X-ray computed tomography of pipe sections by discrete tomography and total variation minimization

Inversio-ongelmien tutkimus on soveltavan matematiikan ala jossa tutkitaan tuntemattoman funktion palauttamista joukosta funtiosta tehtyjä mittauksia, jotka saattavat olla epätäydellisiä ja kohinaisia. Esimerkki käytännön sovelluskohteesta inversio- ongelmien alalla on röntgentomografia, missä yritetään nähdä jonkin kohteen sisäinen rakenne ottamalla useita röntgenprojektiokuvia eri puolilta tutkittavaa kohdetta. Tomografinen rekonstruktiotehtävä on erittäin huonosti asetettu ongelma Hadamardin määritelmän mukaan, mikäli käytettävissä on vain rajoitettu määrä projektiokuvia. Esimerkkejä rajoitetun datan tomografiasta ovat harvan kulman tomografia ja rajoitetun kulman tomografia. Harvan kulman tomografiassa projektioiden määrää on rajoitettu tutkittavan kohteen säteilyaltistuksen rajoittamiseksi tai kuvausprosessin nopeuttamiseksi, ja rajoitetun kulman tomografiassa projektioita on saatavilla vain tietystä kulmasta. Rajoitetun datan tomografiaan on esitetty monia algoritmeja, joista monet usein hyödyntävät ennalta tunnettua a priori- informaatiota tutkittavasta kohteesta. Tällaisia algoritmeja ovat totaalivariaatiominimointi ja diskreetin tomografian algoritmit, joita molempia tutkitaan tässä tutkielmassa. Totaalivariaatiominimoinnissa oletetaan että rekonstruoitavan kuvan totaalivariaatio on pieni. Diskreetin tomografian algoritmeissa oletetaan että kohdeobjekti koostuu rakenteeltaan homogeenisista materiaaleista, joita on vain rajoitettu määrä. Eräs modern diskreetin tomografian algoritmi on pehmeä diskreetti algebrallinen rekonstruktiomenelmä SDART. Tässä tutkielmassa tutkitaan ongelmaa, jossa tavoitteena on palauttaa metalliputken seinämän sisällä sijaitsevien alle millim etrin kokoluokkaa olevien aukkojen koko, muoto ja sijanti röntgentomografian keinoin. Tomografiset rekonstruktiot tehtiin sekä totaalivariaatiominimointimenetelmällä että SDART-algoritmilla, ja lisäksi yhdistelmällä molempia metodeja josta tässä tutkielmassa käytetään nimeä SDART-TV. Tutkimusongelma on peräisin teräsputkien hitsisaumojen laadun tutkimuksesta röntgenkuvantamisella. Hitsausprosessin aikana saumaan saattaa monista syistä syntyä poikkeamia, jotka vaikuttavat haitallisesti sauman kestävyyteen. Monissa teollisuuden sovelluksissa on tärkeää havaita sauman mahdolliset virheet. Putkihitsisaumojen röntgentutkimusta varten kehitettyjen laitteiden kanssa käytettävät röntgenilmaisimet saattavat olla pieniä verrattuna putken halkaisijaan, mikä johtaa vaikeaan rajoitetun kulman kuvausgeometriaan. Putken geometria myös toimii a priori-informaation lähteenä jota voidaan hyödyntää algoritmeissa, sillä putkia tutkiessa usein tiedetään että putken sisäosa on tyhjä. Totaalivariaatio- ja diskreetin tomografian algoritmien toimivuutta kuvatun ongelman ratkaisemisessa tutkittiin sekä laskennallisilla simulaatioilla että kokeilla fyysisellä alumiinisella testikappaleella. Kokeiden tulokset alustavasti vittaavat että modernit röntgentomografiset etukäteistietoa soveltavat algoritmit voivat soveltua putkihitsisaumojen ei-tuhoavaan testaukseen.The applied mathematical field of inverse problems studies how to recover an unknown function from a set of possibly incomplete and noisy observations. One example of practical, real-life inverse problem is X-ray tomography, where one wishes to recover the internal composition of an object by taking several X-ray projection images from different directions around the object. The tomographic inversion task is a severely ill-posed problem in Hadamard's sense if a limited amount of measurement data is available for the reconstruction. Two examples of limited data tomography are sparse tomography and limited angle tomography. In sparse tomography, tomographic projections are taken with a sparse angular sampling, either because one wishes to reduce the radiation exposure of the object or have a faster imaging process. In limited angle tomography, projections are available only from a limited angular range. The numerous algorithms that have been proposed for solving the tomographic problem with limited data are based on taking account a priori information about the object of interest. In this thesis we study two such algorithms, total variation minimization and discrete tomography. In the total variation minimization the prior assumption is that the total variation of the reconstructed image is small. In the discrete tomography, it is assumed that the target object consists of only discrete amount of different, internally homogeneous materials. Smooth Discrete Algebraic Reconstruction Technique or SDART is a modern method for discrete tomography. In this thesis we study the problem of recovering the size, shape and the location of small submillimeter-sized voids enclosed in the wall of a metal pipe section. Tomographic reconstructions were found with the total variation minimization and SDART algorithms and also with a combination of both methods, which we call SDART-TV. The study setup is inspired by the problems involved in the radiographic inspection of steel pipe girth welds. During the welding process, various defects may form in the weld seam and affect negatively the structural properties of the weld. In industrial applications it is important to discover if such defects are present in the weld. The X-ray detectors suited for the existing devices for the radiographic pipe weld inspection can be small compared to the pipe diameter, which results in a difficult limited angle imaging geometry. The geometry of pipes also provides another source of prior information for the algorithms, as the space inside the pipe is often known to contain only air or similar matter. The performance of the total variation and algorithms for discrete tomography in the setup described above was studied with both computational simulations and experiments with an aluminium pipe phantom. The results of the experiments suggest that X-ray tomography algorithms based on a priori information could be applicable for non-destructive testing of pipe welds

Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals

Background:Several small-scale animal studies have suggested that gut microbiota and blood pressure (BP) are linked. However, results from human studies remain scarce and conflicting. We wanted to elucidate the multivariable-adjusted association between gut metagenome and BP in a large, representative, well-phenotyped population sample. We performed a focused analysis to examine the previously reported inverse associations between sodium intake and Lactobacillus abundance and between Lactobacillus abundance and BP.Methods and Results:We studied a population sample of 6953 Finns aged 25 to 74 years (mean age, 49.212.9 years; 54.9% women). The participants underwent a health examination, which included BP measurement, stool collection, and 24-hour urine sampling (N=829). Gut microbiota was analyzed using shallow shotgun metagenome sequencing. In age- and sex-adjusted models, the alpha (within-sample) and beta (between-sample) diversities of taxonomic composition were strongly related to BP indexes (PConclusions:Although the associations between overall gut taxonomic composition and BP are weak, individuals with hypertension demonstrate changes in several genera. We demonstrate strong negative associations of certain Lactobacillus species with sodium intake and BP, highlighting the need for experimental studies.</div

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.</p

Associations of healthy food choices with gut microbiota profiles

Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant.ObjectivesTo assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential.MethodsThis population-based study sample consisted of 4930 participants (ages 25–74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun–sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models.ResultsBoth microbial alpha diversity (β/SD, 0.044; SE, 6.18 × 10−5; P = 2.21 × 10−3) and beta diversity (R2, 0.12; P ≤ 1.00 × 10−3) were associated with the HFC score. For alpha diversity, the strongest associations were observed for fiber-rich breads, poultry, fruits, and low-fat cheeses (all positive). For beta diversity, the most prominent associations were observed for vegetables, followed by berries and fruits. Genera with fiber-degrading and SCFA-producing capacities were positively associated with the HFC score. The HFC score was associated positively with functions such as SCFA metabolism and synthesis, and inversely with functions such as fatty acid biosynthesis and the sulfur relay system.ConclusionsOur results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant- and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.</p

Associations of healthy food choices with gut microbiota profiles

Background: Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant. Objectives: To assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential. Methods: This population-based study sample consisted of 4930 participants (ages 25-74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun-sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models. Results: Both microbial alpha diversity (beta/SD, 0.044; SE, 6.18 x 10(-5); P = 2.21 x 10(-3)) and beta diversity (R-2, 0.12; P Conclusions: Our results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.Peer reviewe

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n=7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status. Gut microbiome composition has a role in health and disease. Here the authors show that microbiome signatures related to the Enterobacteriaceae family are associated with cause-specific mortality risk in a well phenotyped Finish population over a 15-year follow-up.Peer reviewe

Taxonomic signatures of cause-specific mortality risk in human gut microbiome.

The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status