Superhuman cell death detection with biomarker-optimized neural networks.

Cellular events underlying neurodegenerative disease may be captured by longitudinal live microscopy of neurons. While the advent of robot-assisted microscopy has helped scale such efforts to high-throughput regimes with the statistical power to detect transient events, time-intensive human annotation is required. We addressed this fundamental limitation with biomarker-optimized convolutional neural networks (BO-CNNs): interpretable computer vision models trained directly on biosensor activity.

Measurement of the ultrasound attenuation and dispersion in 3D-printed photopolymer materials from 1 to 3.5 MHz.

Over the past decade, the range of applications in biomedical ultrasound exploiting 3D printing has rapidly expanded. For wavefront shaping specifically, 3D printing has enabled a diverse range of new, low-cost approaches for controlling acoustic fields. These methods rely on accurate knowledge of the bulk acoustic properties of the materials; however, to date, robust knowledge of these parameters is lacking for many materials that are commonly used.

Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration.

Cell death is a critical process that occurs normally in health and disease. However, its study is limited due to available technologies that only detect very late stages in the process or specific death mechanisms. Here, we report the development of a family of fluorescent biosensors called genetically encoded death indicators (GEDIs).

Small-Molecule Modulation of TDP-43 Recruitment to Stress Granules Prevents Persistent TDP-43 Accumulation in ALS/FTD.

Stress granules (SGs) form during cellular stress and are implicated in neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). To yield insights into the role of SGs in pathophysiology, we performed a high-content screen to identify small molecules that alter SG properties in proliferative cells and human iPSC-derived motor neurons (iPS-MNs). One major class of active molecules contained extended planar aromatic moieties, suggesting a potential to intercalate in nucleic acids.

Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration.

Current approaches for dynamic profiling of single cells rely on dissociated cultures, which lack important biological features existing in tissues. Organotypic slice cultures preserve aspects of structural and synaptic organisation within the brain and are amenable to microscopy, but established techniques are not well adapted for high throughput or longitudinal single cell analysis. Here we developed a custom-built, automated confocal imaging platform, with improved organotypic slice culture and maintenance.

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images.

Microscopy is a central method in life sciences. Many popular methods, such as antibody labeling, are used to add physical fluorescent labels to specific cellular constituents. However, these approaches have significant drawbacks, including inconsistency; limitations in the number of simultaneous labels because of spectral overlap; and necessary perturbations of the experiment, such as fixing the cells, to generate the measurement.

A Multi-Grid Iterative Method for Photoacoustic Tomography.

Inspired by the recent advances on minimizing nonsmooth or bound-constrained convex functions on models using varying degrees of fidelity, we propose a line search multi-grid (MG) method for full-wave iterative image reconstruction in photoacoustic tomography (PAT) in heterogeneous media. To compute the search direction at each iteration, we decide between the gradient at the target level, or alternatively an approximate error correction at a coarser level, relying on some predefined criteria. To incorporate absorption and dispersion, we derive the analytical adjoint directly from the first-order acoustic wave system.

Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation.

A fast time-difference inverse solver for 3D EIT with application to lung imaging.

A class of sparse optimization techniques that require solely matrix-vector products, rather than an explicit access to the forward matrix and its transpose, has been paid much attention in the recent decade for dealing with large-scale inverse problems. This study tailors application of the so-called Gradient Projection for Sparse Reconstruction (GPSR) to large-scale time-difference three-dimensional electrical impedance tomography (3D EIT). 3D EIT typically suffers from the need for a large number of voxels to cover the whole domain, so its application to real-time imaging, for example monitoring of lung function, remains scarce since the large number of degrees of freedom of the problem extremely increases storage space and reconstruction time.

Sampling of finite elements for sparse recovery in large scale 3D electrical impedance tomography.

This study proposes a method to improve performance of sparse recovery inverse solvers in 3D electrical impedance tomography (3D EIT), especially when the volume under study contains small-sized inclusions, e.g. 3D imaging of breast tumours.

Radial glia require PDGFD-PDGFRβ signalling in human but not mouse neocortex.

Evolutionary expansion of the human neocortex underlies many of our unique mental abilities. This expansion has been attributed to the increased proliferative potential of radial glia (RG; neural stem cells) and their subventricular dispersion from the periventricular niche during neocortical development. Such adaptations may have evolved through gene expression changes in RG.

Compressed sampling for boundary measurements in three-dimensional electrical impedance tomography.

Electrical impedance tomography (EIT) utilizes electrodes on a medium's surface to produce measured data from which the conductivity distribution inside the medium is estimated. For the cases that relocation of electrodes is impractical or no a priori assumptions can be made to optimize the electrodes placement, a large number of electrodes may be needed to cover all possible imaging volume. This may occur in dynamically varying conductivity distribution in 3D EIT.

A cellular model for sporadic ALS using patient-derived induced pluripotent stem cells.

Development of therapeutics for genetically complex neurodegenerative diseases such as sporadic amyotrophic lateral sclerosis (ALS) has largely been hampered by lack of relevant disease models. Reprogramming of sporadic ALS patients' fibroblasts into induced pluripotent stem cells (iPSC) and differentiation into affected neurons that show a disease phenotype could provide a cellular model for disease mechanism studies and drug discovery. Here we report the reprogramming to pluripotency of fibroblasts from a large cohort of healthy controls and ALS patients and their differentiation into motor neurons.

Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing.

There has been a growing interest in using next-generation sequencing (NGS) to profile extracellular small RNAs from the blood and cerebrospinal fluid (CSF) of patients with neurological diseases, CNS tumors, or traumatic brain injury for biomarker discovery. Small sample volumes and samples with low RNA abundance create challenges for downstream small RNA sequencing assays. Plasma, serum, and CSF contain low amounts of total RNA, of which small RNAs make up a fraction.

Induced pluripotent stem cells--opportunities for disease modelling and drug discovery.

The ability to generate induced pluripotent stem cells (iPSCs) from patients, and an increasingly refined capacity to differentiate these iPSCs into disease-relevant cell types, promises a new paradigm in drug development - one that positions human disease pathophysiology at the core of preclinical drug discovery. Disease models derived from iPSCs that manifest cellular disease phenotypes have been established for several monogenic diseases, but iPSCs can likewise be used for phenotype-based drug screens in complex diseases for which the underlying genetic mechanism is unknown. Here, we highlight recent advances as well as limitations in the use of iPSC technology for modelling a 'disease in a dish' and for testing compounds against human disease phenotypes in vitro.

A stem cell niche for intermediate progenitor cells of the embryonic cortex.

The excitatory neurons of the mammalian cerebral cortex arise from asymmetric divisions of radial glial cells in the ventricular zone and symmetric division of intermediate progenitor cells (IPCs) in the subventricular zone (SVZ) of the embryonic cortex. Little is known about the microenvironment in which IPCs divide or whether a stem cell niche exists in the SVZ of the embryonic cortex. Recent evidence suggests that vasculature may provide a niche for adult stem cells but its role in development is less clear.

Coordinated motor neuron axon growth and neuromuscular synaptogenesis are promoted by CPG15 in vivo.

We have used in vivo time-lapse two-photon imaging of single motor neuron axons labeled with GFP combined with labeling of presynaptic vesicle clusters and postsynaptic acetylcholine receptors in Xenopus laevis tadpoles to determine the dynamic rearrangement of individual axon branches and synaptogenesis during motor axon arbor development. Control GFP-labeled axons are highly dynamic during the period when axon arbors are elaborating. Axon branches emerge from sites of synaptic vesicle clusters.