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A mechanistic stochastic framework for regulating bacterial cell division
(Nature Publishing Group, 7/26/16) Ghusinga,Khem Raj; Vargas-Garcia,Cesar A.; Singh,Abhyudai; Khem Raj Ghusinga, Cesar A. Vargas-Garcia,Abhyudai Singh; Singh, Abhyudai
How exponentially growing cells maintain size homeostasis is an important fundamental problem. Recent single-cell studies in prokaryotes have uncovered the adder principle, where cells add a fixed size (volume) from birth to division, irrespective of their size at birth. To mechanistically explain the adder principle, we consider a timekeeper protein that begins to get stochastically expressed after cell birth at a rate proportional to the volume. Cell-division time is formulated as the first-passage time for protein copy numbers to hit a fixed threshold. Consistent with data, the model predicts that the noise in division timing increases with size at birth. Intriguingly, our results show that the distribution of the volume added between successive cell-division events is independent of the newborn cell size. This was dramatically seen in experimental studies, where histograms of the added volume corresponding to different newborn sizes collapsed on top of each other. The model provides further insights consistent with experimental observations: the distribution of the added volume when scaled by its mean becomes invariant of the growth rate. In summary, our simple yet elegant model explains key experimental findings and suggests a mechanism for regulating both the mean and fluctuations in cell-division timing for controlling size.
A multi-decade record of high-quality fCO(2) data in version 3 of the Surface Ocean CO2 Atlas (SOCAT)
(Copernicus Gesellschaft MBH, 9/15/16) Bakker,Dorothee C. E.; Pfeil,Benjamin; Landa,Camilla S.; Metzl,Nicolas; O'Brien,Kevin M.; Olsen,Are; Smith,Karl; Cosca,Cathy; Harasawa,Sumiko; Jones,Stephen D.; Nakaoka,Shin-ichiro; Nojiri,Yukihiro; Schuster,Ute; Steinhoff,Tobias; Sweeney,Colm; Takahashi,Taro; Tilbrook,Bronte; Wada,Chisato; Wanninkhof,Rik; Alin,Simone R.; Balestrini,Carlos F.; Barbero,Leticia; Bates,Nicholas R.; Bianchi,Alejandro A.; Bonou,Frederic; Boutin,Jacqueline; Bozec,Yann; Burger,Eugene F.; Cai,Wei-Jun; Castle,Robert D.; Chen,Liqi; Chierici,Melissa; Currie,Kim; Evans,Wiley; Featherstone,Charles; Feely,Richard A.; Fransson,Agneta; Goyet,Catherine; Greenwood,Naomi; Gregor,Luke; Hankin,Steven; Hardman-Mountford,Nick J.; Harlay,Jerome; Hauck,Judith; Hoppema,Mario; Humphreys,Matthew P.; Hunt,ChristopherW; Huss,Betty; Ibanhez,J. Severino P.; Johannessen,Truls; Keeling,Ralph; Kitidis,Vassilis; Koertzinger,Arne; Kozyr,Alex; Krasakopoulou,Evangelia; Kuwata,Akira; Landschuetzer,Peter; Lauvset,Siv K.; Lefevre,Nathalie; Lo Monaco,Claire; Manke,Ansley; Mathis,Jeremy T.; Merlivat,Liliane; Millero,Frank J.; Monteiro,Pedro M. S.; Munro,David R.; Murata,Akihiko; Newberger,Timothy; Omar,Abdirahman M.; Ono,Tsuneo; Paterson,Kristina; Pearce,David; Pierrot,Denis; Robbins,Lisa L.; Saito,Shu; Salisbury,Joe; Schlitzer,Reiner; Schneider,Bernd; Schweitzer,Roland; Sieger,Rainer; Skjelvan,Ingunn; Sullivan,Kevin F.; Sutherland,Stewart C.; Sutton,Adrienne J.; Tadokoro,Kazuaki; Telszewski,Maciej; Tuma,Matthias; van Heuven,Steven M. A. C.; Vandemark,Doug; Ward,Brian; Watson,Andrew J.; Xu,Suqing; Dorothee C. E. Bakker, Benjamin Pfeil, Camilla S. Landa, Nicolas Metzl, Kevin M. OBrien,Are Olsen, Karl Smith, Cathy Cosca, Sumiko Harasawa, Stephen D. Jones,Shin-ichiro Nakaoka, Yukihiro Nojiri, Ute Schuster, Tobias Steinhoff, Colm Sweeney, Taro Takahashi, Bronte Tilbrook, Chisato Wada, Rik Wanninkhof, Simone R. Alin,Carlos F. Balestrini, Leticia Barbero, Nicholas R. Bates, Alejandro A. Bianchi,Fr_d_ric Bonou, Jacqueline Boutin, Yann Bozec21, Eugene F. Burger5, Wei-Jun Cai,Robert D. Castle, Liqi Chen, Melissa Chierici, Kim Currie, Wiley Evans, Charles Featherstone, Richard A. Feely, Agneta Fransson, Catherine Goyet,Naomi Greenwood, Luke Gregor, Steven Hankin, Nick J. Hardman-Mountford, J_rome Harlay, Judith Hauck, Mario Hoppema, Matthew P. Humphreys,ChristopherW. Hunt, Betty Huss, J. Severino P. Ibanhez, Truls Johannessen, Ralph Keeling, Vassilis Kitidis, Arne K_rtzinger, Alex Kozyr, Evangelia Krasakopoulou,Akira Kuwata, Peter Landschuetzer, Siv K. Lauvset, Nathalie Lefevre, Claire Lo Monaco,Ansley Manke, Jeremy T. Mathis, Liliane Merlivat, Frank J. Millero, Pedro M. S. Monteiro,David R. Munro, Akihiko Murata, Timothy Newberger, Abdirahman M. Omar,Tsuneo Ono, Kristina Paterson, David Pearce, Denis Pierrot, Lisa L. Robbins, Shu Saito, Joe Salisbury, Reiner Schlitzer, Bernd Schneider, Roland Schweitzer, Rainer Sieger,Ingunn Skjelvan, Kevin F. Sullivan, Stewart C. Sutherland, Adrienne J. Sutton,Kazuaki Tadokoro, Maciej Telszewski, Matthias Tuma, Steven M. A. C. van Heuven,Doug Vandemark, Brian Ward, Andrew J. Watson, and Suqing Xu; Cai, Wei-Jun
