Evaluation of a custom QIAseq targeted DNA panel with 164 ancestry informative markers sequenced with the Illumina MiSeq.

Introduction of new methods requires meticulous evaluation before they can be applied to forensic genetic case work. Here, a custom QIAseq Targeted DNA panel with 164 ancestry informative markers was assessed using the MiSeq sequencing platform. Concordance, sensitivity, and the capability for analysis of mixtures were tested. The assay gave reproducible and nearly concordant results with an input of 10 and 2 ng DNA. Lower DNA input led to an increase in both locus and allele drop-outs, and a higher variation in heterozygote balance. Locus or allele drop-outs in the samples with less than 2 ng DNA input were not necessarily associated with the overall performance of a locus. Thus, the QIAseq assay will be difficult to implement in a forensic genetic setting where the sample material is often scarce and of poor quality. With equal or near equal mixture ratios, the mixture DNA profiles were easily identified by an increased number of imbalanced heterozygotes. For more skewed mixture ratios, the mixture DNA profiles were identified by an increased noise level. Lastly, individuals from Great Britain and the Middle East were investigated. The Middle Eastern individuals showed a greater affinity with South European populations compared to North European populations.

Modulation of Negative Effects of Physiological Stress on Frozen-Thawed Semen with Nutrition of Organic Selenium in Ross 308 Rooster.

Current experiment was carried out in factorial 2×2 arrangement to study the effects of stress (with or without dexamethasone administration) and addition of dietary selenium (with or without selenium supplementation in the diet) in male broiler breeder on the quality of frozen-thawed sperm under oxidative stress induced by dexamethasone. A total of 24 broiler breeder roosters with the age of 28 weeks were used based on a completely randomized design with four therapeutic approaches (factorial 2×2) and six birds in each approach. The experimental treatments were: 1) basal diet without selenium supplementation and injection of saline (CON), 2) basal diet with dexamethasone injection (4 mg/kg BW, three times every other day for one week), (DEX), 3) without dexamethasone injection and supplementation with 0.3 mg/kg selenium (Sel-Plex), and 4) dexamethasone injection and basal diet supplemented with 0.3 mg/kg of diet selenium (Sel-Plex+Dex). Sperm samples were collected from roosters. Motility, progressive motility, plasma membrane integrity, viability, malondialdehyde concentration and antioxidant parameters were evaluated in fresh and frozen-thawed semen. In spite of non-significant interaction effects, factorial analysis indicated the significant effect of every factor on different experimental parameters in fresh and frozen-thawed semen (P<0.05); The results revealed that total and progressive motility, plasma membrane integrity and viability were lower in DEX group when compared with other treatments (P<0.05). On the other hand, malondialdehyde concentration was higher in DEX group in comparison with Con, Sel-Plex and Sel-Plex+DEX groups (P<0.05). Moreover, total antioxidant capacity, level of glutathione peroxidase and superoxide dismutase were lower in DEX group as compared with other treatments (P<0.05). Our findings indicated that administration of selenium in dexamethasone-receiving roosters (Sel-Plex+DEX) improved the parameters of fresh and frozen-thawed sperm; but the best results were observed in Sel-Plex treatment. Therefore, selenium supplementation in the diet of roosters without dexamethasone injection improved total motility, progressive motility, membrane integrity, viability, malondialdehyde, total antioxidant capacity, glutathione peroxidase and superoxide dismutase pre- and post-freezing. It can be concluded, selenium in organic forms in stressed and non-stressed rooster's diet might improve all motility and antioxidant parameters in fresh and frozen-thawed sperm.

Ultrafast dynamics in polycyclic aromatic hydrocarbons: the key case of conical intersections at higher excited states and their role in the photophysics of phenanthrene monomer.

In this study we reveal the detailed photocycle of a phenanthrene monomer. Phenanthrene serves as a popular building block for supramolecular systems and as an archetypal molecule to study the photochemistry of polycyclic aromatic hydrocarbons. By means of femtosecond time-resolved UV-vis transient absorption spectroscopy and molecular modeling, we found that the first bright transition involves the second excited singlet state, which relaxes toward the lowest excited singlet state with a biphasic internal conversion through a conical intersection region: a fast coherent branching followed by an exceptionally slow (∼ps) incoherent internal conversion. We succeeded to pinpoint the complete relaxation pathways and to extract the relevant parameters, e.g., the branching ratio at the conical intersection and internal conversion rates.

