bluuebunny/crossref_metadata_2025 huggingface dataset:
High intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma
Authors: Mroz Edmund A. , Tward Aaron D. , Pickering Curtis R. , Myers Jeffrey N. , Ferris Robert L. , Rocco James W.
Published: May 2013

BACKGROUND

Although the presence of genetic heterogeneity within the tumors of individual patients is established, it is unclear whether greater heterogeneity predicts a worse outcome. A quantitative measure of genetic heterogeneity based on next‐generation sequencing (NGS) data, mutant‐allele tumor heterogeneity (MATH), was previously developed and applied to a data set on head and neck squamous cell carcinoma (HNSCC). Whether this measure correlates with clinical outcome was not previously assessed.

METHODS

The authors examined the association between MATH and clinical, pathologic, and overall survival data for 74 patients with HNSCC for whom exome sequencing was completed.

RESULTS

High MATH (a MATH value above the median) was found to be significantly associated with shorter overall survival (hazards ratio, 2.5; 95% confidence interval, 1.3‐4.8). MATH was similarly found to be associated with adverse outcomes in clinically high‐risk patients with an advanced stage of disease, and in those with tumors classified as high risk on the basis of validated biomarkers including those that were negative for human papillomavirus or having disruptive tumor protein p53 mutations. In patients who received chemotherapy, the hazards ratio for high MATH was 4.1 (95% confidence interval, 1.6‐10.2).

CONCLUSIONS

This novel measure of tumor genetic heterogeneity is significantly associated with tumor progression and adverse treatment outcomes, thereby supporting the hypothesis that higher genetic heterogeneity portends a worse clinical outcome in patients with HNSCC. The prognostic value of some known biomarkers may be the result of their association with high genetic heterogeneity. MATH provides a useful measure of that heterogeneity to be prospectively validated as NGS data from homogeneously treated patient cohorts become available Cancer 2013;119:3034—3042. © 2013 American Cancer Society.
Finite element analysis of balloon‐expandable coronary stent deployment: Influence of angioplasty balloon configuration
Authors: Martin David , Boyle Fergal
Published: May 2013

Today, the majority of coronary stents are balloon‐expandable and are deployed using a balloon‐tipped catheter. To improve deliverability, the membrane of the angioplasty balloon is typically folded about the catheter in a pleated configuration. As such, the deployment of the angioplasty balloon is governed by the material properties of the balloon membrane, its folded configuration and its attachment to the catheter. Despite this observation, however, an optimum strategy for modelling the configuration of the angioplasty balloon in finite element studies of coronary stent deployment has not been identified, and idealised models of the angioplasty balloon are commonly employed in the literature. These idealised models often neglect complex geometrical features, such as the folded configuration of the balloon membrane and its attachment to the catheter, which may have a significant influence on the deployment of a stent. In this study, three increasingly sophisticated models of a typical semi‐compliant angioplasty balloon were employed to determine the influence of angioplasty balloon configuration on the deployment of a stent. The results of this study indicate that angioplasty balloon configuration has a significant influence on both the transient behaviour of the stent and its impact on the mechanical environment of the coronary artery. Copyright © 2013 John Wiley & Sons, Ltd.
Orally Active Aurora A/B Kinase Inhibitor, AM‐005, Suppresses the Growth of Human Colon Carcinoma Cells
Authors: Zheng Ming , Zheng Youguang , Xie Li , Chang Weiwei , Gu Ning , Ji Min
Published: May 2013

Preclinical Research

The Aurora family of serine/threonine kinases plays important roles in process of cell division or mitosis. Overexpression of Aurora A, B, and C has been identified in many human cancers including colon carcinoma cells. To date, a number of small molecular inhibitors have been developed for reducing Aurora kinases activities of tumor cells in preclinical and clinical trials. In this study, we describe the properties of AM‐005, a novel and orally active Aurora A/B kinase inhibitor. AM‐005 irreversibly inhibited the proliferation and levels of phospho‐Histone H3 in human colon carcinoma cell lines. Defective mitosis was also visualized in AM‐005‐treated HT29 cells by microscopy. Flow cytometric analysis showed that AM‐005 induced the accumulation of HT29 cells with >4N DNA content in a time or concentration‐dependent manner, and HT29 cells underwent severe apoptosis at 72 h. Moreover, AM‐005 given intragastrically led to suppression of the proliferative response in the xenograft model of colon carcinoma. These results indicate the utility of AM‐005 as a promising noncytotoxic agent for treating human colon carcinoma.
RNA interference by feeding in vitro–synthesized double‐stranded RNA to planarians: Methodology and dynamics
Authors: Rouhana Labib , Weiss Jennifer A. , Forsthoefel David J. , Lee Hayoung , King Ryan S. , Inoue Takeshi , Shibata Norito , Agata Kiyokazu , Newmark Phillip A.
Published: May 2013

COVER PHOTOGRAPH: Low magnification image of planarian flatworms (Schmidtea mediterranea) fed with liver paste containing either red, green, yellow, or blue food dye. Uptake of colored liver paste containing in vitro synthesized double‐stranded RNA is readily visualized in the planarian gut. Ingestion and processing of double‐stranded RNA in the planarian gut leads to systemic RNA‐interference. Image credit: Labib Rouhana and Phillip A. Newmark, Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana‐Champaign. From RNA Interference by feeding in vitro‐synthesized double‐stranded RNA to planarians, Labib Rouhana, Jennifer A. Weiss, David J. Forsthoefel, Hayoung Lee, Ryan S. King, Takeshi Inoue, Norito Shibata, Kiyokazu Agata, and Phillip A. Newmark, Developmental Dynamics 242:718–730, 2013.
Full‐scale shaking table test of a base‐isolated medical facility subjected to vertical motions
Authors: Furukawa Sachi , Sato Eiji , Shi Yundong , Becker Tracy , Nakashima Masayoshi
Published: May 2013

