Introdução: O estudo dos fatores clínicos associados ao prognóstico da rinossinusite crônica (rsc), seja associada à polipose nasossinusal (RSCcPN) ou não (RSCsPN), ainda é pouco abordado a longo prazo. Objetivo: Avaliar pacientes submetidos à ESS (cirurgia endoscópica nasal, do inglês endoscopic sinus surgery) para o tratamento de RSC no Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo, entre 1996 e 2006, e correlacionar a recidiva em longo prazo com parâmetros como a extensão da doença, atopia, tabagismo, asma, eosinofilia e doença respiratória exacerbada pela aspirina (DREA). Métodos: Duzentos e um pacientes foram seguidos por um período médio de 12 anos. Os dados clínicos foram levantados, assim como exames de endoscopia nasal, Tomografia Computadorizada (TC), exames séricos, prick test e prova de função pulmonar. O tempo de seguimento pós-operatório foi analisado, sendo considerado fator de mau prognóstico a indicação de novo procedimento cirúrgico. Foi realizada comparação entre os fatores pela curva de Kaplan-Meyer, e pós-teste de Log-rank. Resultados e Discussão: Pacientes com RSCcPN tiveram chance de nova cirurgia três vezes maior do que aqueles sem pólipos nasais, no período seguido. Entre os pacientes com RSCsPN, apenas a asma foi um fator de pior prognóstico significativo, levando à chance de cirurgia 5,5 vezes maior do que os não-asmáticos. Já entre os pacientes com RSCcPN, aqueles com recidiva apresentaram maior extensão da doença à TC antes da primeira cirurgia. Foram ainda considerados fatores significativamente de pior prognóstico nos pacientes com RSCcPN: asma (odds ratio [OR] de 3,2); atopia a fungos (OR de 1,9); eosinofilia periférica (considerada como >500/µL, levando a OR de 1,9); e intolerância ao Ácido Acetil Salicílico (AAS) (DREA, apresentando OR de 2,5). Conclusões: Concluiu-se que a presença de pólipos per se é fator de pior prognóstico, aumentando em três vezes a chance de recorrência cirúrgica. Entre os pacientes com RSCsPN, apenas a asma influenciou o prognóstico. Já naqueles com RSCcPN, a asma, eosinofilia periférica, atopia a fungos e DREA aumentaram significativamente a probabilidade de nova intervenção cirúrgica. / Introduction: The analysis of prognostic factors associated with the recurrence of chronic rhinosinusitis (CRS), either with nasal polyps (CRSwNP) or without (CRSsNP), is still poorly discussed in the literature. Objective: To evaluate the patients that underwent endoscopic sinus surgery (ESS) due to CRS in Clinics Hospital of Ribeirão Preto Medical School, University of São Paulo, between 1996 and 2006, and to correlate the long-term recurrence to clinical factors, such as extensiveness of the disease, atopy, smoking habits, eosinophilia, and Aspirinexacerbated respiratory disease (AERD). Methods: We collected data of 201 patients, who were followed during an average period of 12 years. Clinical data collected were: extensiveness of the disease at endoscopy and at CT scans, prick test, blood exams, and pulmonary function. The follow-up period after surgery was assessed, and the indication of a new surgical procedure was considered as a poor prognostic factor. Comparison between factors was performed by Kaplan-Meyer curve, with Log-rank post-test. Results and discussion: CRSwNP patients were 3 times more likely to need a revisional surgery than CRSsNP during the follow-up period. Only asthma was a significant prognostic factor in patients with CRSsNP, leading to 5.5 times higher chance of recurrence than non-asthmatic patients. Among patients with CRSwNP, patients with recurrence presented, prior to surgery, higher CT scan extension of the disease. Other factors that influenced the prognosis on CRSwNP were: asthma (odds ratio [OR]: 3.2); atopy for fungi (OR: 1.9); peripheral eosinophilia (considered as >500/?L, leading to an OR: 1.9); and ASA intolerance (AERD; OR: 2.5). Conclusions: The presence of polyps were related to poor prognosis per se, leading to a higher chance of surgical recurrence. Among patients with CRSsNP, only asthma influenced the prognosis. Among the patients with CRSwNP, asthma, peripheral eosinophilia, fungi atopy, and AERD significantly increased the likelihood of further surgical intervention.

