Showing 661 - 670 of 733 Items
New insights on obtaining phytoplankton concentration and composition from in situ multispectral Chlorophyll fluorescence
Date: 2010-01-01
Creator: Christopher W. Proctor, Collin S. Roesler
Access: Open access
- A three-channel excitation (435 nm, 470 nm, and 532 nm) Chlorophyll fluorometer (695 nm emission) was calibrated and characterized to improve uncertainty in estimated in situ Chlorophyll concentrations. Protocols for reducing sensor-related uncertainties as well as environmental-related uncertainties were developed. Sensor calibrations were performed with thirteen monospecific cultures in the laboratory, grown under limiting and saturating irradiance, and sampled at different growth phases. Resulting uncertainties in the calibration slope induced by natural variations in the in vivo fluorescence per extracted Chlorophyll yield were quantified. Signal variations associated with the sensors (i.e., dark current configurations, drift, and stability) and the environment (i.e., temperature dependent dark currents and contamination by colored dissolved organic matter [CDOM] fluorescence) yielded errors in estimating in situ Chlorophyll concentration exceeding 100%. Calibration protocols and concurrent observations of in situ temperature and CDOM fluorescence eliminate these uncertainties. Depending upon excitation channel, biomass calibration slopes varied between 6-and 10-fold between species and as a function of growth irradiance or growth phase. The largest source of slope variability was due to variations in accessory pigmentation, and thus the variance could be reduced among pigment-based taxonomic lines. Fluorescence ratios were statistically distinct among the pigment-based taxonomic groups, providing not only a means for approximating bulk taxonomic composition, but also for selecting the appropriate calibration slope to statistically improve the accuracy of in situ Chlorophyll concentration estimates. Application to 5 months of deployment in China Lake, Maine, USA reduced the error in estimating extracted Chlorophyll concentration from > 30% to < 6%. © 2010, by the American Society of Limnology and Oceanography, Inc.
Role of iron and organic carbon in mass-specific light absorption by particulate matter from louisiana coastal waters
Date: 2012-01-01
Creator: Margaret L. Estapa, Emmanuel Boss, Lawrence M. Mayer, Collin S. Roesler
Access: Open access
- We investigated the influences of organic content and mineralogical composition on light absorption by mostly mineral suspended particles in aquatic and coastal marine systems. Mass-specific absorption spectra of suspended particles and surface sediments from coastal Louisiana and the lower Mississippi and Atchafalaya rivers were measured with a centered sample-mount integrating sphere and analyzed in conjunction with organic carbon (OC), hydrochloric acid- (HCl-) extractable iron, and dithionite-extractable iron contents. Compositions and absorption properties were comparable to published values for similar particles. Dithionite-extractable iron was strongly correlated with absorption at ultraviolet (UV) and blue wavelengths, while OC and HCl-extractable iron were weakly but positively correlated. Oxidative removal of OC from sediments caused small and variable changes in absorption, while dithionite extraction of iron oxides strongly reduced absorption. Shoulders in the absorption spectra corresponded to absorption bands of iron oxide minerals, and their intensities were well correlated to dithionite-extractable iron contents of the samples. These findings support a primary role for iron oxide and hydroxide minerals in the mass-specific absorption of mostly inorganic particles from the terrestrially influenced coast of Louisiana. Riverine particles had higher dithionite-extractable iron contents and iron oxide- specific absorption features than did marine particles, consistent with current knowledge regarding differential transport of particulate iron oxides and hydroxides through estuarine salinity gradients and reductive alteration of these oxide phases on the Louisiana shelf. The quantifiable dependence of UV absorption features on iron oxide content suggests that, under certain conditions, in situ hyperspectral absorption measurements could be designed to monitor water-column iron mineral transport and transformation. © 2012, by the Association for the Sciences of Limnology and Oceanography, Inc.