Base isolation is a well known technology that has been proven to reduce structural response to horizontal ground accelerations. However, vertical response still remains a topic of concern for base‐isolated buildings, perhaps more so than in fixed‐base buildings as isolation is often used when high performance is required. To investigate the effects of vertical response on building contents and nonstructural components, a series of full‐scale shaking table tests were conducted at the E‐Defense facility in Japan. A four‐story base‐isolated reinforced concrete building was outfitted as a medical facility with a wide variety of contents, and the behavior of the contents was observed. The rubber base isolation system was found to significantly amplify vertical accelerations in some cases. However, the damage caused by the vertical ground motions was not detrimental when peak vertical floor accelerations remained below 2 g with three exceptions: (1) small items placed on shelves slid or toppled; (2) objects jumped when placed on nonrigid furniture, which tended to increase the response; and (3) equipment with vertical eccentricities rocked and jumped. In these tests, all equipment and nonstructural components remained functional after shaking. Copyright © 2013 John Wiley & Sons, Ltd.
Numerical modelling of aeolian erosion over a surface with non‐uniformly distributed roughness elements
Authors: Furieri B. , Harion J. L. , Milliez M. , Russeil S. , Santos J. M.
Published: May 2013

The present study is focused on the analysis of the mean wall friction velocity on a surface including roughness elements exposed to a turbulent boundary layer. These roughness elements represent non‐erodible particles over an erodible surface of an agglomeration of granular material on industrial sites. A first study has proposed a formulation that describes the evolution of the friction velocity as a function of geometrical parameters and cover rate with different uniform roughness distributions. The present simulations deal with non‐uniform distributions of particles with a random sampling of diameters, heights, positions and arrangements. The evolution (relative to geometrical parameters of the roughness elements) of the friction velocity for several non‐uniform distributions of roughness elements was analysed by the equation proposed in the literature and compared to the results obtained with the numerical simulations. This comparison showed very good agreement. Thus, the formulation developed for uniform particles was found also to be valid for a larger spectrum of particles noted on industrial sites. The present work aims also to investigate in detail the fluid mechanics over several roughness particles. Copyright © 2013 John Wiley & Sons, Ltd.
Evaluation of trenching, ground penetrating radar (GPR) and electrical resistivity tomography (ERT) for sinkhole characterization
Authors: Carbonel Domingo , Rodríguez Verónica , Gutiérrez Francisco , McCalpin James P. , Linares Rogelio , Roqué Carles , Zarroca Mario , Guerrero Jesús , Sasowsky Ira
Published: May 2013

This paper explores the suitability and advantages of combining the trenching technique with geophysical surveys [ground penetrating radar (GPR) and electrical resistivity tomography (ERT)] for sinkhole characterization in a mantled karst area. The approach is applied to two active sinkholes concealed by anthropogenic deposits and formed by contrasting subsidence mechanisms; collapse and sagging. The ERT section acquired across the collapse sinkhole images the clayey fill of the depression as an obvious low resistivity area, showing the approximate location of the sinkhole edges. Spatially dense GPR surveys provide information on the position of the boundaries of the concealed subsidence structures and their three‐dimensional (3D) internal geometry, revealing the dominant subsidence mechanism. We illustrate the impact of several factors on the quality of the GPR data such as sinkhole size, nominal frequency of the antennas, antenna shielding, and the presence of backfilled excavations and above‐surface objects. Trenches provided detailed information on the subsurface structure of the sinkhole, subsidence magnitude, partitioning of the strain, and the position of the sinkhole edges, especially when they are deep enough and excavated across the central sector and perpendicular to the boundaries. The stratigraphic and structural relationships observed in the trench were then used to infer the spatial evolution of the sinkholes (e.g. enlargement), their kinematic behavior (episodic versus progressive), and to differentiate discrete subsidence events and their associated magnitude. Numerical dates were used to estimate average subsidence rates and the recurrence of subsidence events. Such integrated data sets may be used as an objective basis to forecast the future behavior of potentially damaging sinkholes and to assess the associated hazard and risk. Copyright © 2013 John Wiley & Sons, Ltd.
GNSS observations of deep convective time scales in the Amazon
Authors: Adams D. K. , Gutman Seth I. , Holub Kirk L. , Pereira Dulcineide S.
Published: May 2013

In the tropics, understanding the shallow‐to‐deep transition and organization of convection on the mesoscale is made difficult due the paucity of long‐term high spatial/temporal resolution data. In this paper, data from the world's first long‐term equatorial Global Navigational Satellite System meteorological station in Manaus (Central Amazon) is used to create a new metric, a water vapor convergence time scale, to characterize the temporal evolution of deep convection over a tropical continental region. From 3.5 years of data, 320 convective events were analyzed using a compositing analysis. Results reveal two characteristic time scales of water vapor convergence; an 8 h time scale of weak convergence and 4 h timescale of intense water vapor convergence associated with the shallow‐to‐deep convection transition. The 4 h shallow‐to‐deep transition time scale is particularly robust, regardless of convective intensity, seasonality, or nocturnal versus daytime convection. This new result provides a useful metric for both high resolution and global climate models to replicate.
Vitamin D nuclear receptor deficiency promotes cholestatic liver injury by disruption of biliary epithelial cell junctions in mice
Authors: Firrincieli Delphine , Zúñiga Silvia , Rey Colette , Wendum Dominique , Lasnier Elisabeth , Rainteau Dominique , Braescu Thomas , Falguières Thomas , Boissan Mathieu , Cadoret Axelle , Housset Chantal , Chignard Nicolas
Published: May 2013

Alterations in apical junctional complexes (AJCs) have been reported in genetic or acquired biliary diseases. The vitamin D nuclear receptor (VDR), predominantly expressed in biliary epithelial cells in the liver, has been shown to regulate AJCs. The aim of our study was thus to investigate the role of VDR in the maintenance of bile duct integrity in mice challenged with biliary-type liver injury.

