Sharif Digital Repository

Organ-on-a-chip technology tries to mimic the complexity of native tissues in vitro. Important progress has recently been made in using this technology to study the gut with and without microbiota. These in vitro models can serve as an alternative to animal models for studying physiology, pathology, and pharmacology. While these models have greater physiological relevance than two-dimensional (2D) cell systems in vitro, endocrine and immunological functions in gut-on-a-chip models are still poorly represented. Furthermore, the construction of complex models, in which different cell types and structures interact, remains a challenge. Generally, gut-on-a-chip models have the potential to... 

Contrast induced nephropathy (CIN) has been reported to be the third foremost cause of acute renal failure. Metabolomics is a robust technique that has been used to identify potential biomarkers for the prediction of renal damage. We aim to analyze the serum and urine metabolites changes, before and after using contrast for coronary angiography, to determine if metabolomics can predict early development of CIN. 66 patients undergoing elective coronary angiography were eligible for enrollment. Urine and serum samples were collected prior to administration of CM and 72 h post procedure and analyzed by nuclear magnetic resonance. The significant differential metabolites between patients who... 

The search for efficient chemotherapy drugs and other anti-cancer treatments would benefit from a deeper understanding of the tumor microenvironment (TME) and its role in tumor progression. Because in vivo experimental methods are unable to isolate or control individual factors of the TME and in vitro models often do not include all the contributing factors, some questions are best addressed with systems biology mathematical models. In this work, we present a new fully-coupled, agent-based, multi-scale mathematical model of tumor growth, angiogenesis and metabolism that includes important aspects of the TME spanning subcellular-, cellular- and tissue-level scales. The mathematical model is... 

A new approach, based on Adaptive-Network-based Fuzzy Inference System (ANFIS), is presented for the classification of arthrometric data of normal/ACL-ruptured knees, considering the insufficiency of existing criteria. An ANFIS classifier was developed and tested on a total of 4800 arthrometric data points collected from 40 normal and 40 injured subjects. The system consisted of 5 layers and 8 rules, based on the results of subtractive data clustering, and trained using the hybrid algorithm method. The performance of the system was evaluated in four runs, in the framework of a 4-fold cross validation algorithm. The results indicated a definite correct diagnosis for typical injured and normal... 

Using an iterative kinematics-driven nonlinear finite element model, relative efficiency of individual abdominal muscles in spinal stability in upright standing posture was investigated. Effect of load height on stability and muscle activities was also computed under different coactivity levels in abdominal muscles. The internal oblique was the most efficient muscle (compared with the external oblique and rectus abdominus) in providing stability while generating smaller spinal loads with lower fatigue rate of muscles. As the weight was held higher, stability deteriorated requiring additional flexor-extensor activities. The stabilising efficacy of abdominal muscles diminished at higher... 

The effect of the variation in the femoral groove geometry on patellofemoral joint stability was studied using a two dimensional transverse plane model with deformable articular surfaces. The femoral and patellar bony structures were modelled as rigid bodies with their profiles expressed by splines. The articular cartilage was discretized into compression springs, distributed along the femoral and patellar profiles, based on the rigid-body spring model. The medial and lateral retinacula were modelled as linear tensile springs, and the quadriceps muscles and patellar tendon as strings with known tension. The anatomical data were obtained from the transverse plane magnetic resonance images of... 

We simulated the knee arthrometry test to obtain a deeper understanding of the joint's stability behavior and interpret the arthrometric results more effectively. A 2D sagittal plane finite element model of the lower limb in the standard configuration of knee arthrometry was developed using ANSYS APDL. A detailed model of the knee joint was considered including the femoral articulating contour represented by an ellipse, the tibial plateau represented by a circular arc, and four major knee ligaments and their individual bundles represented by linear and nonlinear tensile springs. A deformable layer of articular cartilage was also considered over the tibial plateau to simulate the bones... 

Patellar lateral stability was studied using a 2D transverse plane model with deformable articular surfaces. Quadriceps muscles and patellar tendon were considered as strings with predefined forces and lateral and medial retinaculum as tensile springs. Deformation behavior of articular cartilage was modeled by a set of compression springs perpendicular to articular surfaces, based on rigid body spring model method (RBSM). Patellar lateral stability was investigated using restraining force method (the external force required to cause up to 10 mm lateral displacement on patella). The results were in good agreement with experimental reports for normal joint, vastus lateralis and vastus medialis... 

