MMMNA-Net for Overall Survival Time Prediction of Brain Tumor Patients

Overall survival (OS) time is one of the most important evaluation indices for gliomas situations. Multimodal Magnetic Resonance Imaging (MRI) scans play an important role in the study of glioma prognosis OS time. Several deep learning-based methods are proposed for the OS time prediction on multi-modal MRI problems. However, these methods usually fuse multi-modal information at the beginning or at the end of the deep learning networks and lack the fusion of features from different scales. In addition, the fusion at the end of networks always adapts global with global (eg. fully connected after concatenation of global average pooling output) or local with local (eg. bilinear pooling), which loses the information of local with global. In this paper, we propose a novel method for multi-modal OS time prediction of brain tumor patients, which contains an improved nonlocal features fusion module introduced on different scales. Our method obtains a relative 8.76% improvement over the current state-of-art method (0.6989 vs. 0.6426 on accuracy). Extensive testing demonstrates that our method could adapt to situations with missing modalities. The code is available at https://github.com/TangWen920812/mmmna-net.Comment: Accepted EMBC 202

Heightfields for Efficient Scene Reconstruction for AR

3D scene reconstruction from a sequence of posed RGB images is a cornerstone task for computer vision and augmented reality (AR). While depth-based fusion is the foundation of most real-time approaches for 3D reconstruction, recent learning based methods that operate directly on RGB images can achieve higher quality reconstructions, but at the cost of increased runtime and memory requirements, making them unsuitable for AR applications. We propose an efficient learning-based method that refines the 3D reconstruction obtained by a traditional fusion approach. By leveraging a top-down heightfield representation, our method remains real-time while approaching the quality of other learning-based methods. Despite being a simplification, our heightfield is perfectly appropriate for robotic path planning or augmented reality character placement. We outline several innovations that push the performance beyond existing top-down prediction baselines, and we present an evaluation framework on the challenging ScanNetV2 dataset, targeting AR tasks

Mechanisms of Sorting and Trafficking for Melanosome Biogenesis as Revealed by Studies of the Human Pigment Cell Protein Oca2

Version:1.0 StartHTML:0000000224 EndHTML:0000004814 StartFragment:0000002412 EndFragment:0000004778 SourceURL:file://localhost/Users/hastha82/Desktop/temporary%20desktop%20folder/MARKS%20LAB/THESIS/final%20changes.doc Certain cell types harbor specialized lysosome-related organelles (LROs) that derive from the endocytic system like conventional lysosomes but have unique functions. The coexistence of LROs and lysosomes in some cell types implies the existence of sorting mechanisms that divert resident cargo proteins to LROs. Based on the pigment-synthesizing melanosome in melanocytes as a model LRO and two melanosomal resident proteins as model cargoes, current models suggest that cargoes are sorted from early endosomes to melanosomes via one of two independent pathways mediated by the multisubunit complexes AP-3 or BLOC-1, each of which is defective in subtypes of the LRO biogenesis disease Hermansky-Pudlak Syndrome (HPS). An AP-3-related protein complex, AP-1, is thought to function in concert with BLOC-1. In this thesis, I assess the pigment-cell-specific putative transporter protein OCA2, as a third potential cargo protein with which to further dissect the relationships between AP-3, AP-1 and BLOC-1 in melanosomal transport. I first investigate the localization and site of action of OCA2. I use biochemical approaches in combination with site-directed mutagenesis and indirect immunofluorescence microscopic analysis of exogenously-expressed OCA2 in melanocytes to show that OCA2 is indeed a melanosome resident protein and does not function within the endoplasmic reticulum as has been suggested by other models. I show that melanosome localization is essential for OCA2 function and requires an acidic dileucine motif in the N-terminal cytoplasmic domain that can bind to both AP-3 and AP-1. Using site-directed mutagenesis in combination with yeast three hybrid assays and immunofluorescence microscopy analyses in melanocytes derived from mouse models of HPS and controls, I define the features of the OCA2 sorting signal that direct binding to AP-1 or AP-3 and show that OCA2 requires both AP-3 interaction and BLOC-1 for melanosomal localization. My results resolve a controversy regarding OCA2 localization, shed light on the interplay between AP-1 and AP-3 in melanosomal trafficking, and provide the first direct evidence for cooperation between BLOC-1 and AP-3 in trafficking to a LRO

New insights into organ-specific oxidative stress mechanisms using a novel biosensor zebrafish