Retinoic acid expands the evolutionarily reduced dentition of zebrafish
Date: 2012-12-01
Creator: Pawat Seritrakul, Eric Samarut, Tenzing T.S. Lama, Yann Gibert, Vincent, Laudet, William R. Jackman
Access: Open access
- Zebrafish lost anterior teeth during evolution but retain a posterior pharyngeal dentition that requires retinoic acid (RA) cell-cell signaling for its development. The purposes of this study were to test the sufficiency of RA to induce tooth development and to assess its role in evolution. We found that exposure of embryos to exogenous RA induces a dramatic anterior expansion of the number of pharyngeal teeth that later form and shifts anteriorly the expression patterns of genes normally expressed in the posterior tooth-forming region, such as pitx2 and dlx2b. After RA exposure, we also observed a correlation between cartilage malformations and ectopic tooth induction, as well as abnormal cranial neural crest marker gene expression. Additionally, we observed that the RA-induced zebrafish anterior teeth resemble in pattern and number the dentition of fish species that retain anterior pharyngeal teeth such as medaka but that medaka do not express the aldh1a2 RA-synthesizing enzyme in tooth-forming regions. We conclude that RA is sufficient to induce anterior ectopic tooth development in zebrafish where teeth were lost in evolution, potentially by altering neural crest cell development, and that changes in the location of RA synthesis correlate with evolutionary changes in vertebrate dentitions. © FASEB.
Initial experiments in using communication swarms to improve the performance of swarm systems
Date: 2012-01-01
Creator: Stephen M. Majercik
Access: Open access
- Swarm intelligence can provide robust, adaptable, scalable solutions to difficult problems. The distributed nature of swarm activity is the basis of these desirable qualities, but it also prevents swarm-based techniques from having direct access to global knowledge that could facilitate the task at hand. Our experiments indicate that a swarm system can use an auxiliary swarm, called a communication swarm, to create and distribute an approximation of useful global knowledge, without sacrificing robustness, adaptability, and scalability. We describe a communication swarm and validate its effectiveness on a simple problem.
Correction: CO2 induced phase transitions in diamine-appended metal-organic frameworks (Chemical Science (2015) 6 (5177-5185) DOI: 10.1039/c5sc01828e)
Date: 2019-01-01
Creator: Bess Vlaisavljevich, Sondre K. Schnell, Allison L. Dzubak, Kyuho Lee, Nora, Planas, Jeffrey B. Neaton, Laura Gagliardi, Berend Smit
Access: Open access
- The authors regret that there are some discrepancies reproducing the data in the original article due to the determined coordinates not being the fully optimised geometries. The authors have provided more information as follows. In the manuscript entitled 'CO2 induced phase transitions in diamine-appended metal-organic frameworks', minor errors with the attached coordinates and energies reported in the paper have recently been identified. In this communication, we correct these errors. Here, we present updated optimized geometries and binding energies. We also take this opportunity to include an extended computational details section to ensure reproducibility. In addition, we show that the overall conclusions of the paper are not affected by these changes. A detailed comparison with the results reported by Lee et al.1 revealed that the DFT optimization of the coordinates provided with the manuscript do not lead to the values reported in the manuscript, and they warrant correction. Corrected coordinates and updated tables (Tables 1-7) and figures (Fig. 1, 2, 4 and 5) are included here for calculations using the PBE functional. These structures have been repeated using a slightly tighter force threshold than in the original manuscript (details below). The M06-L calculations reported in the original manuscript are not revisited since they were performed to assess the role of dispersion. Since the publication of our work in 2015, a far more detailed study of this effect has been published by one of the authors rendering these M06-L calculations unnecessary and we refer readers interested in the role of dispersion on the carbamate formation to this more recent study by Lee et al.1 In addition to correcting our DFT calculations, we examine the effects of the revised DFT values on the lattice model in this work.We recompute the lattice model with the M06-L and PBE values fromthe original manuscript as well as the corrected PBE values reported below (Fig. 6-8 and Tables 8-10). In all three sets of isotherm plots the ordering is preserved but the inflection points are spaced differently with the new PBE numbers, leading to quantitative differences that are nonetheless qualitatively similar to previous work. Finally, we discuss different ways that CO2 can coordinate to the metal binding site, as shown in Fig. 3. We should have notedmore clearly in ourmanuscript that these were starting configurations and not necessarily the final converged structures since our goal was to try several starting geometries to determine which coordination environment around the metal site was lowest in energy. Take for example bidentate insertion. Chemical intuition suggests that this structure could rotate to one that has only one CO2 oxygen center closer to the metal than the other and we observe this in our optimized structure. The resulting geometries we obtained for the starting arrangements noted in the figure are higher in energy than the chain model as reported in our original paper.We wish to emphasize that at the time of our 2015 study, our objective was to understand whether or