The Surface Ocean CO2 Atlas (SOCAT) is a synthesis of quality-controlled fCO(2) (fugacity of carbon dioxide) values for the global surface oceans and coastal seas with regular updates. Version 3 of SOCAT has 14.7 million fCO(2) values from 3646 data sets covering the years 1957 to 2014. This latest version has an additional 4.6 million fCO(2) values relative to version 2 and extends the record from 2011 to 2014. Version 3 also significantly increases the data availability for 2005 to 2013. SOCAT has an average of approximately 1.2 million surface water fCO(2) values per year for the years 2006 to 2012. Quality and documentation of the data has improved. A new feature is the data set quality control (QC) flag of E for data from alternative sensors and platforms. The accuracy of surface water fCO(2) has been defined for all data set QC flags. Automated range checking has been carried out for all data sets during their upload into SOCAT. The upgrade of the interactive Data Set Viewer (previously known as the Cruise Data Viewer) allows better interrogation of the SOCAT data collection and rapid creation of high-quality figures for scientific presentations. Automated data upload has been launched for version 4 and will enable more frequent SOCAT releases in the future. High-profile scientific applications of SOCAT include quantification of the ocean sink for atmospheric carbon dioxide and its long-term variation, detection of ocean acidification, as well as evaluation of coupled-climate and ocean-only biogeochemical models. Users of SOCAT data products are urged to acknowledge the contribution of data providers, as stated in the SOCAT Fair Data Use Statement. This ESSD (Earth System Science Data) "living data" publication documents the methods and data sets used for the assembly of this new version of the SOCAT data collection and compares these with those used for earlier versions of the data collection (Pfeil et al., 2013; Sabine et al., 2013; Bakker et al., 2014).Individual data set files, included in the synthesis product, can be downloaded here: doi:10.1594/PANGAEA.849770. The gridded products are available here: doi: 10.3334/CDIAC/OTG.SOCAT_V3_GRID.
A multiscale 3D finite element analysis of fluid/solute transport in mechanically loaded bone
(Nature Publishing Group, 9/27/16) Fan,Lixia; Pei,Shaopeng; Lu,X. Lucas; Wang,Liyun; Lixia Fan, Shaopeng Pei,X Lucas Lu,Liyun Wang; Wang, Liyun
The transport of fluid, nutrients, and signaling molecules in the bone lacunar-canalicular system (LCS) is critical for osteocyte survival and function. We have applied the fluorescence recovery after photobleaching (FRAP) approach to quantify load-induced fluid and solute transport in the LCS in situ, but the measurements were limited to cortical regions 30-50 mu m underneath the periosteum due to the constrains of laser penetration. With this work, we aimed to expand our understanding of load-induced fluid and solute transport in both trabecular and cortical bone using a multiscaled image-based finite element analysis (FEA) approach. An intact murine tibia was first re-constructed from microCT images into a three-dimensional (3D) linear elastic FEA model, and the matrix deformations at various locations were calculated under axial loading. A segment of the above 3D model was then imported to the biphasic poroelasticity analysis platform (FEBio) to predict load-induced fluid pressure fields, and interstitial solute/fluid flows through LCS in both cortical and trabecular regions. Further, secondary flow effects such as the shear stress and/or drag force acting on osteocytes, the presumed mechano-sensors in bone, were derived using the previously Developmenteloped ultrastructural model of Brinkman flow in the canaliculi. The material properties assumed in the FEA models were validated against previously obtained strain and FRAP transport data measured on the cortical cortex. Our results demonstrated the feasibility of this computational approach in estimating the fluid flux in the LCS and the cellular stimulation forces (shear and drag forces) for osteocytes in any cortical and trabecular bone locations, allowing further studies of how the activation of osteocytes correlates with in vivo functional bone formation. The study provides a promising platform to reveal potential cellular mechanisms underlying the anabolic power of exercises and physical activities in treating patients with skeletal deficiencies.
