Search results

Title: Multi-stage optimization of a deep model: A case study on ground motion modeling..
Creator: Tahmassebi, Amirhessam, Gandomi, Amir H, Fong, Simon, Meyer-Baese, Anke, Foo, Simon Y
Abstract/Description: In this study, a multi-stage optimization procedure is proposed to develop deep neural network models which results in a powerful deep learning pipeline called intelligent deep learning (iDeepLe). The proposed pipeline is then evaluated by a challenging real-world problem, the modeling of the spectral acceleration experienced by a particle during earthquakes. This approach has three main stages to optimize the deep model topology, the hyper-parameters, and its performance, respectively. This...
Show moreIn this study, a multi-stage optimization procedure is proposed to develop deep neural network models which results in a powerful deep learning pipeline called intelligent deep learning (iDeepLe). The proposed pipeline is then evaluated by a challenging real-world problem, the modeling of the spectral acceleration experienced by a particle during earthquakes. This approach has three main stages to optimize the deep model topology, the hyper-parameters, and its performance, respectively. This pipeline optimizes the deep model via adaptive learning rate optimization algorithms for both accuracy and complexity in multiple stages, while simultaneously solving the unknown parameters of the regression model. Among the seven adaptive learning rate optimization algorithms, Nadam optimization algorithm has shown the best performance results in the current study. The proposed approach is shown to be a suitable tool to generate solid models for this complex real-world system. The results also show that the parallel pipeline of iDeepLe has the capacity to handle big data problems as well.
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Date Issued: 2018-09-19
Identifier: FSU_pmch_30231077, 10.1371/journal.pone.0203829, PMC6145533, 30231077, 30231077, PONE-D-18-08965
Format: Citation

Title: Bias caused by sampling error in meta-analysis with small sample sizes.
Creator: Lin, Lifeng
Abstract/Description: Meta-analyses frequently include studies with small sample sizes. Researchers usually fail to account for sampling error in the reported within-study variances; they model the observed study-specific effect sizes with the within-study variances and treat these sample variances as if they were the true variances. However, this sampling error may be influential when sample sizes are small. This article illustrates that the sampling error may lead to substantial bias in meta-analysis results. We...
Show moreMeta-analyses frequently include studies with small sample sizes. Researchers usually fail to account for sampling error in the reported within-study variances; they model the observed study-specific effect sizes with the within-study variances and treat these sample variances as if they were the true variances. However, this sampling error may be influential when sample sizes are small. This article illustrates that the sampling error may lead to substantial bias in meta-analysis results. We conducted extensive simulation studies to assess the bias caused by sampling error. Meta-analyses with continuous and binary outcomes were simulated with various ranges of sample size and extents of heterogeneity. We evaluated the bias and the confidence interval coverage for five commonly-used effect sizes (i.e., the mean difference, standardized mean difference, odds ratio, risk ratio, and risk difference). Sampling error did not cause noticeable bias when the effect size was the mean difference, but the standardized mean difference, odds ratio, risk ratio, and risk difference suffered from this bias to different extents. The bias in the estimated overall odds ratio and risk ratio was noticeable even when each individual study had more than 50 samples under some settings. Also, Hedges' g, which is a bias-corrected estimate of the standardized mean difference within studies, might lead to larger bias than Cohen's d in meta-analysis results. Cautions are needed to perform meta-analyses with small sample sizes. The reported within-study variances may not be simply treated as the true variances, and their sampling error should be fully considered in such meta-analyses.
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Date Issued: 2018-09-13
Identifier: FSU_pmch_30212588, 10.1371/journal.pone.0204056, PMC6136825, 30212588, 30212588, PONE-D-18-14403
Format: Citation

Title: Interactive effects of precipitation and nitrogen enrichment on multi-trophic dynamics in plant-arthropod communities.
Creator: Griffith, Kaitlin A, Grinath, Joshua B
Abstract/Description: Patterns of precipitation and nitrogen (N) deposition are changing in ecosystems worldwide. Simultaneous increases in precipitation and N deposition can relieve co-limiting soil resource conditions for plants and result in synergistic plant responses, which may affect animals and plant responses to higher trophic levels. However, the potential for synergistic effects of precipitation and N deposition on animals and plant responses to herbivores and predators (via trophic cascades) is unclear....
Show morePatterns of precipitation and nitrogen (N) deposition are changing in ecosystems worldwide. Simultaneous increases in precipitation and N deposition can relieve co-limiting soil resource conditions for plants and result in synergistic plant responses, which may affect animals and plant responses to higher trophic levels. However, the potential for synergistic effects of precipitation and N deposition on animals and plant responses to herbivores and predators (via trophic cascades) is unclear. We investigated the influence of precipitation and N enrichment on ecological dynamics across three trophic levels, hypothesizing that herbivores and plants would exhibit synergistic responses to the combined influence of precipitation, N amendments and predators. To test this, we conducted a field experiment with arthropods on two model plant species, Nicotiana tabacum and Nicotiana rustica. First, we characterized the plant-arthropod assemblages, finding that N. tabacum hosted greater abundances of caterpillars, while N. rustica hosted more sap-sucking herbivores. Next, we evaluated the effects of rainwater, soil N, and predatory spider manipulations for both plant-arthropod assemblages. On N. tabacum, water and N availability had an interactive effect on caterpillars, where caterpillars were most abundant with rainwater additions and least abundant when both rainwater and N were added. For N. rustica, foliar chemistry had a synergistic response to all three experimental factors. Compared to spider-absent conditions, leaf N concentration increased and C/N decreased when spiders were present, but this response only occurred under high water and N availability. Spiders indirectly altered plant chemistry via a facilitative effect of spiders on sap-sucking herbivores, potentially due to intra-guild predation, and a positive effect of sap-suckers on foliar N concentration. Our study suggests that predictions of the ecological impacts of altered precipitation and N deposition may need to account for the effects of resource co-limitation on dynamics across trophic levels.
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Date Issued: 2018-08-02
Identifier: FSU_pmch_30070991, 10.1371/journal.pone.0201219, PMC6072000, 30070991, 30070991, PONE-D-17-40079
Format: Citation

Title: An experimental study of turtle shell rattle production and the implications for archaeofaunal assemblages.
Creator: Gillreath-Brown, Andrew, Peres, Tanya M
Abstract/Description: Turtle shell rattles are percussion instruments used by Indigenous peoples of the Americas in ceremonial contexts to keep rhythm. Archaeological investigations in the southeastern United States produced several complete and partial Eastern box turtle (Terrapene carolina) shell rattles from mortuary contexts dating from the Archaic (ca. 8000-1000 BC) through Mississippian periods (ca. AD 800-1500). Fragmentary turtle remains, some identified as Eastern box turtle, are frequently recovered from...
Show moreTurtle shell rattles are percussion instruments used by Indigenous peoples of the Americas in ceremonial contexts to keep rhythm. Archaeological investigations in the southeastern United States produced several complete and partial Eastern box turtle (Terrapene carolina) shell rattles from mortuary contexts dating from the Archaic (ca. 8000-1000 BC) through Mississippian periods (ca. AD 800-1500). Fragmentary turtle remains, some identified as Eastern box turtle, are frequently recovered from non-mortuary contexts. Traditionally, these fragmentary remains are attributed to food waste. Given the archaeological and ethnographic evidence for turtle shell rattles, we need to consider how fragmentary remains might fit into the chaîne opératoire of rattle production. This paper presents the results of an experimental study designed to identify one such chaîne opératoire of rattle production. During this experiment, the data on taphonomic processes such as manufacturing marks, use-wear, and breakage patterns, were recorded. We then tested the taphonomic findings from the experimental study and an object trait list we compiled from known rattle specimens and documentary sources with archaeological turtle remains recovered from non-mortuary contexts at two Mississippian period (ca. AD 1000-1450) sites in Middle Tennessee. Historic indigenous groups are known to have, and still do into the present-day, make and use turtle shell rattles in the region. Ultimately, we determined that "food refuse" should not be the default interpretation of fragmentary box turtle remains, and instead the taphonomic history and contextual associations must be considered in full. The experimental process of crafting turtle shell rattles enhances our understanding of an ancient musical instrument and the success rate of identifying musical artifacts and distinguishing between other modified turtle remains in the archaeological record. This study expands our knowledge of ancient music in North America and prompts re-analysis of curated turtle remains in museums for rattle-related modifications.
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Date Issued: 2018-08-02
Identifier: FSU_pmch_30071068, 10.1371/journal.pone.0201472, PMC6072095, 30071068, 30071068, PONE-D-18-01501
Format: Citation

Title: Pockets of progress amidst persistent racial disparities in low birthweight rates.
Creator: Goldfarb, Samantha S, Houser, Kelsey, Wells, Brittny A, Brown Speights, Joedrecka S, Beitsch, Les, Rust, George
Abstract/Description: Racial disparities persist in adverse perinatal outcomes such as preterm birth, low birthweight (LBW), and infant mortality across the U.S. Although pervasive, these disparities are not universal. Some communities have experienced significant improvements in black (or African American) birth outcomes, both in absolute rates and in rate ratios relative to whites. This study assessed county-level progress on trends in black and white LBW rates as an indicator of progress toward more equal birth...
Show moreRacial disparities persist in adverse perinatal outcomes such as preterm birth, low birthweight (LBW), and infant mortality across the U.S. Although pervasive, these disparities are not universal. Some communities have experienced significant improvements in black (or African American) birth outcomes, both in absolute rates and in rate ratios relative to whites. This study assessed county-level progress on trends in black and white LBW rates as an indicator of progress toward more equal birth outcomes for black infants. County-level LBW data were obtained from the 2003 to 2013 U.S. Natality files. Black LBW rates, black-white rate ratios and percent differences over time were calculated. Trend lines were first assessed for significant differences in slope (i.e., converging, diverging, or parallel trend lines). For counties with parallel trend lines, intercepts were tested for statistically significant differences (sustained equality vs. persistent disparities). To assess progress, black LBW rates were compared to white LBW rates, and the trend lines were tested for significant decline. Each county's progress toward black-white equality was ultimately categorized into five possible trend patterns (n = 408): (1) converging LBW rates with reductions in the black LBW rate (decreasing disparities, n = 4, 1%); (2) converging LBW rates due to worsening white LBW rates (n = 5, 1%); (3) diverging LBW rates (increasing disparities, n = 9, 2%); (4) parallel LBW rates (persistent disparities, n = 373, 91%); and (5) overlapping trend lines (sustained equality, n = 18, 4%). Only four counties demonstrated improvement toward equality with decreasing black LBW rates. There is significant county-level variation in progress toward racial equality in adverse birth outcomes such as low birthweight. Still, some communities are demonstrating that more equitable outcomes are possible. Further research is needed in these positive exemplar communities to identify what works in accelerating progress toward more equal birth outcomes.
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Date Issued: 2018-07-31
Identifier: FSU_pmch_30063767, 10.1371/journal.pone.0201658, PMC6067759, 30063767, 30063767, PONE-D-18-00353
Format: Citation

Title: A new approach for incorporating 15N isotopic data into linear inverse ecosystem models with Markov Chain Monte Carlo sampling.
Creator: Stukel, Michael R, Décima, Moira, Kelly, Thomas B
Abstract/Description: Oceanographic field programs often use δ15N biogeochemical measurements and in situ rate measurements to investigate nitrogen cycling and planktonic ecosystem structure. However, integrative modeling approaches capable of synthesizing these distinct measurement types are lacking. We develop a novel approach for incorporating δ15N isotopic data into existing Markov Chain Monte Carlo (MCMC) random walk methods for solving linear inverse ecosystem models. We test the ability of this approach to...
Show moreOceanographic field programs often use δ15N biogeochemical measurements and in situ rate measurements to investigate nitrogen cycling and planktonic ecosystem structure. However, integrative modeling approaches capable of synthesizing these distinct measurement types are lacking. We develop a novel approach for incorporating δ15N isotopic data into existing Markov Chain Monte Carlo (MCMC) random walk methods for solving linear inverse ecosystem models. We test the ability of this approach to recover food web indices (nitrate uptake, nitrogen fixation, zooplankton trophic level, and secondary production) derived from forward models simulating the planktonic ecosystems of the California Current and Amazon River Plume. We show that the MCMC with δ15N approach typically does a better job of recovering ecosystem structure than the standard MCMC or L2 minimum norm (L2MN) approaches, and also outperforms an L2MN with δ15N approach. Furthermore, we find that the MCMC with δ15N approach is robust to the removal of input equations and hence is well suited to typical pelagic ecosystem studies for which the system is usually vastly under-constrained. Our approach is easily extendable for use with δ13C isotopic measurements or variable carbon:nitrogen stoichiometry.
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Date Issued: 2018-06-18
Identifier: FSU_pmch_29912928, 10.1371/journal.pone.0199123, PMC6005467, 29912928, 29912928, PONE-D-18-03219
Format: Citation

Title: Looking behind the score: Skill structure explains sex differences in skilled video game performance..
Creator: Harwell, Kyle W, Boot, Walter R, Ericsson, K Anders
Abstract/Description: Some have explained large sex differences in visuospatial abilities by genetic adaptations to different roles in primitive hunter-gatherer societies and the interaction of innate biological differences and environmental factors. We explored the extent to which variations in behavior and acquired skills can provide alternative accounts for sex differences in the performance of a complex spatially-demanding video game (Space Fortress). Men and women with limited video game experience were given...
Show moreSome have explained large sex differences in visuospatial abilities by genetic adaptations to different roles in primitive hunter-gatherer societies and the interaction of innate biological differences and environmental factors. We explored the extent to which variations in behavior and acquired skills can provide alternative accounts for sex differences in the performance of a complex spatially-demanding video game (Space Fortress). Men and women with limited video game experience were given 30 hours of training, and latent curve analyses examined the development of their ship control performance and behavior. Men had significantly better control performance than women before and after training, but differences diminished substantially over the training period. An analysis of participants' joystick behaviors revealed that initially men and women relied on different patterns of control behaviors, but changes in these behaviors over time accounted for the reduced sex differences in performance. When we controlled for these differences in behavior, sex effects after training were no longer significant. Finally, examining the development of control performance and control behaviors of men and women categorized as initially high and low performers revealed the lower-performing women may have been controlling their ship using an approach that was very different from the men and higher-performing women. The potential problems of analyzing men and women's spatial performance as homogenous groups are discussed, as well as how these issues may account for sex differences in skilled video game performance and perhaps other domains involving spatial abilities.
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Date Issued: 2018-05-30
Identifier: FSU_pmch_29847565, 10.1371/journal.pone.0197311, PMC5976164, 29847565, 29847565, PONE-D-17-30687
Format: Citation

Title: Attention and working memory deficits in a perinatal nicotine exposure mouse model.
Creator: Zhang, Lin, Spencer, Thomas J, Biederman, Joseph, Bhide, Pradeep G
Abstract/Description: Cigarette smoking by pregnant women is associated with a significant increase in the risk for cognitive disorders in their children. Preclinical models confirm this risk by showing that exposure of the developing brain to nicotine produces adverse behavioral outcomes. Here we describe behavioral phenotypes resulting from perinatal nicotine exposure in a mouse model, and discuss our findings in the context of findings from previously published studies using preclinical models of developmental...
Show moreCigarette smoking by pregnant women is associated with a significant increase in the risk for cognitive disorders in their children. Preclinical models confirm this risk by showing that exposure of the developing brain to nicotine produces adverse behavioral outcomes. Here we describe behavioral phenotypes resulting from perinatal nicotine exposure in a mouse model, and discuss our findings in the context of findings from previously published studies using preclinical models of developmental nicotine exposure. Female C57Bl/6 mice received drinking water containing nicotine (100μg/ml) + saccharin (2%) starting 3 weeks prior to breeding and continuing throughout pregnancy, and until 3 weeks postpartum. Over the same period, female mice in two control groups received drinking water containing saccharin (2%) or plain drinking water. Offspring from each group were weaned at 3-weeks of age and subjected to behavioral analyses at 3 months of age. We examined spontaneous locomotor activity, anxiety-like behavior, spatial working memory, object based attention, recognition memory and impulsive-like behavior. We found significant deficits in attention and working memory only in male mice, and no significant changes in the other behavioral phenotypes in male or female mice. Exposure to saccharin alone did not produce significant changes in either sex. The perinatal nicotine exposure produced significant deficits in attention and working memory in a sex-dependent manner in that the male but not female offspring displayed these behaviors. These behavioral phenotypes are associated with attention deficit hyperactivity disorder (ADHD) and have been reported in other studies that used pre- or perinatal nicotine exposure. Therefore, we suggest that preclinical models of developmental nicotine exposure could be useful tools for modeling ADHD and related disorders.
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Date Issued: 2018-05-24
Identifier: FSU_pmch_29795664, 10.1371/journal.pone.0198064, PMC5967717, 29795664, 29795664, PONE-D-17-44266
Format: Citation

Title: Isotope niche dimension and trophic overlap between bigheaded carps and native filter-feeding fish in the lower Missouri River, USA.
Creator: Wang, Jianzhu, Chapman, Duane, Xu, Jun, Wang, Yang, Gu, Binhe
Abstract/Description: Stable carbon and nitrogen isotope values (δ13C and δ15N) were used to evaluate trophic niche overlap between two filter-feeding fishes (known together as bigheaded carp) native to China, silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), and three native filter-feeding fish including bigmouth buffalo (Ictiobus cyprinellus), gizzard shad (Dorosoma cepedianum) and paddlefish (Polyodon spathula) in the lower Missouri River, USA, using the Bayesian Stable...
Show moreStable carbon and nitrogen isotope values (δ13C and δ15N) were used to evaluate trophic niche overlap between two filter-feeding fishes (known together as bigheaded carp) native to China, silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), and three native filter-feeding fish including bigmouth buffalo (Ictiobus cyprinellus), gizzard shad (Dorosoma cepedianum) and paddlefish (Polyodon spathula) in the lower Missouri River, USA, using the Bayesian Stable Isotope in R statistics. Results indicate that except for bigmouth buffalo, all species displayed similar trophic niche size and trophic diversity. Bigmouth buffalo occupied a small trophic niche and had the greatest trophic overlap with silver carp (93.6%) and bighead carp (94.1%) followed by gizzard shad (91.0%). Paddlefish had a trophic niche which relied on some resources different from those used by other species, and therefore had the lowest trophic overlap with bigheaded carp and other two native fish. The trophic overlap by bigheaded carp onto native fish was typically stronger than the reverse effects from native fish. Average niche overlap between silver carp and native species was as high as 71%, greater than niche overlap between bighead carp and native fish (64%). Our findings indicate that bigheaded carps are a potential threat to a diverse and stable native fish community.
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Date Issued: 2018-05-21
Identifier: FSU_pmch_29782547, 10.1371/journal.pone.0197584, PMC5962084, 29782547, 29782547, PONE-D-17-44424
Format: Citation

Title: Hippocampal protein kinase D1 is necessary for DHPG-induced learning and memory impairments in rats.
Creator: Wang, Wei, Duclot, Florian, Groveman, Bradley R, Carrier, Nicole, Qiao, Haifa, Fang, Xiao-Qian, Wang, Hui, Xin, Wenkuan, Jiang, Xing-Hong, Salter, Michael W, Ding, Xin-Sheng,...
Show moreWang, Wei, Duclot, Florian, Groveman, Bradley R, Carrier, Nicole, Qiao, Haifa, Fang, Xiao-Qian, Wang, Hui, Xin, Wenkuan, Jiang, Xing-Hong, Salter, Michael W, Ding, Xin-Sheng, Kabbaj, Mohamed, Yu, Xian-Min
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Abstract/Description: Understanding molecular mechanisms underlying the induction of learning and memory impairments remains a challenge. Recent investigations have shown that the activation of group I mGluRs (mGluR1 and mGluR5) in cultured hippocampal neurons by application of (S)-3,5-Dihydroxyphenylglycine (DHPG) causes the regulated internalization of N-methyl-D-aspartate receptors (NMDARs), which subsequently activates protein kinase D1 (PKD1). Through phosphorylating the C-terminals of the NMDAR GluN2...
Show moreUnderstanding molecular mechanisms underlying the induction of learning and memory impairments remains a challenge. Recent investigations have shown that the activation of group I mGluRs (mGluR1 and mGluR5) in cultured hippocampal neurons by application of (S)-3,5-Dihydroxyphenylglycine (DHPG) causes the regulated internalization of N-methyl-D-aspartate receptors (NMDARs), which subsequently activates protein kinase D1 (PKD1). Through phosphorylating the C-terminals of the NMDAR GluN2 subunits, PKD1 down-regulates the activity of remaining (non-internalized) surface NMDARs. The knockdown of PKD1 does not affect the DHPG-induced inhibition of AMPA receptor-mediated miniature excitatory post-synaptic currents (mEPSCs) but prevents the DHPG-induced inhibition of NMDAR-mediated mEPSCs in vitro. Thus, we investigated the in vivo effects of bilateral infusions of DHPG into the hippocampal CA1 area of rats in the Morris water maze (MWM) and the novel object discrimination (NOD) tests. A total of 300 adult male Sprague Dawley rats (250-280 g) were used for behavioral tests. One hundred ninety four were used in MWM test and the other 106 rats in the NOD test. Following one week of habituation to the vivarium, rats were bilaterally implanted under deep anesthesia with cannulas aimed at the CA1 area of the hippocampus (CA1 coordinates in mm from Bregma: AP -3.14; lateral +/-2; DV -3.0). Through implanted cannulas artificial cerebrospinal fluid (ACSF), the group1 mGluR antagonist 6-Methyl-2-(phenylethynyl)pyridine (MPEP), the dynamin-dependent internalization inhibitor Dynasore, or the PKD1 inhibitor CID755673 were infused into the bilateral hippocampal CA1 areas (2 μL per side, over 5 min). The effects of these infusions and the effects of PKD1 knockdown were examined in MWM or NOD test. DHPG infusion increased the latency to reach the platform in the MWM test and reduced the preference for the novel object in the NOD task. We found that the DHPG effects were dose-dependent and could be maintained for up to 2 days. Notably, these effects could be prevented by pre-infusion of the group1 mGluR antagonist MPEP, the dynamin-dependent internalization inhibitor Dynasore, the PKD1 inhibitor CID755673, or by PKD1 knockdown in the hippocampal CA1 area. Altogether, these findings provide direct evidence that PKD1-mediated signaling may play a critical role in the induction of learning and memory impairments by DHPG infusion into the hippocampal CA1 area.
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Date Issued: 2018-04-03
Identifier: FSU_pmch_29614089, 10.1371/journal.pone.0195095, PMC5882104, 29614089, 29614089, PONE-D-17-33748
Format: Citation

Title: Researchers' participation in and motivations for engaging with research information management systems.
Creator: Stvilia, Besiki, Wu, Shuheng, Lee, Dong Joon
Abstract/Description: This article examined how researchers participated in research information management systems (RIMSs), their motivations for participation, and their priorities for those motivations. Profile maintenance, question-answering, and endorsement activities were used to define three cumulatively increasing levels of participation: Readers, Record Managers, and Community Members. Junior researchers were more engaged in RIMSs than were senior researchers. Postdocs had significantly higher odds of...
Show moreThis article examined how researchers participated in research information management systems (RIMSs), their motivations for participation, and their priorities for those motivations. Profile maintenance, question-answering, and endorsement activities were used to define three cumulatively increasing levels of participation: Readers, Record Managers, and Community Members. Junior researchers were more engaged in RIMSs than were senior researchers. Postdocs had significantly higher odds of endorsing other researchers for skills and being categorized as Community Members than did full and associate professors. Assistant professors were significantly more likely to be Record Managers than were members of any other seniority categories. Finally, researchers from the life sciences showed a significantly higher propensity for being Community Members than Readers and Record Managers when compared with researchers from engineering and the physical sciences, respectively. When performing activities, researchers were motivated by the desire to share scholarship, feel competent, experience a sense of enjoyment, improve their status, and build ties with other members of the community. Moreover, when researchers performed activities that directly benefited other members of a RIMS, they assigned higher priorities to intrinsic motivations, such as perceived self-efficacy, enjoyment, and building community ties. Researchers at different stages of their academic careers and disciplines ranked some of the motivations for engaging with RIMSs differently. The general model of research participation in RIMSs; the relationships among RIMS activities; the motivation scales for activities; and the activity, seniority, and discipline-specific priorities for the motivations developed by this study provide the foundation for a framework for researcher participation in RIMSs. This framework can be used by RIMSs and institutional repositories to develop tools and design mechanisms to increase researchers' engagement in RIMSs.
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Date Issued: 2018-02-23
Identifier: FSU_pmch_29474438, 10.1371/journal.pone.0193459, PMC5825153, 29474438, 29474438, PONE-D-17-30486
Format: Citation

Title: Impacts of the Deepwater Horizon oil spill evaluated using an end-to-end ecosystem model.
Creator: Ainsworth, Cameron H, Paris, Claire B, Perlin, Natalie, Dornberger, Lindsey N, Patterson, William F, Chancellor, Emily, Murawski, Steve, Hollander, David, Daly, Kendra, Romero,...
Show moreAinsworth, Cameron H, Paris, Claire B, Perlin, Natalie, Dornberger, Lindsey N, Patterson, William F, Chancellor, Emily, Murawski, Steve, Hollander, David, Daly, Kendra, Romero, Isabel C, Coleman, Felicia, Perryman, Holly
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Abstract/Description: We use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the...
Show moreWe use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the oil spill with fisheries independent data. The model suggests that recruitment effects and fishery closures had little influence on biomass dynamics. However, at the assumed level of oil concentrations and toxicity, impacts on fish mortality and growth rates were large and commensurate with observations. Sensitivity analysis suggests the biomass of large reef fish decreased by 25% to 50% in areas most affected by the spill, and biomass of large demersal fish decreased even more, by 40% to 70%. Impacts on reef and demersal forage caused starvation mortality in predators and increased reliance on pelagic forage. Impacts on the food web translated effects of the spill far away from the oiled area. Effects on age structure suggest possible delayed impacts on fishery yields. Recovery of high-turnover populations generally is predicted to occur within 10 years, but some slower-growing populations may take 30+ years to fully recover.
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Date Issued: 2018-01-25
Identifier: FSU_pmch_29370187, 10.1371/journal.pone.0190840, PMC5784916, 29370187, 29370187, PONE-D-17-15401
Format: Citation

Title: The absence of specific yeast heat-shock proteins leads to abnormal aggregation and compromised autophagic clearance of mutant Huntingtin proteins.
Creator: Higgins, Ryan, Kabbaj, Marie-Helene, Hatcher, Alexa, Wang, Yanchang
Abstract/Description: The functionality of a protein depends on its correct folding, but newly synthesized proteins are susceptible to aberrant folding and aggregation. Heat shock proteins (HSPs) function as molecular chaperones that aid in protein folding and the degradation of misfolded proteins. Trinucleotide (CAG) repeat expansion in the Huntingtin gene (HTT) results in the expression of misfolded Huntingtin protein (Htt), which contributes to the development of Huntington's disease. We previously found that...
Show moreThe functionality of a protein depends on its correct folding, but newly synthesized proteins are susceptible to aberrant folding and aggregation. Heat shock proteins (HSPs) function as molecular chaperones that aid in protein folding and the degradation of misfolded proteins. Trinucleotide (CAG) repeat expansion in the Huntingtin gene (HTT) results in the expression of misfolded Huntingtin protein (Htt), which contributes to the development of Huntington's disease. We previously found that the degradation of mutated Htt with polyQ expansion (Htt103QP) depends on both ubiquitin proteasome system and autophagy. However, the role of heat shock proteins in the clearance of mutated Htt remains poorly understood. Here, we report that cytosolic Hsp70 (Ssa family), its nucleotide exchange factors (Sse1 and Fes1), and a Hsp40 co-chaperone (Ydj1) are required for inclusion body formation of Htt103QP proteins and their clearance via autophagy. Extended induction of Htt103QP-GFP leads to the formation of a single inclusion body in wild-type yeast cells, but mutant cells lacking these HSPs exhibit increased number of Htt103QP aggregates. Most notably, we detected more aggregated forms of Htt103QP in sse1Δ mutant cells using an agarose gel assay. Increased protein aggregates are also observed in these HSP mutants even in the absence Htt103QP overexpression. Importantly, these HSPs are required for autophagy-mediated Htt103QP clearance, but are less critical for proteasome-dependent degradation. These findings suggest a chaperone network that facilitates inclusion body formation of misfolded proteins and the subsequent autophagic clearance.
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Date Issued: 2018-01-18
Identifier: FSU_pmch_29346421, 10.1371/journal.pone.0191490, PMC5773196, 29346421, 29346421, PONE-D-17-24723
Format: Citation

Title: Hyperspectral imaging for simultaneous measurements of two FRET biosensors in pancreatic β-cells.
Creator: Elliott, Amicia D, Bedard, Noah, Ustione, Alessandro, Baird, Michelle A, Davidson, Michael W, Tkaczyk, Tomasz, Piston, David W
Abstract/Description: Fluorescent protein (FP) biosensors based on Förster resonance energy transfer (FRET) are commonly used to study molecular processes in living cells. There are FP-FRET biosensors for many cellular molecules, but it remains difficult to perform simultaneous measurements of multiple biosensors. The overlapping emission spectra of the commonly used FPs, including CFP/YFP and GFP/RFP make dual FRET measurements challenging. In addition, a snapshot imaging modality is required for simultaneous...
Show moreFluorescent protein (FP) biosensors based on Förster resonance energy transfer (FRET) are commonly used to study molecular processes in living cells. There are FP-FRET biosensors for many cellular molecules, but it remains difficult to perform simultaneous measurements of multiple biosensors. The overlapping emission spectra of the commonly used FPs, including CFP/YFP and GFP/RFP make dual FRET measurements challenging. In addition, a snapshot imaging modality is required for simultaneous imaging. The Image Mapping Spectrometer (IMS) is a snapshot hyperspectral imaging system that collects high resolution spectral data and can be used to overcome these challenges. We have previously demonstrated the IMS's capabilities for simultaneously imaging GFP and CFP/YFP-based biosensors in pancreatic β-cells. Here, we demonstrate a further capability of the IMS to image simultaneously two FRET biosensors with a single excitation band, one for cAMP and the other for Caspase-3. We use these measurements to measure simultaneously cAMP signaling and Caspase-3 activation in pancreatic β-cells during oxidative stress and hyperglycemia, which are essential components in the pathology of diabetes.
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Date Issued: 2017-12-06
Identifier: FSU_pmch_29211763, 10.1371/journal.pone.0188789, PMC5718502, 29211763, 29211763, PONE-D-17-26284
Format: Citation

Title: Vertical organization of the division of labor within nests of the Florida harvester ant, Pogonomyrmex badius.
Creator: Tschinkel, Walter R, Hanley, Nicholas
Abstract/Description: In the Florida harvester ant, Pogonomyrmex badius, foragers occur only in the top 15 cm of the nest, whereas brood and brood-care workers reside mostly in the deepest regions, yet the food and seeds foragers collect must be transported downward 30 to 80 cm to seed chambers and up to 2 m to brood chambers. Using mark-recapture techniques with fluorescent printer's ink, we identified a class of workers that ranges widely within the vertical structure of the nest, rapidly moving materials...
Show moreIn the Florida harvester ant, Pogonomyrmex badius, foragers occur only in the top 15 cm of the nest, whereas brood and brood-care workers reside mostly in the deepest regions, yet the food and seeds foragers collect must be transported downward 30 to 80 cm to seed chambers and up to 2 m to brood chambers. Using mark-recapture techniques with fluorescent printer's ink, we identified a class of workers that ranges widely within the vertical structure of the nest, rapidly moving materials dropped by foragers in the upper regions downward, and excavated soil from deeper upward. Within the nest, only 5% of foragers were recovered below 20 cm depth, but about 30% of transfer workers and 82% of unmarked workers were found there. Below 70 cm depth, 90% of workers were unmarked, and were probably involved mostly in brood care. During the summer, the transfer workers comprise about a quarter of the nest population, while foragers make up about 40%. Workers marked as transfer workers later appear as foragers, while those marked as foragers die and disappear from the foraging population, suggesting that transfer workers are younger, and age into foraging. The importance of these findings for laboratory studies of division of labor are discussed. The efficient allocation of labor is a key component of superorganismal fitness.
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Date Issued: 2017-11-28
Identifier: FSU_pmch_29182686, 10.1371/journal.pone.0188630, PMC5705139, 29182686, 29182686, PONE-D-17-32984
Format: Citation

Title: Aggregate-level lead exposure, gun violence, homicide, and rape.
Creator: Boutwell, Brian B, Nelson, Erik J, Qian, Zhengmin, Vaughn, Michael G, Wright, John P, Beaver, Kevin M, Barnes, J C, Petkovsek, Melissa, Lewis, Roger, Schootman, Mario, Rosenfeld...
Show moreBoutwell, Brian B, Nelson, Erik J, Qian, Zhengmin, Vaughn, Michael G, Wright, John P, Beaver, Kevin M, Barnes, J C, Petkovsek, Melissa, Lewis, Roger, Schootman, Mario, Rosenfeld, Richard
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Abstract/Description: An increasing body of research has linked the geographic distribution of lead with various indicators of criminal and antisocial behavior. The current study, using data from an ongoing project related to lead exposure in St. Louis City, MO, analyzed the association between aggregate blood lead levels and specific indicators violent crime within the city. Ecological study. St. Louis, Missouri. Blood lead levels. Official reports of violent crimes were categorized as 1) crimes involving a...
Show moreAn increasing body of research has linked the geographic distribution of lead with various indicators of criminal and antisocial behavior. The current study, using data from an ongoing project related to lead exposure in St. Louis City, MO, analyzed the association between aggregate blood lead levels and specific indicators violent crime within the city. Ecological study. St. Louis, Missouri. Blood lead levels. Official reports of violent crimes were categorized as 1) crimes involving a firearm (yes/no), 2) assault crimes (with or without a firearm), 3) robbery crimes (with or without a firearm), 4) homicides and 5) rape. With the exception of rape, aggregate blood-lead levels were statistically significant predictors of violent crime at the census tract level. The risk ratios for each of the outcome measures were as follows: firearm crimes 1.03 (1.03-1.04), assault crimes 1.03 (1.02-1.03), robbery crimes 1.03 (1.02-1.04), homicide 1.03 (1.01, 1.04), and rape 1.01 (0.99-1.03). Extending prior research in St. Louis, results suggest that aggregated lead exposure at the census tract level predicted crime outcomes, even after accounting for important sociological variables. Moving forward, a more developed understanding of aggregate level crime may necessitate a shift toward studying the synergy between sociological and biological risk factors such as lead exposure.
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Date Issued: 2017-11-27
Identifier: FSU_pmch_29176826, 10.1371/journal.pone.0187953, PMC5703470, 29176826, 29176826, PONE-D-16-40412
Format: Citation

Title: Distinguishing neuronal from astrocytic subcellular microstructures using in vivo Double Diffusion Encoded 1H MRS at 21.1 T.
Creator: Shemesh, Noam, Rosenberg, Jens T, Dumez, Jean-Nicolas, Grant, Samuel C, Frydman, Lucio
Abstract/Description: Measuring cellular microstructures non-invasively and achieving specificity towards a cell-type population within an interrogated in vivo tissue, remains an outstanding challenge in brain research. Magnetic Resonance Spectroscopy (MRS) provides an opportunity to achieve cellular specificity via the spectral resolution of metabolites such as N-Acetylaspartate (NAA) and myo-Inositol (mI), which are considered neuronal and astrocytic markers, respectively. Yet the information typically obtained...
Show moreMeasuring cellular microstructures non-invasively and achieving specificity towards a cell-type population within an interrogated in vivo tissue, remains an outstanding challenge in brain research. Magnetic Resonance Spectroscopy (MRS) provides an opportunity to achieve cellular specificity via the spectral resolution of metabolites such as N-Acetylaspartate (NAA) and myo-Inositol (mI), which are considered neuronal and astrocytic markers, respectively. Yet the information typically obtained with MRS describes metabolic concentrations, diffusion coefficients or relaxation rates rather than microstructures. Understanding how these metabolites are compartmentalized is a challenging but important goal, which so far has been mainly addressed using diffusion models. Here, we present direct in vivo evidence for the confinement of NAA and mI within sub-cellular components, namely, the randomly oriented process of neurons and astrocytes, respectively. Our approach applied Relaxation Enhanced MRS at ultrahigh (21.1 T) field, and used its high 1H sensitivity to measure restricted diffusion correlations for NAA and mI using a Double Diffusion Encoding (DDE) filter. While very low macroscopic anisotropy was revealed by spatially localized Diffusion Tensor Spectroscopy, DDE displayed characteristic amplitude modulations reporting on confinements in otherwise randomly oriented anisotropic microstructures for both metabolites. This implies that for the chosen set of parameters, the DDE measurements had a biased sensitivity towards NAA and mI sited in the more confined environments of neurites and astrocytic branches, than in the cell somata. These measurements thus provide intrinsic diffusivities and compartment diameters, and revealed subcellular neuronal and astrocytic morphologies in normal in vivo rat brains. The relevance of these measurements towards human applications-which could in turn help understand CNS plasticity as well as diagnose brain diseases-is discussed.
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Date Issued: 2017-10-02
Identifier: FSU_pmch_28968410, 10.1371/journal.pone.0185232, PMC5624579, 28968410, 28968410, PONE-D-17-12913
Format: Citation

Title: Smart thermosensitive liposomes for effective solid tumor therapy and in vivo imaging.
Creator: Affram, Kevin, Udofot, Ofonime, Singh, Mandip, Krishnan, Sunil, Reams, Renee, Rosenberg, Jens, Agyare, Edward
Abstract/Description: In numerous studies, liposomes have been used to deliver anticancer drugs such as doxorubicin to local heat-triggered tumor. Here, we investigate: (i) the ability of thermosensitive liposomal nanoparticle (TSLnp) as a delivery system to deliver poorly membrane-permeable anticancer drug, gemcitabine (Gem) to solid pancreatic tumor with the aid of local mild hyperthermia and, (ii) the possibility of using gadolinium (Magnevist®) loaded-TSLnps (Gd-TSLnps) to increase magnetic resonance imaging ...
Show moreIn numerous studies, liposomes have been used to deliver anticancer drugs such as doxorubicin to local heat-triggered tumor. Here, we investigate: (i) the ability of thermosensitive liposomal nanoparticle (TSLnp) as a delivery system to deliver poorly membrane-permeable anticancer drug, gemcitabine (Gem) to solid pancreatic tumor with the aid of local mild hyperthermia and, (ii) the possibility of using gadolinium (Magnevist®) loaded-TSLnps (Gd-TSLnps) to increase magnetic resonance imaging (MRI) contrast in solid tumor. In this study, we developed and tested gemcitabine-loaded thermosensitive liposomal nanoparticles (Gem-TSLnps) and gadolinium-loaded thermosensitive liposomal nanoparticles (Gd-TSLnps) both in in-vitro and in-vivo. The TSLnps exhibited temperature-dependent release of Gem, at 40-42°C, 65% of Gem was released within 10 min, whereas < 23% Gem leakage occurred at 37°C after a period of 2 h. The pharmacokinetic parameters and tissue distribution of both Gem-TSLnps and Gd-TSLnps were significantly greater compared with free Gem and Gd, while Gem-TSLnps plasma clearance was reduced by 17-fold and that of Gd-TSLpns was decreased by 2-fold. Area under the plasma concentration time curve (AUC) of Gem-TSLnps (35.17± 0.04 μghr/mL) was significantly higher than that of free Gem (2.09 ± 0.01 μghr/mL) whereas, AUC of Gd-TSLnps was higher than free Gd by 3.9 fold high. TSLnps showed significant Gem accumulation in heated tumor relative to free Gem. Similar trend of increased Gd-TSLnps accumulation was observed in non-heated tumor compared to that of free Gd; however, no significant difference in MRI contrast enhancement between free Gd and Gd-TSLnps ex-vivo tumor images was observed. Despite Gem-TSLnps dose being half of free Gem dose, antitumor efficacy of Gem-TSLnps was comparable to that of free Gem(Gem-TSLnps 10 mg Gem/kg compared with free Gem 20 mg/kg). Overall, the findings suggest that TSLnps may be used to improve Gem delivery and enhance its antitumor activity. However, the formulation of Gd-TSLnp needs to be fully optimized to significantly enhance MRI contrast in tumor.
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Date Issued: 2017-09-21
Identifier: FSU_pmch_28934281, 10.1371/journal.pone.0185116, PMC5608370, 28934281, 28934281, PONE-D-17-14628
Format: Citation

Title: The prevalence of discrimination across racial groups in contemporary America: Results from a nationally representative sample of adults..
Creator: Boutwell, Brian B, Nedelec, Joseph L, Winegard, Bo, Shackelford, Todd, Beaver, Kevin M, Vaughn, Michael, Barnes, J C, Wright, John P
Abstract/Description: A large body of social science research is devoted to understanding the causes and correlates of discrimination. Comparatively less effort has been aimed at providing a general prevalence estimate of discrimination using a nationally representative sample. The current study is intended to offer such an estimate using a large sample of American respondents (N = 14,793) while also exploring perceptions regarding why respondents felt they were discriminated against. The results provide a broad...
Show moreA large body of social science research is devoted to understanding the causes and correlates of discrimination. Comparatively less effort has been aimed at providing a general prevalence estimate of discrimination using a nationally representative sample. The current study is intended to offer such an estimate using a large sample of American respondents (N = 14,793) while also exploring perceptions regarding why respondents felt they were discriminated against. The results provide a broad estimate of self-reported discrimination experiences-an event that was only reported by about one-quarter of all sample members-across racial and ethnic categories.
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Date Issued: 2017-08-24
Identifier: FSU_pmch_28837680, 10.1371/journal.pone.0183356, PMC5570361, 28837680, 28837680, PONE-D-17-06599
Format: Citation

Title: Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates..
Creator: Steppan, Scott J, Schenk, John J
Abstract/Description: We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences...
Show moreWe combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.
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Date Issued: 2017-08-16
Identifier: FSU_pmch_28813483, 10.1371/journal.pone.0183070, PMC5559066, 28813483, 28813483, PONE-D-16-50122
Format: Citation

Title: Identification of a common Ara h 3 epitope recognized by both the capture and the detection monoclonal antibodies in an ELISA detection kit.
Creator: Zhao, Lipei, Zhao, Liang, Zhang, Buchang, Robotham, Jason M, Roux, Kenneth H, Tang, Hengli
Abstract/Description: Allergy to peanuts has become a common and severe problem, especially in westernized countries. In this study, we evaluated the target and epitope specificity of the capture and detection mouse monoclonal antibodies (mAbs) used in a commercial peanut allergen detection platform. We first identified the target of these antibodies as Ara h 3 and then used an overlapping peptide array of Ara h 3 to determine the antibody-binding epitopes. Further amino acids critical for the binding via alanine...
Show moreAllergy to peanuts has become a common and severe problem, especially in westernized countries. In this study, we evaluated the target and epitope specificity of the capture and detection mouse monoclonal antibodies (mAbs) used in a commercial peanut allergen detection platform. We first identified the target of these antibodies as Ara h 3 and then used an overlapping peptide array of Ara h 3 to determine the antibody-binding epitopes. Further amino acids critical for the binding via alanine substitutions at individual amino acid residues within the epitope were mapped. Finally, inhibition ELISA and inhibition immunoblotting using a recombinant Ara h 3 protein were performed to confirm these results. Surprisingly, the capture and detection mAbs showed identical binding characteristics and were presumed to represent two isolates of the same clone, a notion supported by both isoelectric focusing electrophoresis and Liquid chromatography-mass spectrometry experiments. The simultaneous binding of a pair of identical mAbs to an individual allergen such as Ara h3 is attributed to the multivalency of the analyte and has implications for developing diagnostic assays for additional multimeric allergens.
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Date Issued: 2017-08-11
Identifier: FSU_pmch_28800361, 10.1371/journal.pone.0182935, PMC5553815, 28800361, 28800361, PONE-D-17-08766
Format: Citation

Title: Mapping the contact surfaces in the Lamin A:AIMP3 complex by hydrogen/deuterium exchange FT-ICR mass spectrometry.
Creator: Tao, Yeqing, Fang, Pengfei, Kim, Sunghoon, Guo, Min, Young, Nicolas L, Marshall, Alan G
Abstract/Description: Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3...
Show moreAminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear. Here we report solution-phase hydrogen/deuterium exchange (HDX) for AIMP3, LmnA, and AIMP3 in association with the LmnA C-terminus. Reversed-phase LC coupled with LTQ 14.5 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) results in high mass accuracy and resolving power for comparing the D-uptake profiles for AIMP3, LmnA, and their complex. The results show that the AIMP3-LmnA interaction involves one of the two putative binding sites and an adjacent novel interface on AIMP3. LmnA binds AIMP3 via its extreme C-terminus. Together these findings provide a structural insight for understanding the interaction between AIMP3 and LmnA in AIMP3 degradation.
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Date Issued: 2017-08-10
Identifier: FSU_pmch_28797100, 10.1371/journal.pone.0181869, PMC5552228, 28797100, 28797100, PONE-D-17-10096
Format: Citation

Title: The association of post-discharge adverse events with timely follow-up visits after hospital discharge.
Creator: Tsilimingras, Dennis, Ghosh, Samiran, Duke, Ashley, Zhang, Liying, Carretta, Henry, Schnipper, Jeffrey
Abstract/Description: There has been little research to examine the association of post-discharge adverse events (AEs) with timely follow-up visits after hospital discharge. We aimed to examine whether having a timely follow-up outpatient visit would reduce the risk for post-discharge AEs. This was a methods study of patients at risk for post-discharge AEs from December 2011 through October 2012. Five hundred and forty-five patients who were under the care of hospitalist physicians and were discharged home from a...
Show moreThere has been little research to examine the association of post-discharge adverse events (AEs) with timely follow-up visits after hospital discharge. We aimed to examine whether having a timely follow-up outpatient visit would reduce the risk for post-discharge AEs. This was a methods study of patients at risk for post-discharge AEs from December 2011 through October 2012. Five hundred and forty-five patients who were under the care of hospitalist physicians and were discharged home from a community hospital, spoke English, and could be contacted after discharge were evaluated. The aim of the study was to examine the association of post-discharge AEs with timely follow-up visits after hospital discharge based on structured telephone interviews, health record review, and adjudication by two blinded, trained physicians using a previously established methodology. We observed a higher incidence of AEs with patients that had their first follow-up visit within 7 days after hospital discharge (33.5% vs. 23.0%, p = 0.007). This effect was attenuated somewhat but remained significant when adjusted for several patient factors (adjusted OR 1.33, 95% confidence interval 1.16-2.71). This observational study paradoxically showed an increase in post-discharge AEs with early follow-up, likely a result of confounding by indication and/or information bias that could not be completely adjusted for. This study illustrates the potential hazards with conducting observational studies to determine the efficacy of various transitional care interventions, such as early follow-up, where risk for confounding by indication is high.
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Date Issued: 2017-08-10
Identifier: FSU_pmch_28796810, 10.1371/journal.pone.0182669, PMC5552135, 28796810, 28796810, PONE-D-17-08560
Format: Citation

Title: Demographics as predictors of suicidal thoughts and behaviors: A meta-analysis..
Creator: Huang, Xieyining, Ribeiro, Jessica D, Musacchio, Katherine M, Franklin, Joseph C
Abstract/Description: Certain demographic factors have long been cited to confer risk or protection for suicidal thoughts and behaviors. However, many studies have found weak or non-significant effects. Determining the effect strength and clinical utility of demographics as predictors is crucial for suicide risk assessment and theory development. As such, we conducted a meta-analysis to determine the effect strength and clinical utility of demographics as predictors. We searched PsycInfo, PubMed, and GoogleScholar...
Show moreCertain demographic factors have long been cited to confer risk or protection for suicidal thoughts and behaviors. However, many studies have found weak or non-significant effects. Determining the effect strength and clinical utility of demographics as predictors is crucial for suicide risk assessment and theory development. As such, we conducted a meta-analysis to determine the effect strength and clinical utility of demographics as predictors. We searched PsycInfo, PubMed, and GoogleScholar for studies published before January 1st, 2015. Inclusion criteria required that studies use at least one demographic factor to longitudinally predict suicide ideation, attempt, or death. The initial search yielded 2,541 studies, 159 of which were eligible. A total of 752 unique statistical tests were included in analysis. Suicide death was the most commonly studied outcome, followed by attempt and ideation. The average follow-up length was 9.4 years. The overall effects of demographic factors studied in the field as risk factors were significant but weak, and that of demographic factors studied as protective factors were non-significant. Adjusting for publication bias further reduced effect estimates. No specific demographic factors appeared to be strong predictors. The effects were consistent across multiple moderators. At least within the narrow methodological constraints of the existing literature, demographic factors were statistically significant risk factors, but not protective factors. Even as risk factors, demographics offer very little improvement in predictive accuracy. Future studies that go beyond the limitations of the existing literature are needed to further understand the effects of demographics.
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Date Issued: 2017-07-10
Identifier: FSU_pmch_28700728, 10.1371/journal.pone.0180793, PMC5507259, 28700728, 28700728, PONE-D-16-37915
Format: Citation

Title: Magmatic evolution of Panama Canal volcanic rocks: A record of arc processes and tectonic change..
Creator: Farris, David W, Cardona, Agustin, Montes, Camilo, Foster, David, Jaramillo, Carlos
Abstract/Description: Volcanic rocks along the Panama Canal present a world-class opportunity to examine the relationship between arc magmatism, tectonic forcing, wet and dry magmas, and volcanic structures. Major and trace element geochemistry of Canal volcanic rocks indicate a significant petrologic transition at 21-25 Ma. Oligocene Bas Obispo Fm. rocks have large negative Nb-Ta anomalies, low HREE, fluid mobile element enrichments, a THI of 0.88, and a H2Ocalc of >3 wt. %. In contrast, the Miocene Pedro Miguel...
Show moreVolcanic rocks along the Panama Canal present a world-class opportunity to examine the relationship between arc magmatism, tectonic forcing, wet and dry magmas, and volcanic structures. Major and trace element geochemistry of Canal volcanic rocks indicate a significant petrologic transition at 21-25 Ma. Oligocene Bas Obispo Fm. rocks have large negative Nb-Ta anomalies, low HREE, fluid mobile element enrichments, a THI of 0.88, and a H2Ocalc of >3 wt. %. In contrast, the Miocene Pedro Miguel and Late Basalt Fm. exhibit reduced Nb-Ta anomalies, flattened REE curves, depleted fluid mobile elements, a THI of 1.45, a H2Ocalc of <1 wt. %, and plot in mid-ocean ridge/back-arc basin fields. Geochemical modeling of Miocene rocks indicates 0.5-0.1 kbar crystallization depths of hot (1100-1190°C) magmas in which most compositional diversity can be explained by fractional crystallization (F = 0.5). However, the most silicic lavas (Las Cascadas Fm.) require an additional mechanism, and assimilation-fractional-crystallization can reproduce observed compositions at reasonable melt fractions. The Canal volcanic rocks, therefore, change from hydrous basaltic pyroclastic deposits typical of mantle-wedge-derived magmas, to hot, dry bi-modal magmatism at the Oligocene-Miocene boundary. We suggest the primary reason for the change is onset of arc perpendicular extension localized to central Panama. High-resolution mapping along the Panama Canal has revealed a sequence of inward dipping maar-diatreme pyroclastic pipes, large basaltic sills, and bedded silicic ignimbrites and tuff deposits. These volcanic bodies intrude into the sedimentary Canal Basin and are cut by normal and subsequently strike-slip faults. Such pyroclastic pipes and basaltic sills are most common in extensional arc and large igneous province environments. Overall, the change in volcanic edifice form and geochemistry are related to onset of arc perpendicular extension, and are consistent with the idea that Panama arc crust fractured during collision with South America forming the observed Canal extensional zone.
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Date Issued: 2017-05-10
Identifier: FSU_pmch_28489866, 10.1371/journal.pone.0176010, PMC5425183, 28489866, 28489866, PONE-D-16-09080
Format: Citation

Title: How plant neighborhood composition influences herbivory: Testing four mechanisms of associational resistance and susceptibility..
Creator: Kim, Tania N
Abstract/Description: Neighboring plants can decrease or increase each other's likelihood of damage from herbivores through associational resistance or susceptibility, respectively. Associational effects (AE) can transpire through changes in herbivore or plant traits that affect herbivore movement, densities, and feeding behaviors to ultimately affect plant damage. While much work has focused on understanding the mechanisms that underlie associational effects, we know little about how these mechanisms are...
Show moreNeighboring plants can decrease or increase each other's likelihood of damage from herbivores through associational resistance or susceptibility, respectively. Associational effects (AE) can transpire through changes in herbivore or plant traits that affect herbivore movement, densities, and feeding behaviors to ultimately affect plant damage. While much work has focused on understanding the mechanisms that underlie associational effects, we know little about how these mechanisms are influenced by neighborhood composition, i.e., plant density or relative frequency which is necessary to make predictions about when AE should occur in nature. Using a series of field and greenhouse experiments, I examined how plant density and relative frequency affected plant damage to Solanum carolinense and four mechanisms that underlie AE; (i) accumulation of insect herbivores and arthropod predators, (ii) microclimate conditions, (iii) plant resistance, and (iv) specialist herbivore preference. I found a positive relationship between S. carolinense damage and the relative frequency of a non-focal neighbor (Solidago altissima) and all four AE mechanisms were influenced by one or multiple neighborhood components. Frequency-dependence in S. carolinense damage is most likely due to greater generalist herbivore load on S. carolinense (through spillover from S. altissima) with microclimate variables, herbivore preference, predation pressures, and plant resistance having relatively weaker effects. Associational effects may have long-term consequences for these two plant species during plant succession and understanding context-dependent herbivory has insect pest management implication for other plant species in agriculture and forestry.
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Date Issued: 2017-05-09
Identifier: FSU_pmch_28486538, 10.1371/journal.pone.0176499, PMC5423596, 28486538, 28486538, PONE-D-17-02864
Format: Citation

Title: A simulated annealing heuristic for maximum correlation core/periphery partitioning of binary networks.
Creator: Brusco, Michael, Stolze, Hannah J, Hoffman, Michaela, Steinley, Douglas
Abstract/Description: A popular objective criterion for partitioning a set of actors into core and periphery subsets is the maximization of the correlation between an ideal and observed structure associated with intra-core and intra-periphery ties. The resulting optimization problem has commonly been tackled using heuristic procedures such as relocation algorithms, genetic algorithms, and simulated annealing. In this paper, we present a computationally efficient simulated annealing algorithm for maximum...
Show moreA popular objective criterion for partitioning a set of actors into core and periphery subsets is the maximization of the correlation between an ideal and observed structure associated with intra-core and intra-periphery ties. The resulting optimization problem has commonly been tackled using heuristic procedures such as relocation algorithms, genetic algorithms, and simulated annealing. In this paper, we present a computationally efficient simulated annealing algorithm for maximum correlation core/periphery partitioning of binary networks. The algorithm is evaluated using simulated networks consisting of up to 2000 actors and spanning a variety of densities for the intra-core, intra-periphery, and inter-core-periphery components of the network. Core/periphery analyses of problem solving, trust, and information sharing networks for the frontline employees and managers of a consumer packaged goods manufacturer are provided to illustrate the use of the model.
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Date Issued: 2017-05-09
Identifier: FSU_pmch_28486475, 10.1371/journal.pone.0170448, PMC5423590, 28486475, 28486475, PONE-D-16-02050
Format: Citation

Title: Dpb11 may function with RPA and DNA to initiate DNA replication.
Creator: Bruck, Irina, Dhingra, Nalini, Martinez, Matthew P, Kaplan, Daniel L
Abstract/Description: Dpb11 is required for the initiation of DNA replication in budding yeast. We found that Dpb11 binds tightly to single-stranded DNA (ssDNA) or branched DNA structures, while its human homolog, TopBP1, binds tightly to branched-DNA structures. We also found that Dpb11 binds stably to CDK-phosphorylated RPA, the eukaryotic ssDNA binding protein, in the presence of branched DNA. A Dpb11 mutant specifically defective for DNA binding did not exhibit tight binding to RPA in the presence of DNA,...
Show moreDpb11 is required for the initiation of DNA replication in budding yeast. We found that Dpb11 binds tightly to single-stranded DNA (ssDNA) or branched DNA structures, while its human homolog, TopBP1, binds tightly to branched-DNA structures. We also found that Dpb11 binds stably to CDK-phosphorylated RPA, the eukaryotic ssDNA binding protein, in the presence of branched DNA. A Dpb11 mutant specifically defective for DNA binding did not exhibit tight binding to RPA in the presence of DNA, suggesting that Dpb11-interaction with DNA may promote the recruitment of RPA to melted DNA. We then characterized a mutant of Dpb11 that is specifically defective in DNA binding in budding yeast cells. Expression of dpb11-m1,2,3,5,ΔC results in a substantial decrease in RPA recruitment to origins, suggesting that Dpb11 interaction with DNA may be required for RPA recruitment to origins. Expression of dpb11-m1,2,3,5,ΔC also results in diminished GINS interaction with Mcm2-7 during S phase, while Cdc45 interaction with Mcm2-7 is like wild-type. The reduced GINS interaction with Mcm2-7 may be an indirect consequence of diminished origin melting. We propose that the tight interaction between Dpb11, CDK-phosphorylated RPA, and branched-DNA may be required for the essential function of stabilizing melted origin DNA in vivo. We also propose an alternative model, wherein Dpb11-DNA interaction is required for some other function in DNA replication initiation, such as helicase activation.
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Date Issued: 2017-05-03
Identifier: FSU_pmch_28467467, 10.1371/journal.pone.0177147, PMC5415106, 28467467, 28467467, PONE-D-17-03239
Format: Citation

Title: Practices of research data curation in institutional repositories: A qualitative view from repository staff..
Creator: Lee, Dong Joon, Stvilia, Besiki
Abstract/Description: The importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research...
Show moreThe importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research data providers and user communities around those IRs, it is essential to study current data curation practices and provide rich descriptions of the sociotechnical factors and relationships shaping those practices. Based on 13 interviews with 15 IR staff members from 13 large research universities in the United States, this paper provides a rich, qualitative description of research data curation and use practices in IRs. In particular, the paper identifies data curation and use activities in IRs, as well as their structures, roles played, skills needed, contradictions and problems present, solutions sought, and workarounds applied. The paper can inform the development of best practice guides, infrastructure and service templates, as well as education in research data curation in Library and Information Science (LIS) schools.
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Date Issued: 2017-03-16
Identifier: FSU_pmch_28301533, 10.1371/journal.pone.0173987, PMC5354423, 28301533, 28301533, PONE-D-16-20742
Format: Citation

Title: An illustrated guide to seeds found in nests of the Florida harvester ant, Pogonomyrmex badius.
Creator: Tschinkel, Walter R, Domínguez, Daniel J
Abstract/Description: The Florida harvester ant, Pogonomyrmex badius collects the seeds of many plant species and stores them in underground nest chambers for later consumption. Seeds taken from multiple nests in 1989, 2014 and 2015 were separated by size and species and identified through published keys, comparison with herbarium specimens and with identified seed collections. Harvester ants stored at least 58 species of seeds from 20 plant families in their chambers. This paper presents images of each seed...
Show moreThe Florida harvester ant, Pogonomyrmex badius collects the seeds of many plant species and stores them in underground nest chambers for later consumption. Seeds taken from multiple nests in 1989, 2014 and 2015 were separated by size and species and identified through published keys, comparison with herbarium specimens and with identified seed collections. Harvester ants stored at least 58 species of seeds from 20 plant families in their chambers. This paper presents images of each seed species in several aspects, their relative abundance in P. badius nests, their size relative to the smallest, and links to online data and images of the parent plant species, as well as to herbarium specimens. A number of seeds and plant families present at the site were not found in ant nests. These data and images will be valuable for future studies and experiments to untangle the choices the ants make in relation to what the plants and the seasons offer them.
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Date Issued: 2017-03-01
Identifier: FSU_pmch_28248988, 10.1371/journal.pone.0171419, PMC5331987, 28248988, 28248988, PONE-D-16-37099
Format: Citation

Title: Oxytocin receptor binding sites in the periphery of the neonatal mouse.
Creator: Greenwood, Maria A, Hammock, Elizabeth A D
Abstract/Description: Oxytocin (OXT) is a pleiotropic regulator of physiology and behavior. An emerging body of evidence demonstrates a role for OXT in the transition to postnatal life of the infant. To identify potential sites of OXT action via the OXT receptor (OXTR) in the newborn mouse, we performed receptor autoradiography on 20 μm sagittal sections of whole postnatal day 0 male and female mice on a C57BL/6J background using the 125iodinated ornithine vasotocin analog ([125I]-OVTA) radioligand. A competitive...
Show moreOxytocin (OXT) is a pleiotropic regulator of physiology and behavior. An emerging body of evidence demonstrates a role for OXT in the transition to postnatal life of the infant. To identify potential sites of OXT action via the OXT receptor (OXTR) in the newborn mouse, we performed receptor autoradiography on 20 μm sagittal sections of whole postnatal day 0 male and female mice on a C57BL/6J background using the 125iodinated ornithine vasotocin analog ([125I]-OVTA) radioligand. A competitive binding assay on both wild-type (WT) and OXTR knockout (OXTR KO) tissue was used to assess the selectivity of [125I]-OVTA for neonatal OXTR. Radioactive ligand (0.05 nM [125I]-OVTA) was competed against concentrations of 0 nM, 10 nM, and 1000 nM excess unlabeled OXT. Autoradiographs demonstrated the high selectivity of the radioligand for infant peripheral OXTR. Specific ligand binding activity for OXTR was observed in the oronasal cavity, the eye, whisker pads, adrenal gland, and anogenital region in the neonatal OXTR WT mouse, but was absent in neonatal OXTR KO. Nonspecific binding was observed in areas with a high lipid content such as the scapular brown adipose tissue and the liver: in these regions, binding was present in both OXTR WT and KO mice, and could not be competed away with OXT in either WT or KO mice. Collectively, these data confirm novel OXT targets in the periphery of the neonate. These peripheral OXTR sites, coupled with the immaturity of the neonate's own OXT system, suggest a role for exogenous OXT in modulating peripheral physiology and development.
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Date Issued: 2017-02-24
Identifier: FSU_pmch_28235051, 10.1371/journal.pone.0172904, PMC5325587, 28235051, 28235051, PONE-D-16-44673
Format: Citation

Title: A new synthetic matrix metalloproteinase inhibitor reduces human mesenchymal stem cell adipogenesis.
Creator: Bosco, Dale B, Roycik, Mark D, Jin, Yonghao, Schwartz, Martin A, Lively, Ty J, Zorio, Diego A R, Sang, Qing-Xiang Amy
Abstract/Description: Development of adipose tissue requires the differentiation of less specialized cells, such as human mesenchymal stem cells (hMSCs), into adipocytes. Since matrix metalloproteinases (MMPs) play critical roles in the cell differentiation process, we conducted investigations to determine if a novel mercaptosulfonamide-based MMP inhibitor (MMPI), YHJ-7-52, could affect hMSC adipogenic differentiation and lipid accumulation. Enzyme inhibition assays, adipogenic differentiation experiments, and...
Show moreDevelopment of adipose tissue requires the differentiation of less specialized cells, such as human mesenchymal stem cells (hMSCs), into adipocytes. Since matrix metalloproteinases (MMPs) play critical roles in the cell differentiation process, we conducted investigations to determine if a novel mercaptosulfonamide-based MMP inhibitor (MMPI), YHJ-7-52, could affect hMSC adipogenic differentiation and lipid accumulation. Enzyme inhibition assays, adipogenic differentiation experiments, and quantitative PCR methods were employed to characterize this inhibitor and determine its effect upon adipogenesis. YHJ-7-52 reduced lipid accumulation in differentiated cells by comparable amounts as a potent hydroxamate MMPI, GM6001. However, YHJ-7-82, a non-inhibitory structural analog of YHJ-7-52, in which the zinc-binding thiol group is replaced by a hydroxyl group, had no effect on adipogenesis. The two MMPIs (YHJ-7-52 and GM6001) were also as effective in reducing lipid accumulation in differentiated cells as T0070907, an antagonist of peroxisome-proliferator activated receptor gamma (PPAR-gamma), at a similar concentration. PPAR-gamma is a typical adipogenic marker and a key regulatory protein for the transition of preadiopocyte to adipocyte. Moreover, MMP inhibition was able to suppress lipid accumulation in cells co-treated with Troglitazone, a PPAR-gamma agonist. Our results indicate that MMP inhibitors may be used as molecular tools for adipogenesis and obesity treatment research.
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Date Issued: 2017-02-24
Identifier: FSU_pmch_28234995, 10.1371/journal.pone.0172925, PMC5325569, 28234995, 28234995, PONE-D-16-48797
Format: Citation

Title: Biochemical and biophysical investigations of the interaction between human glucokinase and pro-apoptotic BAD.
Creator: Rexford, Alix, Zorio, Diego A R, Miller, Brian G
Abstract/Description: The glycolytic enzyme glucokinase (GCK) and the pro-apoptotic protein BAD reportedly reside within a five-membered complex that localizes to the mitochondria of mammalian hepatocytes and pancreatic β-cells. Photochemical crosslinking studies using a synthetic analog of BAD's BH3 domain and in vitro transcription/translation experiments support a direct interaction between BAD and GCK. To investigate the biochemical and biophysical consequences of the BAD:GCK interaction, we developed a method...
Show moreThe glycolytic enzyme glucokinase (GCK) and the pro-apoptotic protein BAD reportedly reside within a five-membered complex that localizes to the mitochondria of mammalian hepatocytes and pancreatic β-cells. Photochemical crosslinking studies using a synthetic analog of BAD's BH3 domain and in vitro transcription/translation experiments support a direct interaction between BAD and GCK. To investigate the biochemical and biophysical consequences of the BAD:GCK interaction, we developed a method for the production of recombinant human BAD. Consistent with published reports, recombinant BAD displays high affinity for Bcl-xL (KD = 7 nM), and phosphorylation of BAD at S118, within the BH3 domain, abolishes this interaction. Unexpectedly, we do not detect association of recombinant, full-length BAD with recombinant human pancreatic GCK over a range of protein concentrations using various biochemical methods including size-exclusion chromatography, chemical cross-linking, analytical ultracentrifugation, and isothermal titration calorimetry. Furthermore, fluorescence polarization assays and isothermal titration calorimetry detect no direct interaction between GCK and BAD BH3 peptides. Kinetic characterization of GCK in the presence of high concentrations of recombinant BAD show modest (<15%) increases in GCK activity, observable only at glucose concentrations well below the K0.5 value. GCK activity is unaffected by BAD BH3 peptides. These results raise questions as to the mechanism of action of stapled peptide analogs modeled after the BAD BH3 domain, which reportedly enhance the Vmax value of GCK and stimulate insulin release in BAD-deficient islets. Based on our results, we postulate that the BAD:GCK interaction, and any resultant regulatory effect(s) upon GCK activity, requires the participation of additional members of the mitochondrial complex.
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Date Issued: 2017-02-09
Identifier: FSU_pmch_28182770, 10.1371/journal.pone.0171587, PMC5300155, 28182770, 28182770, PONE-D-16-49439
Format: Citation

Title: Enacted Reading Comprehension: Using Bodily Movement to Aid the Comprehension of Abstract Text Content..
Creator: Kaschak, Michael P, Connor, Carol M, Dombek, Jennifer L
Abstract/Description: We report a design study that assessed the feasibility of Enacted Reading Comprehension (ERC), an intervention designed to teach 3rd and 4th grade students (n = 40 and 25, respectively) to use gestures to understand an increasingly abstract set of texts. Students were taught to use gestures to understand the idea of "opposing forces" in a concrete setting-the forces at play as tectonic plates move past each other-and then taught to use the gestures to understand opposing forces in more...
Show moreWe report a design study that assessed the feasibility of Enacted Reading Comprehension (ERC), an intervention designed to teach 3rd and 4th grade students (n = 40 and 25, respectively) to use gestures to understand an increasingly abstract set of texts. Students were taught to use gestures to understand the idea of "opposing forces" in a concrete setting-the forces at play as tectonic plates move past each other-and then taught to use the gestures to understand opposing forces in more abstract situations. For example, students were taught to use gestures to understand the opposing sides of an argument, and to understand the internal conflicts that arise as individuals are faced with moral dilemmas. The results of our design study suggest that ERC has promise as a method for introducing students to the idea of using gesture to understand text content, and to employ this strategy in a range of reading contexts.
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Date Issued: 2017-01-20
Identifier: FSU_pmch_28107474, 10.1371/journal.pone.0169711, PMC5249083, 28107474, 28107474, PONE-D-16-36185
Format: Citation

Title: Understanding the Home Math Environment and Its Role in Predicting Parent Report of Children's Math Skills.
Creator: Hart, Sara A, Ganley, Colleen M, Purpura, David J
Abstract/Description: There is a growing literature concerning the role of the home math environment in children's math development. In this study, we examined the relation between these constructs by specifically addressing three goals. The first goal was to identify the measurement structure of the home math environment through a series of confirmatory factor analyses. The second goal was to examine the role of the home math environment in predicting parent report of children's math skills. The third goal was to...
Show moreThere is a growing literature concerning the role of the home math environment in children's math development. In this study, we examined the relation between these constructs by specifically addressing three goals. The first goal was to identify the measurement structure of the home math environment through a series of confirmatory factor analyses. The second goal was to examine the role of the home math environment in predicting parent report of children's math skills. The third goal was to test a series of potential alternative explanations for the relation between the home math environment and parent report of children's skills, specifically the direct and indirect role of household income, parent math anxiety, and parent math ability as measured by their approximate number system performance. A final sample of 339 parents of children aged 3 through 8 drawn from Mechanical Turk answered a questionnaire online. The best fitting model of the home math environment was a bifactor model with a general factor representing the general home math environment, and three specific factors representing the direct numeracy environment, the indirect numeracy environment, and the spatial environment. When examining the association of the home math environment factors to parent report of child skills, the general home math environment factor and the spatial environment were the only significant predictors. Parents who reported doing more general math activities in the home reported having children with higher math skills, whereas parents who reported doing more spatial activities reported having children with lower math skills.
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Date Issued: 2016-12-22
Identifier: FSU_pmch_28005925, 10.1371/journal.pone.0168227, PMC5179117, 28005925, 28005925, PONE-D-16-10081
Format: Citation

Title: Eastern Mediterranean Economic Exchange during the Iron Age: Portable X-Ray Fluorescence and Neutron Activation Analysis of Cypriot-Style Pottery in the Amuq Valley, Turkey..
Creator: Karacic, Steven, Osborne, James F
Abstract/Description: Two markers of regional exchange in the Eastern Mediterranean during the first millennium BCE are the White Painted and Bichrome Wares from Cyprus's Cypro-Geometric and Cypro-Archaic periods. Although these ceramics are often assumed to be imports from Cyprus, excavations in southern Turkey at sites such as Tarsus-Gözlükule, Kilise Tepe, Sirkeli Höyük, and Kinet Höyük suggest that at least some of this pottery was produced locally, requiring a major revision of our understanding of economic...
Show moreTwo markers of regional exchange in the Eastern Mediterranean during the first millennium BCE are the White Painted and Bichrome Wares from Cyprus's Cypro-Geometric and Cypro-Archaic periods. Although these ceramics are often assumed to be imports from Cyprus, excavations in southern Turkey at sites such as Tarsus-Gözlükule, Kilise Tepe, Sirkeli Höyük, and Kinet Höyük suggest that at least some of this pottery was produced locally, requiring a major revision of our understanding of economic interaction in the Eastern Mediterranean. We employ a combination of portable x-ray fluorescence and neutron activation analysis to investigate the White Painted and Bichrome Wares recovered from Tell Tayinat, Çatal Höyük, and Tell Judaidah, three sites in the Amuq Valley of southeastern Anatolia. Our results demonstrate that a clear geochemical distinction exists between imported and local versions of this pottery. Through comparison with legacy datasets, we locate the likely origin of the imported pottery in the Circum-Troodos sediments of central and southern Cyprus. The secondary and tertiary settlements of Çatal Höyük and Tell Judaidah had access only to this imported material. In contrast, the inhabitants of Tell Tayinat, capital city of the region, consumed both imported and locally produced White Painted and Bichrome Wares. This pattern cannot be explained in purely economic terms whereby the frequency of imports decreases as distance from the point of production increases. Instead, we suggest that elite feasting practices drove demand, resulting in either local potters producing Cypriot-style pottery or Cypriot potters settling in the vicinity of Tell Tayinat. These findings offer new insights into the relationship between historically attested Iron Age kingdoms in southern Turkey and Cyprus and complicate our understanding of exchange in the Eastern Mediterranean during the Iron Age.
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Date Issued: 2016-11-30
Identifier: FSU_pmch_27902729, 10.1371/journal.pone.0166399, PMC5130191, 27902729, 27902729, PONE-D-16-37930
Format: Citation

Title: The Florida Harvester Ant, Pogonomyrmex badius, Relies on Germination to Consume Large Seeds.
Creator: Tschinkel, Walter R, Kwapich, Christina L
Abstract/Description: The Florida harvester ant, Pogonomyrmex badius, is one of many ant species and genera that stores large numbers of seeds in damp, underground chambers for later consumption. A comparison of the sizes of seeds recovered from storage chambers with those of seed husks discarded following consumption revealed that the used seeds are far smaller than stored seeds. This difference in use-rate was confirmed in field and laboratory colonies by offering marked seeds of various sizes and monitoring the...
Show moreThe Florida harvester ant, Pogonomyrmex badius, is one of many ant species and genera that stores large numbers of seeds in damp, underground chambers for later consumption. A comparison of the sizes of seeds recovered from storage chambers with those of seed husks discarded following consumption revealed that the used seeds are far smaller than stored seeds. This difference in use-rate was confirmed in field and laboratory colonies by offering marked seeds of various sizes and monitoring the appearance of size-specific chaff. Because foragers collect a range of seed sizes but only open small seeds, large seeds accumulate, forming 70% or more of the weight of seed stores. Major workers increase the rates at which small and medium seeds are opened, but do not increase the size range of opened seeds. Experiments limiting ant access to portions of natural seed chambers showed that seeds germinate during storage, but that the ants rapidly remove them. When offered alongside non germinating seeds, germinating seeds were preferentially fed to larvae. The rate of germination during the annual cycle was determined by both burial in artificial chambers at various depths and under four laboratory temperatures. The germination rate depends upon the species of seed, the soil/laboratory temperature and/or the elapsed time. The seasonal soil temperature cycle generated germination patterns that vary with the mix of locally-available seeds. Taken together, exploitation of germination greatly increases the resources available to the ants in space and time. While the largest seeds may have the nutritional value of 15 small seeds, the inability of workers to open large seeds at will precludes them from rapid use during catastrophic events. The harvester ant's approach to seed harvesting is therefore two-pronged, with both immediate and delayed payoffs arising from the tendency to forage for a wide variety of seeds sizes.
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Date Issued: 2016-11-28
Identifier: FSU_pmch_27893844, 10.1371/journal.pone.0166907, PMC5125654, 27893844, 27893844, PONE-D-16-33448
Format: Citation

Title: Statistical Models for Tornado Climatology: Long and Short-Term Views..
Creator: Elsner, James B, Jagger, Thomas H, Fricker, Tyler
Abstract/Description: This paper estimates regional tornado risk from records of past events using statistical models. First, a spatial model is fit to the tornado counts aggregated in counties with terms that control for changes in observational practices over time. Results provide a long-term view of risk that delineates the main tornado corridors in the United States where the expected annual rate exceeds two tornadoes per 10,000 square km. A few counties in the Texas Panhandle and central Kansas have annual...
Show moreThis paper estimates regional tornado risk from records of past events using statistical models. First, a spatial model is fit to the tornado counts aggregated in counties with terms that control for changes in observational practices over time. Results provide a long-term view of risk that delineates the main tornado corridors in the United States where the expected annual rate exceeds two tornadoes per 10,000 square km. A few counties in the Texas Panhandle and central Kansas have annual rates that exceed four tornadoes per 10,000 square km. Refitting the model after removing the least damaging tornadoes from the data (EF0) produces a similar map but with the greatest tornado risk shifted south and eastward. Second, a space-time model is fit to the counts aggregated in raster cells with terms that control for changes in climate factors. Results provide a short-term view of risk. The short-term view identifies a shift of tornado activity away from the Ohio Valley under El Niño conditions and away from the Southeast under positive North Atlantic oscillation conditions. The combined predictor effects on the local rates is quantified by fitting the model after leaving out the year to be predicted from the data. The models provide state-of-the-art views of tornado risk that can be used by government agencies, the insurance industry, and the general public.
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Date Issued: 2016-11-22
Identifier: FSU_pmch_27875581, 10.1371/journal.pone.0166895, PMC5119788, 27875581, 27875581, PONE-D-16-27805
Format: Citation

Title: The BDNF Val66Met Polymorphism Influences Reading Ability and Patterns of Neural Activation in Children.
Creator: Jasińska, Kaja K, Molfese, Peter J, Kornilov, Sergey A, Mencl, W Einar, Frost, Stephen J, Lee, Maria, Pugh, Kenneth R, Grigorenko, Elena L, Landi, Nicole
Abstract/Description: Understanding how genes impact the brain's functional activation for learning and cognition during development remains limited. We asked whether a common genetic variant in the BDNF gene (the Val66Met polymorphism) modulates neural activation in the young brain during a critical period for the emergence and maturation of the neural circuitry for reading. In animal models, the bdnf variation has been shown to be associated with the structure and function of the developing brain and in humans...
Show moreUnderstanding how genes impact the brain's functional activation for learning and cognition during development remains limited. We asked whether a common genetic variant in the BDNF gene (the Val66Met polymorphism) modulates neural activation in the young brain during a critical period for the emergence and maturation of the neural circuitry for reading. In animal models, the bdnf variation has been shown to be associated with the structure and function of the developing brain and in humans it has been associated with multiple aspects of cognition, particularly memory, which are relevant for the development of skilled reading. Yet, little is known about the impact of the Val66Met polymorphism on functional brain activation in development, either in animal models or in humans. Here, we examined whether the BDNF Val66Met polymorphism (dbSNP rs6265) is associated with children's (age 6-10) neural activation patterns during a reading task (n = 81) using functional magnetic resonance imaging (fMRI), genotyping, and standardized behavioral assessments of cognitive and reading development. Children homozygous for the Val allele at the SNP rs6265 of the BDNF gene outperformed Met allele carriers on reading comprehension and phonological memory, tasks that have a strong memory component. Consistent with these behavioral findings, Met allele carriers showed greater activation in reading-related brain regions including the fusiform gyrus, the left inferior frontal gyrus and left superior temporal gyrus as well as greater activation in the hippocampus during a word and pseudoword reading task. Increased engagement of memory and spoken language regions for Met allele carriers relative to Val/Val homozygotes during reading suggests that Met carriers have to exert greater effort required to retrieve phonological codes.
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Date Issued: 2016-08-23
Identifier: FSU_pmch_27551971, 10.1371/journal.pone.0157449, PMC4995017, 27551971, 27551971, PONE-D-15-48171
Format: Citation

Title: Influence of Repressive Histone and DNA Methylation upon D4Z4 Transcription in Non-Myogenic Cells.
Creator: Das, Sunny, Chadwick, Brian P
Abstract/Description: We looked at a disease-associated macrosatellite array D4Z4 and focused on epigenetic factors influencing its chromatin state outside of the disease-context. We used the HCT116 cell line that contains the non-canonical polyadenylation (poly-A) signal required to stabilize somatic transcripts of the human double homeobox gene DUX4, encoded from D4Z4. In HCT116, D4Z4 is packaged into constitutive heterochromatin, characterized by DNA methylation and histone H3 tri-methylation at lysine 9 ...
Show moreWe looked at a disease-associated macrosatellite array D4Z4 and focused on epigenetic factors influencing its chromatin state outside of the disease-context. We used the HCT116 cell line that contains the non-canonical polyadenylation (poly-A) signal required to stabilize somatic transcripts of the human double homeobox gene DUX4, encoded from D4Z4. In HCT116, D4Z4 is packaged into constitutive heterochromatin, characterized by DNA methylation and histone H3 tri-methylation at lysine 9 (H3K9me3), resulting in low basal levels of D4Z4-derived transcripts. However, a double knockout (DKO) of DNA methyltransferase genes, DNMT1 and DNMT3B, but not either alone, results in significant loss of DNA and H3K9 methylation. This is coupled with upregulation of transcript levels from the array, including DUX4 isoforms (DUX4-fl) that are abnormally expressed in somatic muscle in the disease Facioscapulohumeral muscular dystrophy (FSHD) along with DUX4 protein, as indicated indirectly by upregulation of bondafide targets of DUX4 in DKO but not HCT116 cells. Results from treatment with a chemical inhibitor of histone methylation in HCT116 suggest that in the absence of DNA hypomethylation, H3K9me3 loss alone is sufficient to facilitate DUX4-fl transcription. Additionally, characterization of a cell line from a patient with Immunodeficiency, Centromeric instability and Facial anomalies syndrome 1 (ICF1) possessing a non-canonical poly-A signal and DNA hypomethylation at D4Z4 showed DUX4 target gene upregulation in the patient when compared to controls in spite of retention of H3K9me3. Taken together, these data suggest that both DNA methylation and H3K9me3 are determinants of D4Z4 silencing. Moreover, we show that in addition to testis, there is appreciable expression of spliced and polyadenylated D4Z4 derived transcripts that contain the complete DUX4 open reading frame (ORF) along with DUX4 target gene expression in the thymus, suggesting that DUX4 may provide normal function in this somatic tissue.
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Date Issued: 2016-07-28
Identifier: FSU_pmch_27467759, 10.1371/journal.pone.0160022, PMC4965136, 27467759, 27467759, PONE-D-15-54558
Format: Citation

Title: Bioturbation by the Fungus-Gardening Ant, Trachymyrmex septentrionalis.
Creator: Tschinkel, Walter R, Seal, Jon N
Abstract/Description: Soil invertebrates such as ants are thought to be important manipulators of soils in temperate and tropical ecosystems. The fungus gardening ant, Trachymyrmex septentrionalis, is an important agent of biomantling, that is, of depositing soil excavated from below onto the surface, and has been suggested as an agent of bioturbation (moving soil below ground) as well. The amount of bioturbation by this ant was quantified by planting queenright colonies in sand columns consisting of 5 layers of...
Show moreSoil invertebrates such as ants are thought to be important manipulators of soils in temperate and tropical ecosystems. The fungus gardening ant, Trachymyrmex septentrionalis, is an important agent of biomantling, that is, of depositing soil excavated from below onto the surface, and has been suggested as an agent of bioturbation (moving soil below ground) as well. The amount of bioturbation by this ant was quantified by planting queenright colonies in sand columns consisting of 5 layers of different colored sand. The amount of each color of sand deposited on the surface was determined from April to November 2015. In November, colonies were excavated and the color and amount of sand deposited below ground (mostly as backfill in chambers) was determined. Extrapolated to one ha, T. septentrionalis deposited 800 kg of sand per annum on the surface, and an additional 200 kg (17% of the total excavated) below ground. On average, this mixes 1.3% of the sand from other layers within the top meter of soil per millennium, but this mixing is unlikely to be homogeneous, and probably occurs as "hotspots" in both horizontal and vertical space. Such mixing is discussed as a challenge to sediment dating by optically stimulated luminescence (OSL).
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Date Issued: 2016-07-08
Identifier: FSU_pmch_27391485, 10.1371/journal.pone.0158920, PMC4938500, 27391485, 27391485, PONE-D-16-06201
Format: Citation

Title: Mining Twitter to Assess the Public Perception of the "Internet of Things".
Creator: Bian, Jiang, Yoshigoe, Kenji, Hicks, Amanda, Yuan, Jiawei, He, Zhe, Xie, Mengjun, Guo, Yi, Prosperi, Mattia, Salloum, Ramzi, Modave, François
Abstract/Description: Social media analysis has shown tremendous potential to understand public's opinion on a wide variety of topics. In this paper, we have mined Twitter to understand the public's perception of the Internet of Things (IoT). We first generated the discussion trends of the IoT from multiple Twitter data sources and validated these trends with Google Trends. We then performed sentiment analysis to gain insights of the public's attitude towards the IoT. As anticipated, our analysis indicates that...
Show moreSocial media analysis has shown tremendous potential to understand public's opinion on a wide variety of topics. In this paper, we have mined Twitter to understand the public's perception of the Internet of Things (IoT). We first generated the discussion trends of the IoT from multiple Twitter data sources and validated these trends with Google Trends. We then performed sentiment analysis to gain insights of the public's attitude towards the IoT. As anticipated, our analysis indicates that the public's perception of the IoT is predominantly positive. Further, through topic modeling, we learned that public tweets discussing the IoT were often focused on business and technology. However, the public has great concerns about privacy and security issues toward the IoT based on the frequent appearance of related terms. Nevertheless, no unexpected perceptions were identified through our analysis. Our analysis was challenged by the limited fraction of tweets relevant to our study. Also, the user demographics of Twitter users may not be strongly representative of the population of the general public.
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Date Issued: 2016-07-08
Identifier: FSU_pmch_27391760, 10.1371/journal.pone.0158450, PMC4938510, 27391760, 27391760, PONE-D-15-54733
Format: Citation

Title: Spatial and Temporal Variation in the Effects of Climatic Variables on Dugong Calf Production.
Creator: Fuentes, Mariana M P B, Delean, Steven, Grayson, Jillian, Lavender, Sally, Logan, Murray, Marsh, Helene
Abstract/Description: Knowledge of the relationships between environmental forcing and demographic parameters is important for predicting responses from climatic changes and to manage populations effectively. We explore the relationships between the proportion of sea cows (Dugong dugon) classified as calves and four climatic drivers (rainfall anomaly, Southern Oscillation El Niño Index [SOI], NINO 3.4 sea surface temperature index, and number of tropical cyclones) at a range of spatially distinct locations in...
Show moreKnowledge of the relationships between environmental forcing and demographic parameters is important for predicting responses from climatic changes and to manage populations effectively. We explore the relationships between the proportion of sea cows (Dugong dugon) classified as calves and four climatic drivers (rainfall anomaly, Southern Oscillation El Niño Index [SOI], NINO 3.4 sea surface temperature index, and number of tropical cyclones) at a range of spatially distinct locations in Queensland, Australia, a region with relatively high dugong density. Dugong and calf data were obtained from standardized aerial surveys conducted along the study region. A range of lagged versions of each of the focal climatic drivers (1 to 4 years) were included in a global model containing the proportion of calves in each population crossed with each of the lagged versions of the climatic drivers to explore relationships. The relative influence of each predictor was estimated via Gibbs variable selection. The relationships between the proportion of dependent calves and the climatic drivers varied spatially and temporally, with climatic drivers influencing calf counts at sub-regional scales. Thus we recommend that the assessment of and management response to indirect climatic threats on dugongs should also occur at sub-regional scales.
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Date Issued: 2016-06-29
Identifier: FSU_pmch_27355367, 10.1371/journal.pone.0155675, PMC4927176, 27355367, 27355367, PONE-D-15-52097
Format: Citation

