bluuebunny/crossref_metadata_2025 huggingface dataset:
Cost-Effective Cloud Computing: A Case Study Using the Comparative Genomics Tool, Roundup
Authors: Kudtarkar Parul , DeLuca Todd F. , Fusaro Vincent A. , Tonellato Peter J. , Wall Dennis P.
Published: December 2010

Background

Comparative genomics resources, such as ortholog detection tools and repositories are rapidly increasing in scale and complexity. Cloud computing is an emerging technological paradigm that enables researchers to dynamically build a dedicated virtual cluster and may represent a valuable alternative for large computational tools in bioinformatics. In the present manuscript, we optimize the computation of a large-scale comparative genomics resource—Roundup—using cloud computing, describe the proper operating principles required to achieve computational efficiency on the cloud, and detail important procedures for improving cost-effectiveness to ensure maximal computation at minimal costs.

Methods

Utilizing the comparative genomics tool, Roundup, as a case study, we computed orthologs among 902 fully sequenced genomes on Amazon's Elastic Compute Cloud. For managing the ortholog processes, we designed a strategy to deploy the web service, Elastic MapReduce, and maximize the use of the cloud while simultaneously minimizing costs. Specifically, we created a model to estimate cloud runtime based on the size and complexity of the genomes being compared that determines in advance the optimal order of the jobs to be submitted.

Results

We computed orthologous relationships for 245,323 genome-to-genome comparisons on Amazon's computing cloud, a computation that required just over 200 hours and cost $8,000 USD, at least 40% less than expected under a strategy in which genome comparisons were submitted to the cloud randomly with respect to runtime. Our cost savings projections were based on a model that not only demonstrates the optimal strategy for deploying RSD to the cloud, but also finds the optimal cluster size to minimize waste and maximize usage. Our cost-reduction model is readily adaptable for other comparative genomics tools and potentially of significant benefit to labs seeking to take advantage of the cloud as an alternative to local computing infrastructure.
Language Learner Strategies and Linguistic Competence as Factors Affecting Achievement Test Scores in English for Specific Purposes
Authors: JURKOVIČ VIOLETA
Published: December 2010

The article examines the effect of two factors on achievement test scores in English as a foreign language for specific purposes in higher education: preexisting linguistic competence and frequency of use of language learner strategies. The rationale for the analysis of language learner strategies as a factor affecting achievement test outcomes is outlined, and then language learner strategies and linguistic competence are defined. Results of international studies that have confirmed the correlation between these two variables are also presented. The results of this study indicate a statistically significant positive effect of general linguistic competence on achievement test scores. Among the constructs of language learner strategies, however, the only construct having a statistically significant effect on achievement test scores is metacognitive strategies. The article concludes with a discussion of findings and presentation of measures that could help students at lower levels of linguistic competence improve their achievement test scores.
Toward a Conversation Between ESL Teachers and Intensive English Program Administrators
Authors: MOUSSU LUCIE
Published: December 2010

Several scholars have investigated the strengths and weaknesses of native‐English‐speaking (NES) and nonnative‐English‐speaking (NNES) teachers of English as a second language (ESL), but few researchers have explored intensive English program (IEP) administrators' and ESL teachers' perspectives on teacher training and the strengths and weaknesses of NES and NNES teachers. Through online questionnaires, this study examined 96 ESL teachers' perceptions regarding their (MA TESOL) teacher education and 21 IEP administrators' perspectives about teacher training and their resulting hiring practices. Results show similarities between IEP administrators' and ESL teachers' perceptions of NNES teachers' strengths and weaknesses. Participants also wished that preservice teachers were given more firsthand teaching opportunities. IEP administrators emphasized experience, not first language, as a determining factor in hiring decisions. Recommendations to improve teacher education and the teaching experience of NES and NNES teachers are offered.
Volatile organic compound emissions from Larrea tridentata (creosotebush)
Authors: Jardine K. , Abrell L. , Kurc S. A. , Huxman T. , Ortega J. , Guenther A.
Published: December 2010

Abstract. We present results from the CREosote ATmosphere Interactions through Volatile Emissions (CREATIVE 2009) field study in southern Arizona aimed at quantifying emission rates of VOCs from creosotebush (Larrea tridentata) during the summer 2009 monsoon season. This species was chosen because of its vast distribution in North and South American deserts and because its resins have been reported to contain a rich set of volatile organic compounds (VOC). While a variety of ecosystems have been investigated for VOC emissions, deserts remain essentially unstudied, partially because of their low biomass densities and water limitations. However, during the North American monsoon, a pronounced increase in rainfall from an extremely dry June (<5 mm precipitation) to a rainy July (>80 mm) occurs over large areas of the Sonoran desert in the southwestern United States and northwestern Mexico. We observed a strong diurnal pattern of branch emissions and ambient concentrations of an extensive suite of VOCs with maxima in early afternoon. These include VOCs typically observed in forest sites (oxygenated VOCs and volatile isoprenoids) as well as a large number of other compounds, some of which have not been previously described from any plant including 1-chloro-2-methoxy-benzene and isobutyronitrile. Although generally considered to be derived from anthropogenic sources, we observed emissions of aromatic compounds including benzene, and a broad range of phenolics. Dimethyl sulfide emissions from creosotebush were higher than reported from any previously studied plant suggesting that terrestrial ecosystems should be reconsidered as an important source of this climatically important gas. We also present direct, primary emission measurements of isoprene and its apparent oxidation products methyl vinyl ketone, methacrolein, and 3-methyl furan (the later three compounds are typically assumed to form from secondary reactions within the atmosphere), as well as a group of compounds considered to be fatty acid oxidation products. These results suggest that one important function of some VOCs in creosotebush is as an antioxidant. We also find that emissions of nitriles from creosotebush could represent a significant but previously unaccounted nitrogen loss from this arid ecosystem. Our results demonstrate the richness of creosotebush volatile emissions and highlight the need for further research into their atmospheric and ecological impacts.
Technical Note: Formal blind intercomparison of HO2 measurements in the atmosphere simulation chamber SAPHIR during the HOxComp campaign
Authors: Fuchs H. , Brauers T. , Dorn H.-P. , Harder H. , Häseler R. , Hofzumahaus A. , Holland F. , Kanaya Y. , Kajii Y. , Kubistin D. , Lou S. , Martinez M. , Miyamoto K. , Nishida S. , Rudolf M. , Schlosser E. , Wahner A. , Yoshino A. , Schurath U.
Published: December 2010

