CIDI-Lung-Seg: A Single-Click Annotation Tool for Automatic Delineation of Lungs from CT Scans

Accurate and fast extraction of lung volumes from computed tomography (CT) scans remains in a great demand in the clinical environment because the available methods fail to provide a generic solution due to wide anatomical variations of lungs and existence of pathologies. Manual annotation, current gold standard, is time consuming and often subject to human bias. On the other hand, current state-of-the-art fully automated lung segmentation methods fail to make their way into the clinical practice due to their inability to efficiently incorporate human input for handling misclassifications and praxis. This paper presents a lung annotation tool for CT images that is interactive, efficient, and robust. The proposed annotation tool produces an "as accurate as possible" initial annotation based on the fuzzy-connectedness image segmentation, followed by efficient manual fixation of the initial extraction if deemed necessary by the practitioner. To provide maximum flexibility to the users, our annotation tool is supported in three major operating systems (Windows, Linux, and the Mac OS X). The quantitative results comparing our free software with commercially available lung segmentation tools show higher degree of consistency and precision of our software with a considerable potential to enhance the performance of routine clinical tasks.Comment: 4 pages, 6 figures; to appear in the proceedings of 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2014

CAVASS: A Computer-Assisted Visualization and Analysis Software System

The Medical Image Processing Group at the University of Pennsylvania has been developing (and distributing with source code) medical image analysis and visualization software systems for a long period of time. Our most recent system, 3DVIEWNIX, was first released in 1993. Since that time, a number of significant advancements have taken place with regard to computer platforms and operating systems, networking capability, the rise of parallel processing standards, and the development of open-source toolkits. The development of CAVASS by our group is the next generation of 3DVIEWNIX. CAVASS will be freely available and open source, and it is integrated with toolkits such as Insight Toolkit and Visualization Toolkit. CAVASS runs on Windows, Unix, Linux, and Mac but shares a single code base. Rather than requiring expensive multiprocessor systems, it seamlessly provides for parallel processing via inexpensive clusters of work stations for more time-consuming algorithms. Most importantly, CAVASS is directed at the visualization, processing, and analysis of 3-dimensional and higher-dimensional medical imagery, so support for digital imaging and communication in medicine data and the efficient implementation of algorithms is given paramount importance

Segmentation and Evaluation of Adipose Tissue from Whole Body MRI Scans

Accurate quantification of total body and the distribution of regional adipose tissue using manual segmentation is a challenging problem due to the high variation between manual delineations. Manual segmentation also requires highly trained experts with knowledge of anatomy. We present a hybrid segmentation method that provides robust delineation results for adipose tissue from whole body MRI scans. A formal evaluation of accuracy of the segmentation method is performed. This semi-automatic segmentation algorithm reduces significantly the time required for quantification of adipose tissue, and the accuracy measurements show that the results are close to the ground truth obtained from manual segmentations

Novel 2,5-disubstituted-1,3,4-oxadiazole derivatives induce apoptosis in HepG2 cells through p53 mediated intrinsic pathway

AbstractA series of novel 1,3,4-oxadiazole derivatives (OSD, OCOD, ONOD, OPD, COD, PMOD, and PCOD) were synthesized and characterized. Their structures were confirmed on the basis of IR, NMR and mass spectroscopy and molecular weights were found in the range 300–325g/mol. Cancerous cell lines (MCF-7, HepG2) and non-cancerous cell lines (Chang liver cells) were treated with these compounds for 48h, which caused dose dependent decrease in the cell viability. From the seven derivatives, OSD was found to be most potent with IC50 value close to 50μM on all tested cell lines. Hence, this compound was selected for mechanistic study on HepG2 cell lines. Fluorescent cell staining and DNA fragmentation study of 50μM OSD on HepG2 cells, showed events marked by apoptosis such as nuclear fragmentation, cytoplasm shrinkage and DNA damage. Further, the cells with same treatment were quantified for apoptosis using annexin V-PI flow cytometric technique. The percentage of apoptotic cells was significantly higher (p<0.05) after OSD treatment compared to control cells. OSD induced a significant increase (p<0.05) in the expression of the tumor suppressor p53 in HepG2 cells. The constitutive expression of anti-apoptotic protein Bcl-2 significantly decreased (p<0.05) after treatment, while the expression of proapoptotic protein Bax significantly increased (p<0.05). The change in Bax to Bcl-2 ratio suggested involvement of Bcl-2 family in induction of apoptosis. Furthermore, the levels of caspase-9 and caspase-3 were significantly (p<0.05) up regulated in HepG2 cells after OSD treatment. The data suggest that 1,3,4-oxadiazole derivatives induce apoptosis mediated by intrinsic pathway of apoptosis. The findings strengthen the potential of the 1,3,4-oxadiazole scaffold OSD, as an agent with chemotherapeutic and cytostatic activity in human hepatocellular carcinoma in vitro

