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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
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Description

Humans are able to modulate digit forces as a function of position despite changes in digit placement that might occur from trial to trial or when changing grip type for object manipulation. Although this phenomenon is likely to rely on sensing the position of the digits relative to each other

Humans are able to modulate digit forces as a function of position despite changes in digit placement that might occur from trial to trial or when changing grip type for object manipulation. Although this phenomenon is likely to rely on sensing the position of the digits relative to each other and the object, the underlying mechanisms remain unclear. To address this question, we asked subjects (n = 30) to match perceived vertical distance between the center of pressure (CoP) of the thumb and index finger pads (dy) of the right hand (“reference” hand) using the same hand (“test” hand). The digits of reference hand were passively placed collinearly (dy = 0 mm). Subjects were then asked to exert different combinations of normal and tangential digit forces (Fn and Ftan, respectively) using the reference hand and then match the memorized dy using the test hand. The reference hand exerted Ftan of thumb and index finger in either same or opposite direction. We hypothesized that, when the tangential forces of the digits are produced in opposite directions, matching error (1) would be biased toward the directions of the tangential forces; and (2) would be greater when the remembered relative contact points are matched with negligible digit force production. For the test hand, digit forces were either negligible (0.5–1 N, 0 ± 0.25 N; Experiment 1) or the same as those exerted by the reference hand (Experiment 2).Matching error was biased towards the direction of digit tangential forces: thumb CoP was placed higher than the index finger CoP when thumb and index finger Ftan were directed upward and downward, respectively, and vice versa (p < 0.001). However, matching error was not dependent on whether the reference and test hand exerted similar or different forces. We propose that the expected sensory consequence of motor commands for tangential forces in opposite directions overrides estimation of fingertip position through haptic sensory feedback.

ContributorsShibata, Daisuke (Author) / Kappers, Astrid M. L. (Author) / Santello, Marco (Author) / College of Health Solutions (Contributor)
Created2014-08-04
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Description

Recent studies about sensorimotor control of the human hand have focused on how dexterous manipulation is learned and generalized. Here we address this question by testing the extent to which learned manipulation can be transferred when the contralateral hand is used and/or object orientation is reversed. We asked subjects to

Recent studies about sensorimotor control of the human hand have focused on how dexterous manipulation is learned and generalized. Here we address this question by testing the extent to which learned manipulation can be transferred when the contralateral hand is used and/or object orientation is reversed. We asked subjects to use a precision grip to lift a grip device with an asymmetrical mass distribution while minimizing object roll during lifting by generating a compensatory torque. Subjects were allowed to grasp anywhere on the object’s vertical surfaces, and were therefore able to modulate both digit positions and forces. After every block of eight trials performed in one manipulation context (i.e., using the right hand and at a given object orientation), subjects had to lift the same object in the second context for one trial (transfer trial).

Context changes were made by asking subjects to switch the hand used to lift the object and/or rotate the object 180° about a vertical axis. Therefore, three transfer conditions, hand switch (HS), object rotation (OR), and both hand switch and object rotation (HS+OR), were tested and compared with hand matched control groups who did not experience context changes. We found that subjects in all transfer conditions adapted digit positions across multiple transfer trials similar to the learning of control groups, regardless of different changes of contexts. Moreover, subjects in both HS and HS+OR group also adapted digit forces similar to the control group, suggesting independent learning of the left hand. In contrast, the OR group showed significant negative transfer of the compensatory torque due to an inability to adapt digit forces. Our results indicate that internal representations of dexterous manipulation tasks may be primarily built through the hand used for learning and cannot be transferred across hands.

ContributorsFu, Qiushi (Author) / Choi, Jason (Author) / Gordon, Andrew M. (Author) / Jesunathadas, Mark (Author) / Santello, Marco (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-09-18
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Description

MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3′untranslated regions (3′UTRs) of mRNAs. Individual miRNAs can regulate networks of hundreds of genes, yet for the majority of miRNAs few, if any, targets are known. Misexpression of miRNAs is

MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3′untranslated regions (3′UTRs) of mRNAs. Individual miRNAs can regulate networks of hundreds of genes, yet for the majority of miRNAs few, if any, targets are known. Misexpression of miRNAs is also a major contributor to cancer progression, thus there is a critical need to validate miRNA targets in high-throughput to understand miRNAs' contribution to tumorigenesis. Here we introduce a novel high-throughput assay to detect miRNA targets in 3′UTRs, called Luminescent Identification of Functional Elements in 3′UTRs (3′LIFE). We demonstrate the feasibility of 3′LIFE using a data set of 275 human 3′UTRs and two cancer-relevant miRNAs, let-7c and miR-10b, and compare our results to alternative methods to detect miRNA targets throughout the genome. We identify a large number of novel gene targets for these miRNAs, with only 32% of hits being bioinformatically predicted and 27% directed by non-canonical interactions. Functional analysis of target genes reveals consistent roles for each miRNA as either a tumor suppressor (let-7c) or oncogenic miRNA (miR-10b), and preferentially target multiple genes within regulatory networks, suggesting 3′LIFE is a rapid and sensitive method to detect miRNA targets in high-throughput.

