Estimation and tracking of rapidly time-varying broadband acoustic communication channels

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2006This thesis develops methods for estimating wideband shallow-water acoustic communication channels. The very shallow water wideband channel has three distinct features: large dimension caused by extensive delay spread; limited number of degrees of freedom (DOF) due to resolvable paths and inter-path correlations; and rapid fluctuations induced by scattering from the moving sea surface. Traditional LS estimation techniques often fail to reconcile the rapid fluctuations with the large dimensionality. Subspace based approaches with DOF reduction are confronted with unstable subspace structure subject to significant changes over a short period of time. Based on state-space channel modeling, the first part of this thesis develops algorithms that jointly estimate the channel as well as its dynamics. Algorithms based on the Extended Kalman Filter (EKF) and the Expectation Maximization (EM) approach respectively are developed. Analysis shows conceptual parallels, including an identical second-order innovation form shared by the EKF modification and the suboptimal EM, and the shared issue of parameter identifiability due to channel structure, reflected as parameter unobservability in EKF and insufficient excitation in EM. Modifications of both algorithms, including a two-model based EKF and a subspace EM algorithm which selectively track dominant taps and reduce prediction error, are proposed to overcome the identifiability issue. The second part of the thesis develops algorithms that explicitly find the sparse estimate of the delay-Doppler spread function. The study contributes to a better understanding of the channel physical constraints on algorithm design and potential performance improvement. It may also be generalized to other applications where dimensionality and variability collide.Financial support for this thesis research was provided by the Office of Naval Research and the WHOI Academic Program Office

Challenges of scale down model for disposable bioreactors: Case studies on growth & product quality impacts

Despite wide-spread use of disposable bioreactors, there is a lack of well-established scale-down model for larger scale SUBs. Here we report a case of NS0 cell culture process transfer from 2000L stainless steel bioreactor (SST) to 2000L disposable bioreactor (SUB). Initial attempts in trying to grow the NS0 cells in the small scale 2D bags yielded non-satisfactory results, as growth was impacted by bag material type as well as by suppliers of the same bag material type. However, 3D bags of 50L and above proved to be supportive of the NS0 cell line growth. Even for cell lines that do not have growth issues in SUBs, surprising product quality difference between SUBs and traditional bench top glass bioreactors are still being observed, thus making the bench top glass bioreactors non-ideal as scale down models. We report two cases where glycan profiles of the expressed antibody products show such dramatic differences. In one case, extensive testing of glass bioreactors from various suppliers led to a particular type being able to mimic the glycan profiles from the SUB, whereas in the other case, alternative scale down model had to be identified and the process had to be modified to maintain the glycan profiles when scaling up to the 200L SUB

Advances in omics research on peanut response to biotic stresses

Peanut growth, development, and eventual production are constrained by biotic and abiotic stresses resulting in serious economic losses. To understand the response and tolerance mechanism of peanut to biotic and abiotic stresses, high-throughput Omics approaches have been applied in peanut research. Integrated Omics approaches are essential for elucidating the temporal and spatial changes that occur in peanut facing different stresses. The integration of functional genomics with other Omics highlights the relationships between peanut genomes and phenotypes under specific stress conditions. In this review, we focus on research on peanut biotic stresses. Here we review the primary types of biotic stresses that threaten sustainable peanut production, the multi-Omics technologies for peanut research and breeding, and the recent advances in various peanut Omics under biotic stresses, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics and phenomics, for identification of biotic stress-related genes, proteins, metabolites and their networks as well as the development of potential traits. We also discuss the challenges, opportunities, and future directions for peanut Omics under biotic stresses, aiming sustainable food production. The Omics knowledge is instrumental for improving peanut tolerance to cope with various biotic stresses and for meeting the food demands of the exponentially growing global population

Focus detection from digital in-line holograms based on spectral l1 norms

Author Posting. © Optical Society of America, 2007. This is the author's version of the work. It is posted here by permission of Optical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Optical Society of America A, 24 (2007): 3054-3062, doi:10.1364/JOSAA.24.003054.In this paper a rapid focus detection technique is developed for objects imaged using digital in-line holograms. It differs from previous approaches in that it is based directly on the spectral content of the object images and does not need a full reconstruction of the actual images. It is based on new focus metrics defined as the l1 norms of the object spectral components associated with the real and imaginary parts of the reconstruction kernel. Furthermore, these l1 norms can be computed efficiently in the frequency domain using a polar coordinate system, yielding a drastic speedup of about two orders of magnitude compared with image-based focus detection. The subsequent reconstruction, when done selectively over these detected focus distances, leads to significant computational savings. Focus detection results from holograms of plankton are demonstrated showing that the technique is both accurate and robust

Vasculogenic mimicry score identifies the prognosis and immune landscape of lung adenocarcinoma

Background: Lung cancer has a high incidence and mortality rate worldwide. Vasculogenic mimicry (VM) is a specific modality of tumor angiogenesis that could potentially be a new target for tumor therapy. The purpose of this study was to explore the role of VM-related genes in assessing the prognosis and immune landscape of lung cancer.Methods: VM-related genes were obtained from previous studies, and the expression data and clinical data of lung adenocarcinoma (LUAD) patients were obtained from the TCGA database and GEO database. We performed enrichment analysis of 24 VM-related genes and screened hub genes by constructing a protein–protein interaction network and using Cytoscape software. Subsequently, we developed the VM score based on univariate Cox regression analysis and Lasso analysis and validated the VM score on the GSE72094 dataset. In addition, we constructed a nomogram based on the VM score in the TCGA cohort. Finally, we explored the correlation between the VM score and the tumor microenvironment, immune cell infiltration, immune checkpoints, and drug sensitivity.Results: Enrichment analysis revealed that VM-related genes were associated with the HIF signaling pathway and angiogenic pathway. We developed a VM score based on 3 genes (EPHA2, LAMC2 and LOXL2) in LUAD patients. Kaplan-Meier analysis showed that the VM score was associated with poor prognosis in LUAD patients. The receiver operating characteristic curve suggested that the VM score and nomogram are valid predictors for the overall survival of LUAD patients. The VM score was significantly correlated with immune cell infiltration, such as naïve B cells, neutrophils, and eosinophils, and there was a difference in the TME between the high VM score group and the low VM score group. LUAD patients in the high VM score group were more sensitive to antitumor drugs.Conclusion: In summary, the VM score developed in this study is a valuable indicator for evaluating the prognosis and immune landscape of LUAD patients. VM may be a potential target for antitumor therapy in lung cancer

