Sharif Digital Repository

The role of quantum tunneling in altering the structure of nucleotides to each other and causing a mutational event in DNA has been a topic of debate for years. Here, we introduce a new quantum mechanical approach for analyzing a typical point-mutation in DNA strands. Assuming each codon as a base state, a superposition of codon states could provide a physical description for a set of codons encoding the same amino acid and there are transition amplitudes between them. We choose the amino acids Phe and Ile as our understudy bio-systems which are encoded by two and three codons, respectively. We treat them as large quantum systems and use double- and triple-well potential models to study the... 

Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized as a mathematical model for gene regulatory networks. This paper provides an algorithm to solve the control problem in Boolean networks. The proposed algorithm is implemented and applied on two biological systems: T-cell receptor network and Drosophila melanogaster network. Results show that the proposed algorithm works faster in solving the control problem over these networks, while having similar accuracy, in comparison to previous exact methods. Source... 

Background: Skeletal muscle mass, which is regulated by a balance between muscle protein synthesis and degradation, is an important factor for movement to meet everyday needs, especially in pathological conditions and aging. The purpose of the present investigation was to compare the alterations of the gene expression involved in muscle protein synthesis and degradation signaling pathways induced by two exercise training protocols. Methods: Eight weeks old Wistar rats have been assigned to the present experimental study, which was conducted from August 2018 to October 2018 at the animal laboratory of Tehran University. They were randomly divided into two resistance and endurance training... 

Cardiovascular diseases are the number one cause of heart failure and death in the world, and the transplantation of the heart is an effective and viable choice for treatment despite presenting many disadvantages (most notably, transplant heart availability). To overcome this problem, cardiac tissue engineering is considered a promising approach by using implantable artificial blood vessels, injectable gels, and cardiac patches (to name a few) made from biodegradable polymers. Biodegradable polymers are classified into two main categories: natural and synthetic polymers. Natural biodegradable polymers have some distinct advantages such as biodegradability, abundant availability, and... 

Naïve pluripotency can be established in human pluripotent stem cells (hPSCs) by manipulation of transcription factors, signaling pathways, or a combination thereof. However, differences exist in the molecular and functional properties of naïve hPSCs generated by different protocols, which include varying similarities with pre-implantation human embryos, differentiation potential, and maintenance of genomic integrity. We show here that short treatment with two chemical agonists (2a) of nuclear receptors, liver receptor homologue-1 (LRH-1) and retinoic acid receptor gamma (RAR-γ), along with 2i/LIF (2a2iL) induces naïve-like pluripotency in human cells during reprogramming of fibroblasts,... 

This chapter covers a part of the spectrum of neural-network uses in analytical chemistry. Different architectures of neural networks are described briefly. The chapter focuses on the development of three-layer artificial neural network for modeling the anti-HIV activity of the HETP derivatives and activity parameters (pIC 50) of heparanase inhibitors. The use of a genetic algorithm-kernel partial least squares algorithm combined with an artificial neural network (GA-KPLS-ANN) is described for predicting the activities of a series of aromatic sulfonamides. The retention behavior of terpenes and volatile organic compounds and predicting the response surface of different detection systems are... 

Based on the force-deflection equation for a beam subjected to lateral point loads, a C2 continuous piecewise bicubic mathematical representation was proposed to model complicated geometrical surfaces, e.g. the articular surfaces of human joints. The method was then extended so that it could be used for mathematical modelling of incomplete nets of data points, as well as smoothing of noisy and/or filtering of erroneous data points. Mathematical techniques were also developed to calculate the required unknown parameters explicitly, with no need to solve the system of equations simultaneously. The performance of the proposed method was evaluated on a number of surface modelling problems,... 

Diatoms are unicellular microalga found in soil and almost every aquatic environment (marine and fresh water). Biogenic silica and diatoms are attractive for biotechnological and industrial applications, especially in the field of biomedicine, industrial/synthetic manufacturing processes, and biomedical/pharmaceutical sciences. Deposition of silica by diatoms allows them to create micro- or nanoscale structures which may be utilized in nanomedicine and especially in drug/gene delivery. Diatoms with their unique architectures, good thermal stability, suitable surface area, simple chemical functionalization/modification procedures, ease of genetic manipulations, optical/photonic... 

Accumulation of amyloid beta (Aβ) soluble forms in the cerebral parenchyma is the mainstream concept underlying memory deficit in the early phase of Alzheimer's disease (AD). PKMζ plays a critical role in the maintenance of long-term memory. Yet, the role of this brain-specific enzyme has not been addressed in AD. We examined the impact of hippocampal PKMζ overexpression on AD-related memory impairment in rats. Oligomeric form of Aβ (oAβ) or vehicle was bilaterally microinjected into the dorsal hippocampus of male Wistar rats under stereotaxic surgery. One week later, 2 μl of lentiviral vector (108 T.U. / ml.) encoding PKMζ genome was microinjected into the dorsal hippocampus. Seven days... 

Self-repairing is not an advanced ability of articular cartilage. Tissue engineering has provided a novel way for reconstructing cartilage using natural polymers because of their biocompatibility and bio-functionality. The purpose of cartilage tissue engineering is to design a scaffold with proper pore structure and similar biological and mechanical properties to the native tissue. In this study, porous scaffolds prepared from gelatin, chitosan and silk fibroin were blended with varying ratios. Between the blends of chitosan (C), gelatin (G) and silk fibroin (S), the scaffold with the weight per volume ratio of 2:2:3 (w/v) showed the most favorable and higher certain properties than the... 

