Inverse RNA folding solution based on multi-objective genetic algorithm and Gibbs sampling method

In living systems, RNAs play important biological functions. The functional form of an RNA frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule. Here, we concentrate on the inverse RNA folding problem. In this problem, an RNA secondary structure is given as a target structure and the goal is to design an RNA sequence that its structure is the same (or very similar) to the given target structure. Different heuristic search methods have been proposed for this problem. One common feature among these methods is to use a folding algorithm to evaluate the accuracy of the designed RNA sequence during the generation process. The well known folding algorithms take O(n3) times where n is the length of the RNA sequence. In this paper, we introduce a new algorithm called GGI-Fold based on multiobjective genetic algorithm and Gibbs sampling method for the inverse RNA folding problem. Our algorithm generates a sequence where its structure is the same or very similar to the given target structure. The key feature of our method is that it never uses any folding algorithm to improve the quality of the generated sequences. We compare our algorithm with RNA-SSD for some biological test samples. In all test samples, our algorithm outperforms the RNA-SSD method for generating a sequence where its structure is more stable

<NOTES>Schedule Rating System for the Insurance of Impaired Lives

Nanowires have the potential to play an important role for next-generation light-emitting diodes. In this work, we present a growth scheme for radial nanowire quantum-well structures in the AlGaInP material system using a GaInP nanowire core as a template for radial growth with GaInP as the active layer for emission and AlGaInP as charge carrier barriers. The different layers were analyzed by X-ray diffraction to ensure lattice-matched radial structures. Furthermore, we evaluated the material composition and heterojunction interface sharpness by scanning transmission electron microscopy energy dispersive X-ray spectroscopy. The electro-optical properties were investigated by injection luminescence measurements. The presented results can be a valuable track toward radial nanowire light-emitting diodes in the AlGaInP material system in the red/orange/yellow color spectrum

Comparing the healing properties of intra-articular injection of human dental pulp stem cells and cell-free-secretome on induced knee osteoarthritis in male rats

Objective: Osteoarthritis (OA) is a common and painful joint disease with multifactorial causes. Stem cells, due to their high ability to reproduce and differentiate, have created a new horizon in tissue engineering of cartilage and bone. Secretions are one of the new therapies that can be used with stem cells or separately. This study aimed to compare the healing effects of human dental pulp stem cells, cell-free secretome, and human dental pulp mesenchymal stem cells with secretome in the induced OA in male rats. Methods: Dental pulp mesenchymal stem cells were isolated and prepared from human dental pulp. The collagenase type II was injected into the knee of twenty-five male Sprague-Dawley rats, and after 10 weeks, OA was confirmed. Rats were divided into five groups (n = 5): 1) Human dental pulp stem cells plus secretome (HDP+Sec); 2) Human dental pulp stem cells (HDP); 3) Secretome (Sec); 4) Hyalgan as the positive control (Hya); 5) No treatment as the negative control (Ctrl). After 12 weeks since OA was confirmed, the healing process was examined by histopathology and radiology evaluations. Results: Histopathological evaluations, radiological assessments, and matrix indexes in three treatment groups significantly improved compared to the Ctrl and Hya groups. Surface in HDP+Sec was significantly better than the Ctrl group. In radiological evaluations, a significant decrease in OA was observed in the three treatment groups in comparison with the Ctrl groups. There was no significant difference between the treatment groups in any radiological and histopathological evaluations. HDP + Sec group slightly records better results compared to Sec or HDP treatment groups. Conclusion: It was concluded that human dental pulp stem cells and their secretome promote cartilage regeneration due to their cell protective potential as well as matrix degeneration reduction capacity. © 2023 Elsevier Lt

A Serological and Molecular study on Toxoplasma gondii infection in sheep and goat in Tabriz

Toxoplasmosis is an important zoonotic diseases in human and animals. The disease caused by the protozoan Toxoplasma gondii. To determine the infection rate of toxoplasmosis in sheep and goats in east Azarbaijan province of Iran a total of 186 sera, 13 fetal brains, 13 cotyledons and 34 whole blood samples were collected from sheep and goats in Tabriz abattoir during the year 2010. Serum samples were tested for IgG antibodies against Toxoplasma gondii by Enzyme Linked Immunosorbent Assay (ELISA). This test is used in conjunction with direct and nested PCR techniques for detection of T. gondii DNA in blood,cotyledon and brain of fetuses, using 4 pairs of universal and specific primers, 18SrRNA, ITS-1, (Tg1,Tg2)and (Tg3,Tg4). Antibodies against T. gondii were found in 18.3% serum samples. DNA of T. gondii was detected in 69% of fetal brains, 23% of cotyledons and 14.7% of blood samples. The prevalence rate of T. gondii in sheep was 24.8% and in goats was 10.6% and the significant difference was observed between sheep and goats groups (p≤0.05). The prevalence of toxoplasmosis antibodies was significantly higher in adult sheep and goats than younger animals. There was significant difference between male (10.5%) andfemale (19.2%) sheep and goat was observed (p≤0.05). Detection of T. gondii DNA using PCR minimizes the problems which the researcher may face when using serological methods and facilitates diagnosis incomplex cases. The presence of T. gondii in blood, fetal tissues and neonatal specimens strongly suggests active and or congenital infection

