214 research outputs found
Optimizing representations for integrative structural modeling using Bayesian model selection
No full text<p>Integrative structural modeling combines data from experiments, physical principles, statistics of previous structures, and prior models to obtain structures of macromolecular assemblies that are challenging to characterize experimentally. The choice of model representation is a key decision in integrative modeling, as it dictates the accuracy of scoring, efficiency of sampling, and resolution of analysis. But currently, the choice is usually made <i>ad hoc</i>, manually. Here, we have deposited NestOR (<strong>Nest</strong>ed Sampling for <strong>O</strong>ptimizing <strong>R</strong>epresentation), a fully automated, statistically rigorous method based on Bayesian model selection to identify the optimal coarse-grained representation for a given integrative modeling setup. We have also deposited a benchmark of four macromolecular assemblies which was used to assess the performance of NestOR.</p>
Migration studies and chemical characterization of short chain cyclic polyester oligomers from food packaging laminate adhesives
No full textLaminates are extensively used for food packaging applications such as retort pouches and retort packaging, boil in the bag, microwavable packaging, military meals ready to eat (MRE’s), single serving dispensers, etc. Laminates are manufactured by bonding multiple layers of films together using adhesives, where each layer acts as a functional component and contributes to overall integrity of the package. Polyurethane adhesive, the most common choice of adhesive for flexible packaging, is the reaction product of polyurethane pre-polymer and/or diisocyanate with polyester. The polyester component reacts with isocyanate, forming urethane bonds and introduces soft chain segments into the final, cured polyurethane. During the formation of polyester, low molecular weight cyclic diesters and oligoesters are formed as unwanted byproducts. These low molecular weight species often migrate out of packaging into the contents of the package. Since these species are novel compounds, the safety and toxicological properties have not been investigated. Our research focused on studying the chemistry and migratory properties of these compounds. We conducted migration testing of laminates using USFDA recommended food simulants such as 10% Ethanol for aqueous and acid foods and 95% Ethanol for the fatty foods. Single side extraction cell assembly was used for the purpose of extraction which was conditioned at 100 °C for 30 min. In our research GC-MS analysis was used to determine chemical structures, gas chromatography retention time indices and the average migratory concentration levels of ten short chain cyclic diesters and oligoesters. The chemical structures were deduced by analyzing the characteristic fragmentation pattern. Also to investigate the predicted metabolic fate of short chain cyclic diesters and oligoesters after their ingestion and potential absorption into the bloodstream, they were treated with non-specific porcine esterase enzyme at 37 °C for 1 h. In our research it was also shown that the enzyme treatment metabolized the short chain cyclic diesters and oligoesters back into their original corresponding diol and dicarboxylic acid precursors.M.S.Includes bibliographical referencesby Aditi Shrikhand
Occupational Therapy Within an Intensive Comprehensive Aphasia Program: Outcomes for People Living With Chronic Stroke
No full textAbstract
Date Presented 4/1/2017
This poster presents findings from a study that supports inclusion of occupational therapy in an intensive, comprehensive aphasia program to increase performance of and satisfaction with valued occupations focusing on instrumental activities of daily living, leisure, work, and social participation for people with chronic stroke and aphasia.
Primary Author and Speaker: Anne Escher
Additional Authors and Speakers: Aditi Amlani, Angela Viani, Sue Berger</jats:p
Women in HPC Australasia, 3 years on
No full textThe Australasian Chapter of the global organisation Women in High Performance Computing (WHPC) began as a collaboration between New Zealand eScience Infrastructure, NCI Australia, Pawsey Supercomputing Research Centre, Monash University, and Australasian eResearch Organisations (AeRO). Launched in 2020, the Chapter (WHPC+ AusNZ)* is celebrating three years of hosting events and creating spaces where anyone interested in supporting diversity & inclusion in our HPC and eResearch communities can feel welcome, connect with others, and contribute to discussions and positive change. This lightning talk will share:an overview of the Chapter's purpose and objectiveshighlights from the last three years of activityways you can get involved We welcome anyone interested in learning more about the Chapter or who is keen to connect with others interested in supporting diversity & inclusion in HPC and eResearch.*Our Chapter has added a "+" to our name to encourage people from all walks of life, not just gender, to join and participate in our community.ABOUT THE AUTHOR(S)Based at the University of Auckland, Jana Makar coordinates communications and engagement strategies for New Zealand eScience Infrastructure (NeSI). She has a degree in Communications from the University of Calgary and spent the early part of her career working as a newspaper journalist.Based at the Pawsey Supercomputing Centre, Aditi Subramanya is a communicator in the digital world. Aditi loves tech and is passionate about creating diverse, inclusive mindsets and cultures. Aditi’s goal is to break global barriers to create fair opportunities for all.For more information about eResearch NZ / eRangahau Aotearoa, visit:https://eresearchnz.co.nz/</p
Development of photochemical etching and its application in fabrication of integrated reflector metal semiconductor metal photodetectors
No full text"Photolithography and etching form the basis of any microfabrication process. Consequently, there is a lot of interest in the research community to improve and innovate on these crucial steps so as to realize the fabrication of complex devices. Once limited to use as physical photomasks for producing planar features, photolithography and etching are now being expanded to function with virtual programmable masks and to produce complex non-planar structures. These ""3-D"" structures are of great interest in fields like photonics, microfluidics and microelectromechanical systems (MEMS). A number of competitive solutions have been proposed to enable this ""grayscale"" processing of materials.
