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BACKGROUND: Türkiye is a country in the world ranking in terms of sheep breeding. Hamdani crossbred sheep breed is one of the sheep breeds that can adapt to the difficult conditions in our country. In addition, the sentence may be corrected as 'Especially in the southeastern part of the Türkiye, crossbreeding is preferred by breeders to increase the yield characteristics of sheep'. OBJECTIVES: In our study, it was aimed to perform a pelvimetric analysis of Hamdani crossbred sheep fetuses in the second and third trimesters by three-dimensional modelling method. METHODS: For this purpose, a total of 40 second-trimester (10 females, 10 males) and third-trimester (10 females, 10 males) fetuses were used. The pelvises of the fetuses were imaged with CT and 3D models were created. Sixteen pelvimetric measurements were performed from the models. The results obtained were evaluated statistically. RESULTS: The study found statistically significant differences between male and female fetuses in terms of vertical diameter (VD) and foramen obturatum width (FOW) measurement parameters in the second trimester. In the third trimester, there were statistically significant differences between genders in acetabulum (AC) (p < 0.01), medial ischial tuberosities (MIT), and ischiatic arch (IA) (p < 0.05) parameters. As a result of the correlation analysis, it was determined that the pelvis length (PL) measurement parameter was positively correlated with different parameters in varying degrees in both periods, while the IA parameter did not show significant correlations with the other parameter in the last two periods of pregnancy. CONCLUSION: In conclusion, the data obtained will be useful in pelvimetric evaluations of human and animal fetuses, anatomy education, zooarchaeology and taxonomy studies.

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OBJECTIVES: The aortic root (AoR) rotation and its spatial morphology at the base of the heart were postulated but not described in every detail. AoR rotation modalities may play an important role in decision-making during AoR surgery and its outcome. The aim was to provide a detailed spatial anatomy of the AoR rotation and its relation to the vital surrounding structure. METHODS: The AoR rotation and its relation to the surrounding structure were assessed in 104 patients with tricuspid aortic valve. The interatrial septum was chosen as a reference to describe AoR rotation that marked the midline of the heart base as a landmark for the AoR rotation direction. Intermediate, clockwise and counterclockwise AoR rotations were defined based on the mentioned reference structures. RESULTS: The AoR rotation was successfully assessed in 104 patients undergoing ascending aorta and or AoR intervention by multidetector row computed tomography. AoR was positioned normally in 53.8% of cases (n = 56) and rotated counterclockwise in 5.8% (n = 6) and clockwise in 40.4% (n = 42) of cases. In clockwise AoR rotation, the right coronary sinus was positioned in proximity to the right atrium and of the tricuspid valve, whereas in a counterclockwise rotation, the noncoronary sinus was placed over the tricuspid valve just over the membranous septum. CONCLUSIONS: The AoR's rotation can be diagnosed using multidetector row computed tomography. Understanding the anatomy of the aortic valve related to rotational position helps guide surgical decision-making in performing AoR reconstruction.

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The development of objective biomarkers for the qualitative assessment of oocytes prior to in-vitro fertilisation procedures is crucial, and in this respect the mechanical response of cells has already emerged as a promising and valid measure. The test setups derived from this conceptual approach usually induce complex, partly asymmetric deformation states, so that the process of material parameter identification can only be realised via three-dimensional, mathematical models. In the present study, a three-dimensional model for oocytes is proposed and implemented in the form of the finite element method. In particular, the contribution of each cellular component to the overall mechanical response is considered by including an anisotropic poro-, viscoelastic approach for the zona pellucida and an incompressible neo-Hookean material for the ooplasm. The model is calibrated and validated using experiments on porcine oocytes under plate-plate compression and indentation during quasi-static cyclic and relaxation tests. In addition to investigating the influence of glycoprotein orientation on the shape and extent of deformation, the applicability of the model to identify mechanical properties is demonstrated and discussed in relation to real, complex testing devices.

