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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

Periodicities (repeating patterns) are observed in many human behaviors. Their strength may capture untapped patterns that incorporate sleep, sedentary, and active behaviors into a single metric indicative of better health. We present a framework to detect periodicities from longitudinal wrist-worn accelerometry data. GENEActiv accelerometer data were collected from 20 participants

Periodicities (repeating patterns) are observed in many human behaviors. Their strength may capture untapped patterns that incorporate sleep, sedentary, and active behaviors into a single metric indicative of better health. We present a framework to detect periodicities from longitudinal wrist-worn accelerometry data. GENEActiv accelerometer data were collected from 20 participants (17 men, 3 women, aged 35–65) continuously for 64.4±26.2 (range: 13.9 to 102.0) consecutive days. Cardiometabolic risk biomarkers and health-related quality of life metrics were assessed at baseline. Periodograms were constructed to determine patterns emergent from the accelerometer data. Periodicity strength was calculated using circular autocorrelations for time-lagged windows. The most notable periodicity was at 24 h, indicating a circadian rest-activity cycle; however, its strength varied significantly across participants. Periodicity strength was most consistently associated with LDL-cholesterol (r’s = 0.40–0.79, P’s < 0.05) and triglycerides (r’s = 0.68–0.86, P’s < 0.05) but also associated with hs-CRP and health-related quality of life, even after adjusting for demographics and self-rated physical activity and insomnia symptoms. Our framework demonstrates a new method for characterizing behavior patterns longitudinally which captures relationships between 24 h accelerometry data and health outcomes.

ContributorsBuman, Matthew (Author) / Hu, Feiyan (Author) / Newman, Eamonn (Author) / Smeaton, Alan F. (Author) / Epstein, Dana R. (Author) / College of Health Solutions (Contributor)
Created2016-01-04
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Description

Background: Falls are a major public health concern in older adults. Recent fall prevention guidelines recommend the use of multifactorial fall prevention programs (FPPs) that include exercise for community-dwelling older adults; however, the availability of sustainable, community-based FPPs is limited.

Methods: We conducted a 24-week quasi-experimental study to evaluate the efficacy

Background: Falls are a major public health concern in older adults. Recent fall prevention guidelines recommend the use of multifactorial fall prevention programs (FPPs) that include exercise for community-dwelling older adults; however, the availability of sustainable, community-based FPPs is limited.

Methods: We conducted a 24-week quasi-experimental study to evaluate the efficacy of a community-based, multifactorial FPP [Stay in Balance (SIB)] on dynamic and functional balance and muscular strength. The SIB program was delivered by allied health students and included a health education program focused on fall risk factors and a progressive exercise program emphasizing lower-extremity strength and balance. All participants initially received the 12-week SIB program, and participants were non-randomly assigned at baseline to either continue the SIB exercise program at home or as a center-based program for an additional 12 weeks. Adults aged 60 and older (n = 69) who were at-risk of falling (fall history or 2+ fall risk factors) were recruited to participate. Mixed effects repeated measures using Statistical Application Software Proc Mixed were used to examine group, time, and group-by-time effects on dynamic balance (8-Foot Up and Go), functional balance (Berg Balance Scale), and muscular strength (30 s chair stands and 30 s arm curls). Non-normally distributed outcome variables were log-transformed.

Results: After adjusting for age, gender, and body mass index, 8-Foot Up and Go scores, improved significantly over time [F(2,173) = 8.92, p = 0.0; T0 − T2 diff = 1.2 (1.0)]. Berg Balance Scores [F(2,173) = 29.0, p < 0.0001; T0 − T2 diff = 4.96 (0.72)], chair stands [F(2,171) = 10.17, p < 0.0001; T0 − T2 diff = 3.1 (0.7)], and arm curls [F(2,171) = 12.7, p < 0.02; T0 − T2 diff = 2.7 (0.6)] also all improved significantly over time. There were no significant group-by-time effects observed for any of the outcomes.

Conclusion: The SIB program improved dynamic and functional balance and muscular strength in older adults at-risk for falling. Our findings indicate continuing home-based strength and balance exercises at home after completion of a center-based FPP program may be an effective and feasible way to maintain improvements in balance and strength parameters.

