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With the advancement of 3-dimensionally (3D) printing technology, orthodontists can design and fabricate 3D-printed indirect bonding trays and transfer jigs for lingual brackets independently from the laboratory. The present article describes, in detail, the digital workflows for designing and fabricating 3D-printed lingual bracket indirect bonding trays and transfer jigs. Additionally, it aims to demonstrate the effectiveness of this approach in managing common orthodontic issues in adult patients. The first case report exemplifies the successful management of moderate crowding in a Class I adult patient using a non-extraction approach with lingual brackets and flexible 3D-printed indirect bonding trays. The second case illustrates the application of lingual brackets and rigid 3D-printed indirect bonding trays in managing a skeletal Class II adult patient with mouth protrusion requiring four-bicuspid extractions. The achieved good treatment results might demonstrate the high transfer accuracy of 3D-printed lingual bracket indirect bonding trays. Additional studies with large sample sizes should be conducted to compare the effectiveness and efficiency of 3D-printed trays with other tray types.
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The leading cause of vision loss globally is diabetic retinopathy. Researchers are making great efforts to automatically detect and diagnose correctly diabetic retinopathy. Diabetic retinopathy includes five stages: no diabetic retinopathy, mild diabetic retinopathy, moderate diabetic retinopathy, severe diabetic retinopathy and proliferative diabetic retinopathy. Recent studies have offered several multi-tasking deep learning models to detect and assess the level of diabetic retinopathy. However, the explanation for the assessment of disease severity of these models is limited, and only stops at showing lesions through images. These studies have not explained on what basis the appraisal of disease severity is based. In this article, we present a system for assessing and interpreting the five stages of diabetic retinopathy. The proposed system is built from internal models including a deep learning model that detects lesions and an explanatory model that assesses disease stage. The deep learning model that detects lesions uses the Mask R-CNN deep learning network to specify the location and shape of the lesion and classify the lesion types. This model is a combination of two networks: one used to detect hemorrhagic and exudative lesions, and one used to detect vascular lesions like aneurysm and proliferation. The explanatory model appraises disease severity based on the severity of each type of lesion and the association between types. The severity of the disease will be decided by the model based on the number of lesions, the density and the area of the lesions. The experimental results on real-world datasets show that our proposed method achieves high accuracy of assessing five stages of diabetic retinopathy comparable to existing state-of-the-art methods and is capable of explaining the causes of disease severity.
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Progress toward Sustainable Development Goals for global access to safe sanitation is lagging significantly. In this Feature, we propose that misleading terminology leads to errors of categorization and hinders progress toward sanitation service provision in urban areas. Binary classifications such as "offsite/onsite" and "sewered/nonsewered" do not capture the need for "transport to treatment" or the complexity of urban sanitation and should be discarded. "Fecal sludge management" is used only in the development context of low- or middle-income countries, implying separate solutions for "poor" or "southern" contexts, which is unhelpful. Terminology alone does not solve problems, but rather than using outdated or "special" terminology, we argue that a robust terminology that is globally relevant across low-, middle-, and upper-income contexts is required to overcome increasingly unhelpful assumptions and stereotypes. The use of accurate, technically robust vocabulary and definitions can improve decisions about management and selection of treatment, promote a circular economy, provide a basis for evidence-based science and technology research, and lead to critical shifts and transformations to set policy goals around truly safely managed sanitation. In this Feature, the three current modes of sanitation are defined, examples of misconceptions based on existing terminology are presented, and a new terminology for collection and conveyance is proposed: (I) fully road transported, (II) source-separated mixed transport, (III) mixed transport, and (IV) fully pipe transported.
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Saneamento , Esgotos , FezesRESUMO
Predictive models, based upon epidemiological principles and fitted to surveillance data, play an increasingly important role in shaping regulatory and operational policies for emerging outbreaks. Data for parameterising these strategically important models are often scarce when rapid actions are required to change the course of an epidemic invading a new region. We introduce and test a flexible epidemiological framework for landscape-scale disease management of an emerging vector-borne pathogen for use with endemic and invading vector populations. We use the framework to analyse and predict the spread of Huanglongbing disease or citrus greening in the U.S. We estimate epidemiological parameters using survey data from one region (Texas) and show how to transfer and test parameters to construct predictive spatio-temporal models for another region (California). The models are used to screen effective coordinated and reactive management strategies for different regions.