not CO2 was bound to the metal and if one-dimensional chain formation could lead to a step in the adsorption isotherm. It has since become clear that a far more thorough study of the arrangements of the amines is required to truly understand competing amine arrangements preset in experiment. This was outside the scope of our work. Once more, these calculations are perhaps now outdated given work in the field in recent years. We again refer interested readers to a more recent study by Lee et al.1 1. Extended computational details to ensure reproducibility In the course of rectifying the error in our calculations, we wanted to ensure that all revised calculations were converged using the exact same protocol; therefore, we repeated the PBE calculations for the pair and chain models using updated computational details given here to ensure reproducibility. The M2(dobpdc) MOF contains six unsaturated metal sites per unit cell. To calculate the binding energies of CO2 in its amine appended analogue mmen-M2(dobpdc), one mmen ligand per CO2 was added per unit cell. The smaller sized ethylenediamine (en) was used to saturate the remaining amines not involved in CO2 binding. In the case of the pair mode, two mmen-amines are included per unit cell only. All DFT calculations were performed with periodic boundary conditions carried out using the VASP 5.4.4 package (original calculations were performed with VASP 5.3.3). The PBE functional was employed to examine the energetics of CO2 adsorption.3 On-site Hubbard U corrections were employed for metal d electrons.4 The U values are determined to reproduce oxidation energies in the respective metal oxides and are given in the tables below. The electron-ion interactions in these calculations were described with the projector augmented wave (PAW) method developed by Blöchl with an energy cutoff of 550 eV.5 This combination of the PBE functional, PAW scheme, and energy cutoff was used for full geometry optimization of the various species investigated until the forces on all atoms were smaller than 0.02 eV Å-1 and the SCF convergence was set to 1 × 10-7 eV. Given the large size of the unit cell and the tests with other numbers of K-points from the original study, only results obtained from G-point calculations are reported here. Finally, heats of adsorption are now reported below along with E + ZPE values, while in the original manuscript only E + ZPE were reported. No changes were made to how the vibrational corrections were computed; however, we have included some additional details to ensure reproducibility.6 Harmonic vibrational modes (ωi) were computed for CO2 in the gas phase and its bound product state (amine-CO2-MOF complex). The framework itself was taken to be rigid and only the vibrational modes associated with the motion of the amine, the metal center, first coordination sphere (oxygen atoms bound to the metal in the MOF backbone), and (if present) the bound CO2 were computed. Since the harmonic approximation breaks down for low frequency modes, we replaced all modes less than 50 cm-1 with 50 cm-1 when computing the zero-point and thermal energies. The following standard harmonic expressions were used to compute the vibrational corrections: Zero-point vibrational energy (ZPE) is: [Equation presented here] While for the bound product, the rotational and translational degrees of freedom of CO2 have been converted to additional vibrational modes allowing one to compute the thermal correction simply as: [Equation presented here] 2. Values for the chain model The chain model used in our original study included 1 mmen- and 5 en-amines. The values from the original paper are reported in Table 1. When we repeat these calculations using the procedure described in Section 1, we obtain the values in Table 2. In addition to the chain model described above (1 mmen- and 5 en-amines per unit cell), during our original study we performed calculations with another model that was not included in the manuscript since its values yielded results further from experiment. This model includes only 1 mmen-amine per unit cell (no other amines) and was used to test the assumption that the five enamines are indeed spectators with respect to the metal dependence of the binding energy. We present the results from this model in Table 3. In the original paper we noted that the energy and bond length trends are correlated and are consistent with the Irving-Williams series. This is no longer true for all metals under investigation, with Zn being an outlier. The results for Zn can be explained by more recent work.1 3. Values for the pair model The model used to compute the "pair" adsorption mechanisms included 2 mmen-amines and 0 en-amines. The values in the original paper are presented in Table 5. 4. Lattice model plots The lattice models to generate adsorption isotherms for these systems were run at one temperature (∼25 °C) using four different input parameters. First the M06-L and PBE values from the original paper were used once more as it has been some time since we have run the lattice model. Then the model is repeated with the new set of values from PBE. If we compare Fig. 7 and 8, the order is preserved, but the infliction points are spaced a bit differently. This is due to the scaling factor being constant and is something we scaled for each of the different systems as well. The slope is also a bit different, but not more then we should expect for this simple lattice model. Furthermore, we only ever aimed to reproduce the step and the order of the metals. Any finer details cannot be expected to be obtained from this model. The exact values used to compute the isotherms are given in the tables below. The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.
