Journal: bioRxiv

Article Title: Paternal aging affects developmental convergence of vocal behavior in individual mice: machine learning-driven analyses of individuality

doi: 10.1101/738781

Figure Lengend Snippet: (A) The experimental design in the model of paternal aging. (B) Typical sonograms of twelve types of syllables. Scale bar = 60 kHz, 20 ms. (C) Following maternal separation, USVs were recorded from individual pups one by one. The resulting USVs were processed to spectrogram by USVSEG, which segmented the syllables and outputted the syllable images with acoustic parameters. Subsequently, the VAE was trained to learn and encode the syllables. The resulting syllables were visualized and mapped in a latent space.

Article Snippet: Acoustic waveforms were first processed using a GUI-based MATLAB script (“USVSEG”) originally developed for segmenting USVs emitted by rodents ( ) because we found that an audio segmentation method implemented in the original variational autoencoder (VAE) detected large amounts of noise.

Techniques:

Journal: bioRxiv

Article Title: Paternal aging affects developmental convergence of vocal behavior in individual mice: machine learning-driven analyses of individuality

doi: 10.1101/738781

Figure Lengend Snippet: (A) Z scores of syllable number, duration, maximum frequency, maximum amplitude, and interval. The thick horizontal lines indicate the mean value of Z scores. Boxplots represent the range of Z scores. The horizontal lines in the boxes signify respective group medians, boxes are 25 th – 75 th percentiles, and whiskers represent minimum to maximum. The light blue point depicts the outlier. Each point represents the syllable data of one pup. * p < 0.05, ** p < 0.01, *** p < 0.001 indicate a significant difference between the wildtype and Auts2 del8/+ pups (Wilcoxon test). (B) Pie graphs show the percentage composition of the twelve types of syllables in the pups of wildtype and Auts2 del8/+ . The colors indicate the syllable type shown in . (C) A significant decrease of the number of syllable types in Auts2 del8/+ pups. The thick horizontal lines indicate the mean value of the number of syllable types. Boxplots represent the range of the number of syllable types. The horizontal lines in the boxes signify respective group medians, boxes are 25 th – 75 th percentiles, and whiskers represent minimum to maximum. Each point represents the data of one pup. *** p < 0.001 indicates a significant difference (Wilcoxon test). (D) A significant decrease of entropy scores of syllables in Auts2 del8/+ pups. The thick horizontal lines indicate the mean value of entropy scores. Boxplots represent the range of entropy scores. The horizontal lines in the boxes signify respective group medians, boxes are 25 th – 75 th percentiles, and whiskers represent minimum to maximum. Each point represents the data of one pup. *** p < 0.001 indicates a significant difference (Wilcoxon test). (E) The VAE takes spectrograms from the syllables of wildtype and Auts2 del8/+ pups as input and visualizes them as a vector of latent dimensions at P7. Each point in this latent space represents a single spectrogram of a syllable. The distance between points indicates neighbor similarity. (F) Based on the USVSEG, PCA summarized the patterns of individual wildtype and Auts2 del8/+ pups. Each point represents the syllable pattern of one pup. Shorter distances between points indicate higher similarity in syllable patterns. Grey and light blue clusters contain 90% of the population of wildtype and Auts2 del8/+ pups, respectively. (G) Based on the VAE, t-SNE summarized the patterns of individual wildtype and Auts2 del8/+ pups. Each point represents the syllable patterns of one pup. Shorter distances between points indicate higher similarity in syllable patterns. Grey and light blue clusters contain 90% of the population of wildtype and Auts2 del8/+ pups, respectively.

Article Snippet: Acoustic waveforms were first processed using a GUI-based MATLAB script (“USVSEG”) originally developed for segmenting USVs emitted by rodents ( ) because we found that an audio segmentation method implemented in the original variational autoencoder (VAE) detected large amounts of noise.

