Phase Space Engineering in Optical Microcavities I: Preserving near-field uniformity while inducing far-field directionality

Optical microcavities have received much attention over the last decade from different research fields ranging from fundamental issues of cavity QED to specific applications such as microlasers and bio-sensors. A major issue in the latter applications is the difficulty to obtain directional emission of light in the far-field while keeping high energy densities inside the cavity (i.e. high quality factor). To improve our understanding of these systems, we have studied the annular cavity (a dielectric disk with a circular hole), where the distance cavity-hole centers, d, is used as a parameter to alter the properties of cavity resonances. We present results showing how one can affect the directionality of the far-field while preserving the uniformity (hence the quality factor) of the near-field simply by increasing the value of d. Interestingly, the transition between a uniform near- and far-field to a uniform near- and directional far-field is rather abrupt. We can explain this behavior quite nicely with a simple model, supported by full numerical calculations, and we predict that the effect will also be found in a large class of eigenmodes of the cavity.Comment: 12th International Conference on Transparent Optical Network

Étude de l'évolution et de la diversité des poissons d'eau douce de l'Amérique du Nord par une approche génétique comparative

La variation génétique des poissons d’eau douce de l’Amérique du Nord a été analysée aux niveaux intraspécifique et interspécifique afin d’approfondir les connaissances actuelles sur l’évolution de la biodiversité et de faciliter la conservation de cette richesse. Premièrement, une banque de données de séquence d’ADN mitochondrial (codes-barres génétiques) a été générée pour 5674 individus représentant 752 espèces dans le but d’établir un outil d’identification moléculaire et de fournir une calibration de l’incertitude taxonomique. Cette analyse démontre que 90 % des espèces peuvent être délimitées à l’aide de codes-barres génétiques. De plus, il apparait que la taxonomie actuelle pourrait largement sous-estimer la diversité des poissons d’eau douce dans son ensemble tout en surestimant la diversité spécifique de certains groupes particuliers. Deuxièmement, les niveaux de divergences génétiques intraspécifique et interspécifique ont été étudiés afin d’identifier les mécanismes évolutifs responsables des patrons généraux de répartition de la biodiversité. L’hypothèse suggérant un rôle combiné des cycles glaciaires du Pléistocène et de l’activité métabolique influençant les taux de mutation est appuyée par les données représentant la presque totalité des poissons d’eau douce de l’Amérique du Nord. Troisièmement, les patrons de variation aux niveaux de l’ADN mitochondrial et de l’ADN nucléaire (AFLP) ont été analysés parmi plusieurs paires de lignées évolutives codistribuées dans le nord-est de l’Amérique afin de vérifier l’importance du processus de spéciation allopatrique. Les résultats indiquent que l’est du bassin des Grands Lacs représente une zone de suture impliquant plusieurs taxons et que les niveaux de divergence sont variables d’une paire de lignées à l’autre. Parmi ces paires de races glaciaires, celles divergeant par plus de 2 % au niveau de l’ADN mitochondrial présentent d’importants signes d’isolement reproducteur. En décrivant les diverses étapes du processus de spéciation allopatrique au sein de différentes espèces d’une même région, cette étude démontre que le processus de spéciation allopatrique a joué un rôle important parmi les poissons d’eau douce de l’Amérique du Nord. L’ensemble de ces travaux aura donc permis de fournir un nouvel outil d’identification et d’appuyer l’hypothèse stipulant que la spéciation allopatrique est le principal moteur de diversification pour les poissons d’eau douce.Intraspecific and interspecific genetic variation has been studied among North America’s freshwater fishes in order to improve our current knowledge on the evolution of biodiversity and to facilitate the conservation of this richness. Firstly, we generated a standard reference library of mitochondrial DNA sequences (DNA barcodes) for 752 North American freshwater fish species to provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application. This study demonstrates that 90% of known species can be delineated using barcodes. Results further suggest that current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, while artificially creating diversity in others. Secondly, we studied intraspecific and interspecific genetic divergence in order to describe and identify the underlying evolutionary causes of general patterns of biodiversity distribution. This study supports a dual role involving both the late Pliocene-Pleistocene climatic fluctuations and metabolic rate in determining latitudinal gradients of genetic divergence. Thirdly, patterns of mitochondrial DNA and nuclear DNA (AFLP) have been studied among different codistributed pairs of glacial lineages in order to verify the generality of allopatric speciation. This study shows that the Eastern Great-Lakes drainage represents a multi-species suture zone for glacial lineages of freshwater fishes with variable levels of genetic divergence. AFLP analyses among four pairs of lineages indicate that lineages with relatively deep levels of mitochondrial DNA sequence divergence (> 2 %) developed strong reproductive barriers. By describing different levels of divergence and reproductive isolation in different co-occurring fishes, we offer strong evidence that allopatric speciation has contributed significantly to the diversification of North Eastern American freshwater fishes. This thesis therefore offers a new molecular identification tool for freshwater fish of North America and brings strong evidences that allopatric speciation has played a predominant role in generating biodiversity

