EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation

During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank has increased more than 15 fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence however is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D-convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The 2-layer architecture was investigated on a large dataset of 63,558 enzymes from the Protein Data Bank and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet.Comment: 11 pages, 6 figure

Perangkat Pembelajaran Matematika Konstruktivis Berbasis Nilai-nilai Karakter 1 Konservasi Berbantuan E-learning

Peningkatkan penguasaan konsep dan memperbaiki sikap belajar mahasiswa dengan menerapkan pembelajaran konstruktivis berbasis nilai-nilai karakter konservasi berbantuan E-learningi adalah fokus dalam penelitian ini, sebab pembelajaran E-learning dapat menyentuh aspek aktivitas dan kreativitas mahasiswa. Pengembangan yang dipilih adalah pengembangan dengan model 4D yang diadaptasi menjadi 4P, yaitu pendefinisian (analisis awal-akhir, analisis peserta didik, analisis materi, analisis tugas, dan merumuskan tujuan pembelajaran khusus), perancangan (penyusunan kriteria tes, pemilihan media, pemilihan format, dan desain awal), pengembangan (validasi ahli dan uji coba), dan penyebaran. Adapun perangkat yang dikembangkan adalah Rencana Pembelajaran Semester (RPS) dan Rancangan Tatap Muka (RTM), yang dilengkapi dengan Lembar Diskusi dan E-learning. Adapun rata-rata prestasi belajar kelas eksperimen adalah 89,38 yang melebihi batas minimal nilai B, sehingga ratarata prestasi belajar kelas eksperimen lebih baik dari kelas kontrol yang rata-rata prestasi belajarnya adalah 80,50. Sehingga dapat disimpulkan pembelajaran efektif

Visual servoing of an autonomous helicopter in urban areas using feature tracking

We present the design and implementation of a vision-based feature tracking system for an autonomous helicopter. Visual sensing is used for estimating the position and velocity of features in the image plane (urban features like windows) in order to generate velocity references for the flight control. These visual-based references are then combined with GPS-positioning references to navigate towards these features and then track them. We present results from experimental flight trials, performed in two UAV systems and under different conditions that show the feasibility and robustness of our approach

Evaluation of Anti-Platelet Aggregation Effect of Some Allium Species

Epidemiologic studies show that the cardiovascular diseases are associated with multiple factors such as raised serum total cholesterol, increased LDL, increased platelet aggregation, hypertension and smoking. In-vitro studies have confirmed the ability of some plants of Allium species to reduce these parameters. Therefore, we evaluated anti-platelet aggregation effect of some Allium species (Allium ampeloprasum, A. hirtifolium, A. haemanthoides, A. vavillovi, A. atroviolaceum, A. jesdianum, A. shelkovnikovii) using arachidonic acid (AA) and adenosine diphosphate (ADP) as platelet aggregation inducers. The screening results for methanolic extract of Allium species showed that the maximum effect of anti-platelet aggregation was related to A. atroviolaceum. This extract inhibited the in-vitro platelet aggregation induced by AA and ADP with IC50 values of 0.4881 (0.4826-0.4937) mg/ml and 0.4945 (0.4137-0.5911) mg/ml respectively. These results support the hypothesis that the dietary intake of Allium could be beneficial for prevention of cardiovascular diseases

Isolation and Enrichment of Mouse Female Germ Line Stem Cells

Objective: The existence of female germ-line stem cells (FGSCs) has been the subject of a wide range of recent studies. Successful isolation and culture of FGSCs could facilitate studies on regenerative medicine and infertility treatments in the near future. Our aim in the present study was evaluation of the most commonly used techniques in enrichment of FGSCs and in establishment of the best procedure. Materials and Methods: In this experimental study, after digesting neonate ovary from C57BI/6 mice, we performed 2 different isolation experiments: magnetic activated cell sorting (MACS) and pre-plating. MACS was applied using two different antibodies against mouse vasa homolog (MVH) and stage-specific embryonic antigen-1 (SSEA1) markers. After the cells were passaged and proliferated in vitro, colony-forming cells were characterized using reverse transcription-polymerase chain reaction (RT-PCR) (for analysis of expression of Oct4, Nanog, C-kit, Fragilis, Mvh, Dazl, Scp3 and Zp3), alkaline phosphatase (AP) activity test and imnnunocytochemistry. Results: Data showed that colonies can be seen more frequently in pre-plating technique than that in MACS. Using the SSEA1 antibody with MACS, 1.98 +/- 0.49% (Mean +/- SDV) positive cells were yield as compared to the total cells sorted. The colonies formed after pre-plating expressed pluripotency and germ stem cell markers (Oct4, Nanog, C-kit, Fragilis, Mvh and Dazl) whereas did not express Zp3 and Scp3 at the mRNA level. Immunocytochemistry in these colonies further confirmed the presence of OCT4 and MVH proteins, and AP activity measured by AP-kit showed positive reaction. Conclusion: We established a simple and an efficient pre-plating technique to culture and to enrich FGSCs from neonatal mouse ovaries

Effect of educational intervention on self-efficacy for choosing delivery method among pregnant women in 2013

Methods: This quasi-experimental study was conducted on 130 pregnant women who attended urban health centers in Shahrekord city in 2013. Intervention was applied in the experimental group in three sessions in about 60-90 min while control group did not receive any intervention. Fear of childbirth and self-efficacy questionnaire was completed before and after training. Results: While mean scores of the fear of childbirth, expectations and childbirth self-efficacy before the intervention between the two groups were not significantly different (P > 0.05), mean scores of childbirth in intervention group was reduced and expectation and childbirth self-efficacy had a significant increase after intervention (P 0.05) and self-efficacy (P < 0.001) than those who chose normal method. Conclusions: Our findings showed that training-based self-efficacy procedure has been effective in encouraging mothers to choose natural childbirth. Therefore, the design and implementation of curriculum-based strategies for increasing self-efficacy is suggested for pregnant women. Background: Nowadays, there has been a growing trend of caesarean sections in Iran. One reason would be the mother’s desire. Increased maternal self-efficacy can be an important step to reduce percentage of cesarean. This study aimed to determine the effectiveness of training-based strategies to increase the self-efficacy for choosing delivery method among pregnant women in Shahrekord city. © 2014, Isfahan University of Medical Sciences(IUMS). All rights reserved