Vdr−/−

mice subjected to bile duct ligation (BDL) displayed increased liver damage compared to wildtype BDL mice. Adaptation to cholestasis, ascertained by expression of genes involved in bile acid metabolism and tissue repair, was limited in

Vdr−/−

BDL mice. Furthermore, evaluation of

Vdr−/−

BDL mouse liver tissue sections indicated altered E-cadherin staining associated with increased bile duct rupture. Total liver protein analysis revealed that a truncated form of E-cadherin was present in higher amounts in

Vdr−/−

mice subjected to BDL compared to wildtype BDL mice. Truncated E-cadherin was also associated with loss of cell adhesion in biliary epithelial cells silenced for VDR. In these cells, E-cadherin cleavage occurred together with calpain 1 activation and was prevented by the silencing of calpain 1. Furthermore, VDR deficiency led to the activation of the epidermal growth factor receptor (EGFR) pathway, while EGFR activation by EGF induced both calpain 1 activation and E-cadherin cleavage in these cells. Finally, truncation of E-cadherin was blunted when EGFR signaling was inhibited in VDR-silenced cells.

Conclusion

: Biliary-type liver injury is exacerbated in

Vdr−/−

mice by limited adaptive response and increased bile duct rupture. These results indicate that loss of VDR restricts the adaptation to cholestasis and diminishes bile duct integrity in the setting of biliary-type liver injury. (Hepatology 2013;58:1401–1412)
Lipocalin-2 negatively modulates the epithelial-to-mesenchymal transition in hepatocellular carcinoma through the epidermal growth factor (TGF-beta1)/Lcn2/Twist1 pathway
Authors: Wang Yun-Peng , Yu Goung-Ran , Lee Mi-Jin , Lee Sang-Yeop , Chu In-Sun , Leem Sun-Hee , Kim Dae-Ghon
Published: May 2013

Lipocalin-2 (Lcn2) is preferentially expressed in hepatocellular carcinoma (HCC). However, the functional role of Lcn2 in HCC progression is still poorly understood, particularly with respect to its involvement in invasion and metastasis. The purpose of this study was to investigate whether Lcn2 is associated with the epithelial-mesenchymal transition (EMT) in HCC and to elucidate the underlying signaling pathway(s). Lcn2 was preferentially expressed in well-differentiated HCC versus liver cirrhosis tissues, and its expression was positively correlated with the stage of HCC. The characteristics of EMT were reversed by adenoviral transduction of Lcn2 into SH-J1 cells, including the down-regulation of N-cadherin, vimentin, alpha-smooth muscle actin, and fibronectin, and the concomitant up-regulation of CK8, CK18, and desmoplakin I/II. Knockdown of Lcn2 by short hairpin RNA (shRNA) in HKK-2 cells expressing high levels of Lcn2 was associated with EMT. Epidermal growth factor (EGF) or transforming growth factor beta1 (TGF-β1) treatment resulted in down-regulation of Lcn2, accompanied by an increase in Twist1 expression and EMT in HCC cells. Stable Lcn2 expression in SH-J1 cells reduced Twist1 expression, inhibited cell proliferation and invasion

in vitro

, and suppressed tumor growth and metastasis in a mouse model. Furthermore, EGF or TGF-β1 treatment barely changed EMT marker expression in SH-J1 cells ectopically expressing Lcn2. Ectopic expression of Twist1 induced EMT marker expression even in cells expressing Lcn2, indicating that Lcn2 functions downstream of growth factors and upstream of Twist1.

Conclusion

: Together, our findings indicate that Lcn2 can negatively modulate the EMT in HCC cells through an EGF (or TGF-β1)/Lcn2/Twist1 pathway. Thus, Lcn2 may be a candidate metastasis suppressor and a potential therapeutic target in HCC. (Hepatology 2013;58:1349–1361)
Donor risk index for African American liver transplant recipients with hepatitis C virus
Authors: Shores Nathan J. , Dodge Jennifer L. , Feng Sandy , Terrault Norah A.
Published: May 2013

African American (AA) liver transplant (LT) recipients with hepatitis C virus (HCV) have higher rates of graft loss than other racial/ethnic groups. The Donor Risk Index (DRI) predicts graft loss but is neither race- nor disease-specific and may not be optimal for assessing donor risk for AA HCV-positive LT recipients. We developed a DRI for AA with HCV with the goal of enhancing graft loss predictions. All U.S. HCV-positive adult AA first deceased donor LTs surviving ≥30 days from March 2002 to December 2009 were included. A total of 1,766 AA LT recipients were followed for median 2.8 (interquartile range [IQR] 1.3-4.9) years. Independent predictors of graft loss were donor age (40-49 years: hazard ratio [HR] 1.54; 50-59 years: HR 1.80; 60+ years: HR 2.34,

P

< 0.001), non-AA donor (HR 1.66,

P

< 0.001), and cold ischemia time (CIT) (HR 1.03 per hour >8 hours,

P

= 0.03). Importantly, the negative effect of increasing donor age on graft and patient survival among AAs was attenuated by receipt of an AA donor. A new donor risk model for AA (AADRI-C) consisting of donor age, race, and CIT yielded 1-year, 3-year, and 5-year predicted graft survival rates of 91%, 77%, and 68% for AADRI <1.60; 86%, 67%, and 55% for AADRI 1.60-2.44; and 78%, 53%, and 39% for AADRI >2.44. In the validation dataset, AADRI-C correctly reclassified 27% of patients (net reclassification improvement

P

= 0.04) compared to the original DRI.