Abstract. Hydroperoxy radical (HO2) concentrations were measured during the formal blind intercomparison campaign HOxComp carried out in Jülich, Germany, in 2005. Three instruments detected HO2 via chemical conversion to hydroxyl radicals (OH) and subsequent detection of the sum of OH and HO2 by laser induced fluorescence (LIF). All instruments were based on the same detection and calibration scheme. Because measurements by a MIESR instrument failed during the campaign, no absolute reference measurement was available, so that the accuracy of individual instruments could not be addressed. Instruments sampled ambient air for three days and were attached to the atmosphere simulation chamber SAPHIR during the second part of the campaign. Six experiments of one day each were conducted in SAPHIR, where air masses are homogeneously mixed, in order to investigate the performance of instruments and to determine potential interferences of measurements under well-controlled conditions. Linear correlation coefficients (R2) between measurements of the LIF instruments are generally high and range from 0.82 to 0.98. However, the agreement between measurements is variable. The regression analysis of the entire data set of measurements in SAPHIR yields slopes between 0.69 to 1.26 and intercepts are smaller than typical atmospheric daytime concentrations (less than 1 pptv). The quality of fit parameters improves significantly, when data are grouped into data subsets of similar water vapor concentrations. Because measurements of LIF instruments were corrected for a well-characterized water dependence of their sensitivities, this indicates that an unknown factor related to water vapor affected measurements in SAPHIR. Measurements in ambient air are also well-correlated, but regression parameters differ from results obtained from SAPHIR experiments. This could have been caused by differences in HO2 concentrations in the sampled air at the slightly different locations of instruments.
Wintertime pollution over the Eastern Indo-Gangetic Plains as observed from MOPITT, CALIPSO and tropospheric ozone residual data
Authors: Kar J. , Deeter M. N. , Fishman J. , Liu Z. , Omar A. , Creilson J. K. , Trepte C. R. , Vaughan M. A. , Winker D. M.
Published: December 2010

Abstract. A large wintertime increase in pollutants has been observed over the eastern parts of the Indo Gangetic Plains. We use improved version 4 carbon monoxide (CO) retrievals from the Measurements of Pollution in the Troposphere (MOPITT) along with latest version 3 aerosol data from the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) lidar instrument and the tropospheric ozone residual products to characterize this pollution pool. The feature is seen primarily in the lower troposphere from about November to February with strong concomitant increases in CO and aerosol optical depth (AOD). The signature of the feature is also observed in tropospheric ozone column data. The height resolved aerosol data from CALIPSO confirm the trapping of the pollution pool at the lowest altitudes. The observations indicate that MOPITT can capture this low altitude phenomenon even in winter conditions as indicated by the averaging kernels.
Ozone, carbon monoxide and nitrogen oxides time series at four alpine GAW mountain stations in central Europe
Authors: Gilge S. , Plass-Duelmer C. , Fricke W. , Kaiser A. , Ries L. , Buchmann B. , Steinbacher M.
Published: December 2010

Abstract. Long-term, ground based in-situ observations of ozone (O3) and its precursor gases nitrogen dioxide (NO2) and carbon monoxide (CO) from the four sites Hohenpeissenberg and Zugspitze (D), Sonnblick (A) and Jungfraujoch (CH) are presented for the period 1995–2007. These Central European alpine mountain observatories cover an altitude range of roughly 1000 to 3500 m. Comparable analytical methods and common quality assurance (QA) procedures are used at all sites. For O3 and CO, calibration is linked to primary calibrations (O3) or CO standards provided by the Central Calibration Laboratory (CCL) at NOAA/ESRL. All stations have been audited by the World Calibration Centre (WCC) for CO and O3 (WCC-Empa; CH). Data from long-term measurements of NO2 and CO are only available from Hohenpeissenberg and Jungfraujoch. Both sites show slightly decreasing mixing ratios of the primarily emitted NO2 and the partly anthropogenically emitted CO between 1995 and 2007. The findings are generally consistent with shorter observation periods at Zugspitze and Sonnblick and thus are considered to represent regional changes in Central European atmospheric composition at this altitude range. Over the same period, 1995–2007, the O3 mixing ratios have slightly increased at three of the four sites independent of wind sector. Trends are often more pronounced in winter and less in summer; highest declines of NO2 and CO are observed in winter and the lowest in summer, whereas the strongest O3 increase was detected in winter and lowest or even decline in summer, respectively. Weekly cycles demonstrate anthropogenic impact at all elevations with enhanced NO2 on working days compared to weekends. Enhanced O3 values on working days indicating photochemical production from anthropogenic precursors are only observed in summer, whereas in all other seasons anti-correlation with NO2 was found due to reduced O3 values on working days. Trends are discussed with respect to anthropogenic impacts and vertical mixing. The observed trends for NO2 at the alpine mountain sites are less pronounced than trends estimated based on emission inventories.
Determination of the averaged charge-to-mass ratio of the heavy charged constituents of a magnetoplasma using whistler wave measurements
Authors: Krafft C. , Lundin B. V.
Published: December 2010