This thesis discusses digital projection photochemical etching as a possible tool for maskless, grayscale lithography and etching in a single step. It is based on light-assisted etching of semiconductors placed in a suitable chemical solution. By projecting spatially varying intensity light, grayscale etching can be achieved. The thesis begins with the motivation and literature review of this area of study, and then discusses the fundamental mechanisms of the photochemical etching process. Finally, an application of the fabrication of high-responsivity metal-semiconductor-metal (MSM) photodetectors is discussed to show how photochemical etching can be integrated with conventional microfabrication to enhance device fabrication capability."Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2019-05-01The student, Aditi Udupa, accepted the attached license on 2017-04-25 at 14:27.The student, Aditi Udupa, submitted this Thesis for approval on 2017-04-25 at 14:31.This Thesis was approved for publication on 2017-04-26 at 12:16.DSpace SAF Submission Ingestion Package generated from Vireo submission #11051 on 2017-08-10 at 15:07:00Made available in DSpace on 2017-08-10T20:33:24Z (GMT). No. of bitstreams: 2
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Editing by leucyl-trna synthetase: Discrimination of norvaline and isoleucine
No full textAminoacyl tRNA-synthetases (AARS) are housekeeping enzymes that are tasked with accurate synthesis of aminoacylated tRNA for protein synthesis and other cellular functions. The specificity of amino acid attachment challenges the AARSs that need to distinguish between structurally similar amino acids. In such cases, AARSs have developed editing mechanisms to circumvent the issue of misaminoacylation.
Leucyl-tRNA synthetase (LeuRS), for instance selectively edits misactivated and mischarged non-leucine amino acids via pre-transfer editing of misactivated adenylates in the synthetic site or by hydrolyzing mischarged amino acids in the CP1 editing domain. The enzyme’s dependence between the two editing mechanisms can shift based on the origin from which the AARS is derived, the amino acid that is targeted for editing, or presence of a mutation in the enzyme. In the absence of the CP1 domain, E. coli LeuRS (LeuRS-ΔCP1) maintains fidelity by clearing non-leucine aminoacyl-adenylates in the enzyme’s synthetic site. The intact tRNA 3’-terminal adenosine (A76) residue is a prerequisite for aminoacylation.
Leveraging A76 essentiality tRNA analogues were designed to investigate amino acid dependent specificity of editing by LeuRS. The tRNA analogues were synthesized by addition of a modified adenosine triphosphate to an in vitro transcribed E. coli tRNALeuUAA using the CCA-adding enzyme from E. coli. Incorporation of unchargeable tRNA analogues stimulated ATP hydrolysis by wild type LeuRS in the presence of norvaline. In contrast, pre-transfer editing occurs independent of the tRNA for LeuRS-ΔCP1, which lacks the CP1 domain. Therefore it is hypothesized that the CP1 domain of LeuRS plays a critical role for tRNA-dependent pre-transfer editing.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2020-12-01The student, Aditi Banerjee, accepted the attached license on 2018-12-04 at 09:13.The student, Aditi Banerjee, submitted this Dissertation for approval on 2018-12-04 at 09:24.This Dissertation was approved for publication on 2018-12-05 at 08:43.DSpace SAF Submission Ingestion Package generated from Vireo submission #13192 on 2019-02-07 at 14:18:57Made available in DSpace on 2019-02-07T20:44:09Z (GMT). No. of bitstreams: 3
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Automated profile builder: one stop portal for creating and sharing your personal profiles
No full textThe explosive growth in digital presence have changed the way people form and stay connected to their professional networks, leading to the rise in multiple online profile management tools each catering to custom profile generation needs. With digital presence being split across multiple online tools, the challenge to maintain, update and customize details of all online profiles has been a challenge, perhaps more so in the academic researcher and professional community where a long list of publication and multiple pages of online profile is the norm. Today a typical researcher can have profiles that range from 1-2 pages like the typical industry standard to several pages as per typical academic standards where publications, patents, talks, workshops, etc are all part of a researchers profile. Maintaining this profile online across various independently run profile management system has created the problem of tedious multiple locations of data managements. As no existing profile management