Superpixel labeling for medical image segmentation

openNowadays, most methods for image segmentation consider images in a pixel- wise manner, which is a huge job and also time-consuming. On the other hand, superpixel labeling can make the segmentation task easier in some aspects. First, superpixels carry more information than pixels because they usually follow the edges present in the image. Furthermore, superpixels have perceptual meaning, and finally, they can be very useful in computationally demanding problems, since by mapping pixels to superpixels we are reducing the complexity of the problem. In this thesis, we propose to do superpixel-wise labeling on two med- ical image datasets including ISIC Lesion Skin and Chest X-ray, then we feed them to the U-Net Convolutional Neural Network (CNN) DoubleU-Net and Dual-Aggregation Transformer (DuAT) network to segment our images in term of superpixels. Three different methods of labeling are used in this thesis: Su- perpixel labeling, Extended Superpixel Labeling (Distance-base Labeling), and Random Walk Superpixel labeling. The Superpixel labeled ground truths are used just for training. For the evaluation, we consider the original image and also the original binary ground truth. We considered four different superpixel algorithms, namely Simple Linear Iterative Clustering (SLIC), Felsenszwalb Hut- tenlocher (FH), QuickShift (QS) , and Superpixels Extracted via Energy-Driven Sampling (SEEDS). We evaluate the segmentation result with metrics such as Dice Coefficient, Precision, Intersection Over Union (IOU), and Sensitivity. Our results show the accuracy of 0.89 and 0.95 percent in dice coefficient for skin lesion and chest X-ray datasets respectively. Key Words: Superpixels, Medical Images, U-Net, DoubleU-Net, Image seg- mentation, CNN, DuAT, SEEDS.Nowadays, most methods for image segmentation consider images in a pixel- wise manner, which is a huge job and also time-consuming. On the other hand, superpixel labeling can make the segmentation task easier in some aspects. First, superpixels carry more information than pixels because they usually follow the edges present in the image. Furthermore, superpixels have perceptual meaning, and finally, they can be very useful in computationally demanding problems, since by mapping pixels to superpixels we are reducing the complexity of the problem. In this thesis, we propose to do superpixel-wise labeling on two med- ical image datasets including ISIC Lesion Skin and Chest X-ray, then we feed them to the U-Net Convolutional Neural Network (CNN) DoubleU-Net and Dual-Aggregation Transformer (DuAT) network to segment our images in term of superpixels. Three different methods of labeling are used in this thesis: Su- perpixel labeling, Extended Superpixel Labeling (Distance-base Labeling), and Random Walk Superpixel labeling. The Superpixel labeled ground truths are used just for training. For the evaluation, we consider the original image and also the original binary ground truth. We considered four different superpixel algorithms, namely Simple Linear Iterative Clustering (SLIC), Felsenszwalb Hut- tenlocher (FH), QuickShift (QS) , and Superpixels Extracted via Energy-Driven Sampling (SEEDS). We evaluate the segmentation result with metrics such as Dice Coefficient, Precision, Intersection Over Union (IOU), and Sensitivity. Our results show the accuracy of 0.89 and 0.95 percent in dice coefficient for skin lesion and chest X-ray datasets respectively. Key Words: Superpixels, Medical Images, U-Net, DoubleU-Net, Image seg- mentation, CNN, DuAT, SEEDS

Effect of harvesting frequency and maturity stage of Jerusalem artichoke forage on yield, chemical composition and in vitro fermentation of the tubers and forage