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Citrus , Epidemias , Doenças das Plantas/prevenção & controle , Surtos de DoençasRESUMO
This study evaluated the experience of implementing water safety plans (WSPs) in Vietnam. WSPs were introduced in Vietnam by the World Health Organization (WHO) in collaboration with the Ministry of Construction in 2006 and have been a mandatory requirement for municipal water supplies since 2012. Using a mixed-methods approach, we collected data on the perceived benefits and challenges of WSP implementation from 23 provincial water companies between August and November 2021. Potential public health benefits of improved water quality were a key motivation; 87% of the water utilities were also motivated by the risk of climate change and prepared response plans to climate-related extreme events as part of WSPs. A decrease in E. coli and an improvement in disinfectant residual in treated water were reported by 61 and 83% of the water supplies, respectively. Sixty-five percent of the water supplies also reported improved revenue and cost recovery. Key barriers to WSP implementation were a lack of WSP guidance suitable for the local context (87%) and insufficient funds for WSP implementation (43%). Our study highlights the need for improved support and capacity building along with locally suited guidance on WSP implementation and audit.
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Escherichia coli , Abastecimento de Água , Vietnã , Qualidade da Água , Saúde PúblicaRESUMO
Pit latrines are used by billions of people globally, often in developing countries where they provide a low-tech and low-cost sanitation method. However, health and social problems can arise from a lack of emptying or maintenance of these facilities. A better understanding of the biological and environmental parameters within pit latrines could inform attempts to enhance material decomposition rates, and therefore slow fill-up rate. In this study, we have performed a spatial analysis of 35 Tanzanian pit latrines to identify bacteria and environmental factors that are associated with faster or slower pit latrine fill-up rates. Using ordination of microbial community data, we observed a linear gradient in terms of beta diversity with increasing pit latrine sample depth, corresponding to a shift in microbial community structure from gut-associated families in the top layer to environmental- and wastewater-associated taxa at greater depths. We also investigated the bacteria and environmental parameters associated with fill-up rates, and identified pH, volatile solids, and volatile fatty acids as features strongly positively correlated with pit latrine fill-up rates, whereas phosphate was strongly negatively correlated with fill-up rate. A number of pit latrine microbiota taxa were also correlated with fill-up rates. Using a multivariate regression, we identified the Lactobacillaceae and Incertae_Sedis_XIII taxa as particularly strongly positively and negatively correlated with fill-up rate, respectively. This study therefore increases knowledge of the microbiota within pit latrines, and identifies potentially important bacteria and environmental variables associated with fill-up rates. These new insights may be useful for future studies investigating the decomposition process within pit latrines.
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The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global health concern. The development of vaccines with high immunogenicity and safety is crucial for controlling the global COVID-19 pandemic and preventing further illness and fatalities. Here, we report the development of a SARS-CoV-2 vaccine candidate, Nanocovax, based on recombinant protein production of the extracellular (soluble) portion of the spike (S) protein of SARS-CoV-2. The results showed that Nanocovax induced high levels of S protein-specific IgG and neutralizing antibodies in three animal models: BALB/c mouse, Syrian hamster, and a non-human primate (Macaca leonina). In addition, a viral challenge study using the hamster model showed that Nanocovax protected the upper respiratory tract from SARS-CoV-2 infection. Nanocovax did not induce any adverse effects in mice (Mus musculus var. albino) and rats (Rattus norvegicus). These preclinical results indicate that Nanocovax is safe and effective.
