Framework for 4D medical data compression

U ovom radu predložen je novi programski okvir za kompresiju četvero-dimenzionalnih (4D) medicinskih podataka. Arhitektura ovog programskog okvira temelji se na različitim procedurama i algoritmima koji detektiraju vremenske i prostorne zalihosti u ulaznim 4D medicinskim podacima. Pokret kroz vrijeme analizira se pomoću vektora pomaka koji predstavljaju ulazne parametre za neuronske mreže koje se koriste za procjenu pokreta. Kombinacijom segmentacije, pronalaženja odgovarajućih blokova i predikcijom vektora pomaka, zajedno s ekspertnim znanjem moguće je optimirati performanse sustava. Frekvencijska svojstva se analiziraju proširenjem wavelet transformacije na tri dimenzije. Za mirne volumetrijske objekte, moguće je konstruirati različite wavelet pakete s različitim filtrima koji omogućavaju širok raspon analiza frekvencijskih zalihosti. Kombinacijom uklanjanja vremenskih i prostornih zalihosti moguće je postići vrlo visoke omjere kompresije.This work presents a novel framework for four-dimensional (4D) medical data compression architecture. This framework is based on different procedures and algorithms that detect time and spatial (frequency) redundancy in recorded 4D medical data. Motion in time is analyzed through the motion fields that produce input parameters for the neural network used for motion estimation. Combination of segmentation, block matching and motion field prediction along with expert knowledge are incorporated to achieve better performance. Frequency analysis is done through an extension of one dimensional wavelet transformation to three dimensions. For still volume objects different wavelet packets with different filter banks can be constructed, providing a wide range of frequency analysis. With combination of removing temporal and spatial redundancies, very high compression ratio is achieved

Kompresija slika bez gubitaka uz iskorištavanje tokovnog modela za izvođenje na višejezgrenim računalima

Image and video coding play a critical role in present multimedia systems ranging from entertainment to specialized applications such as telemedicine. Usually, they are hand–customized for every intended architecture in order to meet performance requirements. This approach is neither portable nor scalable. With the advent of multicores new challenges emerged for programmers related to both efficient utilization of additional resources and scalable performance. For image and video processing applications, streaming model of computation showed to be effective in tackling these challenges. In this paper, we report the efforts to improve the execution performance of the CBPC, our compute intensive lossless image compression algorithm described in [1]. The algorithm is based on highly adaptive and predictive modeling, outperforming many other methods in compression efficiency, although with increased complexity. We employ a high–level performance optimization approach which exploits streaming model for scalability and portability. We obtain this by detecting computationally demanding parts of the algorithm and implementing them in StreamIt, an architecture–independent stream language which goal is to improve programming productivity and parallelization efficiency by exposing the parallelism and communication pattern. We developed an interface that enables the integration and hosting of streaming kernels into the host application developed in general–purpose language.Postupci obrade slikovnih podataka su iznimno zastupljeni u postojećim multimedijskim sustavima, počev od zabavnih sustava pa do specijaliziranih aplikacija u telemedicini. Vrlo često, zbog svojih računskih zahtjeva, ovi programski odsječci su iznimno optimirani i to na niskoj razini, što predstavlja poteškoće u prenosivosti i skalabilnosti konačnog rješenja. Nadolaskom višejezgrenih računala pojavljuju se novi izazovi kao što su učinkovito iskorištavanje računskih jezgri i postizanje skalabilnosti rješenja obzirom na povećanje broja jezgri. U ovom radu prikazan je novi pristup poboljšanja izvedbenih performansi metode za kompresiju slika bez gubitaka CBPC koja se odlikuje adaptivnim modelom predviđanja koji omogućuje postizanje boljih stupnjeva kompresije uz povećanje računske složenosti [1]. Pristup koji je primjenjen sastoji se u implementaciji računski zahtjevnog predikcijskog modela u tokovnom programskom jeziku koji omogućuje paralelizaciju izvornog programa. Ovako projektiran predikcijski model može se iskoristiti kroz sučelje koje smo razvili a koje omogućuje pozivanje tokovnih računskih modula i njihovo paralelno izvođenje uz iskorištavanje više jezgri

3D Surface Analysis and Classification in Neuroimaging Segmentation

This work emphasizes new algorithms for 3D edge and corner detection used in surface extraction and new concept of image segmentation in neuroimaging based on multidimensional shape analysis and classification. We propose using of NifTI standard for describing input data which enables interoperability and enhancement of existing computing tools used widely in neuroimaging research. In methods section we present our newly developed algorithm for 3D edge and corner detection, together with the algorithm for estimating local 3D shape. Surface of estimated shape is analyzed and segmented according to kernel shapes

