Manifold learning based spectral unmixing of hyperspectral remote sensing data

Nonlinear mixing effects inherent in hyperspectral data are not properly represented in linear spectral unmixing models. Although direct nonlinear unmixing models provide capability to capture nonlinear phenomena, they are difficult to formulate and the results are not always generalizable. Manifold learning based spectral unmixing accommodates nonlinearity in the data in the feature extraction stage followed by linear mixing, thereby incorporating some characteristics of nonlinearity while retaining advantages of linear unmixing approaches. Since endmember selection is critical to successful spectral unmixing, it is important to select proper endmembers from the manifold space. However, excessive computational burden hinders development of manifolds for large-scale remote sensing datasets. This dissertation addresses issues related to high computational overhead requirements of manifold learning for developing representative manifolds for the spectral unmixing task. Manifold approximations using landmarks are popular for mitigating the computational complexity of manifold learning. A new computationally effective landmark selection method that exploits spatial redundancy in the imagery is proposed. A robust, less costly landmark set with low spectral and spatial redundancy is successfully incorporated with a hybrid manifold which shares properties of both global and local manifolds. While landmark methods reduce computational demand, the resulting manifolds may not represent subtle features of the manifold adequately. Active learning heuristics are introduced to increase the number of landmarks, with the goal of developing more representative manifolds for spectral unmixing. By communicating between the landmark set and the query criteria relative to spectral unmixing, more representative and stable manifolds with less spectrally and spatially redundant landmarks are developed. A new ranking method based on the pixels with locally high spectral variability within image subsets and convex-geometry finds a solution more quickly and precisely. Experiments were conducted to evaluate the proposed methods using the AVIRIS Cuprite hyperspectral reference dataset. A case study of manifold learning based spectral unmixing in agricultural areas is included in the dissertation.Remotely sensed data collected by airborne or spaceborne sensors are utilized to quantify crop residue cover over an extensive area. Although remote sensing indices are popular for characterizing residue amounts, they are not effective with noisy Hyperion data because the effect of residual striping artifacts is amplified in ratios involving band differences. In this case study, spectral unmixing techniques are investigated for estimating crop residue as an alternative approach to empirical models developed using band based indices. The spectral unmixing techniques, and especially the manifold learning approaches, provide more robust, lower RMSE estimates for crop residue cover than the hyperspectral index based method for Hyperion data

On the Electrostatics of Pneumatic Conveying of Granular Materials

In this work the electrostatics of the pneumatic conveying of granular materials in a non-conducting (PVC) vertical pipe is studied using Electrical Capacitance Tomography (ECT) system. The non-conducting wall in general attains static charges arising from particle-wall collisions in the initial periods of conveying process and then reaches equilibrium with the surroundings. The polarity of particles and conveying pipe inner wall agrees reasonably well with the contact potential difference measurements. The perturbations in the capacitance signal due to charge accumulation are larger with smaller air superficial velocity. The denser flow regimes give larger wall residual charge. Wall charging process shows similar trend by surface potential and ECT measurements. The addition of small amount (0.5% by weight) of anti-static agent (Larostat-519) in the powder form decreases the electrostatic charge generation by altering the patterns for particle-particle and particle-wall collisions.Singapore-MIT Alliance (SMA

Granular Attrition due to Rotary Valve in a Pneumatic Conveying System

The rotary valve is a widely used mechanical device in many solids-handling industrial processes. However, it may also be responsible for most of the attrition effects occurring in a typical process. In this study, the attrition effects occurring in a rotary valve operating as a stand-alone device and as part of a pneumatic conveying system were investigated. In the former case granular attrition was carried out at three different rotary valve speeds and the experimental results obtained were found to be in good agreement with the Gwyn correlation. In the latter case three typical air flow rates were used in the pneumatic conveying system. The size distribution of the attrition product obtained at the lowest air flow rate used was not adequately described by the Gwyn correlation. The attrition process and mechanisms involved were analysed and the minimum size of the attrition product obtained from both modes of operations was found to be similar.Singapore-MIT Alliance (SMA

