Coupled Two-Way Clustering Analysis of Gene Microarray Data

We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant partitions emerge. The search for such subsets is a computationally complex task: we present an algorithm, based on iterative clustering, which performs such a search. This analysis is especially suitable for gene microarray data, where the contributions of a variety of biological mechanisms to the gene expression levels are entangled in a large body of experimental data. The method was applied to two gene microarray data sets, on colon cancer and leukemia. By identifying relevant subsets of the data and focusing on them we were able to discover partitions and correlations that were masked and hidden when the full dataset was used in the analysis. Some of these partitions have clear biological interpretation; others can serve to identify possible directions for future research

Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods

Bacterial infection is considered a predisposing factor for disorders of the biliary tract. This study aimed to determine the diversity of bacterial communities in bile samples and their involvement in the occurrence of biliary tract diseases. A total of 102 bile samples were collected during endoscopic retrograde cholangiopancreatography (ERCP). Characterization of bacteria was done using culture and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methods. Antimicrobial susceptibility of the isolates was determined based on the Clinical and Laboratory Standards Institute (CLSI) guidelines and identity of the nucleotide sequences of differentiated bands from the DGGE gels was determined based on GenBank data. In total, 41.2 (42/102) of the patients showed bacterial infection in their bile samples. This infection was detected in 21 (4/19), 45.4 (5/11), 53.5 (15/28), and 54.5 (24/44) of patients with common bile duct stone, microlithiasis, malignancy, and gallbladder stone, respectively. Escherichia coli showed a significant association with gallstones. Polymicrobial infection was detected in 48 of the patients. While results of the culture method established coexistence of biofilm-forming bacteria (Pseudomonas aeruginosa, E. coli, Klebsiella pneumoniae, Enterococcus spp., and Acinetobacter spp.) in different combinations, the presence of Capnocytophaga spp., Lactococcus spp., Bacillus spp., Staphylococcus haemolyticus, Enterobacter or Citrobacter spp., Morganella spp., Salmonella spp., and Helicobacter pylori was also characterized in these samples by the PCR-DGGE method. Multidrug resistance phenotypes (87.5 ) and resistance to third- and fourth-generation cephalosporins and quinolones were common in these strains, which could evolve through their selection by bile components. Ability for biofilm formation seems to be a need for polymicrobial infection in this organ. © 2016 Springer-Verlag Berlin Heidelber

An Investigation of the Effect of Ventilation Inlet and Outlet Arrangement on Heat Concentration in a Ship Engine Room

Τhe ventilation in the ship engine rooms is an essential issue concerning finest performance of engines and diesel generators as well as electric motors. The present study has aimed at the analysis of temperature distribution inside the ship main engine room. In the same way, attempts have been made to identify those points with considerable thermal concentration in main engine room space, so that proper ventilation systems could be engineered and utilized and favorable thermal conditions could be realized. The CFD approach has been utilized in order to analyze impact of the designed ventilation system on the temperature distribution pattern. The Inlet layout and area have been analyzed under a variety of scenarios in order to decrease the average temperature and eliminate the heat concentrations in various points of the engine room. The temperature distribution and location and area of ventilation air inlet have been studied in different modes resulted in temperature distribution pattern, heat concentration outline and average volumetric temperature level in each mode. The results indicated that considerable circulating air volume is required compared to those levels suggested by common practices, calculations and standards in order to eliminate the heat concentration

A CFD Study of Industrial Double-Cyclone in HDPE Drying Process

Double-cyclone in fluidized bed drying is an important equipment which reflects the conditions of drying in HDPE slurry process. Cyclone is an important unite of fluidized bed drying in order to move the solid particles outward to its wall. Therefore, flow pattern created in fluidized bed will affect industrial cyclones installed in dryer for dust removing. Pressure drop of the cyclones is an effective parameter represents the drying behavior. Substantially, geometry of cyclone, inlet flow rate of gas, density and particle size distribution (PSD) can affect the pressure drop value. Fluidized bed hydrodynamic regime is very complex and must be understood to improve fluidized bed operations through theoretical, industrial and CFD study of double-cyclone. Pressure drop is introduced as parameter related to the cyclone efficiency can be calculated with ANSYS Fluent software in the Eulerian-Lagrangian framework with RNG k-ɛ turbulence model used as a mathematical method. Proper pressure drop concluded from industrial experiments and CFD calculation shows good fluidization of HDPE particles in the bed of nitrogen and powder  to reach the best fluidized bed situation and suitable quality of HDPE powdery product

Multi-criteria decision making (MCDM) model for seismic vulnerability assessment (SVA) of urban residential buildings

