Gene expression profiles and pathway enrichment analysis to identification of differentially expressed gene and signaling pathways in epithelial ovarian cancer based on high-throughput RNA-seq data.

Epithelial ovarian cancer (EOC) can be considered as a stressful and challenging disease among all women in the world, which has been associated with a poor prognosis and its molecular pathogenesis has remained unclear. In recent years, RNA Sequencing (RNA-seq) has become a functional and amazing technology for profiling gene expression. In the present study, RNA-seq raw data from Sequence Read Archive (SRA) of six tumor and normal ovarian sample was extracted, and then analysis and statistical interpretation was done with Linux and R Packages from the open-source Bioconductor. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied for the identification of key genes and pathways involved in EOC. We identified 1091 Differential Expression Genes (DEGs) which have been reported in various studies of ovarian cancer as well as other types of cancer. Among them, 333 genes were up-regulated and 273 genes were down-regulated. In addition, Differentially Expressed Genes (DEGs) including RPL41, ALDH3A2, ERBB2, MIEN1, RBM25, ATF4, UPF2, DDIT3, HOXB8 and IL17D as well as Ribosome and Glycolysis/Gluconeogenesis pathway have had the potentiality to be used as targets for EOC diagnosis and treatment. In this study, unlike that of any other studies on various cancers, ALDH3A2 was most down-regulated gene in most KEGG pathways, and ATF4 was most up-regulated gene in leucine zipper domain binding term. In the other hand, RPL41 as a regulatory of cellular ATF4 level was up-regulated in many term and pathways and augmentation of ATF4 could justify the increase of RPL41 in the EOC. Pivotal pathways and significant genes, which were identified in the present study, can be used for adaptation of different EOC study. However, further molecular biological experiments and computational processes are required to confirm the function of the identified genes associated with EOC.

Achromatic nanostructured gradient index microlenses.

We present a development of microlenses achromatically corrected in near-infrared spectral windows. We show that the standard fiber drawing technology can be successfully applied to the development achromatic gradient index microlenses by means of internal nanostructurization. These gradient index microlenses can achieve similar performance to standard aspheric doublets, while utilizing a simpler, singlet element geometry with flat surfaces. A nanostructured lens with a parabolic profile was designed using a combination of the simulated annealing method and the effective medium approximation theory. Measurements on the fabricated lenses show that the microlenses have a nearly wavelength-independent focal plane at a distance of about 35 µm from the lens facet over the wavelength range of 600-1550 nm. The successful design and fabrication of achromatic flat-parallel rod microlenses opens new perspectives for micro-imaging systems and wavelength-independent coupling into optical fibers.

Selenium Supplementation Affects Insulin Resistance and Serum hs-CRP in Patients with Type 2 Diabetes and Coronary Heart Disease.

To our knowledge, this study is the first indicating the effects of selenium supplementation on metabolic status of patients with type 2 diabetes mellitus (T2DM) and coronary heart disease (CHD). This study was conducted to evaluate the effects of selenium supplementation on metabolic profiles, biomarkers of inflammation, and oxidative stress of patients with T2DM and CHD. This randomized, double-blind, placebo-controlled trial was performed among 60 patients with T2DM and CHD aged 40-85 years. Participants were randomly divided into 2 groups. Group A received 200 µg selenium supplements (n=30) and group B received placebo per day (n=30) for 8 weeks. Fasting blood samples were taken at the beginning of the study and after 8-week intervention to quantify metabolic profiles. After 8 weeks, compared with the placebo, selenium supplementation resulted in a significant decrease in serum insulin levels (- 2.2±4.6 vs. + 3.6±8.4 µIU/ml, p=0.001), homeostasis model of assessment-insulin resistance (HOMA-IR) (- 0.7±1.3 vs. + 0.9±2.4, p=0.004), homeostatic model assessment-beta cell function (HOMA-B) (- 7.5±17.2 vs. + 15.1±34.5, p=0.002) and a significant increase in quantitative insulin sensitivity check index (QUICKI) (+0.01±0.03 vs. - 0.01±0.03, p=0.02). In addition, patients who received selenium supplements had a significant reduction in serum high-sensitivity C-reactive protein (hs-CRP) (- 1 372.3±2 318.8 vs. - 99.8±1 453.6 ng/ml, p=0.01) and a significant rise in plasma total antioxidant capacity (TAC) concentrations (+ 301.3±400.6 vs. - 127.2±428.0 mmol/l, p<0.001) compared with the placebo. A 200 µg/day selenium supplementation among patients with T2DM and CHD resulted in a significant decrease in insulin, HOMA-IR, HOMA-B, serum hs-CRP, and a significant increase in QUICKI score and TAC concentrations.