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Vacinas contra COVID-19/imunologia , Vacinas contra COVID-19/toxicidade , COVID-19/prevenção & controle , Imunogenicidade da Vacina/imunologia , Glicoproteína da Espícula de Coronavírus/imunologia , Animais , Anticorpos Neutralizantes/imunologia , Anticorpos Antivirais/imunologia , Cricetinae , Macaca , Camundongos , Ratos , SARS-CoV-2 , Vacinas Sintéticas/imunologia , Vacinas Sintéticas/toxicidadeRESUMO
Background: Little is known about video-assisted thoracoscopic surgery in the Nuss procedure (VATS-NUSS) and its postoperative outcomes in the resource-scarce conditions in clinical practice such as Vietnam. Available evidence in the literature was mostly reported from large institutions in developed countries. Hence, this study was conducted to review our initial large single-center experience in the use of the VATS-NUSS for patients with pectus excavatum (PE) within 5 years. Methods: Data from 365 consecutive PE patients between January 2015 and December 2019 who were surgically treated with VATS-NUSS were retrospectively analyzed. Results: Of 365 patients, median age at operation was 15.61 ± 3.73 years (range = 5-27 years), most being child and adolescent. Three hundred nine patients (84.65%) were male. PE was commonly detected at puberty (n = 328, 89.9%). Postoperatively, early complications consisted of pneumothorax (n = 5, 1.37%), pleural bleeding/pleural fluid (n = 2, 0.55%), pleural hematoma (n = 1, 0.27%), pneumonia (n = 1, 0.27%), surgical wound infection (n = 1, 0.27%), incision fluid accumulation (n = 3, 0.82%), metal bar infection (n = 1, 0.27%), atelectasis (n = 3, 0.82%), and fever (n = 8, 2.19%). Late complications included surgical wound infection (n = 2, 0.55%), metal bar deviation (n = 5, 1.37%), metal bar allergy (n = 10, 2.74%), recurrent PE (n = 2, 0.55%), and persistent PE (n = 5, 1.37%). No deaths occurred. In 175 patients (47.95%) experiencing bar removal, mean operative time for bar removal was 34.09 ± 10.61 min, and the length of hospitalization following bar removal was 2.4 ± 1.34 days; the most frequent complication was pneumothorax (n = 19, 10.85%). One wound infection and one incision fluid accumulation happened following bar removal. Favorable midterm to long-term postoperative outcomes were achieved. Conclusions: From the beginning of the Vietnamese surgeons' experience, VATS-NUSS application obtained favorable outcomes with minimizing the occurrence of serious intraoperative and postoperative complications. Current rare evidence enables to give a real picture in the application, modification, and development of VATS-NUSS in the countries having similar resource-scarce conditions.
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This study assessed the performance of rainwater-harvesting systems installed for selected public utilities in the northern provinces of Vietnam where rainwater was collected, stored in stainless steel tanks, and treated with a complex filtration unit and Ultraviolet (UV) disinfection system (full system). Results from an operation of over 5 years show that the untreated rainwater could not be used directly for drinking purposes as it was contaminated with bacteria (total coliforms TC = 200-300 CFU/100 ml, Pseudomonas aeruginosa PA = 40-160 CFU/100 ml), and turbidity = 2-4 NTU. Most of the heavy metals detected were found below the standard limits. Phenol and its derivatives were detected occasionally as higher than the standard value (1 µg/L). After treatment, all parameters met the drinking water standards. The capital costs of the rainwater systems were approximately US$200/m3 and US$180/m3 for a full system and simplified system (without complex filtration unit), respectively, while the operation and maintenance (O&M) costs were 3 cents/L and 0.8 cents/L on average for a full system and simplified one, correspondingly.
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Água Potável , Desinfecção , Chuva , Vietnã , Abastecimento de ÁguaRESUMO
This case report describes the lingual orthodontic treatment of an adult patient with Angle Class I malocclusion, agenesis of mandibular right central incisor, severe overjet and deep overbite, excessive proclination of maxillary and mandibular incisors, and midline discrepancy. Because of unique presentation, symmetric extraction could not be performed in the lower arch of this 34-year-old patient. She was treated with three premolar extractions and absolute anchorage with temporary anchorage devices for maximum retraction of upper anterior teeth. To correct the midline deviation and Bolton tooth-size discrepancy, the mandibular right lateral incisor, canine, and premolars were reshaped to reduce the mesiodistal width. The treatment approach greatly improved the patient's facial and dental appearance and provided a stable occlusion.
