Phylodynamic modelling of foot-and-mouth disease virus sequence data

The under-reporting of cases of infectious diseases is a substantial impediment to the control and management of infectious diseases in both epidemic and endemic contexts. Information about infectious disease dynamics can be recovered from sequence data using time-varying coalescent approaches, and phylodynamic models have been developed in order to reconstruct demographic changes of the numbers of infected hosts through time. In this study I have demonstrated the general concordance between empirically observed epidemiological incidence data and viral demography inferred through analysis of foot-and-mouth disease virus VP1 coding sequences belonging to the CATHAY topotype over large temporal and spatial scales. However a more precise and robust relationship between the effective population size (

Provision of care services for rheumatic and musculoskeletal diseases-related foot and ankle problems: a survey from sixteen european countries

Background: The increased prevalence of foot and ankle pathologies in Rheumatic and Musculoskeletal diseases (RMDs) is well documented1, however the provision of foot & ankle (F&A) healthcare services for people with RMDs in Europe has not been evaluated. Objectives: To assess the current healthcare systems for providing foot & ankle healthcare services for people with RMDs in Europe. Methods: A survey was undertaken to evaluate current provision of F&A health care services for people with RMDs across Europe. A questionnaire was distributed to all 22 country presidents representing HP associations within EULAR. The questionnaire used was developed and piloted (in 7 countries) by the EULAR F&A Study Group, and structured to capture the provision and type of F&A services for people with RMDs. When the HP presidents felt unable to answer specific questions they were encouraged to consult a colleague who may be better placed to provide the answers. Results: Sixteen questionnaires were completed (Norway, Ireland, Sweden, Hungary, Netherlands, UK, Denmark, Portugal, Italy, Switzerland, Austria, France, Czech Republic, Spain, Belgium, Malta). Of the 16, 13 respondents indicated provision of F&A health care services in their country, but only three countries had services specialising in RMD-related F&A problems (Netherlands, UK, Malta). The professions providing the care for patients with RMD-related F&A problems were different depending on the pathology and the country (Table1). Podiatrists provided care for F&A pain and deformity problems in 11 countries, but provided F&A ulcer care in only 8 countriesConclusions: Only 3 countries have F&A health care services specialised to the needs of people with RMDs. The professions providing the care varied between countries, and also depended on the F&A pathology. Interestingly, F&A healthcare services were provided by professions that do not solely specialised in F&A care. Further research is needed to assess the variation of F&A healthcare services between and within European countries and the impact on healthcare of various F&A healthcare service designs. References: Woodburn, J. & Helliwell, P. Foot problems in rheumatology. Rheumatology 36, 932-934 (1997).

The epidemiology of foot-and-mouth disease at the wildlife-livestock interface in northern Tanzania