Thesis (MMed) -- Stellenbosch University, 2010. / ENGLISH ABSTRACT: Introduction: Limited facilities exist at rural hospitals for the management of newborn infants with respiratory distress syndrome (RDS). Furthermore, the secondary and tertiary hospitals are under severe strain to accept all the referrals from rural hospitals. Many of these infants require intubation and ventilation with a resuscitation bag which must be sustained for hours until the transport team arrives. Not only is lung damage inflicted by the prolonged ventilation, but transferring the infant by helicopter and ambulance is expensive. CPAP (continuous positive airway pressure), a non-invasive form of ventilatory support, has been used successfully at regional (Level 2) and tertiary (Level 3) neonatal units, to manage infants with RDS. It is cost-effective for infants with mild to moderate grades of RDS to be managed at the rural hospital instead of being transferred to the regional secondary or tertiary hospital. CPAP was introduced to Ceres Hospital, a rural Level 1 hospital, in February 2008 for the management of infants with RDS. Aim: To determine the impact of CPAP on the management of infants with RDS in a rural level 1 hospital and whether it can reduce the number of referrals to regional hospitals. Study setting: Nursery at Ceres District Hospital, Cape Winelands District, Western Cape. Study design: Prospective cohort analytical study with an historic control group (HCG). Patients and Methods: The study group (SG) comprised all neonates with respiratory distress born between 27/02/2008 and 26/02/2010. The infants were initially resuscitated with a Neopuff® machine in labour-ward and CPAP was commenced for those with RDS. The survival and referral rates of the SG were compared to an historic control group (HCG) of infants born between 1/2/2006 to 31/01/2008 at Ceres Hospital. Results: During the 2 years of the study, 51 neonates received CPAP (34 <1800g, 17>1800g). Twenty (83%) of the SG infants between 1000g and 1800g and 23 (68%) of the infants between 500g and 1800g survived. Those <1800g that failed CPAP, had either a severe grade of RDS which required intubation and ventilation or were <1000g. Seventeen (33%) of the infants that received CPAP, were in the >1800g group. Thirteen (76%) of these infants were successfully treated with CPAP only. The four infants that failed CPAP suffered from congenital abnormalities and would not have benefited from CPAP. There was no statistically significant difference in the survival between the SG and HCG (80%) (p=0.5490) but the number of referrals decreased significantly from 21% in the HCG to 7% in the SG (p=0.0003). No complications related to CPAP treatment, such as pneumothorax, were noted. The nursing and medical staff quickly became proficient and confident in applying CPAP and were committed to the project. Conclusion: CPAP can be safely and successfully practised in infants with mild to moderate RDS in a rural Level 1 hospital. The survival rate stayed the same as the HCG, even though a higher risk infants were treated in the SG. The transfers were significantly reduced from 21% to 7%. This resulted in significant cost savings for the hospital. / AFRIKAANSE OPSOMMING: geen opsomming

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The most common viruses involved in acute respiratory diseases among young children are the respiratory syncytial virus (RSV), influenzavirus (FLU), parainfluenzavirus (PIV), adenovirus (AdV) and human rhinovirus (HRV). The purpose of the present study was to identify the main respiratory viruses that affected children younger than five years old in Uberlândia, in Midwestern Brazil. Nasopharyngeal aspirates from 379 children attended at Hospital de Clínicas (HC/UFU), from 2001 to 2004, with acute respiratory disease, were collected and tested by either immunofluorescence assay (IFA) or reverse transcription polymerase chain reaction (RT-PCR). RSV was detected in 26.4% (100/379) of samples, FLU A and B in 9.5% (36/379), PIV 1, 2 and 3 in 6.3% (24/379) and AdV in 3.7% (14/379). Negative and indeterminate samples (205) by IFA were tested by RT-PCR for detection of HRV, and 29.6% (112/379) was positive. RSV, particularly among children in their first 6 months of life, and HRV cases showed highest incidence. For both virus, bronchiolitis and pneumonia/bronchopneumonia were the main nosological presentation among children less than 6 months, were RSV responded for 40,3% and 34,6% of the cases, respectively, and the HRV were detected in 25,0% of bronchiolitis cases and 15,4% of pneumonia/bronchopneumonia cases at the same referred age group. Negative samples by both IFA and RT-PCR might be indicative that other pathogens, such as coronavirus, human metapneumovirus and bacteria, could be the causative agent in these infections. Laboratorial diagnosis constituted an essential instrument to determine the incidence of the most common viruses in respiratory infections among young children in this region. / Os vírus mais comumente envolvidos em doenças respiratórias agudas em crianças são os vírus respiratório sincicial (VRS), influenzavírus