cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1420620.v1
title: Clinical Strains of Listeria monocytogenes From the 2011 Cantaloupe Outbreak Show Evidence of Biofilm Formation on Cantaloupe Food-Conditioning Film

description: In 2011 an outbreak of listeriosis associated with cantaloupes was recorded as the deadliest foodborne disease outbreak in the United States in 90 years1. Interestingly, this was also the first recorded incident associated with cantaloupe, and one of comparatively few outbreaks of listeriosis associated with produce. It is known that Listeria monocytogenes can be isolated from food processing plants, and biofilm formation is thought to be a factor in how particular strains persist in these plants. Previous work from our lab2 has demonstrated that Listeria monocytogenes outbreak strains on food-conditioning films can grow to high cell densities to form biofilms composed of web-like extracellular polymeric substances. Therefore, we sought to identify biological factors that might facilitate Listeria monocytogenes biofilm formation on cantaloupe food-conditioning films. Four clinical strains associated with the cantaloupe outbreak were obtained from the Center for Disease Control and Prevention (CDC). Three of the four strains were also found in the cantaloupe processing plant. Molecular subtyping of the four outbreak strains revealed that they shared key molecular markers with isolates seen in previous outbreaks (Lomonaco et al., unpublished data). One outbreak strain represented a novel outbreak strain and the other three strains were identified as representing two novel epidemic clones. All strains were analyzed using an epifluorescence microscopy biofilm assay. Cantaloupe food-conditioning films enhanced biofilm formation, similar to that seen before with conditioning films made from ready-to-eat meat and poultry products. In particular, cantaloupe rind appeared to enhance attachment, growth and biofilm formation. Interestingly, there was some variability in the growth patterns of different strains, e.g. a strain containing the comK prophage region produced more extracellular polymeric substance. The two epidemic clones included serotype 1/2a and 1/2b strains that had also been previously isolated together from a poultry processing plant, and thus might represent a mix-serotype biofilm.
DOI: 10.6084/m9.figshare.1420576
title: Update to the Brenden et al. (2012) Statistical Catch-at-age Assessment for Chinook salmon in the Main Basin of Lake Huron

description: Bence, J. R., and Ji X. He. 2015. Update to the Brenden et al. (2012) Statistical Catch-at-age Assessment for Chinook salmon in the Main Basin of Lake Huron. Quantitative Fisheries Center Technical Report T2015-01. These reports available at the Quantitative Fisheries Center web site as of May 2015. This represents initial exploration of publishing these through figshare for permanence and wider distribution.
DOI: 10.6084/m9.figshare.1420577.v1
title: Physician Financial Relationships with Industry 2011

description: This dataset contains the industry payments and financial relationships with U.S. physicians from 432 for-profit companies that publically reported data. These data were derived from Kyruus, is a software-based solutions company that uses big data to optimize patient access and provider network operations for large health systems across the country. These data contain individual-level information on physicians’ financial relationships with industry in 2011, including companies from whom they received money, the monetary value of these interactions, and the reason for the financial tie (consulting, research funding, meals and travel, etc.). Additionally, these data include demographic information such as age, gender, medical specialty and primary location. We merged these individual-level data with institution-level data from the American Hospitals Association (AHA) 2011 Annual Survey (which has to be obtained independently due to liscense restrictions) and the National Institutes of Health (NIH) 2011 publically searchable database. Kyruus provided permission for data sharing.
DOI: 10.6084/m9.figshare.1420565
title: Analysis of genetic and environmental risk factors and their interactions in Korean patients with age-related macular degeneration

