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Additional file 1: Figure S1. of Feasibility of cardiovascular magnetic resonance derived coronary wave intensity analysis

Claire Raphael, Jennifer Keegan, Kim Parker, Robin Simpson, Julian Collinson, , Ricardo Wage, Peter Drivas, Stephen Strain, Robert Cooper, , Rod Stables, Carlo Di Mario, Michael Frenneaux, Dudley Pennell, Justin Davies, Alun Hughes, David Firmin & Sanjay Prasad
Stepwise analysis of invasive and CMR data. Ad = diastolic aortic area, As = systolic aortic area, Ps = brachial systolic pressure, Pd = brachial diastolic pressure, ∝ = scaling factor. ρ = blood density (taken as 1050 kg/m3). (PPTX 103 kb)

Additional file 4: Video 2. of Morphological change of CD4+ T cell during contact with DC modulates T-cell activation by accumulation of F-actin in the immunology synapse

Wei Lin, , , , , &
The morphology of a CD4+ T cell changes from round to round-flattened during the IS formation. TCR is shown red, ICAM-1 is green, and scale bar is 2Â Îźm. Before IS formation, TCR was uniformed on the surface of T cell. After IS formation, TCR and ICAM-1 was accumulated at the interface of T-DC.

Additional file 10: of Genome-wide analysis of lectin receptor-like kinases in Populus

, Jessy LabbĂŠ, , , Sara Jawdy, Megan Kennedy, Jenifer Johnson, Avinash Sreedasyam, Jeremy Schmutz, Gerald Tuskan &
The amino acid sequence alignment and conserved motifs of G-type PtLecRLKs. (A) Amino acid sequence alignment via CLUSTALW. To determine conserved amino acid regions, 50Â % sequence identity was used as a cutoff. Note that the amino acid sequence in the protein kinase domain is highly conserved in most G-type PtLecRLKs whereas the other domains such as S-locus glycoprotein, EGF, PAN, TM and signal peptide varied. Highly conserved motifs are boxed with labels a, b,...

Additional file 4: Figure S2. of Genetic Mapping of Anaerobic Germination-Associated QTLs Controlling Coleoptile Elongation in Rice

Sheng-Kai Hsu & Chih-Wei Tung
Manhattan plot from GWAS of anaerobic response index within and across subspecies. (PPTX 3009Â kb)

Additional file 9: Figure S4. of Time-resolved pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae

, , , Sang Lee, &
Time-resolved expression of two component system (TCS) genes. (A) phoB-phoR genes were upregulated within 5 min. (B) ppk was upregulated within 5 min whereas ppx expression was not changed. (C) phoP-phoQ genes were also upregulated within 5 min. The unit of time is min. Red lines indicate the expression levels of genes in control (untreated) Xoo cells. Y-axis represents fold-change. (PPTX 71 kb)

Additional file 3: Figure S2. of Interactions between the oomycete Pythium arrhenomanes and the rice root-knot nematode Meloidogyne graminicola in aerobic Asian rice varieties

, , , , , , & Tina Kyndt
Nematode development at 20 DAI from greenhouse experiment for Palawan (A,C,E) and IR81413-BB-75-4 (B,D,F) under different infection schemes. (A,B) Total number of nematodes, (C,D) number of galls, and (E,F) the developmental stages of M. graminicola per plant at 20 days after transplanting. Statistics were performed with Mann-Whitney U test (α = 0.05), different letters indicate significant differences (n = 12). Statistics for (E,F) were performed by giving each group a total score; where the percentage of each stage has...

Additional file 9: Figure S3. of Identification of therapeutic targets applicable to clinical strategies in ovarian cancer

Marianne Kim, Natasha Caplen, , Lidia Hernandez, Carrie House, Georgios Pongas, Elizabeth Jordan & Christina Annunziata
Two-way ANOVA with REGWQ post-hoc test for cisplatin dose effect. (PPTX 65Â kb)

Additional file 1: Figure S1. of Serum biomarkers VEGF-C and IL-6 are associated with severe human Peripheral Artery Stenosis

, Lei Han, , , & Bin Wei
Serum concentrations of glucose (A), triglyceride (B), HDL, LDL, VLDL (C) and cholesterol (D) from 18 healthy subjects, 23 moderate PAS patients and 20 severe PAS patients were examined. (PPT 732Â kb)

Additional file 1: Figure S1. of Granzyme B-inhibitor serpina3n induces neuroprotection in vitro and in vivo