A new tribe of Tropiduchidae (Hemiptera: Fulgoroidea) with revision of the genus Buca and description of asymmetric hind leg spinulation
(Florida Entomological Society, 2016-9) Gnezdilov,Vladimir M.; Bartlett,Charles R.; Bourgoin,Thierry; Vladimir M. Gnezdilov, Charles R. Bartlett, Thierry Bourgoin; Bartlett, Charles R
A new tribe Bucini trib. nov. is erected for the genus Buca Walker, 1858 in Tropiduchidae (Elicinae), with a discussion of tribal features with respect to the New World fauna. Two new species of Buca are described from Ecuador (Buca asymmetrospinata sp. nov.) and French Guiana (Buca truncoptera sp. nov.). Keys to Buca species and to higher taxa of New World Tropiduchidae are provided. Male and female genitalia of Buca species are illustrated for the first time.
A parallel fictitious domain method for the interface-resolved simulation of particle-laden flows and its application to the turbulent channel flow
(Hong Kong Polytechnic University, Department of Civil and Structural Engineering, 1/20/16) Yu,Zhaosheng; Lin,Zhaowu; Shao,Xueming; Wang,Lian-Ping; Zhaosheng Yu, Zhaowu Lin, Xueming Shao , Lian-Ping Wang; Wang, Lian-Ping
A parallel direct-forcing (DF) fictitious domain (FD) method for the simulation of particulate flows is reported in this paper. The parallel computing strategies for the solution of flow fields and particularly the distributed Lagrange multiplier are presented, and the high efficiency of the parallel code is demonstrated. The new code is then applied to study the effects of particle density (or particle inertia) on the turbulent channel flow. The results show that the large-scale vortices are weakened more severely, and the flow friction drag increases first and then reduces, as particle inertia is increased.
A Simple Adaptive Transfer Function for Deriving the Central Blood Pressure Waveform from a Radial Blood Pressure Waveform
(Nature Publishing Group, 9/14/16) Gao,Mingwu; Rose,William C.; Fetics,Barry; Kass,David A.; Chen,Chen-Huan; Mukkamala,Ramakrishna; Mingwu Gao, William C. Rose, Barry Fetics, David A. Kass, Chen-Huan Chen, Ramakrishna Mukkamala; Rose, William C
Generalized transfer functions (GTFs) are available to compute the more relevant central blood pressure (BP) waveform from a more easily measured radial BP waveform. However, GTFs are population averages and therefore may not adapt to variations in pulse pressure (PP) amplification (ratio of radial to central PP). A simple adaptive transfer function (ATF) was Developmenteloped. First, the transfer function is defined in terms of the wave travel time and reflection coefficient parameters of an arterial model. Then, the parameters are estimated from the radial BP waveform by exploiting the observation that central BP waveforms exhibit exponential diastolic decays. The ATF was assessed using the original data that helped popularize the GTF. These data included radial BP waveforms and invasive reference central BP waveforms from cardiac catheterization patients. The data were divided into low, middle, and high PP amplification groups. The ATF estimated central BP with greater accuracy than GTFs in the low PP amplification group (e.g., central systolic BP and PP root-mean-square-errors of 3.3 and 4.2 mm Hg versus 6.2 and 7.1 mm Hg; p <= 0.05) while showing similar accuracy in the higher PP amplification groups. The ATF may permit more accurate, non-invasive central BP monitoring in elderly and hypertensive patients.
