Matching Items (53)
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Description
In an effort to begin validating the large number of discovered candidate biomarkers, proteomics is beginning to shift from shotgun proteomic experiments towards targeted proteomic approaches that provide solutions to automation and economic concerns. Such approaches to validate biomarkers necessitate the mass spectrometric analysis of hundreds to thousands of human

In an effort to begin validating the large number of discovered candidate biomarkers, proteomics is beginning to shift from shotgun proteomic experiments towards targeted proteomic approaches that provide solutions to automation and economic concerns. Such approaches to validate biomarkers necessitate the mass spectrometric analysis of hundreds to thousands of human samples. As this takes place, a serendipitous opportunity has become evident. By the virtue that as one narrows the focus towards "single" protein targets (instead of entire proteomes) using pan-antibody-based enrichment techniques, a discovery science has emerged, so to speak. This is due to the largely unknown context in which "single" proteins exist in blood (i.e. polymorphisms, transcript variants, and posttranslational modifications) and hence, targeted proteomics has applications for established biomarkers. Furthermore, besides protein heterogeneity accounting for interferences with conventional immunometric platforms, it is becoming evident that this formerly hidden dimension of structural information also contains rich-pathobiological information. Consequently, targeted proteomics studies that aim to ascertain a protein's genuine presentation within disease- stratified populations and serve as a stepping-stone within a biomarker translational pipeline are of clinical interest. Roughly 128 million Americans are pre-diabetic, diabetic, and/or have kidney disease and public and private spending for treating these diseases is in the hundreds of billions of dollars. In an effort to create new solutions for the early detection and management of these conditions, described herein is the design, development, and translation of mass spectrometric immunoassays targeted towards diabetes and kidney disease. Population proteomics experiments were performed for the following clinically relevant proteins: insulin, C-peptide, RANTES, and parathyroid hormone. At least thirty-eight protein isoforms were detected. Besides the numerous disease correlations confronted within the disease-stratified cohorts, certain isoforms also appeared to be causally related to the underlying pathophysiology and/or have therapeutic implications. Technical advancements include multiplexed isoform quantification as well a "dual- extraction" methodology for eliminating non-specific proteins while simultaneously validating isoforms. Industrial efforts towards widespread clinical adoption are also described. Consequently, this work lays a foundation for the translation of mass spectrometric immunoassays into the clinical arena and simultaneously presents the most recent advancements concerning the mass spectrometric immunoassay approach.
ContributorsOran, Paul (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Ros, Alexandra (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Signal processing techniques have been used extensively in many engineering problems and in recent years its application has extended to non-traditional research fields such as biological systems. Many of these applications require extraction of a signal or parameter of interest from degraded measurements. One such application is mass spectrometry immunoassay

Signal processing techniques have been used extensively in many engineering problems and in recent years its application has extended to non-traditional research fields such as biological systems. Many of these applications require extraction of a signal or parameter of interest from degraded measurements. One such application is mass spectrometry immunoassay (MSIA) which has been one of the primary methods of biomarker discovery techniques. MSIA analyzes protein molecules as potential biomarkers using time of flight mass spectrometry (TOF-MS). Peak detection in TOF-MS is important for biomarker analysis and many other MS related application. Though many peak detection algorithms exist, most of them are based on heuristics models. One of the ways of detecting signal peaks is by deploying stochastic models of the signal and noise observations. Likelihood ratio test (LRT) detector, based on the Neyman-Pearson (NP) lemma, is an uniformly most powerful test to decision making in the form of a hypothesis test. The primary goal of this dissertation is to develop signal and noise models for the electrospray ionization (ESI) TOF-MS data. A new method is proposed for developing the signal model by employing first principles calculations based on device physics and molecular properties. The noise model is developed by analyzing MS data from careful experiments in the ESI mass spectrometer. A non-flat baseline in MS data is common. The reasons behind the formation of this baseline has not been fully comprehended. A new signal model explaining the presence of baseline is proposed, though detailed experiments are needed to further substantiate the model assumptions. Signal detection schemes based on these signal and noise models are proposed. A maximum likelihood (ML) method is introduced for estimating the signal peak amplitudes. The performance of the detection methods and ML estimation are evaluated with Monte Carlo simulation which shows promising results. An application of these methods is proposed for fractional abundance calculation for biomarker analysis, which is mathematically robust and fundamentally different than the current algorithms. Biomarker panels for type 2 diabetes and cardiovascular disease are analyzed using existing MS analysis algorithms. Finally, a support vector machine based multi-classification algorithm is developed for evaluating the biomarkers' effectiveness in discriminating type 2 diabetes and cardiovascular diseases and is shown to perform better than a linear discriminant analysis based classifier.
ContributorsBuddi, Sai (Author) / Taylor, Thomas (Thesis advisor) / Cochran, Douglas (Thesis advisor) / Nelson, Randall (Committee member) / Duman, Tolga (Committee member) / Arizona State University (Publisher)
Created2012
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Description
Cancer claims hundreds of thousands of lives every year in US alone. Finding ways for early detection of cancer onset is crucial for better management and treatment of cancer. Thus, biomarkers especially protein biomarkers, being the functional units which reflect dynamic physiological changes, need to be discovered. Though important, there

