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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

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/).
ContributorsLessios-Damerow, Julia (Contributor) / Peirson, Erick (Contributor) / Laubichler, Manfred (Contributor) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2017-09-28
Description

On-going efforts to understand the dynamics of coupled social-ecological (or more broadly, coupled infrastructure) systems and common pool resources have led to the generation of numerous datasets based on a large number of case studies. This data has facilitated the identification of important factors and fundamental principles which increase our

On-going efforts to understand the dynamics of coupled social-ecological (or more broadly, coupled infrastructure) systems and common pool resources have led to the generation of numerous datasets based on a large number of case studies. This data has facilitated the identification of important factors and fundamental principles which increase our understanding of such complex systems. However, the data at our disposal are often not easily comparable, have limited scope and scale, and are based on disparate underlying frameworks inhibiting synthesis, meta-analysis, and the validation of findings. Research efforts are further hampered when case inclusion criteria, variable definitions, coding schema, and inter-coder reliability testing are not made explicit in the presentation of research and shared among the research community. This paper first outlines challenges experienced by researchers engaged in a large-scale coding project; then highlights valuable lessons learned; and finally discusses opportunities for further research on comparative case study analysis focusing on social-ecological systems and common pool resources. Includes supplemental materials and appendices published in the International Journal of the Commons 2016 Special Issue. Volume 10 - Issue 2 - 2016.

ContributorsRatajczyk, Elicia (Author) / Brady, Ute (Author) / Baggio, Jacopo (Author) / Barnett, Allain J. (Author) / Perez Ibarra, Irene (Author) / Rollins, Nathan (Author) / Rubinos, Cathy (Author) / Shin, Hoon Cheol (Author) / Yu, David (Author) / Aggarwal, Rimjhim (Author) / Anderies, John (Author) / Janssen, Marco (Author) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2016-09-09
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Description

At the end of the dark ages, anatomy was taught as though everything that could be known was known. Scholars learned about what had been discovered rather than how to make discoveries. This was true even though the body (and the rest of biology) was very poorly understood. The renaissance

At the end of the dark ages, anatomy was taught as though everything that could be known was known. Scholars learned about what had been discovered rather than how to make discoveries. This was true even though the body (and the rest of biology) was very poorly understood. The renaissance eventually brought a revolution in how scholars (and graduate students) were trained and worked. This revolution never occurred in K-12 or university education such that we now teach young students in much the way that scholars were taught in the dark ages, we teach them what is already known rather than the process of knowing. Citizen science offers a way to change K-12 and university education and, in doing so, complete the renaissance. Here we offer an example of such an approach and call for change in the way students are taught science, change that is more possible than it has ever been and is, nonetheless, five hundred years delayed.

Created2016-03-01
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Description

Background: Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial

Background: Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rRNA gene PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the “buildings” in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons.

Results: Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rRNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project.

Conclusions: While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are OTU-rich with 1,036–4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

ContributorsLang, Jenna M. (Author) / Coil, David A. (Author) / Neches, Russell Y. (Author) / Brown, Wendy E. (Author) / Cavalier, Darlene (Author) / Severance, Mark (Author) / Hampton-Marcell, Jarrad T. (Author) / Gilbert, Jack A. (Author) / Eisen, Jonathan A. (Author) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2017-12-05
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Description

We find that the flow of attention on the Web forms a directed, tree-like structure implying the time-sensitive browsing behavior of users. Using the data of a news sharing website, we construct clickstream networks in which nodes are news stories and edges represent the consecutive clicks between two stories. To

We find that the flow of attention on the Web forms a directed, tree-like structure implying the time-sensitive browsing behavior of users. Using the data of a news sharing website, we construct clickstream networks in which nodes are news stories and edges represent the consecutive clicks between two stories. To identify the flow direction of clickstreams, we define the “flow distance” of nodes (Li), which measures the average number of steps a random walker takes to reach the ith node. It is observed that Li is related with the clicks (Ci) to news stories and the age (Ti) of stories. Putting these three variables together help us understand the rise and decay of news stories from a network perspective. We also find that the studied clickstream networks preserve a stable structure over time, leading to the scaling between users and clicks. The universal scaling behavior is confirmed by the 1,000 Web forums. We suggest that the tree-like, stable structure of clickstream networks reveals the time-sensitive preference of users in online browsing. To test our assumption, we discuss three models on individual browsing behavior, and compare the simulation results with empirical data.

