Topology-Aware Loss for Aorta and Great Vessel Segmentation in Computed Tomography Images

Segmentation networks are not explicitly imposed to learn global invariants of an image, such as the shape of an object and the geometry between multiple objects, when they are trained with a standard loss function. On the other hand, incorporating such invariants into network training may help improve performance for various segmentation tasks when they are the intrinsic characteristics of the objects to be segmented. One example is segmentation of aorta and great vessels in computed tomography (CT) images where vessels are found in a particular geometry in the body due to the human anatomy and they mostly seem as round objects on a 2D CT image. This paper addresses this issue by introducing a new topology-aware loss function that penalizes topology dissimilarities between the ground truth and prediction through persistent homology. Different from the previously suggested segmentation network designs, which apply the threshold filtration on a likelihood function of the prediction map and the Betti numbers of the ground truth, this paper proposes to apply the Vietoris-Rips filtration to obtain persistence diagrams of both ground truth and prediction maps and calculate the dissimilarity with the Wasserstein distance between the corresponding persistence diagrams. The use of this filtration has advantage of modeling shape and geometry at the same time, which may not happen when the threshold filtration is applied. Our experiments on 4327 CT images of 24 subjects reveal that the proposed topology-aware loss function leads to better results than its counterparts, indicating the effectiveness of this use

DETERMINATION OF THE AGRICULTURAL CHARACTERISTICS OF THE POLE FRESH BEAN POPULATION IN GREENHOUSE

WOS: 000302001100002In this study, improvement of pole fresh bean populations gathered from the Middle Black Sea Region was attempted using pure-line selection method under greenhouse conditions. The aim was to regain the populations that have lost their distinctive typical properties through breeding and bring them into use of local farmers. Fresh pole bean populations collected from Carsamba Plain of Middle-Black Sea region in 2003 were evaluated in terms of their agricultural characteristics under greenhouse conditions. In 2006 observation gardens were established in greenhouses; pre-yield and yield experiments were performed in the following 3 years (2007-2009). Eleven lines were selected according to UPOV criteria. In addition to best phenological and morphological traits being presented by C4-3. TK9-4 and TK43-4 lines in comparison to the control varieties; C4-3, TK43-4, L4 and TK50-3 lines outperformed the control varieties in terms of yield following stage 1 and stage II regional yield experiments on 11 lines between 2010-2011, and certain lines were selected to be candidates for certification.TAGEMGida Tarim Ve Hayvancilik BakanligiThis research was supported by TAGEM as part of a project titled "Reclaiming Local Dwarf fresh Bean Populations with Selection Method and Improving New Bean Types with Hybrid resistance against Anthracnose Disease". The research was conducted at Agricultural Research Institute of Black Sea Region, Samsun. We would like to thank Assoc. Prof. Muge Turet Sayar for her valuable criticisms during the preparation of the manuscript

Prenatal diagnosis of beta-thalassaemia and sickle cell anaemia in Turkey.

This paper reports our experience of molecular analysis and diagnosis of beta-thalassaemia and sickle cell anaemia (HbS) in 70 prospective parents of Turkish descent and their fetuses. Molecular screening was carried out by allele-specific oligonucleotide (ASO) hybridization of amplified DNA to the 12 most common mutations in the Turkish population. By using this approach, we were able to define the mutation in 95 per cent of chromosomes investigated. Genomic sequencing led to the additional detection of three rare mutations: Cd 44 (- C), IVS-I-5 (G-C), and IVS-I-116 (T-G). All diagnoses were successfully accomplished and no misdiagnosis occurred. Consanguineous marriage appears to contribute significantly to the frequency of affected births in Turkey. Out of the 14 homozygous fetuses, six were the result of close consanguinity. This study indicates that fetal diagnosis of P-thalassaemia and HbS may be obtained in practically all cases, even in a heterogeneous population like the Turkish population, when early methods of fetal sampling are combined with polymerase chain reaction (PCR)-based techniques. Until gene therapy becomes a reality, the only approaches to the control of haemoglobinopathies are prevention and avoidance. The most relevant and common aspects of the programmes, which have been very effective in reducing the birth rate of beta-thalassaemia major in several at-risk areas of the Mediterranean basin, are the continuous educational campaigns directed at the population at large, the voluntary basis, and non-directive counseling. The most important challenge for the eradication of the haemoglobin-opathies in Turkey is the organization of a nation-wide and comprehensive genetic preventive programme based on DNA technology