tipos A e B (FLU A e B), parainfluenzavírus tipos 1, 2 e 3 (PIV-1, -2 e -3), adenovírus (AdV) e os rinovírus (HRV). O objetivo geral do presente estudo foi identificar os principais vírus respiratórios envolvidos em doenças respiratórias aguda (DRA) em crianças de até cinco anos de idade no período de 2001 a 2004. Aspirados de nasofaringe de 379 crianças atendidas no Hospital de Clínicas da Universidade Federal de Uberlândia (HC/UFU) com doença respiratória aguda foram coletadas e testadas pelas reações de imunofluorescência indireta (IFI) ou transcrição reversa da reação em cadeia da polimerase (RT-PCR). O VRS foi detectado em 26,4% (100/379) dessas amostras, FLU tipos A e B em 9,5% (36/379), PIV 1, 2 e 3 em 6,3% (24/379) e AdV em 3,7% (14/379). As amostras negativas e inconclusivas pela IFI (205) foram testadas por RT-PCR para detecção dos HRV, sendo que 26,9% (112/379) foram positivas. Neste estudo, os vírus mais comumente detectados em quadros clínicos de bronquiolite e pneumonia/broncopneumonia em crianças menores de seis meses de idade foram o VRS, respondendo por 40,3% e 34,6% do total de casos, respectivamente, e o HRV, identificado em 25,0% dos casos de bronquiolite e em 15,4% dos casos de pneumonia/broncopneumonia na mesma faixa etária. Relacionado à sazonalidade, a circulação dos vírus identificados predominou nos meses de temperaturas mais baixas. Esse padrão foi evidente para o VRS, que apresentou um pico de ocorrência em abril e maio, enquanto que o pico do FLU e HRV ocorreu em julho. Amostras negativas tanto pela IFI quanto pela RT-PCR indicam que outros patógenos, incluindo coronavírus, metapneumovirus humano além de bactérias, podem ter sido os responsáveis pelas infecções. Finalizando, este estudo foi essencial para um diagnóstico conclusivo de DRAs causadas por vírus, bem como para determinar quais agentes virais circularam nesta região. / Mestre em Imunologia e Parasitologia Aplicadas

In Brazil, the few studies conducted have used viral etiology, in general, traditional methods (imunofluorescense techniques and and viral cultures) in hospitalized children. The purpose of the present study was to investigate the presence of respiratory viruses using indirect immunofluorescence techniques and the reverse transcription followed by polymerase chain reaction in nasopharyngeal aspirates of children with acute respiratory disease attendet in public institutions of primary and secondary care in the city of Uberlândia. Between february, 2008 to may, 2010 were obtained a convenience sample, nasopharyngeal aspirates from children under five years old with symptoms of acute respiratory disease, attended at Unidade Básica de Saúde da Família - Granada 1, Unidade de Atendimento Integrado-Pampulha and in Clinica Infantil Don Bosco in Uberlândia. Acute respiratory disease was defined by the presence of coryza, coughing, breathing difficulties and/or sibilance, with or without fever. The indirect immunofluorescence techniques and the reverse transcription followed by polymerase chain reaction were used to test for the presence of respiratory viruses. A total of 43 children (53,5% male and 46,5% female) between two and 60 months of age (average: 18,3 months; median 15 months; DP±16). The clinical diagnosis for admission was common cold for 23 children (53,4%), tracheobronchitis in four (9,3%); pneumonia in 12 (28%) and bronchiolitis in four (9,3%). At least one respiratory virus was detected in 22 (51,1%) of the samples. A total of 26 viruses were identified. Ten (38,4%) samples were positive for the respiratory syncytial virus; ten (38,4%) for rhinovirus, three (11,5%) for parainfluenzavirus; two (7,7%) for adenovirus and one (3,8%) for influenzavirus. Co-infection occurred in three of the samples. The indirect immunofluorescence techniques identified nine (21,0%) and the reverse transcription followed by polymerase chain reaction 19 (44,1%) of the respiratory viruses. The rhinovirus and respiratory syncytial virus were the respiratory virus most prevalent in children with acute respiratory disease in public institutions of primary and secondary care. The use of molecular method permitted a two fold increase in the capacity for detection of the viral agent collected from the nasopharyngeal aspirates. / No Brasil, os poucos estudos conduzidos com o objetivo de verificar a etiologia viral das doenças respiratórias agudas utilizaram, em geral, métodos tradicionais (imunofluorescência e cultura viral) em crianças hospitalizadas. O objetivo geral do presente estudo foi investigar a presença de vírus respiratórios por meio das técnicas de imunofluorescência indireta e da transcrição reversa seguida da reação em cadeia da polimerase em aspirados de nasofaringe de crianças com doença respiratória aguda atendidas em serviços públicos de atenção primária e secundária na cidade de Uberlândia, MG. Entre fevereiro de 2008 a maio de 2010 foram obtidos, por meio de uma amostra de conveniência, aspirados de nasofaringe de crianças menores de cinco anos com sintomas de doença respiratória aguda, atendidas na Unidade Básica de Saúde da Família - Granada 1, Unidade de Atendimento Integrado-Pampulha