Étude du comportement des bifilms lors de solidifications contrôlées d'alliages d'Al-Fe et d'Al-Fe-Si avec et sans centrifugation

Les bifilms sont des inclusions solides, présentes en très grand nombre dans l'aluminium et sont néfastes au niveau des propriétés mécaniques des alliages. Il a été observé que lors de solidification s'approchant de l'équilibre, les intermétalliques Al3Fe et Al5FeSi-? ne peuvent germer que sur les films d'oxyde présents. Ayant une masse volumique bien plus élevée que l'aluminium liquide, ces intermétalliques entament une sédimentation dès leur formation et entrainent donc avec eux les bifilms sur lesquels ils ont germé. L'objectif principal de ce projet est l'étude du comportement des bifilms dans des alliages d'aluminium enrichi en fer lors de solidifications lentes. Un alliage Al-3.74%Fe faisant germer Al3Fe et un autre Al-1.16%Fe-13.5%Si faisant germer Al5FeSi-? ont été produits et coulés en barreaux. Un appareillage capable de centrifuger les barreaux a été utilisé pour générer une force G supérieure à l'accélération gravitationnelle terrestre lors de la solidification. Certains barreaux ont été centrifugés lors de leur solidification, d'autres non. Tous les barreaux ont été découpés perpendiculairement à l'axe en séparant les différentes zones d'accumulation de particules des zones de métal sans particules accumulées. Les résultats de cartographie élémentaire XRF permettent de confirmer que la sédimentation des intermétalliques s'opère pour chaque alliage créant une zone d'accumulation de particules au bas des échantillons. Une technique a été développée pour quantifier et localiser les bifilms dans ces zones découpées; le Test à Pression Réduite Modifié - TPRM. Ce test révèle les bifilms en les faisant gonfler lors d'une refusion sous pression contrôlée. Une fois solidifiés, les échantillons ont été coupés et polis, les pores ont été dénombrés et la surface de métal mesurée pour connaitre le nombre de pores/cm2 de métal. Les résultats de TPRM nous montrent que les intermétalliques ont aussi entrainé avec eux les bifilms. Les zones nettoyées de leurs bifilms montrent une réduction de leur nombre de pores/cm2 allant jusqu'à 53 % pour l'alliage Al-Fe et de 63 % pour l'alliage de Al-Fe-Si en comparaison à leur échantillon de référence respectif. Cette diminution atteint minimalement 40% chez tous les échantillons nettoyés de leur bifilms, qu'ils soient centrifugés ou non.Bifilms are solid inclusions, present in large numbers in aluminum and are detrimental to the mechanical properties of alloys. It has been observed that upon solidification approaching equilibrium, the intermetallic Al3Fe and Al5FeSi-B can only nucleate on the oxide films present. Having a much higher density than liquid aluminum, these intermetallic particles start sedimentation as soon as they are formed and therefore carry with them the bifilms on which they have nucleated. The main objective of this project is the study of the behavior of bifilms in iron-enriched aluminum alloys during slow solidifications approaching equilibrium. An Al-3.74%Fe alloy which nucleates Al3Fe and another Al-1.16%Fe-12.6%Si alloy which nucleates Al5FeSi-B were cast into bars. An apparatus capable of centrifuging the bars was used to generate a G force greater than the Earth's gravitational acceleration during solidification. Some bars were centrifuged during solidification, others were not. All the bars were cut perpendicular to the axis, separating the different areas of particle accumulation from the areas of metal without accumulated particles. The XRF elemental mapping results allow us to confirm that intermetallic sedimentation occurs for each alloy, creating a zone of particle accumulation at the bottom of the samples. A technique has been developed to quantify and locate the bifilms in these areas; the Modified Reduced Pressure Test - MRPT. This test reveals bifilms by swelling them during re-fusion under controlled pressure. Once solidified, the samples were cut and polished, the pores were counted, and the metal surface measured to calculate the number of pores/cm2 of metal. The results of TPRM allow us to say that the intermetallic also carried the bifilms with them. The bifilm-cleaned areas show a reduction in their number of pores/cm2 of up to 53 % for the Al-Fe alloy and 63 % for the Al-Fe-Si alloy in comparison to the value of their respective reference sample. This reduction reaches a minimum of 40 % in all samples cleaned of their bifilms, whether they were centrifuged or not

