Matching Items (21)

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The Giles Ecosystem – Storage, Text Extraction, and OCR of Documents

Description

In the digital humanities, there is a constant need to turn images and PDF files into plain text to apply analyses such as topic modelling, named entity recognition, and other

In the digital humanities, there is a constant need to turn images and PDF files into plain text to apply analyses such as topic modelling, named entity recognition, and other techniques. However, although there exist different solutions to extract text embedded in PDF files or run OCR on images, they typically require additional training (for example, scholars have to learn how to use the command line) or are difficult to automate without programming skills. The Giles Ecosystem is a distributed system based on Apache Kafka that allows users to upload documents for text and image extraction. The system components are implemented using Java and the Spring Framework and are available under an Open Source license on GitHub (https://github.com/diging/).

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Created

Date Created
  • 2017-09-28

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The Comet Cometh: Evolving Developmental Systems

Description

In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these

In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology (EvoDevo) may easily take another 100 years. He identifies methodological, epistemological, and social differences as causes for this supposed separation. Our article provides a contrasting view. We argue that Duboule’s prediction is based on a one-sided understanding of systems biology as a science that is only interested in functional, not evolutionary, aspects of biological processes. Instead, we propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems. We call this approach—which is based on reverse engineering, simulation, and mathematical analysis—the natural history of configuration space. We discuss a number of illustrative examples that demonstrate the past success of local exploration, as opposed to global mapping, in different biological contexts. We argue that this pragmatic mode of inquiry can be extended and applied to the mathematical analysis of the developmental repertoire and evolutionary potential of evolving developmental mechanisms and that evolutionary systems biology so conceived provides a pragmatic epistemological framework for the EvoDevo synthesis.

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Date Created
  • 2015-02-17

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Computational Analysis of Research in Mammalian Neocortical Neurogenesis

Description

Studies in neocortical neurogenesis have experienced an explosive growth since the early 2000s, measured by the increasing number of publications each year. I examine here the influence of Arnold Kriegstein

Studies in neocortical neurogenesis have experienced an explosive growth since the early 2000s, measured by the increasing number of publications each year. I examine here the influence of Arnold Kriegstein in the field using Topic Modeling, a set of algorithms that can be applied to a collection of texts to elucidate the central themes of said collection. Using a Java-based software called MALLET, I obtained data for his corpus, and compared it to the texts of other researchers in the field. This latter collection, which I dub "General Corpus", was separated by year from 2000 to 2014. I found that Kriegstein's most frequently discussed topic concerned highly unique terms such as GABA, glutamate, and receptor, which did not appear in any of the primary topics of the General Corpus. This was in contrast to my initial hypothesis that Kriegstein's importance stemmed from his examination of different phenomena that constitute the broader aspect of neocortical neurogenesis. I predicted that the terms in Kriegstein's primary topic would appear many times throughout the topics of the General Corpus, but it was not so, aside from the common ones such as neurons, cortical, and development. Taken in tandem with NIH Reporter data, these results suggest that Kriegstein obtains a large amount of research funding because his studies concern unique topics when compared to others in the field. The implications of these findings are especially relevant in a world where funding is becoming increasingly difficult to come by.

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Created

Date Created
  • 2015-05

Institutional Complexity and Efficiency: How Universities Scale

Description

As the US and the rest of the world face a growing need for affordable and accessible higher education, we must more deeply examine the scalability of our universities: how

As the US and the rest of the world face a growing need for affordable and accessible higher education, we must more deeply examine the scalability of our universities: how do they change with size? How do different institutional types vary? What makes ASU number one in innovation? At least two of these questions have immediate relevance to not only higher education, but political economy and sustainability as well. We apply to institutions the exciting complex systems framework of scaling, which has led to deep theoretical insight into the structure of biological systems and cities (West, Brown and Enquist 1997, Bettencourt 2013). First we group universities into seven distinct sectors, from public research universities to professional schools. Then we examine the returns to scale of university revenues, expenditures, and graduation rates, by correlating these key variables versus total enrollment. We discover that the sectors exhibit some important similarities, but overall leverage different economies of scale to serve their own priorities. These results imply shared mechanisms and constraints among the entire class of institutions. Furthermore, the uniqueness of each sector reveals their "speciation" into diverse institutional models, offering a fresh (though limited) first look at their scale-dependent complementary roles and competitive advantages. Accordingly, we outline what additional data and analyses might sufficiently strengthen these results to make recommendations, at levels ranging from student and family decisions to individual university strategies to sector-wide and system-wide policies. Promising future directions include longitudinal analysis of university growth patterns, detailed outlier analysis, and deeper theoretical investigation of mechanisms that drive the observed scaling.