system leverages data from other systems it has been difficult for researchers to maintain and update online profiles. In addition, most of the profile management system have a fixed schema while creating online profile so the user does not have the flexibility to create a customized profile. In this thesis, we propose an Automated Profile Builder(AutoPB) which acts as a one stop portal for all the online profile management system. AutoPB aims to solve the issues surrounding current distributed and scattered profile management systems by its three main features: a) schema sharing, b) centralized multi format data in/out portal and c) client-side data retrieval system. First concept is known as schema sharing, which is a unique feature that no other profile management system has. This feature lets user to learn and share schema that are used while building an online profile. Secondly, the system provides flexible Import and Export feature. The user can import data from external sources as well as export the profile in different formats. Lastly, the profile builder performs client-side searching, crawling and parsing to minimize the server work load. Using our profile builder users can import data from their existing online profile and would not need to manually type their information which is easily available in the internet. In this thesis, we demonstrate that AutoPB with these features can act as a one stop portal especially for researchers to more easily manage their online profile by centralized data management paired with distribution of multiple custom profiles.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2019-08-01The student, Aditi Adhikari, accepted the attached license on 2017-07-12 at 00:56.The student, Aditi Adhikari, submitted this Thesis for approval on 2017-07-12 at 01:22.This Thesis was approved for publication on 2017-07-12 at 16:45.DSpace SAF Submission Ingestion Package generated from Vireo submission #11418 on 2017-09-29 at 11:19:05Made available in DSpace on 2017-09-29T16:39:46Z (GMT). No. of bitstreams: 2
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New vaccines for infectious diseases: immunological targeting of the quorum sensing system of Pseudomonas aeruginosa
No full textPseudomonas aeruginosa is an opportunistic pathogen of animals and humans causing medical complications in burns, wounds, and cystic fibrosis. P. aeruginosa is efficient at adapting its virulence phenotype depending on the site of infection. Emerging multi-drug resistant strains and a limited number of effective anti-pseudomonal antibiotics renders P. aeruginosa infections increasingly difficult to treat.
To address this need, this thesis considers targeting bacterial quorum sensing, which regulates the production of virulence factors, as an alternative prophylactic strategy. The P. aeruginosa quorum sensing system is compromised of three interlinked but independent systems, Las, Rhl and Pqs, which produce and utilise quorum sensing system molecules, 3OC12-HSL, C4-HSL and PQS respectively. Immunological targeting of the quorum sensing system molecule 3OC12-HSL, through active immunisation (vaccines), inhibits the Las system, resulting in a longer life expectancy in mice infected with P. aeruginosa in vivo.
However, P. aeruginosa has the capacity to develop resistance, through compensatory mechanisms, towards quorum sensing inhibition that targets the Las system only. This emphasises the need to target all three quorum sensing systems, Las, Rhl, and the Pqs, in order to inhibit quorum sensing. The present study focuses particularly on the development of a multi-component anti-quorum sensing system vaccine that would target the three main quorum sensing system molecules, effectively compromising the quorum sensing system and minimising compensatory mechanisms.
This involved the synthesis of haptens based on the quorum sensing system molecules, which were used to haptenise the immunogenic carrier keyhole limpet haemocyanin. Syntheses of the haptens, AP1 (derivative of 3OC8-HSL) and AP2 (derivative of PQS), were conducted using adapted published methods. The resulting conjugates, AP1-keyhole limpet haemocyanin and AP2-keyhole limpet haemocyanin were immunogenic in mice and rabbits. The specific anti-hapten polyclonal antibodies that were generated demonstrated cross-reactivity with the natural quorum sensing system molecules of P. aeruginosa that translated in significant and specific anti-quorum sensing system molecule activity in bioluminescence reporter assays. Anti-AP1 polyclonal antibodies were able to reduce biofilm formation at high concentrations, however, significant reduction of biofilm formation was seen when the anti-hapten antibodies were used in combination.
