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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

This study explored the relation between visual processing and word-decoding ability in a normal reading population. Forty participants were recruited at Arizona State University. Flicker fusion thresholds were assessed with an optical chopper using the method of limits by a 1-deg diameter green (543 nm) test field. Word decoding was

This study explored the relation between visual processing and word-decoding ability in a normal reading population. Forty participants were recruited at Arizona State University. Flicker fusion thresholds were assessed with an optical chopper using the method of limits by a 1-deg diameter green (543 nm) test field. Word decoding was measured using reading-word and nonsense-word decoding tests. A non-linguistic decoding measure was obtained using a computer program that consisted of Landolt C targets randomly presented in four cardinal orientations, at 3-radial distances from a focus point, for eight compass points, in a circular pattern. Participants responded by pressing the arrow key on the keyboard that matched the direction the target was facing. The results show a strong correlation between critical flicker fusion thresholds and scores on the reading-word, nonsense-word, and non-linguistic decoding measures. The data suggests that the functional elements of the visual system involved with temporal modulation and spatial processing may affect the ease with which people read.

ContributorsHolloway, Steven (Author) / Nanez, Jose (Author) / Seitz, Aaron R. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2013-12-20
Description

The World Health Organization recently proposed the inclusion of brominated congeners in addition to chlorinated congeners when computing the toxic equivalency (TEQ) of dioxin-like compounds (DLCs) in assessments of human health risks. In the present study, 12 polybrominated dibenzo-p-dioxins and furans (PBDD/Fs) were analyzed by gas chromatography/high resolution mass spectrometry

The World Health Organization recently proposed the inclusion of brominated congeners in addition to chlorinated congeners when computing the toxic equivalency (TEQ) of dioxin-like compounds (DLCs) in assessments of human health risks. In the present study, 12 polybrominated dibenzo-p-dioxins and furans (PBDD/Fs) were analyzed by gas chromatography/high resolution mass spectrometry in the composited, archived biosolids that were collected in 32 U.S. states and the District of Columbia from 94 wastewater treatment plants by the United States Environmental Protection Agency in its 2001 national sewage sludge survey. Two PBDDs and five PBDFs were detected in the biosolids composites at varying frequencies (40–100%) with a total mean concentration of 10,000 ng/kg dry weight (range: 630–42,800), of which 1,2,3,4,6,7,8-hepta-BDF constituted about 95% by mass. Relative to commercial polybrominated diphenyl ether (PBDE) formulations, the ratio of PBDD/Fs to PBDEs in biosolids was 55-times higher (∼0.002% vs ∼0.11%), which indicates potential PBDE transformation or possibly additional sources of PBDD/Fs in the environment. The TEQ contribution of PBDD/Fs was estimated at 162 ng/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (range: 15–672), which is equivalent to 75% (range: 12–96%) of the total TEQ in biosolids. The TEQ of DLCs released annually to U.S. soils as a result of the land application of biosolids was estimated at 720 g (range: 530–1600 g). Among all known DLCs determined in biosolids, brominated analogs contributed 370% more TEQ than did chlorinated congeners, which indicates the need to include brominated DLCs in the exposure and risk assessment of land-applied biosolids.

ContributorsVenkatesan, Arjunkrishna (Author) / Halden, Rolf (Author) / Center for Environmental Security (Contributor)
Created2014-09-16
Description

Widespread contamination of groundwater by chlorinated ethenes and their biological dechlorination products necessitates the reliable monitoring of liquid matrices; current methods approved by the U.S. Environmental Protection Agency (EPA) require a minimum of 5 mL of sample volume and cannot simultaneously detect all transformative products. This paper reports on the