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Created

Date Created
  • 2017-12

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From Monsters to Medicine: A Historical Analysis of Changes in the Field of Teratology Over the Twentieth Century

Description

This project focuses on the history of how teratogens, or agents which have the potential to cause birth defects, have been understood and tested for teratogenic potential in the US

This project focuses on the history of how teratogens, or agents which have the potential to cause birth defects, have been understood and tested for teratogenic potential in the US over the twentieth century. Prior to this time, teratogen studies were primarily concerned with cataloguing defects rather than exploring possible causes. At the turn of the twentieth century, experimental teratogen studies with the aim of elucidating mechanisms commenced. However, these early studies did not aim to discover human pregnancy outcomes and ways to prevent them, but simply focused on the results of exposing pregnant mammals to various physical and chemical insults. My project documents the change in understanding of teratogens over the twentieth century, the advancement of testing methods, and the causes of these advancements. Through the Embryo Project at Arizona State University (embryo.asu.edu), a digital encyclopedia for topics related to embryology, development, and reproductive medicine, I wrote ten encyclopedic articles that focused on chemical mechanisms of various teratogens, testing limitations in animal models, and legal and regulatory responses to well-known teratogens. As an extension of my previous work, this project bridges the current gap in research and focuses on contextualizing major events in the field of teratology to determine how these events led to various shifts in the understanding of birth defects and their causes, and how those conceptual shifts led to the creation of teratological testing guidelines. Results show that throughout the twentieth century, there are four distinct shifts in the understanding of teratogens: the first being 1900-1945, the second being 1946-1960, the third being 1961-1980, and the fourth being 1981-2000.

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Created

Date Created
  • 2014-05

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Cultural Competence in the Medical Education Cycle

Description

Mentions of diversity have become an essential part of every university and medical school’s mission statement. Yet, with such an emphasis on diversity, there is an evident absence of<br/>cultural competence

Mentions of diversity have become an essential part of every university and medical school’s mission statement. Yet, with such an emphasis on diversity, there is an evident absence of<br/>cultural competence education in the curricula of medical education. There is no clear answer of<br/>what is expected of physicians and no direct transitions for the different stages of medical<br/>training when it comes to cultural competence education. This is a vital issue, as there is a close<br/>relationship between the quality of patient care, patient adherence, and medical providers’ levels<br/>of cultural competence. This research analyzes the extent that cultural competence is taught at<br/>various points of the medical education cycle through a data analysis of an IRB approved<br/>questionnaire given to students within the medical education cycle and their value versus<br/>exposure of cultural competence.

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Created

Date Created
  • 2021-05

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Preliminary Results and the Unconsidered Potential of the 2014 Open Payments Research Dataset: Introducing a Complex Systems Framework for Extracting Meaningful Information from Big Data

Description

This work challenges the conventional perceptions surrounding the utility and use of the CMS Open Payments data. I suggest unconsidered methodologies for extracting meaningful information from these data following an

This work challenges the conventional perceptions surrounding the utility and use of the CMS Open Payments data. I suggest unconsidered methodologies for extracting meaningful information from these data following an exploratory analysis of the 2014 research dataset that, in turn, enhance its value as a public good. This dataset is favored for analysis over the general payments dataset as it is believed that generating transparency in the pharmaceutical and medical device R&D process would be of the greatest benefit to public health. The research dataset has been largely ignored by analysts and this may be one of the few works that have accomplished a comprehensive exploratory analysis of these data. If we are to extract valuable information from this dataset, we must alter both our approach as well as focus our attention towards re-conceptualizing the questions that we ask. Adopting the theoretical framework of complex systems serves as the foundation for our interpretation of the research dataset. This framework, in conjunction with a methodological toolkit for network analysis, may set a precedent for the development of alternative perspectives that allow for novel interpretations of the information that big data attempts to convey. By thus proposing a novel perspective in interpreting the information that this dataset contains, it is possible to gain insight into the emergent dynamics of the collaborative relationships that are established during the pharmaceutical and medical device R&D process.