ContributorsWang, Cheng-Jun (Author) / Wu, Lingfei (Author) / Zhang, Jiang (Author) / Janssen, Marco (Author) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2016-09-28
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Description

Many adaptive systems sit near a tipping or critical point. For systems near a critical point small changes to component behaviour can induce large-scale changes in aggregate structure and function. Criticality can be adaptive when the environment is changing, but entails reduced robustness through sensitivity. This tradeoff can be resolved

Many adaptive systems sit near a tipping or critical point. For systems near a critical point small changes to component behaviour can induce large-scale changes in aggregate structure and function. Criticality can be adaptive when the environment is changing, but entails reduced robustness through sensitivity. This tradeoff can be resolved when criticality can be tuned. We address the control of finite measures of criticality using data on fight sizes from an animal society model system (Macaca nemestrina, n=48). We find that a heterogeneous, socially organized system, like homogeneous, spatial systems (flocks and schools), sits near a critical point; the contributions individuals make to collective phenomena can be quantified; there is heterogeneity in these contributions; and distance from the critical point (DFC) can be controlled through biologically plausible mechanisms exploiting heterogeneity. We propose two alternative hypotheses for why a system decreases the distance from the critical point.

ContributorsDaniels, Bryan (Author) / Krakauer, David (Author) / Flack, Jessica (Author) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2017-02-10
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Description

National and state organizations have developed policies calling upon afterschool programs (ASPs, 3–6 pm) to serve a fruit or vegetable (FV) each day for snack, while eliminating foods and beverages high in added-sugars, and to ensure children accumulate a minimum of 30 min/d of moderate-to-vigorous physical activity (MVPA). Few efficacious

National and state organizations have developed policies calling upon afterschool programs (ASPs, 3–6 pm) to serve a fruit or vegetable (FV) each day for snack, while eliminating foods and beverages high in added-sugars, and to ensure children accumulate a minimum of 30 min/d of moderate-to-vigorous physical activity (MVPA). Few efficacious and cost-effective strategies exist to assist ASP providers in achieving these important public health goals. This paper reports on the design and conceptual framework of Making Healthy Eating and Physical Activity (HEPA) Policy Practice in ASPs, a 3-year group randomized controlled trial testing the effectiveness of strategies designed to improve snacks served and increase MVPA in children attending community-based ASPs. Twenty ASPs, serving over 1800 children (6–12 years) will be enrolled and match-paired based on enrollment size, average daily min/d MVPA, and days/week FV served, with ASPs randomized after baseline data collection to immediate intervention or a 1-year delayed group. The framework employed, STEPs (Strategies To Enhance Practice), focuses on intentional programming of HEPA in each ASPs' daily schedule, and includes a grocery store partnership to reduce price barriers to purchasing FV, professional development training to promote physical activity to develop core physical activity competencies, as well as ongoing technical support/assistance. Primary outcome measures include children's accelerometry-derived MVPA and time spend sedentary while attending an ASP, direct observation of staff HEPA promoting and inhibiting behaviors, types of snacks served, and child consumption of snacks, as well as, cost of snacks via receipts and detailed accounting of intervention delivery costs to estimate cost-effectiveness.

ContributorsBeets, Michael W. (Author) / Weaver, R. Glenn (Author) / Turner-McGrievy, Gabrielle (Author) / Huberty, Jennifer (Author) / Ward, Dianne S. (Author) / Freedman, Darcy A. (Author) / Saunders, Ruth (Author) / Pate, Russell R. (Author) / Beighle, Aaron (Author) / Hutto, Brent (Author) / Moore, Justin B. (Author) / College of Health Solutions (Contributor)
Created2014-07-01
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Description

Background: GoGirlGo! (GGG) is designed to increase girls’ physical activity (PA) using a health behavior and PA-based curriculum and is widely available for free to afterschool programs across the nation. However, GGG has not been formally evaluated. The purpose of this pilot study was to evaluate the effectiveness of the GGG

Background: GoGirlGo! (GGG) is designed to increase girls’ physical activity (PA) using a health behavior and PA-based curriculum and is widely available for free to afterschool programs across the nation. However, GGG has not been formally evaluated. The purpose of this pilot study was to evaluate the effectiveness of the GGG curricula to improve PA, and self-efficacy for and enjoyment of PA in elementary aged girls (i.e., 5-13 years).