Worldwide comparison of survival from childhood leukaemia for 1995–2009, by subtype, age, and sex (CONCORD-2): a population-based study of individual data for 89 828 children from 198 registries in 53 countries

Background Global inequalities in access to health care are reflected in differences in cancer survival. The CONCORD programme was designed to assess worldwide differences and trends in population-based cancer survival. In this population-based study, we aimed to estimate survival inequalities globally for several subtypes of childhood leukaemia. Methods Cancer registries participating in CONCORD were asked to submit tumour registrations for all children aged 0-14 years who were diagnosed with leukaemia between Jan 1, 1995, and Dec 31, 2009, and followed up until Dec 31, 2009. Haematological malignancies were defined by morphology codes in the International Classification of Diseases for Oncology, third revision. We excluded data from registries from which the data were judged to be less reliable, or included only lymphomas, and data from countries in which data for fewer than ten children were available for analysis. We also excluded records because of a missing date of birth, diagnosis, or last known vital status. We estimated 5-year net survival (ie, the probability of surviving at least 5 years after diagnosis, after controlling for deaths from other causes [background mortality]) for children by calendar period of diagnosis (1995-99, 2000-04, and 2005-09), sex, and age at diagnosis (< 1, 1-4, 5-9, and 10-14 years, inclusive) using appropriate life tables. We estimated age-standardised net survival for international comparison of survival trends for precursor-cell acute lymphoblastic leukaemia (ALL) and acute myeloid leukaemia (AML). Findings We analysed data from 89 828 children from 198 registries in 53 countries. During 1995-99, 5-year agestandardised net survival for all lymphoid leukaemias combined ranged from 10.6% (95% CI 3.1-18.2) in the Chinese registries to 86.8% (81.6-92.0) in Austria. International differences in 5-year survival for childhood leukaemia were still large as recently as 2005-09, when age-standardised survival for lymphoid leukaemias ranged from 52.4% (95% CI 42.8-61.9) in Cali, Colombia, to 91.6% (89.5-93.6) in the German registries, and for AML ranged from 33.3% (18.9-47.7) in Bulgaria to 78.2% (72.0-84.3) in German registries. Survival from precursor-cell ALL was very close to that of all lymphoid leukaemias combined, with similar variation. In most countries, survival from AML improved more than survival from ALL between 2000-04 and 2005-09. Survival for each type of leukaemia varied markedly with age: survival was highest for children aged 1-4 and 5-9 years, and lowest for infants (younger than 1 year). There was no systematic difference in survival between boys and girls. Interpretation Global inequalities in survival from childhood leukaemia have narrowed with time but remain very wide for both ALL and AML. These results provide useful information for health policy makers on the effectiveness of health-care systems and for cancer policy makers to reduce inequalities in childhood survival

Global surveillance of cancer survival 1995-2009: analysis of individual data for 25,676,887 patients from 279 population-based registries in 67 countries (CONCORD-2)