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The habitat preferences of many reef fishes are well established, but the use of space within these habitats by non-site-attached species is poorly studied. The authors examined the space use of a functionally important mesopredator, graysby (Cephalopholis cruentata), on six patch reefs in the Florida Keys. A 1 m2 -scale grid was constructed on each reef and 16 individual C. cruentata were tracked diurnally in situ to identify space use. At the patch reef scale, larger C. cruentata were more active and had larger observed home ranges, although home ranges were also affected by fish density and the abundances of prey and predators. The total time in each 1 m2 grid cell was regressed against a range of fine-scale biotic variables, including multiple variables derived from structure-from-motion three-dimensional digital reconstructions of each reef. Nonetheless, time in grid cells (preferred microhabitats) was only significantly positively correlated with the height of carbonate structures, likely because the cavities they enclose are particularly suitable for predator avoidance, resting and ambushing prey. The ongoing flattening of reefs in the region caused by negative carbonate budgets is thus likely to have significant effects on the abundance and space use of C. cruentata. In addition to examining spatial patterns, we analysed C. cruentata waiting times in each grid cell before moving. These times were best approximated by a truncated power-law (heavy-tailed) distribution, indicating a "bursty" pattern of relatively long periods of inactivity interspersed with multiple periods of activity. Such a pattern has previously been identified in a range of temperate ambush predators, and the authors extend this move-wait behaviour, which may optimize foraging success, to a reef fish for the first time. Understanding how C. cruentata uses space and time is critical to fully identify their functional role and better predict the implications of fishing and loss of reef structure.

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Introduction: A number of studies on using both three-dimensional printing and virtual models in assessment of aortic coarctation have been published, yet none of them uses virtual modelling as a planning tool in a blind retrospective analysis. Aim: Assessment of virtual modelling and virtual reality in planning interventional treatment of aortic coarctation. Material and methods: The study involved computed tomography scans of 20 patients performed prior to interventional treatment of aortic coarctation, which were used to create a virtual three-dimensional model of the aorta in Materialise Mimics. A group of potential stents was modelled in Materialise 3-Matic and complete simulations were assessed in Mimics Viewer using a virtual reality headset in order to choose an optimal stent, which was later compared with the implanted one. Results: In 5 cases identical or very similar stents were proposed, in 12 cases simulations had slight, potentially avoidable misestimations either in stent length or diameter, and in 3 cases differences were more considerable. Overall, in 14 cases the location of the stent was concordant between the simulation and reality and in the remaining 6 cases the simulated stent was located lower than the actual one. Conclusions: The method of computer modelling provided a satisfactory success rate of predicting the possible stents to use during the procedure. Differences in chosen stents may have been caused by individual experience in interventional cardiology, the lack of availability of certain stents in the heart catheterization laboratory, the lack of information about the diameter of the vascular access and differences in dimensions measured on the model, tomography and angiography.

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The paper presents effective numerical modelling of multi-layered plates with orthotropic properties. The method called the FEM23 is employed to construct the numerical model. The approach enables a full 3D analysis to be performed while using a 2D finite element mesh. The numerical model for a multi-layered plate is constructed by an assembling procedure, where each layer with orthotropic properties is added to the global numerical model. The paper demonstrates that the FEM23 method is very flexible in defining the multilayered plate, where the thickness of each layer as well as its mechanical orthotropic properties can be defined independently. Several examples of three-layered or nine-layered plates are analyzed in this paper. The results obtained by the FEM23 method coincide with the ones taken from the published papers or calculated with the standard 3D FEM approach. The orthotropic version of the FEM23 can be quite easily applied for other kinds of problems including thermo-mechanics, free vibrations, buckling analysis, or delamination.

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Reef squids belong to a group reputed for polarization sensitivity, yet polarization patterns of reef squid have not been quantified in situ. To quantify polarization patterns from video polarimetric data, we developed a protocol to map two-dimensional polarization data onto squid-shaped three-dimensional tessellated surfaces. This protocol provided a robust data container used to investigate three-dimensional regions-of-interest, producing data lineouts derived from the squid's geometry. This protocol also extracted polarimeter and squid body orientations and the solar heading from polarization images. When averaged over the solar heading, the ventral midline gave a low degree of polarization (2.4 ± 5.3%), and the area between the ventral and flank midlines had higher values (9.0 ± 5.3%). These averaged data had a large discontinuity in the angle of polarization (AoP) at the mantle's ventral midline (64 ± 55°), with larger discontinuities measured on individual squid. Ray-tracing calculations demonstrated that the AoP pattern was not related to the squid's surface-normal geometry. However, the AoP followed virtual striation axes on the squid's surface oriented 24° to the squid's long axis, similar in angle (27°) to the striations of birefringent collagen fibres documented in other squid species' skin.

