日期:2018-02-14 00:00:00

  • Behavioural responses of spinner dolphins to human interactions.

    abstract::There is increasing evidence that whale and dolphin watching activities have detrimental effects on targeted cetacean populations. In Egypt, spinner dolphins regularly occur in the resting areas of Samadai, Satayah and Qubbat'Isa reefs. In-water human interactions with dolphins are regulated with a time-area closure s...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.172044

    authors: Fumagalli M,Cesario A,Costa M,Harraway J,Notarbartolo di Sciara G,Slooten E

    更新日期:2018-04-25 00:00:00

  • A giant dapediid from the Late Triassic of Switzerland and insights into neopterygian phylogeny.

    abstract::A new Triassic neopterygian is described on the basis of a large three-dimensional neurocranium from the Rhaetian (Late Triassic) of the Kössen Formation (Schesaplana, Grisons, Switzerland). CT scanning reveals neurocranial features similar to Dapedium, suggesting that this new genus, Scopulipiscis saxciput gen. et sp...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.180497

    authors: Latimer AE,Giles S

    更新日期:2018-08-15 00:00:00

  • Spatial heterogeneity of the shorebird gastrointestinal microbiome.

    abstract::The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestin...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.191609

    authors: Grond K,Guilani H,Hird SM

    更新日期:2020-01-15 00:00:00

  • Muscle-tendon unit length changes differ between young and adult sprinters in the first stance phase of sprint running.

    abstract::The aim of this study was to compare young and adult sprinters on several biomechanical parameters that were previously highlighted as performance-related and to determine the behaviour of several muscle-tendon units (MTU) in the first stance phase following a block start in sprint running. The ground reaction force (...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.180332

    authors: Aeles J,Jonkers I,Debaere S,Delecluse C,Vanwanseele B

    更新日期:2018-06-13 00:00:00

  • The roles of contact conformity, temperature and displacement amplitude on the lubricated fretting wear of a steel-on-steel contact.

    abstract::This paper investigates the effect of contact geometry, temperature and displacement amplitude on the fretting behaviour of an aero-turbo oil lubricated cylinder-on-flat contact. To be effective, the lubricant needed both to penetrate the contact and then offer protection. Lubricant penetration into the fretting conta...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.150637

    authors: Warmuth AR,Sun W,Shipway PH

    更新日期:2016-10-19 00:00:00

  • Neutral genetic variation in adult Chinook salmon (Oncorhynchus tshawytscha) affects brain-to-body trade-off and brain laterality.

    abstract::Low levels of heterozygosity can have detrimental effects on life history and growth characteristics of organisms but more subtle effects such as those on trade-offs of expensive tissues and morphological laterality, especially of the brain, have not been explicitly tested. The objective of the current study was to in...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.170989

    authors: Wiper ML,Lehnert SJ,Heath DD,Higgs DM

    更新日期:2017-12-06 00:00:00

  • A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals.

    abstract::Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. H...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.150156

    authors: Tsagkogeorga G,McGowen MR,Davies KT,Jarman S,Polanowski A,Bertelsen MF,Rossiter SJ

    更新日期:2015-09-30 00:00:00

  • Pathogen avoidance and prey discrimination in ants.

    abstract::Insect societies have developed sanitary strategies, one of which is the avoidance of infectious food resources as a primary line of defence. Using binary choices, we investigated whether Myrmica rubra ants can identify prey that has been artificially infected with the entomopathogenic fungus, Metarhizium brunneum. We...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.191705

    authors: Pereira H,Detrain C

    更新日期:2020-02-19 00:00:00

  • The positive side of a negative reference: the delay between linguistic processing and common ground.

    abstract::Interlocutors converge on names to refer to entities. For example, a speaker might refer to a novel looking object as the jellyfish and, once identified, the listener will too. The hypothesized mechanism behind such referential precedents is a subject of debate. The common ground view claims that listeners register th...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.160827

    authors: Kronmüller E,Noveck I,Rivera N,Jaume-Guazzini F,Barr D

    更新日期:2017-02-08 00:00:00

  • Ferromagnetically filled carbon nano-onions: the key role of sulfur in dimensional, structural and electric control.

    abstract::A key challenge in the fabrication of ferromagnetically filled carbon nano-onions (CNOs) is the control of their thickness, dimensions and electric properties. Up to now literature works have mainly focused on the encapsulation of different types of ferromagnetic materials including α-Fe, Fe3C, Co, FeCo, FePd3 and oth...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.170981

    authors: Medranda D,Borowiec J,Zhang X,Wang S,Yan K,Zhang J,He Y,Ivaturi S,Boi FS

    更新日期:2018-01-17 00:00:00

  • Comparing and modelling land use organization in cities.

    abstract::The advent of geolocated information and communication technologies opens the possibility of exploring how people use space in cities, bringing an important new tool for urban scientists and planners, especially for regions where data are scarce or not available. Here we apply a functional network approach to determin...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.150449

    authors: Lenormand M,Picornell M,Cantú-Ros OG,Louail T,Herranz R,Barthelemy M,Frías-Martínez E,San Miguel M,Ramasco JJ

    更新日期:2015-12-02 00:00:00

  • Huygens' clocks revisited.

    abstract::In 1665, Huygens observed that two identical pendulum clocks, weakly coupled through a heavy beam, soon synchronized with the same period and amplitude but with the two pendula swinging in opposite directions. This behaviour is now called anti-phase synchronization. This paper presents an analysis of the behaviour of ...

    journal_title:Royal Society open science

    pub_type: 杂志文章

    doi:10.1098/rsos.170777

    authors: Willms AR,Kitanov PM,Langford WF

    更新日期:2017-09-06 00:00:00