TuNet: End-to-end Hierarchical Brain Tumor Segmentation using Cascaded Networks

Glioma is one of the most common types of brain tumors; it arises in the glial cells in the human brain and in the spinal cord. In addition to having a high mortality rate, glioma treatment is also very expensive. Hence, automatic and accurate segmentation and measurement from the early stages are critical in order to prolong the survival rates of the patients and to reduce the costs of the treatment. In the present work, we propose a novel end-to-end cascaded network for semantic segmentation that utilizes the hierarchical structure of the tumor sub-regions with ResNet-like blocks and Squeeze-and-Excitation modules after each convolution and concatenation block. By utilizing cross-validation, an average ensemble technique, and a simple post-processing technique, we obtained dice scores of 88.06, 80.84, and 80.29, and Hausdorff Distances (95th percentile) of 6.10, 5.17, and 2.21 for the whole tumor, tumor core, and enhancing tumor, respectively, on the online test set.Comment: Accepted at MICCAI BrainLes 201

A nano-particle based approach to improve filtration control of water based muds under high pressure high temperature conditions

There have been many attempts to improve the filtration control of water based muds under High Pressure High Temperature (HPHT) condition using a cost effective approach. Nano particles are perhaps the best option considering their successful applications reported in many studies. However, they are often expensive and pose unfavourably changes on the rheology of the muds. In this paper, an attempt was made to show the application of Nano Glass Flakes (NGFs) as a cheap but effective nano particle to control the filtration of water based muds under HPHT conditions. Performing a series of rheology, filtration and conductivity tests on the mud samples with unmodified NGFs revealed that this nano particle increases the mud rheology, yield point and gel strength of the mud with a slight impact on the filtration loss. However, by modifying the surface charges of NGFs with a cationic surfactant, filtration loss was significantly reduced without any severe impacts on the mud rheology. Considering the conductivity of the mud which increases by adding the modified NGF, this nano particle might be a good choice to improve the overall performance of water based muds under HPHT conditions

Entropic forces generated by grafted semiflexible polymers

The entropic force exerted by the Brownian fluctuations of a grafted semiflexible polymer upon a rigid smooth wall are calculated both analytically and by Monte Carlo simulations. Such forces are thought to play an important role for several cellular phenomena, in particular, the physics of actin-polymerization-driven cell motility and movement of bacteria like Listeria. In the stiff limit, where the persistence length of the polymer is larger than its contour length, we find that the entropic force shows scaling behavior. We identify the characteristic length scales and the explicit form of the scaling functions. In certain asymptotic regimes we give simple analytical expressions which describe the full results to a very high numerical accuracy. Depending on the constraints imposed on the transverse fluctuations of the filament there are characteristic differences in the functional form of the entropic forces; in a two-dimensional geometry the entropic force exhibits a marked peak.Comment: 21 pages, 18 figures, minor misprints correcte

Swarm intelligence optimization of the group method of data handling using the cuckoo search and whale optimization algorithms to model and predict landslides

The robustness of landslide prediction models has become a major focus of researchers worldwide. We developed two novel hybrid predictive models that combine the self-organizing, deep-learning group method of data handling (GMDH) with two swarm intelligence optimization algorithms, i.e., cuckoo search algorithm (CSA) and whale optimization algorithm (WOA) for spatially explicit prediction of landslide susceptibility. Eleven landslide-causing factors and 334 historic landslides in a 31,340 km2 landslide-prone area in Iran were used to produce geospatial training and validation datasets. The GMDH model was employed to develop a basic predictive model that was then restructured and its parameters were optimized using the CSA and WOA algorithms, yielding the novel hybrid GMDH-CSA and GMDH-WOA models. The hybrid models were validated and compared to the standalone GMDH model by calculating the area under the receiver operating characteristic (AUC) curve and root mean square error (RMSE). The results demonstrated that the hybrid models overcame the computational shortcomings of the basic GMDH model and significantly improved landslide susceptibility prediction (GMDH-CSA, AUC = 0.909 and RMSE = 0.089; GMDH-WOA, AUC = 0.902 and RMSE = 0.129; standalone GMDH, AUC = 0.791 and RMSE = 0.226). Further, the hybrid models were more robust than the standalone GMDH model, showing consistently excellent performance when the training and validation datasets were changed. Overall, the swarm intelligence-optimized models, but not the standalone model, identified the best trade-offs among objectives, accuracy, and robustness

Dynamics of an Intruder in Dense Granular Fluids

We investigate the dynamics of an intruder pulled by a constant force in a dense two-dimensional granular fluid by means of event-driven molecular dynamics simulations. In a first step, we show how a propagating momentum front develops and compactifies the system when reflected by the boundaries. To be closer to recent experiments \cite{candelier2010journey,candelier2009creep}, we then add a frictional force acting on each particle, proportional to the particle's velocity. We show how to implement frictional motion in an event-driven simulation. This allows us to carry out extensive numerical simulations aiming at the dependence of the intruder's velocity on packing fraction and pulling force. We identify a linear relation for small and a nonlinear regime for high pulling forces and investigate the dependence of these regimes on granular temperature

Bio-nanotechnology application in wastewater treatment

The nanoparticles have received high interest in the field of medicine and water purification, however, the nanomaterials produced by chemical and physical methods are considered hazardous, expensive, and leave behind harmful substances to the environment. This chapter aimed to focus on green-synthesized nanoparticles and their medical applications. Moreover, the chapter highlighted the applicability of the metallic nanoparticles (MNPs) in the inactivation of microbial cells due to their high surface and small particle size. Modifying nanomaterials produced by green-methods is safe, inexpensive, and easy. Therefore, the control and modification of nanoparticles and their properties were also discussed

Knowledge translation in Iranian universities: Need for serious interventions

Background: The aim of this study was to assess the status of knowledge translation (KT) in Iranian medical science universities in order to assess the strengths and weaknesses of the most important organizations responsible for producing knowledge in the country.Methods: The KT activities were assessed qualitatively and quantitatively in nine universities using the Self-Assessment Tool for Research Institutes.Results: The strengths and weaknesses of universities were determined using seven main themes: priority setting; research quality and timeliness; researchers' KT capacities; interaction with research users; the facilities and prerequisites of KT; the processes and regulations supporting KT; and promoting and evaluating the use of evidence.The quantitative and qualitative results showed that the Iranian universities did not have an appropriate context for KT. There were significant shortcomings in supportive regulations, facilities for KT activities, and the level of interaction between the researchers and research users.Conclusions: The shortcomings in KT were mostly in the area of stewardship and policymaking (macro level), followed by planning and implementation at the universities. In order to strengthen KT in Iran, it should occupy a prominent and focused role in the strategies of the country's health research system. © 2013 Gholami et al.; licensee BioMed Central Ltd