Protective effect of Zingiber officinale extract on rat testis after cyclophosphamide treatment.

Decreasing the side effects of chemotherapy in testis has been the subjects of many studies. In this study, the protective effects of Zingiber officinale extract on rat testis were investigated after chemotherapy with cyclophosphamide. Histological and biochemical parameters were compared in cyclophosphamide-treated rats with or without ginger extract intake. Wistar male rats were randomly divided into four groups each 10. The control group received a single injection of 1 ml isotonic saline intraperitoneally. The Cyclophosphamide (CP) group received a single dose of cyclophosphamide (100 mg kg(-1) BW) intraperitoneally. CP + 300 and CP + 600 groups received orally 300 or 600 mg of ginger extract, respectively, for a period of 6 weeks after cyclophosphamide injection. The morphologic and histological structure of the testis was compared in different groups of the rats. Also, factors like malondialdehyde, reactive oxygen species, total antioxidant capacity and testosterone level were assessed in blood serum as well. Our results showed that although ginger extract could not change testis weight, malondialdehyde (MDA) and ROS, but antioxidant and testosterone levels in serum were increased significantly. Also, an obvious improved histological change was seen in CP + 300 and CP + 600 groups in comparison with CP group. These protective effects of ginger on rat testis after cyclophosphamide treatment could be attributed to the higher serum level of antioxidants.

Protective effect of pumpkin seed extract on sperm characteristics, biochemical parameters and epididymal histology in adult male rats treated with cyclophosphamide.

Cancer treatment with cyclophosphamide (CP) may result in reproductive toxicity as one of its side effects. The pumpkin seed is a rich natural source of antioxidant. We have assessed the possible protective efficacy of pumpkin seed extract on sperm characteristics, biochemical parameters and epididymal histology of CP-treated rats. Male adult Wistar rats were categorised into four groups. Group 1 served as control and received intraperitoneal (IP) injection of isotonic saline solution. Group 2 rats were treated with CP by IP injection in a single dose of 100 mg/kg body weight, only once. Group 3 and 4 received CP plus 300 and 600 mg/kg pumpkin seed extract respectively. Six weeks after treatment, sperm characteristics, biochemical parameters and histopathological changes were examined. Results showed that, sperm characteristics in CP-treated rats were significantly decreased. Biochemical analysis results showed that the co-administration of 300 mg pumpkin seed extract could increase the total antioxidant capacity (TAC) level significantly. In CP-treated rats, histopathological changes such as vacuolisation, disorganisation and separation of epididymal epithelium were observed as well. Interestingly, pumpkin seed extract could improve the above-mentioned parameters remarkably in CP-treated rats. Our findings indicated that pumpkin seed extract might be used as protective agent against CP-induced reproductive toxicity.

Compared to Aluminum Hydroxide Adjuvant, Montanide ISA 206 VG Induces a Higher and More Durable Neutralizing Antibody Response against FMDV in Goats.

Foot-and-mouth disease (FMD) has a high prevalence in cloven-hoofed animals. It is also highly contagious and remains a serious threat to livestock worldwide. Despite the widespread vaccination program in Iran, outbreaks of FMD continue to occur. Vaccination is one of the most effective methods of preventing FMD. The vaccines used in Iran are of the inactivated type and contain several serotypes. Since inactivated vaccines without adjuvants do not induce a high and durable antibody response, it is necessary to use adjuvants. Montanide ISA 206 VG is a mineral oil-based adjuvant that produces a water-in-oil-in-water (w:o:w) emulsion in vaccine preparations. However, a large number of manufacturers in Iran and around the world still use alum adjuvant (with or without saponin) to produce the FMD vaccine. This study used Montanide ISA 206 and alum adjuvants to administer the O2010 serotype of the FMD virus to goats. A total of six goats were divided randomly into three groups. Vaccines were administered subcutaneously twice, at a one-month interval. Blood sampling was done at different times, and the micro-neutralization method was used to measure the neutralizing antibody titer in each serum. Seven days after the second vaccination, the alum group's antibody titer was higher but not statistically significant. However, from the 28th day after the second injection until the end of the study, the Montanide ISA 206 group's antibody titer was significantly higher than that of the alum group. Six months after the second injection, the antibody titer in the ISA 206 group remained at the peak level, while in the alum group, it decreased and reached the minimum protective level. Nine months after the second injection, the antibody titer remained at its peak level in the ISA 206 group, whereas it dropped significantly in the alum group. Based on the findings, ISA 206 VG is capable of generating long-term humoral immunity in goats against the FMD serotype O2010 and could replace aluminum hydroxide adjuvants in FMD vaccine preparations.