Abstract. In a cold magnetized plasma with two light ions of comparable gyrofrequencies and any species of heavy ions and/or charged dust particulates, a technique is developed to recover the relative charge density of the heavy plasma population and to estimate its effective averaged charge-to-mass ratio. Such results can be obtained without using mass spectrometer data but only the measurements of the ion plasma frequency, the electron gyro- and plasma frequencies as well as the two highest ion cutoff frequencies.
Fluorescence and absorption properties of chromophoric dissolved organic matter (CDOM) in coastal surface waters of the northwestern Mediterranean Sea, influence of the Rhône River
Authors: Para J. , Coble P. G. , Charrière B. , Tedetti M. , Fontana C. , Sempéré R.
Published: December 2010

Abstract. Seawater samples were collected monthly in surface waters (2 and 5 m depths) of the Bay of Marseilles (northwestern Mediterranean Sea; 5°17'30" E, 43°14'30" N) during one year from November 2007 to December 2008 and studied for total organic carbon (TOC) as well as chromophoric dissolved organic matter (CDOM) optical properties (absorbance and fluorescence). The annual mean value of surface CDOM absorption coefficient at 350 nm [aCDOM(350)] was very low (0.10 ± 0.02 m−1) in comparison to values usually found in coastal waters, and no significant seasonal trend in aCDOM(350) could be determined. By contrast, the spectral slope of CDOM absorption (SCDOM) was significantly higher (0.023 ± 0.003 nm−1) in summer than in fall and winter periods (0.017 ± 0.002 nm−1), reflecting either CDOM photobleaching or production in surface waters during stratified sunny periods. The CDOM fluorescence, assessed through excitation emission matrices (EEMs), was dominated by protein-like component (peak T; 1.30–21.94 QSU) and marine humic-like component (peak M; 0.55–5.82 QSU), while terrestrial humic-like fluorescence (peak C; 0.34–2.99 QSU) remained very low. This reflected a dominance of relatively fresh material from biological origin within the CDOM fluorescent pool. At the end of summer, surface CDOM fluorescence was very low and strongly blue shifted, reinforcing the hypothesis of CDOM photobleaching. Our results suggested that unusual Rhône River plume eastward intrusion events might reach Marseilles Bay within 2–3 days and induce local phytoplankton blooms and subsequent fluorescent CDOM production (peaks M and T) without adding terrestrial fluorescence signatures (peaks C and A). Besides Rhône River plumes, mixing events of the entire water column injected relative aged (peaks C and M) CDOM from the bottom into the surface and thus appeared also as an important source of CDOM in surface waters of the Marseilles Bay. Therefore, the assessment of CDOM optical properties, within the hydrological context, pointed out several biotic (in situ biological production, biological production within Rhône River plumes) and abiotic (photobleaching, mixing) factors controlling CDOM transport, production and removal in this highly urbanized coastal area.
Implications for chloro- and pheopigment synthesis and preservation from combined compound-specific δ13C, δ15N, and Δ14C analysis
Authors: Kusch S. , Kashiyama Y. , Ogawa N. O. , Altabet M. , Butzin M. , Friedrich J. , Ohkouchi N. , Mollenhauer G.
Published: December 2010

Abstract. Chloropigments and their derivative pheopigments preserved in sediments can directly be linked to photosynthesis. Their carbon and nitrogen stable isotopic compositions have been shown to be a good recorder of recent and past surface ocean environmental conditions tracing the carbon and nitrogen sources and dominant assimilation processes of the phytoplanktonic community. In this study we report results from combined compound-specific radiocarbon and stable carbon and nitrogen isotope analysis to examine the time-scales of synthesis and fate of chlorophyll-a and its degradation products pheophytin-a, pyropheophytin-a, and 132,173-cyclopheophorbide-a-enol until burial in Black Sea core-top sediments. The pigments are mainly of marine phytoplanktonic origin as implied by their stable isotopic compositions. Pigment δ15N values indicate nitrate as the major uptake substrate but 15N-depletion towards the open marine setting indicates either contribution from N2-fixation or direct uptake of ammonium from deeper waters. Radiocarbon concentrations translate into minimum and maximum pigment ages of approximately 40 to 1200 years. This implies that protective mechanisms against decomposition such as association with minerals, storage in deltaic anoxic environments, or eutrophication-induced hypoxia and light limitation are much more efficient than previously thought. Moreover, seasonal variations of nutrient source, growth period, and habitat and their associated isotopic variability are likely at least as strong as long-term trends. Combined triple isotope analysis of sedimentary chlorophyll and its primary derivatives is a powerful tool to delineate biogeochemical and diagenetic processes in the surface water and sediments, and to assess their precise time-scales.
Development and validation of a size-resolved particle dry deposition scheme for application in aerosol transport models
Authors: Petroff A. , Zhang L.
Published: December 2010