Cancer claims hundreds of thousands of lives every year in US alone. Finding ways for early detection of cancer onset is crucial for better management and treatment of cancer. Thus, biomarkers especially protein biomarkers, being the functional units which reflect dynamic physiological changes, need to be discovered. Though important, there are only a few approved protein cancer biomarkers till date. To accelerate this process, fast, comprehensive and affordable assays are required which can be applied to large population studies. For this, these assays should be able to comprehensively characterize and explore the molecular diversity of nominally "single" proteins across populations. This information is usually unavailable with commonly used immunoassays such as ELISA (enzyme linked immunosorbent assay) which either ignore protein microheterogeneity, or are confounded by it. To this end, mass spectrometric immuno assays (MSIA) for three different human plasma proteins have been developed. These proteins viz. IGF-1, hemopexin and tetranectin have been found in reported literature to show correlations with many diseases along with several carcinomas. Developed assays were used to extract entire proteins from plasma samples and subsequently analyzed on mass spectrometric platforms. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric techniques where used due to their availability and suitability for the analysis. This resulted in visibility of different structural forms of these proteins showing their structural micro-heterogeneity which is invisible to commonly used immunoassays. These assays are fast, comprehensive and can be applied in large sample studies to analyze proteins for biomarker discovery.
ContributorsRai, Samita (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Borges, Chad (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2012
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Description
The transforming skills that lead to exceptional academic results are writing and research. While it is the role of academic librarians to provide the appropriate resources to facilitate research, arguably students are more willing to rely on their fellow students than professional library assistance. At Arizona State University’s Barrett, The

The transforming skills that lead to exceptional academic results are writing and research. While it is the role of academic librarians to provide the appropriate resources to facilitate research, arguably students are more willing to rely on their fellow students than professional library assistance. At Arizona State University’s Barrett, The Honors College, trained and motivated students are serving as Peer Mentors who assist student research needs without the "stigma" of asking a Librarian for help.

The panel discusses and elucidate components of a student-to-student peer program and cover comprehensive planning aspects of personnel, communication and workflow methodologies, interdisciplinary representation, and competency building activities. They will share training and work protocols, focusing on the evolution of the program from conceptualization through implementation. The presentation is an interactive conversation between the panelists (covering varying aspects and perspectives of the program) and the audience.
ContributorsOetting, Edward C. (Author) / Harp, Matthew (Author) / Hernandez, Maximilliano (Author)
Created2019-10-31
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Description
The ASU Library is actively building relationships around and increasing its expertise in research data services. We have established a collaboration with our university’s research administration in order to coordinate our distinct areas of expertise in research data services so that both entities can better support researchers all the way

The ASU Library is actively building relationships around and increasing its expertise in research data services. We have established a collaboration with our university’s research administration in order to coordinate our distinct areas of expertise in research data services so that both entities can better support researchers all the way through the research data lifecycle. The Library embedded itself into research administration’s learning management system and works with their research advancement officers to engage with researchers and staff we have not traditionally reached. Forging this new collaboration increased expectations that the Library will expand existing research data services to more investigators, so we have grown Library professionals’ internal competencies by providing research data management training opportunities to meet these demands. In addition, the Library’s Research Services Working Group established data competencies, workflows, and trainings so more librarians gain skills necessary to answer and assist patrons with data needs. Greater expertise throughout the Library enables us to authentically and confidently scale our research data services and form new collaborations.
The substance of this article is based upon a lightning talk given at RDAP Summit 2019.
ContributorsHarp, Matthew (Author) / Ogborn, Matt (Author)
Created2019-12-18
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Description
As academic libraries focus on delivering new services in such areas as research data, digital preservation, and data curation, they have begun to explore alternative funding models and approaches to research. The Arizona State University (ASU) Library in Tempe works with the university's Office of Knowledge Enterprise Development to collaborate

As academic libraries focus on delivering new services in such areas as research data, digital preservation, and data curation, they have begun to explore alternative funding models and approaches to research. The Arizona State University (ASU) Library in Tempe works with the university's Office of Knowledge Enterprise Development to collaborate and support ASU's researchers at scale. The library's ongoing collaboration and its specialized services, consultations, and training have led it to consider becoming a core facility, a centralized service that would provide consultation and other help to the university's researchers. As a core facility, the library would gain the ability to fund new initiatives and functions that would expand its reach and improve its support for research.
ContributorsOgborn, Matt (Author) / Harp, Matthew (Author) / Kurtz, Debra Hanken (Author)
Created2019-10
Description

In 2014/2015, Arizona State University (ASU) Libraries, the Labriola National American Indian Data Center, and the ASU American Indian Studies Department completed an ASU Institute for Humanities Research (IHR) seed grant entitled “Carlos Montezuma’s Wassaja Newsletter: Digitization, Access and Context” to digitize all ASU held issues of the newsletter Wassaja

In 2014/2015, Arizona State University (ASU) Libraries, the Labriola National American Indian Data Center, and the ASU American Indian Studies Department completed an ASU Institute for Humanities Research (IHR) seed grant entitled “Carlos Montezuma’s Wassaja Newsletter: Digitization, Access and Context” to digitize all ASU held issues of the newsletter Wassaja Freedom’s Signal for the Indian, which Yavapai activist-intellectual Carlos Montezuma, MD (1866-1923) self-published during 1916-1922. The grant team additionally selected a portion of the ASU Libraries Carlos Montezuma archival collection for digitization to provide a more complete picture of Dr. Carlos Montezuma’s life and work.