description: Purpose: To investigate the association of genetic and environmental factors, and their interactions in Korean patients with exudative age-related macular degeneration (AMD). Methods: A total of 314 robustly characterized exudative AMD patients, including 111 PCV (polypoidal choroidal vasculopathy) and 154 typical choroidal neovascularization (CNV), and 395 control subjects without any evidence of AMD were enrolled. Full ophthalmologic examinations including fluorescein angiography (FA), indocyanine green angiography (ICG) and optical coherence tomography (OCT) were done, according to which patients were divided into either PCV or typical CNV. Standardized questionnaires were used to collect information regarding underlying systemic diseases, dietary habits, smoking history and body mass index (BMI). A total of 86 SNPs from 31 candidate genes were analyzed. Genotype association and logistic regression analyses were done and stepwise regression models to best predict disease for each AMD subtype were constructed. Results: Age, spherical equivalent and ever smoking were associated with risk of exudative AMD (OR=1.034, 1.118 and 1.582, P=5.25E-05, 0.0084 and 0.0025, respectively). Age, hypertension and hyperlipidemia were risk factors for typical CNV (OR=1.049, 1.588 and 0.584, P=3.76E-06, 0.0154, and 0.0429, respectively) while increased education and ever smoking were significantly associated with PCV (OR=1.475 and 2.364, P=0.0002 and 9.89E-05, respectively). Four SNPs, ARMS2/HTRA1 rs10490924, rs11200638, and rs2736911, and CFH rs800292, showed association with exudative AMD. Two of these SNPs, ARMS2/HTRA1 rs10490924 and rs11200638, showed significant association with typical CNV and PCV specifically. There were no significant interactions between environmental and genetic factors. The most predictive disease model for exudative AMD included spherical equivalent (refractive error), smoking, CFH rs800292, and ARMS2 rs10490924 while that for typical CNV included age and ARMS2 rs10490924. Smoking, education, and ARMS2 rs10490924 were the most predictive variables for PCV. Conclusions: Only one locus, the ARMS2/HTRA1 was a significant genetic risk factor for Korean exudative AMD, including its subtypes, PCV and typical CNV. Stepwise regression revealed that CFH was important to risk of exudative AMD in general but not to any specific subtype. While increased education was a unique risk factor to PCV, this association was independent of refractive error in this homogenous population from South Korea. No significant interactions between environmental and genetic risk factors were observed.
DOI: 10.6084/m9.figshare.1420575
title: Post-fire recovery in the Cape Floristic Region of South Africa

description: This document describes the data associated with the manuscript <em>Climatic controls on ecosystem resilience: post-fire regeneration in the Cape Floristic Region of South Africa</em>.
DOI: 10.6084/m9.figshare.1420576.v1
title: Update to the Brenden et al. (2012) Statistical Catch-at-age Assessment for Chinook salmon in the Main Basin of Lake Huron

description: Bence, J. R., and Ji X. He. 2015. Update to the Brenden et al. (2012) Statistical Catch-at-age Assessment for Chinook salmon in the Main Basin of Lake Huron. Quantitative Fisheries Center Technical Report T2015-01. These reports available at the Quantitative Fisheries Center web site as of May 2015. This represents initial exploration of publishing these through figshare for permanence and wider distribution.
DOI: 10.6084/m9.figshare.1420565.v1
title: Analysis of genetic and environmental risk factors and their interactions in Korean patients with age-related macular degeneration

description: Purpose: To investigate the association of genetic and environmental factors, and their interactions in Korean patients with exudative age-related macular degeneration (AMD). Methods: A total of 314 robustly characterized exudative AMD patients, including 111 PCV (polypoidal choroidal vasculopathy) and 154 typical choroidal neovascularization (CNV), and 395 control subjects without any evidence of AMD were enrolled. Full ophthalmologic examinations including fluorescein angiography (FA), indocyanine green angiography (ICG) and optical coherence tomography (OCT) were done, according to which patients were divided into either PCV or typical CNV. Standardized questionnaires were used to collect information regarding underlying systemic diseases, dietary habits, smoking history and body mass index (BMI). A total of 86 SNPs from 31 candidate genes were analyzed. Genotype association and logistic regression analyses were done and stepwise regression models to best predict disease for each AMD subtype were constructed. Results: Age, spherical equivalent and ever smoking were associated with risk of exudative AMD (OR=1.034, 1.118 and 1.582, P=5.25E-05, 0.0084 and 0.0025, respectively). Age, hypertension and hyperlipidemia were risk factors for typical CNV (OR=1.049, 1.588 and 0.584, P=3.76E-06, 0.0154, and 0.0429, respectively) while increased education and ever smoking were significantly associated with PCV (OR=1.475 and 2.364, P=0.0002 and 9.89E-05, respectively). Four SNPs, ARMS2/HTRA1 rs10490924, rs11200638, and rs2736911, and CFH rs800292, showed association with exudative AMD. Two of these SNPs, ARMS2/HTRA1 rs10490924 and rs11200638, showed significant association with typical CNV and PCV specifically. There were no significant interactions between environmental and genetic factors. The most predictive disease model for exudative AMD included spherical equivalent (refractive error), smoking, CFH rs800292, and ARMS2 rs10490924 while that for typical CNV included age and ARMS2 rs10490924. Smoking, education, and ARMS2 rs10490924 were the most predictive variables for PCV. Conclusions: Only one locus, the ARMS2/HTRA1 was a significant genetic risk factor for Korean exudative AMD, including its subtypes, PCV and typical CNV. Stepwise regression revealed that CFH was important to risk of exudative AMD in general but not to any specific subtype. While increased education was a unique risk factor to PCV, this association was independent of refractive error in this homogenous population from South Korea. No significant interactions between environmental and genetic risk factors were observed.
DOI: 10.6084/m9.figshare.1420536
title: High resolution locomotor time series in Japanese quail in a home-cage environment over a 6.5 day period (# 11-group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has both a fractal pattern, as well as ultradian and circadian rhythms. <strong>This is the data from quail number 11, of the second experimental group.</strong> Note that in the total experiment the locomotor behavior of 24 quail was studied in two independent experimental groups. See details in project "Quail locomotor time series in a home-cage environment over a 6.5 day period sampled at 0.5s intervals."
DOI: 10.6084/m9.figshare.1420537
title: High resolution locomotor time series in Japanese quail in a home-cage environment over a 6.5 day period (# 12-group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has both a fractal pattern, as well as ultradian and circadian rhythms. This is the data from quail number 12, of the second experimental group. Note that in the total experiment the locomotor behavior of 24 quail was studied in two independent experimental groups. See details in project.
DOI: 10.6084/m9.figshare.1420534
title: High resolution locomotor time series in Japanese quail in a home-cage environment over a 6.5 day period (#9-group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has both a fractal pattern, as well as ultradian and circadian rhythms. <strong>This is the data from quail number 9, of the second experimental group.</strong> In this experiment in a whole, the locomotor activity of 24 adult females quail (100-140 days old) was evaluated in a home-cage environment in a white wooden box measuring 40 x 40 x 40 cm (width x length x height, respectively) with a wire mesh floor. A metal bar wall divided the box in two same-size zones (feeding, nesting), and an opening served as a door allowing the bird to move freely between compartments. A video camera that automatically switched to infrared recording after lights were turned off was suspended 1.5m above the box. It was connected to a computer in an adjacent room and could be accessed remotely by experimenters. Testing began at approximately 1:00 PM, when 12 quail were placed in a box, and transported to a nearby experimental room. Each bird was then placed individually in the feeding zone of one of the boxes. During the following 6.5 days, the birds’ locomotor activity was continuously recorded. Testing ended at 9 PM the 7th day. Daily maintenance activities (egg collection, cleaning and feeding) were performed between 12 and 12:30 PM; the activity during this period was not included in time series, which in total implied a loss of 2% from the data set. Since only 12 birds could be tested simultaneously, two consecutive groups of 12 individuals were evaluated (group 1 and group 2). We used the commercially available ANY-MAZE@ computer program to register locomotion at 0.5 s intervals (xi). The locomotor time series (1.07e6 time intervals) of each bird was obtained by assigning a number one (xi = 1) if during the interval the bird was ambulating, or a zero (xi = 0) if immobile. 0.5s intervals."
DOI: 10.6084/m9.figshare.1420535