Long-term clinical course of a patient with mucopolysaccharidosis type IIIB

Mucopolysaccharidosis type III (MPS III) is a rare genetic disorder caused by lysosomal storage of heparan sulfate. MPS IIIB results from a deficiency in the enzyme alpha-N-acetyl-D-glucosaminidase (NAGLU). Affected patients begin showing behavioral changes, progressive profound mental retardation, and severe disability from the age of 2 to 6 years. We report a patient with MPS IIIB with a long-term follow-up duration. He showed normal development until 3 years. Subsequently, he presented behavioral changes, sleep disturbance, and progressive motor dysfunction. He had been hospitalized owing to recurrent pneumonia and epilepsy with severe cognitive dysfunction. The patient had compound heterozygous c.1444C>T (p.R482W) and c.1675G>T (p.D559Y) variants of NAGLU. Considering that individuals with MPS IIIB have less prominent facial features and skeletal changes, evaluation of long-term clinical course is important for diagnosis. Although no effective therapies for MPS IIIB have been developed yet, early and accurate diagnosis can provide important information for family planning in families at risk of the disorder

Deep Learning for Simulating Harmful Algal Blooms Using Ocean Numerical Model

In several countries, the public health and fishery industries have suffered from harmful algal blooms (HABs) that have escalated to become a global issue. Though computational modeling offers an effective means to understand and mitigate the adverse effects of HABs, it is challenging to design models that adequately reflect the complexity of HAB dynamics. This paper presents a method involving the application of deep learning to an ocean model for simulating blooms of Alexandrium catenella. The classification and regression convolutional neural network (CNN) models are used for simulating the blooms. The classification CNN determines the bloom initiation while the regression CNN estimates the bloom density. GoogleNet and Resnet 101 are identified as the best structures for the classification and regression CNNs, respectively. The corresponding accuracy and root means square error values are determined as 96.8% and 1.20 [log(cells L-1)], respectively. The results obtained in this study reveal the simulated distribution to follow the Alexandrium catenella bloom. Moreover, Grad-CAM identifies that the salinity and temperature contributed to the initiation of the bloom whereas NH4-N influenced the growth of the bloom.</p&gt

Detection of betanodaviruses in apparently healthy aquarium fishes and invertebrates

Betanodaviruses are the causative agents of viral nervous necrosis (VNN) in cultured marine fish. A total of 237 apparently healthy aquarium fish, marine (65 species) and freshwater (12 species) fishes and marine invertebrates (4 species), which were stocked in a commercial aquarium in Seoul, South Korea, were collected from November 2005 to February 2006. The brains of the fish and other tissues of the invertebrates were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR to detect betanodavirus. Positive nested PCR results were obtained from the brains of 8 marine fish species (shrimp fish Aeoliscus strigatus, milkfish Chanos chanos, three spot damsel Dascyllus trimaculatus, Japanese anchovy Engraulis japonicus, pinecone fish Monocentris japonica, blue ribbon eel Rhinomuraena quaesita, look down fish Selene vomer, yellow tang Zebrasoma flavesenes), 1 marine invertebrate species (spiny lobster Pamulirus versicolor), and 2 freshwater fish species (South American leaf fish Monocirrhus polyacanthus and red piranha Pygocentrus nattereri). The detection rate in nested PCR was 11/237 (4.64%). These subclinically infected aquarium fish and invertebrates may constitute an inoculum source of betanodaviruses for cultured fishes in the Korean Peninsula

Identification of MYC as an antinecroptotic protein that stifles RIPK1-RIPK3 complex formation

The underlying mechanism of necroptosis in relation to cancer is still unclear. Here, MYC, a potent oncogene, is an antinecroptotic factor that directly suppresses the formation of the RIPK1-RIPK3 complex. Gene set enrichment analyses reveal that the MYC pathway is the most prominently down-regulated signaling pathway during necroptosis. Depletion or deletion of MYC promotes the RIPK1-RIPK3 interaction, thereby stabilizing the RIPK1 and RIPK3 proteins and facilitating necroptosis. Interestingly, MYC binds to RIPK3 in the cytoplasm and inhibits the interaction between RIPK1 and RIPK3 in vitro. Furthermore, MYC-nick, a truncated form that is mainly localized in the cytoplasm, prevented TNF-induced necroptosis. Finally, down-regulation of MYC enhances necroptosis in leukemia cells and suppresses tumor growth in a xenograft model upon treatment with birinapant and emricasan. MYC-mediated suppression of necroptosis is a mechanism of necroptosis resistance in cancer, and approaches targeting MYC to induce necroptosis represent an attractive therapeutic strategy for cancer

The genome sequence of the orchid Phalaenopsis equestris

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers. (Résumé d'auteur

Disruption of nucleocytoplasmic trafficking as a cellular senescence driver

Senescent cells exhibit a reduced response to intrinsic and extrinsic stimuli. This diminished reaction may be explained by the disrupted transmission of nuclear signals. However, this hypothesis requires more evidence before it can be accepted as a mechanism of cellular senescence. A proteomic analysis of the cytoplasmic and nuclear fractions obtained from young and senescent cells revealed disruption of nucleocytoplasmic trafficking (NCT) as an essential feature of replicative senescence (RS) at the global level. Blocking NCT either chemically or genetically induced the acquisition of an RS-like senescence phenotype, named nuclear barrier-induced senescence (NBIS). A transcriptome analysis revealed that, among various types of cellular senescence, NBIS exhibited a gene expression pattern most similar to that of RS. Core proteomic and transcriptomic patterns common to both RS and NBIS included upregulation of the endocytosis-lysosome network and downregulation of NCT in senescent cells, patterns also observed in an aging yeast model. These results imply coordinated aging-dependent reduction in the transmission of extrinsic signals to the nucleus and in the nucleus-to-cytoplasm supply of proteins/RNAs. We further showed that the aging-associated decrease in Sp1 transcription factor expression was critical for the downregulation of NCT. Our results suggest that NBIS is a modality of cellular senescence that may represent the nature of physiological aging in eukaryotes. © 2021, The Author(s).1

The 5p15.33 Locus Is Associated with Risk of Lung Adenocarcinoma in Never-Smoking Females in Asia

Genome-wide association studies of lung cancer reported in populations of European background have identified three regions on chromosomes 5p15.33, 6p21.33, and 15q25 that have achieved genome-wide significance with p-values of 10−7 or lower. These studies have been performed primarily in cigarette smokers, raising the possibility that the observed associations could be related to tobacco use, lung carcinogenesis, or both. Since most women in Asia do not smoke, we conducted a genome-wide association study of lung adenocarcinoma in never-smoking females (584 cases, 585 controls) among Han Chinese in Taiwan and found that the most significant association was for rs2736100 on chromosome 5p15.33 (p = 1.30×10−11). This finding was independently replicated in seven studies from East Asia totaling 1,164 lung adenocarcinomas and 1,736 controls (p = 5.38×10−11). A pooled analysis achieved genome-wide significance for rs2736100. This SNP marker localizes to the CLPTM1L-TERT locus on chromosome 5p15.33 (p = 2.60×10−20, allelic risk = 1.54, 95% Confidence Interval (CI) 1.41–1.68). Risks for heterozygote and homozygote carriers of the minor allele were 1.62 (95% CI; 1.40–1.87), and 2.35 (95% CI: 1.95–2.83), respectively. In summary, our results show that genetic variation in the CLPTM1L-TERT locus of chromosome 5p15.33 is directly associated with the risk of lung cancer, most notably adenocarcinoma