Socializing the Semantic Gap: A Comparative Survey on Image Tag Assignment, Refinement and Retrieval

Where previous reviews on content-based image retrieval emphasize on what can be seen in an image to bridge the semantic gap, this survey considers what people tag about an image. A comprehensive treatise of three closely linked problems, i.e., image tag assignment, refinement, and tag-based image retrieval is presented. While existing works vary in terms of their targeted tasks and methodology, they rely on the key functionality of tag relevance, i.e. estimating the relevance of a specific tag with respect to the visual content of a given image and its social context. By analyzing what information a specific method exploits to construct its tag relevance function and how such information is exploited, this paper introduces a taxonomy to structure the growing literature, understand the ingredients of the main works, clarify their connections and difference, and recognize their merits and limitations. For a head-to-head comparison between the state-of-the-art, a new experimental protocol is presented, with training sets containing 10k, 100k and 1m images and an evaluation on three test sets, contributed by various research groups. Eleven representative works are implemented and evaluated. Putting all this together, the survey aims to provide an overview of the past and foster progress for the near future.Comment: to appear in ACM Computing Survey

Making Ribosomes: Biochemical and Structural Studies of Early Ribosome Biogenesis in Yeast

The ribosome is a complex macromolecule responsible for the synthesis of all proteins in the cell. In yeast, it is made of four ribosomal RNAs and 79 proteins, asymmetrically divided in a small and large subunit. In a growing yeast cell, more than 2000 ribosomes are assembled every minute. The ribosome is assembled through a highly complex process involving more than 200 trans-acting factors. Ribosome assembly begins in the nucleolus where RNA polymerase I transcribes a long polycistronic RNA, the 35S preribosomal RNA which contains the sequences for three of the four ribosomal RNAs, as well as spacer sequences which are transcribed and removed during assembly. Ribosome assembly factors bind co-transcriptionally to the nascent chains of preribosomal RNA and coordinate its correct folding, modification and cleavage. While most ribosome assembly factors have been identified, the function of numerous factors is still unknown. The timing of their involvement in ribosome assembly has not been characterized, limiting our understanding of their function. To further our knowledge of this essential cellular process, we set out to characterize the order of assembly of ribosomal assembly factors on the first half of the nascent preribosomal RNA, which forms the earliest precursors of the small subunit (Chapter II). Moreover, using state-of-the-art cryo-electron microscopy we determined the structure at near-atomic resolution of the earliest yet intermediate of small subunit assembly, the small subuit processome (Chapter III). The combined insights from the structure of this early intermediate and co-transcriptional assembly of pre-ribosomal complexes has redefined our understanding of early ribosome assembly. The cell invests more than 70 factors into the early events of small subunit assembly, with a combined molecular weight of more than 5 megadalton, four times the size of the mature small subunit. This impressive number of factors form a structural blueprint for the spatial segregation and individual maturation of the domains of the 18S. Ribosome assembly factors perform a multitude of functions within this platform, including specific modification of the ribosomal RNA and the concerted coordination of important RNA elements. We have also determined a new mechanism by which cells regulate ribosome biogenesis in response to nutritional depletion. We finally set out characterize the timing of recruitment of assembly factors to the second half of the 35S pre-ribosomal RNA, which leads to the formation of the earliest large subunit precursors (Chapter IV). This has allowed us to complete a new model for the co-transcriptional assembly of pre-ribosomal complexes. Our work has not only provided new insights into the role of more than 100 factors of early ribosome biogenesis but will serve as a platform for the further characterization of individual factors, as well as the regulation of ribosome assembly

Functional analysis and structural investigations of MTB DosS sensory domain.

Mycobacterium tuberculosis (MTB) is a very successful pathogen, causing the deaths of approximately two million people a year world-wide. Survival of the pathogen in vivo is dependant on its ability to respond and adapt to changes within its environment. One method of adaptation is through two-component signal transduction systems, the phosphotransfer pathways that couple stimuli to responses. Generic two-component systems involve two conserved elements, a membrane bound histidine kinase, which is the sensory protein, and a response-regulator protein that controls the response usually by altering the expression of genes required for adaptive responses. The aim of this thesis is to investigate the structure and function of the sensory protein DosS (DevS). DosS is induced by exposure to hypoxia, NO and ethanol and is the only one of the 11 paired MTB two component systems for which inducers have been identified but the precise chemical nature of the signal is unknown. The N-terminal input region of the DosS sensor contains two putative GAF domains. Various fragments of the N-terminal region were cloned, expressed and purified to homogeneity. Ultraviolet-Visible spectral analysis reveals that full length DosS binds a classical high spin b haem cofactor. Mutagenesis identified histidine 149 of DosS, which is within the N-terminal GAF domain, as critical to haem-binding. This is the first known GAF domain to bind haem and the presence of a haem co-factor is consistent with the postulated involvement of DosS in oxygen and redox sensing. Based on this data a model for histidine kinase activation is suggested. The second GAF domain of DosS was analysed using NMR spectroscopy. Triple resonance NMR experiments enabled the identification and sequential assignment for 99 out of the 141 backbone amide proton and nitrogen resonances. In addition, both of the GAF domains were also subjected to protein crystallisation while the full length DosS was investigated using electron microscopy