a Center of Excellence in Biomathematics,

Several biological features are presented by different types of trees. Two types of such trees are considered in this paper. the first type is trees with n external nodes that each internal node have at least two children, and are used in neuro-science and called neuronal dendritic trees. The second type is trees with n internal nodes and m external nodes. This type of trees represent the secondary structure of RNA sequences, and called RNA trees. In this paper, we present two new parallel algorithms for generation of these two biological trees. Both algorithms are adoptive and cost-optimal and generate the trees in B-order. Computations run in an SM SIMD model. Keywords: Neuronal Dendritic Trees, RNA Trees, Parallel Algorithm, B-order.

Processing and characterization of nanowire arrays for photodetectors

We present a fabrication scheme of contacting arrays of vertically standing nanowires (NW) for LEDs (Duan et al. Nature 409:66–69, 2001), photodetectors (Wang et al. Science (NY) 293:1455–1457, 2001) or solar cell applications (Wallentin et al. Science (NY) 339:1057–1060, 2013). Samples were prepared by depositing Au films using nano-imprint lithography (Ma rtensson et al. Nano Lett 4:699–702, 2004) which are used as catalysts for NW growth in a low-pressure metal organic vapour phase epitaxy system where III-V precursors and dopant gases are flown at elevated temperatures which lead to the formation of NWs with different segments (Borgstrom et al. Nano Res 3:264–270, 2010). An insulating SiO2 layer is then deposited and etched from the top segments of the NWs followed by sputtering of a transparent top conducting oxide and opening up 1 1mm2 device areas through a UV lithography step and etching of the top contact from non-device areas. A second UV lithography step was subsequently carried out to open up smaller windows on the ITO squares for bond pad definition, followed by metallization and lift-off; and the substrate is used as back contact. We also report on the electrical and optical properties of near-infrared p+-i-n+photodetectors/solar cells based on square millimeter ensembles of InP nanowires grown on InP substrates. The study includes a sample series where the p+-segment length was varied between 0 and 250 nm, as well as solar cell samples with 9.3% efficiency with similar design. The NWs have a complex modulated crystal structure of alternating wurtzite and zincblende segments, a polytypism that depends on dopant type. The electrical data for all samples display excellent rectifying behavior with an ideality factor of about 2 at 300 K. From spectrally resolved photocurrent measurements, we conclude that the photocurrent generation process depends strongly on the p+- segment length.Without p+-segment in the NWs, photogenerated carriers funneled from the substrate into the NWs contribute significantly to the photocurrent. Adding a pC-segment shifts the depletion region up into the i -region of the NWs reducing the substrate contribution to photocurrent while strongly improving the collections of carriers generated in the NWs, in agreement with theoretical modeling (Fig. 48.1)

Guided tissue regeneration using a polylactic acid barrier. Part II: Predictors influencing treatment outcome

Objectives: The purpose of this study was to determine the relative impact of various predictors responsible for the variability in treatment outcome after guided tissue regeneration (GTR) in intraosseous periodontal defects. Patients and methods: 30 patients with chronic periodontitis and at least one intraosseous periodontal lesion (≥;4 mm) were enrolled. Following full-mouth scaling, GTR using polylactic acid membranes was performed at one site in each patient. Main periodontal pathogens, defect morphology, membrane exposure and smoking habit were assessed as predictor variables. Alveolar bone level change served as the primary outcome variable in a multiple regression analysis. Results: After 12 months, the 29 patients completing the study showed alveolar bone changes ranging from 4 mm bone gain to 1 mm bone loss (mean: 1.6 ± 0.4 mm gain). Active smoking (β-weight:-0.49, P = 0.003) and persistence of subgingival infection with P. gingivalis (P.g.) (β-weight:-0.25, P = 0.11) were associated with poor treatment outcome. Deep initial intraosseous defects (β-weight: 0.32, P = 0.045) were associated with favorable treatment outcome, and membrane exposure had no impact on bone gain. Conclusion: Active smoking was the strongest predictor variable negatively affecting alveolar bone gain following GTR in the treatment of periodontal defects. It was followed by a positive influence of a deeper intraosseous defect and by a negative effect by persistent subgingival infection of P. gingivalis. The relative impact of these factors may be useful in assessing the prosgnosis of GTR in intraosseous periodontal defects.link_to_subscribed_fulltex