ContributorsWolter, Justin (Author) / Kotagama, Kasuen (Author) / Pierre-Bez, Alexandra C. (Author) / Firago, Mari (Author) / Mangone, Marco (Author) / College of Liberal Arts and Sciences (Contributor)
Created2014-09-29
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Description

Sensorimotor control theories propose that the central nervous system exploits expected sensory consequences generated by motor commands for movement planning, as well as online sensory feedback for comparison with expected sensory feedback for monitoring and correcting, if needed, ongoing motor output. In our study, we tested this theoretical framework by

Sensorimotor control theories propose that the central nervous system exploits expected sensory consequences generated by motor commands for movement planning, as well as online sensory feedback for comparison with expected sensory feedback for monitoring and correcting, if needed, ongoing motor output. In our study, we tested this theoretical framework by quantifying the functional role of expected vs. actual proprioceptive feedback for planning and regulation of gait in humans. We addressed this question by using a novel methodological approach to deliver fast perturbations of the walking surface stiffness, in conjunction with a virtual reality system that provided visual feedback of upcoming changes of surface stiffness. In the “predictable” experimental condition, we asked subjects to learn associating visual feedback of changes in floor stiffness (sand patch) during locomotion to quantify kinematic and kinetic changes in gait prior to and during the gait cycle. In the “unpredictable” experimental condition, we perturbed floor stiffness at unpredictable instances during the gait to characterize the gait-phase dependent strategies in recovering the locomotor cycle. For the “unpredictable” conditions, visual feedback of changes in floor stiffness was absent or inconsistent with tactile and proprioceptive feedback. The investigation of these perturbation-induced effects on contralateral leg kinematics revealed that visual feedback of upcoming changes in floor stiffness allows for both early (preparatory) and late (post-perturbation) changes in leg kinematics. However, when proprioceptive feedback is not available, the early responses in leg kinematics do not occur while the late responses are preserved although in a, slightly attenuated form. The methods proposed in this study and the preliminary results of the kinematic response of the contralateral leg open new directions for the investigation of the relative role of visual, tactile, and proprioceptive feedback on gait control, with potential implications for designing novel robot-assisted gait rehabilitation approaches.

ContributorsFrost, Ryan (Author) / Skidmore, Jeffrey (Author) / Santello, Marco (Author) / Artemiadis, Panagiotis (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2015-02-09
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Description

What's a profession without a code of ethics? Being a legitimate profession almost requires drafting a code and, at least nominally, making members follow it. Codes of ethics (henceforth “codes”) exist for a number of reasons, many of which can vary widely from profession to profession - but above all

What's a profession without a code of ethics? Being a legitimate profession almost requires drafting a code and, at least nominally, making members follow it. Codes of ethics (henceforth “codes”) exist for a number of reasons, many of which can vary widely from profession to profession - but above all they are a form of codified self-regulation. While codes can be beneficial, it argues that when we scratch below the surface, there are many problems at their root. In terms of efficacy, codes can serve as a form of ethical window dressing, rather than effective rules for behavior. But even more that, codes can degrade the meaning behind being a good person who acts ethically for the right reasons.

Created2013-11-30
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Description

The intact nervous system has an exquisite ability to modulate the activity of multiple muscles acting at one or more joints to produce an enormous range of actions. Seemingly simple tasks, such as reaching for an object or walking, in fact rely on very complex spatial and temporal patterns of

The intact nervous system has an exquisite ability to modulate the activity of multiple muscles acting at one or more joints to produce an enormous range of actions. Seemingly simple tasks, such as reaching for an object or walking, in fact rely on very complex spatial and temporal patterns of muscle activations. Neurological disorders such as stroke and focal dystonia affect the ability to coordinate multi-joint movements. This article reviews the state of the art of research of muscle synergies in the intact and damaged nervous system, their implications for recovery and rehabilitation, and proposes avenues for research aimed at restoring the nervous system’s ability to control movement.