Conclusion

: AADRI-C identifies grafts at higher risk of failure and this information is useful for risk-benefit discussions with recipients. Use of AA donors allows consideration of older donors. (Hepatology 2013;58:1263–1269)
Ketamine attenuates cytochrome p450 aromatase gene expression and estradiol‐17β levels in zebrafish early life stages
Authors: Trickler William J. , Guo Xiaoqing , Cuevas Elvis , Ali Syed F. , Paule Merle G. , Kanungo Jyotshna
Published: May 2013

Ketamine, a dissociative anesthetic, is a noncompetitive antagonist of N‐methyl‐D‐aspartate‐type glutamate receptors. In rodents and non‐human primates as well as in zebrafish embryos, ketamine has been shown to be neurotoxic. In cyclic female rats, ketamine has been shown to decrease serum estradiol‐17β (E2) levels. E2 plays critical roles in neurodevelopment and neuroprotection. Cytochrome p450 (CYP) aromatase catalyzes E2 synthesis from androgens. Although ketamine down‐regulates a number of CYP enzymes in rodents, its effect on the CYP aromatase (CYP19) is not known. Zebrafish have been used as a model system for examining mechanisms underlying drug effects. Here, using wild‐type (WT) zebrafish (Danio rerio) embryos, we demonstrate that ketamine significantly reduced E2 levels compared with the control. However, the testosterone level was elevated in ketamine‐treated embryos. These results are concordant with data from mammalian studies. Ketamine also attenuated the expression of the ovary form of CYP aromatase (cyp19a1a) at the transcriptional level but not the brain form of aromatase, cyp19a1b. Exogenous E2 potently induced the expression of cyp19a1b and vtg 1, both validated biomarkers of estrogenicity and endocrine disruption, but not cyp19a1a expression. Attenuation of activated ERK/MAPK levels, reportedly responsible for reduced human cyp19 transcription, was also observed in ketamine‐treated embryos. These results suggest that reduced E2 levels in ketamine‐treated embryos may have resulted from the suppression of cyp19a1a transcription. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
Inhibition of cytochrome P450s enhances (+)‐usnic acid cytotoxicity in primary cultured rat hepatocytes
Authors: Shi Qiang , Greenhaw James , Salminen William F.
Published: May 2013

(+)‐Usnic acid (UA) is consumed as a dietary supplement to promote weight loss; however, dietary supplements containing UA have been associated with clinical cases of severe liver injury. UA has been shown to be hepatotoxic in rats and is extensively metabolized by hepatic cytochrome P450s (CYPs); therefore, we examined if UA metabolism results in the formation of cytotoxic metabolites or if metabolism is a detoxification process in primary rat hepatocytes. When CYP activity was suppressed by the non‐isoenzyme‐selective inhibitor SKF‐525A (20 μM), or the CYP1A inhibitor alpha‐naphthoflavone (10 μM), or the CYP3A inhibitor ketoconazole (25 μM), the cytotoxicity of UA at 3 ~ 6 μM after 3 ~ 20 h of exposure was significantly increased as measured by lactate dehydrogenase (LDH) leakage. At 2 h after UA exposure, an earlier time point prior to LDH release, these CYP inhibitors potentiated UA‐induced inhibition of cellular respiration as determined by the Clark type oxygen electrode. Cellular adenosine triphosphate (ATP) depletion by UA was also exacerbated by these CYP inhibitors. The CYP2B/2C inhibitor, ticlopidine at 20 μM, showed no effects in parallel experiments. These data demonstrate that UA is bio‐transformed to less toxic metabolites in rat primary hepatocytes, probably mainly by CYP1A and 3A, but not 2B/2C. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
Double laminar and turbulent meteor trails observed in space and simulated in the laboratory
Authors: Kelley M. C. , Williamson C. H. K. , Vlasov M. N.
Published: May 2013

One of nature's most interesting and beautiful sights is meteor trails that are visible to the naked eye. The first published sketches of trails appeared in 1869 after the Leonids storm of 1868. One of the perplexing features of these trails is that very often they are double trails and seldom triple or quadruple, which rules out breaking up or fractioning as a source. The original observations were visual and reproduced in artwork. The photographs used now reveal the accuracy of the original 1868 drawings. Since 1907, scientific explanations have ruled out physical breakup as a source. The long‐standing explanation by Trowbridge (1907) has also been ruled out using modern cameras, and several new explanations have been proposed. Here we modify the explanation by Zinn and Drummond (2005), who modeled the event as an explosion followed by buoyancy, and instead, explain the effect by showing that the trails are severely convectively unstable, leading to the vortices proposed by these authors. This idea is supported by lidar‐based measurements of the temperature gradient in the trail. We also show laboratory experiments that are remarkably similar to the meteor trails in appearance, although we argue that buoyancy is not the effect in the natural case.
Longitudinal modulation of the brightness of Io's auroral footprint emission: Comparison with models
Authors: Wannawichian S. , Clarke J. T. , Bagenal F. , Smyth W. H. , Peterson C. A. , Nichols J. D.
Published: May 2013

