Benchmarking off-the-shelf statistical shape modeling tools in clinical applications

Statistical shape modeling (SSM) is widely used in biology and medicine as a new generation of morphometric approaches for the quantitative analysis of anatomical shapes. Technological advancements of in vivo imaging have led to the development of open-source computational tools that automate the modeling of anatomical shapes and their population-level variability. However, little work has been done on the evaluation and validation of such tools in clinical applications that rely on morphometric quantifications(e.g., implant design and lesion screening). Here, we systematically assess the outcome of widely used, state-of-the-art SSM tools, namely ShapeWorks, Deformetrica, and SPHARM-PDM. We use both quantitative and qualitative metrics to evaluate shape models from different tools. We propose validation frameworks for anatomical landmark/measurement inference and lesion screening. We also present a lesion screening method to objectively characterize subtle abnormal shape changes with respect to learned population-level statistics of controls. Results demonstrate that SSM tools display different levels of consistencies, where ShapeWorks and Deformetrica models are more consistent compared to models from SPHARM-PDM due to the groupwise approach of estimating surface correspondences. Furthermore, ShapeWorks and Deformetrica shape models are found to capture clinically relevant population-level variability compared to SPHARM-PDM models.

Efficient Segmentation Pipeline Using Diffeomorphic Image Registration: A Validation Study

Functional measurements of the left atrium (LA) in atrial fibrillation (AF) patients is limited to a single CINE slice midway through the LA. Nonetheless, a full 3D characterization of atrial functional measurements would provide more insights into LA function. But this improved modeling capacity comes at a price of requiring LA segmentation of each 3D time point,a time-consuming and expensive task that requires anatomy-specific expertise.We propose an efficient pipeline which requires ground truth segmentation of a single (or limited) CINE time point to accurately propagate it throughout the sequence. This method significantly saves human effort and enable better characterization of LA anatomy. From a gated cardiac CINE MRI sequence we select a single CINE time point with ground truth segmentation, and assuming cyclic motion, we register other images corresponding to all time points using diffeomorphic registration in ANTs. The diffeomorphic registration fields allow us to map a given anatomical shape (segmentation) to each CINE time point, facilitating the construction of a 4D shape model.

Interatrial Septum and Appendage Ostium in Atrial Fibrillation Patients: A Population Study

Left atrial appendage (LAA) closure is performed in atrial fibrillation (AF) patients to help prevent stroke. LAA closure using an occlusion implant is performed under imaging guidance. However, occlusion can be a complicated process due to the highly variable and heterogeneous LAA shapes across patients. Patient-specific implant selection and insertion processes are keys to the success of the procedure, yet subjective in nature. A population study of the angle of entry at the interatrial septum relative to the appendage can assist in both catheter design and patient-specific implant choice. In our population study, we analyzed the inherent clusters of the angles that were obtained between the septum normal and the LAA ostium plane. The number of inherent angle clusters matched the LAA four morphological classifications reported in the literature. Further, our exploratory analysis revealed that the normal from the ostium plane does not intersect the septum in all the samples under study. The insights gained from this study can help assist in making objective decisions during LAA closure.

On the Evaluation and Validation of Off-the-shelf Statistical Shape Modeling Tools: A Clinical Application

Statistical shape modeling (SSM) has proven useful in many areas of biology and medicine as a new generation of morphometric approaches for the quantitative analysis of anatomical shapes. Recently, the increased availability of high-resolution in vivo images of anatomy has led to the development and distribution of open-source computational tools to model anatomical shapes and their variability within populations with unprecedented detail and statistical power. Nonetheless, there is little work on the evaluation and validation of such tools as related to clinical applications that rely on morphometric quantifications for treatment planning. To address this lack of validation, we systematically assess the outcome of widely used off-the-shelf SSM tools, namely ShapeWorks, SPHARM-PDM, and Deformetrica, in the context of designing closure devices for left atrium appendage (LAA) in atrial fibrillation (AF) patients to prevent stroke, where an incomplete LAA closure may be worse than no closure. This study is motivated by the potential role of SSM in the geometric design of closure devices, which could be informed by population-level statistics, and patient-specific device selection, which is driven by anatomical measurements that could be automated by relating patient-level anatomy to population-level morphometrics. Hence, understanding the consequences of different SSM tools for the final analysis is critical for the careful choice of the tool to be deployed in real clinical scenarios. Results demonstrate that estimated measurements from ShapeWorks model are more consistent compared to models from Deformetrica and SPHARM-PDM. Furthermore, ShapeWorks and Deformetrica shape models capture clinically relevant population-level variability compared to SPHARM-PDM models.

