A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes.

While there are >2 million publicly-available human microarray gene-expression profiles, these profiles were measured using a variety of platforms that each cover a pre-defined, limited set of genes. Therefore, key to reanalyzing and integrating this massive data collection are methods that can computationally reconstitute the complete transcriptome in partially-measured microarray samples by imputing the expression of unmeasured genes. Current state-of-the-art imputation methods are tailored to samples from a specific platform and rely on gene-gene relationships regardless of the biological context of the target sample. We show that sparse regression models that capture sample-sample relationships (termed SampleLASSO), built on-the-fly for each new target sample to be imputed, outperform models based on fixed gene relationships. Extensive evaluation involving three machine learning algorithms (LASSO, k-nearest-neighbors, and deep-neural-networks), two gene subsets (GPL96-570 and LINCS), and multiple imputation tasks (within and across microarray/RNA-seq datasets) establishes that SampleLASSO is the most accurate model. Additionally, we demonstrate the biological interpretability of this method by showing that, for imputing a target sample from a certain tissue, SampleLASSO automatically leverages training samples from the same tissue. Thus, SampleLASSO is a simple, yet powerful and flexible approach for harmonizing large-scale gene-expression data.

Multimodal nonlinear optical imaging of unstained retinas in the epi-direction with a sub-40 fs Yb-fiber laser.

Ultrafast lasers have potential use in ophthalmology for diagnoses through non-invasive imaging as well as for surgical therapies or for evaluating pharmacological therapies. New ultrafast laser sources, operating at 1.07 µm and sub-40 fs pulse durations, offer exciting possibilities in multiphoton imagining of the retina as the bulk of the eye is relatively transparent to this wavelength, three-photon excitation is not absorbed by DNA, and this wavelength has a greater penetration depth compared to the commonly used 800 nm Ti:Sapphire laser. In this work, we present the first epi-direction detected cross-section and depth-resolved images of unstained isolated retinas obtained using multiphoton microscopy with an ultrafast fiber laser centered at 1.07 µm and a ~38 fs pulse duration. Spectral and temporal characterization of the autofluorescence signals show two distinct regions; the first one from the nerve fiber layer to the inner receptor layer, and the second being the retinal pigmented epithelium and choroid.