Widespread contamination of groundwater by chlorinated ethenes and their biological dechlorination products necessitates the reliable monitoring of liquid matrices; current methods approved by the U.S. Environmental Protection Agency (EPA) require a minimum of 5 mL of sample volume and cannot simultaneously detect all transformative products. This paper reports on the simultaneous detection of six chlorinated ethenes and ethene itself, using a liquid sample volume of 1 mL by concentrating the compounds onto an 85-µm carboxen-polydimenthylsiloxane solid-phase microextraction fiber in 5 min and subsequent chromatographic analysis in 9.15 min. Linear increases in signal response were obtained over three orders of magnitude (∼0.05 to ∼50 µM) for simultaneous analysis with coefficient of determination (R2) values of ≥ 0.99. The detection limits of the method (1.3–6 µg/L) were at or below the maximum contaminant levels specified by the EPA. Matrix spike studies with groundwater and mineral medium showed recovery rates between 79–108%. The utility of the method was demonstrated in lab-scale sediment flow-through columns assessing the bioremediation potential of chlorinated ethene-contaminated groundwater. Owing to its low sample volume requirements, good sensitivity and broad target analyte range, the method is suitable for routine compliance monitoring and is particularly attractive for interpreting the bench-scale feasibility studies that are commonly performed during the remedial design stage of groundwater cleanup projects.

ContributorsZiv-El, Michal (Author) / Kalinowski, Tomasz (Author) / Krajmalnik-Brown, Rosa (Author) / Halden, Rolf (Author) / Biodesign Institute (Contributor)
Created2014-02-01
Description

Important antibiotics in human medicine have been used for many decades in animal agriculture for growth promotion and disease treatment. Several publications have linked antibiotic resistance development and spread with animal production. Aquaculture, the newest and fastest growing food production sector, may promote similar or new resistance mechanisms. This review

Important antibiotics in human medicine have been used for many decades in animal agriculture for growth promotion and disease treatment. Several publications have linked antibiotic resistance development and spread with animal production. Aquaculture, the newest and fastest growing food production sector, may promote similar or new resistance mechanisms. This review of 650+ papers from diverse sources examines parallels and differences between land-based agriculture of swine, beef, and poultry and aquaculture. Among three key findings was, first, that of 51 antibiotics commonly used in aquaculture and agriculture, 39 (or 76%) are also of importance in human medicine; furthermore, six classes of antibiotics commonly used in both agriculture and aquaculture are also included on the World Health Organization’s (WHO) list of critically important/highly important/important antimicrobials. Second, various zoonotic pathogens isolated from meat and seafood were observed to feature resistance to multiple antibiotics on the WHO list, irrespective of their origin in either agriculture or aquaculture. Third, the data show that resistant bacteria isolated from both aquaculture and agriculture share the same resistance mechanisms, indicating that aquaculture is contributing to the same resistance issues established by terrestrial agriculture. More transparency in data collection and reporting is needed so the risks and benefits of antibiotic usage can be adequately assessed.

ContributorsDone, Hansa (Author) / Venkatesan, Arjunkrishna (Author) / Halden, Rolf (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2015-05-01
Description

A meta-analysis was conducted to inform the epistemology, or theory of knowledge, of contaminants of emerging concern (CECs). The CEC terminology acknowledges the existence of harmful environmental agents whose identities, occurrences, hazards, and effects are not sufficiently understood. Here, data on publishing activity were analyzed for 12 CECs, revealing a

A meta-analysis was conducted to inform the epistemology, or theory of knowledge, of contaminants of emerging concern (CECs). The CEC terminology acknowledges the existence of harmful environmental agents whose identities, occurrences, hazards, and effects are not sufficiently understood. Here, data on publishing activity were analyzed for 12 CECs, revealing a common pattern of emergence, suitable for identifying past years of peak concern and forecasting future ones: dichlorodiphenyltrichloroethane (DDT; 1972, 2008), trichloroacetic acid (TCAA; 1972, 2009), nitrosodimethylamine (1984), methyl tert-butyl ether (2001), trichloroethylene (2005), perchlorate (2006), 1,4-dioxane (2009), prions (2009), triclocarban (2010), triclosan (2012), nanomaterials (by 2016), and microplastics (2022 ± 4). CECs were found to emerge from obscurity to the height of concern in 14.1 ± 3.6 years, and subside to a new baseline level of concern in 14.5 ± 4.5 years. CECs can emerge more than once (e.g., TCAA, DDT) and the multifactorial process of emergence may be driven by inception of novel scientific methods (e.g., ion chromatography, mass spectrometry and nanometrology), scientific paradigm shifts (discovery of infectious proteins), and the development, marketing and mass consumption of novel products (antimicrobial personal care products, microplastics and nanomaterials). Publishing activity and U.S. regulatory actions were correlated for several CECs investigated.

