Evaluation of Retinal Image Quality Assessment Networks in Different Color-spaces

Retinal image quality assessment (RIQA) is essential for controlling the quality of retinal imaging and guaranteeing the reliability of diagnoses by ophthalmologists or automated analysis systems. Existing RIQA methods focus on the RGB color-space and are developed based on small datasets with binary quality labels (i.e., `Accept' and `Reject'). In this paper, we first re-annotate an Eye-Quality (EyeQ) dataset with 28,792 retinal images from the EyePACS dataset, based on a three-level quality grading system (i.e., `Good', `Usable' and `Reject') for evaluating RIQA methods. Our RIQA dataset is characterized by its large-scale size, multi-level grading, and multi-modality. Then, we analyze the influences on RIQA of different color-spaces, and propose a simple yet efficient deep network, named Multiple Color-space Fusion Network (MCF-Net), which integrates the different color-space representations at both a feature-level and prediction-level to predict image quality grades. Experiments on our EyeQ dataset show that our MCF-Net obtains a state-of-the-art performance, outperforming the other deep learning methods. Furthermore, we also evaluate diabetic retinopathy (DR) detection methods on images of different quality, and demonstrate that the performances of automated diagnostic systems are highly dependent on image quality.Comment: Accepted by MICCAI 2019. Corrected two typos in Table 1 as: (1) in training set, the number of "Usable + All" should be '1,876'; (2) In testing set, the number of "Total + DR-0" should be '11,362'. Project page: https://github.com/hzfu/Eye

Cell sorting in a Petri dish controlled by computer vision.

Fluorescence-activated cell sorting (FACS) applying flow cytometry to separate cells on a molecular basis is a widespread method. We demonstrate that both fluorescent and unlabeled live cells in a Petri dish observed with a microscope can be automatically recognized by computer vision and picked up by a computer-controlled micropipette. This method can be routinely applied as a FACS down to the single cell level with a very high selectivity. Sorting resolution, i.e., the minimum distance between two cells from which one could be selectively removed was 50-70 micrometers. Survival rate with a low number of 3T3 mouse fibroblasts and NE-4C neuroectodermal mouse stem cells was 66 +/- 12% and 88 +/- 16%, respectively. Purity of sorted cultures and rate of survival using NE-4C/NE-GFP-4C co-cultures were 95 +/- 2% and 62 +/- 7%, respectively. Hydrodynamic simulations confirmed the experimental sorting efficiency and a cell damage risk similar to that of normal FACS

Improved genome editing in human cell lines using the CRISPR method

The Cas9/CRISPR system has become a popular choice for genome editing. In this system, binding of a single guide (sg) RNA to a cognate genomic sequence enables the Cas9 nuclease to induce a double-strand break at that locus. This break is next repaired by an error-prone mechanism, leading to mutation and gene disruption. In this study we describe a range of refinements of the method, including stable cell lines expressing Cas9, and a PCR based protocol for the generation of the sgRNA. We also describe a simple methodology that allows both elimination of Cas9 from cells after gene disruption and re-introduction of the disrupted gene. This advance enables easy assessment of the off target effects associated with gene disruption, as well as phenotype-based structure-function analysis. In our study, we used the Fan1 DNA repair gene as control in these experiments. Cas9/CRISPR-mediated Fan1 disruption occurred at frequencies of around 29%, and resulted in the anticipated spectrum of genotoxin hypersensitivity, which was rescued by re-introduction of Fan1

Wnt5a induces ROR1 to associate with 14-3-3ζ for enhanced chemotaxis and proliferation of chronic lymphocytic leukemia cells.

Wnt5a can activate Rho GTPases in chronic lymphocytic leukemia (CLL) cells by inducing the recruitment of ARHGEF2 to ROR1. Mass spectrometry on immune precipitates of Wnt5a-activated ROR1 identified 14-3-3ζ, which was confirmed by co-immunoprecipitation. The capacity of Wnt5a to induce ROR1 to complex with 14-3-3ζ could be blocked in CLL cells by treatment with cirmtuzumab, a humanized mAb targeting ROR1. Silencing 14-3-3ζ via small interfering RNA impaired the capacity of Wnt5a to: (1) induce recruitment of ARHGEF2 to ROR1, (2) enhance in vitro exchange activity of ARHGEF2 and (3) induce activation of RhoA and Rac1 in CLL cells. Furthermore, CRISPR/Cas9 deletion of 14-3-3ζ in ROR1-negative CLL cell-line MEC1, and in MEC1 cells transfected to express ROR1 (MEC1-ROR1), demonstrated that 14-3-3ζ was necessary for the growth/engraftment advantage of MEC1-ROR1 over MEC1 cells. We identified a binding motif (RSPS857SAS) in ROR1 for 14-3-3ζ. Site-directed mutagenesis of ROR1 demonstrated that serine-857 was required for the recruitment of 14-3-3ζ and ARHGEF2 to ROR1, and activation of RhoA and Rac1. Collectively, this study reveals that 14-3-3ζ plays a critical role in Wnt5a/ROR1 signaling, leading to enhanced CLL migration and proliferation