A stochastic model of solid state thin film deposition: Application to chalcopyrite growth
(Americanican Institute of Physics, 4/26/16) Lovelett,Robert J.; Pang,Xueqi; Roberts,Tyler M.; Shafarman,William N.; Birkmire,Robert W.; Ogunnaike,Babatunde A.; Robert J. Lovelett, Xueqi Pang, Tyler M. Roberts, William N. Shafarman,Robert W. Birkmire, and Babatunde A. Ogunnaike; Shafarman, William N; Birkmire, Robert W; Ogunnaike Babatunde A
Developmenteloping high fidelity quantitative models of solid state reaction systems can be challenging, especially in deposition systems where, in addition to the multiple competing processes occurring simultaneously, the solid interacts with its atmosphere. In this work, we Developmentelop a model for the growth of a thin solid film where species from the atmosphere adsorb, diffuse, and react with the film. The model is mesoscale and describes an entire film with thickness on the order of microns. Because it is stochastic, the model allows us to examine inhomogeneities and agglomerations that would be impossible to characterize with deterministic methods. We demonstrate the modeling approach with the example of chalcopyrite Cu(InGa)(SeS)(2) thin film growth via precursor reaction, which is a common industrial method for fabricating thin film photovoltaic modules. The model is used to understand how and why through-film variation in the composition of Cu(InGa)(SeS)(2) thin films arises and persists. We believe that the model will be valuable as an effective quantitative description of many other materials systems used in semiconductors, energy storage, and other fast-growing industries. (C) 2016 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
A Structural Equation Model of HIV-Related Stigma, Racial Discrimination, Housing Insecurity and Wellbeing among African and Caribbean Black Women Living with HIV in Ontario, Canada
(Public Library of Science, 9/26/16) Logie,Carmen H.; Jenkinson,Jesse I. R.; Earnshaw,Valerie; Tharao,Wangari; Loutfy,Mona R.; Carmen H. Logie, Jesse I. R. Jenkinson, Valerie Earnshaw, Wangari Tharao, Mona R. Loutfy; Earnshaw, Valerie A
African and Caribbean Black women in Canada have new HIV infection rates 7 times higher than their white counterparts. This overrepresentation is situated in structural contexts of inequities that result in social, economic and health disparities among African and Caribbean Black populations. Economic insecurity is a distal driver of HIV vulnerability, reducing access to HIV testing, prevention and care. Less is known about how economic insecurity indicators, such as housing security, continue to influence the lives of women living with HIV following HIV-positive diagnoses. The aim of this study was to test a conceptual model of the pathways linking HIV-related stigma, racial discrimination, housing insecurity, and wellbeing (depression, social support, self-rated health). We implemented a cross-sectional survey with African and Caribbean Black women living with HIV in 5 Ontario cities, and included 157 participants with complete data in the analyses. We conducted structural equation modeling using maximum likelihood estimation to evaluate the hypothesized conceptual model. One-fifth (22.5%; n = 39) of participants reported housing insecurity. As hypothesized, racial discrimination had significant direct effects on: HIV-related stigma, depression and social support, and an indirect effect on self-rated health via HIV-related stigma. HIV-related stigma and housing insecurity had direct effects on depression and social support, and HIV-related stigma had a direct effect on self-rated health. The model fit the data well: chi(2) (45, n = 154) = 54.28, p = 0.387; CFI = 0.997; TLI = 0.996; RMSEA = 0.016. Findings highlight the need to address housing insecurity and intersecting forms of stigma and discrimination among African and Caribbean Black women living with HIV. Understanding the complex relationships between housing insecurity, HIV-related stigma, racial discrimination, and wellbeing can inform multi-level interventions to reduce stigma and enhance health.
Adsorption of 2-propanol on ice probed by ambient pressure X-ray photoelectron spectroscopy
(Royal Society of Chemistry, 2015-08-18) Newberg, John T.; Bluhm, Hendrik; John T. Newberg and Hendrik Bluhm; Newberg, John T.