Foot-and-mouth disease (FMD), a disease of cloven hooved animals caused by FMD virus (FMDV), is one of the most economically devastating diseases of livestock worldwide. The global burden of disease is borne largely by livestock-keepers in areas of Africa and Asia where the disease is endemic and where many people rely on livestock for their livelihoods and food-security. Yet, there are many gaps in our knowledge of the drivers of FMDV circulation in these settings. In East Africa, FMD epidemiology is complicated by the circulation of multiple FMDV serotypes (distinct antigenic variants) and by the presence of large populations of susceptible wildlife and domestic livestock. The African buffalo (Syncerus caffer) is the only wildlife species with consistent evidence of high levels of FMDV infection, and East Africa contains the largest population of this species globally. To inform FMD control in this region, key questions relate to heterogeneities in FMD prevalence and impacts in different livestock management systems and to the role of wildlife as a potential source of FMDV for livestock. To develop FMD control strategies and make best use of vaccine control options, serotype-specific patterns of circulation need to be characterised. In this study, the impacts and epidemiology of FMD were investigated across a range of traditional livestock-keeping systems in northern Tanzania, including pastoralist, agro-pastoralist and rural smallholder systems. Data were generated through field studies and laboratory analyses between 2010 and 2015. The study involved analysis of existing household survey data and generated serological data from cross-sectional livestock and buffalo samples and longitudinal cattle samples. Serological analyses included non-structural protein ELISAs, serotype-specific solid-phase competitive ELISAs, with optimisation to detect East African FMDV variants, and virus neutralisation testing. Risk factors for FMDV infection and outbreaks were investigated through analysis of cross-sectional serological data in conjunction with a case-control outbreak analysis. A novel Bayesian modeling approach was developed to infer serotype-specific infection history from serological data, and combined with virus isolation data from FMD outbreaks to characterise temporal and spatial patterns of serotype-specific infection. A high seroprevalence of FMD was detected in both northern Tanzanian livestock (69%, [66.5 - 71.4%] in cattle and 48.5%, [45.7-51.3%] in small ruminants) and in buffalo (80.9%, [74.7-86.1%]). Four different serotypes of FMDV (A, O, SAT1 and SAT2) were isolated from livestock. Up to three outbreaks per year were reported by households and active surveillance highlighted up to four serial outbreaks in the same herds within three years. Agro-pastoral and pastoral livestock keepers reported more frequent FMD outbreaks compared to smallholders. Households in all three management systems reported that FMD outbreaks caused significant impacts on milk production and sales, and on animals’ draught power, hence on crop production, with implications for food security and livelihoods. Risk factor analyses showed that older livestock were more likely to be seropositive for FMD (Odds Ratio [OR] 1.4 [1.4-1.5] per extra year) and that cattle (OR 3.3 [2.7-4.0]) were more likely than sheep and goats to be seropositive. Livestock managed by agro-pastoralists (OR 8.1 [2.8-23.6]) or pastoralists (OR 7.1 [2.9-17.6]) were more likely to be seropositive compared to those managed by smallholders. Larger herds (OR: 1.02 [1.01-1.03] per extra bovine) and those that recently acquired new livestock (OR: 5.57 [1.01 – 30.91]) had increased odds of suffering an FMD outbreak. Measures of potential contact with buffalo or with other FMD susceptible wildlife did not increase the likelihood of FMD in livestock in either the cross-sectional serological analysis or case-control outbreak analysis. The Bayesian model was validated to correctly infer from ELISA data the most recent serotype to infect cattle. Consistent with the lack of risk factors related to wildlife contact, temporal and spatial patterns of exposure to specific FMDV serotypes were not tightly linked in cattle and buffalo. In cattle, four serial waves of different FMDV serotypes that swept through southern Kenyan and northern Tanzanian livestock populations over a four-year period dominated infection patterns. In contrast, only two serotypes (SAT1 and SAT2) dominated in buffalo populations. Key conclusions are that FMD has a substantial impact in traditional livestock systems in East Africa. Wildlife does not currently appear to act as an important source of FMDV for East African livestock, and control efforts in the region should initially focus on livestock management and vaccination strategies. A novel modeling approach greatly facilitated the interpretation of serological data and may be a potent epidemiological tool in the African setting. There was a clear temporal pattern of FMDV antigenic dominance across northern Tanzania and southern Kenya. Longer-term research to investigate whether serotype-specific FMDV sweeps are truly predictable, and to shed light on FMD post-infection immunity in animals exposed to serial FMD infections is warranted.

Having The Foot at Risk:Experience Report

Resumo As alterações à sensibilidade do pé tornam o diabético mais vulnerável a traumatismos que tendem a evoluir para lesões por vezes, com consequências graves, influenciando negativamente o bem-estar e a qualidade de vida. Objetivo: Avaliar a implicação da úlcera no pé diabético, na qualidade de vida. Métodos: Estudo de caso. Recorreu-se à entrevista informal e esquema de Cardiff de Impacto da Ferida. Resultados: Através dos dados qualitativos identificaram-se quatro categorias: Preocupação com o futuro, Tranquilidade perante a doença, Recursos e Conhecimento sobre os riscos. Dos dados do questionário, percebeu-se que a mobilidade foi a atividade de vida mais afetada. Conclusões: Tem havido uma preocupação em empoderar e informar a cliente, o que ajuda a melhor se adaptar às transformações pelas quais passa no decurso da sua doença. Seria vantajoso o acompanhamento da utente nos cuidados de saúde primários com vigilância do enfermeiro de família.