The auroral emission close to the foot of Io's magnetic flux tube has been known for over a decade to be one of the key parameters characterizing the electrodynamic interaction between the satellite and Jupiter's magnetosphere. Ten years of observations of Io's magnetic footprint brightness have been conducted via far ultraviolet imaging by two instruments, the Space Telescope Imaging Spectrograph and the Advanced Camera for Surveys, on board the Hubble Space Telescope. The variation of Io's magnetic footprint brightness was found to have a strong correlation with the satellite's location in system III longitude. The persistent pattern of the variation of the brightness of the auroral emission at Io's magnetic footprint with longitude over 10 years of observations implies that the footprint emissions are primarily determined by processes other than temporal variations of the plasma torus. The changing location of Io in the plasma torus with longitude corresponds to changes in centrifugal latitude and to the plasma density in the vicinity of Io, likely affecting the electrodynamic interaction at the satellite. To test this, quantitative models of electron density and the generated power near Io are applied to simulate the observed footprint brightness variation pattern. We find, however, that the longitudinal variations in plasma conditions needed to produce changes in the electrodynamic interaction comparable to the observed modulation of the footprint emissions would require an unrealistically colder plasma torus than previously measured. We quantify the additional energy needed to produce the asymmetric emission peaks at 110° and 270° longitudes.
Observational constraints on Arctic Ocean clouds and radiative fluxes during the early 21st century
Authors: Kay Jennifer E. , L'Ecuyer Tristan
Published: May 2013

Arctic Ocean observations are combined to create a cloud and radiation climatology for the early 21st century (March 2000 to February 2011). Data sources include: active (CloudSat, CALIPSO) and passive (MODIS) satellite cloud observations, observed top‐of‐atmosphere (TOA) radiative fluxes (CERES‐EBAF), observationally constrained radiative flux calculations (2B‐FLXHR‐LIDAR), and observationally constrained cloud forcing calculations (CERES‐EBAF, 2B‐FLXHR‐LIDAR). Uncertainty in flux calculations is dominated by cloud uncertainty, not surface albedo uncertainty. The climatology exposes large geographic, seasonal, and interannual variability cloud forcing, but on average, Arctic Ocean clouds warm the surface (+10 W m−2, in 2B‐FLXHR‐LIDAR) and cool the TOA (−12 W m−2, in CERES‐EBAF and 2B‐FLXHR‐LIDAR). Shortwave TOA cloud cooling and longwave TOA cloud warming are stronger in 2B‐FLXHR‐LIDAR than in CERES‐EBAF, but these two differences compensate each other, yielding similar net TOA values. During the early 21st century, summer TOA albedo decreases are consistent with sea ice loss but are unrelated to summer cloud trends that are statistically insignificant. In contrast, both sea ice variability and cloud variability contribute to interannual variability in summer shortwave radiative fluxes. Summer 2007 had the largest persistent cloud, radiation, and sea ice anomalies in the climatology. During that summer, positive net shortwave radiation anomalies exceeded 20 W m−2 over much of the Arctic Ocean. This enhanced shortwave absorption resulted primarily from cloud reductions during early summer and sea ice loss during late summer. In summary, the observations show that while cloud variability influences absorbed shortwave radiation variability, there is no summer cloud trend affecting summer absorbed shortwave radiation.
Pollutant transport among California regions
Authors: Angevine Wayne M. , Brioude Jerome , McKeen Stuart , Holloway John S. , Lerner Brian M. , Goldstein Allen H. , Guha Abhinav , Andrews Arlyn , Nowak John B. , Evan Stephanie , Fischer Marc L. , Gilman Jessica B. , Bon Daniel
Published: May 2013

Several regions within California have significant air quality issues. Transport of pollutants emitted in one region to another region may add to the impact of local emissions. In this work, Lagrangian particle dispersion model simulations show the amounts of tracers that are transported within and among four regions, Southern California, the San Francisco Bay Area, the Central Valley, and the rest of the state. The simulations cover May and June of 2010, the California Research at the Nexus of Air Quality and Climate Change experiment period. Tracers of automobile emissions and one type of agricultural emission are used. Tracer mixing ratios are compared to airborne and ground‐based measurements. The age of tracers in each location is also presented. Vertical profiles and diurnal cycles help to clarify the transport process. As is well known, Southern California emissions are transported to the east and affect the desert areas, and Bay Area automobile emissions are an important source of pollutants in the San Joaquin Valley. A novel result is that the Southern California Bight is filled with a mixture of well‐aged carbon monoxide tracer from Southern California and the Bay Area. Air over the Bight is also affected by the agricultural emissions represented by the agricultural tracer, dominantly from the Central Valley where its sources are largest. There is no indication of transport from Southern California to the Central Valley. Emissions from the Central Valley do make their way to Southern California, as shown by the agricultural tracer, but automobile emissions from the Valley are insignificant in Southern California.
A seasonal trend of single scattering albedo in southern African biomass‐burning particles: Implications for satellite products and estimates of emissions for the world's largest biomass‐burning source
Authors: Eck T. F. , Holben B. N. , Reid J. S. , Mukelabai M. M. , Piketh S. J. , Torres O. , Jethva H. T. , Hyer E. J. , Ward D. E. , Dubovik O. , Sinyuk A. , Schafer J. S. , Giles D. M. , Sorokin M. , Smirnov A. , Slutsker I.
Published: May 2013

