Influence of reconstruction parameters for FBP in semiquantification of brain studies with 123I-FPCIT

Brain dopamine transporters imaging by Single Photon Emission Tomography (SPECT) with 123I-FP-CIT has become an important tool in the diagnosis and evaluation of parkinsonian syndromes, since this radiopharmaceutical exhibits high affinity for membrane transporters responsible for cellular reabsorption of dopamine on the striatum. However, Ordered Subset Expectation Maximization (OSEM) is the method recommended in the literature for imaging reconstruction. Filtered Back Projection (FBP) is still used due to its fast processing, even if it presents some disadvantages. The aim of this work is to investigate the influence of reconstruction parameters for FBP in semiquantification of Brain Studies with 123I-FPCIT compared with those obtained with OSEM recommended reconstruction.

Paleoambiental reconstruction based on mineralogical data of quaternary littoral deposits occuring at Cortegaça and Maceda beaches (Ovar, Portugal)

The main goal of the present work is the use of mineralogical data corresponding to sediment fine fractions (silt and clay) of Quaternary littoral deposits for the definition of a more detailed vertical zonography and to discriminate the most significant morphoclimatic changes concerned with sediment source areas and sediment deposition areas. The analysis of the available mineralogical data reveals a vertical evolution of the mineral composition. The following aspects deserve particular reference: 1) fine fractions (<38 nm) are composed of quartz and phyllosilicates associated to feldspars, prevailing over other minerals; however in certain sections iron hydroxides and evaporitic minerals occur in significant amounts; 2) clay fractions (<2 nm) show a general prevalence of illite associated with kaolinite and oscillations, in relative terms, of kaolinite and illite contents. Qualitative and quantitative lateral and vertical variations of clay and non clay minerals allow the discrimination of sedimentary sequences and the establishment of the ritmicity and periodicity of the morphoclimatic Quaternary episodes that occurred in the Cortegaça and Maceda beaches. To each one of the sedimentary sequences corresponds, in a first stage, a littoral environment that increasingly became more continental. Climate would be mild to cold, sometimes with humidity - aridity oscillations. Warmer and moister episodes alternated with cooler and dryer ones.

Upper Eyelid Reconstruction With a Horizontal V-Y Myotarsocutaneous Advancement Flap

Upper eyelid tumours, particularly basal cell carcinomas, are relatively frequent. Surgical ablation of these lesions creates defects of variable complexity. Although several options are available for lower eyelid reconstruction, fewer surgical alternatives exist for upper eyelid reconstruction. Large defects of this region are usually reconstructed with two-step procedures. In 1997, Okada et al. described a horizontal V-Y myotarsocutaneous advancement flap for reconstruction of a large upper eyelid defect in a single operative time. However, no further studies were published regarding the use of this particular flap in upper eyelid reconstruction. In addition, this flap is not described in most plastic surgery textbooks. The authors report here their experience of 16 cases of horizontal V-Y myotarsocutaneous advancement flaps used to reconstruct full-thickness defects of the upper eyelid after tumour excision. The tumour histological types were as follows: 12 basal cell carcinomas, 2 cases of squamous cell carcinomas, 1 case of sebaceous cell carcinoma and 1 of malignant melanoma. This technique allowed closure of defects of up to 60% of the eyelid width. None of the flaps suffered necrosis. The mean operative time was 30 min. No additional procedures were necessary as good functional and cosmetic results were achieved in all cases. No recurrences were noted. In this series, the horizontal V-Y myotarsocutaneous advancement flap proved to be a technically simple, reliable and expeditious option for reconstruction of full-thickness upper eyelid defects (as wide as 60% of the eyelid width) in a single operative procedure. In the future this technique may become the preferential option for such defects.

Reconstruction of Large Defect of Foot with Extensive Bone Loss Exclusively Using a Latissimus Dorsi Muscle Free Flap: a Potential New Indication for this Flap

In cases of extensive damage to the foot, with significant bone loss, it is generally accepted that reconstruction must include bone flaps or grafts either in the emergency setting or subsequently. In this report, we describe the case of an 18-year-old student with an avulsion injury of the dorsum of his right foot. Consequently, he lost most of the soft tissue over the dorsum of the foot and the cuboid, navicular, and cuneiform bones. A latissimus dorsi free flap was used to reconstruct the defect. A functional pseudoarthrosis developed between the remaining bones of the foot, and the patient experienced satisfactory foot function after rehabilitation. For this reason, no additional reconstructive procedure was undertaken. This case suggests that it might be adequate to use the latissimus dorsi muscle flap more liberally than previously reported in the reconstruction of extensive defects of the dorsum of the foot, including cases with significant bone loss. This option could avoid the morbidity and inconvenience of a second surgery and the need to harvest a bone flap or graft.

