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Additional file 4:Figure S1. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
Length distribution of the unique sRNA sequences in the four libraries. RCK and YACK: ROC22 and YA05-179 under sterile water stress after 48 h, respectively; RT and YAT: ROC22 and YA05-179 under Sporisorium scitamineum stress after 48 h, respectively. (TIF 35 kb)

Additional file 16: Figure S4. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
GO categories and distribution of novel miRNAs targets in RT/RCK (A) and YAT/YACK (B), respectively. RCK and YACK: ROC22 and YA05-179 under sterile water stress after 48 h, respectively; RT and YAT: ROC22 and YA05-179 under Sporisorium scitamineum stress after 48 h, respectively. (TIF 1606 kb)

Additional file 15: Figure S3. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
GO categories and distribution of known miRNAs targets in RT/RCK (A) and YAT/YACK (B), respectively. RCK and YACK: ROC22 and YA05-179 under sterile water stress after 48 h, respectively; RT and YAT: ROC22 and YA05-179 under Sporisorium scitamineum stress after 48 h, respectively. (TIF 3774 kb)

MOESM2 of Process relevant screening of cellulolytic organisms for consolidated bioprocessing

Elena Antonov, Ivan Schlembach, Lars Regestein, Miriam Rosenbaum & Jochen Büchs
Additional file 2: Figure S2. Characteristic growth and enzyme production properties of T. terrestris. (A) Biological duplicates of oxygen transfer rate (OTR) and cumulative oxygen transfer. For clarity of the depicted values, only every third measuring point of OTR and every eighth measuring point of cumulative oxygen transfer over time is represented by a symbol. (B) pH value and protein content in the culture supernatant; (C) Residual cellulose concentration and standard filter paper activity; RAMOS...

MOESM1 of Process relevant screening of cellulolytic organisms for consolidated bioprocessing

Elena Antonov, Ivan Schlembach, Lars Regestein, Miriam Rosenbaum & Jochen Büchs
Additional file 1: Figure S1. Screening for cellulase synergism with A. terreus culture broth using the freeze assay. Freeze assay was performed at the indicated cultivation temperatures with 0.5 mL suspended full culture broth of A. terreus mixed with 0.5 mL full culture broth of different candidate organisms. Full culture broth was harvested after 5 days of cultivation in modified Pakula medium with 5 g L−1 glucose and 30 g L−1 α-cellulose. Bars show overall carbon release rate calculated as...

Additional file 6 of The PINK1 p.I368N mutation affects protein stability and ubiquitin kinase activity

Maya Ando, Fabienne Fiesel, Roman Hudec, Thomas Caulfield, Kotaro Ogaki, Paulina Górka-Skoczylas, Dariusz Koziorowski, Andrzej Friedman, Li Chen, Valina Dawson, Ted Dawson, Guojun Bu, Owen Ross, Zbigniew Wszolek & Wolfdieter Springer
Figure S2. Expression of PINK1-V5 WT and p.I368N mutation at different levels in HeLa cells. (A) HeLa cells were transfected with PINK1 siRNA and with different amounts (0.5 or 1 μg per well of a 12-well plate) of V5 empty vector, PINK1-V5 WT or p.I368N, as indicated. Cells were left untreated or incubated with 10 μM CCCP for 4 h and lysates were analyzed on WB with anti-V5 and PINK1 antibodies. GAPDH was used as a loading control....

Additional file 5: Figure S1. of The PINK1 p.I368N mutation affects protein stability and ubiquitin kinase activity

Maya Ando, Fabienne Fiesel, Roman Hudec, Thomas Caulfield, Kotaro Ogaki, Paulina Górka-Skoczylas, Dariusz Koziorowski, Andrzej Friedman, Li Chen, Valina Dawson, Ted Dawson, Guojun Bu, Owen Ross, Zbigniew Wszolek & Wolfdieter Springer
Reduced full-length PINK1 levels in p.I368N mutant fibroblasts upon treatment with valinomycin. (A) Representative confocal IF images of control and two PINK1 p.I368N fibroblasts showing mitochondrial localization but greatly reduced levels of the mutant protein. Cells were left untreated (-) or treated with 10 μM CCCP for 6 days (+) and stained with antibodies against PINK1 (green) and TOM20 (mitochondria, red). Nuclei were counterstained with Hoechst (blue). Scale bars represent 10 μm. (B) Subcellular fractionation of WT control...