Liposomi rivastigmina za isporuku u mozak intranazalnim putem

The present study is mainly aimed at delivering a drug into the brain via the intranasal route using a liposomal formulation. For this purpose, rivastigmine, which is used in the management of Alzheimer’s disease, was selectd as a model drug. Conventional liposomes were formulated by lipid layer hydration method using cholesterol and soya lecithin as lipid components. The concentration of rivastigmine in brain and plasma was studied in rat models after intranasal and oral administration of liposomes and free drug. A significantly higher level of drug was found in the brain with intranasal liposomes of rivastigmine compared to the intranasal free drug and the oral route. Intranasal liposomes had a longer half-life in the brain than intranasally or orally administered free drug. Delivering rivastigmine liposomes through the intranasal route for the treatment of Alzheimer’s disease might be a new approach to the management of this condition.Glavni cilj rada je razvoj liposoma za intranazalnu primjenu za isporuku lijeka u mozak. U tu svrhu izabran je rivastigmin kao modelni lijek koji se upotrebljava u terapiji Alzheimerove bolesti. Liposomi su pripravljeni metodom hidratacije lipidnog sloja koristeći kolesterol i lecitin iz soje kao lipidne komponente. Praćena je koncentracija rivastigmina u mozgu i plazmi nakon intranazalne i peroralne primjene liposoma i slobodnog lijeka. S intranazalnim liposomima rivastigmina postignuta je značajno veća koncentracija lijeka u mozgu. Osim toga intranazalni liposomi imaju dulje vrijeme poluživota u mozgu. Intranazalna primjena liposoma rivastigmina mogla bi predstavljati novi pristup terapiji Alzheimerove bolesti

Chest Fat Quantification via CT Based on Standardized Anatomy Space in Adult Lung Transplant Candidates