Mapping the likelihood of foot-and-mouth disease introduction along the border between Brazil and Paraguay.

The objective of this work was to apply fuzzy majority multicriteria group decision?making to determine risk areas for foot?and?mouth disease (FMD) introduction along the border between Brazil and Paraguay. The study was conducted in three municipalities in the state of Mato Grosso do Sul, Brazil, located along the border with Paraguay. Four scenarios were built, applying the following linguistic quantifiers to describe risk factors: few, half, many, and most. The three criteria considered to be most likely to affect the vulnerability to introduction of FMD, according to experts? opinions, were: the introduction of animals in the farm, the distance from the border, and the type of property settlements. The resulting maps show a strong spatial heterogeneity in the risk of FMD introduction. The used methodology brings out a new approach that can be helpful to policy makers in the combat and eradication of FMD.

A black foot extract can delay downy mildew progress in grapevine under greenhouse conditions.

2011

The FOOT experiment: Trigger and Data Acquisition (TDAQ) development and data analysis

Hadrontherapy employs high-energy beams of charged particles (protons and heavier ions) to treat deep-seated tumours: these particles have a favourable depth-dose distribution in tissue characterized by a low dose in the entrance channel and a sharp maximum (Bragg peak) near the end of their path. In these treatments nuclear interactions have to be considered: beam particles can fragment in the human body releasing a non-zero dose beyond the Bragg peak while fragments of human body nuclei can modify the dose released in healthy tissues. These effects are still in question given the lack of interesting cross sections data. Also space radioprotection can profit by fragmentation cross section measurements: the interest in long-term manned space missions beyond Low Earth Orbit is growing in these years but it has to cope with major health risks due to space radiation. To this end, risk models are under study: however, huge gaps in fragmentation cross sections data are currently present preventing an accurate benchmark of deterministic and Monte Carlo codes. To fill these gaps in data, the FOOT (FragmentatiOn Of Target) experiment was proposed. It is composed by two independent and complementary setups, an Emulsion Cloud Chamber and an electronic setup composed by several subdetectors providing redundant measurements of kinematic properties of fragments produced in nuclear interactions between a beam and a target. FOOT aims to measure double differential cross sections both in angle and kinetic energy which is the most complete information to address existing questions. In this Ph.D. thesis, the development of the Trigger and Data Acquisition system for the FOOT electronic setup and a first analysis of 400 MeV/u 16O beam on Carbon target data acquired in July 2021 at GSI (Darmstadt, Germany) are presented. When possible, a comparison with other available measurements is also reported.

Caratterizzazione di un sistema di veto per un rilvelatore di neutroni nell'ambito dell'esperimento FOOT

L’adroterapia è un tipo di terapia oncologica in cui il tumore è irraggiato con particelle cariche (adroni) quali protoni e ioni carbonio. Il vantaggio principale rispetto alla radioterapia convenzionale a raggi X consiste nel fatto che l’irraggiamento con adroni non coinvolge i tessuti sani circostanti quelli malati. Tuttavia, si conosce ancora poco sui processi di frammentazione nucleare che avvengono tra gli adroni del fascio usato nel trattamento e i nuclei presenti nel corpo umano. Così, nel 2017 nasce l’esperimento FOOT (FragmentatiOn Of Target) con lo scopo di misurare le sezioni d’urto differenziali dei frammenti nucleari prodotti nell’interazione a energie di 200-400 MeV/u (tipicamente impiegate in adroterapia). Attualmente l’apparato sperimentale di FOOT è in grado di compiere misure accurate solo per frammenti carichi, ma nell’ultimo anno si è cominciata ad esplorare la possibilità di rivelare anche i neutroni. Per questa operazione è necessario servirsi di scintillatori liquidi affiancati ad un sistema di veto costituito da scintillatori plastici sottili accoppiati a sensori che segnalano il passaggio di eventuali frammenti carichi. In una precedente campagna di misure con la collaborazione FOOT, si sono utilizzati come sensori dei tubi fotomoltiplicatori (PMT). Per migliorare le prestazioni del sistema di veto si è reso necessario l’utilizzo di scintillatori plastici veloci, letti da sensori fotomoltiplicatori al silicio (SiPM). In questa tesi mi sono occupato della risoluzione temporale dei segnali acquisiti con scintillatori plastici EJ-204 di 3 mm di spessore, letti da SiPM SenseL®.