Introduction: This study was conducted to investigate the relationship of glomerular and tubular dysfunctions with glycaemic control, lipid, lipoprotein, apolipoproteins and antioxidant status in 72 patients with type 2 diabetes mellitus. Methods: Urine albumin concentration was measured by immunoturbidimetric and urine N-acetyl-beta-D-glucosaminidase (NAG) and alanine aminopeptidase (AAP) activities with colorimetric methods. Glycated haemoglobin was measured using affinity chromatography. Erythrocyte glu ta thione reductase and glutathione peroxidase activities and serum levels of malondialdehyde, lipids, lipoproteins and apolipoproteins were determined in patients with type 2 diabetes... 

Human infertility is a multifactorial disease that affects 8%–12% of reproductive-aged couples worldwide. However, the genetic causes of human infertility are still poorly understood. Synaptonemal complex (SC) is a conserved tripartite structure that holds homologous chromosomes together and plays an indispensable role in the meiotic progression. Here, we identified three homozygous mutations in the SC coding gene C14orf39/SIX6OS1 in infertile individuals from different ethnic populations by whole-exome sequencing (WES). These mutations include a frameshift mutation (c.204_205del [p.His68Glnfs∗2]) from a consanguineous Pakistani family with two males suffering from non-obstructive... 

Mechanical ventilation (MV) can result in long-term brain impairments that are resistant to treatment. The mechanisms underlying MV-induced brain function impairment remain unclear. Since nasal airflow modulates brain activity, here we evaluated whether reinstating airflow during MV could influence the memory performance of rats after recovery. Rats were allocated into two study groups: one group received rhythmic air-puff into the nasal cavity during MV and a control group that underwent ventilation without air-puff. During MV, air-puffs induced time-locked event potentials in OB, mPFC and vHPC and significantly increased the oscillatory activity at the air-puff frequency. Furthermore, in... 

Irregular hemodynamics affects the progression of various vascular diseases, such atherosclerosis or aneurysms. Despite the extensive hemodynamics studies on animal models, the inter-species differences between humans and animals hamper the translation of such findings. Recent advances in vascular tissue engineering and the suitability ofin vitromodels for interim analysis have increased the use ofin vitrohuman vascular tissue models. Although the effect of flow on endothelial cell (EC) pathophysiology and EC-flow interactions have been vastly studied in two-dimensional systems, they cannot be used to understand the effect of other micro- and macro-environmental parameters associated with... 

Anxiety is among the most debilitating nonmotor symptoms of Parkinson's disease (PD). This study aimed to determine how PD patients with low and high levels of anxiety (LA-PD and HA-PD, respectively) compare with age- and sex-matched controls at the level of motor control of reach-to-grasp movements during single- and dual-task conditions with varying complexity. Reach-to-grasp movement kinematics were assessed in 20 LA-PD, 20 HA-PD, and 20 sex- and age-matched healthy controls under single- as well as easy and difficult dual-task conditions. Assessment of PD patients was performed during both the on- and off-drug phases. The results obtained during dual-task conditions reveal deficits in... 

The NF-κB family includes some transcription factors which have important functions in the regulation of immune responses, therefore participating in the pathophysiology of inflammatory conditions such as peripheral neuropathies. We have quantified expression of a number of NF-κB-related transcripts in patients with Guillain-Barré syndrome (GBS) or chronic inflammatory demyelinating polyneuropathy (CIDP) versus healthy subjects. These transcripts have been previously shown to be functionally related with this family of transcription factors. Expressions of ATG5, DICER-AS1, PACER, DILC, NKILA and ADINR have been increased in both CIDP and GBS patients compared with controls. However,... 

The relative vulnerability of spinal motion segments to different loading combinations remains unknown. The meta-analysis described here using the results of a validated L2-L3 nonlinear viscoelastic finite element model was designed to investigate the critical loading and its effect on the internal mechanics of the human lumbar spine. A Box-Behnken experimental design was used to design the magnitude of seven independent variables associated with loads, rotations and velocity of motion. Subsequently, an optimization method was used to find the primary and secondary variables that influence spine mechanical output related to facet forces, disc pressure, ligament forces, annulus matrix... 

In this paper, we discuss modeling issues of the Parkinson's tremor. Through the work we have employed physiological structure as well as functioning of the parts in brain that are involved in the disease. To obtain more practical similarity, random behaviors of the connection paths are also considered. Medication or treatment of the disease both by drug prescription and electrical signal stimulation are modeled based on the same model introduced for the disease itself. Two new medication strategies are proposed based on the model to reduce the side effects caused by the present drug prescription. © 2005 Elsevier Ltd. All rights reserved