Trends in marine survival of Atlantic salmon populations in eastern Canada

Declines in wild Atlantic salmon (Salmo salar) abundance throughout the north Atlantic are primarily attributed to decreases in survival at sea. However, comparing trends in marine survival among populations is challenging as data on both migrating smolts and returning adults are sparse and models are difficult to parameterize due to their varied life histories. We fit a hierarchical Bayesian maturity schedule model to data from seven populations in eastern Canada to estimate numbers of out-migrating smolts, survival in the first and second year at sea, and the proportion returning after 1 year. Trends in survival at sea were not consistent among populations; we observe positive, negative, and no correlations in these, suggesting that large-scale patterns of changes in marine survival are not necessarily representative for individual populations. Variation in return abundances was mostly explained by marine survival in the first winter at sea in all but one population. However, variation in the other components were not negligible and their relative importance differed among populations. If salmon populations do not respond in a uniform manner to changing environmental conditions throughout their range, future research initiatives should explore why.publishedVersio

Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation

Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open

A Review of Pink Salmon in the Pacific, Arctic, and Atlantic Oceans

The Northern Hemisphere Pink Salmon Expert Group Meeting was held on October 2–3, 2022 in Vancouver, Canada, immediately preceding the International Year of the Salmon (IYS) Synthesis Symposium. The rapid expansion of pink salmon was the theme for the meeting, and experts came together to discuss the current state of knowledge for pink salmon. Specific topics of focus included the range expansion into the Atlantic and Arctic oceans, trends in distribution and abundance, research and monitoring approaches, potential inter-specific interactions, mitigation efforts, and plans for future collaborations. The outcomes of the meeting were presented at the IYS Synthesis Symposium and are further disseminated through this NPAFC Technical Report. The Executive Summary section of this report provides a brief background, a condensed overview of each topic, and concludes with overarching takeaway messages that are intended to guide future collaborations.publishedVersio

A Review of Pink Salmon in the Pacific, Arctic, and Atlantic Oceans

The Northern Hemisphere Pink Salmon Expert Group Meeting was held on October 2–3, 2022 in Vancouver, Canada, immediately preceding the International Year of the Salmon (IYS) Synthesis Symposium. The rapid expansion of pink salmon was the theme for the meeting, and experts came together to discuss the current state of knowledge for pink salmon. Specific topics of focus included the range expansion into the Atlantic and Arctic oceans, trends in distribution and abundance, research and monitoring approaches, potential inter-specific interactions, mitigation efforts, and plans for future collaborations. The outcomes of the meeting were presented at the IYS Synthesis Symposium and are further disseminated through this NPAFC Technical Report. The Executive Summary section of this report provides a brief background, a condensed overview of each topic, and concludes with overarching takeaway messages that are intended to guide future collaborations.publishedVersio

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Identifying Canadian Freshwater Fishes through DNA Barcodes

BACKGROUND: DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. METHODOLOGY/PRINCIPAL FINDINGS: We bi-directionally sequenced the standard 652 bp "barcode" region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. CONCLUSIONS/SIGNIFICANCE: The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication