Supervised machine learning based multi-task artificial intelligence classification of retinopathies

Artificial intelligence (AI) classification holds promise as a novel and affordable screening tool for clinical management of ocular diseases. Rural and underserved areas, which suffer from lack of access to experienced ophthalmologists may particularly benefit from this technology. Quantitative optical coherence tomography angiography (OCTA) imaging provides excellent capability to identify subtle vascular distortions, which are useful for classifying retinovascular diseases. However, application of AI for differentiation and classification of multiple eye diseases is not yet established. In this study, we demonstrate supervised machine learning based multi-task OCTA classification. We sought 1) to differentiate normal from diseased ocular conditions, 2) to differentiate different ocular disease conditions from each other, and 3) to stage the severity of each ocular condition. Quantitative OCTA features, including blood vessel tortuosity (BVT), blood vascular caliber (BVC), vessel perimeter index (VPI), blood vessel density (BVD), foveal avascular zone (FAZ) area (FAZ-A), and FAZ contour irregularity (FAZ-CI) were fully automatically extracted from the OCTA images. A stepwise backward elimination approach was employed to identify sensitive OCTA features and optimal-feature-combinations for the multi-task classification. For proof-of-concept demonstration, diabetic retinopathy (DR) and sickle cell retinopathy (SCR) were used to validate the supervised machine leaning classifier. The presented AI classification methodology is applicable and can be readily extended to other ocular diseases, holding promise to enable a mass-screening platform for clinical deployment and telemedicine.Comment: Supplemental material attached at the en

C1q-targeted inhibition of the classical complement pathway prevents injury in a novel mouse model of acute motor axonal neuropathy

Introduction Guillain-Barré syndrome (GBS) is an autoimmune disease that results in acute paralysis through inflammatory attack on peripheral nerves, and currently has limited, non-specific treatment options. The pathogenesis of the acute motor axonal neuropathy (AMAN) variant is mediated by complement-fixing anti-ganglioside antibodies that directly bind and injure the axon at sites of vulnerability such as nodes of Ranvier and nerve terminals. Consequently, the complement cascade is an attractive target to reduce disease severity. Recently, C5 complement component inhibitors that block the formation of the membrane attack complex and subsequent downstream injury have been shown to be efficacious in an in vivo anti-GQ1b antibody-mediated mouse model of the GBS variant Miller Fisher syndrome (MFS). However, since gangliosides are widely expressed in neurons and glial cells, injury in this model was not targeted exclusively to the axon and there are currently no pure mouse models for AMAN. Additionally, C5 inhibition does not prevent the production of early complement fragments such as C3a and C3b that can be deleterious via their known role in immune cell and macrophage recruitment to sites of neuronal damage. Results and Conclusions In this study, we first developed a new in vivo transgenic mouse model of AMAN using mice that express complex gangliosides exclusively in neurons, thereby enabling specific targeting of axons with anti-ganglioside antibodies. Secondly, we have evaluated the efficacy of a novel anti-C1q antibody (M1) that blocks initiation of the classical complement cascade, in both the newly developed anti-GM1 antibody-mediated AMAN model and our established MFS model in vivo. Anti-C1q monoclonal antibody treatment attenuated complement cascade activation and deposition, reduced immune cell recruitment and axonal injury, in both mouse models of GBS, along with improvement in respiratory function. These results demonstrate that neutralising C1q function attenuates injury with a consequent neuroprotective effect in acute GBS models and promises to be a useful new target for human therapy

Differential binding patterns of anti-sulfatide antibodies to glial membranes

Sulfatide is a major glycosphingolipid in myelin and a target for autoantibodies in autoimmune neuropathies. However neuropathy disease models have not been widely established, in part because currently available monoclonal antibodies to sulfatide may not represent the diversity of anti-sulfatide antibody binding patterns found in neuropathy patients. We sought to address this issue by generating and characterising a panel of new anti-sulfatide monoclonal antibodies. These antibodies have sulfatide reactivity distinct from existing antibodies in assays and in binding to peripheral nerve tissues and can be used to provide insights into the pathophysiological roles of anti-sulfatide antibodies in demyelinating neuropathies

Chemical and enzymatic tools to study proteins in their native cellular environment

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2013.Cataloged from PDF version of thesis. Vita.Includes bibliographical references.A detailed understating of living systems requires methods to probe molecular processes in cells and whole organisms. A set of technologies that combines chemical and genetic probes have been developed to address the need for dynamic and noninvasive assay of biological processes. In addition to be able to visualize the localization, trafficking, and turnover of individual proteins, strategies that allow the tagging, and imaging, and identification of entire proteomes have also offered valuable insights into disease biology. Since protein visualization serves as a complement to protein identification, this thesis first describes the development of a protein labeling technique that is able to specifically target diverse fluorophores to proteins inside live cells. The methodology uses the E. coli lipoic acid ligase (LplA) that we have engineered to accept and ligate an azide functional handle onto a 13-amino acid ḺplA a̲cceptor peptide (LAP). Subsequent derivatization of the azide with fluorophores functionalized with cyclooctyne via strain-promoted azide-alkyne cycloaddition allowed us to target many bright and photostable fluorophores that could be used in super resolution imaging. Due to the numerous applications to which cyclooctynes are being applied, our observation of the behavior of different cyclooctynes inside cells should also prove useful to the protein labeling community and beyond. For protein identification, we describe our work of engineering and using LplA to site-specifically target a benzophenone photocrosslinker. Our observations led us to the conclusion that although benzophenone is generally regarded as the more efficient and specific photocrosslinker than aryl azide and diazirine, its high geometric constraint to its proximal crosslinkable C-H bonds may decrease its crosslinking yield. Knowing the protein structure and amino acid environment surrounding benzophenone could help in choosing the most optimal position for the photocrosslinker. Finally, in a different crosslinking approach, we discuss our effort towards using a promiscuous peroxidase enzyme that generates biotin-phenol radicals to study membrane protein topology.by Jennifer Zhengzheng Yao.Ph.D

DNA sequence to a million doses of COVID-19 therapeutic antibody in 9 months – Making the seemingly impossible, possible

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Microplastic Contamination of Three Commonly Consumed Seafood Species from Taiwan: A Pilot Study

Microplastics have already been detected in various human foods, especially seafood. This problem should be especially pertinent to the Taiwanese public because a relatively high proportion of people’s diet comes from seafood. Therefore, a pilot study of microplastic contamination of seafood products commonly consumed by Taiwanese people is presented. Six batches of three seafood species were examined for the presence of microplastics using FTIR spectroscopy. A total of 107 seafood individuals from three species (hard clam Meretrix lusoria, oyster Crassostrea gigas, Loligo squid Loliginidae spp.) weighing a total of 994 g yielded a total of 100 microplastic particles consisting of nine different polymer types. The most common polymer types were polypropylene, poly(ethylene:propylene:diene), and polyethylene terephthalate; we also detected six additional, but less common polymer types. A total of 91% of microplastic particles were fragments that likely originated from fragmented plastic debris which was then consumed by the seafood species; the remaining particles were fibers and a pellet. The mean number of microplastics kg−1 was 87.9 microplastics kg−1 across the three examined species. Given that the Taiwanese public average about 10 kg of seafood consumption per year, a few thousand microplastic particles are estimated to be annually consumed on average. The methodology of this pilot study can now be used to conduct examinations of more seafood species and samples

pHLIP-Mediated Delivery of PEGylated Liposomes to Cancer Cells

We develop a method for pH-dependent fusion between liposomes and cellular membranes using pHLIP (pH Low Insertion Peptide), which inserts into lipid bilayer of membrane only at low pH. Previously we establish the molecular mechanism of peptide action and show that pHLIP can target acidic diseased tissue. Here we investigate how coating of PEGylated liposomes with pHLIP might affect liposomal uptake by cells. The presence of pHLIP on the surface of PEGylated-liposomes enhanced membrane fusion and lipid exchange in a pH dependent fashion, leading to increase of cellular uptake and payload release, and inhibition of cell proliferation by liposomes containing ceramide. A novel type of pH-sensitive, “fusogenic” pHLIP-liposomes was developed, which could be used to selectively deliver various diagnostic and therapeutic agents to acidic diseased cells

Direct Control of Cell Cycle Gene Expression by Proto-oncogene Product ACTR, and Its Autoregulation Underlies Its Transforming Activity

ACTR (also called AIB1 and SRC-3) was identified as a coactivator for nuclear receptors and is linked to multiple types of human cancer due to its frequent overexpression. However, the molecular mechanism of ACTR oncogenicity and its function independent of nuclear receptors remain to be defined. We demonstrate here that ACTR is required for both normal and malignant human cells to effectively enter S phase. RNA interference-mediated depletion and chromatin immunoprecipitation assays show that endogenous ACTR directly controls the expression of genes important for initiation of DNA replication, which include cdc6, cdc25A, MCM7, cyclin E, and Cdk2. Moreover, consistent with its critical role in cell cycle control, ACTR expression appears to be cell cycle regulated, which involves E2F. Interestingly, ACTR is recruited to its own promoter at the G1/S transition and activates its own expression, suggesting a positive feedback mechanism for ACTR action in the control of cell cycle progression and for its aberrant expression in cancers. Importantly, overexpression of ACTR alone transforms human mammary epithelial cells, which requires its association with E2F. These findings reveal a novel role for ACTR in cell cycle control and support the notion that the ability of aberrant ACTR to deregulate the cell cycle through E2F underlies its oncogenicity in human cancers

Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia

The expression profiles of umbilical cords from premature newborns reveal distinct patterns, including changes in the expression of chromatin remodeling factors, associated with the development of bronchopulmonary dysplasia