Monitoring of Newcastle Disease Virus Vaccine Strain Replication in Embryonated Chicken Eggs by Reverse Transcription-Polymerase Chain Reaction.

The knowledge of virus and replication kinetics plays a key role in developing a vaccine. This study aimed to monitor the replication process and determine the best harvesting time of the Newcastle disease virus (NDV) V4 vaccine strain in the allantoic fluids of specific pathogen-free (SPF)-embryonated chicken eggs (ECEs) by reverse transcription-polymerase chain reaction (RT-PCR), hemagglutination (HA), and egg infective dose 50% (EID50) tests. For this purpose, the V4 vaccine strain of the virus was intra-allantoically inoculated into 96 10-day-old SPF-ECEs at the rate of 0.1 mL/ECE. The allantoic fluids of the inoculated eggs were collected from six eggs at six-hour intervals up to 96 hours post-infection (hpi). The harvested suspensions were confirmed to contain the NDV by the mentioned serologic and molecular techniques. Based on the results, the virus was first detected at 36 hpi in ECEs by RT-PCR. The peak of HA and EID50 titers in allantoic fluids started at 42 hpi, and the titers were at the highest level until the end of the experiment. The results indicated that the best virus harvesting time for the NDV V4 vaccine strain in ECEs is between 42-60 hpi. These findings pave the way for adequate and enhanced production rate, immunogenicity, and cost-related parameters in the V4 Newcastle vaccine development.

Evaluation of Immunogenicity of Clostridium perfringens Type B Toxoid and Inactivated FMD (O) Virus with Adjuvant (ISA70-MF59).

Foot and mouth disease (FMD) and enterotoxemia are important diseases of hoofed animals. Vaccination against livestock pathogens, especially these two diseases, plays a key role in the prevention and control of these diseases. The use of combined vaccines with the aim of creating a better immune response and producing cheaper vaccines is a great contribution to Vaccine industry. This research aimed to compare the immunogenicity of FMD (O) and Clostridium perfringens type B toxoid along with adjuvant (MF59) and Montanide (ISA70) to create the best immunogenicity. To investigate the immune responses of vaccines, it was injected into an animal model, and the antibody titer was measured by enzyme-linked immunosorbent assay (ELISA) test and VN antibody titer. The results showed that the formulation with MF59 adjuvant brought more stable immunogenicity against FMD and Clostridium perfringens type B, and the length of the immunogenicity period also increased significantly. Therefore, the combined vaccine (Clostridium perfringens + FMD) could play a major role invaccine industry as an alternative vaccine against Clostridium perfringens and FMD in livestock.

Nasal Administration of M2e/CpG-ODN Encapsulated in N-Trimethyl Chitosan (TMC) Significantly Increases Specific Immune Responses in a Mouse Model.