Characterization and surface reconstruction of objects in tomographic images of composite materials

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Optimization of breast tomosynthesis image reconstruction using parallel computing

Breast cancer is the most common cancer among women, being a major public health problem. Worldwide, X-ray mammography is the current gold-standard for medical imaging of breast cancer. However, it has associated some well-known limitations. The false-negative rates, up to 66% in symptomatic women, and the false-positive rates, up to 60%, are a continued source of concern and debate. These drawbacks prompt the development of other imaging techniques for breast cancer detection, in which Digital Breast Tomosynthesis (DBT) is included. DBT is a 3D radiographic technique that reduces the obscuring effect of tissue overlap and appears to address both issues of false-negative and false-positive rates. The 3D images in DBT are only achieved through image reconstruction methods. These methods play an important role in a clinical setting since there is a need to implement a reconstruction process that is both accurate and fast. This dissertation deals with the optimization of iterative algorithms, with parallel computing through an implementation on Graphics Processing Units (GPUs) to make the 3D reconstruction faster using Compute Unified Device Architecture (CUDA). Iterative algorithms have shown to produce the highest quality DBT images, but since they are computationally intensive, their clinical use is currently rejected. These algorithms have the potential to reduce patient dose in DBT scans. A method of integrating CUDA in Interactive Data Language (IDL) is proposed in order to accelerate the DBT image reconstructions. This method has never been attempted before for DBT. In this work the system matrix calculation, the most computationally expensive part of iterative algorithms, is accelerated. A speedup of 1.6 is achieved proving the fact that GPUs can accelerate the IDL implementation.

Genome-scale metabolic network reconstruction of Polaromonas sp. strain JS666: analysis of cDCE degradation rates and design of experiments for bioremediation improvement

Release of chloroethene compounds into the environment often results in groundwater contamination, which puts people at risk of exposure by drinking contaminated water. cDCE (cis-1,2-dichloroethene) accumulation on subsurface environments is a common environmental problem due to stagnation and partial degradation of other precursor chloroethene species. Polaromonas sp. strain JS666 apparently requires no exotic growth factors to be used as a bioaugmentation agent for aerobic cDCE degradation. Although being the only suitable microorganism found capable of such, further studies are needed for improving the intrinsic bioremediation rates and fully comprehend the metabolic processes involved. In order to do so, a metabolic model, iJS666, was reconstructed from genome annotation and available bibliographic data. FVA (Flux Variability Analysis) and FBA (Flux Balance Analysis) techniques were used to satisfactory validate the predictive capabilities of the iJS666 model. The iJS666 model was able to predict biomass growth for different previously tested conditions, allowed to design key experiments which should be done for further model improvement and, also, produced viable predictions for the use of biostimulant metabolites in the cDCE biodegradation.

GEOCHEMISTRY AND GEOCHRONOLOGY OF SURFICIAL ACRE BASIN SEDIMENTS (WESTERN AMAZONIA): KEY INFORMATION FOR CLIMATE RECONSTRUCTION.

Geochemical and geochronological analyses of samples of surficial Acre Basin sediments and fossils indicate an extensive fluvial-lacustrine system, occupying this region, desiccated slowly during the last glacial cycle (LGC). This research documents direct evidence for aridity in western Amazonia during the LGC and is important in establishing boundary conditions for LGC climate models as well as in correlating marine and continental (LGC) climate conditions.

