An evolutionary approach to optimising neural network predictors for passive sonar target tracking

Object tracking is important in autonomous robotics, military applications, financial time-series forecasting, and mobile systems. In order to correctly track through clutter, algorithms which predict the next value in a time series are essential. The competence of standard machine learning techniques to create bearing prediction estimates was examined. The results show that the classification based algorithms produce more accurate estimates than the state-of-the-art statistical models. Artificial Neural Networks (ANNs) and K-Nearest Neighbour were used, demonstrating that this technique is not specific to a single classifier. [Continues.

MOESM2 of Screening of melatonin, Îą-tocopherol, folic acid, acetyl-l-carnitine and resveratrol for anti-dengue 2 virus activity

Additional file 2. Effect of folic acid on DENV2 infection of HEK293T/17 and HepG2 cells

MOESM1 of Screening of melatonin, Îą-tocopherol, folic acid, acetyl-l-carnitine and resveratrol for anti-dengue 2 virus activity

Additional file 1. Effect of acetyl-l-carnitine on DENV2 infection of HEK293T/17 and HepG2 cells

Johnson et al. 2018 Functional Ecol data

This file contains all pressure-volume curve, leaf hydraulic vulnerability curve and water potential data used in this study

Additional file 2: Figure S1. of Involvement of fatty acid synthase in dengue virus infection

Real-time PCR validation of siRNA mediated gene silencing of fatty acid synthase (FASN) gene. HEK293T/17 cells were not treated (mock) or treated with a siRNA control (GFP) or treated with one of four siRNAs directed to FASN (FASN1 to FASN 4). On days 1 to 5 post transfection the level of FASN transcript was determined by real time PCR. Normalization expression data relative to actin is shown. Bars show mean +/−SD. (a) 1 day post transfection, (b) 2 days post transfection, (c) 3 days post transfection, (d) 4 days post transfection and (e) 5 days post transfection. Bars show mean +/−SD (*; p value <0.05). Figure S2. Assessment of cell viability after siRNA transfection. HEK293T/17 cells were not treated (mock) or treated with a siRNA control (GFP) or treated with siRNAs directed to FASN (FASN1 and FASN 4). On day 2 post transfection cell viability was assessed by trypan blue staining and counting cells using a hemocytometer. Bars show mean +/−SD. Figure S3. Real-time PCR validation of siRNA mediated gene silencing of fatty acid synthase (FASN) gene. HEK293T/17 cells were not treated (mock) or treated with a siRNA control (GFP) or treated with one of four siRNAs directed to FASN (FASN1 to FASN 4). On day 2 post transfection (a) the level of FASN transcript was determined by real time PCR and (b) amplification product was run on an agarose gel and products visualized after ethidium bromide staining. Normalization expression data relative to actin is shown. Bars show mean +/−SD (*; p value <0.05). Figure S4. Western analysis of FASN expression after siRNA treatment. HEK293T/17 cells were not treated (mock) or treated with a siRNA control (GFP) or treated with one of four siRNAs directed to FASN (FASN1 to FASN 4). On days 1 to 4 post transfection the level of FASN protein was determined by western blot analysis. Normalization expression data relative to actin is shown. Bars show mean +/−SD (* p value <0.05; ** p value <0.01). Figure S5. Determination of orlistat cytotoxicity to HEK293T/17 cells. HEK293T/17 cells were incubated with different concentrations of orlistat or not treated (−) for (a) 24 h or (b) 36 h followed by MTT cell viability assays. Data is derived from 8 replicates. Treatment with 5% DMSO was used as a positive control. Bars show mean +/−SD (*; p value <0.05). Figure S6. The morphology of HEK293T/17 cells after orlistat treatment. HEK293T/17 cells were incubated with different concentrations of orlistat or not treated (mock) for (a) 24 h or (b) 36 h followed by observation under an inverted microscope. Magnification × 20. Figure S7. Evaluation of virucidal activity of orlistat. Stock DENV-2 was incubated with orlistat at concentrations of 1, 10, 20, 50 μM for 1 h and then used in the standard infection protocol. At 24 h.p.i (a) flow cytometry was performed to determine the percentage of infection and (b) supernatants were used to determine the virus titers. No deficit was observed in either percentage cell infection or virus titer. (PDF 2701 kb

Summary of proteins identified by mass spectrometry that co-purified with TAP-Ulp2.