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Anodontia/complicações , Incisivo/anormalidades , Má Oclusão Classe I de Angle/complicações , Má Oclusão Classe I de Angle/terapia , Sobremordida/complicações , Sobremordida/terapia , Adulto , Dente Pré-Molar/cirurgia , Estética Dentária , Feminino , Humanos , Contenções Ortodônticas , Fios Ortodônticos , Extração Dentária , Técnicas de Movimentação DentáriaRESUMO
The bacterial type VI secretion system (T6SS) is a macromolecular machine that injects effectors into prokaryotic and eukaryotic cells. The mode of action of the T6SS is similar to contractile phages: the contraction of a sheath structure pushes a tube topped by a spike into target cells. Effectors are loaded onto the spike or confined into the tube. In enteroaggregative Escherichia coli, the Tle1 phospholipase binds the C-terminal extension of the VgrG trimeric spike. Here, we purify the VgrG-Tle1 complex and show that a VgrG trimer binds three Tle1 monomers and inhibits their activity. Using covalent cross-linking coupled to high-resolution mass spectrometry, we provide information on the sites of contact and further identify the requirement for a Tle1 N-terminal secretion sequence in complex formation. Finally, we report the 2.6-Å-resolution cryo-electron microscopy tri-dimensional structure of the (VgrG)3 -(Tle1)3 complex revealing how the effector binds its cargo, and how VgrG inhibits Tle1 phospholipase activity. The inhibition of Tle1 phospholipase activity once bound to VgrG suggests that Tle1 dissociation from VgrG is required upon delivery.
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Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Fosfolipases/metabolismo , Sistemas de Secreção Tipo VI/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Fosfolipases/genética , Sistemas de Secreção Tipo VI/genéticaRESUMO
The importance of faecal sludge management is gaining recognition. However, methods are still lacking to reasonably estimate the quantities and qualities (Q&Q) that need to be managed, which makes the planning for and implementing of management solutions quite difficult. The objective of this study was to collect and analyse Q&Q of faecal sludge at a citywide scale, and to evaluate whether "SPA-DET" data (=> spatially analysable - demographic, environmental and technical) could then be used as predictors of Q&Q of faecal sludge. 60 field samples and questionnaires from Hanoi and 180 from Kampala were analysed. Software tools were used in an iterative process to predict total solids (TS) and emptying frequency in both Hanoi, Vietnam and Kampala, Uganda. City-specific data could be predicted with types of "SPA-DET" data as input variables, and model performance was improved by analysing septic tanks and pit latrines separately. Individual models were built for TS concentrations and emptying frequency. In addition, a model was built across both cities for emptying frequency of septic tanks based on number of users and containment volume, indicating predictive models can be relevant for multiple cities. Number of users, containment volume, truck volume and income level were identified as the most common variables for the correction function. Results confirm the high intrinsic variability of faecal sludge characteristics, and illustrate the importance of moving beyond simple reporting of city-wide average values for estimations of Q&Q. The collected data and developed scripts have been made available for replication in future studies.
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Saneamento , Esgotos , Cidades , Uganda , VietnãRESUMO
High-quality meso/micropore-controlled hierarchical porous carbon (HPC) was synthesized by a hard template method utilizing rice husk biochar and then used to adsorb copper ions from an aqueous solution. The preparation procedure included two main steps: base leaching and physicochemical activation. During the activation process, the porosity characteristics (i.e., specific surface area and meso/micropore ratio) were controlled by altering the KOH impregnation ratio, activation time, and temperature under the CO2 atmosphere. In addition, a copper adsorption study was performed using three HPC samples with different pore structures and characteristics. The results of this study indicate that the adsorption capacity of HPC material derived from rice husk biochar is strongly influenced by its meso/micropore ratio. As evidenced, HPC 3-0.5-800, which was impregnated by a KOH:biochar ratio of 3 and activated at 800°C for 0.5h under a CO2 atmosphere, has a very high specific surface area of 2330 m2g-1 with an 81% mesopore to total specific surface area. Importantly, it exhibited a superior adsorption capacity of 265mgg-1 and rapid adsorption kinetics for copper ions. The improvement is ascribed to the high specific surface area and favorable hierarchical structure. The findings demonstrate the feasibility of controlling the hierarchical pore structure of rice husk biochar-derived carbons as high-performance adsorbents for copper ion removal from water.