The nasal passage is the primary entry point for many infectious agents. Therefore, nasal vaccines that can overcome the limitations associated with antigen uptake are likely to play an important role in protecting these infectious agents. Thus, adjuvants and antigen-carrying systems that can induce a suitable mucosal and systemic immune response against their accompanying antigens are highly important. In this study, synthetic oligodeoxynucleotides containing CpG motifs (CpG-ODN) accompanied by the recombinant ectodomain of influenza M2 protein were encapsulated in N-trimethyl chitosan (TMC) nanoparticles. After the preparation of TMC nanoparticles, the morphological characteristics and loading efficiency and in vitro antigen release, as well as their ability to induce efficient immune responses against M2e in intranasal inoculation in the mouse model, were studied. Based on the size and zeta potential of the nanoparticles prepared in this study, it was determined that they were all nanosized, and their positive zeta potential ranged from 25 to 28 mV, while their polydispersity index was between 0.1 to 0.2, indicating a narrow range of particle sizes. A significant increase in serum levels of the total M2e-specific IgG antibody and BALF anti-M2e IgA was observed in mice intranasally immunized with M2e/CpG-ODN/TMC as opposed to those that were intranasally immunized with M2e/TMC, M2e/CpG-ODN, free M2e, and CpG-ODN/TMC. There was also a significant change in the IgG2a/IgG1 ratio in favour of IgG2a seems that CpG-ODN is responsible for directing the immune system towards Th1. Our findings show that CpG-ODN can significantly enhance the mucosal and systemic humoral immune response against M2e when encapsulated in a suitable carrier such as TMC for intranasal administration. In conclusion, when combined with a suitable carrier, CpG-ODN can be considered an effective adjuvant for mucosal administration.

Comparative Study on the Efficacy of MF 59, ISA70 VG, and Nano-Aluminum Hydroxide Adjuvants, Alone and with Nano-Selenium on Humoral Immunity Induced by a Bivalent Newcastle+Avian Influenza Vaccine in Chickens.

Newcastle disease (ND) and Avian influenza (AI) are the major problems and the most economically important viral diseases in the poultry industry; therefore, vaccination against these diseases is considered one of the most effective ways of prevention. Extensive studies have been conducted to improve the performance of vaccines, and one of the major achievements of these studies is the preparation of adjuvants as stimulants of the immune system and one of the most important compounds in killed vaccines. An immunogenicity comparison of three adjuvants including, ISA70VG, Nano-Aluminum Hydroxide (Nano-Alum), and MF59 alone or with Nano-Selenium (Nano-Se), was performed using bivalent Newcastle plus Avian Influenza (ND+AI) killed vaccine. In this study, 105 specific-pathogen-free chicks (Ross-308) were divided into 7 treatments, including T1 (control group), T2 (ISA70VG), T3 (ISA70VG plus Nano-Se), T4 (Nano-Alum Hydroxide), T5 (Nano-Alum+Nano-Se), T6 (MF59), and T7 (MF59+Nano-Se). The vaccine was injected subcutaneously on day 21 in the back of the neck area. The blood samples were taken on days 14, 21, 28, 35, 42, and 49 post-vaccination. Serums of the samples were titrated by the haemagglutination inhibition (HI) test against Newcastle and Avian influenza. Based on the results, the highest HI test titers were observed for the T2 and T3 treatments, while the T6 and T7 treatments had the lowest titers. Moreover, regardless of the type of the adjuvants, adding Nano-Se increased the antibody titer in the vaccinated groups. In conclusion, a combination of the ISA70VG adjuvant and Nano-Se induced excellent antibody titers using bivalent ND+AI killed vaccine.

Nanostructured elliptical gradient-index microlenses.

We show theoretical and experimental characterizations of a nanostructured gradient-index lens. The elliptical lens is a nonguiding element fabricated using the mosaic method, which is widely used for the fabrication of photonic crystal fibers. For the first time we show experimental data in the optics regime that confirm the effective medium approximation for discrete mosaic structures with subwavelength feature size. This opens the door for the development of general asymmetric gradient-index materials.

Design and fabrication of nano-structured gradient index microlenses.

We present a novel fabrication technology for nano-structured graded index micro-optical components, based on the stack-and-draw method used for photonic crystal fibres. These discrete structures can be described with an effective refractive index distribution. Furthermore we present spherical nano-structured microlenses with a flat facet fabricated with this method and designed using an algorithm based on the Maxwell-Garnett mixing formula. Finally we show theoretical verification by using FDTD simulations for a nano-structured lens as well as experimental data obtained in the microwave regime.

Effect of molecular weight on the ultrasonic degradation of poly(vinyl-pyrrolidone).