Techniques: Plasmid Preparation

Journal: bioRxiv

Article Title: Paternal aging affects developmental convergence of vocal behavior in individual mice: machine learning-driven analyses of individuality

doi: 10.1101/738781

Figure Lengend Snippet: (A) Based on the USVSEG, PCA summarized the patterns of individual YFO and AFO at P3, P6, P9, and P12. Each point represents the syllable pattern of one pup. Shorter distances between points indicate higher similarity in syllable patterns. Grey and light red clusters contain 90% of the population of the YFO and AFO, respectively. The M and F mean male and female, respectively. (B) Based on the VAE, t-SNE summarized the patterns of individual YFO and AFO at P3, P6, P9, and P12. Each point represents the syllable features of one pup. Shorter distances between points indicate higher similarity in vocal repertoire. Grey and light red clusters contain 90% of the population of the YFO and AFO, respectively. The M and F mean male and female, respectively. (C) Summary of individual traces at P3 and P12 based on (A) and (B). Each point represents the syllable pattern of one pup.

Article Snippet: Acoustic waveforms were first processed using a GUI-based MATLAB script (“USVSEG”) originally developed for segmenting USVs emitted by rodents ( ) because we found that an audio segmentation method implemented in the original variational autoencoder (VAE) detected large amounts of noise.

Techniques:

Journal: Scientific Reports

Article Title: NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models

doi: 10.1038/s41598-019-52451-8

Figure Lengend Snippet: Summary of existing NMR lineshape software. The shown MATLAB version is known to work with the indicated software but may not be the only version. “?” indicates unknown version. “N/A”: not available in the indicated software.

Article Snippet: TITAN , NMRPipe MATLAB R2016b* , Spec. acqu. parameters 2D lineshape only , Scripts-based Up to 4 states , GUI-based Up to 4 states.

Techniques: Software

Journal: Materials Today Bio

Article Title: Viridibacillus culture derived silver nanoparticles exert potent anticancer action in 2D and 3D models of lung cancer via mitochondrial depolarization-mediated apoptosis

doi: 10.1016/j.mtbio.2024.100997

Figure Lengend Snippet: Study of migration of 2D cultured A549 cells in absence and presence of epidermal growth factor (EGF) and V-AgNPs at LD50-2D. (A) The schematic shows creation of cell-free area using cell inserts and addition of cell culture medium (control group), EGF (positive control group), and EGF + V-AgNPs (treatment group). Upon these treatments, the time lapse imaging was done to understand A549 cell migration in cell-free area using IncuCyte S3 live cell imaging platform. (B) The schematic shows the image analysis pipeline for time lapse images obtained from IncuCyte S3 instrument. The image analysis was done using our previously developed macro script for understanding % cell-free are over time as well as using a Matlab-GUI based CellTracker program for understanding cell migration pattern and migration velocities under various treatments. (C) The binary time lapse images obtained after image analysis show percent reduction of cell-free area (white area in the images) due to migration of A549 cells (black area in the images) in presence of only cell culture medium (black, upper row), EGF (blue, middle row), and EGF + V-AgNPs (red, lower row). The % cell-free areas were calculated by considering the cell-free area of 0 th h images as 100%. (D) The line graph shows the cell migration kinetics under the influence of various treatments, where each line represents mean ± std. error of 3 replicates ( n = 3). The yellow box indicates the time frame within which significant differences (two-way ANOVA, p-value <0.05) were observed in each treatment. The bar graph showing these differences is given in supporting information, . (E) The bar graph represents average cell migration velocities obtained from CellTracker program and each bar represents mean velocity ± std. error of randomly selected cells ( n = 10). The cell migration patterns and directionalities in presence of aforementioned treatments are given in the supporting information, . The asterisks in the bar graph represent significantly different observations (One-way ANOVA test: **** p-value<0.0001). (Abbreviations – V-AgNPs: Viridibacilli derived silver nanoparticles, EGF: Epidermal growth factor, t 0 : initial time or start time, t’: time point other that t 0 , h: hours, ns: not significant) (Schematics were created with BioRender.com ). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: The image analysis was done using our previously developed macro script for understanding % cell-free are over time as well as using a Matlab-GUI based CellTracker program for understanding cell migration pattern and migration velocities under various treatments. (C) The binary time lapse images obtained after image analysis show percent reduction of cell-free area (white area in the images) due to migration of A549 cells (black area in the images) in presence of only cell culture medium (black, upper row), EGF (blue, middle row), and EGF + V-AgNPs (red, lower row).

Techniques: Migration, Cell Culture, Control, Positive Control, Imaging, Live Cell Imaging, Derivative Assay