Towards Layer-Selective Quantum Spin Hall Channels in Weak Topological Insulator Bi4Br2I2

Weak topological insulators, constructed by stacking quantum spin Hall insulators with weak interlayer coupling, offer promising quantum electronic applications through topologically nontrivial edge channels. However, the currently available weak topological insulators are stacks of the same quantum spin Hall layer with translational symmetry in the out-of-plane direction, leading to the absence of the channel degree of freedom for edge states. Here, we study a candidate weak topological insulator, Bi4Br2I2, which is alternately stacked by three different quantum spin Hall insulators, each with tunable topologically non-trivial edge states. Our angle-resolved photoemission spectroscopy and first-principles calculations show that an energy gap opens at the crossing points of different Dirac cones correlated with different layers due to the interlayer interaction. This is essential to achieve the tunability of topological edge states as controlled by varying the chemical potential. Our work offers a perspective for the construction of tunable quantized conductance devices for future spintronic applications

Exogenous trehalose improves growth under limiting nitrogen through upregulation of nitrogen metabolism

The trehalose (Tre) pathway has strong effects on growth and development in plants through regulation of carbon metabolism. Altering either Tre or trehalose 6-phosphate (T6P) can improve growth and productivity of plants as observed under different water availability. As yet, there are no reports of the effects of modification of Tre orT6P on plant performance under limiting nutrition. Here we report that nitrogen (N) metabolism is positively affected by exogenous application of Tre in nitrogen-deficient growing conditions. Spraying foliage of tobacco (Nicotiana tabacum) with trehalose partially alleviated symptoms of nitrogen deficiency through upregulation of nitrate and ammonia assimilation and increasing activities of nitrate reductase (NR), glycolate oxidase (GO), glutamine synthetase (GS) and glutamine oxoglutarate aminotransferase (GOGAT) with concomitant changes in ammonium (NH4 +) and nitrate (NO3 −) concentrations, glutamine and amino acids. Chlorophyll and total nitrogen content of leaves and rates of photosynthesis were increased compared to nitrogen-deficient plants without applied Tre. Total plant biomass accumulation was also higher in Tre -fed nitrogen-deficient plants, with a smaller proportion of dry weight partitioned to roots, compared to nitrogen-deficient plants without applied Tre. Consistent with higher nitrogen assimilation and growth, Tre application reduced foliar starch. Minimal effects of Tre feeding were observed on nitrogen-sufficient plants. The data show, for the first time, significant stimulatory effects of exogenous Tre on nitrogen metabolism and growth in plants growing under deficient nitrogen. Under such adverse conditions metabolism is regulated for survival rather than productivity. Application of Tre can alter this regulation towards maintenance of productive functions under low nitrogen. This has implications for considering approaches to modifying the Tre pathway for to improve crop nitrogen-use efficiency and production

A comparison of the burden of knee osteoarthritis attributable to high body mass index in China and globally from 1990 to 2019

BackgroundExcess body mass index (BMI) plays a key role in the onset and progression of knee osteoarthritis (knee OA). However, the burden of knee OA attributable to high BMI at the global, Chinese, and regional levels have received far too little attention. The aim of this study is to provide evidence to support the design of policy by investigating long-term trends of years lived with disability (YLDs) for knee OA.MethodsTo illustrate the trends of YLDs for knee OA attributable to high BMI and the temporal trends of the YLDs rate by age, period, and cohort, Joinpoint regression software and age-period-cohort (APC) were used to analyze the YLDs data of knee OA from the Global Burden of Disease (GBD) 2019.ResultsIn China, there were 549,963.5 YLDs for knee OA attributable to high BMI in 2019, which had increased by 460.7% since 1990. From 1990 to 2019, age-standardized disability-adjusted life year rate (ASDR) of knee OA attributable to high BMI trended upwards. The average annual percent change (AAPC) of knee OA attributable to high BMI in China and globe were 3.019, 1.419%, respectively. The longitudinal age curve of the APC model showed that the YLDs rates of knee OA due to high BMI increased with age, and YLDs rates were higher among females than males. The period rate ratios (RRs) of knee OA due to high BMI increased significantly. The cohort RRs of knee OA due to high BMI increased among those born between 1900 and 1970. The net drifts of knee OA attributable to high BMI in China and globe were above 1. Compared with global condition, the net drift values of knee OA attributable to high BMI in China was higher. Compared with females, males had higher net drift value. Countries with high socio-demographic index (SDI) have a much higher burden of knee OA caused by high BMI than countries with low SDI.ConclusionIn China, high BMI is a substantial cause of knee OA, the incidence of which has been increasing since 1990. In addition, women and the elderly are more vulnerable to knee OA caused by high BMI. The Chinese government must take the long-term impact of high BMI on knee OA into account and implement effective public health policies and resort to interventions to reduce the burden as soon as possible