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Carvão Vegetal/química , Cobre/análise , Eliminação de Resíduos Líquidos/métodos , Poluentes Químicos da Água/análise , Purificação da Água/métodos , Adsorção , Hidróxidos/química , Cinética , Oryza/química , Porosidade , Compostos de Potássio/química , Eliminação de Resíduos Líquidos/instrumentação , Purificação da Água/instrumentaçãoRESUMO
This paper presents the design of a constructed wetland (CW) system in an area with limited land availability, resulting in high hydraulic loads. The CW was constructed to act as a buffering/ polishing step after stabilization ponds for steel industry wastewater post-treatment. A pilot test with two different filter media (50-100mm vs 40-60mm diameter) indicated that a flow rate increase from 49.5 m3/h to 122.4 m3/h would lead to a head loss increase from 2.9cm to 8.7cm, and more than double that for the finer gravel. This was substantially higher than the calculated theoretical values, though the relation with flow rate was similar. Four full scale wetland cells (CW1, CW2, CW3 and CW4) were constructed using the coarser gravel. A design value of total head loss of 1.01m over the total system length, with a design flow of 36,000 m3/day, was expected based on pilot test results. During the first operation year (September 2017 to July 2018), the pond-CW system has received wastewater already meeting required discharge standards. The effluent from the CWs had consistently lower concentrations of all measured variables, and met the predicted values for biochemical oxygen demand (BOD5), total nitrogen (TN) and NH4 +-N. Highest removal efficiencies were achieved for NH4 +-N (>90%), Mn (>60%) and Fe (45%) with removal efficiencies for TN (14%), BOD5 and chemical oxygen demand (COD) (around 30%). Concentrations of phenol, CN- and Cr6+ were below 10, 4 and 3µg/l, respectively, in in- and outflows. An appreciated benefit of the wetland was the 'green element' in the industrial landscape.
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Aço , Eliminação de Resíduos Líquidos/métodos , Águas Residuárias , Áreas Alagadas , Análise da Demanda Biológica de Oxigênio , Metalurgia , NitrogênioRESUMO
BACKGROUND: After levelling and alignment in skeletal Class III patients with upper anterior crowding, the upper incisors usually have excessive proclination. In these cases, the upper incisors' axial proclination need to be reduced to improve esthetics. CASE REPORT: This case report presents an invisible orthodontic treatment of a 24-year-old adult female patient with skeletal Class III relationship, anterior crossbite, proclined upper incisors, and reduced incisor showing. Patients denied extraction and interproximal reduction. With multi-slotted lingual brackets and straight archwires, we applied lingual crown torque to upper anterior teeth to reduce axial proclination. The resulting uprighted position of upper incisors led to increased incisor showing. A good smile and stable occlusion were obtained after 15 months of active treatment. CONCLUSION: The use of lingual brackets to apply lingual crown torque helps to reduce axial proclination and increasing upper incisor showing without interproximal reduction nor extraction in skeletal Class III patients with upper anterior crowding.
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Dewatering of faecal sludge (FS) is indispensable for adequate FS management. However, comprehensive knowledge is lacking on FS dewatering performance. This study compared the dewatering performance of FS from different countries and onsite sanitation technologies, to assess influential characteristics on dewatering, and to compare dewatering performance of FS with wastewater sludge. We collected 73 FS samples from septic tanks, lined pit latrines, unlined pit latrines and johkasou tanks in Uganda, Vietnam and Japan, and 18 samples of wastewater sludge in Switzerland. Capillary suction time (CST) and total solids (TS) of centrifuged sludge (%TSfinal) were determined as metrics of dewatering rate and dewaterability, respectively, together with relevant sludge characteristics. Data were analysed by bootstrapping comparison of median results of each sample category and by bootstrapping multiple regression analysis to quantify the relative importance of sludge characteristics on dewatering performance. Results showed that the dewatering rate was significantly different between FS from different technologies, whereas dewaterability was significantly different within the same technology. FS had a significantly lower dewatering rate than wastewater sludge. In contrast, FS dewaterability was greater than wastewater sludge. However, this could be attributed to higher concentrations of sand in FS. Electrochemical properties such as NH4-N and surface charge had the strongest correlation to dewatering rate, and solid properties such as sand content and total volatile solids to dewaterability. The results identify potential characteristics that could explain and predict the high variability of FS dewatering performance that is observed in the field.