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Created

Date Created
  • 2016-05

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University Student Knowledge and Perception of Influenza

Description

Influenza has shown its potential to affect and even kill millions of people within an extremely short time frame, yet studies and surveys show that the general public is not

Influenza has shown its potential to affect and even kill millions of people within an extremely short time frame, yet studies and surveys show that the general public is not well educated about the facts about influenza, including prevention and treatment. For this reason, public perception of influenza is extremely skewed, with people generally not taking the disease as seriously as they should given its severity. To investigate the inconsistencies between action and awareness of best available knowledge regarding influenza, this study conducted literature review and a survey of university students about their knowledge, perceptions, and action taken in relationship to influenza. Due to their dense living quarters, constant daily interactions, and mindset that they are "immune" to fairly common diseases like influenza, university students are a representative sample of urban populations. According to the World Health Organization (WHO), 54% of the world's population lived in cities as of 2014 (Urban population growth). Between 2015 and 2020, the global urban population is expected to grow 1.84% per year, 1.63% between 2020 and 2025, and 1.44% between 2025 and 2030 (Urban population growth). Similar projections estimate that by 2017, an overwhelming majority of the world's population, even in less developed countries, will be living in cities (Urban population growth). Results of this study suggest possible reasons for the large gap between best available knowledge and the perceptions and actions of individuals on the other hand. This may lead to better-oriented influenza education initiatives, more effective prevention and treatment plans, and generally raise excitement and awareness surrounding public health and scientific communication.

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Created

Date Created
  • 2014-12

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The Inimical Unintended Consequences of Fiduciary Duty, A Business Case for Sustainability

Description

Pressure from fiduciary duty leads agents within organizational systems to make decisions that result in positive feedback loops that often have inimical unintended consequences. The current corporate climate that often

Pressure from fiduciary duty leads agents within organizational systems to make decisions that result in positive feedback loops that often have inimical unintended consequences. The current corporate climate that often puts the bottom line ahead of environmental and social concerns in the name of fiduciary duty is doing so based on a revised interpretation of the term that is clearly to the benefit of the corporations. It is important to note that this modern interpretation is a radical misinterpretation of the intent of the law as our forefathers defined it. However, in spite of the fact that the modern interpretation is leading to inimical unintended consequences, providing the systems agents with the proper training and tools necessary to recognize the cost benefit of implementing sustainable solutions may mitigate some of these positive feedback loops and their associated unintended consequences. By developing tools based on sustainable frameworks we may be able to return these organizations to the original intent of fiduciary duty, which was designed to encourage investment in organizations that worked for the public benefit. A concept that is remarkably similar to the triple bottom line framework that many sustainability professionals advocate on behalf of today.

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Created

Date Created
  • 2015-05

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The Genesis Mechanism: an explorative undertaking across academic disciplines in the effort to synthesize a more comprehensive understanding of complexity and the role it has served in the gensis of life

Description

The field of biologic research is particularly concerned with understanding nature's complex dynamics. From deducing anatomical structures to studying behavioral patterns, evolutionary theory has developed greatly beyond the simple notions

The field of biologic research is particularly concerned with understanding nature's complex dynamics. From deducing anatomical structures to studying behavioral patterns, evolutionary theory has developed greatly beyond the simple notions proposed by Charles Darwin. However, because it rarely considers the concept of complexity, modern evolutionary theory retains some descriptive weakness. This project represents an explorative approach for considering complexity and whether it plays an active role in the development of biotic systems. A novel theoretical framework, titled the Genesis Mechanism, was formulated reconsidering the major tenets of evolutionary theory to include complexity as a universal tendency. Within this framework, a phenomenon, referred to as "social transitioning," occurs between higher orders of complexity. Several potential properties of social transitions were proposed and analyzed in order to validate the theoretical concepts proposed within the Genesis Mechanism. The successful results obtained through this project's completion help demonstrate the scientific necessity for understanding complexity from a more fundamental, biologic standpoint.

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Created

Date Created
  • 2013-05