This is the final version. Available from Elsevier via the DOI in this record. Background: Reactive oxygen species (ROS) arise as a result from, and are essential in, numerous cellular processes. ROS, however, are highly reactive and if left unneutralised by endogenous antioxidant systems, can result in extensive cellular damage and/or pathogenesis. In addition, exposure to a wide range of environmental stressors can also result in surplus ROS production leading to oxidative stress (OS) and downstream tissue toxicity. Objectives: Our aim was to produce a stable transgenic zebrafish line, unrestricted by tissue-specific gene regulation, which was capable of providing a whole organismal, real-time read-out of tissue-specific OS following exposure to a wide range of OS-inducing environmental contaminants and conditions. This model could, therefore, serve as a sensitive and specific mechanistic in vivo biomarker for all environmental conditions that result in OS. Methods: To achieve this aim, we exploited the pivotal role of the electrophile response element (EpRE) as a globally-acting master regulator of the cellular response to OS. To test tissue specificity and quantitative capacity, we selected a range of chemical contaminants known to induce OS in specific organs or tissues, and assessed dose-responsiveness in each using microscopic measures of mCherry fluorescence intensity. Results: We produced the first stable transgenic zebrafish line Tg (3EpRE:hsp70:mCherry) with high sensitivity for the detection of cellular RedOx imbalances, in vivo in near-real time. We applied this new model to quantify OS after exposure to a range of environmental conditions with high resolution and provided quantification both of compound- and tissue-specific ROS-induced toxicity. Discussion: Our model has an extremely diverse range of potential applications not only for biomonitoring of toxicants in aqueous environments, but also in biomedicine for identifying ROS-mediated mechanisms involved in the progression of a number of important human diseases, including cancer.Natural Environmental Research CouncilEuropean Unio

Various Aspects of Silicon Polymer Chemistry

This special issue of Molecules is dedicated to Professor Julian Chojnowski on the occasion of his 85th birthday for his outstanding achievements in the field of organosilicon chemistry. This issue contains one review and eleven original articles written by eminent experts on various aspects of silicon polymer chemistry, which reflect the tireless passion of Professor Chojnowski to the development of organosilicon chemistry

Doctor of Philosophy

dissertationThe ESCRT (endosomal sorting complexes required for transport) protein complexes are required for the sorting of proteins into the MVB (multivesicular body) pathway, a protein trafficking pathway that is critical for the degradation of plasma membrane proteins. As a result, the ESCRTs plays an important role in the regulation of nutrient import and cell signaling events by influencing the expression of nutrient transporters and signaling receptors on the surface of the cell. In this study we present a novel in vitro technique based on SFG (sumfrequency generation) capable of analyzing the dynamic assembly of the ESCRT complexes on planar supported lipid bilayers. We present evidence to support that this novel approach has the potential to provide information about the dynamics of the ESCRT network and to obtain data regarding the function of these protein complexes. Furthermore, we elucidated a regulatory connection between the nutrient sensing system, TORC1 (target of rapamycin complex 1), and the MVB pathway. Our results demonstrate that the MVB pathway functions to degrade non-essential biomass during starvation to replenish depleted amino acid levels. We further propose that ESCRT-dependent protein turnover is regulated by the metabolic state of the cell through TORC1 signaling. Surprisingly, we found indications that endocytosis and subsequent degradation of plasma membrane proteins is regulated by a novel starvation pathway that acts independently of TORC1. Based on our results, we present a model in which during starvation TORC1, together with an unknown regulatory pathway, increases the sorting efficiency and degradation of cargo proteins through the MVB pathway by suppressing recycling pathways. The increase in protein turnover replenishes the free amino acid pool, which allows the cell to produce stress-response proteins required to adapt to starvation conditions

A Comprehensive Survey on Orbital Edge Computing: Systems, Applications, and Algorithms

The number of satellites, especially those operating in low-earth orbit (LEO), is exploding in recent years. Additionally, the use of COTS hardware into those satellites enables a new paradigm of computing: orbital edge computing (OEC). OEC entails more technically advanced steps compared to single-satellite computing. This feature allows for vast design spaces with multiple parameters, rendering several novel approaches feasible. The mobility of LEO satellites in the network and limited resources of communication, computation, and storage make it challenging to design an appropriate scheduling algorithm for specific tasks in comparison to traditional ground-based edge computing. This article comprehensively surveys the significant areas of focus in orbital edge computing, which include protocol optimization, mobility management, and resource allocation. This article provides the first comprehensive survey of OEC. Previous survey papers have only concentrated on ground-based edge computing or the integration of space and ground technologies. This article presents a review of recent research from 2000 to 2023 on orbital edge computing that covers network design, computation offloading, resource allocation, performance analysis, and optimization. Moreover, having discussed several related works, both technological challenges and future directions are highlighted in the field.Comment: 18 pages, 9 figures and 5 table

Enhancing spatial resolution of remotely sensed data for mapping freshwater environments