BACKGROUND: Worldwide data for cancer survival are scarce. We aimed to initiate worldwide surveillance of cancer survival by central analysis of population-based registry data, as a metric of the effectiveness of health systems, and to inform global policy on cancer control. METHODS: Individual tumour records were submitted by 279 population-based cancer registries in 67 countries for 25·7 million adults (age 15-99 years) and 75,000 children (age 0-14 years) diagnosed with cancer during 1995-2009 and followed up to Dec 31, 2009, or later. We looked at cancers of the stomach, colon, rectum, liver, lung, breast (women), cervix, ovary, and prostate in adults, and adult and childhood leukaemia. Standardised quality control procedures were applied; errors were corrected by the registry concerned. We estimated 5-year net survival, adjusted for background mortality in every country or region by age (single year), sex, and calendar year, and by race or ethnic origin in some countries. Estimates were age-standardised with the International Cancer Survival Standard weights. FINDINGS: 5-year survival from colon, rectal, and breast cancers has increased steadily in most developed countries. For patients diagnosed during 2005-09, survival for colon and rectal cancer reached 60% or more in 22 countries around the world; for breast cancer, 5-year survival rose to 85% or higher in 17 countries worldwide. Liver and lung cancer remain lethal in all nations: for both cancers, 5-year survival is below 20% everywhere in Europe, in the range 15-19% in North America, and as low as 7-9% in Mongolia and Thailand. Striking rises in 5-year survival from prostate cancer have occurred in many countries: survival rose by 10-20% between 1995-99 and 2005-09 in 22 countries in South America, Asia, and Europe, but survival still varies widely around the world, from less than 60% in Bulgaria and Thailand to 95% or more in Brazil, Puerto Rico, and the USA. For cervical cancer, national estimates of 5-year survival range from less than 50% to more than 70%; regional variations are much wider, and improvements between 1995-99 and 2005-09 have generally been slight. For women diagnosed with ovarian cancer in 2005-09, 5-year survival was 40% or higher only in Ecuador, the USA, and 17 countries in Asia and Europe. 5-year survival for stomach cancer in 2005-09 was high (54-58%) in Japan and South Korea, compared with less than 40% in other countries. By contrast, 5-year survival from adult leukaemia in Japan and South Korea (18-23%) is lower than in most other countries. 5-year survival from childhood acute lymphoblastic leukaemia is less than 60% in several countries, but as high as 90% in Canada and four European countries, which suggests major deficiencies in the management of a largely curable disease. INTERPRETATION: International comparison of survival trends reveals very wide differences that are likely to be attributable to differences in access to early diagnosis and optimum treatment. Continuous worldwide surveillance of cancer survival should become an indispensable source of information for cancer patients and researchers and a stimulus for politicians to improve health policy and health-care systems

Arhitektura sustava za kompresiju četverodimenzionalnih medicinskih podataka

This thesis presents a novel framework for four-dimensional medical data compression architecture. This framework is based on different procedures and algorithms that detect time and spatial redundancy in recorded MRI volumes. Motion in time is analyzed through motion estimation based on neural networks. Motion estimation is used to eliminate a large amount of temporal and frequency redundancies that exists in sequences of 3D data. Combination of segmentation, block matching and motion field prediction along with expert knowledge are incorporated to achieve better performance. Frequency analysis is done through an extension of wavelet transformations to three dimensions. For still volume objects different wavelet packets with different filter banks can be constructed, providing a wide range of frequency analysis. With combination of removing temporal and spatial redundancies, very high compression ratio is achived. The suggested data compression architecture can be implemented in telemedicine to improve the quality of service. It incorporates operations for frequency and time analysis of datasets, creating kernel shapes and models, and fitting of medical 4D datasets. Each part of the system architecture is implemented independently and can be used for other approaches such as entertainment applications and other new applications that use 4D data.U ovom doktorskom radu prezentirane su osnovne značajke arhitekture za četverodimenzionalnu kompresiju medicinskih podataka koja se temelji na različitim procedurama i algoritmima za analizu vremenske i prostorne zalihosti MR zapisa u NIfTI podatkovnom formatu. Za analizu i procjenu pokreta, a u cilju uklanjanja vremenske zalihosti koja postoji u slijedu 3D prostornih podataka koriste se neuronske mreže. Da bi se ostvarila kompresija takvih podataka, koristi se ekspertno znanje u različitim algoritmima segmentacije podataka, procjene oblika, predviđanja i definiranja polja pokreta. Frekvencijska analiza je ostvarena proširenjem transformacije temeljene na teoriji valića u tri dimenzije. Za statičke 3D prostorne podatke koriste se različite baze i paketi valića koji pružaju širok raspon frekvencijske analize. Uklanjanjem vremenske i prostorne zalihosti postiže se visok stupanj kompresije. Predložena arhitektura kompresije služi u podizanju razine kvalitete usluga u telemedicini. Svaki dio ove arhitekture predstavlja zasebnu cjelinu te se može primijeniti nezavisno i u druge svrhe, kao što su aplikacije namijenjene zabavi i druge aplikacije koje koriste četverodimenzionalne podatke

Economic thermal insulation thickness and price comparison between a classically built and a prefabricated house