ContributorsSantello, Marco (Author) / Lang, Catherine E. (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2015-01-06
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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
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Description

Studies have shown that internal representations of manipulations of objects with asymmetric mass distributions that are generated within a specific orientation are not generalizable to novel orientations, i.e., subjects fail to prevent object roll on their first grasp-lift attempt of the object following 180° object rotation. This suggests that representations

Studies have shown that internal representations of manipulations of objects with asymmetric mass distributions that are generated within a specific orientation are not generalizable to novel orientations, i.e., subjects fail to prevent object roll on their first grasp-lift attempt of the object following 180° object rotation. This suggests that representations of these manipulations are specific to the reference frame in which they are formed. However, it is unknown whether that reference frame is specific to the hand, the body, or both, because rotating the object 180° modifies the relation between object and body as well as object and hand. An alternative, untested explanation for the above failure to generalize learned manipulations is that any rotation will disrupt grasp performance, regardless if the reference frame in which the manipulation was learned is maintained or modified. We examined the effect of rotations that (1) maintain and (2) modify relations between object and body, and object and hand, on the generalizability of learned two-digit manipulation of an object with an asymmetric mass distribution. Following rotations that maintained the relation between object and body and object and hand (e.g., rotating the object and subject 180°), subjects continued to use appropriate digit placement and load force distributions, thus generating sufficient compensatory moments to minimize object roll. In contrast, following rotations that modified the relation between (1) object and hand (e.g. rotating the hand around to the opposite object side), (2) object and body (e.g. rotating subject and hand 180°), or (3) both (e.g. rotating the subject 180°), subjects used the same, yet inappropriate digit placement and load force distribution, as those used prior to the rotation. Consequently, the compensatory moments were insufficient to prevent large object rolls. These findings suggest that representations of learned manipulation of objects with asymmetric mass distributions are specific to the body- and hand-reference frames in which they were learned.

ContributorsMarneweck, Michelle (Author) / Knelange, Elisabeth (Author) / Lee-Miller, Trevor (Author) / Santello, Marco (Author) / Gordon, Andrew M. (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2015-09-16
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Description

Background: Counselor behaviors that mediate the efficacy of motivational interviewing (MI) are not well understood, especially when applied to health behavior promotion. We hypothesized that client change talk mediates the relationship between counselor variables and subsequent client behavior change.

Methods: Purposeful sampling identified individuals from a prospective randomized worksite trial using an MI

Background: Counselor behaviors that mediate the efficacy of motivational interviewing (MI) are not well understood, especially when applied to health behavior promotion. We hypothesized that client change talk mediates the relationship between counselor variables and subsequent client behavior change.

Methods: Purposeful sampling identified individuals from a prospective randomized worksite trial using an MI intervention to promote firefighters’ healthy diet and regular exercise that increased dietary intake of fruits and vegetables (n = 21) or did not increase intake of fruits and vegetables (n = 22). MI interactions were coded using the Motivational Interviewing Skill Code (MISC 2.1) to categorize counselor and firefighter verbal utterances. Both Bayesian and frequentist mediation analyses were used to investigate whether client change talk mediated the relationship between counselor skills and behavior change.

Results: Counselors’ global spirit, empathy, and direction and MI-consistent behavioral counts (e.g., reflections, open questions, affirmations, emphasize control) significantly correlated with firefighters’ total client change talk utterances (rs = 0.42, 0.40, 0.30, and 0.61, respectively), which correlated significantly with their fruit and vegetable intake increase (r = 0.33). Both Bayesian and frequentist mediation analyses demonstrated that findings were consistent with hypotheses, such that total client change talk mediated the relationship between counselor’s skills—MI-consistent behaviors [Bayesian mediated effect: αβ = .06 (.03), 95% CI = .02, .12] and MI spirit [Bayesian mediated effect: αβ = .06 (.03), 95% CI = .01, .13]—and increased fruit and vegetable consumption.

Conclusion: Motivational interviewing is a resource- and time-intensive intervention, and is currently being applied in many arenas. Previous research has identified the importance of counselor behaviors and client change talk in the treatment of substance use disorders. Our results indicate that similar mechanisms may underlie the effects of MI for dietary change. These results inform MI training and application by identifying those processes critical for MI success in health promotion domains.

ContributorsPirlott, Angela (Author) / Kisbu-Sakarya, Yasemin (Author) / DeFrancesco, Carol A. (Author) / Elliot, Diane L. (Author) / MacKinnon, David (Author) / College of Liberal Arts and Sciences (Contributor)
Created2012-06-08