MOESM2 of Metformin exhibits the anti-proliferation and anti-invasion effects in hepatocellular carcinoma cells after insufficient radiofrequency ablation

Qingyun Zhang, Jian Kong, Shuying Dong, Wenlei Xu & Wenbing Sun
Additional file 2: Figure S2. Metformin may regulate SMMC7721 cells proliferation, migration and invasion after insufficient RFA by promoting AMPK/PTEN/Akt pathway. Metformin was used to treat SMMC7721 cells, and western blot was used to determined the expression of p-AMPK, PTEN, p-Akt, E-cadherin, PCNA and VEGF.

MOESM1 of Metformin exhibits the anti-proliferation and anti-invasion effects in hepatocellular carcinoma cells after insufficient radiofrequency ablation

Qingyun Zhang, Jian Kong, Shuying Dong, Wenlei Xu & Wenbing Sun
Additional file 1: Figure S1. Metformin suppressed the insufficient RFA-induced proliferation, migration and invasion of SMMC7721 cells. SMMC7721 cells were treated with insufficient RFA (47 °C 5, 10, 15, 20 and 25 min) gradually. Residual SMMC7721 (named as SMMC7721-H) cells were collected and used for the next experiments. (A) The effect of metformin on proliferation rate of SMMC7721 and SMMC7721-H cells was evaluated by MTT assay. Error bars represent the SEM of data obtained in five independent...

Additional file 3: of DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli

Michelle Madelung, Tina Kronborg, Thomas Doktor, Carsten Struve, Karen Krogfelt & Jakob Møller-Jensen
Figure S3. Muatnts with no cell adhesion defect. The standard error of the mean of three independent invasion assays are shown, P > 0.05 (the exact p-value can be seen in Additional file 9: Table S4). Unpaired t tests with two-tailed p-values were performed using GraphPad Prism 5 software. (JPG 3905 kb)

Additional file 2: of DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli

Michelle Madelung, Tina Kronborg, Thomas Doktor, Carsten Struve, Karen Krogfelt & Jakob Møller-Jensen
Figure S2. Mutants with no cell invasion defect. The standard error of the mean of three independent invasion assays are shown, P > 0.05 (the exact p-value can be seen in Additional file 8: Table S5). Unpaired t tests with two-tailed p-values were performed using GraphPad Prism 5 software. (JPG 3856 kb)

Additional file 2: Table S2. of Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery

Nathaniel Crabtree, Jason Moore, John Bowyer & Nysia George
Genes chosen by CES using 227 selected immune-related genes expressed in rat blood. Description of data: A list of the most frequently selected genes in the rat blood immune-related dataset along with the tissues in which they are most highly expressed, their function in relation to the immune system, and the reason why their expression would be increased. (TIF 4.17 kb)

Additional file 1: of DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli

Michelle Madelung, Tina Kronborg, Thomas Doktor, Carsten Struve, Karen Krogfelt & Jakob MøLler-Jensen
Figure S1. Mutants with no growth defect. The standard error of the mean of two independent 24-h growth experiments is shown. The exact p-value can be seen Additional file 7: Table S3. Unpaired t tests with two-tailed p-values were performed using GraphPad Prism 5 software. (JPG 1007 kb)

Additional file 2: Figure S2. of Specific and quantitative detection of Human polyomaviruses BKPyV and JCPyV in the healthy Pakistani population

Iqra Hussain, Fareeda Tasneem, Muhammed Umer, Ayesha Pervaiz, Muslim Raza, Muhammad Arshad & Naveed Shahzad
Cross reactivity between BKPyV and JCPyV primers. The BKPyV and JCPyV primers specificity was checked by PCR using BKPyV and JCPyV templates for each primer set. All primers were specific having no cross reactivity with other viruses. Lane 1: molecular mass marker; Lane 2,3: LT-BKPyV-pcDNA3 template with BKPyV and JCPyV LT antigen primers, respectively; Lane 6,7: LT-JCPyV-pcDNA3 template with BKPyV and JCPyV LT antigen primers, respectively; Lane 4, 8: non template control pcDNA3 for BKPyV...