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Geometric plant modelling is crucial in in silico plants. Existing geometric modelling methods have focused on the topological structure and basic organ profiles, simplifying the morphological features. However, the models cannot effectively differentiate cultivars, limiting FSPM application in crop breeding and management. This study proposes a 3D phytomer-based geometric modelling method with maize (Zea Mays) as the representative plant. Specifically, conversion methods between skeleton and mesh models of 3D phytomer are specified. This study describes the geometric modelling of maize shoots and populations by assembling 3D phytomers. Results show that the method can quickly and efficiently construct 3D models of maize plants and populations, with the ability to show morphological, structural and functional differences among four representative cultivars. The method takes into account both the geometric modelling efficiency and 3D detail features to achieve automatic operation of geometric modelling through the standardized description of 3D phytomers. Therefore, this study provides a theoretical and technical basis for the research and application of in silico plants.

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Central nervous system (CNS) tumors are a variety of distinct neoplasms that present multiple challenges in terms of treatment and prognosis. Glioblastoma, the most common primary tumor in adults, is associated with poor survival and remains one of the least treatable neoplasms. These tumors are highly heterogenous and complex in their nature. Due to this complexity, traditional cell culturing techniques and methods do not provide an ideal recapitulating model for the study of these tumors' behavior in vivo. Two-dimensional models lack the spatial arrangement, the heterogeneity in cell types, and the microenvironment that play a large role in tumor cell behavior and response to treatment. Recently, scientists have turned towards three-dimensional culturing methods, namely spheroids and organoids, as they have been shown to recapitulate tumors in a more faithful manner to their in vivo counterparts. Moreover, tumor-on-a-chip systems have lately been employed in CNS tumor modeling and have shown great potential in both studying the pathophysiology and therapeutic testing. In this review, we will discuss the current available literature on in vitro three-dimensional culturing models in CNS tumors, in addition to presenting their advantages and current limitations. We will also elaborate on the future implications of these models and their benefit in the clinical setting.

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BACKGROUND: Three-dimensional (3D) modelling technology translates the patient-specific anatomical information derived from two-dimensional radiological images into virtual or physical 3D models, which more closely resemble the complex environment encountered during surgery. It has been successfully applied to surgical planning and navigation, as well as surgical training and patient education in several surgical specialties, but its uptake lags behind in colorectal surgery. Rectal cancer surgery poses specific challenges due to the complex anatomy of the pelvis, which is difficult to comprehend and visualise. AIM: To review the current and emerging applications of the 3D models, both virtual and physical, in rectal cancer surgery. METHODS: Medline/PubMed, Embase and Scopus databases were searched using the keywords "rectal surgery", "colorectal surgery", "three-dimensional", "3D", "modelling", "3D printing", "surgical planning", "surgical navigation", "surgical education", "patient education" to identify the eligible full-text studies published in English between 2001 and 2020. Reference list from each article was manually reviewed to identify additional relevant papers. The conference abstracts, animal and cadaveric studies and studies describing 3D pelvimetry or radiotherapy planning were excluded. Data were extracted from the retrieved manuscripts and summarised in a descriptive way. The manuscript was prepared and revised in accordance with PRISMA 2009 checklist. RESULTS: Sixteen studies, including 9 feasibility studies, were included in the systematic review. The studies were classified into four categories: feasibility of the use of 3D modelling technology in rectal cancer surgery, preoperative planning and intraoperative navigation, surgical education and surgical device design. Thirteen studies used virtual models, one 3D printed model and 2 both types of models. The construction of virtual and physical models depicting the normal pelvic anatomy and rectal cancer, was shown to be feasible. Within the clinical context, 3D models were used to identify vascular anomalies, for surgical planning and navigation in lateral pelvic wall lymph node dissection and in management of recurrent rectal cancer. Both physical and virtual 3D models were found to be valuable in surgical education, with a preference for 3D printed models. The main limitations of the current technology identified in the studies were related to the restrictions of the segmentation process and the lack of 3D printing materials that could mimic the soft and deformable tissues. CONCLUSION: 3D modelling technology has potential to be utilised in multiple aspects of rectal cancer surgery, however, it is still at the experimental stage of application in this setting.