Studio delle interazioni nel rivelatore e selezione degli eventi nelle misure di sezione d'urto nell'esperimento FOOT

L’adroterapia è una tecnica di cura tumorale basata sull’irraggiamento della zona cancerosa tramite ioni pesanti e particelle cariche. Queste permettono di massimizzare il danno nella zona tumorale e limitare invece quello subito dalle cellule sane. Il più grande ostacolo risiede nella limitata reperibilità di informazioni in letteratura sulla frammentazione del target. I frammenti così prodotti infatti hanno una mobilità di µm e per questo motivo sono molto difficili da rivelare. In questo contesto nel 2017 l’esperimento FOOT, approvato dall’INFN nasce con l’obiettivo di misurare la sezione d’urto differenziale di tutti i prodotti emessi dalla frammentazione nucleare fra il fascio ed il paziente. Operando in condizione di cinematica inversa l’esperimento riesce a rivelare questi frammenti ed a misurarne l’abbondanza e l’energia. E’ stata effettuata a questo proposito, un’analisi dati volta ad eliminare le frammentazioni in aria precedenti ed interne al rivelatore MSD per poter ottenere misure più accurate delle sezioni d’urto di frammentazione.

Studio delle interazioni in aria nelle misure di sezione d'urto nell'esperimento FOOT

L’adroterapia è una terapia medica oncologica che consiste nell’irraggiamento della massa tumorale tramite un fascio di particelle cariche, come protoni o ioni pesanti. Ad oggi però, non è ancora stata fatta una stima completa degli effetti causati dagli eventi di frammentazione nucleare tra le particelle del fascio e i nuclei del corpo umano. A tale scopo è nato nel 2017 l’esperimento FOOT (FragmentatiOn Of Target), con l’obiettivo di misurare la sezione d’urto differenziale di tutti i prodotti emessi nella frammentazione nucleare tra il fascio e il paziente. In questa tesi sono stati analizzati i dati acquisiti relativi all’interazione tra un fascio di ioni ossigeno a 400MeV/n su un bersaglio di grafite. Per ottenere una misura quanto migliore delle sezioni d’urto è necessario eliminare gli eventi di frammentazione che avvengono tra il fascio e i nuclei dell’aria posta tra i rivelatori dell’apparato sperimentale. Confrontando l’energia rilasciata in due rivelatori consecutivi si può capire se nell’aria posta fra questi vi sono stati tali eventi.

Analisi di un metodo per la discriminazione delle particelle neutre nell'ambito dell'esperimento FOOT

