Journal: Micromachines

Article Title: Design of an FPGA-Based Fuzzy Feedback Controller for Closed-Loop FES in Knee Joint Model

doi: 10.3390/mi12080968

Figure Lengend Snippet: Hardware measurement setup using an Intel field-programmable gate array (FPGA) (DE2-115) board, an ADC (ADC0804) circuit, a rotary 10k ohm potentiometer and a digital oscilloscope.

Article Snippet: This section discusses the results of synthesized digital FFC using the Intel FPGA (Cyclone IV E) chip (Terasic Inc., Hsinchu, Taiwan), register transfer level (RTL) simulation results in a digital simulator timing waveform, real-time hardware measurement, comparative analyses between hardware measurement and simulation results, and HDL co-simulations for system level verification in MATLAB Simulink.

Techniques:

Journal: Micromachines

Article Title: Design of an FPGA-Based Fuzzy Feedback Controller for Closed-Loop FES in Knee Joint Model

doi: 10.3390/mi12080968

Figure Lengend Snippet: Schematics of the synthesized digital FFC using the Intel FPGA (Cyclone IV E) chip; ( a ) Internal architecture of the digital FFC; ( b ) Internal architecture of the digital FLC.

Article Snippet: This section discusses the results of synthesized digital FFC using the Intel FPGA (Cyclone IV E) chip (Terasic Inc., Hsinchu, Taiwan), register transfer level (RTL) simulation results in a digital simulator timing waveform, real-time hardware measurement, comparative analyses between hardware measurement and simulation results, and HDL co-simulations for system level verification in MATLAB Simulink.

Techniques: Synthesized

Journal: Micromachines

Article Title: Design of an FPGA-Based Fuzzy Feedback Controller for Closed-Loop FES in Knee Joint Model

doi: 10.3390/mi12080968

Figure Lengend Snippet: Synthesis summary report of the digital Fuzzy Feedback Controller (FFC) using the Intel field-programmable gate array (FPGA) (Cyclone IV E) chip.

Article Snippet: This section discusses the results of synthesized digital FFC using the Intel FPGA (Cyclone IV E) chip (Terasic Inc., Hsinchu, Taiwan), register transfer level (RTL) simulation results in a digital simulator timing waveform, real-time hardware measurement, comparative analyses between hardware measurement and simulation results, and HDL co-simulations for system level verification in MATLAB Simulink.

Techniques:

Journal: Nucleic Acids Research

Article Title: Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair

doi: 10.1093/nar/gkv327

Figure Lengend Snippet: Neil1 protein and RNA abundance in mES and human prostate cancer cells with inherent or reduced levels of Rad9 protein. ( A ) Immunoblotting analyses used to measure indicated DDR proteins in Rad9 +/+ and Rad9 −/− mES cells. β-Actin, loading control. ( B ) Immunoblotting used to measure NEIL1 protein abundance in DU145 cells with inherent or sh RAD9 knocked down RAD9 levels. β-Actin, loading control. ( C ) Same as B, but PC-3 cells were examined. ( D ) qRT-PCR used to assess Neil1 and Rad9 RNA levels in Rad9 +/+ and Rad9 −/− mES cells, plotted relative to β-Actin levels. ( E, F ) Same as D, but using DU145 and PC-3 cells, respectively, with inherent or shRNA-reduced levels of RAD9. Error bars in D, E and F represent standard deviation of three independent experiments.

Article Snippet: Mouse Neil1 and human NEIL1 ORF clones were purchased from Origene (#MC211355) and Genecopoeia (#A3833), respectively.

Techniques: Western Blot, Control, Quantitative Proteomics, Quantitative RT-PCR, shRNA, Standard Deviation

Journal: Nucleic Acids Research

Article Title: Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair

doi: 10.1093/nar/gkv327

Figure Lengend Snippet: Rad9 controls Neil1 protein stability in mES but not in DU145 cells. ( A ) Neil1 and Rad9 protein levels were detected by immunoblotting in Rad9 +/+ and Rad9 −/− mES cells after treating with CHX (50 μg/ml) for indicated time intervals. β-Actin was the loading control. ( B ) Same as A, but using DU145 cells with or without sh RAD9 . ( C ) Average Neil1 protein level relative to β-Actin was calculated by densitometric measurements of bands from three independent experiments (as in A, B). Error bars represent standard deviation. ( D ) Neil1 and Rad9 abundance was assessed by immunoblotting analyses using Rad9 +/+ and Rad9 −/− mES cells grown in the presence or absence of proteasomal inhibitor MG132 at concentrations indicated. β-Actin is the loading control. ( E ) Average Neil1 protein level relative to β-Actin was calculated by densitometric measurements of bands from three independent experiments (as in D).

Article Snippet: Mouse Neil1 and human NEIL1 ORF clones were purchased from Origene (#MC211355) and Genecopoeia (#A3833), respectively.

Techniques: Western Blot, Control, Standard Deviation

Journal: Nucleic Acids Research

Article Title: Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair

doi: 10.1093/nar/gkv327

Figure Lengend Snippet: RAD9 protein binds the NEIL1 promoter. Binding of RAD9 and Rad9 to their corresponding NEIL1/Neil1 promoter was tested by ChIP-qPCR, using DU145 and mES cells, respectively. ( A ) Schematic representation of NEIL1/Neil1 promoters with the approximate position of primer pairs used for ChIP-qPCR experiments (see Supplementary Table S1 for primer details); each letter represents the primer pair; asterisk indicates reverse orientation primer of pair. TSS is the transcription start site. ( B ) Fold enrichment of RAD9 or Rad9 relative to IgG in ChIP-qPCR experiments. Error bars represent the standard deviation of three independent experiments.

