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Article ; Online: A Parallel Framework with Block Matrices of a Discrete Fourier Transform for Vector-Valued Discrete-Time Signals.

Soto-Quiros, Pablo

TheScientificWorldJournal

2015 Volume 2015, Page(s) 348517

Abstract: This paper presents a parallel implementation of a kind of discrete Fourier transform (DFT): the vector-valued DFT. The vector-valued DFT is a novel tool to analyze the spectra of vector-valued discrete-time signals. This parallel implementation is ... ...

Abstract	This paper presents a parallel implementation of a kind of discrete Fourier transform (DFT): the vector-valued DFT. The vector-valued DFT is a novel tool to analyze the spectra of vector-valued discrete-time signals. This parallel implementation is developed in terms of a mathematical framework with a set of block matrix operations. These block matrix operations contribute to analysis, design, and implementation of parallel algorithms in multicore processors. In this work, an implementation and experimental investigation of the mathematical framework are performed using MATLAB with the Parallel Computing Toolbox. We found that there is advantage to use multicore processors and a parallel computing environment to minimize the high execution time. Additionally, speedup increases when the number of logical processors and length of the signal increase.
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1537-744X
ISSN (online)	1537-744X
DOI	10.1155/2015/348517
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Article ; Online: Contribution of cropland to the spread of Shiga toxin phages and the emergence of new Shiga toxin-producing strains.

Quirós, Pablo / Muniesa, Maite

Scientific reports

2017 Volume 7, Issue 1, Page(s) 7796

Abstract: A growing interest in healthy eating has lead to an increase in the consumption of vegetables, associated with a rising number of bacterial outbreaks related to fresh produce. This is the case of the outbreak in Germany, caused by a O104:H4 ... ...

Abstract	A growing interest in healthy eating has lead to an increase in the consumption of vegetables, associated with a rising number of bacterial outbreaks related to fresh produce. This is the case of the outbreak in Germany, caused by a O104:H4 enteroaggregative E. coli strain lysogenic for a Stx phage. Temperate Stx phages released from their hosts occur as free particles in various environments. This study reports the occurrence of Stx phages in vegetables (lettuce, cucumber, and spinach) and cropland soil samples. Infectious Stx2 phages were found in all samples and many carried also Stx1 phages. Their persistence in vegetables, including germinated sprouts, of Stx phage 933 W and an E. coli C600 (933 W∆stx::gfp-cat) lysogen used as surrogate, showed reductions below 2 log
MeSH term(s)	Bacteriophages/genetics ; Bacteriophages/isolation & purification ; Crops, Agricultural/virology ; Food Microbiology ; Germany ; Lysogeny ; Shiga Toxin/genetics ; Shiga-Toxigenic Escherichia coli/virology ; Soil Microbiology ; Transduction, Genetic ; Vegetables/virology
Chemical Substances	Shiga Toxin (75757-64-1)
Language	English
Publishing date	2017-08-10
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/s41598-017-08169-6
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Article ; Online: Erratum for Quirós et al., "Improving Detection of Shiga Toxin-Producing Escherichia coli by Molecular Methods by Reducing the Interference of Free Shiga Toxin-Encoding Bacteriophages".

Quirós, Pablo / Martínez-Castillo, Alexandre / Muniesa, Maite

Applied and environmental microbiology

2017 Volume 83, Issue 16

Language	English
Publishing date	2017-08-01
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.01407-17
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Article ; Online: Spread of bacterial genomes in packaged particles.

Quirós, Pablo / Brown-Jaque, Maryury / Muniesa, Maite

Future microbiology

2016 Volume 11, Issue 2, Page(s) 171–173

MeSH term(s)	Bacteria/genetics ; Bacteriophages/genetics ; Gene Transfer, Horizontal ; Genetic Vectors ; Genome, Bacterial ; Humans
Language	English
Publishing date	2016
Publishing country	England
Document type	Editorial ; Research Support, Non-U.S. Gov't
ISSN	1746-0921
ISSN (online)	1746-0921
DOI	10.2217/fmb.15.145
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Article ; Online: Identification of a virulent phage infecting species of Nitrosomonas.

Quirós, Pablo / Sala-Comorera, Laura / Gómez-Gómez, Clara / Ramos-Barbero, María Dolores / Rodríguez-Rubio, Lorena / Vique, Gloria / Yance-Chávez, Tula / Atarés, Sergio / García-Gutierrez, Sandra / García-Marco, Sonia / Vallejo, Antonio / Salaet, Ignasi / Muniesa, Maite

The ISME journal

2023 Volume 17, Issue 5, Page(s) 645–648

Abstract: In the first and limiting step of nitrification, ammonia ( ... ...