L'adroterapia è una delle tecniche utilizzate ad oggi per trattare i tumori ed è basata sull'utilizzo di fasci di particelle cariche, come protoni e ioni carbonio, accelerati sulla zona da trattare. A differenza dei fotoni, utilizzati in radioterapia, le particelle cariche permettono un rilascio di energia più mirato, danneggiando il DNA delle cellule tumorali fino ad impedirne la duplicazione, senza intaccare i tessuti sani circostanti. Per sfruttare al meglio questa tecnica è necessario conoscere a fondo i processi di frammentazione nucleare che possono avere luogo durante il trattamento, sui quali si hanno ancora insufficienti dati sperimentali, in particolare a proposito della frammentazione del bersaglio. L'esperimento FOOT (FragmentatiOn Of Target) nasce proprio per poter misurare le sezioni d'urto differenziali dei processi di frammentazione nucleare alle tipiche energie dell'adroterapia, dai 60 MeV/u ai 400 MeV/u. Allo stato attuale l'esperimento è dotato di un apparato per la rivelazione di frammenti carichi pesanti e uno per quelli leggeri, mentre non ha un sistema di rivelazione per le particelle neutre. Si sta quindi valutando la possibilità di aggiungere rivelatori di neutroni, per esempio gli scintillatori liquidi BC-501A, i quali permettono di discriminare fotoni da neutroni grazie alla diversa forma del segnale prodotto (Pulse Shape Discrimination). Per studiare le prestazioni di questi rivelatori, essi si stanno attualmente testando alla facility n_TOF del CERN con diverse sorgenti di particelle. In questo lavoro di tesi mi sono occupata di analizzare i segnali raccolti da due BC-501A con una sorgente AmBe di raggi γ e neutroni, con schermo in piombo, e con una sorgente 88Y di soli raggi γ, evidenziando le buone capacità di questi rivelatori di identificare correttamente neutroni e fotoni.

Analysis of fragmentation cross sections of GSI 2021 data for the FOOT experiment

Hadrontherapy is a medical treatment based on the use of charged particles beams accelerated towards deep-seated tumors on clinical patients. The reason why it is increasingly used is the favorable depth dose profile following the Bragg Peak distribution, where the release of dose is almost sharply focused near the end of the beam path. However, nuclear interactions between the beam and the human body constituents occur, generating nuclear fragments which modify the dose profile. To overcome the lack of experimental data on nuclear fragmentation reactions in the energy range of hadrontherapy interest, the FOOT (FragmentatiOn Of Target) experiment has been conceived with the main aim of measuring differential nuclear fragmentation cross sections with an uncertainty lower than 5\%. The same results are of great interest also in the radioprotection field, studying similar processes. Long-term human missions outside the Earth’s orbit are going to be planned in the next years, among which the NASA foreseen travel to Mars, and it is fundamental to protect astronauts health and electronics from radiation exposure .\\ In this thesis, a first analysis of the data taken at the GSI with a beam of $^{16}O$ at 400 $MeV/u$ impinging on a target of graphite ($C$) will be presented, showing the first preliminary results of elemental cross section and angular differential cross section. A Monte Carlo dataset was first studied to test the performance of the tracking reconstruction algorithm and to check the reliability of the full analysis chain, from hit reconstruction to cross section measurement. An high agreement was found between generated and reconstructed fragments, thus validating the adopted procedure. A preliminary experimental cross section was measured and compared with MC results, highlighting a good consistency for all the fragments.

Impact Of Pregabalin Treatment On Synaptic Plasticity And Glial Reactivity During The Course Of Experimental Autoimmune Encephalomyelitis.

Multiple sclerosis (MS) is an autoimmune and neurodegenerative disease that affects young adults. It is characterized by generating a chronic demyelinating autoimmune inflammation in the central nervous system. An experimental model for studying MS is the experimental autoimmune encephalomyelitis (EAE), induced by immunization with antigenic proteins from myelin. The present study investigated the evolution of EAE in pregabalin treated animals up to the remission phase. The results demonstrated a delay in the onset of the disease with statistical differences at the 10th and the 16th day after immunization. Additionally, the walking track test (CatWalk) was used to evaluate different parameters related to motor function. Although no difference between groups was obtained for the foot print pressure, the regularity index was improved post treatment, indicating a better motor coordination. The immunohistochemical analysis of putative synapse preservation and glial reactivity revealed that pregabalin treatment improved the overall morphology of the spinal cord. A preservation of circuits was depicted and the glial reaction was downregulated during the course of the disease. qRT-PCR data did not show immunomodulatory effects of pregabalin, indicating that the positive effects were restricted to the CNS environment. Overall, the present data indicate that pregabalin is efficient for reducing the seriousness of EAE, delaying its course as well as reducing synaptic loss and astroglial reaction.