Abstract. A size-resolved particle dry deposition scheme is developed for inclusion in large-scale air quality and climate models where the size distribution and fate of atmospheric aerosols is of concern. The "resistance" structure is similar to what is proposed by Zhang et al. (2001), while a new "surface" deposition velocity (or surface resistance) is derived by simplification of a one-dimensional aerosol transport model (Petroff et al., 2008b, 2009). Compared to Zhang et al.'s model, the present model accounts for the leaf size, shape and area index as well as the height of the vegetation canopy. Consequently, it is more sensitive to the change of land covers, particularly in the accumulation mode (0.1–1 micron). A drift velocity is included to account for the phoretic effects related to temperature and humidity gradients close to liquid and solid water surfaces. An extended comparison of this model with experimental evidence is performed over typical land covers such as bare ground, grass, coniferous forest, liquid and solid water surfaces and highlights its adequate prediction. The predictions of the present model differ from Zhang et al.'s model in the fine mode, where the latter tends to over-estimate in a significant way the particle deposition, as measured by various investigators or predicted by the present model. The present development is thought to be useful to modellers of the atmospheric aerosol who need an adequate parameterization of aerosol dry removal to the earth surface, described here by 26 land covers. An open source code is available in Fortran90.
The impact of in-canopy wind profile formulations on heat flux estimation in an open orchard using the remote sensing-based two-source model
Authors: Cammalleri C. , Anderson M. C. , Ciraolo G. , D'Urso G. , Kustas W. P. , La Loggia G. , Minacapilli M.
Published: December 2010

Abstract. For open orchard and vineyard canopies containing significant fractions of exposed soil (>50%), typical of Mediterranean agricultural regions, the energy balance of the vegetation elements is strongly influenced by heat exchange with the bare soil/substrate. For these agricultural systems a "two-source" approach, where radiation and turbulent exchange between the soil and canopy elements are explicitly modelled, appears to be the only suitable methodology for reliably assessing energy fluxes. In strongly clumped canopies, the effective wind speed profile inside and below the canopy layer can strongly influence the partitioning of energy fluxes between the soil and vegetation components. To assess the impact of in-canopy wind profile on model flux estimates, an analysis of three different formulations is presented, including algorithms from Goudriaan (1977), Massman (1987) and Lalic et al. (2003). The in-canopy wind profile formulations are applied to the thermal-based two-source energy balance (TSEB) model developed by Norman et al. (1995) and modified by Kustas and Norman (1999). High resolution airborne remote sensing images, collected over an agricultural area located in the western part of Sicily (Italy) comprised primarily of vineyards, olive and citrus orchards, are used to derive all the input parameters needed to apply the TSEB. The images were acquired from June to October 2008 and include a relatively wide range of meteorological and soil moisture conditions. A preliminary sensitivity analysis of the three wind profile algorithms highlights the dependence of wind speed just above the soil/substrate to leaf area index and canopy height over the typical range of canopy properties encountered in these agricultural areas. It is found that differences among the models in wind just above the soil surface are most significant under sparse and medium fractional cover conditions (15–50%). The TSEB model heat flux estimates are compared with micro-meteorological measurements from a small aperture scintillometer and an eddy covariance tower collected over an olive orchard characterized by moderate fractional vegetation cover (≈35%) and relatively tall crop (≈3.5 m). TSEB fluxes for the 7 image acquisition dates generated using both the Massman and Goudriaan in-canopy wind profile formulations give close agreement with measured fluxes, while the Lalic et al. equations yield poor results. The Massman wind profile scheme slightly outperforms that of Goudriaan, but it requires an additional parameter accounting for the roughness sub-layer of the underlying vegetative surface. The analysis also suggests that within-canopy wind profile model discrepancies become important, in terms of impact on modelled sensible heat flux, only for sparse canopies with moderate vegetation coverage.
HESS Opinions "Topography driven conceptual modelling (FLEX-Topo)"
Authors: Savenije H. H. G.
Published: December 2010

Abstract. Heterogeneity and complexity of hydrological processes offer substantial challenges to the hydrological modeller. Some hydrologists try to tackle this problem by introducing more and more detail in their models, or by setting-up more and more complicated models starting from basic principles at the smallest possible level. As we know, this reductionist approach leads to ever higher levels of equifinality and predictive uncertainty. On the other hand, simple, lumped and parsimonious models may be too simple to be realistic or representative of the dominant hydrological processes. In this commentary, a new approach is proposed that tries to find the middle way between complex distributed and simple lumped modelling approaches. Here we try to find the right level of simplification while avoiding over-simplification. Paraphrasing Einstein, the maxim is: make a model as simple as possible, but not simpler than that. The approach presented is process based, but not physically based in the traditional sense. Instead, it is based on a conceptual representation of the dominant physical processes in certain key elements of the landscape. The essence of the approach is that the model structure is made dependent on a limited number of landscape classes in which the topography is the main driver, but which can include geological, geomorphological or land-use classification. These classes are then represented by lumped conceptual models that act in parallel. The advantage of this approach over a fully distributed conceptualisation is that it retains maximum simplicity while taking into account observable landscape characteristics.
Energy-based predictions in Lorenz system by a unified formalism and neural network modelling
Authors: Pasini A. , Langone R. , Maimone F. , Pelino V.
Published: December 2010

