Ontological Levels in Histological Imaging

Paper presented at the 9th edition of the Formal Ontology in Information Systems conference, FOIS 2016, July 6–9, 2016, Annecy, FranceThis is the author accepted manuscript. The final version is available from IOS Press via the DOI in this record.In this paper we present an ontological perspective on ongoing work in histological and histopathological imaging involving the quantitative and algorithmic analysis of digitised images of cells and tissues. We present the derivation of consistent histological models from initially captured images of prepared tissue samples as a progression through a number of ontological levels, each populated by its distinctive classes of entities related in systematic ways to entities at other levels. We see this work as contributing to ongoing efforts to provide a consistent and widely accepted suite of ontological resources such as those currently constituting the OBO Foundry, and where possible we draw links between our work and existing ontologies within that suite.This research is supported by EPSRC through funding under grant EP/M023869/1 “Novel context-based segmentation algorithms for intelligent microscopy”

Automatic thresholding from the gradients of region boundaries

We present an approach for automatic threshold segmentation of greyscale images. The procedure is inspired by a reinterpretation of the strategy observed in human operators when adjusting thresholds manually and interactively by means of ‘slider’ controls. The approach translates into two methods. The first one is suitable for single or multiple global thresholds to be applied globally to images and consists of searching for a threshold value that generates a phase whose boundary coincides with the largest gradients in the original image. The second method is a variation, implemented to operate on the discrete connected components of the thresholded phase (i.e. the binary regions) independently. Consequently, this becomes an adaptive local threshold procedure, which operates relative to regions, rather than to local image subsets as is the case in most local thresholding methods previously published. Adding constraints for specifying certain classes of expected objects in the images can improve the output of the method over the traditional ‘segmenting first, then classify’ approach.The research reported in this paper was supported by the Engineering and Physical Sciences Research Council (EPSRC), UK through funding under grant EP/M023869/1 ‘Novel contextbased segmentation algorithms for intelligent microscopy’

Hypoxia Preconditioning Increases Survival and Decreases Expression of Toll-like Receptor 4 in Pulmonary Artery Endothelial Cells Exposed to Lipopolysaccharide

Pulmonary or systemic infections and hypoxemic respiratory failure are among the leading causes of admission to intensive care units, and these conditions frequently exist in sequence or in tandem. Inflammatory responses to infections are reproduced by lipopolysaccharide (LPS) engaging Toll-like receptor 4 (TLR4). Apoptosis is a hallmark of lung injury in sepsis. This study was conducted to determine whether preexposure to LPS or hypoxia modulated the survival of pulmonary artery endothelial cells (PAECs). We also investigated the role TLR4 receptor expression plays in apoptosis due to these conditions. Bovine PAECs were cultured in hypoxic or normoxic environments and treated with LPS. TLR4 antagonist TAK-242 was used to probe the role played by TLR4 receptors in cell survival. Cell apoptosis and survival were measured by caspase 3 activity and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) incorporation. TLR4 expression and tumor necrosis factor α (TNF-α) production were also determined. LPS increased caspase 3 activity in a TAK-242-sensitive manner and decreased MTT incorporation. Apoptosis was decreased in PAECs preconditioned with hypoxia prior to LPS exposure. LPS increased TNF-α production, and hypoxic preconditioning blunted it. Hypoxic preconditioning reduced LPS-induced TLR4 messenger RNA and TLR4 protein. TAK-242 decreased to baseline the LPS-stimulated expression of TLR4 messenger RNA regardless of environmental conditions. In contrast, LPS followed by hypoxia substantially increased apoptosis and cell death. In conclusion, protection from LPS-stimulated PAEC apoptosis by hypoxic preconditioning is attributable in part to reduction in TLR4 expression. If these signaling pathways apply to septic patients, they may account for differing sensitivities of individuals to acute lung injury depending on oxygen tensions in PAECs in vivo

Comparison of Direct Fluorescence Assay and Real-Time RT-PCR as Diagnostics for Respiratory Syncytial Virus in Young Children

Respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children worldwide. Early detection of RSV is critical to initiate proper care. Two methods, the direct fluorescence assay (DFA) and the real-time reverse-transcription polymerase chain reaction (rt-RT-PCR), that are used for RSV detection were compared. A total of 451 nasopharyngeal aspirates from children 5 years of age or less were tested for RSV using both methods. The overall prevalence rate of the RSV among the children was 23.7% with a significantly higher prevalence among children under the age of 6 months of age when compared to other age groups. The sensitivity of DFA in comparison to rt-RT-PCR was highest (86%) during the first 3 days of symptoms onset and decreased gradually till it reached 65% after the first week. The specificity of DFA in comparison to rt-RT-PCR ranged between 99 and 100% irrespective of the date of collection. We concluded that, although the rt-RT-PCR is more sensitive for RSV detection, the DFA offers a reliable point-of-care alternative detection method especially during the first few days of illness

An interactive boundary element analysis system

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Civil Engineering, 1985.MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING.Includes bibliographical references.by Fouad G. Tamer.M.S

Compressive behavior of refractory ceramics at elevated temperatures

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil Engineering, 1989.Title as it appears in M.I.T. Graduate List, Feb. 1989: Compressive behavior of refractory ceramics at high temperatures.Includes bibliographical references.by Fouad George Tamer.Ph.D