© 2018 by the authors. Earthquakes are among the most catastrophic natural geo-hazards worldwide and endanger numerous lives annually. Therefore, it is vital to evaluate seismic vulnerability beforehand to decrease future fatalities. The aim of this research is to assess the seismic vulnerability of residential houses in an urban region on the basis of the Multi-Criteria Decision Making (MCDM) model, including the analytic hierarchy process (AHP) and geographical information system (GIS). Tabriz city located adjacent to the North Tabriz Fault (NTF) in North-West Iran was selected as a case study. The NTF is one of the major seismogenic faults in the north-western part of Iran. First, several parameters such as distance to fault, percent of slope, and geology layers were used to develop a geotechnical map. In addition, the structural construction materials, building materials, size of building blocks, quality of buildings and buildings-floors were used as key factors impacting on the building’s structural vulnerability in residential areas. Subsequently, the AHP technique was adopted to measure the priority ranking, criteria weight (layers), and alternatives (classes) of every criterion through pair-wise comparison at all levels. Lastly, the layers of geotechnical and spatial structures were superimposed to design the seismic vulnerability map of buildings in the residential area of Tabriz city. The results showed that South and Southeast areas of Tabriz city exhibit low to moderate vulnerability, while some regions of the north-eastern area are under severe vulnerability conditions. In conclusion, the suggested approach offers a practical and effective evaluation of Seismic Vulnerability Assessment (SVA) and provides valuable information that could assist urban planners during mitigation and preparatory phases of less examined areas in many other regions around the world

Intralobular pulmonary sequestration

Background: A 59-year-old non-smoking woman, with a history of gall stones, type 2 diabetes mellitus and hypertension, was referred to our hospital because of persistent coughing, night sweats, headaches and weight loss. Clinical examination revealed no abnormalities. The laboratory findings on admission were as follows: erythrocyte sedimentation rate was 39 mm/h, C-reactive protein level was 62 mg/mL and leukocyte count was 8.0 x 109/L. Bronchoscopic examination showed a normal bronchial tree

Neural Differentiation of Whartonś Jelly Stem Cells in Three-Dimensional Chitosan Based Culture Environment

BACKGROUND AND OBJECTIVE: Wharton Jelly Stem Cells (WJSCs) can be a good option for differentiating and regeneration of nervous system damage. Three dimensional (3D) cell cultures by providing a body-like environment have more advantages than the two dimensional (2D) cell cultures. The aim of this study was to investigate the neural differentiation of these cells in a 3D chitosan based culture environment. METHODS: This experimental study was performed in 4 groups of 2&3D with and without differentiation media on WJSCs. First, to construct the hydrogel, hydroxyl ethyl cellulose was added to chitosan-beta-glycerophosphate solution (8.4: 0.8) (HEC: CH-β-GF). Human WJSCs after isolation by enzymatic method from wartons' jelly of born infant in Imam Khomeini hospital in Tehran and characterization with flow cytometry, were cultured 510 5 cell in each well of 24-well plate in a 2D and 3D environment using the hydrogel in neural differentiation media for 4 days. Then, the neural differentiation of WJSCs was evaluated by quantitative analysis of β-Tubulin III, Nestin and β-actin (internal control) genes expression by Real Time PCR (RT-PCR). FINDINGS: The results of RT-PCR showed that expression of β-Tubulin III and Nestin genes in WJSCs was significantly increased by the influence of the neural differentiation media in both 2D (more than 4 folds)and 3D (more than 2 folds) culture conditions (p <0.005). But the expression of β-Tubulin III and Nestin in 3D cell culture condition (more than 1.5 folds) was greater than that in the 2D cell culture condition under the influence of the neural differentiation media (p <0.01). CONCLUSION: The results showed that neural differentiation of WJSCs in a chitosan based 3D environment is higher than 2D

Investigating the post-yield behavior of mineralized bone fibril arrays using a 3D non-linear finite element unit-cell model

Data availability: Data will be made available on request.Copyright © 2023 The Authors. In this study, we propose a 3D non-linear finite element (FE) unit-cell model to investigate the post-yield behavior of mineralized collagen fibril arrays (FAY). We then compare the predictions of the model with recent micro-tensile and micropillar compression tests in both axial and transverse directions. The unit cell consists of mineralized collagen fibrils (MCFs) embedded in an extrafibrillar matrix (EFM), and the FE mesh is equipped with cohesive interactions and a custom plasticity model. The simulation results confirm that MCF plays a dominant role in load bearing prior to yielding under axial tensile loading. Damage was initiated via debonding in shear and progressive sliding at the MCF/EFM interface, and resulted in MCF pull-out until brittle failure. In transverse tensile loading, EFM carried most of the load in pre-yield deformation, and then mixed normal/shear debonding between MCF and EFM began to form, which eventually produced brittle delamination of the two phases. The loading/unloading FE analysis in compression along both axial and transverse directions demonstrated perfect plasticity without any reduction in elastic modulus, i.e., damage due to the interfaces as seen in micropillar compression. Beyond the brittle and ductile nature of the stress–strain curves, in tensile and compressive loading, the simulated post-yield behavior and failure mechanism are in good quantitative agreement with the experimental observations. Our rather simple but efficient unit-cell FE model can reproduce qualitatively and quantitatively the mechanical behavior of bone ECM under tensile and compressive loading along the two main orientations. The model's integration into higher length scales may be useful in describing the macroscopic post-yield and failure behavior of trabecular and cortical bone in greater detail.Swiss Government Excellence Scholarship, Grant/Award Number (2021.0686)