Multiple parallel skin markers for minimal incision lumbar disc surgery; a technical note

BACKGROUND: Spinal surgery depends on accurate localization to prevent incorrect surgical approaches. The trend towards minimally invasive surgery that minimizes surgical exposure and reduces postoperative pain increasingly requires surgeons to accurately determine the operative level before an incision is made. Preoperative localization with a C-arm image intensifier is popular, but the exposure of both patients and theatre staff to radiation is a disadvantage, as well as being time-consuming. METHODS: We describe a simple surgical tool developed to help localize exact spinal levels in conjunction with a simple AP X-ray film immediately before surgery. Multiple parallel skin markers were made using a circular oven rack comprising multiple 1.5 cm spaced parallel wires attached to a circular outside rim. The longest line was placed on the line of the postero-superior iliac spine (PSIS) over the junction of the L5-S1 region. RESULTS AND CONCLUSIONS: Based on the film taken, the incision can be accurately made at the intended level. The incision wound can be minimized to 3.0 cm even when using conventional disc surgery instruments

Mechanical activation of vinculin binding to talin locks talin in an unfolded conformation

The force-dependent interaction between talin and vinculin plays a crucial role in the initiation and growth of focal adhesions. Here we use magnetic tweezers to characterise the mechano-sensitive compact N-terminal region of the talin rod, and show that the three helical bundles R1-R3 in this region unfold in three distinct steps consistent with the domains unfolding independently. Mechanical stretching of talin R1-R3 enhances its binding to vinculin and vinculin binding inhibits talin refolding after force is released. Mutations that stabilize R3 identify it as the initial mechano-sensing domain in talin, unfolding at ~5 pN, suggesting that 5 pN is the force threshold for vinculin binding and adhesion progression

Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1-Top3

double Holliday junction (dHJ) is a central intermediate of homologous recombination that can be processed to yield crossover or non-crossover recombination products. To preserve genomic integrity, cells possess mechanisms to avoid crossing over. We show that Saccharomyces cerevisiae Sgs1 and Top3 proteins are sufficient to migrate and disentangle a dHJ to produce exclusively non-crossover recombination products, in a reaction termed "dissolution." We show that Rmi1 stimulates dHJ dissolution at low Sgs1-Top3 protein concentrations, although it has no effect on the initial rate of Holliday junction (HJ) migration. Rmi1 serves to stimulate DNA decatenation, removing the last linkages between the repaired and template DNA molecules. Dissolution of a dHJ is a highly efficient and concerted alternative to nucleolytic resolution that prevents crossing over of chromosomes during recombinational DNA repair in mitotic cells and thereby contributes to genomic integrity

Aerosol Assisted Solvent Treatment: A Universal Method for Performance and Stability Enhancements in Perovskite Solar Cells

Abstract: Metal‐halide perovskite solar cells (PSCs) have had a transformative impact on the renewable energy landscape since they were first demonstrated just over a decade ago. Outstanding improvements in performance have been demonstrated through structural, compositional, and morphological control of devices, with commercialization now being a reality. Here the authors present an aerosol assisted solvent treatment as a universal method to obtain performance and stability enhancements in PSCs, demonstrating their methodology as a convenient, scalable, and reproducible post‐deposition treatment for PSCs. Their results identify improvements in crystallinity and grain size, accompanied by a narrowing in grain size distribution as the underlying physical changes that drive reductions of electronic and ionic defects. These changes lead to prolonged charge‐carrier lifetimes and ultimately increased device efficiencies. The versatility of the process is demonstrated for PSCs with thick (>1 µm) active layers, large‐areas (>1 cm2) and a variety of device architectures and active layer compositions. This simple post‐deposition process is widely transferable across the field of perovskites, thereby improving the future design principles of these materials to develop large‐area, stable, and efficient PSCs

Hydrologically-driven crustal stresses and seismicity in the New Madrid Seismic Zone

The degree to which short-term non-tectonic processes, either natural and anthropogenic, influence the occurrence of earthquakes in active tectonic settings or ‘stable’ plate interiors, remains a subject of debate. Recent work in plate-boundary regions demonstrates the capacity for long-wavelength changes in continental water storage to produce observable surface deformation, induce crustal stresses and modulate seismicity rates. Here we show that a significant variation in the rate of microearthquakes in the intraplate New Madrid Seismic Zone at annual and multi-annual timescales coincides with hydrological loading in the upper Mississippi embayment. We demonstrate that this loading, which results in geodetically observed surface deformation, induces stresses within the lithosphere that, although of small amplitude, modulate the ongoing seismicity of the New Madrid region. Correspondence between surface deformation, hydrological loading and seismicity rates at both annual and multi-annual timescales indicates that seismicity variations are the direct result of elastic stresses induced by the water load