The Value of 18 Fluorine-fluorodeoxyglucose Positron Emission Tomography/Computed Tomography Imaging in Breast Cancer Staging

BACKGROUND: Accurate staging is important for management decisions in patients with newly diagnosed breast cancer. AIM: This study was conducted to evaluate the value of 18 fluorine-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) imaging in breast cancer staging.. METHODS: A prospective study of 80 patients (1 male and 79 female) mean age 51.13 years with histologically confirmed breast cancer. The staging procedures included history, physical examination, mammography, and CT of neck, chest, abdomen, and pelvis; then, PET/CT was performed in a time interval <30 days. The findings of PET/CT were compared with those of the other conventional methods. RESULTS: The agreement between conventional methods (mammography, breast ultrasound, contrast-enhanced CT of the neck, chest, abdomen, and pelvis) and 18F FDG-PET/CT was 0.6 for assessing the T stage, 0.39 for N stage, and 0.75 for M stage. There was moderate agreement between CT and 18F FDG-PET/CT in the detection of nodal lesions (K=0.6) and pulmonary lesions (K=0.51), while a perfect agreement was noted for detecting osseous (K=0.82) and liver lesions (K=0.81). In total, 50 patients (62.5%) were concordantly staged between the conventional imaging and 18F-FDG PET/CT, while 30 patients (37.5%) showed a different tumor, node, and metastasis stage. The changes were driven by the detection of additional findings (n=26) or exclusion of findings (n=4), mainly at the lymph nodes (LNs) and/or distant sites. Regarding N status, 18F FDG-PET/CT revealed previously unknown regional lymphatic spread in supraclavicular (n=4; 5%), infraclavicular (n=11; 13.7%), and internal mammary (n=12; 15%) lymph node groups. 18F-FDG PET/CT changed M status in a total of four patients (5%); three of them were upstaged by detecting distant metastases, while osseous deposits were excluded in one patient leading to downstaging. CONCLUSION: 18F-FDG-PET/CT is considered a valuable imaging tool in the initial staging of breast cancer, which significantly impacts the overall American Joint Committee on Cancer staging in 37.5% of our study population

Hepatic Arterial Therapy with Drug-Eluting Beads in the Management of Metastatic Bronchogenic Carcinoma to the Liver: A Multi-Institutional Registry

Introduction. There has been limited information reported on the use of hepatic arterial therapy in liver dominant hepatic metastases arising from lung cancer. The aim of this study was to evaluate the safety and efficacy of hepatic arterial therapy in the treatment of liver dominant hepatic metastases arising from lung cancer. Methods. Thirteen patients underwent a total of 30 treatment sessions with Drug-Eluting Beads. Eight of the thirteen received only doxorubicin DEB (17 of the total treatments), and four patients received Irinotecan DEB (7 of the total treatments). Results. The planned preprocedural dosage was a median of 75 mg (range 19–200), with total hepatic dose exposure being a median of 150 mg (range 0–458), with a technical success rate of 97% in all 29 treatments. There were 4 adverse events related to treatment, but no evidence of hepatic insufficiency. Overall 6-month and 12-month response rates were 50%. After a median followup of 24 months, the median overall survival in this cohort was 14 months (range 7–48 months). Conclusion. Drug-eluting beads loaded with doxorubicin (DEBDOX) or irinotecan (DEBIRI) can be safely and effectively used in treatment of patients with liver predominant metastatic disease from lung cancer

Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions

Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy εW/k = 220 K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E—εW/k = 78.2 K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally

Augmentation of tibial plateau fractures with Trabecular Metal™: a biomechanical study

<p>Abstract</p> <p>Background</p> <p>Restoration and maintenance of the plateau surface are the key points in the treatment of tibial plateau fractures. Any deformity of the articular surface jeopardizes the future of the knee by causing osteoarthritis and axis deviation. The purpose of this study is to evaluate the effect of Trabecular Metal (porous tantalum metal) on stability and strength of fracture repair in the central depression tibial plateau fracture.</p> <p>Method</p> <p>Six matched pairs of fresh frozen human cadaveric tibias were fractured and randomly assigned to be treated with either the standard of treatment (impacted cancellous bone graft stabilized by two 4.5 mm screws under the comminuted articular surface) or the experimental method (the same screws supporting a 2 cm diameter Trabecular Metal (TM) disc placed under the comminuted articular surface). Each tibia was tested on a MTS machine simulating immediate postoperative load transmission with 500 Newton for 10,000 cycles and then loaded to failure to determine the ultimate strength of the construct.</p> <p>Results</p> <p>The trabecular metal construct showed 40% less caudad displacement of the articular surface (1, 32 ± 0.1 mm vs. 0, 80 ± 0.1 mm) in cyclic loading (p < 0.05). Its mechanical failure occurred at a mean of 3275 N compared to 2650 N for the standard of care construct (p < 0, 05).</p> <p>Conclusion</p> <p>The current study shows the biomechanical superiority of the trabecular metal construct compared to the current standard of treatment with regards to both its resistance to caudad displacement of the articular surface in cyclic loading and its strength at load to failure.</p