In this study, it has been demonstrated that the inhibition of the quorum sensing system should include the three systems, Las, Rhl and PQS, and that this can be done by a multi-component anti-quorum sensing system vaccine. These data suggest that a multi-component anti-quorum sensing system vaccine takes us a step forward to a viable prophylaxis against P. aeruginosa for susceptible patients
New vaccines for infectious diseases : immunological targeting of the quorum sensing system of Pseudomonas aeruginosa
No full textPseudomonas aeruginosa is an opportunistic pathogen of animals and humans causing medical complications in burns, wounds, and cystic fibrosis. P. aeruginosa is efficient at adapting its virulence phenotype depending on the site of infection. Emerging multi-drug resistant strains and a limited number of effective anti-pseudomonal antibiotics renders P. aeruginosa infections increasingly difficult to treat. To address this need, this thesis considers targeting bacterial quorum sensing, which regulates the production of virulence factors, as an alternative prophylactic strategy. The P. aeruginosa quorum sensing system is compromised of three interlinked but independent systems, Las, Rhl and Pqs, which produce and utilise quorum sensing system molecules, 3OC12-HSL, C4-HSL and PQS respectively. Immunological targeting of the quorum sensing system molecule 3OC12-HSL, through active immunisation (vaccines), inhibits the Las system, resulting in a longer life expectancy in mice infected with P. aeruginosa in vivo. However, P. aeruginosa has the capacity to develop resistance, through compensatory mechanisms, towards quorum sensing inhibition that targets the Las system only. This emphasises the need to target all three quorum sensing systems, Las, Rhl, and the Pqs, in order to inhibit quorum sensing. The present study focuses particularly on the development of a multi-component anti-quorum sensing system vaccine that would target the three main quorum sensing system molecules, effectively compromising the quorum sensing system and minimising compensatory mechanisms. This involved the synthesis of haptens based on the quorum sensing system molecules, which were used to haptenise the immunogenic carrier keyhole limpet haemocyanin. Syntheses of the haptens, AP1 (derivative of 3OC8-HSL) and AP2 (derivative of PQS), were conducted using adapted published methods. The resulting conjugates, AP1-keyhole limpet haemocyanin and AP2-keyhole limpet haemocyanin were immunogenic in mice and rabbits. The specific anti-hapten polyclonal antibodies that were generated demonstrated cross-reactivity with the natural quorum sensing system molecules of P. aeruginosa that translated in significant and specific anti-quorum sensing system molecule activity in bioluminescence reporter assays. Anti-AP1 polyclonal antibodies were able to reduce biofilm formation at high concentrations, however, significant reduction of biofilm formation was seen when the anti-hapten antibodies were used in combination. In this study, it has been demonstrated that the inhibition of the quorum sensing system should include the three systems, Las, Rhl and PQS, and that this can be done by a multi-component anti-quorum sensing system vaccine. These data suggest that a multi-component anti-quorum sensing system vaccine takes us a step forward to a viable prophylaxis against P. aeruginosa for susceptible patients.EThOS - Electronic Theses Online ServiceGBUnited Kingdo
Methodology and applications of topology optimization in nanophotonics
No full textAs photonic integrated circuits are becoming more diverse in functionality and compact in size, the traditional design approach based on physical intuition becomes limited. There is a great interest in the research and development of inverse design for nanophotonics as it can surpass the limitations of brute-force design by intuition and few-parameter sweeps. We studied the inverse design approach to photonic device design, and this dissertation presents our work in advancing current topology optimization approaches for nanophotonics and applying it to several versatile applications.
We discuss the extension of conventional topology optimization both from a methodology perspective as well as an application perspective. From a methodology perspective, we develop an approach to generalize topology optimization to include grayscale structures and discrete-height structures, which expands the design space. We apply this broader form of topology optimization to different cases both in integrated photonics to design ultra-compact power splitters and polarization splitters, and in free-space optics to design chiro-optic devices. We also extend inverse design to heterogeneous photonic integration for a compact edge-coupler for coupling the light from an edge-emitting transistor laser to a passive waveguide. This study demonstrates that for complex device architectures with multiple materials and constraints, inverse design can alleviate the load on the designer. We designed an ultra-compact spot-size converter with misalignment tolerances within the margin of the proposed fabrication tools. We also developed designs for an ultra-compact ring resonator by utilizing conventional topology optimization but applied in a unique way. By optimizing only the 90-degree bend and cascading it to form a ring, the physics and interpretability of the device are maintained. Finally, we discuss our efforts to develop an open-source, cluster-deployable inverse design code so that topology optimization can be done for large devices.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2022-08-01The student, Aditi Udupa, accepted the attached license on 2020-07-16 at 12:09.The student, Aditi Udupa, submitted this Dissertation for approval on 2020-07-16 at 12:49.This Dissertation was approved for publication on 2020-07-16 at 13:49.DSpace SAF Submission Ingestion Package generated from Vireo submission #15654 on 2020-10-02 at 15:51:12Made available in DSpace on 2020-10-07T22:50:02Z (GMT). No. of bitstreams: 3
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