Elucidation of the Functional Architecture of the Early Pre-Ribosomal Processing Machinery in Yeast

Ribosomes carry out one of the most fundamental functions of life - the translation of genetic information into functional proteins. The pivotal role of the ribosome in the cell is reflected in its immensely complicated and energy-consuming assembly pathway. The maturation of a eukaryotic ribosome involves more than 200 non-ribosomal factors and the activity of all three RNA polymerases. In yeast, ribosome biogenesis starts with the transcription of the 35S pre-ribosomal RNA in the nucleolus. This large RNA molecule contains three of the four ribosomal RNAs separated by several internal and external transcribed spacer regions. The 5’ external transcribed spacer (5’ETS) is the first RNA domain of the 35S pre-rRNA being transcribed. As it emerges from the RNA polymerase it is bound by UtpA, a 660 kDa complex consisting of 7 essential subunits in yeast. 9 By binding to the nascent pre-rRNA, UtpA triggers the association of multiple other proteins and complexes, which leads to the formation of the ~2 MDa 5’ ETS particle. As transcription continues through the ensuing small subunit rRNA gene more ribosome biogenesis factors as well as ribosomal proteins are recruited and the 5’ ETS particle evolves into the small subunit processome. The small subunit processome, a giant particle, unique and essential to eukaryotes, coordinates the cleavage of the 35S pre-rRNA to separate the maturation of the small and large ribosomal subunit. So far, a functional understanding of the initial events in ribosome biogenesis has been impeded by a lack of structural and biochemical data about the protein complexes facilitating this process and the pre-ribosomal particles they form. To gain mechanistic insights into these earliest steps we set out to delineate the role of UtpA as first building block, vital structural component and organizer of the 5’ ETS particle and the small subunit processome. By using protein-protein and RNA-protein cross-linking techniques combined with negative stain electron microscopy and biochemical assays we were able to define the composite RNA binding site of UtpA and characterize its molecular architecture in the absence of high-resolution structural data (Chapter II). Subsequent structure determination of the small subunit processome by cryoelectron microscopy has not only provided the first fully assigned atomic model of UtpA but visualized how ribosome biogenesis factors keep the ribosomal RNA domains in spatially separated compartments of this large particle (Chapter III). In the small subunit processome, the 5’ ETS particle forms the base onto which the segregated ribosomal RNA domains are folded. To investigate whether the 5’ ETS particle serves as a structural mold for the maturing rRNA domains during earlier assembly stages, we solved the cryo-EM structures of the 5’ ETS particle in intermediates preceding the formation of the small subunit processome (Chapter IV). Combined with the in vivo analysis of artificial pre-rRNA fragments, the architecture of the 5’ ETS particle shows that the initial steps of ribosome assembly are governed by the functional independence of all rRNA domains and the 5’ ETS particle. Completion of ribosomal gene transcription then leads to a conformational change in the 5’ ETS particle and small subunit processome formation. In summary, our work provides structural snapshots and biochemical information on more than 50 ribosome assembly factors during different stages of the initiating steps in eukaryotic ribosome biogenesis. These data form the basis for a three-dimensional model of these essential events in the eukaryotic cell

Structural studies of eukaryotic ribosome biogenesis and the sec and Bcs1 protein translocation systems