Freshwater environments are important for ecosystem services and biodiversity. These environments are subject to many natural and anthropogenic changes, which influence their quality; therefore, regular monitoring is required for their effective management. High biotic heterogeneity, elongated land/water interaction zones, and logistic difficulties with access make field based monitoring on a large scale expensive, inconsistent and often impractical. Remote sensing (RS) is an established mapping tool that overcomes these barriers. However, complex and heterogeneous vegetation and spectral variability due to water make freshwater environments challenging to map using remote sensing technology. Satellite images available for New Zealand were reviewed, in terms of cost, and spectral and spatial resolution. Particularly promising image data sets for freshwater mapping include the QuickBird and SPOT-5. However, for mapping freshwater environments a combination of images is required to obtain high spatial, spectral, radiometric, and temporal resolution. Data fusion (DF) is a framework of data processing tools and algorithms that combines images to improve spectral and spatial qualities. A range of DF techniques were reviewed and tested for performance using panchromatic and multispectral QB images of a semi-aquatic environment, on the southern shores of Lake Taupo, New Zealand. In order to discuss the mechanics of different DF techniques a classification consisting of three groups was used - (i) spatially-centric (ii) spectrally-centric and (iii) hybrid. Subtract resolution merge (SRM) is a hybrid technique and this research demonstrated that for a semi aquatic QuickBird image it out performed Brovey transformation (BT), principal component substitution (PCS), local mean and variance matching (LMVM), and optimised high pass filter addition (OHPFA). However some limitations were identified with SRM, which included the requirement for predetermined band weights, and the over-representation of the spatial edges in the NIR bands due to their high spectral variance. This research developed three modifications to the SRM technique that addressed these limitations. These were tested on QuickBird (QB), SPOT-5, and Vexcel aerial digital images, as well as a scanned coloured aerial photograph. A visual qualitative assessment and a range of spectral and spatial quantitative metrics were used to evaluate these modifications. These included spectral correlation and root mean squared error (RMSE), Sobel filter based spatial edges RMSE, and unsupervised classification. The first modification addressed the issue of predetermined spectral weights and explored two alternative regression methods (Least Absolute Deviation, and Ordinary Least Squares) to derive image-specific band weights for use in SRM. Both methods were found equally effective; however, OLS was preferred as it was more efficient in processing band weights compared to LAD. The second modification used a pixel block averaging function on high resolution panchromatic images to derive spatial edges for data fusion. This eliminated the need for spectral band weights, minimised spectral infidelity, and enabled the fusion of multi-platform data. The third modification addressed the issue of over-represented spatial edges by introducing a sophisticated contrast and luminance index to develop a new normalising function. This improved the spatial representation of the NIR band, which is particularly important for mapping vegetation. A combination of the second and third modification of SRM was effective in simultaneously minimising the overall spectral infidelity and undesired spatial errors for the NIR band of the fused image. This new method has been labelled Contrast and Luminance Normalised (CLN) data fusion, and has been demonstrated to make a significant contribution in fusing multi-platform, multi-sensor, multi-resolution, and multi-temporal data. This contributes to improvements in the classification and monitoring of fresh water environments using remote sensing

The use of monotheism in the shaping of Christian identities vis-à-vis Judaism in the second century

This thesis argues that early Christians actively engaged rhetoric and symbols of monotheism in diverse literary strategies as an ideological tool for resisting, repositioning, and rereading Judaism in order to shape their own collective identity from 100 to 200 CE (ch. 1). Belief and confession of one God provides an important basis for social comparison between Jews and Christians because it represents a fundamental Jewish identity marker also shared by Christians (ch. 2). A survey of divine unity and uniqueness rhetoric in early Christian literature revealed three broad trajectories in which monotheistic motifs assumed significance in shaping Christian literature and thereby the production of "Christianness" itself. This thesis examines specific moments in each trajectory that highlight particularly well the functionality of monotheism in the process of forming Christianness relative to Judaism.Ignatius of Antioch provides the first example (ch. 3). The literary shaping of Philadelphians and Magnesians reveals that for Ignatius what fundamentally distinguished "Judaism" and "Christianism" was not monotheism but their respective response to the revelation of God through Jesus in the gospel. Monotheism was not a tool for classifying difference but a powerful weapon for resisting threatening Jewish influence within the Christian church. Only as an element of resistance brought to bear on an already established "Judaism"-"Christianism" divide did monotheism represent, reflexively and secondarily, a means of shaping Christian identity.Another trajectory overtly utilised "knowledge" of the one God as primary criterion for indexing sameness and difference between Christianity, Judaism, and other groups (ch. 4). Kerygma Petrou and Aristides' Apology employ such monotheistic classification strategies to situate Christianity in a global framework alongside other religious and/or ethnic collectivities. Both texts locate the "newness" of Christianity alongside the more well-known status of Jews. In so doing, they effectively reposition Judaism within the global framework of religious and ethnic groups to clarify and legitimate the meaning of belonging to Christian identity.Some Christians employed "two powers" hermeneutic strategies to reinterpret Jewish scriptural traditions of exclusivist monotheism by insinuating into scripture a second figure, Jesus, alongside the one God (ch. 5). Aristo's Disputation of Jason and Papiscus and Justin's Dialogue demonstrate awareness that the scriptures are shared intellectual property and the proper locus for Christian-Jewish debate. "Two powers" interpretations thus reflect conscious attempts to reread Jewish monotheistic textual traditions in a new way. Through them an entire reconstruction of the symbolic universe of monotheism can take place in explicitly Christian terms.These diverse strategies reveal a complex network of early Christian literary production that used monotheistic symbols and rhetoric as an implement to resist, reposition, and reread Judaism, thereby producing distinctly Christian identities (ch. 6)