title: High resolution locomotor time series in Japanese quail in a home-cage environment (#8 - group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has been shown to present both a fractal pattern, as well as ultradian and circadian rhythms.<strong> This is the data from quail number 5, of the second experimental group</strong>. In this experiment in a whole, the locomotor activity of 24 adult females quail (100-140 days old) was evaluated in a home-cage environment in a white wooden box measuring 40 x 40 x 40 cm (width x length x height, respectively) with a wire mesh floor. A metal bar wall divided the box in two same-size zones (feeding, nesting), and an opening served as a door allowing the bird to move freely between compartments. A video camera that automatically switched to infrared recording after lights were turned off was suspended 1.5m above the box. It was connected to a computer in an adjacent room and could be accessed remotely by experimenters. Testing began at approximately 1:00 PM, when 12 quail were placed in a box, and transported to a nearby experimental room. Each bird was then placed individually in the feeding zone of one of the boxes. During the following 6.5 days, the birds’ locomotor activity was continuously recorded. Testing ended at 9 PM the 7th day. Daily maintenance activities (egg collection, cleaning and feeding) were performed between 12 and 12:30 PM; the activity during this period was not included in time series, which in total implied a loss of 2% from the data set. Since only 12 birds could be tested simultaneously, two consecutive groups of 12 individuals were evaluated (group 1 and group 2). We used the commercially available ANY-MAZE@ computer program to register locomotion at 0.5 s intervals (xi). The locomotor time series (1.07e6 time intervals) of each bird was obtained by assigning a number one (xi = 1) if during the interval the bird was ambulating, or a zero (xi = 0) if immobile. 0.5s intervals."
DOI: 10.6084/m9.figshare.1420537.v2
title: High resolution locomotor time series in Japanese quail in a home-cage environment over a 6.5 day period (# 12-group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has both a fractal pattern, as well as ultradian and circadian rhythms. This is the data from quail number 12, of the second experimental group. Note that in the total experiment the locomotor behavior of 24 quail was studied in two independent experimental groups. See details in project.
DOI: 10.6084/m9.figshare.1420534.v2
title: High resolution locomotor time series in Japanese quail in a home-cage environment over a 6.5 day period (#9-group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has both a fractal pattern, as well as ultradian and circadian rhythms. <strong>This is the data from quail number 9, of the second experimental group.</strong> In this experiment in a whole, the locomotor activity of 24 adult females quail (100-140 days old) was evaluated in a home-cage environment in a white wooden box measuring 40 x 40 x 40 cm (width x length x height, respectively) with a wire mesh floor. A metal bar wall divided the box in two same-size zones (feeding, nesting), and an opening served as a door allowing the bird to move freely between compartments. A video camera that automatically switched to infrared recording after lights were turned off was suspended 1.5m above the box. It was connected to a computer in an adjacent room and could be accessed remotely by experimenters. Testing began at approximately 1:00 PM, when 12 quail were placed in a box, and transported to a nearby experimental room. Each bird was then placed individually in the feeding zone of one of the boxes. During the following 6.5 days, the birds’ locomotor activity was continuously recorded. Testing ended at 9 PM the 7th day. Daily maintenance activities (egg collection, cleaning and feeding) were performed between 12 and 12:30 PM; the activity during this period was not included in time series, which in total implied a loss of 2% from the data set. Since only 12 birds could be tested simultaneously, two consecutive groups of 12 individuals were evaluated (group 1 and group 2). We used the commercially available ANY-MAZE@ computer program to register locomotion at 0.5 s intervals (xi). The locomotor time series (1.07e6 time intervals) of each bird was obtained by assigning a number one (xi = 1) if during the interval the bird was ambulating, or a zero (xi = 0) if immobile. 0.5s intervals."
DOI: 10.6084/m9.figshare.1420535.v2
title: High resolution locomotor time series in Japanese quail in a home-cage environment (#8 - group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has been shown to present both a fractal pattern, as well as ultradian and circadian rhythms.<strong> This is the data from quail number 5, of the second experimental group</strong>. In this experiment in a whole, the locomotor activity of 24 adult females quail (100-140 days old) was evaluated in a home-cage environment in a white wooden box measuring 40 x 40 x 40 cm (width x length x height, respectively) with a wire mesh floor. A metal bar wall divided the box in two same-size zones (feeding, nesting), and an opening served as a door allowing the bird to move freely between compartments. A video camera that automatically switched to infrared recording after lights were turned off was suspended 1.5m above the box. It was connected to a computer in an adjacent room and could be accessed remotely by experimenters. Testing began at approximately 1:00 PM, when 12 quail were placed in a box, and transported to a nearby experimental room. Each bird was then placed individually in the feeding zone of one of the boxes. During the following 6.5 days, the birds’ locomotor activity was continuously recorded. Testing ended at 9 PM the 7th day. Daily maintenance activities (egg collection, cleaning and feeding) were performed between 12 and 12:30 PM; the activity during this period was not included in time series, which in total implied a loss of 2% from the data set. Since only 12 birds could be tested simultaneously, two consecutive groups of 12 individuals were evaluated (group 1 and group 2). We used the commercially available ANY-MAZE@ computer program to register locomotion at 0.5 s intervals (xi). The locomotor time series (1.07e6 time intervals) of each bird was obtained by assigning a number one (xi = 1) if during the interval the bird was ambulating, or a zero (xi = 0) if immobile. 0.5s intervals."
DOI: 10.6084/m9.figshare.1420536.v1
title: Long- high resolution locomotor time series quail (# 11-group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has both a fractal pattern, as well as ultradian and circadian rhythms. <strong>This is the data from quail number 11, of the second experimental group.</strong> Note that in the total experiment the locomotor behavior of 24 quail was studied in two independent experimental groups. See details in project "Quail locomotor time series in a home-cage environment over a 6.5 day period sampled at 0.5s intervals."
DOI: 10.6084/m9.figshare.1420537.v1
title: Long- high resolution locomotor time series quail (# 12-group 2)

description: Each data point represents a 0.5s time interval (xi) in which the quail could either been ambulating (xi=1) or immobile (xi=0), over a 6.5 day period .The total number of data points is approximately 1.070.000. This time series has both a fractal pattern, as well as ultradian and circadian rhythms. This is the data from quail number 12, of the second experimental group. Note that in the total experiment the locomotor behavior of 24 quail was studied in two independent experimental groups. See details in project.