Aim of study: To evaluate the effect of maturity stage and harvesting frequency of Jerusalem artichoke (JA) forage on the nutritional quality of the tubers and forages.Area of study: The plant cultivation and laboratory experiments were carried out in Karaj (Alborz, Iran) and Tehran (Tehran, Iran), respectively.Material and methods: Forages were harvested every 60, 90 and 120 days during the growing season (four, three and two harvests per year, respectively). Tubers were harvested just once, at the end of the growing season, from plots with four, three and two forage cuts per year. Biomass production, chemical composition and in vitro ruminal fermentation of the forages and tubers were assessed.Main results: Compared to 90 and 120 days, the forages harvested every 60 days contained the highest (p<0.05) yearly dry matter (DM) biomass (27.16 t/ha), crude protein (98.6 to 145 g/kg DM), organic matter digestibility (0.607 to 0.691) and microbial biomass production (350 to 369 g/kg DM). Compared to 60 and 90 days, harvesting JA forage every 120 days caused the tubers with the higher (p<0.05) water-soluble carbohydrates (WSC), in vitro digestibility and DM yield (7.63 t/ha). Jerusalem artichoke forages and tubers contained the low phenolics (4.93 to 13.2 g/kg DM) and nitrate (1.12 to 3.19 g/kg DM). Overall, the best harvesting interval of JA forage to achieve tubers with the highest yearly yield, WSC and digestibility was every 120 days, while the highest nutritive value and yield of the forages were observed with harvesting JA every 60 days.Research highlights: The best harvesting interval of JA forage to obtain the highest yearly DM, protein and energy biomass from both tubers and forage was every 60 days

High Speed Train Geotechnics: Numerical and Experimental Simulation of Some Embankment Problems

This dissertation explores some of the geotechnical challenges associated with implementing high-speed railway (HSR) systems. These challenges are mostly related to HSR embankments. Three special geotechnical issues addressed in this project are long-term softening of compacted unsaturated embankments due to water absorption, potential derailment when trains break through the Rayleigh wave barrier, and the tolerable bump (or any other type of irregularity) in the track. Soil softening due to water level rise in compacted embankments is investigated through an extensive experimental study that provides a better understanding of unsaturated soil and its impact on soil modulus degradation, which has a great impact on the other two issues. In fact, too much water content in the natural soil under the embankment can cause serious problems, such as unexpected large, uneven deflections. Through these experiments, it was confirmed that the soil modulus can considerably change as the water content in the soil varies. To evaluate both the track responses to breaking the Rayleigh wave barrier and bump along HSR lines, a series of four-dimensional (4-D) finite element models (FEMs) using LS-DYNA have been developed. These 4-D FEMs include all track substructural and superstrucural components. Breaking the Rayleigh wave barrier, especially when traveling on soft soils, results in large deflection in the track structures and substructure components due to the combination of static and dynamic loads. Using the developed 4-D FEMs, the effect of train speed on the large track deflection is investigated. Through this study, it was confirmed that at a particular speed called the critical speed, the maximum track deflection occurs. This train speed should be avoided because the resultant maximum track deflection leads to either high maintenance cost or, in the worst-case scenario, train derailment. These extensive numerical simulation results are compiled into proposed guideline charts to enable the design of safe embankment for HSR lines while keeping the train speed below 70% of the critical speed, which is considered as the safe train speed zone. The problems of stiffness transition and irregularity along HSR are investigated using a 4-D FEM of both faulted and non-faulted track, considering passenger safety and comfort criteria. Although the main source of bump development is found to be the track modulus differential alone, track modulus variation alone has only minor impact on the train/track responses. It should be noted that track modulus differential instigates the formation of different types of irregularities along HSR, which significantly increases the wheel/rail interaction force and train body acceleration. The parametric study conducted to look at the effect of different parameters such as train speed, subsoil modulus, and irregularity type and size on the train/track responses results in proposed guideline charts defining tolerable irregularity size for HSR lines such that the vertical train body acceleration and wheel/rail interaction force are kept below the permissible values

The Study of the Level of Harmony of Rhyme and Content in the Poems of Hakim Sanaei