Characterization Of Cumulative Joint Damage Patterns In Patients With Rheumatoid Arthritis: A Clinical, Serological, And Gene Polymorphism Perspective.

To characterize cumulative joint damage (CJD) patterns in rheumatoid arthritis (RA) and determine their associations with demographic/clinical features and HLA-DRB1 gene polymorphism. Hand and foot radiographs were obtained from 404 patients with RA. CJD patterns were determined by 3 derivations from Sharp/van der Heijde scores, obtained by the mathematical division of scores for hands/feet (Sharp-h/f score), fingers/wrists (Sharp-f/w score), and erosion/space narrowing (Sharp-e/sn score), respectively. DNA and serum were obtained for determination of HLA-DRB1 polymorphism, rheumatoid factor (RF), and anticitrullinated protein antibodies (ACPA). Patients with wrist-dominant CJD pattern were more likely to have severe RA than those with finger-dominant pattern (68.4% vs 46.0%; p = 0.036) as were those with foot-dominant vs hand-dominant CJD pattern (76.5% vs 56.4%; p = 0.044). HLA-DRB1 shared epitope (SE) alleles were associated with erosion-dominant CJD pattern (p = 0.021). Patients with erosion-dominant CJD pattern had higher levels of RF and ACPA than those with space-narrowing-dominant CJD pattern (median RF 71.35 U/ml vs 22.05 U/ml, respectively; p = 0.003; median ACPA 187.9 U/ml vs 143.2 U/ml, respectively; p < 0.001). The majority of triple-positive patients (SE+, RF+, ACPA+) had erosion-dominant CJD pattern (62.3%) while the majority of triple-negative patients (SE-, FR-, ACPA-) had space narrowing-dominant CJD pattern (75%; p = 0.017). ACPA was associated with HLA-DRB1 SE alleles (p < 0.05). Patients with foot-dominant CJD pattern were taller than those with hand-dominant CJD pattern (p = 0.002); those with erosion-dominant CJD pattern had higher weight and body mass index than those with space narrowing-dominant CJD pattern (p = 0.014, p = 0.001). CJD patterns were associated with disease severity, HLA-DRB1 SE status, presence and titer of ACPA and RF, and morphometric features.

Reduced Lrp6 Expression And Increase In The Interaction Of Gsk3β With P53 Contribute To Podocyte Apoptosis In Diabetes Mellitus And Are Prevented By Green Tea.

In diabetes mellitus (DM), podocyte apoptosis leads to albuminuria and nephropathy progression. Low-density lipoprotein receptor-related protein 6 (LRP6) is WNT pathway receptor that is involved in podocyte death, adhesion and motility. Glycogen synthase kinase 3 (GSK3) interaction with p53 (GSK3-p53) promotes apoptosis in carcinoma cells. It is unknown if GSK3-p53 contributes to podocyte apoptosis in DM. In experimental DM, green tea (GT) reduces albuminuria by an unknown mechanism. In the present study, we assessed the role of the GSK3β-p53 in podocyte apoptosis and the effects of GT on these abnormalities. In diabetic spontaneously hypertensive rats (SHRs), GT prevents podocyte's p-LRP6 expression reduction, increased GSK3β-p53 and high p53 levels. In diabetic SHR rats, GT reduces podocyte apoptosis, foot process effacement and albuminuria. In immortalized mouse podocytes (iMPs), high glucose (HG), silencing RNA (siRNA) or blocking LRP6 (DKK-1) reduced p-LRP6 expression, leading to high GSK3β-p53, p53 expression, apoptosis and increased albumin influx. GSK3β blockade by BIO reduced GSK3β-p53 and podocyte apoptosis. In iMPs under HG, GT reduced apoptosis and the albumin influx by blocking GSK3β-p53 following the rise in p-LRP6 expression. These effects of GT were prevented by LRP6 siRNA or DKK-1. In conclusion, in DM, WNT inhibition, via LRP6, increases GSK3β-p53 and podocyte apoptosis. Maneuvers that inactivate GSK3β-p53, such as GT, may be renoprotective in DM.