Abstract. In the framework of a unified formalism for Kolmogorov-Lorenz systems, predictions of times of regime transitions in the classical Lorenz model can be successfully achieved by considering orbits characterised by energy or Casimir maxima. However, little uncertainties in the starting energy usually lead to high uncertainties in the return energy, so precluding the chance of accurate multi-step forecasts. In this paper, the problem of obtaining good forecasts of maximum return energy is faced by means of a neural network model. The results of its application show promising results.
Comparison of Movement of the Upper Dentition According to Anchorage Method: Orthodontic Mini-Implant versus Conventional Anchorage Reinforcement in Class I Malocclusion
Authors: Lee Ah-Young , Kim Young Ho
Published: December 2010

Objective. To compare the amounts of anchorage loss in the upper first molar (U6) and of retraction of the upper central incisor (U1) in cases with Class I malocclusion between orthodontic mini-implants (OMIs) and conventional anchorage reinforcements (CARs). Methods. The subjects were 40 female adult patients with Class I malocclusion who were treated with extraction of the first premolars and sliding mechanics. The subjects were divided into Groups 1 (N=20, CAR) and 2 (N=20, OMI) according to anchorage method. Lateral cephalograms were taken before (T0) and after treatment (T1). Seven skeletal and dental variables and ten anchorage variables were measured. Mann-Whitney test was used for statistical analysis. Results. Group 2 showed significantly larger retraction of U1 (U1E-sag, 9.5 mm : 7.1 mm, P<.05) and less anchorage loss of U6 (U6M-sag, 0.2 mm : 2.2 mm, P<.05; U6A-sag, 0.3 mm versus 2.4 mm, P<.01) than Group 1. There was opposite vertical movement in U1 and U6 between Groups 1 and 2 (U1E-ver, 0.9 mm intrusion : 0.7 mm extrusion; U6F-ver, 1.0 mm intrusion : 0.9 mm extrusion, P<.05). Conclusion. Although OMI could not reduce the treatment duration, it could provide better maximum anchorage of U6, greater retraction of U1, intrusion of U1 and U6 than CAR.
N‐Doped CsTaWO6 as a New Photocatalyst for Hydrogen Production from Water Splitting Under Solar Irradiation
Authors: Mukherji Aniruddh , Marschall Roland , Tanksale Akshat , Sun Chenghua , Smith Sean C. , Lu Gao Qing , Wang Lianzhou
Published: December 2010

Photocatalysts for efficient solar hydrogen production are highly sought after. Here a new type of nitrogen‐doped tantalum tungstenate (CsTaWO6) material, which demonstrates excellent visible light absorption and improved photocatalytic activity, is demonstrated. X‐ray diffraction (XRD) patterns reveal that the defect pyrochlore‐type structure of CsTaWO6 remained intact upon nitrogen doping. UV‐vis spectra indicate that nitrogen doping in the compound results in a red‐shift of the absorption edge from 358 nm to 580 nm, thus offering significantly increased visible light absorption. X‐ray photoelectron spectroscopy (XPS) further indicates that [Ta/W]–N bonds were formed by inducing nitrogen to replace a small amount of oxygen in the material, resulting in a compound of CsTaWO6‐xNx. The explanation of the experimental results is supported by density functional theory calculations. The density of states (DOS) and the projected DOS after substitutional doping of nitrogen in CsTaWO6 indicated that N‐doping reduces the bandgap significantly from 3.8 to 2.3 eV due to N 2p and O 2p orbital mixing. The role of the new N 2p states is also investigated by studying the production of the •OH radicals in the visible light region (>420 nm). In CsTaWO6‐xNx, the N 2p orbitals are the main contributors to the top of the valence band, causing bandgap narrowing while the bottom of conduction band, due to Ta 4d orbitals, remains almost unchanged. Compared with its undoped counterpart, nitrogen‐doped CsTaWO6‐xNx exhibits a nearly 100% increase in solar hydrogen production efficiency.
3D Microperiodic Hydrogel Scaffolds for Robust Neuronal Cultures
Authors: Hanson Shepherd Jennifer N. , Parker Sara T. , Shepherd Robert F. , Gillette Martha U. , Lewis Jennifer A. , Nuzzo Ralph G.
Published: December 2010

Three‐dimensional (3D) microperiodic scaffolds of poly(2‐hydroxyethyl methacrylate) (pHEMA) have been fabricated by direct‐write assembly of a photopolymerizable hydrogel ink. The ink is initially composed of physically entangled pHEMA chains dissolved in a solution of HEMA monomer, comonomer, photoinitiator and water. Upon printing 3D scaffolds of varying architecture, the ink filaments are exposed to UV light, where they are transformed into an interpenetrating hydrogel network of chemically cross‐linked and physically entangled pHEMA chains. These 3D microperiodic scaffolds are rendered growth compliant for primary rat hippocampal neurons by absorption of polylysine. Neuronal cells thrive on these scaffolds, forming differentiated, intricately branched networks. Confocal laser scanning microscopy reveals that both cell distribution and extent of neuronal process alignment depend upon scaffold architecture. This work provides an important step forward in the creation of suitable platforms for in vitro study of sensitive cell types.
Modeling the depleting mechanism of urea‐water‐solution droplet for automotive selective catalytic reduction systems
Authors: Abu‐Ramadan Ehab , Saha Kaushik , Li Xianguo
Published: December 2010