e Clínica Infantil Dom Bosco Uberlândia. Doença respiratória aguda foi definida pela presença de coriza, tosse, dificuldade para respirar ou sibilância, com ou sem febre. A imunofluorescência e a transcrição reversa seguida da reação em cadeia da polimerase foram utilizadas para testar a presença de vírus respiratórios. Partiparam do estudo 43 crianças (53,5% do gênero masculino e 46,5% gênero feminino) com idade entre dois a 60 meses (média = 18,3 meses; mediana = 15 meses; DP=±16). O diagnóstico clínico à admissão foi de resfriado comum em 23 crianças (53,4%), traqueobronquite, em quatro (9,3%), pneumonia, em doze (28%) e bronquiolite, em quatro (9,3%). Pelo menos um vírus respiratório foi detectado em 22 (51,1%) amostras, sendo que 26 vírus foram identificados. Dez (38,4%) amostras foram positivas para o vírus respiratório sincicial, dez (38,4%) para o rinivirus, três (11,5%) para o parainfluenzavírus; duas (7,7%) para adenovírus e uma (3,8%), para o influenzavírus. A presença de co-infecção ocorreu em três amostras. A imunofluorescência identificou nove (21%) e a transcrição reversa seguida da reação em cadeia da polimerase dezenove (44,1%) vírus respiratórios. O rinovírus e o vírus respiratório sincicial foram os vírus mais prevalentes em crianças com doença respiratória aguda em serviços de atenção primária e secundária. A utilização de método molecular permitiu dobrar a capacidade de detecção de agente viral nos aspirados de nasofaringe. / Mestre em Ciências da Saúde

Made available in DSpace on 2014-08-20T14:37:53Z (GMT). No. of bitstreams: 1 dissertacao_nathalia_assis_brasil_resumo.pdf: 8786 bytes, checksum: 29067eed0bac7715d60b7e64baf7f05f (MD5) Previous issue date: 2013-12-07 / This study aimed to survey the major diseases that affect calves under one year of age in area of influence of the Regional Diagnostic Laboratory, Faculty of Veterinary Medicine, Federal University of Pelotas, from 2000 to 2011. The results of this study are presented in the form of two scientific papers. The first one refers to the data of a general survey of the main causes of death in this animal category, establishing the epidemiological conditions in which they occur. The second paper describes the epidemiology, clinical signs and pathology of respiratory diseases occuring in the same animal category. Immunohistochemical of cases of enzootic pneumonia suspected to be caused by bovine respiratory syncytial virus were also performed. / Este trabalho teve como objetivo realizar um levantamento das principais enfermidades que acometem bezerros até um ano de idade na área de influência do Laboratório Regional de Diagnóstico da Faculdade de Veterinária da Universidade Federal de Pelotas no período de 2000 a 2011. O trabalho está apresentado na forma de dois artigos científicos. O primeiro deles refere-se os dados de um levantamento geral das principais causas de morte nesta categoria animal, estabelecendo-se as condições epidemiológicas em que as mesmas ocorrem. O segundo trabalho apresenta a epidemiologia, sinais clínicos e patologia das pneumonias que ocorrem nesta mesma categoria animal. Foi realizado também um estudo imuno-histoquímico dos casos de pneumonia enzoótica suspeitos de serem causados pelo vírus respiratório sincicial bovino.

Abstract Each year in Finland, approximately 5.7% of infants are born preterm, i.e., before 37 completed weeks of gestation. Preterm birth is a major cause of mortality and several neonatal morbidities, especially the respiratory diseases. Infants born very preterm (&#60;32 wk) are at higher risk of developing a chronic lung disease called bronchopulmonary dysplasia (BPD). The genetic factors predisposing to spontaneous preterm birth (SPTB) and BPD are incompletely known. The aims of this thesis project were to identify genetic factors that affect susceptibility to SPTB and BPD. Genetic case-control association studies were performed in mothers and infants of northern Finnish origin (SPTB study), or in multiple populations of very preterm infants of Finnish or European origin (BPD study). The candidate genes were selected based on their proposed roles in inflammation which is involved in both SPTB and BPD susceptibility. Additionally, the aim was to study the possible functional role of polymorphisms in the gene encoding surfactant protein B (SP-B) that have been shown previously to associate with pulmonary function. An association between Met31Thr polymorphisms in the gene encoding SP-D (SFTPD) and SPTB infants was found. The other collectin genes that were studied, encoding SP-A and mannose-binding lectin, did not associate with SPTB in mothers or infants. An intronic polymorphism in the gene encoding Kit ligand (KITLG) was associated with the risk of BPD in the northern Finnish and in the combined population that originated from Finland, Canada and Hungary. The role of KITLG in BPD was further supported by biomarker data, which showed higher concentrations of Kit ligand at the time of birth in infants that later developed BPD. The genes encoding interleukin 6 (IL-6), its receptors, IL-10, tumor necrosis factor alpha or glucocorticoid receptor did not associate