Genetic algorithm for shipping route estimation with long-range tracking data : automatic reconstruction of shipping routes based on the historical ship positions for maritime safety applications

Ship tracking systems allow Maritime Organizations that are concerned with the Safety at Sea to obtain information on the current location and route of merchant vessels. Thanks to Space technology in recent years the geographical coverage of the ship tracking platforms has increased significantly, from radar based near-shore traffic monitoring towards a worldwide picture of the maritime traffic situation. The long-range tracking systems currently in operations allow the storage of ship position data over many years: a valuable source of knowledge about the shipping routes between different ocean regions. The outcome of this Master project is a software prototype for the estimation of the most operated shipping route between any two geographical locations. The analysis is based on the historical ship positions acquired with long-range tracking systems. The proposed approach makes use of a Genetic Algorithm applied on a training set of relevant ship positions extracted from the long-term storage tracking database of the European Maritime Safety Agency (EMSA). The analysis of some representative shipping routes is presented and the quality of the results and their operational applications are assessed by a Maritime Safety expert.

The role of temporary accommodation buildings for post-disaster housing reconstruction

The number of houses damaged or destroyed after disasters is frequently large, and re-housing of homeless people is one of the most important tasks of reconstruction programmes. Reconstruction works often last long and during that time, it is essential to provide victims with the minimum conditions to live with dignity, privacy, and protection. This research intends to demonstrate the crucial role of temporary accommodation buildings to provide spaces where people can live and gradually resume their life until they have a permanent house. The study also aims to identify the main problems of temporary accommodation strategies and to discuss some principles and guidelines in order to reach better design solutions. It is found that temporary accommodation is an issue that goes beyond the simple provision of buildings, since the whole space for temporary settlement is important. Likewise, temporary accommodation is a process that should start before a disaster occurs, as a preventive pre-planning. In spite of being temporary constructions, these housing buildings are one of the most important elements to provide in emergency scenarios, contributing for better recovery and reconstruction actions.

Modeling microbes: New methods for integrated metabolic and regulatory network reconstruction

PhD Thesis in Bioengineering

Self-narrative reconstruction after dilemma-focused therapy for depression: a comparison of good and poor outcome cases

Objective: The aim of this study is to improve the understanding of self-changes after an intervention for depression focused on implicative dilemmas, a type of cognitive conflict related to identity. As recent research has highlighted the relevance of identity-related dilemmas in clients with depression, we sought to assess the way in which clients resolve such inner conflicts after a tailored dilemma-focused intervention and how this is reflected in the clients’ self-narratives. Method: We used three instruments to observe differences between good (n = 5) and poor (n = 5) outcome cases: (i) the Repertory Grid Technique to track the resolution of dilemmas, (ii) the Change Interview to compile clients’ accounts of changes at posttreatment, and (iii) the Innovative Moments Coding System to examine the emergence of clients’ novelties at the Change Interview. Results: Groups did not differ in terms of the number and relevance of client-identified significantly helpful events. However, between-group differences were found for the resolution of dilemmas and for the proportion of high-level innovative moment (IM) types. Furthermore, a greater self-narrative reconstruction was associated with higher levels of symptom improvement. Conclusions: Good outcome cases seem to be associated with the resolution of conflicts and high-level IMs.

Dynamic three-dimensional reconstruction of the heart by transesophageal echocardiography

OBJECTIVE: To evaluate echocardiography accuracy in performing and obtaining images for dynamical three-dimensional (3D) reconstruction. METHODS: Three-dimensional (3D) image reconstruction was obtained in 20 consecutive patients who underwent transesophageal echocardiography. A multiplanar 5 MHz transducer was used for 3D reconstruction. RESULTS: Twenty patients were studied consecutively. The following cardiac diseases were present: valvar prostheses-6 (2 mitral, 2 aortic and 2 mitral and aortic); mitral valve prolapse- 3; mitral and aortic disease - 2; aortic valve disease- 5; congenital heart disease- 3 (2 atrial septal defect- ASD - and 1 transposition of the great arteries -TGA); arteriovenous fistula- 1. In 7 patients, color Doppler was also obtained and used for 3D flow reconstruction. Twenty five cardiac structures were acquired and 60 reconstructions generated (28 of mitral valves, 14 of aortic valves, 4 of mitral prostheses, 7 of aortic prostheses and 7 of the ASD). Fifty five of 60 (91.6%) reconstructions were considered of good quality by 2 independent observers. The 11 reconstructed mitral valves/prostheses and the 2 reconstructed ASDs provided more anatomical information than two dimensional echocardiography (2DE) alone. CONCLUSION: 3D echocardiography using a transesophageal transducer is a feasible technique, which improves detection of anatomical details of cardiac structures, particularly of the mitral valve and atrial septum.

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2016.00275

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.