Additional file 1: Figure S1. of Specific and quantitative detection of Human polyomaviruses BKPyV and JCPyV in the healthy Pakistani population

Iqra Hussain, Fareeda Tasneem, Muhammed Umer, Ayesha Pervaiz, Muslim Raza, Muhammad Arshad & Naveed Shahzad
Analysis of genomic DNA (gDNA). A) Analysis by agarose gel. The genomic DNA was isolated from the whole blood and loaded on 1% agarose gel. The compact and brighter bands indicate the intact gDNA. Lane 1: molecular mass marker; Lane 2–10 representative genomic DNA from blood samples. B). Quality assay by β-globin amplification. Lane 1: molecular mass marker; Lane 2: Negative control; Lane 3–10; β-globin amplified product from representative genomic DNA. (JPG 66 kb)

Additional file 2: Figure S1. of Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans

Rajini Haraksingh, Alexej Abyzov & Alexander Urban
Effects of tuning parameters in Nexus software on overlap of autosomal CNV calls with gold standard CNVs for a select set of arrays. Overlap data is shown for CNV call sets of two technical replicates for the Affymetrix CytoScan HD, Agilent 2Ă 400 K and 4Ă 180 K, and Illumina HumanOmni1Quad, HumanOmni2.5, HumanOmni2.5Exome and HumanOmni5Exome arrays using at least two different parameter settings. The number of array CNV calls that overlap a gold standard CNV...

2015 01 11 Comparison Sequence for 2014 07 01-02 Time-Lapse Sequence and Resulting Size Comparison

John Kosinski
11 January 2015 - Complete sequence of Reconyx HC600 HyperFire trail camera images using both the motion sensor and time-lapse to trigger the camera. Comparison shoot of a human subject and an 11" x 17" target placed close to the location at which an unknown animal is visible in image 6891 obtained on 1-2 July 2014. The camera is placed in the same location (just below a fork in the tree) on the same tree.
Project...

2015 01 11 Field Notes

John Kosinski
Field notes including image and/or video records. Original versions of all videos are available as of 20 Jan 2016 following the increase in allowed file size by figshare.
Project order 54a

2015 01 03 Field Notes

John Kosinski
Field notes including image and/or video records. Original versions of all videos are available as of 20 Jan 2016 following the increase in allowed file size by figshare.
Project order 51a

electronic supplementary material file 1.docx

Shuhong Zhao
Figure S1. NJ tree. Figure S2. Bayesian treeFigure S2. Models used to calculate phylogeny-based Ka/Ks

electronic supplementary material file 1.docx

Shuhong Zhao
Figure S1. NJ tree. Figure S2. Bayesian treeFigure S2. Models used to calculate phylogeny-based Ka/Ks

2014 12 22 Field Notes

John Kosinski
Field notes including image and/or video records. Original versions of all videos are available as of 20 Jan 2016 following the increase in allowed file size by figshare.
Project order 50a

2014 10 17 Field Notes

John Kosinski
Field notes including image and/or video records.

Project order 49a

2014 09 26 Field Notes

John Kosinski
Field notes including image and/or video records.

Project order 48a

2014 09 20 VID00043 Discussion

John Kosinski
Discussion notes on video VID00043 taken on 20 September 2014. This video is notable for documenting an eye-to-eye observation of an anomalous large non-human primate.
Original and two versions of adjusted frames for the entire VID00043 are posted in separate folders. For convenience, additional processed images are made available in this folder.
The original video is located in the 20 September 2014 Field Notes folder. For convenience, it is also included here along with two enhanced versions...

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