Expression profiling of plac1 in murine cancer cell lines

AIM: Placenta-specific 1 (PLAC1) is among recently-discovered placental antigens which exerts fundamental role in placental function and development. Increasing body of literature shows that PLAC1 is frequently activated and expressed in a wide variety of human cancers and promote cancer progression. However, no data is available regarding the expression of mouse orthologue, plac1, in murine cancer cell lines. Materials and Methods: We investigated the expression of plac1 in a series of murine cell lines from different histological origins, mammary carcinoma (4T1), melanoma (B16F10), colorectal carcinoma (CT26), renal carcinoma (Renca), glioma (GL26), B-cell lymphoma (A20 and BCL1) and also two fibroblast cell lines (NIH3T3 and L929), using RT-PCR, Western blotting and flow cytometry. Results: Our data demonstrated that plac1 transcript and plac1 protein were expressed in all examined cell lines, as judged by RT-PCR and Western blot, respectively. The molecular weight of mouse plac1 was experimentally observed to be approximately 24 kD. Flow cytometric analysis showed surface expression of plac1 in aforesaid cell lines ranging from 2% to 42.5%. Conclusion: Based on the ubiquitous expression of plac1, the investigated cancer cell lines or immortalized cell lines can be used to examine the role of plac1 in the process of immortalization.

Recipients' Experiences after Organ Transplantation.

BACKGROUND: After organ transplantation, many patients have diverse experiences; they face many changes in the physical and emotional aspects of their life. Patients' understandings of the post-transplantation period influence their adaptation to the changes. There is a need to improving the knowledge of patients' unique experiences of post-transplantation period and the changes occur in their life. OBJECTIVE: To explore the experiences of organ recipients in the post-transplantation period. METHODS: In a qualitative research using a hermeneutical phenomenological approach, data were collected from April 2015 to June 2016. Participants were consisted of 15 patients who received organ chosen using a purposive sampling method. In-depth semi-structured interviews were held with them. The collected data were analyzed using Diekelmann's hermeneutical analysis approach. RESULTS: The data analyses led to the development of 3 main themes and 17 subthemes as "back from the grave" with the subthemes of "organ as the God's deposit," "God as the source of life," and "new life"; "chapter of prosperity" with the subthemes of "the spring of the body," "recovery," "peace and joy," "benevolent and good behavior," "renewal," "opportunity of being together again," "golden age," "positive perspective," "the sense of normality," "the return of health," and "spiritual evolution"; and "the fall" with the subthemes of "a lack of energy," "the mirage of transplantation," and "hell on the earth." CONCLUSION: The patients had diverse experiences of the post-transplantation period, which varied from the feeling of exhilaration and youth to losing energy and the wish for not undertaking organ transplantation.

Super RLuc8-sFv; a new luciferase-labeled probe for detection of human CD4+ cells.

The human immunodeficiency virus (HIV) destroys CD4+ lymphocytes and monitoring these cells is one of the best techniques for studying HIV infection. In the present study a novel bioluminescent probe, super RLuc8-sFv, is developed in order to detect human CD4+ cells by fusion of an anti-human CD4 sFv to the C-terminus of super RLuc8. The results indicate that the probe can bind to CD4+ cells via its sFv domain; also it emits visible light through its signalling domain. Super RLuc8-sFv provides a new gateway for detection of human CD4+ cells using luminometric-based assays and may reduce the difficulties involved in, and the cost of, HIV-related diagnostic tests.

On the effect of mucus rheology on the muco-ciliary transport.

A two dimensional numerical model is used to study the muco-ciliary transport process in human respiratory tract. Here, hybrid finite difference-lattice Boltzmann method is used to model the flow physics of the transport of mucus and periciliary liquid (PCL) layer in the airway surface liquid. The immersed boundary method is also used to implement the propulsive effect of the cilia and also the effects of the interface between the mucus and PCL layers. The main contribution of this study is on elucidating the role of the viscoelastic behavior of mucus on the muco-ciliary transport and for this purpose an Oldroyd-B model is used as the constitutive equation of mucus for the first time. Results show that the viscosity and viscosity ratio of mucus have an enormous effect on the muco-ciliary transport process. It is also seen that the mucus velocity is affected by mucus relaxation time when its value is less than 0.002 s. Results also indicate that the variation of these properties on the mucus velocity at lower values of viscosity ratio is more significant.

