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Article: The Use of Interdisciplinary Approaches to Understand the Biology of

Dzianach, Paulina A / Pérez-Reche, Francisco J / Strachan, Norval J C / Forbes, Ken J / Dykes, Gary A

2022 Volume 10, Issue 12

Abstract: Campylobacter ... ...

Abstract	Campylobacter jejuni
Language	English
Publishing date	2022-12-16
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms10122498
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Importance of untested infectious individuals for interventions to suppress COVID-19.

Pérez-Reche, Francisco J / Forbes, Ken J / Strachan, Norval J C

Scientific reports

2021 Volume 11, Issue 1, Page(s) 20728

Abstract: The impact of the extent of testing infectious individuals on suppression of COVID-19 is illustrated from the early stages of outbreaks in Germany, the Hubei province of China, Italy, Spain and the UK. The predicted percentage of untested infected ... ...

Abstract	The impact of the extent of testing infectious individuals on suppression of COVID-19 is illustrated from the early stages of outbreaks in Germany, the Hubei province of China, Italy, Spain and the UK. The predicted percentage of untested infected individuals depends on the specific outbreak but we found that they typically represent 60-80% of all infected individuals during the early stages of the outbreaks. We propose that reducing the underlying transmission from untested cases is crucial to suppress the virus. This can be achieved through enhanced testing in combination with social distancing and other interventions that reduce transmission such as wearing face masks. Once transmission from silent carriers is kept under control by these means, the virus could have been fully suppressed through fast isolation and contact tracing of tested cases.
MeSH term(s)	Basic Reproduction Number ; COVID-19/diagnosis ; COVID-19/prevention & control ; COVID-19/virology ; COVID-19 Testing/methods ; Calibration ; China/epidemiology ; Contact Tracing/methods ; Disease Outbreaks ; Germany/epidemiology ; Humans ; Italy/epidemiology ; Masks ; Models, Theoretical ; Physical Distancing ; Poisson Distribution ; SARS-CoV-2 ; Spain/epidemiology ; United Kingdom/epidemiology
Language	English
Publishing date	2021-10-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-00056-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Identification of the host reservoir of SARS-CoV-2 and determining when it spilled over into humans

Pamjula, Vidyavathi / Strachan, Norval J. C / Perez-Reche, Francisco J.

bioRxiv

Abstract: Since the emergence of SARS-CoV-2 in Wuhan in 2019 its host reservoir has not been established. Phylogenetic analysis was performed on whole genome sequences (WGS) of 71 coronaviruses and a Breda virus. A subset comprising two SARS-CoV-2 Wuhan viruses ... ...

Abstract	Since the emergence of SARS-CoV-2 in Wuhan in 2019 its host reservoir has not been established. Phylogenetic analysis was performed on whole genome sequences (WGS) of 71 coronaviruses and a Breda virus. A subset comprising two SARS-CoV-2 Wuhan viruses and 8 of the most closely related coronavirus sequences were used for host reservoir analysis using Bayesian Evolutionary Analysis Sampling Trees (BEAST). Within these genomes, 20 core genome fragments were combined into 2 groups each with similar clock rates (5.9x10 -3 and 1.1x10 -3 subs/site/year). Pooling the results from these fragment groups yielded a most recent common ancestor (MRCA) shared between SARS-COV-2 and the bat isolate RaTG13 around 2007 (95% HPD: 2003, 2011). Further, the host of the MRCA was most likely a bat (probability 0.64 - 0.87). Hence, the spillover into humans must have occurred at some point between 2007 and 2019 and bats may have been the most likely host reservoir.
Keywords	covid19
Language	English
Publishing date	2023-11-27
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.11.25.568670
Database	COVID19

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Article ; Online: Mining whole genome sequence data to efficiently attribute individuals to source populations.

Pérez-Reche, Francisco J / Rotariu, Ovidiu / Lopes, Bruno S / Forbes, Ken J / Strachan, Norval J C

Scientific reports

2020 Volume 10, Issue 1, Page(s) 12124

Abstract: Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that efficiently mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly ... ...

Abstract	Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that efficiently mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.
MeSH term(s)	Animals ; Campylobacter/genetics ; Campylobacter/isolation & purification ; Campylobacter Infections/genetics ; Campylobacter Infections/pathology ; Databases, Genetic ; Disease Reservoirs/microbiology ; Genome, Bacterial ; Genotype ; Humans ; Multilocus Sequence Typing/methods ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing
Language	English
Publishing date	2020-07-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-68740-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Retention Site Contribution Toward Silver Particle Immobilization in Porous Media

Patiño, Janis E. / Pérez‐Reche, Francisco J. / Morales, Verónica L.