Title: Elevated Resistin Gene Expression in African American Estrogen and Progesterone Receptor Negative Breast Cancer.
Creator: Vallega, Karin A, Liu, NingNing, Myers, Jennifer S, Yu, Kaixian, Sang, Qing-Xiang Amy
Abstract/Description: African American (AA) women diagnosed with breast cancer are more likely to have aggressive subtypes. Investigating differentially expressed genes between patient populations may help explain racial health disparities. Resistin, one such gene, is linked to inflammation, obesity, and breast cancer risk. Previous studies indicated that resistin expression is higher in serum and tissue of AA breast cancer patients compared to Caucasian American (CA) patients. However, resistin expression levels...
Show moreAfrican American (AA) women diagnosed with breast cancer are more likely to have aggressive subtypes. Investigating differentially expressed genes between patient populations may help explain racial health disparities. Resistin, one such gene, is linked to inflammation, obesity, and breast cancer risk. Previous studies indicated that resistin expression is higher in serum and tissue of AA breast cancer patients compared to Caucasian American (CA) patients. However, resistin expression levels have not been compared between AA and CA patients in a stage- and subtype-specific context. Breast cancer prognosis and treatments vary by subtype. This work investigates differential resistin gene expression in human breast cancer tissues of specific stages, receptor subtypes, and menopause statuses in AA and CA women. Differential gene expression analysis was performed using human breast cancer gene expression data from The Cancer Genome Atlas. We performed inter-race resistin gene expression level comparisons looking at receptor status and stage-specific data between AA and CA samples. DESeq was run to test for differentially expressed resistin values. Resistin RNA was higher in AA women overall, with highest values in receptor negative subtypes. Estrogen-, progesterone-, and human epidermal growth factor receptor 2- negative groups showed statistically significant elevated resistin levels in Stage I and II AA women compared to CA women. In inter-racial comparisons, AA women had significantly higher levels of resistin regardless of menopause status. In whole population comparisons, resistin expression was higher among Stage I and III estrogen receptor negative cases. In comparisons of molecular subtypes, resistin levels were significant higher in triple negative than in luminal A breast cancer. Resistin gene expression levels were significantly higher in receptor negative subtypes, especially estrogen receptor negative cases in AA women. Resistin may serve as an early breast cancer biomarker and possible therapeutic target for AA breast cancer.
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Date Issued: 2016-06-17
Identifier: FSU_pmch_27314854, 10.1371/journal.pone.0157741, PMC4912107, 27314854, 27314854, PONE-D-16-17121
Format: Citation

Title: In Wrong Anticipation - Miscalibrated Beliefs between Germans, Israelis, and Palestinians.
Creator: Goerg, Sebastian J, Hennig-Schmidt, Heike, Walkowitz, Gari, Winter, Eyal
Abstract/Description: The reconcilability of actions and beliefs in inter-country relationships, either in business or politics, is of vital importance as incorrect beliefs on foreigners' behavior can have serious implications. We study a typical inter-country interaction by means of a controlled laboratory investment game experiment in Germany, Israel and Palestine involving 400 student participants in total. An investor has to take a risky decision in a foreign country that involves transferring money to an...
Show moreThe reconcilability of actions and beliefs in inter-country relationships, either in business or politics, is of vital importance as incorrect beliefs on foreigners' behavior can have serious implications. We study a typical inter-country interaction by means of a controlled laboratory investment game experiment in Germany, Israel and Palestine involving 400 student participants in total. An investor has to take a risky decision in a foreign country that involves transferring money to an investee/allocator. We found a notable constellation of calibrated and un-calibrated beliefs. Within each country, transfer standards exist, which investees correctly anticipate within their country. However, across countries these standards differ. By attributing the standard of their own environment to the other countries investees are remarkably bad in predicting foreign investors' behavior. The tendency to ignore this potential difference can be a source of misinterpreting motives in cross-country interaction. Foreigners might perceive behavior as unfavorable or favorable differentiation, even though-unknown to them-investors actually treat fellow-country people and foreigners alike.
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Date Issued: 2016-06-16
Identifier: FSU_pmch_27311066, 10.1371/journal.pone.0156998, PMC4911115, 27311066, 27311066, PONE-D-15-27349
Format: Citation

Title: A Critical Evaluation of the Down Syndrome Diagnosis for LB1, Type Specimen of Homo floresiensis.
Creator: Baab, Karen L, Brown, Peter, Falk, Dean, Richtsmeier, Joan T, Hildebolt, Charles F, Smith, Kirk, Jungers, William
Abstract/Description: The Liang Bua hominins from Flores, Indonesia, have been the subject of intense scrutiny and debate since their initial description and classification in 2004. These remains have been assigned to a new species, Homo floresiensis, with the partial skeleton LB1 as the type specimen. The Liang Bua hominins are notable for their short stature, small endocranial volume, and many features that appear phylogenetically primitive relative to modern humans, despite their late Pleistocene age. Recently,...
Show moreThe Liang Bua hominins from Flores, Indonesia, have been the subject of intense scrutiny and debate since their initial description and classification in 2004. These remains have been assigned to a new species, Homo floresiensis, with the partial skeleton LB1 as the type specimen. The Liang Bua hominins are notable for their short stature, small endocranial volume, and many features that appear phylogenetically primitive relative to modern humans, despite their late Pleistocene age. Recently, some workers suggested that the remains represent members of a small-bodied island population of modern Austro-Melanesian humans, with LB1 exhibiting clinical signs of Down syndrome. Many classic Down syndrome signs are soft tissue features that could not be assessed in skeletal remains. Moreover, a definitive diagnosis of Down syndrome can only be made by genetic analysis as the phenotypes associated with Down syndrome are variable. Most features that contribute to the Down syndrome phenotype are not restricted to Down syndrome but are seen in other chromosomal disorders and in the general population. Nevertheless, we re-evaluated the presence of those phenotypic features used to support this classification by comparing LB1 to samples of modern humans diagnosed with Down syndrome and euploid modern humans using comparative morphometric analyses. We present new data regarding neurocranial, brain, and symphyseal shape in Down syndrome, additional estimates of stature for LB1, and analyses of inter- and intralimb proportions. The presence of cranial sinuses is addressed using CT images of LB1. We found minimal congruence between the LB1 phenotype and clinical descriptions of Down syndrome. We present important differences between the phenotypes of LB1 and individuals with Down syndrome, and quantitative data that characterize LB1 as an outlier compared with Down syndrome and non-Down syndrome groups. Homo floresiensis remains a phenotypically unique, valid species with its roots in Plio-Pleistocene Homo taxa.
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Date Issued: 2016-06-08
Identifier: FSU_pmch_27275928, 10.1371/journal.pone.0155731, PMC4898715, 27275928, 27275928, PONE-D-15-42984
Format: Citation

Title: An Unusual Inverted Saline Microbial Mat Community in an Interdune Sabkha in the Rub' al Khali (the Empty Quarter), United Arab Emirates.
Creator: McKay, Christopher P, Rask, Jon C, Detweiler, Angela M, Bebout, Brad M, Everroad, R Craig, Lee, Jackson Z, Chanton, Jeffrey P, Mayer, Marisa H, Caraballo, Adrian A L, Kapili,...
Show moreMcKay, Christopher P, Rask, Jon C, Detweiler, Angela M, Bebout, Brad M, Everroad, R Craig, Lee, Jackson Z, Chanton, Jeffrey P, Mayer, Marisa H, Caraballo, Adrian A L, Kapili, Bennett, Al-Awar, Meshgan, Al-Farraj, Asma
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Abstract/Description: Salt flats (sabkha) are a recognized habitat for microbial life in desert environments and as analogs of habitats for possible life on Mars. Here we report on the physical setting and microbiology of interdune sabkhas among the large dunes in the Rub' al Khali (the Empty Quarter) in Liwa Oasis, United Arab Emirates. The salt flats, composed of gypsum and halite, are moistened by relatively fresh ground water. The result is a salinity gradient that is inverted compared to most salt flat...
Show moreSalt flats (sabkha) are a recognized habitat for microbial life in desert environments and as analogs of habitats for possible life on Mars. Here we report on the physical setting and microbiology of interdune sabkhas among the large dunes in the Rub' al Khali (the Empty Quarter) in Liwa Oasis, United Arab Emirates. The salt flats, composed of gypsum and halite, are moistened by relatively fresh ground water. The result is a salinity gradient that is inverted compared to most salt flat communities with the hypersaline layer at the top and freshwater layers below. We describe and characterize a rich photosynthetically-based microbial ecosystem that is protected from the arid outside environment by a translucent salt crust. Gases collected from sediments under shallow ponds in the sabkha contain methane in concentrations as high as 3400 ppm. The salt crust could preserve biomarkers and other evidence for life in the salt after it dries out. Chloride-filled depressions have been identified on Mars and although surface flow of water is unlikely on Mars today, ground water is possible. Such a near surface system with modern groundwater flowing under ancient salt deposits could be present on Mars and could be accessed by surface rovers.
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Date Issued: 2016-03-16
Identifier: FSU_pmch_26982497, 10.1371/journal.pone.0150342, PMC4794207, 26982497, 26982497, PONE-D-15-26866
Format: Citation

Title: A Landmark-Free Method for Three-Dimensional Shape Analysis.
Creator: Pomidor, Benjamin J, Makedonska, Jana, Slice, Dennis E
Abstract/Description: The tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts. This is...
Show moreThe tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts. This is especially true of those investigating smooth or featureless surfaces. In this paper, we present a new method to perform this transformation for data obtained from high-resolution scanning technology. This method uses surface scans, instead of landmarks, to calculate a shape difference metric analogous to Procrustes distance and perform superimposition. This is accomplished by building upon and extending the Iterative Closest Point algorithm. We also explore some new ways this data can be used; for example, we can calculate an averaged surface directly and visualize point-wise shape information over this surface. Finally, we briefly demonstrate this method on a set of primate skulls and compare the results of the new methodology with traditional geometric morphometric analysis.
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Date Issued: 2016-03-08
Identifier: FSU_pmch_26953573, 10.1371/journal.pone.0150368, PMC4783062, 26953573, 26953573, PONE-D-15-18418
Format: Citation

Title: Nucleosome Repositioning: A Novel Mechanism for Nicotine- and Cocaine-Induced Epigenetic Changes..
Creator: Brown, Amber N, Vied, Cynthia, Dennis, Jonathan H, Bhide, Pradeep G
Abstract/Description: Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or...
Show moreDrugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug naïve positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse.
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Date Issued: 2015-09-28
Identifier: FSU_pmch_26414157, 10.1371/journal.pone.0139103, PMC4586372, 26414157, 26414157, PONE-D-14-52968
Format: Citation

Title: Dopamine receptor and Gα(olf) expression in DYT1 dystonia mouse models during postnatal development.
Creator: Zhang, Lin, McCarthy, Deirdre M, Sharma, Nutan, Bhide, Pradeep G
Abstract/Description: DYT1 dystonia is a heritable, early-onset generalized movement disorder caused by a GAG deletion (ΔGAG) in the DYT1 gene. Neuroimaging studies and studies using mouse models suggest that DYT1 dystonia is associated with dopamine imbalance. However, whether dopamine imbalance is key to DYT1 or other forms of dystonia continues to be debated. We used Dyt1 knock out (Dyt1 KO), Dyt1 ΔGAG knock-in (Dyt1 KI), and transgenic mice carrying one copy of the human DYT1 wild type allele (DYT1 hWT) or...
Show moreDYT1 dystonia is a heritable, early-onset generalized movement disorder caused by a GAG deletion (ΔGAG) in the DYT1 gene. Neuroimaging studies and studies using mouse models suggest that DYT1 dystonia is associated with dopamine imbalance. However, whether dopamine imbalance is key to DYT1 or other forms of dystonia continues to be debated. We used Dyt1 knock out (Dyt1 KO), Dyt1 ΔGAG knock-in (Dyt1 KI), and transgenic mice carrying one copy of the human DYT1 wild type allele (DYT1 hWT) or human ΔGAG mutant allele (DYT1 hMT). D1R, D2R, and Gα(olf) protein expression was analyzed by western blot in the frontal cortex, caudate-putamen and ventral midbrain in young adult (postnatal day 60; P60) male mice from all four lines; and in the frontal cortex and caudate putamen in juvenile (postnatal day 14; P14) male mice from the Dyt1 KI and KO lines. Dopamine receptor and Gα(olf) protein expression were significantly decreased in multiple brain regions of Dyt1 KI and Dyt1 KO mice and not significantly altered in the DYT1 hMT or DYT1 hWT mice at P60. The only significant change at P14 was a decrease in D1R expression in the caudate-putamen of the Dyt1 KO mice. We found significant decreases in key proteins in the dopaminergic system in multiple brain regions of Dyt1 KO and Dyt1 KI mouse lines at P60. Deletion of one copy of the Dyt1 gene (KO mice) produced the most pronounced effects. These data offer evidence that impaired dopamine receptor signaling may be an early and significant contributor to DYT1 dystonia pathophysiology.
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Date Issued: 2015-04-10
Identifier: FSU_pmch_25860259, 10.1371/journal.pone.0123104, PMC4393110, 25860259, 25860259, PONE-D-14-28479
Format: Citation

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