The interaction of 2-propanol with ice was examined via ambient pressure X-ray photoelectron spectroscopy (APXPS), a surface sensitive technique that probes the adsorbed 2-propanol directly with submonolayer resolution. Isothermal uptake experiments were performed on vapor deposited ice at 227 K in the presence of the equilibrium water vapor pressure of 0.05 Torr and 2-propanol partial pressures ranging from 5 × 10−5 to 2 × 10−3 Torr. The C 1s APXPS spectra of adsorbed 2-propanol showed two characteristic peaks associated with the COH alcohol group and CMe methyl groups in a 1 : 2 ratio, respectively. Coverage increased with 2-propanol partial pressure and followed first order Langmuir kinetics with a Langmuir constant of K = 6.3 × 103 Torr−1. The 1 : 2 ratio of COH : CMe remained constant with increasing coverage, indicating there is no chemical reaction upon adsorption. The observed Langmuir kinetics using APXPS is consistent with previous observations of other small chain alcohols via indirect adsorption methods using, e.g., Knudsen cell and coated wall flow tube reactors. Graphical abstract: Adsorption of 2-propanol on ice probed by ambient pressure X-ray photoelectron spectroscopy
Agents of change and temporal nutrient dynamics in the Altamaha River Watershed
(Ecological Society of America, 2017-01-23) Takagi, Kimberly K.; Hunter, Kimberley S.; Cai, Wei-Jun; Joye, Samantha B.; Kimberly K. Takagi, Kimberley S. Hunter, Wei-Jun Cai, and Samantha B. Joye; Cai, Wei-Jun
Nutrient and carbon dynamics in river ecosystems are shifting, and climate change is likely a driving factor; however, some previous studies indicate anthropogenic modification of natural resources may supersede the effects of climate. To understand temporal changes in river ecosystems, consideration of how these agents act independently and collectively to affect watershed biogeochemistry is necessary. Through the Georgia Coastal Ecosystems Long-Term Ecological Research Project, we assessed nutrient (phosphorus, nitrogen, silicate) and carbon dynamics, with specific regard to import and export, in the Altamaha River Basin from 2000 to 2012. This is the first study in the region to document the biogeochemical patterns in the Altamaha’s four main tributaries, the Little Ocmulgee, Ocmulgee, Oconee, and Ohoopee rivers, and the relationships between biogeochemistry and historical precipitation and discharge patterns as well as agricultural and population census data. As discharge patterns are a primary driver of nutrient loads, we determined that water use was a dominant factor in the shifting ecosystem dynamics. Dissolved inorganic nitrogen loads were primarily driven by population density and dissolved inorganic phosphorus loads were strongly influenced by livestock biomass. Taken together, we conclude that both the transportation and biogeochemical cycling of nutrients within the Altamaha River Watershed were highly impacted by anthropogenic influences, which were then further exacerbated by continued climate change. Furthermore, the N-and P-loads in the Altamaha River and tributaries were dominated by dissolved organic nitrogen and dissolved organic phosphorus, emphasizing a need to further study the bioavailability of these species and the mechanisms driving their potential ecological impacts.
An all-copper plasmonic sandwich system obtained through directly depositing copper NPs on a CVD grown graphene/copper film and its application in SERS
(Royal Society of Chemistry, 2015-05-11) Li, Xuanhua; Ren, Xingang; Zhang, Yongxing; Choy, Wallace C. H.; Wei, Bingqing; Xuanhua Li, Xingang Ren, Yongxing Zhang, Wallace C. H. Choy and Bingqing Wei; Wei, Bingqing
A simple, low-cost, all-copper sandwich system has been obtained through directly depositing Cu nanoparticles (NPs) onto a graphene sheet, which has already been grown on a Cu foil (Cu-NGF). The new design inherits two key advantages: (1) the materials of the NGF coupling system are composed of only cheaper Cu instead of Au and Ag, (2) direct fabrication of the system without transferring graphene will greatly lower the fabrication cost. More importantly, the Cu-NFG system shows a high sensitivity in surface-enhanced Raman scattering (SERS) with the highest enhancement factor (EF, over 1.89 × 107) reported to date in Cu plasmonic systems. Experimental and theoretical results reveal that the strong EF is mainly because of the strong near-field coupling between Cu NPs and Cu films at the optimal angle of incidence, opening up a new route for Cu materials in SERS applications.
An Analytical Approach for Levee Underseepage Analysis
(Elsevier B. V., 2012) Meehan, Christopher L.; Benjasupattananan, Sittinan; Meehan, Christopher L., Benjasupattananan, Sittinan; Meehan, Christopher L.
Levee underseepage analyses are commonly performed to assess the risk of erosion and piping of levee foundation soils. They are also commonly used to estimate the quantity of seepage that is expected to pass beneath a levee over time, and to assess the risk of excessively high pore pressures at various points in the foundation. A variety of approaches have historically been utilized to perform steady-state underseepage analyses in levees, including flow-nets, closed-form analytical solutions, and numerical techniques such as finite difference or finite element analyses. This paper provides a derivation of a series of closed-form \blanket theory" analytical equations that can be used to perform a levee underseepage analysis. This derivation starts from a generic confined flow analytical solution, of the type that is common in groundwater flow analyses. The solution is then extended to simulate semiconfined flow beneath a levee in a shallow aquifer. Equations are presented for calculating total head and seepage quantity values for different model boundary conditions. A typical example problem is used to compare the analytical equations that are derived with the analytical equations that are presented in the US Army Corps of Engineers (USACE) levee design manual. The results provide validation for both the equations that are presented and the conventional USACE analytical design approach. Using the results from the example problem, general guidance and suggestions are provided for designers that use closed-form analytical approaches for modeling levee underseepage.