The true poetry is the birth of the unconscious poet without the intervention of his consciousness, as Plato and Aristotle, the critics of the first poetry, point to this point. If poetry is burst from inside the poet's conscience, the rhyme and all the elements of the poetry are followed by the contents of his poem, rather than the poet, with a figure of a pattern. The outer music of poetry follows the poet's feelings on his tongue, and a poem with a conventional weight of poetry identity is indistinguishable from the point of view of the poetry and intuition; as the poems of the great poets of Persian literature is an example of this harmony between elements of poetry. Sanai Ghaznavi is one of the popular poets of Persian literature whose poetry seems to come from his uneasy inside the poetic moments of her life. The purpose of this research is to determine the extent to which weight and content are coordinated in his poems, and whether the two elements of weight and content in the Sanaei poems are in line with each other. In this research which was done by the library method, after reviewing the poetry of Sanai (330 sonnets and verses). Their subject and content were determined. First, the studied poems were divided into four groups of love, mysticism, ethics-preaching-social criticism, and eulogy. After determining their rhyme, the quality of rhyme and content and the level of coordination of these two elements were analyzed in Sanaei's poetry. It is worth noting that Sanaei's poems based on his work were chosen and studied by Modarres Razavi. In considering the weight of a poet's poetry, there are a few points to consider; for example, in the case of the Senaei's poems, he has said that he has undergone a number of existential issues and undoubtedly influenced these changes in his poetic style. Of course, the style of the time should not be ignored. This point should also not be ignored, with the advent of the purposive content of Persian poetry, a new chapter in literature begins with the name of Sanai Ghaznavi. The Sanai Ghaznavi's poems begin with mystical poetry, his lyrics and odes in this study, according to their contents were divided into four groups of preaching, mysticism, Qalandari, and romanticism. He has completed three stages of poetry. He used the great rhymes to compose eulogy, and according to the survey, rhymes can be said to fit into the theme of the eulogy. The important point regarding Sanaei is the romantic that has happy and sad rhyme at the same time. These poems are considered as lyrics that are more exciting. In his mystical and spiritual poems, the rhyme is calm. Although the poems with calm rhymes are more, but the short rhythmic poems are less that is the kind of rhyme in the speech. In the reviewed poems, Bahr-e Raml and Hazj are the most frequent. There is no rhymic forms in these poems

European pond turtle (Emys orbicularis persica) as a biomarker of environmental pollution in Golestan and Mazandaran provinces, Iran

Anthropogenic environmental changes are hypothesized as main reasons for animal species population declines. Heavy metals contamination is one of the worst threats to animals among human-caused threats. As most of the heavy metals bioaccumulate in organisms, analyzing concentrations of heavy metals in long living animals, such as turtles, would be very useful for biomonitoring of environmental quality. The European pond turtle is classified as a Near Threatened in the red list of International Union for Conservation of Nature. The objective of this study was to obtain information on heavy metals contamination in this species, as a sentinels, to evaluate the overall health of both the European pond turtles and their ecosystem in Golestan and Mazandaran provinces. Biological samples of 10 living and 15 dead European pond turtles were analyzed by atomic absorption spectrophotometer for Zn, Pb, Cu, and Cd contaminations. Highest concentration of Zn (202.6 \ub1 58.5 \u3bcg g-1), Cd (4.4 \ub1 1.3 \u3bcg g-1) and Cu (3.8 \ub1 1.7 \u3bcg g-1) was detected in livers and the highest accumulation of Pb (45.6 \ub116.3 \u3bcg g-1) occurred in kidneys. Positive correlations were detected among Zn, Pb and Cd tissue concentrations and carapaces curve length. Heavy metal levels were higher in males than females. Heavy metals contamination of sampled turtles stood in high degree. However, there is clearly a need to evaluate heavy metals physiologic effects on European pond turtles

Evaluation of the Effects of Diabetes Self-Management Education based on 5A Model on the Quality of Life and Blood Glucose of Women with Gestational Diabetes Mellitus

Abstract Introduction: Gestational diabetes mellitus (GDM) is an important condition during pregnancy. The aim of the current study was to evaluate the effects of self-management education based on 5A model on the quality of life and blood glucose level of women with GDM. Methods: This quasi-experimental study was conducted on 54 pregnant women who referred to the urban health care centers affiliated to the Gonabad University of Medical Sciences from March 2019 to March 2020 based on purposive sampling method. Participants were randomly allocated into intervention and control groups based on stratified random sampling using permuted block randomization method. The intervention group received self-management education program based on 5A model in five sessions during two months. Demographic data, blood glucose level, and diabetes quality of life (DQOL) questionnaire were recorded for each participant. Data analysis was performed using the SPSS software version 16 and the level of statistical significance was set at 0.05. Results: Mean age of the participants was 33.11 ± 5.35 years old. At the end of the intervention, the mean blood glucose level of the participants in the intervention group was significantly lower compared to the control group (p<0.001). The quality of life in the intervention group was significantly improved at the end of the intervention compared to the control group (p<0.001). Conclusions: Self-management education based on 5A model can effectively improve quality of life and blood glucose levels in women with GDM