The ASU grant team produced a searchable online collection on the ASU Digital Repository and created an online exhibition in conjunction with the IHR Nexus Lab’s Developing Wassaja Project. The Nexus Lab’s role at ASU is to grow the digital humanities through interdisciplinary collaborations bringing together humanities, science, and technology. The Nexus Lab partnered with the grant team to create the Developing Wassaja Project which provided an opportunity for faculty, staff, and students at ASU to engage in electronic publication through web application development.

The resulting web platform, Wassaja: A Carlos Montezuma Project, provides context for this digitized collection and facilitates community interaction, including a partnership with Dr. Montezuma’s home community the Fort McDowell Yavapai Nation. In this webcast, Digital Projects Librarian Matthew Harp, Developing Wassaja Project team member Joe Buenker (subject librarian), and grant team member Joyce Martin (librarian and curator of the Labriola National American Indian Data Center) will discuss and demonstrate the resources created and the resulting partnership with the Fort McDowell Yavapai Nation. The webcast will focus on identifying collaborators and needed skills to engage in Digital Humanities research and on identifying the stages of a collaborative project.

Participants will gain insight on working directly with diverse communities; overcoming technical limitations of traditional institutional repositories; collaborative strategies with faculty, research centers, and cultural heritage societies; solutions for moving hidden collections into an engaging digital exhibition; integrating digital humanities research and instruction with library curation; and preparing for long term costs and management issues.

ContributorsHarp, Matthew (Author) / Martin, Joyce (Author) / Buenker, Joseph (Author)
Created2016-03-23
Description

Limited to streaming only those videos a vendor hosted, ASU Libraries sought to expand collection options with a trial project for hosting content locally. Kaltura, was selected as the platform, but Kaltura does not work out of the box. This presentation will cover how using Drupal, along with Kaltura, we

Limited to streaming only those videos a vendor hosted, ASU Libraries sought to expand collection options with a trial project for hosting content locally. Kaltura, was selected as the platform, but Kaltura does not work out of the box. This presentation will cover how using Drupal, along with Kaltura, we built a working video hosting solution. The presentation will cover administrative hurdles, stumbling blocks, pitfalls, enhancements, and lessons learned along the way.

ContributorsHarp, Matthew (Author) / farrelly, deg (Author) / Kurtz, Jeremy (Author) / Allgood, Tammy (Author)
Created2012-06-25
Description

While PhD dissertations are typically accessible many other terminal degree projects remain invisible and inaccessible to a greater audience. Over the past year and a half, librarians at Arizona State University collaborated with faculty and departmental administrators across a variety of fields to develop and create institutional repository collections that

While PhD dissertations are typically accessible many other terminal degree projects remain invisible and inaccessible to a greater audience. Over the past year and a half, librarians at Arizona State University collaborated with faculty and departmental administrators across a variety of fields to develop and create institutional repository collections that highlight and authoritatively share this type of student scholarship with schools, researchers, and future employers. This poster will present the benefits, challenges, and considerations required to successfully implement and manage these collections of applied final projects or capstone projects. Specifically, issues/challenges related to metadata consistency, faculty buy-in, and developing an ingest process, as well as benefits related to increased visibility and improved educational and employment opportunities will be discussed. This interactive presentation will also discuss lessons learned from the presenter’s experiences in context of how they can easily apply to benefit their respective institutions.

ContributorsHarp, Matthew (Author) / Dyal, Samuel (Author) / Pardon, Kevin (Author) / Arizona State University. ASU Library (Contributor)
Created2017-05-02
Description

This presentation highlights SHARE’s ongoing initiatives as a free, open data set about research and scholarly activities across their life cycle. It includes information about the SHARE open technology and the ongoing community contributions. A variety of data set use cases and their implementation will be described to allow others

This presentation highlights SHARE’s ongoing initiatives as a free, open data set about research and scholarly activities across their life cycle. It includes information about the SHARE open technology and the ongoing community contributions. A variety of data set use cases and their implementation will be described to allow others to apply similar tools and techniques to their home institution or organization. SHARE aggregates free, open metadata about scholarship that includes proposals, registrations, data, publications, and more from more than 125 sources including ASU.

ContributorsHarp, Matthew (Author) / Hudson-Vitale, Cynthia (Author) / Arizona State University. ASU Library (Contributor)
Created2017-04-19