ContributorsHalden, Rolf (Author) / Biodesign Institute (Contributor)
Created2015-01-23
Description

Processed municipal sewage sludges (MSS) are an abundant, unwanted by-product of wastewater treatment, increasingly applied to agriculture and forestry for inexpensive disposal and soil conditioning. Due to their high organic carbon and lipid contents, MSS not only is rich in carbon and nutrients but also represents a “sink” for recalcitrant,

Processed municipal sewage sludges (MSS) are an abundant, unwanted by-product of wastewater treatment, increasingly applied to agriculture and forestry for inexpensive disposal and soil conditioning. Due to their high organic carbon and lipid contents, MSS not only is rich in carbon and nutrients but also represents a “sink” for recalcitrant, hydrophobic, and potentially bioaccumulative compounds. Indeed, many organics sequestered and concentrated in MSS meet the US Environmental Protection Agency’s definition of being persistent, bioaccumulative, and toxic (PBT). In a strategic effort, our research team at the Biodesign Institute has created the National Sewage Sludge Repository (NSSR), a large repository of digested MSSs from 164 wastewater treatment plants from across the USA, as part of the Human Health Observatory (H2O) at Arizona State University (ASU). The NSSR likely represents the largest archive of digested MSS specimens in the USA. The present study summarizes key findings gleaned thus far from analysis of NSSR samples. For example, we evaluated the content of toxicants in MSS and computed estimates of nationwide inventories of mass produced chemicals that become sequestrated in sludge and later are released into the environment during sludge disposal on land. Ongoing efforts document co-occurrence of a variety of PBT compounds in both MSS and human samples, while also identifying a large number of potentially harmful MSS constituents for which human exposure data are still lacking. Finally, we summarize future opportunities and invite collaborative use of the NSSR by the research community. The H2O at ASU represents a new resource and research tool for environmental scientists and the larger research community. As illustrated in this work, this repository can serve to (i) identify and prioritize emerging contaminants, (ii) provide spatial and temporal trends of contaminants, (iii) inform and evaluate the effectiveness of environmental policy-making and regulations, and (iv) approximate, ongoing exposures and body burdens of mass-produced chemicals in human society.

ContributorsVenkatesan, Arjunkrishna (Author) / Done, Hansa (Author) / Halden, Rolf (Author) / Biodesign Institute (Contributor)
Created2015-02-01
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

Perchloroethylene (PCE) is a highly utilized solvent in the dry cleaning industry because of its cleaning effectiveness and relatively low cost to consumers. According to the 2006 U.S. Census, approximately 28,000 dry cleaning operations used PCE as their principal cleaning agent. Widespread use of PCE is problematic because of its

Perchloroethylene (PCE) is a highly utilized solvent in the dry cleaning industry because of its cleaning effectiveness and relatively low cost to consumers. According to the 2006 U.S. Census, approximately 28,000 dry cleaning operations used PCE as their principal cleaning agent. Widespread use of PCE is problematic because of its adverse impacts on human health and environmental quality. As PCE use is curtailed, effective alternatives must be analyzed for their toxicity and impacts to human health and the environment. Potential alternatives to PCE in dry cleaning include dipropylene glycol n-butyl ether (DPnB) and dipropylene glycol tert-butyl ether (DPtB), both promising to pose a relatively smaller risk. To evaluate these two alternatives to PCE, we established and scored performance criteria, including chemical toxicity, employee and customer exposure levels, impacts on the general population, costs of each system, and cleaning efficacy. The scores received for PCE were 5, 5, 3, 5, 3, and 3, respectively, and DPnB and DPtB scored 3, 1, 2, 2, 4, and 4, respectively. An aggregate sum of the performance criteria yielded a favorably low score of “16” for both DPnB and DPtB compared to “24” for PCE. We conclude that DPnB and DPtB are preferable dry cleaning agents, exhibiting reduced human toxicity and a lesser adverse impact on human health and the environment compared to PCE, with comparable capital investments, and moderately higher annual operating costs.

ContributorsHesari, Nikou (Author) / Francis, Chelsea (Author) / Halden, Rolf (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-04-03
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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