The current work aims to develop a reliable theoretical model capable of simulating the depletion process of urea‐water‐solution (UWS) droplets injected in a hot exhaust stream as experienced in an automotive urea‐based selective catalytic reduction system. A modified multicomponent vaporization model is presented and implemented in the current study to simulate the behavior of UWS droplet in heated environment. Although water depletion is modeled as a vaporization process, urea depletion is modeled using two different approaches: (i) vaporization and (ii) direct thermal decomposition. The suitability of both depletion approaches is assessed in the current study by comparison with experimental data of the decay of a single UWS droplet in a quiescent heated environment. The decay rate of UWS droplet is accurately predicted with the multicomponent vaporization model. The possibility of internal gasification is demonstrated. Based on the complex decomposition behavior of urea, the current study proposes a decomposition mechanism for UWS droplet. The suitability of implementing the rapid mixing approach is assessed through comparison with the diffusion limit approach at various operating conditions and initial UWS droplet sizes. © 2011 American Institute of Chemical Engineers AIChE J, 2011
Activated carbon supported silicotungstic acid catalysts for ethyl‐tert‐butyl ether synthesis
Authors: Degirmenci Levent , Oktar Nuray , Dogu Gulsen
Published: December 2010

Vapor phase ethyl‐tert‐butyl ether (ETBE) production was conducted in the presence of Cesium salts of silicotungstic acid (Cs‐STA), activated carbon supported silicotungstic acid (AC‐STA), and activated carbon supported Cesium salts of silicotungstic acid (AC‐Cs‐STA) catalysts. Isobutene (IB) conversion to ETBE at 373 K were determined as 0.16 and 0.2 for STA and AC‐STA catalysts on constant space time basis. This increase of activity is one of the highlights of this study considering that STA loading in AC‐STA catalysts had been adjusted to 40%. IB conversion to ETBE obtained at 373 K in the presence of AC‐STA catalyst was found to be close to equilibrium. Stability of the synthesized catalysts were tested by applying a washing procedure with ethanol. Repeated ETBE synthesis with thoroughly washed samples indicated quite stable and active catalyts. © 2011 American Institute of Chemical Engineers AIChE J, 2011
The aromatic enhancement in the axial‐flow spherical packed‐bed membrane naphtha reformers in the presence of catalyst deactivation
Authors: Rahimpour Mohammad Reza , Iranshahi Davood , Pourazadi Ehsan , Paymooni Khadijeh , Bahmanpour Ali Mohammad
Published: December 2010

Because of some disadvantages of conventional tubular reactors (CTRs), the concept of spherical membrane reactors is proposed as an alternative. In this study, it is suggested to apply hydrogen perm‐selective membrane in the axial‐flow spherical packed‐bed naphtha reformers. The axial flow spherical packed‐bed membrane reactor (AF‐SPBMR) consists of two concentric spheres. The inner sphere is supposed to be a composite wall coated by a thin Pd‐Ag membrane layer. Set of coupled partial differential equations are developed for the AF‐SPBMR model considering the catalyst deactivation, which are solved by using orthogonal collocation method. Differential evolution optimization technique identifies some decision variables which can manipulate the input parameters to obtain the desired results. In addition to lower pressure drop, the enhancement of aromatics yield by the membrane layer in AF‐SPBMR adds additional superiority to the spherical reactor performance in comparison with CTR. © 2011 American Institute of Chemical Engineers AIChE J, 2011
Disproportionation of toluene on ZSM5 washcoated monoliths
Authors: Mitra B. , Chakraborty Jyoti Prasad , Kunzru Deepak
Published: December 2010

ZSM5 washcoated monoliths with zeolite loading ranging from 10 to 60 wt % were prepared, characterized, and examined for disproportionation of toluene. Toluene conversion increased with temperature and W/FAo but decreased with washcoat thickness. The selectivity of the most desirable isomer (p‐xylene) increased with a decrease in temperature, W/FAo and washcoat thickness. The high selectivity to p‐xylene indicates that the initially formed para isomer is easily removed from the zeolite pores in the thin washcoat to the bulk gas phase preventing further isomerization of the primary product. A reaction scheme has been proposed for this reaction and the kinetic parameters determined for the 10 wt % ZSM5 monolith. A one‐dimensional reactor model was developed to predict the performance of the reactor for disproportionation of toluene. The model equations were coupled with a module to calculate the concentration profile in the washcoat by considering the effect of diffusion and reaction. © 2011 American Institute of Chemical Engineers AIChE J, 00: 000–000, 2011
Supercritical extraction of evening primrose oil: Experimental optimization via response surface methodology
Authors: Ghoreishi Seyyed M. , Bataghva Ehsan
Published: December 2010