Abstract	In the first and limiting step of nitrification, ammonia (NH
MeSH term(s)	Bacteriophages/genetics ; Nitrosomonas ; Nitrosomonas europaea ; Bacteria ; Nitrites ; Ammonia
Chemical Substances	Nitrites ; Ammonia (7664-41-7)
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2406536-5
ISSN	1751-7370 ; 1751-7362
ISSN (online)	1751-7370
ISSN	1751-7362
DOI	10.1038/s41396-023-01380-6
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Article ; Online: Improving detection of Shiga toxin-producing Escherichia coli by molecular methods by reducing the interference of free Shiga toxin-encoding bacteriophages.

Quirós, Pablo / Martínez-Castillo, Alexandre / Muniesa, Maite

Applied and environmental microbiology

2015 Volume 81, Issue 1, Page(s) 415–421

Abstract: Detection of Shiga toxin-producing Escherichia coli (STEC) by culture methods is advisable to identify the pathogen, but recovery of the strain responsible for the disease is not always possible. The use of DNA-based methods (PCR, quantitative PCR [qPCR], ...

Abstract	Detection of Shiga toxin-producing Escherichia coli (STEC) by culture methods is advisable to identify the pathogen, but recovery of the strain responsible for the disease is not always possible. The use of DNA-based methods (PCR, quantitative PCR [qPCR], or genomics) targeting virulence genes offers fast and robust alternatives. However, detection of stx is not always indicative of STEC because stx can be located in the genome of temperate phages found in the samples as free particles; this could explain the numerous reports of positive stx detection without successful STEC isolation. An approach based on filtration through low-protein-binding membranes and additional washing steps was applied to reduce free Stx phages without reducing detection of STEC bacteria. River water, food, and stool samples were spiked with suspensions of phage 933W and, as a STEC surrogate, a lysogen harboring a recombinant Stx phage in which stx was replaced by gfp. Bacteria were tested either by culture or by qPCR for gfp while phages were tested using qPCR targeting stx in phage DNA. The procedure reduces phage particles by 3.3 log10 units without affecting the recovery of the STEC population (culturable or assessed by qPCR). The method is applicable regardless of phage and bacteria densities and is useful in different matrices (liquid or solid). This approach eliminates or considerably reduces the interference of Stx phages in the detection of STEC by molecular methods. The reduction of possible interference would increase the efficiency and reliability of genomics for STEC detection when the method is applied routinely in diagnosis and food analysis.
MeSH term(s)	Bacteriological Techniques/methods ; Bacteriophages/isolation & purification ; Feces/microbiology ; Filtration/methods ; Food Microbiology ; Real-Time Polymerase Chain Reaction ; Rivers/microbiology ; Sensitivity and Specificity ; Shiga Toxin/genetics ; Shiga-Toxigenic Escherichia coli/genetics ; Shiga-Toxigenic Escherichia coli/isolation & purification ; Specimen Handling/methods
Chemical Substances	Shiga Toxin (75757-64-1)
Language	English
Publishing date	2015-01
Publishing country	United States
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.02941-14
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Article ; Online: The Cantabrian capercaillie: A population on the edge.

Jiménez, José / Godinho, Raquel / Pinto, Daniel / Lopes, Susana / Castro, Diana / Cubero, David / Osorio, M Angeles / Piqué, Josep / Moreno-Opo, Rubén / Quiros, Pablo / González-Nuevo, Daniel / Hernandez-Palacios, Orencio / Kéry, Marc

The Science of the total environment

2022 Volume 821, Page(s) 153523

Abstract: The capercaillie Tetrao urogallus - the world's largest grouse- is a circumboreal forest species, which only two remaining populations in Spain: one in the Cantabrian mountains in the west and the other in the Pyrenees further east. Both have shown ... ...

Abstract	The capercaillie Tetrao urogallus - the world's largest grouse- is a circumboreal forest species, which only two remaining populations in Spain: one in the Cantabrian mountains in the west and the other in the Pyrenees further east. Both have shown severe declines, especially in the Cantabrian population, which has recently been classified as "Critically Endangered". To develop management plans, information on demographic parameters is necessary to understand and forecast population dynamics. We used spatial capture-recapture (SCR) modeling and non-invasive DNA samples to estimate the current population size in the whole Cantabrian mountain range. In addition, for the assessment of population status, we analyzed the population trajectory over the last 42 years (1978-2019) at 196 leks on the Southern slope of the range, using an integrated population model with a Dail-Madsen model at its core, combined with a multistate capture-recapture model for survival and a Poisson regression for productivity. For 2019, we estimate the size of the entire population at 191 individuals (95% BCI 165-222) for an estimated 60 (48-78) females and 131 (109-157) males. Since the 1970s, our study estimates a shrinkage of the population range by 83%. The population at the studied leks in 2019 was at about 10% of the size estimated for 1978. Apparent annual survival was estimated at 0.707 (0.677-0.735), and per-capita recruitment at 0.233 (0.207-0.262), and insufficient to maintain a stable population. We suggest work to improve the recruitment (and survival) and manage these mountain forests for capercaillie conservation. Also, in the future, management should assess the genetic viability of this population.
MeSH term(s)	Animals ; DNA ; Female ; Galliformes ; Humans ; Male ; Population Density ; Population Dynamics ; Spain
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-01-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.153523
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Article: The Cantabrian capercaillie: A population on the edge