Water resources research. 2022 May, v. 58, no. 5

2022

Abstract: This work investigates the role that pore structure plays in colloid retention across scales with a novel methodology based on image analysis. Experiments were designed to quantify–with robust statistics–the contribution from commonly proposed retention ... ...

Abstract	This work investigates the role that pore structure plays in colloid retention across scales with a novel methodology based on image analysis. Experiments were designed to quantify–with robust statistics–the contribution from commonly proposed retention sites toward colloid immobilization. Specific retention sites include solid‐water interface, air‐water interface, air‐water‐solid triple point, grain‐to‐grain contacts, and thin films. Variable conditions for pore‐water content, velocity, and chemistry were tested in a model glass bead porous medium with silver microspheres. Concentration signals from effluent breakthrough and spatial profiles of retained particles from micro X‐ray Computed Tomography were used to compute mass balances and enumerate pore‐scale regions of interest in three dimensions. At the Darcy‐scale, retained colloids follow non‐monotonic deposition profiles, which implicates effects from flow‐stagnation zones. The spatial distribution of immobilized colloids along the porous medium depth was analyzed by retention site, revealing depth‐independent partitioning of colloids. At the pore‐scale, dominance and overall saturation of all retention sites considered indicated that the solid‐water interface and wedge‐shaped regions associated with flow‐stagnation (grain‐to‐grain contacts in saturated and air‐water‐solid triple points in unsaturated conditions) are the greatest contributors toward retention under the tested conditions. At the interface‐scale, xDLVO energy profiles were in agreement with pore‐scale observations. Our calculations suggest favorable interactions for colloids and solid‐water interfaces and for weak flocculation (e.g., at flow‐stagnation zones), but unfavorable interactions between colloids and air‐water interfaces. Overall, we demonstrate that pore‐structure plays a critical role in colloid immobilization and that Darcy‐, pore‐ and interface‐scales are consistent when the pore structure is taken into account.
Keywords	X-radiation ; energy ; flocculation ; glass ; image analysis ; liquid-air interface ; microparticles ; porous media ; research ; silver ; water
Language	English
Dates of publication	2022-05
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	5564-5
ISSN	1944-7973 ; 0043-1397
ISSN (online)	1944-7973
ISSN	0043-1397
DOI	10.1029/2021WR031807
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Estimated Dissemination Ratio-A Practical Alternative to the Reproduction Number for Infectious Diseases.

Pérez-Reche, Francisco J / Taylor, Nick / McGuigan, Chris / Conaglen, Philip / Forbes, Ken J / Strachan, Norval J C / Honhold, Naomi

Frontiers in public health

2021 Volume 9, Page(s) 675065

Abstract: Policymakers require consistent and accessible tools to monitor the progress of an epidemic and the impact of control measures in real time. One such measure is the Estimated Dissemination Ratio (EDR), a straightforward, easily replicable, and robust ... ...

Abstract	Policymakers require consistent and accessible tools to monitor the progress of an epidemic and the impact of control measures in real time. One such measure is the Estimated Dissemination Ratio (EDR), a straightforward, easily replicable, and robust measure of the trajectory of an outbreak that has been used for many years in the control of infectious disease in livestock. It is simple to calculate and explain. Its calculation and use are discussed below together with examples from the current COVID-19 outbreak in the UK. These applications illustrate that EDR can demonstrate changes in transmission rate before they may be clear from the epidemic curve. Thus, EDR can provide an early warning that an epidemic is resuming growth, allowing earlier intervention. A conceptual comparison between EDR and the commonly used reproduction number is also provided.
MeSH term(s)	COVID-19 ; Communicable Diseases/epidemiology ; Epidemics ; Humans ; Reproduction ; SARS-CoV-2
Language	English
Publishing date	2021-07-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2021.675065
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Importance of untested infectious individuals for interventions to suppress COVID-19

Francisco J. Pérez-Reche / Ken J. Forbes / Norval J. C. Strachan

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 13

Abstract: Abstract The impact of the extent of testing infectious individuals on suppression of COVID-19 is illustrated from the early stages of outbreaks in Germany, the Hubei province of China, Italy, Spain and the UK. The predicted percentage of untested ... ...