Supercritical carbon dioxide (CO2) effective extraction parameters (pressure, temperature, static extraction time, and dynamic extraction time) of oil recovery from evening primrose seeds were optimized via response surface methodology (RSM). The results of this study indicated that the linear terms of static and dynamic time and the quadratics of temperature and pressure, as well as the interactions of temperature and static time, pressure and temperature had a significant effect on the oil recovery. The optimum extraction conditions of 14.2 MPa, 47.3°C, 30 min (static extraction time) and 150 min (dynamic extraction time) were obtained. Applying the optimum conditions, a mean experimental recovery of 92.98% (triplicate experiment) was achieved, which is well compatible with the RSM‐predicted value (93.61%). The fatty acid composition of extracted evening primrose oil using supercritical CO2 was compared with that obtained by Soxhlet method in which minor difference was observed. © 2011 American Institute of Chemical Engineers AIChE J, 2011
47, XY, +der(Y),t(X;Y)(p21.1;p11.2): A unique case of XY sex reversal
Authors: Zarate Yuri A. , Dwivedi Alka , Bartel Frank O. , Corning Ken , DuPont Barbara R.
Published: December 2010

Translocations involving the short arms of the X and Y chromosomes are rare and can result in a functional disomy of the short arm of the X chromosome, including the dosage‐sensitive sex reversal (DSS) locus. A result of such imbalance may be sex reversal with multiple congenital anomalies. We present the clinical and cytogenetic evaluation of a newborn infant with DSS and additional clinical findings of minor facial anomalies, left abdominal mass, 5th finger clinodactyly, and mild hypotonia. The external genitalia appeared to be normal female. The infant had bilateral corneal opacities and findings suggestive of anterior segment dysgenesis. Ultrasonography showed a small uterus with undetectable ovaries, and a left multicystic dysplastic kidney. High‐resolution chromosome analysis identified the presence of a derivative Y chromosome, 47,XY, +der(Y)t(X;Y)(p21.1;p11.2), which was confirmed by fluorescence in situ hybridization studies. Array CGH showed a 35.1 Mb copy number gain of chromosome region Xp22.33‐p21.1 and a 52.2 Mb copy number gain of Yp11.2‐qter, in addition to the intact X and Y chromosomes. Previously reported patients with XY sex reversal have not had DSS with corneal opacities, dysgenesis of the anterior segment of the eye, and unilateral multicystic dysplastic kidney. These findings represent a new form of XY sex reversal due to an Xp duplication. © 2010 Wiley‐Liss, Inc.
Back to the future: Proceedings from the 2010 NF Conference
Authors: Huson Susan M. , Acosta Maria T. , Belzberg Allan J. , Bernards Andre , Chernoff Jonathan , Cichowski Karen , Gareth Evans D. , Ferner Rosalie E. , Giovannini Marco , Korf Bruce R. , Listernick Robert , North Kathryn N. , Packer Roger J. , Parada Luis F. , Peltonen Juha , Ramesh Vijaya , Reilly Karlyne M. , Risner John W. , Schorry Elizabeth K. , Upadhyaya Meena , Viskochil David H. , Zhu Yuan , Hunter‐Schaedle Kim , Giancotti Filippo G.
Published: December 2010

The neurofibromatoses (NF) encompass the rare diseases NF1, NF2, and schwannomatosis. The NFs affect 100,000 Americans; over 2 million persons worldwide; and are caused by mutation of tumor suppressor genes. Individuals with NF1 in particular may develop tumors anywhere in the nervous system; additional manifestations can include learning disabilities, bone dysplasia, cardiovascular defects, unmanageable pain, and physical disfigurement. Ultimately, the NFs can cause blindness, deafness, severe morbidity, and increased mortality and NF1 includes a risk of malignant cancer. Today there is no treatment for the NFs (other than symptomatic); however, research efforts to understand these genetic conditions have made tremendous strides in the past few years. Progress is being made on all fronts, from discovery studies—understanding the molecular signaling deficits that cause the manifestations of NF—to the growth of preclinical drug screening initiatives and the emergence of a number of clinical trials. An important element in fuelling this progress is the sharing of knowledge, and to this end, for over 20 years the Children's Tumor Foundation has convened an annual NF Conference, bringing together NF professionals to share ideas and build collaborations. The 2010 NF Conference held in Baltimore, MD June 5–8, 2010 hosted over 300 NF researchers and clinicians. This paper provides a synthesis of the highlights presented at the Conference and as such, is a “state‐of‐the‐field” for NF research in 2010. © 2010 Wiley‐Liss, Inc.
How can social network analysis improve the study of primate behavior?
Authors: Sueur Cédric , Jacobs Armand , Amblard Frédéric , Petit Odile , King Andrew J.
Published: December 2010

When living in a group, individuals have to make trade‐offs, and compromise, in order to balance the advantages and disadvantages of group life. Strategies that enable individuals to achieve this typically affect inter‐individual interactions resulting in nonrandom associations. Studying the patterns of this assortativity using social network analyses can allow us to explore how individual behavior influences what happens at the group, or population level. Understanding the consequences of these interactions at multiple scales may allow us to better understand the fitness implications for individuals. Social network analyses offer the tools to achieve this. This special issue aims to highlight the benefits of social network analysis for the study of primate behaviour, assessing it's suitability for analyzing individual social characteristics as well as group/population patterns. In this introduction to the special issue, we first introduce social network theory, then demonstrate with examples how social networks can influence individual and collective behaviors, and finally conclude with some outstanding questions for future primatological research. Am. J. Primatol. 73:703–719, 2011. © 2011 Wiley‐Liss, Inc.
Individuality in male songs of wild black crested Gibbons (Nomascus concolor)
Authors: Sun Guo‐Zheng , Huang Bei , Guan Zhen‐Hua , Geissmann Thomas , Jiang Xue‐Long
Published: December 2010