, Katia Carmine-Simmen, Camille Olechowski, Bradley Kerr, & Fabrizio Giuliani
A representative section from the lumbar part of the spinal cord. The regions under the blue-lined rectangular boxes show the areas where CD4+ T cells and SMI32-positive axons were quantified and analyzed. (PPTX 6495 kb)

Video 1; Extracted locations of predator and prey plotted for several trials (.avi) from The confusion effect when attacking simulated three-dimensional starling flocks

Benedict G. Hogan, Hanno Hildenbrandt, Nicholas E. Scott-Samuel, Innes C. Cuthill & Charlotte K. Hemelrijk
The confusion effect describes the phenomenon of decreasing predator attack success with increasing prey group size. However, there is a paucity of research into the influence of this effect in coherent groups, such as flocks of European starlings (Sturnus vulgaris). Here, for the first time, we use a computer game style experiment to investigate the confusion effect in three dimensions. To date, computerized studies on the confusion effect have used two-dimensional simulations with simplistic prey...

Video 1; Extracted locations of predator and prey plotted for several trials (.avi) from The confusion effect when attacking simulated three-dimensional starling flocks

Benedict G. Hogan, Hanno Hildenbrandt, Nicholas E. Scott-Samuel, Innes C. Cuthill & Charlotte K. Hemelrijk
The confusion effect describes the phenomenon of decreasing predator attack success with increasing prey group size. However, there is a paucity of research into the influence of this effect in coherent groups, such as flocks of European starlings (Sturnus vulgaris). Here, for the first time, we use a computer game style experiment to investigate the confusion effect in three dimensions. To date, computerized studies on the confusion effect have used two-dimensional simulations with simplistic prey...

Supplementary Material for: Five-Port Combined Limbal and Pars Plana Vitrectomy for Infectious Endophthalmitis

K. Xu, E.K. Chin &
Pars plana vitrectomy for acute infectious endophthalmitis can be challenging due to severe inflammation in the anterior chamber creating significant media opacity. We describe a surgical technique combining limbal based vitrectomy and pars plana vitrectomy to manage acute infectious endophthalmitis. Limbal based vitrectomy facilitates removal of anterior chamber fibrin and inflammatory membranes for safe and optimal posterior pars plana vitrectomy.

Additional file 8: of Rab32 and Rab38 genes in chordate pigmentation: an evolutionary perspective

Ugo Coppola, Giovanni Annona, Salvatore D’Aniello & Filomena Ristoratore
Additional syntenic studies. A. Human chromosome 11 and mouse chromosome 7: a focus on Rab38 gene loci with, respectively, a TRIM gene family expansion and an extraordinary clustering of olfactory genes: Vomeronasal 2 receptor (Vmn2r) and Olfactory Receptor (OR) in mouse; B Microsynteny of Rab32LO between echinoderms and cephalochordates. (PPTX 72.8 kb)

MOESM3 of Janus kinase inhibition suppresses PKC-induced cytokine release without affecting HIV-1 latency reversal ex vivo

Adam Spivak, Erin Larragoite, McKenna Coletti, Amanda Macedo, Laura Martins, Alberto Bosque & Vicente Planelles
Additional file 3: Figure 2. Ingenols do not induce pro-inflammatory cytokine release in purified resting CD4+ T cell cultures. Concentrations of pro-inflammatory cytokines TNFα, IFNγ, IL-1β and IL-6 were not significantly elevated in the presence of ingenol-3,20-dibenzoate (ingenol DB) or ingenol B compared to media alone control at 72 h in purified resting CD4+ T cell cultures. Mean values and standard deviation of seven independent experiments using resting CD4+ T cells from aviremic ART-treated HIV...

Clean4Yield eConference teaser

Organic Photovoltaics

Mikkel Jørgensen

Interview with Theresa Spaan-Burke

Theresa Spaan-Burke

Additional file 7: Figure S4. of Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response

Daniel Pastor-Flores, , Anna Bahí, , Ricardo Biondi & Antonio Casamayor
Analysis of the genes up-regulated by heat shock in a Pkh-dependent manner. A: Cluster analysis of the expression profiles of the sub-set of 52 genes that whose expression was up-regulated upon heat stress in a Pkh-dependent manner that were found already up-regulated in SDP8 cells treated with doxycycline for 24 h (“Depletion of Pkh”). Data was hierarchically clustered (complete linkage clustering, uncentered correlation) by means of the Gene Cluster (v. 2.11) software [57] and visualized...