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Esgotos , Águas Residuárias , Japão , Uganda , VietnãRESUMO
Improving the rate and extent of faecal decomposition in basic forms of sanitation such as pit latrines would benefit around 1.7 billion users worldwide, but to do so requires a major advance in our understanding of the biology of these systems. As a critical first step, bacterial diversity and composition was studied in 30 latrines in Tanzania and Vietnam using pyrosequencing of 16S rRNA genes, and correlated with a number of intrinsic environmental factors such as pH, temperature, organic matter content/composition and geographical factors. Clear differences were observed at the operational taxonomic unit, family and phylum level in terms of richness and community composition between latrines in Tanzania and Vietnam. The results also clearly show that environmental variables, particularly substrate type and availability, can exert a strong structuring influence on bacterial communities in latrines from both countries. The origins and significance of these environmental differences are discussed. This work describes the bacterial ecology of pit latrines in combination with inherent latrine characteristics at an unprecedented level of detail. As such, it provides useful baseline information for future studies that aim to understand the factors that affect decomposition rates in pit latrines.
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Bactérias/classificação , Bactérias/genética , Biota , Microbiologia Ambiental , Fezes/microbiologia , Banheiros , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Exposição Ambiental , Geografia , Concentração de Íons de Hidrogênio , Compostos Orgânicos/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tanzânia , Temperatura , VietnãRESUMO
BACKGROUND: The role that hands play in the transmission of Ascaris is not well understood. METHODS: A newly developed method to quantify the presence helminth eggs on hands was tested among a group of farmers in Vietnam. High turbidity in hand rinse samples meant that the adopted sugar solution had to be replaced by zinc sulphate as a flotation solution. RESULTS: The survey found 34% (31/90) of study participant hands' were positive for helminth eggs, though concentrations were low and ranged from 0-10 eggs/2 hands. The use of fresh excreta in agriculture was the only variable that showed an association with the concentrations of eggs found on hands. CONCLUSIONS: The results highlight the need to promote handwashing with soap to prevent the transmission of soil-transmitted helminth infections.
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Doenças dos Trabalhadores Agrícolas/parasitologia , Mãos/parasitologia , Helmintíase/transmissão , Helmintos/isolamento & purificação , Óvulo , Adulto , Animais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Contagem de Ovos de Parasitas , Características de Residência , Fatores de Risco , População Rural , VietnãRESUMO
BACKGROUND: Type 2 diabetes mellitus (T2D) is a common age-related disease, and is a major health concern, particularly in developed countries where the population is aging, including Europe. The multi-scale immune system simulator for the onset of type 2 diabetes (MISSION-T2D) is a European Union-funded project that aims to develop and validate an integrated, multilevel, and patient-specific model, incorporating genetic, metabolic, and nutritional data for the simulation and prediction of metabolic and inflammatory processes in the onset and progression of T2D. The project will ultimately provide a tool for diagnosis and clinical decision making that can estimate the risk of developing T2D and predict its progression in response to possible therapies. Recent data showed that T2D and its complications, specifically in the heart, kidney, retina, and feet, should be considered a systemic disease that is sustained by a pervasive, metabolically-driven state of inflammation. Accordingly, there is an urgent need (1) to understand the complex mechanisms underpinning the onset of this disease, and (2) to identify early patient-specific diagnostic parameters and related inflammatory indicators. OBJECTIVE: We aim to accomplish this mission by setting up a multi-scale model to study the systemic interactions of the biological mechanisms involved in response to a variety of nutritional and metabolic stimuli and stressors. METHODS: Specifically, we will be studying the biological mechanisms of immunological/inflammatory processes, energy intake/expenditure ratio, and cell cycle rate. The overall architecture of the model will exploit an already established immune system simulator as well as several discrete and continuous mathematical methods for modeling of the processes critically involved in the onset and progression of T2D. We aim to validate the predictions of our models using actual biological and clinical data. RESULTS: This study was initiated in March 2013 and is expected to be completed by February 2016. CONCLUSIONS: MISSION-T2D aims to pave the way for translating validated multilevel immune-metabolic models into the clinical setting of T2D. This approach will eventually generate predictive biomarkers for this disease from the integration of clinical data with metabolic, nutritional, immune/inflammatory, genetic, and gut microbiota profiles. Eventually, it should prove possible to translate these into cost-effective and mobile-based diagnostic tools.
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A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.