As a representative site of the southern African biomass‐burning region, sun‐sky data from the 15 year Aerosol Robotic Network (AERONET) deployment at Mongu, Zambia, was analyzed. For the biomass‐burning season months (July–November), we investigate seasonal trends in aerosol single scattering albedo (SSA), aerosol size distributions, and refractive indices from almucantar sky scan retrievals. The monthly mean single scattering albedo at 440 nm in Mongu was found to increase significantly from ~0.84 in July to ~0.93 in November (from 0.78 to 0.90 at 675 nm in these same months). There was no significant change in particle size, in either the dominant accumulation or secondary coarse modes during these months, nor any significant trend in the Ångström exponent (440–870 nm; r2 = 0.02). A significant downward seasonal trend in imaginary refractive index (r2 = 0.43) suggests a trend of decreasing black carbon content in the aerosol composition as the burning season progresses. Similarly, burning season SSA retrievals for the Etosha Pan, Namibia AERONET site also show very similar increasing single scattering albedo values and decreasing imaginary refractive index as the season progresses. Furthermore, retrievals of SSA at 388 nm from the Ozone Monitoring Instrument satellite sensor show similar seasonal trends as observed by AERONET and suggest that this seasonal shift is widespread throughout much of southern Africa. A seasonal shift in the satellite retrieval bias of aerosol optical depth from the Moderate Resolution Imaging Spectroradiometer collection 5 dark target algorithm is consistent with this seasonal SSA trend since the algorithm assumes a constant value of SSA. Multi‐angle Imaging Spectroradiometer, however, appears less sensitive to the absorption‐induced bias.
Quality assessment and assimilation of Megha‐Tropiques SAPHIR radiances into WRF assimilation system
Authors: Singh Randhir , Ojha Satya P. , Kishtawal C. M. , Pal P. K.
Published: May 2013

This study presents an initial assessment of the quality of radiances measured from SAPHIR (Sounder for Probing Vertical Profiles of Humidity) on board Megha‐Tropiques (Indo‐French joint satellite), launched by the Indian Space Research Organisation on 12 October 2011. The radiances measured from SAPHIR are compared with those simulated by the radiative transfer model (RTM) using radiosondes measurements, Atmospheric Infrared Sounder retrievals, and National Centers for Environmental Prediction (NCEP) analyzed fields over the Indian subcontinent, during January to November 2012. The radiances from SAPHIR are also compared with the similar measurements available from Microwave Humidity Sounder (MHS) on board MetOp‐A and NOAA‐18/19 satellites, during January to November 2012. A limited comparison is also carried out between SAPHIR measured and the RTM computed radiances using European Centre for Medium‐Range Weather Forecasts analyzed fields, during May and November 2012. The comparison of SAPHIR measured radiances with RTM simulated and MHS observed radiances reveals that SAPHIR observations are of good quality. After the initial assessment of the quality of the SAPHIR radiances, these radiances have been assimilated within the Weather Research and Forecasting (WRF) three‐dimensional variational data assimilation system. Analysis/forecast cycling experiments with and without SAPHIR radiances are performed over the Indian region during the entire month of May 2012. The assimilation of SAPHIR radiances shows considerable improvements (with moisture analysis error reduction up to 30%) in the tropospheric analyses and forecast of moisture, temperature, and winds when compared to NCEP analyses and radiances measurement obtained from MHS, Advanced Microwave Sounding Unit‐A, and High Resolution Infrared Sounder. Assimilation of SAPHIR radiances also resulted in substantial improvement in the precipitation forecast skill when compared with satellite‐derived rain. Overall, initial results show the usefulness of SAPHIR radiances in the numerical weather prediction data assimilation systems.
SO2 as a possible proxy for volcanic ash in aviation hazard avoidance
Authors: Sears T. M. , Thomas G. E. , Carboni E. , A. Smith A. J. , Grainger R. G.
Published: May 2013

Airborne volcanic ash poses a significant danger to aircraft, but is difficult to quantify accurately using satellite data, while sulphur dioxide is much easier to detect accurately, but is much less of a direct hazard to aviation. This paper investigates the reliability of using SO2 as a proxy for the location of volcanic ash, using an SO2 retrieval from the Infrared Atmospheric Sounding Interferometer (IASI) and ash detections from IASI and the Advanced Along Track Scanning Radiometer (AATSR). Using a numerical “missed ash fraction” applied to the eruptions of Eyjafjallajökull in 2010 and Puyehue‐Cordón Caulle in 2011 reveals that the SO2 flag typically misses ∼30% of the detectable ash. Furthermore, the missed ash fraction is found to be highly variable, both between the two eruptions and over the course of each eruption, with values of over 80% found on some days. The detection threshold of the AATSR ash flag is also investigated using radiative transfer calculations, allowing the threshold of the IASI flag to be inferred, and these are related to the ash contamination levels.
Reconciliation of modeled climate responses to spectral solar forcing
Authors: Wen Guoyong , Cahalan Robert F. , Haigh Joanna D. , Pilewskie Peter , Oreopoulos Lazaros , Harder Jerald W.
Published: May 2013

The SIM (Spectral Irradiance Monitor) on SORCE (Solar Radiation and Climate Experiment) provides more spectrally complete daily SSI (spectral solar irradiance) measurements than ever before, allowing us to explore chemical and physical processes in the Earth's ocean and atmosphere system. However, the newly observed SSI instigated controversies in the Sun‐climate community on whether the SIM‐observed trends are true solar variations and on whether climate responses are in phase or out of phase with solar forcing. In this study, we focus on resolving two apparently contradictory results published on possible temperature responses to SIM‐derived solar forcing. When applying extreme scenarios of SIM‐based spectral solar forcing in a radiative‐convective model (RCM), we find that some apparently contradictory results can be explained by the different methods used to apply the SIM SSI data. It is clear that accurate SSI data are essential for accurate climate simulations and that climate modelers need to take care how they apply these data.
The JPL lunar gravity field to spherical harmonic degree 660 from the GRAIL Primary Mission
Authors: Konopliv Alex S. , Park Ryan S. , Yuan Dah‐Ning , Asmar Sami W. , Watkins Michael M. , Williams James G. , Fahnestock Eugene , Kruizinga Gerhard , Paik Meegyeong , Strekalov Dmitry , Harvey Nate , Smith David E. , Zuber Maria T.
Published: May 2013

The lunar gravity field and topography provide a way to probe the interior structure of the Moon. Prior to the Gravity Recovery and Interior Laboratory (GRAIL) mission, knowledge of the lunar gravity was limited mostly to the nearside of the Moon, since the farside was not directly observable from missions such as Lunar Prospector. The farside gravity was directly observed for the first time with the SELENE mission, but was limited to spherical harmonic degree n ≤ 70. The GRAIL Primary Mission, for which results are presented here, dramatically improves the gravity spectrum by up to ~4 orders of magnitude for the entire Moon and for more than 5 orders‐of‐magnitude over some spectral ranges by using interspacecraft measurements with near 0.03 μm/s accuracy. The resulting GL0660B (n = 660) solution has 98% global coherence with topography to n = 330, and has variable regional surface resolution between n = 371 (14.6 km) and n = 583 (9.3 km) because the gravity data were collected at different spacecraft altitudes. The GRAIL data also improve low‐degree harmonics, and the uncertainty in the lunar Love number has been reduced by ~5× to k2 = 0.02405 ± 0.00018. The reprocessing of the Lunar Prospector data indicates ~3× improved orbit uncertainty for the lower altitudes to ~10 m, whereas the GRAIL orbits are determined to an accuracy of 20 cm.
The Role of Credit, Currency and Debt Crises in Trade Performance: A Product‐Disaggregated Panel Data Analysis
Authors: Prasada D. V. Pahan
Published: May 2013

The impacts of financial crisis shocks on trade performance are investigated for a sample of Asian countries that experienced financial crises during the 1980–2006 period. Credit, currency appreciation, currency depreciation and external debt shocks are considered. The focus is to look beyond aggregates into sub‐sector level exports using disaggregated data for 27 industries. We look at how the shocks affect bilateral exports in general and fluctuation of exports in terms of creation and diversion in particular. Further, the impact of each crisis shock on the level of competitiveness and the degree of diversification of exports is assessed. Copyright © 2013 John Wiley & Sons, Ltd.
Ultrastructure of the male genital tract, spermatogenesis and spermatozoa of hattena cometis domrow (Acari: Gamasida: Ameroseiidae)
Authors: Alberti Gerd , Seeman Owen D. , Di Palma Antonella
Published: May 2013

The ameroseiid mite Hattena cometis has a male genital system that consists of an unpaired, u‐shaped testis and paired deferent ducts leading into an unpaired accessory genital gland and ejaculatory duct. The genital opening is located anteriorly immediately in front of the sternal shield. Spermatogenesis is simple, probably due to the haploid nature of the male. Eight stages of spermatogenesis could be roughly distinguished. Mature spermatozoa as found in the deferent duct lumen are peculiar in having a bisected nucleus and numerous peripheral flat chambers, which were formed from indentations of the plasmalemma. In inseminated females, spermatozoa were observed in the syncytial tissue of the sperm access system and in the somatic cells of the ovary. These spermatozoa have achieved a new structure, i.e., an electron‐dense plate dividing the cell into two unequal halves. The dense plate has an intricate substructure. Its function is unknown. These sperm cells are considered to represent capacitated spermatozoa. The peripheral chambers are reduced in number inside the female. Similar sperm cells, containing a dense plate, were seen in vacuoles within the epithelium of the deferent duct of one male. These cells are evidently under destruction, but before being completely dissolved had undergone a development leading beyond that of the mature sperm cells found in the deferent duct. Apparently, entering the cell of the deferent duct epithelium or the syncytium tissue triggers the production of the dense plate (or the capacitation process). Our observations are compared with results obtained from other anactinotrichid Acari, mainly Gamasida, and confirm and complete the interpretation of the correlated evolution of components of gamasid reproductive systems. J. Morphol. 274:1010–1025, 2013. © 2013 Wiley Periodicals, Inc.
The filter pads and filtration mechanisms of the devil rays: Variation at macro and microscopic scales
Authors: Paig‐Tran E.W. Misty , Kleinteich Thomas , Summers Adam P.
Published: May 2013

Three lineages of cartilaginous fishes have independently evolved filter feeding (Lamniformes: Megachasma and Cetorhinus, Orectolobiformes: Rhincodon, and Mobulidae: Manta and Mobula); and the structure of the branchial filters is different in each group. The filter in Rhincodon typus has been described; species within the Lamniformes have simple filamentous filters, but the anatomy and ultrastructure of the branchial filter in the mobulid rays varies and is of functional interest. In most fishes, branchial gill rakers are elongated structures located along the anterior ceratobranchial and/or epibranchial arches; however, mobulid gill rakers are highly modified, flattened, lobe‐like structures located on the anterior and posterior epibranchial elements as well as the ceratobranchials. The ultrastructure of the filter lobes can be smooth or covered by a layer of microcilia, and some are denticulated along the dorsal and ventral lobe surface. Flow through the mobulid oropharyngeal cavity differs from other filter‐feeding fishes in that water must rapidly deviate from the free stream direction. There is an abrupt 90° turn from the initial inflowing path to move through the laterally directed branchial filter pores, over the gill tissue, and out the ventrally located gill slits. The deviation in the flow must result in tangential shearing stress across the filter surface. This implies that mobulids can use cross‐flow filtration in which this shearing force serves as a mechanism to resuspend food particles initially caught by sieving or another capture mode. These particles will be transported by the cross filter flow toward the esophagus. We propose that species with cilia on the rakers augment the shear mediated movement of particles along the filter with ciliary transport. J. Morphol. 274:1026–1043, 2013. © 2013 Wiley Periodicals, Inc.
Pigments accumulation via light and oxygen in Rhodobacter capsulatus strain XJ‐1 isolated from saline soil
Authors: Lin Zhihua , Cui Xiaohua , Zhao Chungui , Yang Suping , Imhoff Johannes F.
Published: May 2013

A Rhodobacter capsulatus strain, designated XJ‐1, isolated from saline soil, accumulated almost only one kind of bacteriochlorophyll a anaerobically in the light, aerobically in the light and dark, and the relative contents of the bacteriochlorophyll a were 44.61, 74.89, and 77.53% of the total pigments, respectively. A new purple pigment appeared only in aerobic‐light grown cells, exhibited absorption maxima at 355, 389, 520, 621, and 755 nm, especially distinctly unusual peak at 621 nm, whereas vanished in anaerobic‐light and in aerobic‐dark culture. Spheroidene and OH–spheroidene predominated in anaerobic phototrophic cultures. Spheroidenone was the sole carotenoid when exposed to both light and oxygen. The second keto‐carotenoids, OH–spheroidenone, presented only in aerobic‐dark culture in addition to spheroidenone. Strain XJ‐1 would be a good model organism for the further illustration of the regulation of bacteriochlorophyll biosynthesis gene expression in response to unique habitat.
Stress and development in Dictyostelium discoideum: the involvement of the catalytic calcineurin A subunit
Authors: Thewes Sascha , Schubert Sebastian K. , Park Kyuhyeon , Mutzel Rupert
Published: May 2013

Calcium signaling is one of the most important signaling‐pathways in all eukaryotes. One important target activated by an increased intracellular calcium concentration via calmodulin is the protein phosphatase calcineurin, which is composed of a catalytic subunit (calcineurin A) and a regulatory subunit (calcineurin B). The importance of calcium and calcineurin for the differentiation and development of the social amoeba Dictyostelium discoideum has already been shown by pharmacological approaches. However, so far only a RNAi‐silenced calcineurin B mutant has been investigated on a molecular level. Here, we describe the construction and phenotypic investigation of a RNAi‐silenced calcineurin A mutant. Phenotypic aberrations during development resemble those produced by silencing of calcineurin B with ectopic tip formation of the fruiting bodies. Additionally, we tested the response of the mutants under various stress conditions in liquid culture as well as during development. Both, calcineurin A and B RNAi‐mutants, are hypersensitive during development towards cation stress. Besides its role in development, calcineurin is thus also involved in the stress response in D. discoideum. Further, our data imply that many functions of calcineurin are conserved among the eukaryotes.
Optimization of an automatic counting system for the quantification of Staphylococcus epidermidis cells in biofilms
Authors: Freitas Ana Isabel , Vasconcelos Carlos , Vilanova Manuel , Cerca Nuno
Published: May 2013

Biofilm formation is recognized as the main virulence factor in a variety of chronic infections. In vitro evaluation of biofilm formation is often achieved by quantification of viable or total cells. However, these methods depend on biofilm disruption, which is often achieved by vortexing or sonication. In this study, we investigated the effects of sonication on the elimination of Staphylococcus epidermidis cell clusters from biofilms grown over time, and quantification was performed by three distinct analytical techniques. Even when a higher number of sonication cycles was used, some stable cell clusters remained in the samples obtained from 48‐ and 72‐h‐old biofilms, interfering with the quantification of sessile bacteria by plate counting. On the other hand, the fluorescence microscopy automatic counting system allowed proper quantification of biofilm samples that had undergone any of the described sonication cycles, suggesting that this is a more accurate method for assessing the cell concentration in S. epidermidis biofilms, especially in mature biofilms.
Peptide profiling of the route from Mahoney to Sabin, and return
Authors: Kanduc Darja , Fasano Candida , Bavaro Simona Lucia , Novello Giuseppe , Lucchese Guglielmo , Capone Giovanni
Published: May 2013

In order to define poliovirus (PV) neurovirulence at the molecular level, we comparatively analyze the primary amino acid sequence of Mahoney, a neurovirulent PV strain, versus (i) Sabin, an attenuated PV strain, and (ii) IS1, a PV isolate obtained in temporal association to a paralysis event from a polio vaccinated subject. We identify and describe 12 pentapeptides that, originally present in the Mahoney sequence, are changed in the non‐neurovirulent Sabin strain, and, successively, restored in IS1 strain.