Purpose Overweight and underweight conditions are considered relative contraindications to lung transplantation due to their association with excess mortality. Yet, recent work suggests that body mass index (BMI) does not accurately reflect adipose tissue mass in adults with advanced lung diseases. Alternative and more accurate measures of adiposity are needed. Chest fat estimation by routine computed tomography (CT) imaging may therefore be important for identifying high-risk lung transplant candidates. In this paper, an approach to chest fat quantification and quality assessment based on a recently formulated concept of standardized anatomic space (SAS) is presented. The goal of the paper is to seek answers to several key questions related to chest fat quantity and quality assessment based on a single slice CT (whether in the chest, abdomen, or thigh) versus a volumetric CT, which have not been addressed in the literature. Methods Unenhanced chest CT image data sets from 40 adult lung transplant candidates (age 58 ± 12 yrs and BMI 26.4 ± 4.3 kg/m2), 16 with chronic obstructive pulmonary disease (COPD), 16 with idiopathic pulmonary fibrosis (IPF), and the remainder with other conditions were analyzed together with a single slice acquired for each patient at the L5 vertebral level and mid-thigh level. The thoracic body region and the interface between subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) in the chest were consistently defined in all patients and delineated using Live Wire tools. The SAT and VAT components of chest were then segmented guided by this interface. The SAS approach was used to identify the corresponding anatomic slices in each chest CT study, and SAT and VAT areas in each slice as well as their whole volumes were quantified. Similarly, the SAT and VAT components were segmented in the abdomen and thigh slices. Key parameters of the attenuation (Hounsfield unit (HU) distributions) were determined from each chest slice and from the whole chest volume separately for SAT and VAT components. The same parameters were also computed from the single abdominal and thigh slices. The ability of the slice at each anatomic location in the chest (and abdomen and thigh) to act as a marker of the measures derived from the whole chest volume was assessed via Pearson correlation coefficient (PCC) analysis. Results The SAS approach correctly identified slice locations in different subjects in terms of vertebral levels. PCC between chest fat volume and chest slice fat area was maximal at the T8 level for SAT (0.97) and at the T7 level for VAT (0.86), and was modest between chest fat volume and abdominal slice fat area for SAT and VAT (0.73 and 0.75, respectively). However, correlation was weak for chest fat volume and thigh slice fat area for SAT and VAT (0.52 and 0.37, respectively), and for chest fat volume for SAT and VAT and BMI (0.65 and 0.28, respectively). These same single slice locations with maximal PCC were found for SAT and VAT within both COPD and IPF groups. Most of the attenuation properties derived from the whole chest volume and single best chest slice for VAT (but not for SAT) were significantly different between COPD and IPF groups. Conclusions This study demonstrates a new way of optimally selecting slices whose measurements may be used as markers of similar measurements made on the whole chest volume. The results suggest that one or two slices imaged at T7 and T8 vertebral levels may be enough to estimate reliably the total SAT and VAT components of chest fat and the quality of chest fat as determined by attenuation distributions in the entire chest volume

A Methodology for Evaluating Image Segmentation Algorithms

The purpose of this paper is to describe a framework for evaluating image segmentation algorithms. Image segmentation consists of object recognition and delineation. For evaluating segmentation methods, three factors - precision (reproducibility), accuracy (agreement with truth), and efficiency (time taken) – need to be considered for both recognition and delineation. To assess precision, we need to choose a figure of merit (FOM), repeat segmentation considering all sources of variation, and determine variations in FOM via statistical analysis. It is impossible usually to establish true segmentation. Hence, to assess accuracy, we need to choose a surrogate of true segmentation and proceed as for precision. To assess efficiency, both the computational and the user time required for algorithm and operator training and for algorithm execution should be measured and analyzed. Precision, accuracy, and efficiency are interdependent. It is difficult to improve one factor without affecting others. Segmentation methods must be compared based on all three factors. The weight given to each factor depends on application

Chiral Heterocyclic Ligands. XI. Self-assembly and X-Ray Crystal Structures of Chiral Silver Coordination Polymers of (S)-(-)-Nicotine

Three chiral coordination polymers have been prepared by reaction of (S)-(-)-nicotine with silver(I) salts. X-Ray crystal structure determinations revealed that these all contain polymer chains in which the nicotine molecule acts as a bridging ligand between four-coordinate silver atoms. In one case additional bridging by nitrate anions leads to a three-dimensional network structure

Mining the chickpea composite collection for allelic variation

Chickpea, Cicer arietinum L., is believed to have originated in south-east Turkey. However, at present, the major chickpea-growing countries are India, Pakistan, Iran, Turkey, Australia, Ethiopia, and Mexico. Chickpea is a leguminous food crop, self-pollinating, and diploid. Its gene pool consists of 43 species: one annual cultivated (i.e. chickpea), eight annual wild, and 34 perennial wild species. Two types of chickpea are known: desi types with coloured flowers, and angular-shaped and dark-coloured seeds, primarily grown in South Asia and Africa; and kabuli types with white flowers, owl’s head-shaped and beige-coloured seeds, and grown mostly in Mediterranean countries. To study the allelic richness and diversity associated with beneficial traits, a composite set of 3000 chickpea germplasm accessions was constituted. This set included the chickpea core collection, old and new cultivars and traitspecific germplasm accessions from ICRISAT and accessions representing the ICARDA collection