The goal of this study is to investigate the effects of tendon and cannulated drill bit diameter on the strength of the bone and site hold tendon inside (BASHTI) fixation technique for an anterior cruciate ligament (ACL) reconstruction. Bovine digital tendons and Sawbones blocks were used to mimic the ACL reconstruction. Mechanical strength of the specimens was measured using a cyclic loading continued by a single cycle pullout load until failure to simulate the real postsurgical loading conditions. Finally, failure modes of specimens and ultimate failure load were recorded. The maximum possible tendon surface strain (i.e., tendon compression [TC]) for tendon diameters of 6, 7, 8, and 9 mm... 

Neural synchronization has been engaged in several brain mechanisms. Previous studies have shown that the interaction between the time of spiking activity and phase of local field potentials (LFPs) plays a key role in many cognitive functions. However, the potential role of this spike–LFP phase coupling (SPC) in neural coding is not fully understood. Here, we sought to investigate the role of this SPC for encoding the sensory properties of visual stimuli. To this end, we measured SPC strength in the preferred and anti-preferred motion directions of stimulus presented inside the receptive field of middle temporal (MT) neurons. We found a selective response in terms of SPC strength for... 

Theranostic liposomes have recently found a broad range of applications in nanomedicine due to stability, the high solubility of biomacromolecules, bioavailability, efficacy, and low adverse effects. However, the limitations of liposomes concerning the short systemic circulation in the body, limited controllability of the release rate, and the inability of in vivo imaging remain challenging. Herein, the development of novel hybrid ultrasound-activated piezoelectric nanoparticles based on a hybrid liposome nanocarrier composed of poly(vinylidene fluoride‐trifluoroethylene), graphene quantum dots (GQDs), and Silibinin (a hydrophobic drug) is presented. The hybrid nanoparticles are an... 

The gut-brain axis is believed to constitute a bidirectional communication mechanism that affects both mental and digestive processes. Recently, the role of the gut microbiota in cognitive performance has been the focus of much research. In this paper, we discuss the effects of gut microbiota and nutrition on spatial memory and learning. Studies have shown the influence of diet on cognitive capabilities such as spatial learning and memory. It has been reported that a high-fat diet can alter gut microbiota which subsequently leads to changes in spatial learning and memory. Some microorganisms in the gut that can significantly affect spatial learning and memory are Akkermansia muciniphila,... 

In this study, optimized preparation, quality control, cell assessments and biostribution of 188Re-HYNIC-PSMA in normal rats and tumor bearing mice are studied. Optimized conditions for radiolabeling were evaluated and radiochemical purity (> 99%) was investigated using ITLC and HPLC methods. 188Re-HYNIC-PSMA was stable both in PBS (4 °C) and in human serum (37 °C) even after 48 h. The results showed the complex was cleared from the blood very fast via urinary track. This new radiolabeled compound has a high potential to be considered as an agent for the treatment of patients with PSMA expressing tumors however more biological studies are still needed. © 2022, Akadémiai Kiadó, Budapest,... 

Simultaneous recording of activity across brain regions can contain additional information compared to regional recordings done in isolation. In particular, multivariate pattern analysis (MVPA) across voxels has been interpreted as evidence for distributed coding of cognitive or sensorimotor processes beyond what can be gleaned from a collection of univariate effects (UVE) using functional magnetic resonance imaging (fMRI). Here, we argue that regardless of patterns revealed, conventional MVPA is merely a decoding tool with increased sensitivity arising from considering a large number of ‘weak classifiers’ (i.e., single voxels) in higher dimensions. We propose instead that ‘real’ multivoxel... 

Abstract: In recent years, temporary skin grafts (TSG) based on natural biopolymers modified with carbon nanostructures have received considerable attention for wound healing. Developments are required to improve physico-mechanical properties of these materials to match to natural skins. Additionally, in-deep pre-clinical examinations are necessary to ensure biological performance and toxicity effect in vivo. In the present work, we show superior acute-wound healing effect of graphene oxide nanosheets embedded in ultrafine biopolymer fibers (60 nm) on adult male rats. Nano-fibrous chitosan-based skin grafts crosslinked by Genepin with physico-mechanical properties close to natural skins were... 

In this study, superparamagnetic iron oxide nanoparticles (SPION) embedded by folic acid (SPION-folate) were prepared by a modified co-precipitation method. The structure, size, morphology, magnetic property and relaxivity of the SPION-folate were characterized systematically by means of XRD, VSM, HRSEM and TEM and the interaction between folate and iron oxide (Fe3O 4) was characterized by FT-IR. The particle size was shown to be ≈5-10 nm. To ensure biocompatibility, the interaction of these SPION with mouse connective tissue cells (adhesive) was investigated using an MTT assay. Consequently, gallium-67 labeled nanoparticles ([67Ga]-SPION-folate) were prepared using 67Ga with a high labeling... 

Degenerative disc disease, associated with discrete structural changes in the peripheral annulus and vertebral endplate, is one of the most common pathological triggers of acute and chronic low back pain, significantly depreciating an individual's quality of life and instigating huge socioeconomic costs. Novel emerging therapeutic techniques are hence of great interest to both research and clinical communities alike. Exogenous crosslinking, such as Genipin, and platelet-rich plasma therapies have been recently demonstrated encouraging results for the repair and regeneration of degenerated discs, but there remains a knowledge gap regarding the quantitative degree of effectiveness and... 

Microfluidic devices are beneficial in miniaturizing and multiplexing various cellular assays in a single platform. Chondrogenesis is known to pertain to chemical, topographical, and mechanical cues in the microenvironment. Mechanical cues themselves have numerous parameters such as strain magnitude, frequency, and stimulation time. Effects of different strain magnitudes on the chondrogenic differentiation of adult stem cells have not been explored thoroughly. Here, a new multilayer microdevice is presented for the unidirectional compressive stimulation of cells in a three-dimensional cell culture. Numerical simulations were performed to evaluate and optimize the design. Results showed a...