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BACKGROUND: Integrin αV, encoded by ITGAV gene, is one of the most studied protein subunits, closely associated with liver, pancreatic and stomach cancer progression and metastasis via regulation of angiogenesis. The occurrence of Single Nucleotide Polymorphisms (SNPs) in cancer- associated proteins is a key determinant for varied susceptibility of an individual towards cancer. METHODOLOGY: The study investigated the deleterious effects of these cancer-associated SNPs on the protein's structure, stability and cancer causing potential using an in silico approach. Numerous computational tools were employed that identified the most deleterious cancer-associated SNPs and those to get actively involved in post-translational modifications. The impact of these SNPs on the protein structure, function and stability was also examined. Conclusion and Future Scope: A total 63 non-synonymous SNPs in ITGAV gene were observed to be associated in these three gastrointestinal cancers and among this, 63, 19 were the most deleterious ones. The structural and functional importance of residues altered by most damaging SNPs was analyzed through evolutionary conservation and solvent accessibility. The study also elucidated three-dimensional structures of the 19 most damaging mutants. The analysis of conformational variation identified 5 SNPs (D379Y, G188E, G513V, L950P, and R540L) in integrin αV, which influence the protein's structure. Three calcium binding sites were predicted at residues: D379, G384 and G408 and a peptide binding site at residue: R369 in integrin αV. Therefore, SNPs D379Y, G384C, G408R and R369W have the potential to alter the binding properties of the protein. Screening and characterization of deleterious SNPs could advance novel biomarker discovery and therapeutic development in the future.

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In the packaging industry, the barrier property of packaging materials is of paramount importance. The enhancement of barrier properties of materials can be achieved by adding impermeable nanoparticles into thin polymeric films, known as mixed-matrix membranes (MMMs). Three-dimensional numerical simulations were performed to study the barrier property of these MMMs and to estimate the effective membrane gas permeability. Results show that horizontally-aligned thin cuboid nanoparticles offer far superior barrier properties than spherical nanoparticles for an identical solid volume fraction. Maxwell's model predicts very well the relative permeability of spherical and cubic nanoparticles over a wide range of the solid volume fraction. However, Maxwell's model shows an increasingly poor prediction of the relative permeability of MMM as the aspect ratio of cuboid nanoparticles tends to zero or infinity. An artificial neural network (ANN) model was developed successfully to predict the relative permeability of MMMs as a function of the relative thickness and the relative projected area of the embedded nanoparticles. However, since an ANN model does not provide an explicit form of the relation of the relative permeability with the physical characteristics of the MMM, a new model based on multivariable regression analysis is introduced to represent the relative permeability in a MMM with impermeable cuboid nanoparticles. The new model possesses a simple explicit form and can predict, very well, the relative permeability over an extensive range of the solid volume fraction and aspect ratio, compared with many existing models.

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BACKGROUND: Brassica rapeseed crops contain high concentrations of oil in the seed. The remaining meal, following oil extraction, has a high protein content, but is of low value due to the presence of high amounts of napin seed storage proteins. These 2S albumin-like proteins are difficult to digest and have been identified as major allergens in humans. OBJECTIVE: To comprehensively characterize the napin gene (NG) family in Brassica rapa and to gain an understanding of the structural basis of allergenicity of the expressed proteins. METHODS: To identify candidate napin genes in B rapa, 2S albumin-like napin genes of Arabidopsis thaliana were used as query sequences to search for similarity against the B rapa var. pekinensis Chiifu-401 v2 and the var. trilocularis R-o-18 v1.5 genomes. Multiple sequence alignment (MSA) and epitope modelling was carried out to determine structural and evolutionary relationships of NGs and their potential allergenicity. RESULTS: Four candidate napin genes in R-o-18 and ten in Chiifu-401 were identified with high sequence similarity to A thaliana napin genes. Multiple sequence alignment revealed strong conservation among the candidate genes. An epitope survey indicated high conservation of allergenic epitope motifs with known 2S albumin-like allergens. CONCLUSION: Napin is thought to be responsible for a  high prevalence of food allergies. Characterization of the napin gene family in B rapa will give important insight into the protein structure, and epitope modelling will help to advance studies into allergenicity including the development of precise diagnostic screenings and therapies for this potential food allergy as well as the possible manipulation of napin levels in the seed by gene editing technology.