with BPD susceptibility. Finally, a genetic variant 131Thr in the gene encoding SP-B (SFTPB) was associated with lower SP-B levels in vivo and delayed secretion in vitro. To date, there is no effective method to prevent SPTB, and especially the extremely preterm infants are at an increased risk of developing serious respiratory diseases. Better understanding of the mechanisms underlying both SPTB and BPD could help in the successful prediction of risk groups as well as in the design of new preventive and treatment strategies. / Tiivistelmä Noin 5,7 % lapsista syntyy Suomessa ennenaikaisesti, eli ennen kuin raskaus on kestänyt täydet 37 viikkoa. Ennenaikainen syntymä altistaa vastasyntyneen lapsen vakaville pitkäaikaissairauksille. Erityisesti hyvin pienillä keskosilla, jotka ovat syntyneet ennen 32. raskausviikkoa, on suurempi riski sairastua vakavaan hengitysvaikeuteen eli bronkopulmonaaliseen dysplasiaan, joka tunnetaan myös nimellä BPD-tauti. Perinnölliset tekijät vaikuttavat niin spontaanin ennenaikaisen syntymän (SEAS) kuin BPD-taudinkin taustalla, mutta nämä tekijät tunnetaan huonosti. Tässä väitöskirjatyössä pyrittiin tunnistamaan perinnöllisiä tekijöitä, jotka vaikuttavat SEAS:in ja BPD-taudin taustalla. Perinnöllisen taustan selvittämisessä ehdokasgeenien sisältämien muuntelevien kohtien esiintyvyyttä verrattiin terveiden verrokkien ja tautitapausten välillä. SEAS-tutkimuksessa tutkimusväestö koostui suomalaisista äideistä ja heidän lapsistaan. BPD-tutkimuksessa oli mukana hyvin ennenaikaisesti syntyneitä lapsia Suomesta, Kanadasta ja Unkarista. Tämän lisäksi kokeellisten tutkimusten avulla tutkittiin aiemmin keuhkosairauksiin liittyneen geenin muuntelevien kohtien osuutta sen koodaaman surfaktanttiproteiini (SP) B:n toiminnassa. Tutkimuksissa havaittiin SP-D:tä koodaavan geenin Met31Thr-polymorfismin olevan mahdollinen riskitekijä SEAS:lle lapsilla, mutta se ei selittänyt SEAS-riskiä äideissä. SP-A:ta ja mannoosia sitovaa lektiiniä koodaavilla geeneillä ei ollut yhteyttä SEAS-riskiin. Kit-ligandia koodaavan geenin intronissa sijaitseva polymorfismi selitti BPD-tautiriskiä pohjoissuomalaisessa sekä yhdistetyssä tutkimusväestössä. Lisäksi lapsilla, jotka myöhemmin sairastuivat BPD-tautiin, havaittiin suurempia Kit-ligandipitoisuuksia syntymähetkellä. Interleukiini 6:ta (IL-6), sen reseptoreita, IL-10:ta, tuumorinekroosifaktori-alfaa tai glukokortikoidireseptoria koodaavien geenien polymorfismien ja BPD-taudin välillä ei ollut yhteyttä. SP-B:tä koodaavan geenin Ile131Thr-polymorfismin Thr-variaatio liittyi alhaisempaan SP-B:n pitoisuuteen lapsivedessä sekä hidastuneeseen proteiinin tuottoon kokeellisessa solumallissa. Tulokset antavat uutta tietoa SEAS:n ja BPD-taudin perinnöllisestä taustasta. Tämä tieto voi auttaa synnytyksen käynnistymiseen sekä BPD-alttiuteen johtavien biologisten mekanismien selvittämisessä ja uusien hoitokeinojen kehittämisessä.

Objectif : La bronchopneumonie infectieuse (BPI) est une affection des voies respiratoires inférieures due à l’interaction entre des agents microbiens, des facteurs environnementaux et des facteurs propres à l’individu. Malgré des années de recherche, la BPI reste prévalente en élevage de génisses de remplacement et de veaux lourds engendrant des pertes économiques majeures et une forte consommation d’antibiotiques dans ces élevages. Le score clinique respiratoire diagnostique (SCRD), l’auscultation thoracique, l’échographie thoracique et la radiographie thoracique sont des tests couramment utilisés pour détecter la BPI. Cependant, leurs performances diagnostiques actuelles à savoir : leurs facultés à détecter les veaux malades (sensibilité; Se) et leurs facultés à détecter les veaux non malades (spécificité; Sp) sont sous-optimales pour détecter adéquatement les veaux de race laitière nécessitant d’être traités avec des antibiotiques et/ou des anti-inflammatoires. L’objectif général de cette thèse était donc d’améliorer les stratégies de détection du statut actif de la BPI, statut nécessitant un traitement (d’antibiotiques et/ou d’anti-inflammatoires), afin, d’une part, de mieux diagnostiquer les veaux malades, diminuer les impacts économiques de la maladie et améliorer le bien-être des veaux ; et d’autre part, favoriser l’emploi judicieux des antibiotiques en traitant uniquement les veaux qui en ont besoin. Pour répondre à cet objectif général, 3 sous-objectifs spécifiques ont été définis : (1) développer un SCRD, en identifiant et validant les signes cliniques avec une bonne répétabilité interopérateurs pour diagnostiquer le statut actif de la BPI à l’échelle individuelle et populationnelle; (2) Améliorer les stratégies diagnostiques des tests d’imagerie médicale en comparant l’échographie et la radiographie thoracique pour détecter les lésions pulmonaires et le statut actif de la BPI; (3) Améliorer l’échographie thoracique en standardisant la technique (ajout ou non du lobe crânial droit) et l’interprétation (seuil de profondeur) afin d’en optimiser ces performances pour détecter le statut actif de la BPI. Méthodes : (1) 800 veaux lourds de 80 lots ont été filmés à l’aide d’une caméra portative lors de leur évaluation