Analyses of point mutation repair and allelic heterogeneity generated by CRISPR/Cas9 and single-stranded DNA oligonucleotides
(Nature Publishing Group, 9/9/16) Bialk,Pawel; Sansbury,Brett; Rivera-Torres,Natalia; Bloh,Kevin; Man,Dula; Kmiec,Eric B.; Pawel Bialk, Brett Sansbury, Natalia Rivera-Torres, Kevin Bloh, Dula Man,Eric B. Kmiec; Kmiec, Eric
The repair of a point mutation can be facilitated by combined activity of a single-stranded oligonucleotide and a CRISPR/Cas9 system. While the mechanism of action of combinatorial gene editing remains to be elucidated, the regulatory circuitry of nucleotide exchange executed by oligonucleotides alone has been largely defined. The presence of the appropriate CRISPR/Cas9 system leads to an enhancement in the frequency of gene editing directed by single-stranded DNA oligonucleotides. While CRISPR/Cas9 executes double-stranded DNA cleavage efficiently, closure of the broken chromosomes is dynamic, as varying degrees of heterogeneity of the cleavage products appear to accompany the emergence of the corrected base pair. We provide a detailed analysis of allelic variance at and surrounding the target site. In one particular case, we report sequence alteration directed by a distinct member of the same gene family. Our data suggests that single-stranded DNA molecules may influence DNA junction heterogeneity created by CRISPR/Cas9.
An ‘analytic dynamical magnetosphere’ formalism for X-ray and optical emission from slowly rotating magnetic massive stars
(Oxford University Press on behalf of the Royal Astronomical Society., 2016-08-01) Owocki, Stanley P.; ud-Doula, Asif; Sundqvist, Jon O.; Petit, Veronique; Cohen, David H.; Townsend, Richard H. D.; Stanley P. Owocki, Asif ud-Doula, Jon O. Sundqvist, Veronique Petit, David H. Cohen, and Richard H. D. Townsend; Owocki, Stanley P.
Slowly rotating magnetic massive stars develop ‘dynamical magnetospheres’ (DMs), characterized by trapping of stellar wind outflow in closed magnetic loops, shock heating from collision of the upflow from opposite loop footpoints, and subsequent gravitational infall of radiatively cooled material. In 2D and 3D magnetohydrodynamic (MHD) simulations, the interplay among these three components is spatially complex and temporally variable, making it difficult to derive observational signatures and discern their overall scaling trends. Within a simplified, steady-state analysis based on overall conservation principles, we present here an ‘analytic dynamical magnetosphere’ (ADM) model that provides explicit formulae for density, temperature, and flow speed in each of these three components – wind outflow, hot post-shock gas, and cooled inflow – as a function of colatitude and radius within the closed (presumed dipole) field lines of the magnetosphere. We compare these scalings with time-averaged results from MHD simulations, and provide initial examples of application of this ADM model for deriving two key observational diagnostics, namely hydrogen H α emission line profiles from the cooled infall, and X-ray emission from the hot post-shock gas. We conclude with a discussion of key issues and advantages in applying this ADM formalism towards derivation of a broader set of observational diagnostics and scaling trends for massive stars with such dynamical magnetospheres.
Analytical Approach for Modeling Axisymmetric Levee Underseepage
(American Society of Civil Engineers., 2014) Benjasupattananan, Sittinan; Meehan, Christopher L.; Meehan, Christopher L., Benjasupattananan, Sittinan; Meehan, Christopher L. (orcid.org/0000-0002-9721-6275); Benjasupattananan, Sittinan
A variety of real-world levee underseepage problems can best be modeled using an axisymmetric analysis approach. In current practice, axisymmetric levee underseepage analyses are performed using numerical modeling approaches, such as the FEM. In contrast, levee underseepage analyses of planar cross sections are often analyzed using a blanket theory analytical approach, which is quicker and more convenient than numerical modeling. To address this problem, this paper provides a derivation of a series of closed-form blanket theory analytical equations that can be used to perform an axisymmetric levee underseepage analysis. This derivation begins from the governing equation of semiconfined uid ow beneath a levee in a shallow semiconfined aquifer. The equations that result from this derivation can be used to calculate the total head in the pervious foundation layer and the seepage quantity that passes through the levee foundation over time. Different equations are presented for different seepage directions relative to the axis of rotation and different model boundary conditions. A typical example problem is used to compare results from the axisymmetric analytical equations that are derived with those from axisymmetric finite-element analyses. For this example problem, the analytical equations yield results that are equal to or more conservative than those from the finite-element analysis, where conservative results correspond to greater seepage under the levee and higher heads at the levee toe.