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BACKGROUND: This study was aimed to examine the detailed morphometrical and morphological characteristics of the bone by creating three-dimensional images through multidetector computed tomography images of ossa cruris in brown bears. MATERIALS AND METHODS: Four brown bear ossa cruris were used in the study. RESULTS: It was observed that tibia and fibula articulated at proximal and distal epiphysis and they combined, and ossa cruris were shaped in this way. Cochlea tibiae were determined to be sagittally oriented. The length of the tibia was determined to be 268.97 mm and 266.32 mm at right and left sides, respectively. The length of the fibula was determined to be 249.16 mm and 250.19 mm on average at the right and left sides, respectively. In consequence of the correlation analysis, statistical relationships at different rates were detected between the measured values. CONCLUSIONS: Detailed anatomical examinations are very important in terms of determining the similarities and differences of bear bones with those of the other species in the order Carnivora. Therefore, it is thought that this study will reveal detailed characteristics of ossa cruris of bears and provide data for further studies on archaeological and forensic sciences.

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An exceptional property of skeletal muscles that distinguishes them from other soft tissues is their ability to contract by generating active forces, which in turn are initiated by an electrochemical trigger. Some of these so-called active material properties are generally characterised using isometric contraction experiments at various muscle lengths. In this context, experimental observations revealed that unlike the widespread assumption in muscle modelling, reaction forces indeed depend on so-called history effects, which can be classified into force enhancement and force depression. For the experimental settings of force enhancement, two subsequent isometric contractions are interrupted by an isokinetic extension. The isometric reaction force is increased after the isokinetic extension with respect to a reference measurement, while in the case of force depression, isokinetic shortening is responsible for forces below a certain isometric reference measurement. Most theoretical investigations of force enhancement and force depression use one-dimensional models to simulate the force response considering muscle deformation to be homogeneous. In contrast, the aim of the present study is to analyse history effects in skeletal muscle tissue using a three-dimensional geometry model of the whole muscle-tendon unit. Therefore, a purely phenomenological approach is presented. The model is implemented in the finite element framework to analyse history effects for the boundary value problem of the entire three-dimensional muscle-tendon geometry. The constitutive model shows good agreement with the experimental data. Furthermore, the simulations reveal information about the inhomogeneous stretch distributions within the muscle tissues.

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The elongate-necked aquatic plesiosaurs existed for 135 Myr during the Mesozoic. The function of this elongate neck is a point of debate. Using computed tomography and three-dimensional (3D) modelling, the range of motion (ROM) of the plesiosaur Nichollssaura borealis neck was assessed. To quantify the ROM, the intervertebral mobility was measured along the cervical vertebral column. This was done by manipulating the 3D models in the lateral and dorsoventral directions during two trials. The first assessed the mean intervertebral ROM between pairs of cervical vertebrae along the entire column, and the second assessed ROM with reduced intervertebral spaces. The results suggest that there may be preference for lateral neck movements in N. borealis, which could correspond to an ecological function related to prey capture. This study demonstrates that 3D modelling is an effective tool for assessing function morphology for structures where no good modern analogue exists.

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During fossilization, the remains of extinct organisms are subjected to taphonomic and diagenetic processes. As a result, fossils show a variety of preservational artefacts, which can range from small breaks and cracks, disarticulation and fragmentation, to the loss and deformation of skeletal structures and other hard parts. Such artefacts can present a considerable problem, as the preserved morphology of fossils often forms the basis for palaeontological research. Phylogenetic and taxonomic studies, inferences on appearance, ecology and behaviour and functional analyses of fossil organisms strongly rely on morphological information. As a consequence, the restoration of fossil morphology is often a necessary prerequisite for further analyses. Facilitated by recent computational advances, virtual reconstruction and restoration techniques offer versatile tools to restore the original morphology of fossils. Different methodological steps and approaches, as well as software are outlined and reviewed here, and advantages and disadvantages are discussed. Although the complexity of the restorative processes can introduce a degree of interpretation, digitally restored fossils can provide useful morphological information and can be used to obtain functional estimates. Additionally, the digital nature of the restored models can open up possibilities for education and outreach and further research.