Acute Toxicity Assessment of Reactive Red 120 to Certain Aquatic Organisms

Laboratory experiments were conducted to evaluate the acute toxicity of a widely used textile dye namely Reactive Red 120 (RR 120) on certain aquatic species such as Pseudokirchneriella subcapitata (green alga), Lemna gibba (duck weed), Daphnia magna (water flea) and Oncorhynchus mykiss (Rainbow trout). All experiments were performed as per the OECD Guidelines for Testing of Chemicals. The toxicity end points of EC50, LC50, NOEC and LOEC for RR 120 were determined with 95% confidence limits using TOX STAT version 3.5. The EC50 of RR 120 for green alga, duck weed and water flea are >100.00, 64.34, 10.40 mg L(-1), respectively and LC50 for Rainbow trout is 78.84 mg L(-1). Based on the results, the test item RR 120 could be classified as non-toxic to green alga, harmful to duck weed and Rainbow trout, toxic to water flea.

Nanoemulsified ethanolic extract of Pyllanthus amarus Schum & Thonn ameliorates CCl4 induced hepatotoxicity in Wistar rats

Phyllanthus amarus (PA) is commonly used in traditional medicine for hepatoprotectivity. The major limitation is that, treatment requires a large quantity of herbal extract for a longer duration. Aim of the present study was to encapsulate ethanolic plant extract for sustained release of constituents in intestine and facilitate maximum absorption. The efficacy was compared for the hepatoprotective activity of nanoencapsulated ethanolic extract of P. amarus (NPA) and PA in carbon tetrachloride (CCl4) induced hepatotoxic male rats. Based on total phenol content (TPC), the loading efficiency of nanocapsules was 89% (pH 7.0) and optimum concentration was 2:18 (mg/mL) for plant extract: olive oil. Scanning electron microscopy (SEM) showed a spherical morphology, photon correlation spectroscopy (PCS) identified mean particle diameter as 213 nm and Fourier transform infrared spectroscopy (FT-IR) revealed that the phytoconstituents were stable. An oral dose of NPA (20 mg/kg body wt.) showed a better hepatoprotective activity than PA (100 mg/kg body wt.) and also repeated dose oral toxicity proved to be safe. These biochemical assessments were supported by rat biopsy examinations. In conclusion, the nanoemulsification method may be applied for poor water-soluble ethanolic herbal extracts to reduce the dosage and time.

Oxidative stress and inflammatory responses of rat following acute inhalation exposure to iron oxide nanoparticles

In this research, we investigated the toxicity responses of rat following a continuous 4 h inhalation exposure of only the head and nose to iron oxide nanoparticles (Fe(3)O(4) NPs, size = 15-20 nm). The rats for the investigation were exposed to a concentration of 640 mg/m(3) Fe(3)O(4) NPs. Markers of lung injury and proinflammatory cytokines (interleukin-1β, tumor necrosis factor-α, and interleukin-6) in bronchoalveolar lavage fluid (BALF) and blood, oxidative stress in lungs, and histopathology were assessed on 24 h, 48 h, and 14 days of postexposure periods. Our results showed a significant decrease in the cell viability, with the increase in the levels of lactate dehydrogenase, total protein, and alkaline phosphatase in the BALF. Total leukocyte count and the percentage of neutrophils in BALF increased within 24 h of postexposure. Immediately following acute exposure, rats showed increased inflammation with significantly higher levels of lavage and blood proinflammatory cytokines and were consistent throughout the observation period. Fe(3)O(4) NPs exposure markedly increased malondialdehyde concentration, while intracellular reduced glutathione and antioxidant enzyme activities were significantly decreased in lung tissue within 24-h postexposure period. On histological observation, the lung showed an early activation of pulmonary clearance and a size-dependant biphasic nature of the Fe(3)O(4) NPs in causing the structural alteration. Collectively, our data illustrate that Fe(3)O(4) NPs inhalation exposure may induce cytotoxicity via oxidative stress and lead to biphasic inflammatory responses in Wistar rat.

Toxicity Assessment of Expired Pesticides to Green Algae Pseudokirchneriella subcapitata

In order to investigate the effect of expired pesticides on the yield and growth rate of green algae Pseudokirchneriella subcapitata, a study was conducted as per the Organisation for Economic Cooperation and Development (OECD) guideline number 201. Fifteen expired pesticide formulations, most commonly used in Indian agriculture, were tested in comparison with their unexpired counterparts. The expired pesticide formulations studied belonged to various class and functional groups: organophosphate, pyrethroid-based insecticides; azole-based fungicides; acetamide, propionate, acetic acid-based herbicides; fungicides mixtures containing two actives—azole and dithiocarbamate. The toxicity endpoints of yield (E_yC₅₀: 0–72 h) and growth rate (E_rC₅₀: 0–72 h) of Pseudokirchneriella subcapitata for each pesticide formulation (both expired and unexpired pesticides) were determined statistically using TOXSTAT 3.5 version software. The results pointed out that some expired pesticide formulations exhibited higher toxicity to tested algal species, as compared to the corresponding unexpired pesticides. These data thus stress the need for greater care to dispose expired pesticides to water bodies, to avoid the effects on aquatic ecospecies tested.