Nanoparticles Targeting Hematopoietic Stem and Progenitor Cells: Multimodal Carriers for the Treatment of Hematological Diseases

Modern-day hematopoietic stem cell (HSC) therapies, such as gene therapy, modify autologous HSCs prior to re-infusion into myelo-conditioned patients and hold great promise for treatment of hematological disorders. While this approach has been successful in numerous clinical trials, it relies on transplantation of ex vivo modified patient HSCs, which presents several limitations. It is a costly and time-consuming procedure, which includes only few patients so far, and ex vivo culturing negatively impacts on the viability and stem cell-properties of HSCs. If viral vectors are used, this carries the additional risk of insertional mutagenesis. A therapy delivered to HSCs in vivo, with minimal disturbance of the HSC niche, could offer great opportunities for novel treatments that aim to reverse disease symptoms for hematopoietic disorders and could bring safe, effective and affordable genetic therapies to all parts of the world. However, substantial unmet needs exist with respect to the in vivo delivery of therapeutics to HSCs. In the last decade, in particular with the development of gene editing technologies such as CRISPR/Cas9, nanoparticles (NPs) have become an emerging platform to facilitate the manipulation of cells and organs. By employing surface modification strategies, different types of NPs can be designed to target specific tissues and cell types in vivo. HSCs are particularly difficult to target due to the lack of unique cell surface markers that can be utilized for cell-specific delivery of therapeutics, and their shielded localization in the bone marrow (BM). Recent advances in NP technology and genetic engineering have resulted in the development of advanced nanocarriers that can deliver therapeutics and imaging agents to hematopoietic stem- and progenitor cells (HSPCs) in the BM niche. In this review we provide a comprehensive overview of NP-based approaches targeting HSPCs to control and monitor HSPC activity in vitro and in vivo, and we discuss the potential of NPs for the treatment of malignant and non-malignant hematological disorders, with a specific focus on the delivery of gene editing tools

Comparison of Reasoner’s 2A Agar and Muller Hinton Agar Media for Microbiological Monitoring of Dialysis Water

Background and Aim: Microbiological culture of dialysis water is a routine safety measure. In, Khorramabad laboratories perform these cultures on Muller Hinton Agar (MHA) at 35–378C for 48 h, not on the Reasoner’s 2A agar (R2A agar) at 17–238ºC for 7 days recommended by international standards, the objective of the present study was the comparison of the efficiency of R2A and MHA media in the counting of heterotrophic bacteria in the samples of water collected in dialysis centers from 2 hospitals in Khorramabad, from September to November 2019. Methods: A total of 165 samples of treated water in dialysis centers were collected aseptically and then transported in ice‑packs to the Department of Medical Microbiology of the Lorestan University of Medical Sciences and the pour plate technique was carried out for the enumerating of heterotrophic bacteria. Finally, bacterial colonies were counted after incubation at 34±2ºC for 48 hours on MHA and 25ºC for 1 week on R2A. Results: Results showed heterotrophic bacterial counts in R2A were greater than those in MHA in 89% of the samples, so enumeration of heterotrophic bacteria should be carried out in R2A agar associated with longer incubation times, because of the greater sensitivity. The proportion of water samples yielding colony counts ≥200 CFU/mL by R2A -7d was significantly different from the proportion by MHA-48h (p<0.001). Conclusion: The results proposed using R2A agar combined with relative low culture temperature (20-25°C), and an extended incubation time (7-10 days) is more efficient. However, as the spectrum of bacterial contamination is not similar for dialysis centers and countries, many studies using different media and culture parameters are required to confirm this. *Corresponding Author: Faranak Rezaei; Email: [email protected] Please cite this article as: Pouladi I, Delfani S, Hadian B, Soroush S, Anbari K, Rezaei F. Comparison of Reasoner’s 2A Agar and Muller Hinton Agar Media for Microbiological Monitoring of Dialysis Water. Arch Med Lab Sci. 2020;6:1-5 (e10). https://doi.org/10.22037/amls.v6.3290