Raman measurements of substrate temperature in a molecular beam epitaxy growth chamber.

A method is described for directly measuring the temperature of a substrate in a molecular-beam epitaxy (MBE) growth system. The approach relies on the establishment of the temperature dependence of Raman-active phonons of the substrate material using independently known calibration points across the range of interest. An unknown temperature in this range is then determined based on the Raman peak position with the substrate in situ the MBE chamber. The apparatus relies on conventional optics and Raman components. Shifting and broadening of the Raman spectrum are described based on the effects of thermal expansion and anharmonic decay. The choice of reference temperature is discussed. The method is qualified by examining the substrate temperature dependence, relative to that of a standard thermocouple, during a commonly used ramp procedure. Both temperature difference and time lag are obtained.

FcUni-RLuc: an engineered Renilla luciferase with Fc binding ability and light emission activity.

A novel and advanced Fc-binding probe ­ FcUni-RLuc namely ­ has been produced and functionally assayed for labelling IgGs. The Fc antibody binding sequence ­ HWRGWV ­ was fused to Renilla luciferase, and the purified probe was employed for bioluminescence enzyme-linked immunoabsorbance assay of Her2 positive cells.

The estimation of ruminal protein degradation parameters of various feeds using in vitro modified gas production technique.

This study was conducted to determine in vitro crude protein degradation (IVDP) parameters and effective crude protein degradability (EPD) of various feeds using the modified in vitro gas production (GP) technique. Feed samples were alfalfa hay, soybean meal, soybean, rapeseed meal, sunflower meal and fish meal. Rumen fluid was collected before the morning feeding from four rumen fistulated lambs (49.4 ± 3.5 kg, body weight). Approximately 90 ml of buffered rumen fluid (BRF), 400 mg of feed samples and carbohydrates (maltose, xylose and starch) at four concentrations (100, 200, 300, and 400 mg) were added to screw-cap bottles. Gas production (ml) and ammonia nitrogen concentration (mg) in each bottle were measured at 4, 8, 12, 16, 24, and 30 h post incubation and IVDP was calculated via estimated intercept of linear regression between GP (as main variable, X) and ammonia nitrogen (as dependent variable, Y) using the linear regression procedure. Feed, time and feed × time interaction had significant effect on IVDP (P<0.001). Estimated EPD values at the outflow rate of 0.06/h for alfalfa hay, soybean meal, soybean, rapeseed meal, sunflower meal and fish meal were 0.56, 0.77, 0.59, 0.45, 0.50 and 0.38, respectively.

Non-Newtonian unconfined flow and heat transfer over a heated cylinder using the direct-forcing immersed boundary-thermal lattice Boltzmann method.

In this study, the immersed boundary-thermal lattice Boltzmann method has been used to simulate non-Newtonian fluid flow over a heated circular cylinder. The direct-forcing algorithm has been employed to couple the off-lattice obstacles and on-lattice fluid nodes. To investigate the effect of boundary sharpness, two different diffuse interface schemes are considered to interpolate the velocity and temperature between the boundary and computational grid points. The lattice Boltzmann equation with split-forcing term is applied to consider the effects of the discrete lattice and the body force to the momentum flux, simultaneously. A method for calculating the Nusselt number based on diffuse interface schemes is developed. The rheological and thermal properties of non-Newtonian fluids are investigated under the different power-law indices and Reynolds numbers. The effect of numerical parameters on the accuracy of the proposed method has been investigated in detail. Results show that the rheological and thermal properties of non-Newtonian fluids in the presence of a heated immersed body can be suitably captured using the immersed boundary thermal lattice Boltzmann method.

Davey-Stewartson equation with fractional coordinate derivatives.

We have used the homotopy analysis method (HAM) to obtain solution of Davey-Stewartson equations of fractional order. The fractional derivative is described in the Caputo sense. The results obtained by this method have been compared with the exact solutions. Stability and convergence of the proposed approach is investigated. The effects of fractional derivatives for the systems under consideration are discussed. Furthermore, comparisons indicate that there is a very good agreement between the solutions of homotopy analysis method and the exact solutions in terms of accuracy.