ContributorsDer Ananian, Cheryl (Author) / Mitros, Melanie (Author) / Buman, Matthew (Author) / College of Health Solutions (Contributor)
Created2017-02-27
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Description

We present a new approach to computing event shape distributions or, more precisely, charge flow correlations in a generic conformal field theory (CFT). These infrared finite observables are familiar from collider physics studies and describe the angular distribution of global charges in outgoing radiation created from the vacuum by some

We present a new approach to computing event shape distributions or, more precisely, charge flow correlations in a generic conformal field theory (CFT). These infrared finite observables are familiar from collider physics studies and describe the angular distribution of global charges in outgoing radiation created from the vacuum by some source. The charge flow correlations can be expressed in terms of Wightman correlation functions in a certain limit. We explain how to compute these quantities starting from their Euclidean analogues by means of a nontrivial analytic continuation which, in the framework of CFT, can be performed elegantly in Mellin space. The relation between the charge flow correlations and Euclidean correlation functions can be reformulated directly in configuration space, bypassing the Mellin representation, as a certain Lorentzian double discontinuity of the correlation function integrated along the cuts. We illustrate the general formalism in N = 4 SYM, making use of the well-known results on the four-point correlation function of half-BPS scalar operators. We compute the double scalar flow correlation in N = 4 SYM, at weak and strong coupling and show that it agrees with known results obtained by different techniques. One of the remarkable features of the N = 4 theory is that the scalar and energy flow correlations are proportional to each other. Imposing natural physical conditions on the energy flow correlations (finiteness, positivity and regularity), we formulate additional constraints on the four-point correlation functions in N = 4SYM that should be valid at any coupling and away from the planar limit.

ContributorsBelitsky, Andrei (Author) / Hohenegger, S. (Author) / Korchemsky, G. P. (Author) / Sokatchev, E. (Author) / Zhiboedov, A. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2014-04-30
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Description

The Operator Product Expansion for null polygonal Wilson loop in planar maximally supersymmetric Yang–Mills theory runs systematically in terms of multi-particle pentagon transitions which encode the physics of excitations propagating on the color flux tube ending on the sides of the four-dimensional contour. Their dynamics was unraveled in the past

The Operator Product Expansion for null polygonal Wilson loop in planar maximally supersymmetric Yang–Mills theory runs systematically in terms of multi-particle pentagon transitions which encode the physics of excitations propagating on the color flux tube ending on the sides of the four-dimensional contour. Their dynamics was unraveled in the past several years and culminated in a complete description of pentagons as an exact function of the 't Hooft coupling. In this paper we provide a solution for the last building block in this program, the SU(4) matrix structure arising from internal symmetry indices of scalars and fermions. This is achieved by a recursive solution of the Mirror and Watson equations obeyed by the so-called singlet pentagons and fixing the form of the twisted component in their tensor decomposition. The non-singlet, or charged, pentagons are deduced from these by a limiting procedure.

ContributorsBelitsky, Andrei (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-08-31
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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 address the near-collinear expansion of NMHV six-particle scattering amplitudes at strong value of the 't Hooft coupling in planar maximally supersymmetric Yang–Mills theory. We complement recent studies of this observable within the context of the Pentagon Operator Product Expansion, via the dual superWilson loop description, by studying effects of

We address the near-collinear expansion of NMHV six-particle scattering amplitudes at strong value of the 't Hooft coupling in planar maximally supersymmetric Yang–Mills theory. We complement recent studies of this observable within the context of the Pentagon Operator Product Expansion, via the dual superWilson loop description, by studying effects of multiple scalar exchanges that accompany (or not) massive flux-tube excitations. Due to the fact that holes have a very small, nonperturbatively generated mass mh which is exponentially suppressed in the 't Hooft coupling, their exchanges must be resummed in the ultraviolet limit, T <<1/mh. This procedure yields a contribution to the expectation value of the superloop which enters on equal footing with the classical area — a phenomenon which was earlier observed for MHV amplitudes. In all components, the near-massless scalar exchanges factorize from the ones of massive particles, at leading order in strong coupling.

ContributorsBelitsky, Andrei (Author) / College of Liberal Arts and Sciences (Contributor)
Created2016-08-20
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Description

Scattering amplitudes in maximally supersymmetric gauge theory receive a dual description in terms of the expectation value of the super Wilson loop stretched on a null polygonal contour. This makes the analysis amenable to nonperturbative techniques. Presently, we elaborate on a refined form of the operator product expansion in terms

Scattering amplitudes in maximally supersymmetric gauge theory receive a dual description in terms of the expectation value of the super Wilson loop stretched on a null polygonal contour. This makes the analysis amenable to nonperturbative techniques. Presently, we elaborate on a refined form of the operator product expansion in terms of pentagon transitions to compute twist-two contributions to NMHV amplitudes. To start with, we provide a novel derivation of scattering matrices starting from Baxter equations for flux-tube excitations propagating on magnon background. We propose bootstrap equations obeyed by pentagon form factors with nonsinglet quantum numbers with respect to the R-symmetry group and provide solutions to them to all orders in 't Hooft coupling. These are then successfully confronted against available perturbative calculations for NMHV amplitudes to four-loop order.

ContributorsBelitsky, Andrei (Author) / College of Liberal Arts and Sciences (Contributor)
Created2015-05-05