Methods: Nine afterschool programs were recruited to participate in the pilot (within subjects repeated measures design). GGG is a 12-week program, with a once a week, one-hour lesson with 30 minutes of education and 30 minutes of PA). Data collection occurred at baseline, mid (twice), post, and at follow-up (3-months after the intervention ended). PA was assessed via accelerometry at each time point. Self-efficacy for and enjoyment of PA was measured using the Self-Efficacy Scale and the Short-PA enjoyment scale and was assessed at baseline, post, and follow-up. Fidelity was assessed at midpoint.

Results: Across all age groups there was a statistically significant increase in PA. Overall, on days GGG was offered girls accumulated an average of 11 minutes of moderate-to-vigorous PA compared to 8 minutes during non-GGG days. There was a statistically significant difference in girls’ self-efficacy for PA reported between baseline and post, which was maintained at follow-up. An improvement in enjoyment of PA for girls was found between baseline and follow-up. According to fidelity assessment, 89% of the activities within the curriculum were completed each lesson. Girls appeared to respond well to the curriculum but girls 5-7 years had difficulties paying attention and understanding discussion questions.

Conclusions: Even though there were statistically significant differences in self-efficacy for PA and enjoyment of PA, minimal increases in girls’ PA were observed. GGG curricula improvements are warranted. Future GGG programming should explore offering GGG every day, modifying activities so that they are moderate-to-vigorous in intensity, and providing additional trainings that allow staff to better implement PA and improve behavior management techniques. With modifications, GGG could provide a promising no-cost curriculum that afterschool programs may implement to help girls achieve recommendations for PA.

ContributorsHuberty, Jennifer (Author) / Dinkel, Danae M. (Author) / Beets, Michael W. (Author) / College of Health Solutions (Contributor)
Created2014-02-05
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Description

Sequential affect dynamics generated during the interaction of intimate dyads, such as married couples, are associated with a cascade of effects - some good and some bad - on each partner, close family members, and other social contacts. Although the effects are well documented, the probabilistic structures associated with micro-social

Sequential affect dynamics generated during the interaction of intimate dyads, such as married couples, are associated with a cascade of effects - some good and some bad - on each partner, close family members, and other social contacts. Although the effects are well documented, the probabilistic structures associated with micro-social processes connected to the varied outcomes remain enigmatic. Using extant data we developed a method of classifying and subsequently generating couple dynamics using a Hierarchical Dirichlet Process Hidden semi-Markov Model (HDP-HSMM). Our findings indicate that several key aspects of existing models of marital interaction are inadequate: affect state emissions and their durations, along with the expected variability differences between distressed and nondistressed couples are present but highly nuanced; and most surprisingly, heterogeneity among highly satisfied couples necessitate that they be divided into subgroups. We review how this unsupervised learning technique generates plausible dyadic sequences that are sensitive to relationship quality and provide a natural mechanism for computational models of behavioral and affective micro-social processes.

ContributorsGriffin, William (Author) / Li, Xun (Author) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2016-05-17
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Description

Online communities are becoming increasingly important as platforms for large-scale human cooperation. These communities allow users seeking and sharing professional skills to solve problems collaboratively. To investigate how users cooperate to complete a large number of knowledge-producing tasks, we analyze Stack Exchange, one of the largest question and answer systems

Online communities are becoming increasingly important as platforms for large-scale human cooperation. These communities allow users seeking and sharing professional skills to solve problems collaboratively. To investigate how users cooperate to complete a large number of knowledge-producing tasks, we analyze Stack Exchange, one of the largest question and answer systems in the world. We construct attention networks to model the growth of 110 communities in the Stack Exchange system and quantify individual answering strategies using the linking dynamics on attention networks. We identify two answering strategies. Strategy A aims at performing maintenance by doing simple tasks, whereas strategy B aims at investing time in doing challenging tasks. Both strategies are important: empirical evidence shows that strategy A decreases the median waiting time for answers and strategy B increases the acceptance rate of answers. In investigating the strategic persistence of users, we find that users tends to stick on the same strategy over time in a community, but switch from one strategy to the other across communities. This finding reveals the different sets of knowledge and skills between users. A balance between the population of users taking A and B strategies that approximates 2:1, is found to be optimal to the sustainable growth of communities.

ContributorsWu, Lingfei (Author) / Baggio, Jacopo (Author) / Janssen, Marco (Author) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2016-03-02