Comparison of maternal characteristics in low birth weight and normal birth weight infants.

Low birth weight is a key determinant in the risk of morbidity and mortality in the neonatal period and during childhood. This unmatched case-control study in Hamadan, Islamic Republic of Iran, compared the characteristics of mothers of low- and normal-birth-weight infants. Maternal sociodemographic data, pregnancy history, anthropometric data and cord plasma zinc level were collected from 134 mothers of low-birth-weight infants and 134 mothers of normal infants at the time of delivery. Significant differences in maternal characteristics namely gravida, parity, body mass index, maternal weight gain during pregnancy and plasma cord blood zinc were found between low- and normal-birth-weight infants. There were no significant differences in maternal age, maternal education, maternal occupation, family income, previous abortion, previous preterm labour, birth Iinterval, type of clinic and place of residence between the 2 groups.

Anopheline species composition in borderline of Iran-Azerbaijan.

Malaria is still one of the most important health-problems in the world and is endemic in Iran. Since 1994, after collapse of former Soviet Union, a new threat of malaria importation emerged from those countries into the northern Iran. This work was carried out to provide further evidence on the status of anopheline species composition, the malaria parasite species, and natural infectivity of mosquitoes distributed in Pars-Abad district, on the borderline of Azerbaijan in northwestern Iran. Mosquitoes were collected from May to December 2008 in anopheline seasonal activity and were identified at the species level. The genus- and species-specific primers against Plasmodium ssrDNA gene were used for specific amplification on female mosquito head+thorax. Members of the Anoheles maculipennis complex were identified by sequence analysis of the ribosomal internal transcribed spacer II (ITS2-rDNA). Morphological character-based identification showed that out of 1455 anopheline female specimens, 1121 (77%) were of A. maculipennis s.l. and 334 (23%) were of Anoheles hyrcanus. Molecular analysis of the species complex indicated the presence of Anoheles sacharovi 984 (67.6%) and A. maculipennis 137 (9.4%) in the region. None of themosquito's head-thorax was found to be naturally infected by malaria parasite. Results of this study, particularly high dominance of A. sacharovi, suggest a potential risk of malaria epidemic in the region, and the need for a continuous epidemiological surveillance.

A randomized, double-blind, placebo-controlled trial on the efficacy and tolerability of sertraline in Iranian veterans with post-traumatic stress disorder.

BACKGROUND: Unlike civilian post-traumatic stress disorder (PTSD), the efficacy of sertraline for the treatment of combat-related PTSD has not yet been proven. The present study aimed to evaluate the clinical efficacy of sertraline against combat-related PTSD in a randomized, double-blind, placebo-controlled trial. METHOD: Seventy Iranian veterans of the Iran-Iraq war who met the DSM-IV criteria for diagnosis of PTSD were randomized to receive either flexibly dosed sertraline (50-200 mg/day) (n=35, completers=32) or placebo (n=35, completers=30) for 10 weeks. Efficacy was evaluated by the Impact of Event Scale--Revised (IES-R) and the Clinical Global Impression scale--Severity (CGI-S) and Improvement (CGI-I) ratings. Responder criteria were defined as a ≥30% reduction in the IES-R total score plus a CGI-I rating of 'much' or 'very much' improved. RESULTS: On both intention-to-treat (ITT) and per protocol (completer) methods of analysis, the mean reductions in the IES-R total and subscale (re-experiencing/intrusion, avoidance/numbing and hyperarousal) scores (p<0.001) and also in the CGI-S score (p<0.01) were significantly greater in the sertraline group than in the placebo group. For the CGI-I, the mean endpoint score was significantly lower in the sertraline group than in the placebo group (p≤0.001). The number of responders in the sertraline group was significantly higher than in the placebo group (44% v. 3%, p≤0.001). Sertraline was well tolerated, with a 6% discontinuation rate as a result of adverse reactions. CONCLUSIONS: The results of this study suggest that sertraline can be an effective, safe and tolerable treatment for combat-related PTSD in Iranian veterans.

Apolipoprotein E gene polymorphism and total serum cholesterol level in Iranian population.