clinique. Différentes séquences vidéo ont été aléatoirement sélectionnées et soumises à un panel d’évaluateur constitué de producteurs de veaux lourds, techniciens et médecins vétérinaires. La variabilité interopérateurs de chaque signe clinique a été évaluée. Les signes cliniques ayant la meilleure répétabilité ont été retenus pour le développement et la validation d’un SCRD en utilisant un modèle bayésien d’analyse de classe latente. Enfin, des stratégies diagnostiques des BPI au niveau populationnel ont été développées; (2) 50 veaux hospitalisés ont reçu une échographie et une radiographie thoracique. La tomodensitométrie thoracique (CT scan) a été utilisé comme gold standard pour vérifier les individus positifs à l’un des deux tests. Les performances des deux tests ont été comparées pour détecter d’abord les lésions pulmonaires en comparant avec les résultats du CT scan, puis le statut actif de la BPI défini par trois experts; (3) la Se et la Sp pour diagnostiquer le statut actif de BPI de différents sites d’échographie thoracique et différents seuils de profondeur de consolidation pulmonaire ont été évalués à l’aide de modèles utilisant une analyse bayésienne à classe latente dans une population de génisse de remplacement et une population de veaux lourds. Résultats : (1) La position des oreilles et la toux induite étaient les signes cliniques de BPI les plus répétables. Le SCRD développé et validé consiste à évaluer ces deux signes cliniques ainsi que la température rectale (anormale T≥ 39.5◦C) sur 10 veaux d’un lot, deux semaines après leur arrivée en parc d’engraissement. La présence de 3 veaux avec deux de ces prédicteurs implique que le lot a 94 % de chance d’avoir une prévalence du statut actif de BPI ≥ 0.10. Avec moins de 3 veaux, le lot à 95 % de chance de ne pas avoir une prévalence ≥ 0.10; (2) Pour détecter les lésions pulmonaires, les Se et Sp de l’échographie thoracique étaient de 0,81 (intervalle de crédit bayésien à 95 % (ICB95%): 0,65; 0,92) et 0,90 (ICB95 %: 0,81; 0,96), respectivement. Les Se et Sp de la radiographie thoracique étaient de 0,86 (ICB95%: 0,62; 0,99) et 0,89 (ICB95%: 0,67; 0,99), respectivement. Pour détecter le statut actif de la BPI, les Se et Sp de l’échographie thoracique étaient de 0,84 (intervalle de confiance à 95% (IC95%): 0,60; 0,97) et 0,74 (IC95 %: 0,57; 0,86), respectivement. La Se et Sp de la radiographie thoracique étaient de 0,89 (IC95%: 0,67; 0,99) et 0,58 (IC95%: 0,39; 0,75), respectivement. Aucune différence n’était présente entre les deux tests pour détecter les lésions pulmonaires ou le statut actif de BPI; (3) La détection échographique de lésions de consolidation pulmonaire des sites caudaux au cœur avec une profondeur ≥ 3 cm conclut à la présence du statut actif de BPI avec une Se de 0,89 (ICB95%: 0,55; 1,00) et une Sp de 0,95 (ICB95%: 0,92; 0,98). Conclusion : Dans cette thèse, nous avons amélioré les stratégies diagnostiques pour détecter les veaux à traiter de BPI. L’utilisation de ces résultats pour élaborer des algorithmes décisionnels devrait ultimement permettre de diminuer les pertes économiques et de raffiner l’utilisation d’antibiotiques. / Objectives: Infectious bronchopneumonia (BPI) is the infection of the lower respiratory tract implying an interaction between microbial agents, environment, and host. Despite decades of research, BPI remains omnipresent in dairy and veal calves, responsible for major economic losses and antimicrobial consumption. Clinical respiratory scoring system (CRSC), lung auscultation, thoracic ultrasonography, and thoracic radiography are the most popular tests used to detect BPI in calves. However, the sensitivity (Se) (i.e., faculty to detect sick calves) and the specificity (Sp) (i.e., faculty to detect healthy calves) are suboptimal to accurately detecting dairy and veal calves to treat. Our main objective was to improve the diagnostic strategies to detect active BPI (BPI status needed a treatment) in order to: firstly, better diagnose sick calves, reduce BPI economic losses and improve calves’ welfare; secondly, reduce antimicrobial consumption by treating only calves that need it. For this purpose, three sub-objectives have been defined: (1) develop and validate a CRSC including inter-operator reliable respiratory clinical signs to detect active BPI at calf-level and group level; (2) compare thoracic ultrasonography and thoracic radiography to detect lung lesions and active BPI; (3) standardize thoracic ultrasonography technique (sites to ultrasound) and interpretation (lung consolidation depth threshold) to promote thoracic ultrasonography Se and Sp to detect active BPI. Methods: (1) 800 veal calves from 80 batches were filmed with a portative camera during their clinical exam. Videos were randomly selected and assessed by producers, technicians, and veterinarians. The reliability of each respiratory clinical sign was assessed. The most reliable respiratory clinical signs were kept in order to develop and validate a CRSC using latent class Bayesian analysis. Batch-level diagnostic strategies were developed; (2) Fifty hospitalized calves underwent thoracic ultrasonography and thoracic