This is the first study of vocal individuality in male songs of black crested gibbons. The sound recordings were carried out at two field sites, Pinghe, Ailao Mountains, and Dazhaizi, Wuliang Mountains, both located in Yunnan province, China. A total of 127 coda phrases of 38 male songs bouts of eight individual male gibbons were analyzed. Stepwise discriminant function analysis was used to examine the acoustic individuality of the males. We found that individuality among neighbors was very pronounced. Moreover, individuality within a site (i.e. among neighbors) is higher than among individuals between sites. Our finding suggests that black crested gibbons may actively increase their degree of vocal individuality against that of their immediate neighbors by vocal adjustment. Am. J. Primatol. 73:431–438, 2011. © 2010 Wiley‐Liss, Inc.
Talon cusp from two archaic period cemeteries in North America: Implications for comparative evolutionary morphology
Authors: Stojanowski Christopher M. , Johnson Kent M. , Doran Glen H. , Ricklis Robert A.
Published: December 2010

Talon cusps are rare morphological features of the anterior dentition that represent a spectrum of lingual cingulum diversity. In this paper, talon cusp prevalence is described in two Archaic period North American samples, Windover Pond (Florida) and Buckeye Knoll (Texas). Given the early date of these cemeteries (∼7500 BP), these specimens represent the oldest reported cases of lingual talon cusp in the New World, and perhaps globally. Windover preserves three cases of talon cusp (representing three different individuals) affecting the permanent maxillary lateral incisors. The sample frequencies were 1.8% and 3.1% for the left and right maxillary lateral incisors, respectively. Buckeye Knoll preserves four cases of talon cusp representing three individuals. Talon cusps at this site were distributed throughout the maxillary anterior dentition, including a permanent maxillary central incisor, bilateral permanent maxillary lateral incisors, and a deciduous maxillary lateral incisor. The multicomponent nature of this site complicates sample frequency calculation with by‐tooth estimates ranging from 3.6% to 25%. This paper discusses the difficulties with comparative frequency estimation, resulting from a proliferation of terminology that is discipline‐specific. Understanding the evolutionary basis and significance of dental morphological variation requires an inclusive approach to the comparative literature that focuses on homology within the context of odontogenetic process. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.
Are Homo sapiens nonsupranuchal fossa and neanderthal suprainiac fossa convergent traits?
Authors: Nowaczewska Wioletta
Published: December 2010

The autapomorphic status of the Neanderthal suprainiac fossa was recently confirmed. This was a result of a detailed analysis of the internal bone composition in the area of the suprainiac depression on Neanderthal and Homo sapiens specimens. However, while anatomical differences between Neanderthal suprainiac fossa and the depression in the inion region of the occipital bone of fossil and recent Homo sapiens have been discussed in detail, the etiology of these structures has not been resolved. In this article, the hypothesis that the Homo sapiens non‐supranuchal fossa and the Neanderthal suprainiac fossa both formed to maintain the optimal shape of the occipital plane (to minimize strain on the posterior cranial vault) is tested. First, the variation in the expression of the fossa above inion in the crania of recent Homo sapiens from European, African, and Australian samples was examined, and the degree of structural similarity between these depressions and the Neanderthal suprainiac fossa was assessed. Next, the relationship between the shape of the occipital squama in the midsagittal plane and two particular features (the degree of the occipital torus development and the occurrence of a depression in the inion region that is not the supranuchal fossa) were analyzed. Based on the results, it is suggested that the Homo sapiens non‐supranuchal fossa and Neanderthal suprainiac fossa are convergent traits. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.
Chemische Kontrolle des Schicksals und Entwicklungspotenzials von Stammzellen
Authors: Lyssiotis Costas A. , Lairson Luke L. , Boitano Anthony E. , Wurdak Heiko , Zhu Shoutian , Schultz Peter G.
Published: December 2010

Mögliche Anwendungen von Stammzellen in der Medizin reichen von der Modellierung von Krankheiten und der Wirkstoffsuche bis hin zu Zelltransplantation und regenerativen Therapien. Bevor diese Versprechen jedoch eingelöst werden können, müssen noch einige Hindernisse überwunden werden, unter anderem die Kontrolle der Stammzelldifferenzierung, die allogene Abstoßung und die eingeschränkte Zellverfügbarkeit. Dies erfordert ein vertieftes Verständnis der Mechanismen, die das Stammzellpotenzial kontrollieren, und die Entwicklung robuster Methoden, um das Schicksal von Stammzellen effizient zu steuern. In der letzten Zeit wurden eine Reihe niedermolekularer Verbindungen entdeckt, die in vitro und in vivo verwendet werden können, um Stammzellen zu expandieren, ihre Differenzierung zu dirigieren oder somatische Zellen in ein naiveres Stadium zu reprogrammieren. Diese Moleküle haben tiefe Einblicke in Signalwege und epigenetische Mechanismen ermöglicht, die die Stammzellbiologie regulieren, und sie beginnen bereits, zur Entwicklung effizienter Behandlungen für Gewebereparatur und –regeneration beizutragen.