Hedgehog signaling is required at multiple stages of zebrafish tooth development
Date: 2010-12-02
Creator: William R. Jackman, James J. Yoo, David W. Stock
Access: Open access
- Background. The accessibility of the developing zebrafish pharyngeal dentition makes it an advantageous system in which to study many aspects of tooth development from early initiation to late morphogenesis. In mammals, hedgehog signaling is known to be essential for multiple stages of odontogenesis; however, potential roles for the pathway during initiation of tooth development or in later morphogenesis are incompletely understood. Results. We have identified mRNA expression of the hedgehog ligands shha and the receptors ptc1 and ptc2 during zebrafish pharyngeal tooth development. We looked for, but did not detect, tooth germ expression of the other known zebrafish hedgehog ligands shhb, dhh, ihha, or ihhb, suggesting that as in mammals, only Shh participates in zebrafish tooth development. Supporting this idea, we found that morphological and gene expression evidence of tooth initiation is eliminated in shha mutant embryos, and that morpholino antisense oligonucleotide knockdown of shha, but not shhb, function prevents mature tooth formation. Hedgehog pathway inhibition with the antagonist compound cyclopamine affected tooth formation at each stage in which we applied it: arresting development at early stages and disrupting mature tooth morphology when applied later. These results suggest that hedgehog signaling is required continuously during odontogenesis. In contrast, over-expression of shha had no effect on the developing dentition, possibly because shha is normally extensively expressed in the zebrafish pharyngeal region. Conclusion. We have identified previously unknown requirements for hedgehog signaling for early tooth initiation and later morphogenesis. The similarity of our results with data from mouse and other vertebrates suggests that despite gene duplication and changes in the location of where teeth form, the roles of hedgehog signaling in tooth development have been largely conserved during evolution. © 2010 Jackman et al; licensee BioMed Central Ltd.
Probing mucin-type O-linked glycosylation in living animals
Date: 2006-03-28
Creator: Danielle H. Dube, Jennifer A. Prescher, Chi M. Quang, Carolyn R. Bertozzi
Access: Open access
- Changes in O-linked protein glycosylation are known to correlate with disease states but are difficult to monitor in a physiological setting because of a lack of experimental tools. Here, we report a technique for rapid profiling of O-linked glycoproteins in living animals by metabolic labeling with N-azidoacetylgalactosamine (GalNAz) followed by Staudinger ligation with phosphine probes. After injection of mice with a peracetylated form of GalNAz, azide-labeled glycoproteins were observed in a variety of tissues, including liver, kidney, and heart, in serum, and on isolated splenocytes. B cell glycoproteins were robustly labeled with GalNAz but T cell glycoproteins were not, suggesting fundamental differences in glycosylation machinery or metabolism. Furthermore, GalNAz-labeled B cells could be selectively targeted with a phosphine probe by Staudinger ligation within the living animal. Metabolic labeling with GalNAz followed by Staudinger ligation provides a means for proteomic analysis of this posttranslational modification and for identifying O-linked glycoprotein fingerprints associated with disease. © 2006 by The National Academy of Sciences of the USA.
Does Productivity Respond to Exchange Rate Appreciations? A Theoretical and Empirical Investigation
Date: 2010-12-15
Creator: Yao Tang
Access: Open access
- Although real currency appreciations pose direct difficulties for exporters and import-competing firms as they will face more intense competition, is it possible that such competition spurs firms to improve productivity? To answer this question, the paper first constructs a theoretical model to show how the competitive pressures of currency appreciations induce firms to improve productivity by adopting new technologies. In addition, the model predicts that during appreciations there will be a positive relation between market concentration and improvements in productivity for industries highly exposed to trade, because the marginal benefits of productivity improvement will be bigger for firms with a larger market share. The paper then examines Canadian manufacturing data from 1997 to 2006, and finds evidence consistent with model predictions. I find that growth rates of labor productivity were on average higher during the Canadian dollar appreciation between 2002 and 2006, after controlling for industry characteristics. Within the group of highly traded Canadian industries, the more concentrated ones experienced larger growth in labor productivity.
Where do the poor live in cities? Revisiting the role of public transportation on income sorting in US urban areas
Date: 2020-06-03
Creator: Erik Nelson
Access: Open access
- Glaeser et al. (2008) argue that the relative distribution of poor and rich households (HHs) in American cities is "strongly" explained by the spatial location of the cities' public transportation (PT) networks. Among their claims: 1) The broad distribution of poor and rich HHs in the typical American city is consistent with a basic monocentric city model that includes commute technology speeds; 2) Poor commuters will overwhelmingly transition from commuting by PT to car if they experience a substantial increase in their HH’s income; 3) areas in American cities that receive new PT infrastructure become poorer over time. Using 2017 data I find empirical evidence that partially or wholly contradicts these three claims. First, as of 2017, the observed concentration of poor HHs in the inner city and rich HHs in the suburbs of the US’ smaller cities cannot be explained by monocentric model that includes commute speeds. Second, as of 2017, significant increases in poor HHs’ incomes were not expected to lead to a "massive shift" towards car commuting in these HHs; most of these poor workers commute by car already. Third, using data from four cities that expanded their light-rail and rapid-bus network in the early 2000s, I find that neighborhoods surrounding new light-rail or rapid-bus stations either saw little change in their income patterns or became slightly richer after station opening. In conclusion, as of 2017, the spatial distribution of HH incomes within American urban areas is not as intricately linked to the location of PT networks as Glaeser et al. (2008) would have us believe. As an addendum to the analysis I add some thoughts on how the COVID-19 pandemic might affect commuting behavior and income distributions within urban areas over the next decade.
Responses of stomatal features and photosynthesis to porewater N enrichment and elevated atmospheric CO2 in Phragmites australis, the common reed
Date: 2021-04-01
Creator: Julian R. Garrison, Joshua S. Caplan, Vladimir Douhovnikoff, Thomas J. Mozdzer, Barry A. Logan
Access: Open access
- PREMISE: Biological invasions increasingly threaten native biodiversity and ecosystem services. One notable example is the common reed, Phragmites australis, which aggressively invades North American salt marshes. Elevated atmospheric CO2 and nitrogen pollution enhance its growth and facilitate invasion because P. australis responds more strongly to these enrichments than do native species. We investigated how modifications to stomatal features contribute to strong photosynthetic responses to CO2 and nitrogen enrichment in P. australis by evaluating stomatal shifts under experimental conditions and relating them to maximal stomatal conductance (gwmax) and photosynthetic rates. METHODS: Plants were grown in situ in open-top chambers under ambient and elevated atmospheric CO2 (eCO2) and porewater nitrogen (Nenr) in a Chesapeake Bay tidal marsh. We measured light-saturated carbon assimilation rates (Asat) and stomatal characteristics, from which we calculated gwmax and determined whether CO2 and Nenr altered the relationship between gwmax and Asat. RESULTS: eCO2 and Nenr enhanced both gwmax and Asat, but to differing degrees; gwmax was more strongly influenced by Nenr through increases in stomatal density while Asat was more strongly stimulated by eCO2. There was a positive relationship between gwmax and Asat that was not modified by eCO2 or Nenr, individually or in combination. CONCLUSIONS: Changes in stomatal features co-occur with previously described responses of P. australis to eCO2 and Nenr. Complementary responses of stomatal length and density to these global change factors may facilitate greater stomatal conductance and carbon gain, contributing to the invasiveness of the introduced lineage.