Abstract	Abstract The impact of the extent of testing infectious individuals on suppression of COVID-19 is illustrated from the early stages of outbreaks in Germany, the Hubei province of China, Italy, Spain and the UK. The predicted percentage of untested infected individuals depends on the specific outbreak but we found that they typically represent 60–80% of all infected individuals during the early stages of the outbreaks. We propose that reducing the underlying transmission from untested cases is crucial to suppress the virus. This can be achieved through enhanced testing in combination with social distancing and other interventions that reduce transmission such as wearing face masks. Once transmission from silent carriers is kept under control by these means, the virus could have been fully suppressed through fast isolation and contact tracing of tested cases.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Challenges of biofilm control and utilization: lessons from mathematical modelling.

Dzianach, Paulina A / Dykes, Gary A / Strachan, Norval J C / Forbes, Ken J / Pérez-Reche, Francisco J

Journal of the Royal Society, Interface

2019 Volume 16, Issue 155, Page(s) 20190042

Abstract: This article reviews modern applications of mathematical descriptions of biofilm formation. The focus is on theoretically obtained results which have implications for areas including the medical sector, food industry and wastewater treatment. Examples ... ...

Abstract	This article reviews modern applications of mathematical descriptions of biofilm formation. The focus is on theoretically obtained results which have implications for areas including the medical sector, food industry and wastewater treatment. Examples are given as to how models have contributed to the overall knowledge on biofilms and how they are used to predict biofilm behaviour. We conclude that the use of mathematical models of biofilms has demonstrated over the years the ability to significantly contribute to the vast field of biofilm research. Among other things, they have been used to test various hypotheses on the nature of interspecies interactions, viability of biofilm treatment methods or forces behind observed biofilm pattern formations. Mathematical models can also play a key role in future biofilm research. Many models nowadays are analysed through computer simulations and continue to improve along with computational capabilities. We predict that models will keep on providing answers to important challenges involving biofilm formation. However, further strengthening of the ties between various disciplines is necessary to fully use the tools of collective knowledge in tackling the biofilm phenomenon.
MeSH term(s)	Biofilms/growth & development ; Computer Simulation ; Models, Biological
Language	English
Publishing date	2019-06-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2019.0042
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Article ; Online: Immunization and Targeted Destruction of Networks using Explosive Percolation.

Clusella, Pau / Grassberger, Peter / Pérez-Reche, Francisco J / Politi, Antonio

Physical review letters

2016 Volume 117, Issue 20, Page(s) 208301

Abstract: A new method ("explosive immunization") is proposed for immunization and targeted destruction of networks. It combines the explosive percolation (EP) paradigm with the idea of maintaining a fragmented distribution of clusters. The ability of each node to ...

Abstract	A new method ("explosive immunization") is proposed for immunization and targeted destruction of networks. It combines the explosive percolation (EP) paradigm with the idea of maintaining a fragmented distribution of clusters. The ability of each node to block the spread of an infection (or to prevent the existence of a large cluster of connected nodes) is estimated by a score. The algorithm proceeds by first identifying low score nodes that should not be vaccinated or destroyed, analogously to the links selected in EP if they do not lead to large clusters. As in EP, this is done by selecting the worst node (weakest blocker) from a finite set of randomly chosen "candidates." Tests on several real-world and model networks suggest that the method is more efficient and faster than any existing immunization strategy. Because of the latter property it can deal with very large networks.
Language	English
Publishing date	2016-11-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.117.208301
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Estimated Dissemination Ratio—A Practical Alternative to the Reproduction Number for Infectious Diseases

Francisco J. Pérez-Reche / Nick Taylor / Chris McGuigan / Philip Conaglen / Ken J. Forbes / Norval J. C. Strachan / Naomi Honhold

Frontiers in Public Health, Vol

2021 Volume 9

Abstract	Policymakers require consistent and accessible tools to monitor the progress of an epidemic and the impact of control measures in real time. One such measure is the Estimated Dissemination Ratio (EDR), a straightforward, easily replicable, and robust measure of the trajectory of an outbreak that has been used for many years in the control of infectious disease in livestock. It is simple to calculate and explain. Its calculation and use are discussed below together with examples from the current COVID-19 outbreak in the UK. These applications illustrate that EDR can demonstrate changes in transmission rate before they may be clear from the epidemic curve. Thus, EDR can provide an early warning that an epidemic is resuming growth, allowing earlier intervention. A conceptual comparison between EDR and the commonly used reproduction number is also provided.
Keywords	epidemics ; survaillance ; mathematical models ; COVID-19 ; reproduction number R ; estimated dissemination ratio ; Public aspects of medicine ; RA1-1270
Subject code	612
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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