BACKGROUND: Apolipoprotein E (APOE) is known as a major regulator of blood lipid levels in humans. A number of APOE gene allelic variants have been reported including E2, E3 and E4. Recent studies suggested a role for APOE in obesity and increased Body Mass Index (BMI) and plasma lipid levels in obese children. AIM: The aim of this study was to examine the association between APOE genetic variants and the BMI and lipid profile in an Iranian cohort. SETTING AND DESIGN: Samples were obtained from subjects who participated in a study based on the WHO-designed MONICA (multinational monitoring of trends and determinants in cardiovascular disease) study for coronary artery disease risk assessment in Zone 17 of Tehran. The study was approved by the local ethical committee. Informed consent was obtained from all subjects included in this study. MATERIALS AND METHODS: Subjects (n=320) were recruited. The level of triglyceride (TG) and total serum cholesterol was tested for all subjects in this study. Genotyping for APOE was carried using polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP)technique. STATISTICAL ANALYSIS: Levels of significance were determined using contingency tables by either Chi-square or Fisher exact analysis using the STATA (v8) software. The analysis of regression and significance of differences for level of cholesterol and TG was established by one-way analysis of variance followed by Dunnett post hoc multiple comparison tests using SPSS software Version 11.5. RESULTS: The frequency of allele E2 was significantly higher in patients with total serum cholesterol level <200 mg/dl (P 0.01 OR 2.1 95% CI 1.1-4.2). CONCLUSION: The association found in this study between allele E2 and lower total cholesterol level had been reported in previous studies. We have also observed that the frequency of genotype E2/E3 and E2/E4 was significantly higher in patients with normal total serum cholesterol level compared to patients with abnormal cholesterol (P=0.003 OR 2.4 95% CI; 1.3-4.6). Our data needs to be repeated in a larger population with more information for serum LDL and HDL levels and their subgroups.

Visual sensory processing deficit in the occipital region in children with attention-deficit / hyperactivity disorder as revealed by event-related potentials during cued continuous performance test.

AIMS OF THE STUDY: Recent studies described several changes of attention-related components of late frontal event-related potentials (ERPs) during Go/NoGo paradigm in children with attention-deficit/hyperactivity disorder (ADHD). We aimed to determine whether ERP components corresponding to earlier encoding of visual incoming information are also modulated by attentional disorders. METHODS: We recorded high-resolution EEG in 15 children meeting DSM-IV criteria for ADHD, comprising 15 age-matched control groups during an equiprobable Go/NoGo task in a cued continuous performance test (CPT-AX) paradigm. Both P100 and N200 ERP components were measured in response to both Go and NoGo stimuli. We analyzed both components with SwLORETA in order to localize their brain sources. RESULTS: A low rate of Go correct response and high rate of omission errors were observed in ADHD children. When compared to controls, these displayed delayed P100 and N200 latency, and lower P100-NoGo amplitude. In addition, the P100 latency was delayed for NoGo compared to Go condition. The source of P100 was located in occipital area. A sizable decrease in early electrical activity was found in ADHD, especially in the NoGo condition. CONCLUSION: Our results suggest an early deficit in visual sensory integration within the occipital cortex in children with ADHD.

Role of the ventromedial hypothalamic orexin-1 receptors in regulation of gastric Acid secretion in conscious rats.

Orexins play an important role on the central nervous system to modulate gastric acid secretion. The orexin receptors are distributed within the hypothalamus, and expression of orexin-1 receptors (OX1R) is greatest in the anterior hypothalamus and ventromedial nucleus. Therefore, we hypothesised that ventromedial hypothalamic OX1R may be involved in the control of gastric acid secretion. To address this question, we examined the effects of orexin-A and a selective OX1R antagonist, SB-3345867, on gastric acid secretion in pyloric-ligated conscious rats. Intraventromedial injection of orexin-A (0.5-2 microg/microl) stimulated gastric acid secretion in a dose-dependent manner. This stimulatory effect of orexin-A persisted over 3 h. In some experiments, SB-3345867 (10 mg/kg i.p.) was administered 30 min before orexin-A or saline injections. We found that i.p. injection of SB-334867 suppressed stimulated gastric acid secretion induced by orexin-A (2 microg/microl). Atropine (5 mg/kg) also inhibited the stimulatory effect of central injection of orexin-A on acid secretion. In conclusion, the present study suggests that endogenous orexin-A acts on the ventromedial hypothalamus to stimulates acid secretion. This stimulatory effect is probably mediated through OX1R.