radiography. Thoracic tomography (CT scan) was used as a gold standard to check positive calves on one of both tests. Se and Sp of both tests were compared to detect lung lesions and active BPI defined by three experts; (3) Se and Sp of different ultrasound sites and different lung consolidation depth thresholds were estimated to detect active BPI using latent class Bayesian analysis in both dairy calves and veal calves’ populations. Results: (1) Ear droop/head tilt and induced cough were the most reliable respiratory clinical signs. The CRSC developed and validated implies assessing those clinical signs with rectal temperature (abnormal T≥ 39.5◦C) in 10 calves from a batch at two weeks after arriving at the fattening unit. Having two abnormal characteristics of those predictors in three calves implies that a batch has 94% of having an active BPI prevalence ≥ 0.10. A batch with <3 positive calves on 10 has 95% of not having an active BPI prevalence ≥ 0.10; (2) For detecting lung lesions, the Se and Sp of thoracic ultrasonography were 0.81 (95% Bayesian credible interval (95%BCI): 0.65; 0.92) and 0.90 (95%BCI: 0.81; 0.96), respectively. The Se and Sp of thoracic radiography were 0.86 (95%BCI: 0.62; 0.99) and 0.89 (95%BCI: 0.67; 0.99), respectively. For detecting active BPI, the Se and Sp of thoracic ultrasonography were 0.84 (95% confidence interval (95%CI): 0.60; 0.97) and 0.74 (95%CI: 0.57; 0.86), respectively. The Se and Sp of thoracic radiography were 0.89 (95%CI: 0.67; 0.99) and 0.58 (95%CI: 0.39; 0.75), respectively. There was no difference between both tests to detect both lung lesions and active BPI; (3) Thoracic ultrasonography of the sites caudal of the heart with a depth lung consolidation ≥ 3 cm has a Se of 0.89 (95%BCI: 0.55; 1.00) and a Sp of 0.95 (95%BCI: 0.92; 0.98). Conclusion: We improved diagnostic strategies to detect active BPI in this thesis. Using our results to elaborate decisional algorithms would reduce economic losses and antimicrobial consumption of BPI in dairy and veal calves.

Introduction/Background: Guidelines from the World Health Organization currently recommend targeting a body mass index (BMI) between 18.5 and 24.9 kg/m2 based on the lowest risk of mortality observed in epidemiological studies. However, these recommendations are based on population observations and do not take into account potential inter-individual differences. We hypothesized that genetic and non-genetic differences in adiposity, anthropometric, and metabolic measures result in inter-individual variation in the optimal BMI. Methods: Genetic variants associated with BMI as well as related adiposity, anthropometric, and metabolic phenotypes (e.g. triglyceride (TG)) were combined into polygenic risk scores (PRS), cumulative risk scores derived from the weighted contributions of each variant. 387,692 participants in the UK Biobank were split by quantiles of PRS or clinical biomarkers such as C-reactive protein (CRP), and alanine aminotransferase (ALT). The BMI linked with the lowest risk of all-cause and cause-specific mortality outcomes (“nadir value”) was then compared across quantiles (“Cox meta-regression model”). Our results were replicated using the non-linear mendelian randomization (NLMR) model to assess causality. Results: The nadir value for the BMI–all-cause mortality relationship differed across percentiles of BMI PRS, suggesting inter-individual variation in optimal BMI based on genetics (p = 0.005). There was a difference of 1.90 kg/m2 in predicted optimal BMI between individuals in the top and bottom 5th BMI PRS percentile. Individuals having above and below median TG (p = 1.29×10-4), CRP (p = 7.92 × 10-5), and ALT (p = 2.70 × 10-8) levels differed in nadir for this relationship. There was no difference in the computed nadir between the Cox meta-regression or NLMR models (p = 0.102). Conclusions: The impact of BMI on mortality is heterogenous due to individual genetic and clinical biomarker level differences. Although we cannot confirm that are results are causal, genetics and clinical biomarkers have potential use for making more tailored BMI recommendations for patients. / Thesis / Master of Science (MSc) / The World Health Organization (WHO) recommends targeting a body mass index (BMI) between 18.5 - 24.9 kg/m2 for optimal health. However, this recommendation does not take into account individual differences in genetics or biology. Our project aimed to determine whether the optimal BMI, or the BMI associated with the lowest risk of mortality, varies due to genetic or biological variation. Analyses were conducted across 387,692 individuals. We divided participants into groups according to genetic risk for obesity or clinical biomarker profile. Our results show that the optimal BMI varies according to genetic or biomarker profile. WHO recommendations do not account for this variation, as the optimal BMI can fall under the normal 18.5 - 24.9 kg/m2 or overweight 25.0 – 29.0 kg/m2 WHO BMI categories depending on individual genetic or biomarker profile. Thus, there is potential for using genetic and/or biomarker profiles to make more precise BMI recommendations for patients.