Additional file 6: Figure S3. of Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response

Daniel Pastor-Flores, , Anna Bahí, , Ricardo Biondi & Antonio Casamayor
The transcriptional changes caused by heat shock are attenuated in Pkh-depleted cells. A: Graphical representation of the expression values (in log2) for the top 100 most up-regulated genes, after heat shock, in doxycycline-treated wild-type (WT) cells (○) and the corresponding value for the same genes in the SDP8 strain under the same condition (■). B: Similar representation for the top 100 most down-regulated genes after heat shock in doxycycline-treated wild-type (WT) cells (○) and the...

Additional file 3: of The diagnostic value of saccades in movement disorder patients: a practical guide and review

, , Janet Rucker & Steven Frucht
Segment 3. Degenerative ataxias. Spinocerebellar ataxia type 2 (SCA2): This patient with genetically confirmed SCA-2 and a history of mild scanning dysarthria and mild wide-based gait, demonstrates pathognomonic eye findings of SCA-2. Rare square wave jerks are present. She blinks to generate vertical saccades, and vertical saccadic speed is mildly slow. Similar blinks are used to generate horizontal saccades, but horizontal saccades are even slower and more difficult than vertical saccades. Spinocerebellar ataxia type 3...

Additional file 1: Figure S1. of Decreased performance in IDUA knockout mouse mimic limitations of joint function and locomotion in patients with Hurler syndrome

, Min Kwak, Sung Cho, , , , & Dong-Kyu Jin
Radiograph of IDUA KO and wild type mice. Arrows show the area where thickness of the bone is evident. (PPTX 440Â kb)

MOESM2 of PEP-1-MsrA ameliorates inflammation and reduces atherosclerosis in apolipoprotein E deficient mice

Yao Wu, , , Li Ma, , , Fen Du & Hong Yu
Additional file 2: Figure S2. Cell viability analysis of MsrA and PEP-1-MsrA on HeLa cells. Different concentrations of MsrA and PEP-1-MsrA proteins were incubated with HeLa cells for 72 h. Cell viability was analyzed by MTT method, n = 3.

MOESM5 of Janus kinase inhibition suppresses PKC-induced cytokine release without affecting HIV-1 latency reversal ex vivo

Adam Spivak, Erin Larragoite, McKenna Coletti, Amanda Macedo, Laura Martins, Alberto Bosque & Vicente Planelles
Additional file 5: Figure 4. Ruxolitinib-induced cytokine changes in PBMCs from aviremic HIV-1 infected donors. CD25 (IL2r), IL-5, and IL-13 concentrations were significantly decreased in PBMC cultures exposed to ruxolitinib + ingenol-3,20-dibenzoate compared to ingenol-3,20-dibenzoate alone. Ruxolitinib significantly reduced these cytokine concentrations in CD3/28 antibody-treated PBMC cultures as well, along with reduction in IL-10. Ruxolitinib did not decrease pro-inflammatory cytokines induced by CD3/28 antibody stimulation to the same degree as ingenol-stimulated cells (shown in Fig....

MOESM1 of Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

Samuel Oyola, Cristina Ariani, William Hamilton, , Lucas Amenga-Etego, Anita Ghansah, Gavin Rutledge, Seth Redmond, Magnus Manske, , Chris Jacob, Thomas Otto, Kirk Rockett, Chris Newbold, Matthew Berriman & Dominic Kwiatkowski
Additional file 1: Figure S1. A plot of primers (probes) and their binding distribution on the P. falciparum genome. The topmost panel show cumulating binding positions and distribution profile of all the 28 primers. Black dots (1) show positions where the primer binds and Red (0) dots shows positions with no primer binding. Probes are ordered from bottom to top; the first 10 primers is Probe_10, followed by Probe_20 then Probe_28. Figure S2. Coverage depths...

Tutorial: Data sharing from a computer or cluster via SeedMe.org

Amit Chourasia, Mona Wong, Dmitry Mishin, David Nadeau & Michael Norman
High performance computing processes and workflows often have several steps for example input preparation, computation monitoring, output validation, analysis and visualizations. All these processes yield small-scale consumable data such as computation progress, statistics, plots that are of high value for research team. Sharing and accessing this information by team members is often slow and cumbersome in current HPC environment. SeedMe platform lowers these barriers by providing cyberinfrastructure and necessary tools for data sharing.This tutorial will...

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