Three publications of this cumulative dissertation use cryo-electron microscopy (cryo-EM) to dissect the assembly pathway of the eukaryotic large ribosomal subunit (LSU). This pathway commences with freshly transcribed and initially unfolded rRNA in the nucleolus, which folds and incorporates ribosomal proteins while traveling to the cytoplasm, ultimately culminating in the mature LSU. During this highly complex pathway, the yeast cell must assemble four rRNAs and 79 ribosomal proteins with the help of over 200 assembly factors (AFs). Using cryo-EM, structures of nucleo\-plasmic and cytoplasmic assembly intermediates of the LSU could be solved in recent years, thus shedding light on the later stages of LSU formation. Early assembly steps remain enigmatic, as nucleolar LSU assembly intermediates have been biochemically but not structurally characterized. Taken together, we solved the structure of seven nucleolar or early nucleoplasmic intermediates at resolutions ranging from 3.3 to 4.5 Å, showing a linear assembly sequence. The first five structures show how the rRNA of the LSU is incorporated stepwise, in a non-transcriptional sequence, first forming the solvent exposed back side, and later the peptide exit tunnel and parts of the intersubunit surface (ISS). At the late nucleolar stage, the L1-stalk rRNA of domain V blocks the site of central protuberance (CP) assembly and is stabilized in a premature conformation by a range of AFs associated with the meandering, long N-terminal tail of Erb1. Two further structures show progression from this stage after release of the Erb1-Ytm1 complex by the Rea1 remodeling machinery. These intermediates, purified via Nop53, show dissociation of many early AFs from the premature ISS and destabilization of the L1-stalk. After subsequent release of the Spb1 methyltransferase, the L1-stalk rRNA can be accommodated in its mature conformation. This allows the premature CP to form, leading to a previously characterized nucleoplasmic intermediate, with a formed but premature CP. This particle is the substrate for the second Rea1 mediated structural remodeling, an intermediate of which we resolved to molecular resolution revealing Ipi1 as a central integrator for the Rix1-Ipi1-Ipi3 complex on this pre-60S particle. The binding of the Rix1-Rea1 remodeling machinery at this nucleoplasmic stage progresses maturation by inducing a 180$^{\circ}$ rotation of the 5S ribonucleoprotein particle (5S RNP) and CP. Using a combination of yeast genetics and cryo-EM we investigated the function of the AF Cgr1 in this maturation step. We showed that Cgr1 is required for CP rotation to take place, likely by stabilizing the rotated conformation. The Cgr1 function can be bypassed by introducing suppressor mutations in Rpf2 and Rrs1, two factors stabilizing the CP prior to rotation. Apart from ribosome biogenesis, two additional publications of this dissertation address protein translocation machinery, required for transport of proteins across or into membranes. The Sec translocon allows co- and posttranslational translocation of mostly unfolded substrates across the bacterial plasma and the eukaryotic endoplasmic reticulum (ER) membrane. We solved the structure of a stalled 70S ribosome-nascent chain complex (RNC) bound to the SecYEG translocon in a native like environment provided by a large lipid nanodisc. The structure shows all three subunits of the bacterial SecYEG complex and displays the lateral gate at a defined, early stage of opening or unzipping on the cytoplasmic side upon insertion of the signal anchor domain of the nascent chain. Specific pathways, such as the assembly of the mitochondrial bc1 respiratory chain complex, require folding of proteins in one compartment before translocation across a membrane to allow the protein to be active in another compartment. The bc1-complex component Rip1 folds in the mitochondrial matrix and assembles a 2Fe-2S cluster before being translocated across the inner mitochondrial membrane (IM) by the AAA-protein Bcs1. We solved the structure of Bcs1 in an ADP-bound state and two apo states, displaying a heptameric ring of Bcs1 protomers. Bcs1 forms two large aqueous vestibules separated by a seal forming middle domain. One vestibule is accessible from the matrix side and one lies within the inner mitochondrial membrane. The architecture and structural dynamics between the three states suggest an airlock like mechanism, allowing transport of folded Rip1 while maintaining the permeability barrier of the membrane

Study of spaceborne multiprocessing, phase 1

Multiprocessing computer organizations and their application to future space mission

RFID Technology in Intelligent Tracking Systems in Construction Waste Logistics Using Optimisation Techniques

Construction waste disposal is an urgent issue for protecting our environment. This paper proposes a waste management system and illustrates the work process using plasterboard waste as an example, which creates a hazardous gas when land filled with household waste, and for which the recycling rate is less than 10% in the UK. The proposed system integrates RFID technology, Rule-Based Reasoning, Ant Colony optimization and knowledge technology for auditing and tracking plasterboard waste, guiding the operation staff, arranging vehicles, schedule planning, and also provides evidence to verify its disposal. It h relies on RFID equipment for collecting logistical data and uses digital imaging equipment to give further evidence; the reasoning core in the third layer is responsible for generating schedules and route plans and guidance, and the last layer delivers the result to inform users. The paper firstly introduces the current plasterboard disposal situation and addresses the logistical problem that is now the main barrier to a higher recycling rate, followed by discussion of the proposed system in terms of both system level structure and process structure. And finally, an example scenario will be given to illustrate the system’s utilization