Jiménez, José / Godinho, Raquel / Pinto, Daniel / Lopes, Susana / Castro, Diana / Cubero, David / Osorio, M. Angeles / Piqué, Josep / Moreno-Opo, Rubén / Quiros, Pablo / González-Nuevo, Daniel / Hernandez-Palacios, Orencio / Kéry, Marc

Science of the total environment. 2022 May 15, v. 821

2022

Abstract	The capercaillie Tetrao urogallus - the world's largest grouse- is a circumboreal forest species, which only two remaining populations in Spain: one in the Cantabrian mountains in the west and the other in the Pyrenees further east. Both have shown severe declines, especially in the Cantabrian population, which has recently been classified as “Critically Endangered”. To develop management plans, information on demographic parameters is necessary to understand and forecast population dynamics. We used spatial capture-recapture (SCR) modeling and non-invasive DNA samples to estimate the current population size in the whole Cantabrian mountain range. In addition, for the assessment of population status, we analyzed the population trajectory over the last 42 years (1978–2019) at 196 leks on the Southern slope of the range, using an integrated population model with a Dail-Madsen model at its core, combined with a multistate capture-recapture model for survival and a Poisson regression for productivity. For 2019, we estimate the size of the entire population at 191 individuals (95% BCI 165–222) for an estimated 60 (48–78) females and 131 (109–157) males. Since the 1970s, our study estimates a shrinkage of the population range by 83%. The population at the studied leks in 2019 was at about 10% of the size estimated for 1978. Apparent annual survival was estimated at 0.707 (0.677–0.735), and per-capita recruitment at 0.233 (0.207–0.262), and insufficient to maintain a stable population. We suggest work to improve the recruitment (and survival) and manage these mountain forests for capercaillie conservation. Also, in the future, management should assess the genetic viability of this population.
Keywords	DNA ; Tetrao urogallus ; environment ; mark-recapture studies ; models ; mountains ; population dynamics ; population size ; shrinkage ; topographic slope ; viability ; Spain
Language	English
Dates of publication	2022-0515
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.153523
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Article: Investigation on the Evolution of Shiga Toxin-Converting Phages Based on Whole Genome Sequencing.

Zuppi, Michele / Tozzoli, Rosangela / Chiani, Paola / Quiros, Pablo / Martinez-Velazquez, Adan / Michelacci, Valeria / Muniesa, Maite / Morabito, Stefano

Frontiers in microbiology

2020 Volume 11, Page(s) 1472

Abstract: Bacteriophages are pivotal elements in the dissemination of virulence genes. The main virulence determinants of Shiga Toxin ... ...

Abstract	Bacteriophages are pivotal elements in the dissemination of virulence genes. The main virulence determinants of Shiga Toxin producing
Language	English
Publishing date	2020-07-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.01472
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Article: Effectiveness of a calf-selective feeder in preventing wild boar access

Balseiro, Ana / Oleaga, Álvaro / Álvarez Morales, Luis Miguel / González Quirós, Pablo / Gortázar, Christian / Prieto, José Miguel

European journal of wildlife research. 2019 June, v. 65, no. 3

2019

Abstract: Tuberculosis (TB) transmission between wildlife and domestic animals is usually indirect when they share an interface or visit the same location at different times in order to use the same food and water resources. Preventing aggregation and subsequent ... ...

Abstract	Tuberculosis (TB) transmission between wildlife and domestic animals is usually indirect when they share an interface or visit the same location at different times in order to use the same food and water resources. Preventing aggregation and subsequent contact between domestic and wild animals is a valuable and cheap tool for improving farm biosafety. This study was carried out in a beef cattle farm located in Asturias (Atlantic Spain). Wild boar (Sus scrofa) visited the farm facilities every night to feed in the farm’s calf feeders. Our aim was to design and test the efficacy of a selective feeder for calves that could hinder its use by wild boar. We analyzed the effectiveness of the design using camera trapping. Pictures showed a reduction of 97.8% and 56.3% in the number of wild boar accessing to the selective feeder and in the number of wild boar “around” it, respectively. Those data demonstrate that the selective feeder hindered the access of wild boar to the feed and therefore, reduced the feed-mediated indirect interspecies contacts. Biosecurity measures are promising, cheap, and cost-effective tools for preventing TB and other diseases.
Keywords	Sus scrofa ; beef cattle ; biosafety ; biosecurity ; calf feeders ; calves ; camera trapping ; cost effectiveness ; farms ; livestock and meat industry ; tuberculosis ; water resources ; wild boars ; wildlife ; Spain
Language	English
Dates of publication	2019-06
Size	p. 38.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	2141660-6
ISSN	1439-0574 ; 1612-4642
ISSN (online)	1439-0574
ISSN	1612-4642
DOI	10.1007/s10344-019-1276-4
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