<p dir="ltr">ABSTRACT</p><p dir="ltr">Bovine Respiratory Disease (BRD) poses a significant challenge in the dairy and beef industry, contributing to high mortality, morbidity, and economic costs. Extensive research has aimed to enhance BRD diagnosis, focusing on various factors such as predisposition, environment, and epidemiology. While diverse methods have been developed for BRD detection, including clinical signs, behavioral changes, lung consolidation assessment via ultrasonography, and molecular techniques for microbiome analysis, accurate diagnosis remain inconsistent. Notably, many studies lack exploration of microbial interactions (fungi, viruses, and bacteria) within BRD-affected animals compared to healthy ones. Moreover, the impact of age, disease, and antibiotic treatment on the microbiome community remains understudied. Thus, additional analysis is crucial to understand the relationships between these factors and BRD development. This dissertation is divided into two parts, each addressing specific conditions. The first part focuses on characterizing the nasopharyngeal (NP) microbiome of dairy calves, pre-weaned and post-transported, and those diagnosed with BRD within the first two weeks of life. The objective is to identify NP microbiome changes as indicators of disease development, considering antibiotic treatment effects on NP alpha and beta diversity. The second part delves into characterizing the fungal and bacterial nasal cavity among BRD-affected and healthy cattle within the same pen. This section, presented in three chapters, explores the bovine nasal mycobiome in beef cattle, as well as the nasal microbiome in both dairy and beef cattle. The overarching goals of these studies are to evaluate differences in the nasal mycobiome or microbiome community between BRD-affected and healthy cattle, focusing on alpha, beta, and community compositions as potential disease indicators. Additionally, the aim is to determine if BRD-affected cattle exhibit higher abundance of BRD-pathobionts (fungi and bacteria) in the nasal cavity compared to healthy pen-mates. In conclusion, findings from this research emphasize the importance of incorporating both mycobiome and microbiome analyses in understanding BRD development. Future studies should consider geographical influences on nasal microbiome structure, highlighting the need for separate investigations in dairy and beef calves due to breed variations. Ultimately, studying mycobiome and microbiome ecology offers insights into microbial transitions from commensal to pathogenic farms in the bovine upper respiratory tract, supporting advancements in BRD prevention or mitigation strategies.</p>

Chronic obstructive pulmonary disease (COPD) describes a range of lung conditions including emphysema, chronic bronchitis and small airways disease. While COPD is a major cause of death and debilitating illness, current clinical assessment methods are inadequate: they are a poor predictor of patient outcome and insensitive to mild disease. A new imaging technology, hyperpolarised xenon MRI, offers the hope of improved diagnostic techniques, based on regional measurements using functional imaging. There is a need for quantitative analysis techniques to assist in the interpretation of these images. The aim of this work is to develop these techniques as part of a clinical trial into hyperpolarised xenon MRI. In this thesis we develop a fully automated pipeline for deriving regional measurements of lung function, making use of the multiple imaging modalities available from the trial. The core of our pipeline is a novel method for automatically segmenting the pulmonary lobes from CT data. This method combines a Hessian-based filter for detecting pulmonary fissures with anatomical cues from segmented lungs, airways and pulmonary vessels. The pipeline also includes methods for segmenting the lungs from CT and MRI data, and the airways from CT data. We apply this lobar map to the xenon MRI data using a multi-modal image registration technique based on automatically segmented lung boundaries, using proton MRI as an intermediate stage. We demonstrate our pipeline by deriving lobar measurements of ventilated volumes and diffusion from hyperpolarised xenon MRI data. In future work, we will use the trial data to further validate the pipeline and investigate the potential of xenon MRI in the clinical assessment of COPD. We also demonstrate how our work can be extended to build personalised computational models of the lung, which can be used to gain insights into the mechanisms of lung disease.