The ultrasonic degradation of poly(vinyl-pyrrolidone) (PVP) of different initial molecular weights was studied at a fixed temperature. The effect of solution concentration on the rate of degradation was investigated. A method of viscometry was used to study the degradation behavior and kinetic model was developed to estimate the degradation rate constant. The results were indicated that the rate of ultrasonic degradation increased with increasing molecular weight. It was found that rate constant decreases as the concentration increases. The calculated rate constants correlated in terms of inverse concentration and relative viscosity of PVP solutions. This behavior in the rate of degradation was interpreted in terms of viscosity and concentration of polymer solution. With increasing solution concentration, viscosity increases and it causes a reduction in the cavitation efficiency thus, the rate of degradation will be decreased. The experimental results show that the viscosity of polymers decreased with ultrasonic irradiation time and approached a limiting value, below which no further degradation took place. This study confirms the general assumption that the shear forces generated by the rapid motion of the solvent following cavitational collapse are responsible for the breakage of the chemical bonds within the polymer. The effect of polymer concentration can be interpreted in terms of the increase in viscosity with concentration, causing the molecules to become less mobile in solution and the velocity gradients around the collapsing bubbles to, therefore, become smaller.

Evaluation of nutritional status in patients undergoing hematopoietic SCT.

The aims of this study were to establish the nutritional status of patients during hematopoietic SCT (HSCT) and to determine if body mass index (BMI) is a valid indicator of nutritional status in this population when compared with nitrogen balance (NB). In total, 50 patients were enrolled (mean age: 25.7+/-9.0 years). Patients (14%) were underweight (BMI<18.5 kg/m(2)), 58% in a normal BMI (between 18.5 and 24.9 kg/m(2)) and 28% were overweight or obese (BMI >or= 25 kg/m(2)). NB dropped after transplantation and increased from days +5 to +20 after transplantation (P=0.006). There was a significant negative relationship between patients' BMI and time to engraftment (r=-0.45, P=0.001). Engraftment of underweight patients was 3.0 days (P=0.002) and 4.0 days (P<0.001) later than in normal and overweight or obese patients, respectively. There was no significant correlation between NB before transplantation and time to engraftment (r=-0.22, P=0.16). The results of this study demonstrate that patients undergoing HSCT may have suboptimal nutritional status and that pre-HSCT-BMI rather than NB may have a greater correlation in HSCT patients with the time of engraftment. Therefore, it may be useful to consider patient's BMI before transplantation for earlier engraftment time.

Characterization of the interaction between human serum albumin and diazinon via spectroscopic and molecular docking methods.

Human serum albumin (HSA) is a soluble blood protein which binds to small molecules (such as drugs and toxins) and transfers them within the blood circulation. In this research, the interaction of diazinon, as a toxic organophosphate, with HSA was investigated. Various biophysical methods such as fluorescence, ultraviolet-visible (UV-vis), Fourier transform infrared spectroscopy, and molecular docking were utilized to characterize the binding properties of diazinon to HSA under physiological-like condition. The UV-vis spectroscopy showed that the absorption increased and the fluorescence intensity of HSA decreased regularly with regard to the gradual increases of the concentrations of diazinon. Due to the binding constant of ( ka = 3.367 × 10+4 M-1), the α-helix structure for the first day and 35 days of incubation were obtained 66.09-55.4% and 59.99-46.48%, respectively, and their amounts in other secondary structures (ß-sheet, ß-anti, and random (r) coils) were increased. The molecular docking revealed a good binding site in HSA (Trp-214) for diazinon which was related to the considerable alterations in HSA secondary and tertiary structures. There is a close relationship between the secondary structure of protein and its biological activity and after 35 days of incubation, the high toxic concentrations of diazinon can make HSA to be partially unfolded and lose its structure.

The flow properties of honey-malt spread.

In this study, the effect of barley malt extract at two brix levels (74 and 79 °Bx) and three ratios of malt extract/honey (65:35, 70:30 and 75:25) on the flow behavior properties of honey-malt spread at three temperature levels (35 ℃, 45 ℃ and 55 ℃) was investigated. Time-dependent behavior data of the spread samples were appropriately fitted to the Weltman, first-order stress decay with a zero stress value and first-order stress decay with a non-zero stress value models. Also, the Power-law, Herschel-Bulkley, Casson and Bingham models were used for curve fitting the time-independent behavior data. Regarding the R2 and root mean square error coefficients, the first-order stress decay with a non-zero stress value and Herschel-Bulkley models were selected as the suitable models to describe the flow behavior of samples. The results for time-dependent properties showed that spread samples exhibit a thixotropic behaviour, as the viscosity for all samples decreased with increase in shearing time at a constant shear rate of 50 s-1.