<p>Data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094182#pone.0094182-Westman1" target="_blank">[6]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094182#pone.0094182-Hannich1" target="_blank">[7]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094182#pone.0094182-Blomster1" target="_blank">[23]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094182#pone.0094182-Panse1" target="_blank">[26]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094182#pone.0094182-Zhao1" target="_blank">[56]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094182#pone.0094182-Wohlschlegel1" target="_blank">[58]</a>.</p

Analysis of Ulp2 function.

<p>A. Assay for SUMO-processing activity. Lanes 1–4 contain full length SUMO, lane 5 SUMO-GG. Lanes 1,5, unincubated controls, lanes 2–4 were incubated at 20°C for 2 h following addition of 0.72 µg Ulp1 (lane 2), 2.32 µg Ulp2 (lane 3) or 2 µl buffer (lane 4). Proteins were analysed by SDS PAGE followed by staining with Coommassie Brilliant Blue. B. Assay for de-conjugating activity. <i>S. pombe</i> cell extracts were prepared using standard native extraction procedures. Extracts were incubated at 20°C for 2 h (lanes 1–6), lane 1 5 µl of fraction from extract from <i>E. coli</i> cells transformed with empty vector, equivalent in volume to the Ulp2-containing fraction from <i>ulp2</i>-transformed cells, lane 2 0.6 µg Ulp2, lane 3 1.2 µg Ulp2, lane 4 2.4 µg (5 µl) Ulp2, lane 5 4.8 µg Ulp2, lane 6 1.2 µg Ulp2 pre-incubated with 5 mM NEM, lane 7 total cell extract without incubation at 20°C. Assays were analysed by Western blotting with anti-SUMO antisera. C. Western analysis of total cell extracts using anti-SUMO antisera. Both the separating and stacking gels (6% polyacrylamide in the stacking gel) were blotted. D. Ten microlitre of 10 fold serial dilutions of cells were plated onto YEP agar plates with or without additives as indicated. 10x amount of cells of <i>ulp2-d</i> and <i>ulp1-d,pmt3-GG</i> were used compared to wild type.</p

Ulp2 is localised predominantly within the nucleus.

<p>A. Cells containing myc-tagged <i>ulp2</i> as the sole copy of the <i>ulp2</i> gene were incubated with anti-myc antisera (mouse monoclonal) and anti-SUMO antisera (rabbit polyclonal) followed by TRITC-conjugated anti-mouse IgG antisera, FITC-conjugated anti-rabbit IgG antisera and DAPI. Merge  =  overlay of TRITC (red), FITC (green) and DAPI (blue) staining. 1: early G2 cells, 2,3: late G2 cells, 4: mitotic cells, 5: S phase cells. Bar  = 5 µm.</p

eIF4G, but not eIF3h, is sumoylated.

<p>His-tagged SUMO was expressed in cells containing genomically tagged (HA) copies of eIF4G (A) and eIF3h (B). WCE  =  whole cell extract, PD  =  Ni²⁺-agarose pull down. Blots were probed with anti-HA or anti-SUMO antisera. C. Western blot of whole cell extracts from cells containing genomically tagged eIF4G-HA. UT  =  untreated, C, K  =  incubated for 30 min with 100 µg/ml CHX (C) or 1 M KCl (K).</p

Human eIF4G is sumoylated.

<p>A. <i>S. pombe</i> cells containing His-tagged SUMO and HA-tagged eIF4G as indicated were treated with CHX (100 µg/ml) or KCl (1 M), and His-tagged SUMO pulled down, and analysed as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094182#pone-0094182-g005" target="_blank">Figure 5</a>. B. Comparison of human and eIF4G proteins, indicating protein binding domains: PABP =  polyA binding protein, 4E  =  eIF4E, 4A  =  eIF4A, 3 =  eIF3, Mnk  =  MAP kinase-interacting kinase 1. C. Whole cell extracts (WCE) and Ni²⁺ pull-down (PD) from extracts of HeLa cells stably transfected with His-tagged SUMO-1 (S1) or SUMO-2 (S2) or nothing (-). Western blots probed with anti-eIF4GI (KRERK epitope) antisera. D. Representative eIF4G ion mass spectra (MS/MS spectra) showing identification of the <i>in vitro</i> sites of sumoylation.</p