Analytical imaging studies of the migration of degraded orpiment, realgar, and emerald green pigments in historic paintings and related conservation issues
(Springer Open, 2016-04-21) Keune, Katrien; Mass, Jennifer; Mehta, Apurva; Church, Jonathan; Meirer, Florian; Katrien Keune, Jennifer Mass, Apurva Mehta, Jonathan Church and Florian Meirer; Churhc, Jonathan
Yellow orpiment (As2S3) and red–orange realgar (As4S4) photo-degrade and the nineteenth-century pigment emerald green (Cu(C2H3O2)2·3Cu(AsO2)2) degrades into arsenic oxides. Because of their solubility in water, arsenic oxides readily migrate and are found throughout the multi-layered paint system. The widespread arsenic migration has consequences for conservation, and this paper provides better insight into the extent of the problem. Five paint samples containing orpiment, realgar or emerald green pigments deriving from paintings by De Heem (17th C), Van Gogh (19th C), Rousseau (19th C), an unknown 17th C northern European artist and an Austrian painted cupboard (19th C) were investigated using SEM/EDX, imaging ATR-FTIR and arsenic (As) K–edge μ-XANES to obtain the spatial distribution and chemical speciation of arsenic in the paint system. In all of the samples investigated arsenic had migrated throughout the multi-layered paint structure of the art object, from support to varnish. Furthermore, As5+-species were found throughout the entire paint sample. We hypothesize that arsenic trioxide is first formed, dissolves in water, further oxidizes to arsenic pentaoxide, and then reacts with lead, calcium and other ions and is deposited in the paint system as insoluble arsenates. Since the degradation of arsenic pigments such as orpiment, realgar and emerald green occurs through a highly mobile intermediate stage, it not only affects the regions rich in arsenic pigments, but also the entire object, including substrate and top varnish layers. Because of this widespread potential for damage, preventing degradation of arsenic pigments should be prioritized and conservators should minimize exposure of objects containing arsenic pigments to strong light, large fluctuations in relative humidity and water-based cleaning agents.
And on top of all that…: Coping with ocean acidification in the midst of many stressors
(The Oceanography Society., 2015-06-01) Breitburg, Denise L.; Salisbury, Joseph; Bernhard, Joan M.; Cai, Wei-Jun; Dupont, Sam; Doney, Scott C.; Kroeker, Kristy J.; Levin, Lisa A.; Long, Christopher; Milke, Lisa M.; Miller, Seth H.; Phelan, Beth; Passow, Uta; Seibel, Brad A.; Todgham, Anne E.; Tarrant, Ann M.; Denise L. Breitburg, Joseph Salisbury, Joan M. Bernhard, Wei-Jun Cai, Sam Dupont, Scott C. Doney, Kristy J. Kroeker, Lisa A. Levin, W. Christopher Long, Lisa M. Milke, Seth H. Miller, Beth Phelan, Uta Passow, Brad A. Seibel, Anne E. Todgham, and Ann M. Tarrant; Cai, Wei-Jun
Oceanic and coastal waters are acidifying due to processes dominated in the open ocean by increasing atmospheric CO2 and dominated in estuaries and some coastal waters by nutrient-fueled respiration. The patterns and severity of acidification, as well as its effects, are modified by the host of stressors related to human activities that also influence these habitats. Temperature, deoxygenation, and changes in food webs are particularly important co-stressors because they are pervasive, and both their causes and effects are often mechanistically linked to acidification. Development of a theoretical underpinning to multiple stressor research that considers physiological, ecological, and evolutionary perspectives is needed because testing all combinations of stressors and stressor intensities experimentally is impossible. Nevertheless, use of a wide variety of research approaches is a logical and promising strategy for improving understanding of acidification and its effects. Future research that focuses on spatial and temporal patterns of stressor interactions and on identifying mechanisms by which multiple stressors affect individuals, populations, and ecosystems is critical. It is also necessary to incorporate consideration of multiple stressors into management, mitigation, and adaptation to acidification and to increase public and policy recognition of the importance of addressing acidification in the context of the suite of other stressors with which it potentially interacts.
Antarctic sea-ice thickness and volume estimates from ice charts between 1995 and 1998
(International Glaciological Society, 2015-10-01) Bernstein, E. Rachel; Geiger, Cathleen A.; DeLiberty, Tracy L.; Lemcke-Stampone, Mary D.; E. Rachel BERNSTEIN, Cathleen A. GEIGER, Tracy L. DeLIBERTY, Mary D. LEMCKE-STAMPONE; Bernstein, E. Rachel; Geiger, Cathleen A.; DeLiberty, Tracy L.