V diplomski nalogi sem obravnaval ekonomično debelino toplotne izolacije na zunanji steni ter pod temeljno ploščo. Poleg tega pa sem primerjal ceno gradnje klasične in montažne hiše. V prvem delu sem predstavil lastnosti klasično zidane in montažne hiše ter opredelil teoretične osnove energetske učinkovitosti. V drugem delu sem opisal izbrani objekt ter zanj izdelal popis materialov za primera klasično zidane hiše in montažne hiše, pri čemer sem za primerjavo vzel montažno hišo Marles s sestavo zunanje stene Mega N14. Na podlagi izbranega objekta sem izračunal ekonomično debelino toplotne izolacije zunanjih sten v obdobju 60 let, kjer se fasada obnovi dvakrat in ekonomično debelino toplotne izolacije pod temeljno ploščo pri predpostavljeni življenjski dobi 100 let za primer klasično zidane hiše. Upošteval sem tudi možnost, da se toplotna izolacija pod temeljno ploščo ne izvede. Za izračun sem uporabil dinamično metodo iz ekonomije, imenovano neto sedanja vrednost. V nadaljevanju sem izdelal popis del in materialov za izvedbo izbranega objekta ter tako primerjal ceno izvedbe klasične in ceno izvedbe montažne hiše. Pri tem sem zaradi primerljivosti določene postavke klasično zidane hiše poenotil s ponudbo montažne hiše Marles Mega N14, tako da sta oba objekta enaka v smislu energetske varčnosti ter v smislu enake opreme. V diplomskem delu sem prikazal, da se vgrajevanje večje količine toplotne izolacije obrestuje tako na zunanjih stenah kot pod temeljno ploščo. Rezultati cenovne primerjave klasično zidane hiše in montažne hiše so pokazali, da je izvedba zidanega objekta še vedno cenejša za približno 20 %.In the thesis, I discussed the economic thermal insulation thickness on the outer wall and under the base plate. I also compared the prices of constructing a classically built and prefabricated house. In the first part, I presented characteristics of the classically built and the prefabricated house and defined the theoretical bases of energy efficiency. In the second part, I described the chosen object and prepared an inventory of the material for the cases of a classically built house and a prefabricated one, where I compared the prefabricated house by Marles with the N14 composition of the outer wall. Based on the chosen object I calculated the economic thermal insulation thickness of the outer walls for a period of 60 years, where the façade is being renovated twice, and the economic thermal insulation thickness under the base plate with the assumed lifetime of 100 years for the case of a classically built house. I also considered the possibility of no thermal insulation under the base plate. For the calculation, I used the dynamic method, used in economics, called net present value. In continuation I prepared an inventory of the work and material for the construction of the chosen object and so compared the prices for the construction of a classically build and a prefabricated house. For the purpose of comparability, I unified some elements of the classically built house with the offer for the prefabricated house Marles Mega N14, so that both objects are the same in terms of energy efficiency and equipment. In the thesis, I showed that the installation of large amounts of thermal insulation pays off at the outer walls as well as under the base plate. The results of the price comparison for the classically built house and the prefabricated one showed that the construction of a classically built object is still cheaper for about 20%

TUNA FARMING

Cilj ovog rada je predstaviti tekuće probleme i moguća rješenja u održivom razvitku jedne od grana marikulture – uzgoja tune. Danas se uzgajaju tri vrste tuna: atlantska plavoperajna tuna, pacifička plavoperajna tuna i južna plavoperajna tuna, pa će se u radu spomenuti posebnosti uzgoju pojedinih vrsta, kao i proces nabave nasadnog materijala temeljenog na ribolovu, odnosno na umjetnom mrijestu. Zbog dugogodišnjeg prelova ovih vrsta na snagu su stupili određeni propisi koji imaju stanovit utjecaj na proces ribolova i uzgoja. Uzgojenom tunom se najviše trguje na japanskom tržištu na koje se plasira kao sirovina za japanske delikatese, ali posljednjih godina zamjetan je rast drugih tržišta. Tijekom svih procesa uzgoja, od nabave nasadnog materijala do izlova u uzgajalištu javljaju je određeni utjecaji na okoliš. U Republici Hrvatskoj uzgoj tune je relativno mlada djelatnost, ali sa značajnim razvojnim mogućnostima.The aim of this paper is to present the current problems and possible solutions in the sustainable development of one of the branches of mariculture – tuna farming. Today, farming of tuna is based on three species: Atlantic bluefin tuna, pacific bluefin tuna and southern bluefin tuna, so peculiarities of capture-based farming and farming based on artificial spawning will be mentioned. Due to years of overfishing of these species, certain legal regulations came to force. The effects of these regulations on tuna fishing and farming will be provided. Farmed tunas are mostly traded in the Japanese delicacy sushi and sashimi, but in recent years there has been a growth in other markets. During the process of farming, from providing the seed material to harvesting on farms, certain environmental impacts are occurring. In Croatia, tuna farming is a relatively young activity, but with significant developmental capacities