Article Snippet: Mouse Neil1 and human NEIL1 ORF clones were purchased from Origene (#MC211355) and Genecopoeia (#A3833), respectively.

Techniques: Binding Assay, ChIP-qPCR, Standard Deviation

Journal: Nucleic Acids Research

Article Title: Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair

doi: 10.1093/nar/gkv327

Figure Lengend Snippet: NEIL1 promoter-luciferase reporter activity in DU145 and mES cells with inherent or reduced levels of RAD9. Chimeric constructs of the NEIL1 promoter-luciferase reporter are schematically represented on the Y-axis. The X-axis indicates luciferase activity as fold above values obtained for the promoterless vector, pGL-Basic. ( A ) Human NEIL1 promoter sequence. DU145 (dark bar), DU145-sh RAD9 (light bar) host cells. ( B ) Mouse Neil1 promoter sequences. mES Rad9 +/+ (dark bar), Rad9 −/− (light bar) host cells. Error bars represent the standard deviation of three independent experiments. Luc, luciferase. Numbers on constructs in Y-axis correspond to nucleotide positions in promoters relative to the start of transcription. Dark ovals represent intact p53-binding sites; light ovals indicate mutation sites. Pointed regions of promoters contain RAD9 binding sequences, as per the Chip-qPCR data, and are deleted.

Article Snippet: Mouse Neil1 and human NEIL1 ORF clones were purchased from Origene (#MC211355) and Genecopoeia (#A3833), respectively.

Techniques: Luciferase, Activity Assay, Construct, Plasmid Preparation, Sequencing, Standard Deviation, Binding Assay, Mutagenesis, ChIP-qPCR

Journal: Nucleic Acids Research

Article Title: Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair

doi: 10.1093/nar/gkv327

Figure Lengend Snippet: Clonogenic survival of mES and DU145 cells with varying status of Rad9 after UV, menadione, and gamma-ray treatment. ( A, B ) Sensitivity of cells to 254 nm UV light. ( C, D ) Sensitivity of cells to menadione. ( E, F ) Sensitivity of cells to gamma rays. A, C and E, parental DU145 cells or those with shControl or sh RAD9 , and the latter with insertless pCMV6-AC-DDK-His vector, or ectopically expressing Rad9 + or NEIL1 + . B, D and F, mES cells Rad9 +/+ , Rad9 −/− , or the latter with insertless pCMV6-AC-DDK-His vector, or ectopically expressing RAD9 + , Rad9 + , NEIL1 + or Neil1 + . Percent survival after each treatment was calculated as the number of colonies formed in treated versus mock-treated populations, times 100. Points are the average of three independent trials, each with two dishes per point. Error bars, standard deviation.

Article Snippet: Mouse Neil1 and human NEIL1 ORF clones were purchased from Origene (#MC211355) and Genecopoeia (#A3833), respectively.

Techniques: Plasmid Preparation, Expressing, Standard Deviation

Journal: Nucleic Acids Research

Article Title: Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair

doi: 10.1093/nar/gkv327

Figure Lengend Snippet: Glycosylase activity on different substrates in extracts from mES cells with varying Rad9 and Neil1 status. Glycosylase activity (incision) was measured by an in vitro assay using a 24-mer oligo substrate containing either abasic ( A, B ) 5-OH-Uracil ( C, D ) or 8-oxo-dG ( E, F ) modifications, coupled with extracts from mES cells, either Rad9 +/+ , Rad9 −/− , or the latter with insertless pCMV6-AC-DDK-His vector (IV), or ectopically expressing RAD9 + , Rad9 + , NEIL1 + or Neil1 + . Panels A, C, E: in vitro incision assay showing 24-mer oligo substrate and 10-mer product. Average percent incision from three independent experiments shown in panels B, D, F; error bars, standard deviation.

Article Snippet: Mouse Neil1 and human NEIL1 ORF clones were purchased from Origene (#MC211355) and Genecopoeia (#A3833), respectively.

Techniques: Activity Assay, In Vitro, Plasmid Preparation, Expressing, Standard Deviation

Journal: Nucleic Acids Research

Article Title: Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair

doi: 10.1093/nar/gkv327

Figure Lengend Snippet: Deletion analysis used to determine the region of mouse Rad9 protein involved in Rad9–Neil1 binding. ( A ) Ectopically expressed RAD9 and endogenous Neil1 were immunoprecipitated from Rad9 −/− mES cells individually and tested for binding to the other. ( B ) Same as A, but in DU145-sh RAD9 cells ectopically expressing FLAG-Rad9. ( C ) Graphic depiction of amino acids encoded by inherent or truncated Rad9 cloned into pCMV6-AC-DDK-His vector, which adds a C-terminal FLAG-His tag to each protein; numbers represent the amino acid positions. Dark box at C-terminal end represents FLAG-His tag. Rad9, full length; Rad9 N, amino-end fragment; Rad9 C, carboxy-end fragment. ( D ) Binding of intact or deletion mutants of Rad9 to Neil1, shown by IP either with anti-FLAG (upper panel) or anti-Neil1 (lower panel) antibody. ( E ) Immunoblot showing abundance of Rad9 and Neil1 proteins in whole cell extracts from IP experiments in panel B. β-Actin was used as loading control. Rad9 N, amino-terminal fragment; Rad9 C, carboxy-terminal fragment; NS, non-specific; IP, immunoprecipitation; IB, immunoblot.

Article Snippet: Mouse Neil1 and human NEIL1 ORF clones were purchased from Origene (#MC211355) and Genecopoeia (#A3833), respectively.

Techniques: Binding Assay, Immunoprecipitation, Expressing, Clone Assay, Plasmid Preparation, Western Blot, Control