This work evaluates two distinct calculations of central tendency for sea-ice thickness and quantifies the impact such calculations have on ice volume for the Southern Ocean. The first calculation, area-weighted average thickness, is computed from polygonal ice features and then upscaled to regions. The second calculation, integrated thickness, is a measure of the central value of thickness categories tracked across different scales and subsequently summed to chosen regions. Both methods yield the same result from one scale to the next, but subsequent scales develop diverging solutions when distributions are strongly non-Gaussian. Data for this evaluation are sea-ice stage-ofdevelopment records from US National Ice Center ice charts from 1995 to 1998, as proxy records of ice thickness. Results show regionally integrated thickness exceeds area-weighted average thickness by as much as 60% in summer with as few as five bins in thickness distribution. Year-round, the difference between the two calculations yields volume differences consistently >10%. The largest discrepancies arise due to bimodal distributions which are common in ice charts based on current subjective-analysis protocols. We recommend that integrated distribution be used for regional-scale sea-ice thickness and volume estimates from ice charts and encourage similar testing of other large-scale thickness data archives.
Antibody-nanoparticle conjugates to enhance the sensitivity of ELISA-based detection methods
(Public Library of Science (PLOS), 2017-05-11) Billingsley, Margaret M.; Riley, Rachel S.; Day, Emily S.; Margaret M. Billingsley, Rachel S. Riley, Emily S. Day; Billingsley, Margaret M.; Riley, Rachel S.; Day, Emily S.
Accurate antigen detection is imperative for clinicians to diagnose disease, assess treatment success, and predict patient prognosis. The most common technique used for the detection of disease-associated biomarkers is the enzyme linked immunosorbent assay (ELISA). In an ELISA, primary antibodies are incubated with biological samples containing the biomarker of interest. Then, detectible secondary antibodies conjugated with horseradish peroxidase (HRP) bind the primary antibodies. Upon addition of a color-changing substrate, the samples provide a colorimetric signal that directly correlates to the targeted biomarker concentration. While ELISAs are effective for analyzing samples with high biomarker content, they lack the sensitivity required to analyze samples with low antigen levels. We hypothesized that the sensitivity of ELISAs could be enhanced by replacing freely delivered primary antibodies with antibody-nanoparticle conjugates that provide excess binding sites for detectible secondary antibodies, ultimately leading to increased signal. Here, we investigated the use of nanoshells (NS) decorated with antibodies specific to epidermal growth factor receptor (EGFR) as a model system (EGFR-NS). We incubated one healthy and two breast cancer cell lines, each expressing different levels of EGFR, with EGFR-NS, untargeted NS, or unconjugated EGFR antibodies, as well as detectable secondary antibodies. We found that EGFR-NS consistently increased signal intensity relative to unconjugated EGFR antibodies, with a substantial 13-fold enhancement from cells expressing high levels of EGFR. Additionally, 40x more unconjugated antibodies were required to detect EGFR compared to those conjugated to NS. Our results demonstrate that antibody-nanoparticle conjugates lower the detection limit of traditional ELISAs and support further investigation of this strategy with other antibodies and nanoparticles. Owing to their enhanced sensitivity, we anticipate that nanoparticle-modified ELISAs can be used to detect low levels of biomarkers found in various diseases, such as cancers, tuberculosis, and rheumatoid arthritis, and may ultimately enable earlier diagnosis, better prognostication, and improved treatment monitoring
ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis
(Public Library of Science (PLoS), 2017-02-23) Yu, Yu; Ji, Lijuan; Le, Brandon H.; Zhai, Jixian; Chen, Jiayi; Lusche, Elizabeth; Gao, Lei; Liu, Chunyan; Cao, Xiaofeng; Mo, Beixin; Ma, Jinbiao; Meyers, Blake C.; Chen, Xuemei; Yu Yu, Lijuan Ji, Brandon H. Le, Jixian Zhai, Jiayi Chen, Elizabeth Luscher, Lei Gao, Chunyan Liu, Xiaofeng Cao, Beixin Mo, Jinbiao Ma, Blake C. Meyers, Xuemei Chen; Zhai, Jixian; Meyers, Blake C.
The degradation of small RNAs in plants and animals is associated with small RNA 30 truncation and 30 uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) effector in Arabidopsis, and its closest homolog, AGO10, maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we show that SMALL RNA DEGRADING NUCLEASES (SDNs) initiate miRNA degradation by acting on AGO1-bound miRNAs to cause their 30 truncation, and the truncated species are uridylated and degraded. We report that AGO10 reduces miR165/6 accumulation by enhancing its degradation by SDN1 and SDN2 in vivo. In vitro, AGO10-bound miR165/6 is more susceptible to SDN1-mediated 30 truncation than AGO1-bound miR165/ 6. Thus, AGO10 promotes the degradation of miR165/6, which is contrary to the stabilizing effect of AGO1. Our work identifies a class of exonucleases responsible for miRNA 30 truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, suggests that spatially regulated miRNA degradation underlies stem cell maintenance in plants.

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