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Computer assisted technologies offer new opportunities in medical imaging and rapid prototyping in biomechanical engineering. Three dimensional (3D) modelling of soft tissues and bones are becoming more important. The accuracy of the analysis in modelling processes depends on the outline of the tissues derived from medical images. The aim of this study is the evaluation of the accuracy of 3D models of a dog femur derived from computed tomography data by using point cloud method and boundary line method on several modelling software. Solidworks, Rapidform and 3DSMax software were used to create 3D models and outcomes were evaluated statistically. The most accurate 3D prototype of the dog femur was created with stereolithography method using rapid prototype device. Furthermore, the linearity of the volumes of models was investigated between software and the constructed models. The difference between the software and real models manifests the sensitivity of the software and the devices used in this manner.

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BACKGROUND: Reconstructing three-dimensional structures of chromosomes is useful for visualizing their shapes in a cell and interpreting their function. In this work, we reconstruct chromosomal structures from Hi-C data by translating contact counts in Hi-C data into Euclidean distances between chromosomal regions and then satisfying these distances using a structure reconstruction method rigorously tested in the field of protein structure determination. RESULTS: We first evaluate the robustness of the overall reconstruction algorithm on noisy simulated data at various levels of noise by comparing with some of the state-of-the-art reconstruction methods. Then, using simulated data, we validate that Spearman's rank correlation coefficient between pairwise distances in the reconstructed chromosomal structures and the experimental chromosomal contact counts can be used to find optimum conversion rules for transforming interaction frequencies to wish distances. This strategy is then applied to real Hi-C data at chromosome level for optimal transformation of interaction frequencies to wish distances and for ranking and selecting structures. The chromosomal structures reconstructed from a real-world human Hi-C dataset by our method were validated by the known two-compartment feature of the human chromosome organization. We also show that our method is robust with respect to the change of the granularity of Hi-C data, and consistently produces similar structures at different chromosomal resolutions. CONCLUSION: Chromosome3D is a robust method of reconstructing chromosome three-dimensional models using distance restraints obtained from Hi-C interaction frequency data. It is available as a web application and as an open source tool at http://sysbio.rnet.missouri.edu/chromosome3d/ .

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BACKGROUND: The eNOS gene has been extensively screened for important variations in the promoter (-786T/C), Intron 4 (4b/4a) and exon 7 (894G/T) regions in multiple diseases. Prevalence of Coronary Heart Disease (CHD) is much higher in young Indians when compared to other ethnic groups and first-degree relatives (FDRS) of CHD patients are at risk correlating with earlier age-of-onset and poor prognosis. OBJECTIVE: The objective of this study is to understand the genetic mechanism of eNOS -786T/C, Intron 4b/4a and 894G/T polymorphisms/haplotypes in the development of CHD and to identify individuals having coronary risk factors among the FDRS of CHD patients by comparing them with the general population. MATERIALS & METHODS: The study population consisted of 300 CHD patients with angiographically documented, 100 FDRS and 300 age and sex matched healthy controls. Genotyping of eNOS -786T/C, Intron 4b/4a was carried out by Allele specific-Polymerase Chain Reaction (As-PCR) and 894G/T by PCR-restriction fragment length polymorphism (PCR-RFLP) assays. RESULTS: The frequency of risk factors for CHD includes age, blood pressure, obesity, diabetes mellitus, smoking, non-vegetarian diet, family history are higher in CHD patients and FDRS compared to controls (p < 0.01). The genotype distribution, allele frequencies and haplotypes of the eNOS -786T/C, 4b/4a and 894G/T were significantly different between CHD patients, FDRS and controls. eNOS gene haplotypes GCB, TCB (G-allele of 894G/T, C-allele -786T/C, B-allele of Intron 4b/4a respectively) were associated with high nitrite/nitrate levels compared to GTB in both FDRS and CHD patients (p < 0.01). CONCLUSION: The study shows the importance of eNOS polymorphism in the pathogenesis of CHD and predicting the risk of future coronary events in asymptomatic healthy FDRS and suggests the use of new therapeutics and initiating the measures for prevention or delaying the progression of the disease by life style modification or treatment modalities in high-risk individuals.

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