Effect of flaxseed oil on serum systemic and vascular inflammation markers and oxidative stress in hemodialysis patients: a randomized controlled trial.

PURPOSE: The aim of this study was to investigate the effects of flaxseed oil consumption on serum systemic and vascular inflammation markers, and oxidative stress in hemodialysis (HD) patients. METHODS: In this randomized, double-blind, clinical trial, 34 HD patients were randomly assigned to either the flaxseed oil or the control group. The patients in the flaxseed oil group received 6 g/day flaxseed oil for 8 week, whereas the control group received 6 g/day medium-chain triglycerides (MCT) oil. At baseline and the end of week 8, serum concentrations of high-sensitive C-reactive protein (hs-CRP), soluble intercellular adhesion molecule type 1 (sICAM-1), soluble vascular cell adhesion molecule type 1 (sVCAM-1), sE-selectin, and malondialdehyde (MDA) were measured after a 12- to 14-h fast. RESULTS: Serum hs-CRP, a systemic inflammation marker, and sVCAM-1, a vascular inflammation marker, reduced significantly in the flaxseed oil group at the end of week 8 compared to baseline (P < 0.05), and the reductions were significant in comparison with the MCT oil group (P < 0.05). There were no significant differences between the two groups in mean changes in serum sICAM-1, sE-selectin, and MDA. CONCLUSION: This study indicates that daily consumption of 6 g flaxseed oil reduces serum hs-CRP and sVCAM-1, which are two risk factors for CVD. Therefore, the inclusion of flaxseed oil in the usual diet of HD patients can be considered as a strategy for reducing CVD risk factors.

Synthesis of new copper nanoparticle-decorated anchored type ligands: applications as non-enzymatic electrochemical sensors for hydrogen peroxide.

In this work, copper nanoparticles (CuNPs) decorated on two new anchored type ligands were utilized to prepare two electrochemical sensors. These ligands are made from bonding amine chains to silica support including SiO2-pro-NH2 (compound I) and SiO2-pro-NH-cyanuric-NH2 (compound II). The morphology of synthesized CuNPs was characterized by transmission electron microscopy (TEM). The nano-particles were in the range of 13-37 nm with the average size of 23 nm. These materials were used to modify carbon paste electrode. Different electrochemical techniques, including cyclic voltammetry, electrochemical impedance spectroscopy and hydrodynamic chronoamperometry, were used to study the sensor behavior. These electrochemical sensors were used as a model for non-enzymatic detection of hydrogen peroxide (H2O2). To evaluate the abilities of the modified electrodes for H2O2 detection, the electrochemical signals were compared in the absence and presence of H2O2. From them, two modified electrodes showed significant responses vs. H2O2 addition. The amperograms illustrated that the sensors were selective for H2O2 sensing with linear ranges of 5.14-1250 µmol L(-1) and 1.14-1120 µmol L(-1) with detection limits of 0.85 and 0.27 µmol L(-1) H2O2, sensitivities of 3545 and 11,293 µA mmol(-1)L and with response times less than 5s for I/CPE and II/CPE, respectively. As further verification of the selected sensor, H2O2 contained in milk sample was analyzed and the obtained results were comparable with the ones from classical control titration method.

Dual-wavelength operation diffractive phase elements for pattern formation.

We report on the design and fabrication of novel diffractive phase elements that reconstruct distinct intensity patterns in the far-field on illumination with two specific wavelengths. The elements contain deep surface-relief structures that represent phase-delays of greater than 2p radians. The design process incorporates a modified version of the iterative Fourier transform algorithm. A 16 phase-level element for dual wavelength (blue and red) operation, with high diffraction efficiency, is demonstrated experimentally.

A neural-network packet switch controller: scalability, performance, and network optimization.

We examine a novel combination of architecture and algorithm for a packet switch controller that incorporates an experimentally implemented optically interconnected neural network. The network performs scheduling decisions based on incoming packet requests and priorities. We show how and why, by means of simulation, the move from a continuous to a discrete algorithm has improved both network performance and scalability. The system's limitations are examined and conclusions drawn as to its maximum scalability and throughput based on today's technologies.