bluuebunny/crossref_metadata_2025 huggingface dataset:
Is there evidence for an aerosol indirect effect during the recent aerosol optical depth decline in Europe?
Authors: Ruckstuhl Christian , Norris Joel R. , Philipona Rolf
Published: February 2010

Aerosol indirect effects are some of the largest uncertainties of anthropogenic climate change. To estimate the first aerosol indirect radiative effect (or cloud albedo effect), we analyzed global solar irradiance measurements under completely overcast skies during the recent period of aerosol optical depth decline in Europe. Although measurements from 15 Swiss and 8 northern German sites show clear evidence for an aerosol direct radiative effect under cloud‐free skies, trends of transmitted solar irradiance (SWtran) under overcast skies are ambiguous. Time series from 1981 to 2005 of SWtran for all overcast conditions show slightly negative, but nonsignificant trends. SWtran under overcast conditions with “thick” clouds (SWtran smaller than the long‐term mean) exhibit on average an increasing trend of +0.29 [+0.01 to +0.57] W m−2/decade. The increase of SWtran under “thick” overcast skies, however, is about nine times smaller than the increase under cloud‐free skies. Since cirrus clouds are generally excluded from and low‐level stratiform clouds are more frequently represented by “thick” overcast skies, the slight increase in SWtran may possibly result from a weak aerosol indirect effect. Alternatively, the increase in SWtran may be due to a decreasing trend in low‐level stratiform cloud amount under overcast conditions observed for these sites. We further find that solar irradiance changes caused by decreasing aerosol direct effect and increasing sunshine duration can account for most of the observed increasing all‐sky solar radiation trend. This suggests that the first aerosol indirect effect makes little contribution to surface solar radiation changes over Europe.
Spectrally distinct ejecta in Syrtis Major, Mars: Evidence for environmental change at the Hesperian‐Amazonian boundary
Authors: Skok John R. , Mustard John F. , Murchie Scott L. , Wyatt Michael B. , Ehlmann Bethany L.
Published: February 2010

Analysis of visible and near‐infrared (VNIR) imaging spectrometer data of the Syrtis Major volcanic complex on Mars shows spectrally distinct ejecta (SDE) around a subset of the region's impact craters. We explore the nature of this spectral difference with the intention of constraining the physical cause of the distinction and the significance of their near random spatial distribution. Crater counting performed by Baratoux et al. (2007) indicated that the craters with SDE are systematically younger than craters without SDE. Extensive crater counts of the craters with SDE show that they fit a consistent Hartmann (2005) isochron indicting that they represent temporally continuous population. This population was dated near 2 Ga, consistent with the counts of Baratoux et al. (2007). This modeled age corresponds to just after the Hesperian‐Amazonian boundary, indicating that it may be related to a global event. We explore possible explanations for the lack of SDE around older craters, including atmospheric changes, significant but brief regional emplacement of materials, and volcanic activity. We conclude that the preferred explanation is that the SDE represent the true composition of the Syrtis Major volcanics and that surfaces older than 2 Ga were altered by interactions with water vapor or volcanic gases under different Hesperian climatic and atmospheric conditions leading to all craters formed after this alteration event to display SDE.
Reorganization of the ocean overturning in a colder climate
Authors: Saenko Oleg A. , Lee Warren G.
Published: February 2010

Using a climate model, the effect of strong cooling on the ocean overturning circulation is investigated. The cooling has a profound impact. Essentially, the conversion of dense water of Northern Hemisphere origin to lighter water shifts from taking place predominantly in the Southern Ocean in the present day, relatively warm climate to the low‐latitude oceans in the cold climate. The main factors contributing to this reorganization of oceanic overturning are related to the changes in oceanic stratification and wind field.
A complex symmetry arises at a spin chain’s quantum critical point
Authors: Levi Barbara Goss
Published: February 2010

The relation between the E8 Lie group and the mass excitations in the Ising model was predicted more than 20 years ago, but seeing it is an experimental coup.
Diffraction around the head makes hearers mislocate sound sources
Authors: Schwarzschild Bertram
Published: February 2010

When light is obstructed by a small sphere, diffraction creates a bright spot at the center of the sphere’s shadow. Psychoacousticians are studying the acoustic analogue of that bright spot.
Model sheds light on the language of color
Authors: Miller Johanna
Published: February 2010

The process by which human societies collectively decide which segments of the visible spectrum get their own names can be studied by computer simulation.
Roundtable participants find near-consensus on free access to results of publicly funded research
Authors: Kramer David
Published: February 2010

Publishers and subscribers urge agencies to freely distribute scientific journal articles based on federally sponsored research.
ArXiv survival tied to new funding model
Authors: Guinnessy Paul
Published: February 2010

Publishers and subscribers urge agencies to freely distribute scientific journal articles based on federally sponsored research.
Physics in China
Authors: Day Charles
Published: February 2010

In its range and depth, physics in China is much like physics in other big, technologically advanced countries. The historical, political, and social contexts, however, are China’s own.
Universal insights from few-body land
Authors: Greene Chris H.
Published: February 2010

The ability to tune atomic interactions has inspired theorists and experimentalists to investigate those properties of few-particle systems that hold universally, regardless of the specific nature of the interparticle force.
Ultracold neutral plasmas
Authors: Killian Thomas C. , Rolston Steven L.
Published: February 2010

By ionizing cold atoms or molecules with a laser, researchers get a glimpse of one of nature’s extreme regimes, in which many usual rules and approximations no longer apply.
Holograms tie optical vortices in knots
Authors: Wilson Mark
Published: February 2010

Using techniques from mathematics and optical wavefront engineering, researchers demonstrate that lines of zero intensity in a light beam can be shaped into links and loops of arbitrary topology.
UV-A and Simulated Sunlight Photo-activity of TiO2 Nanoparticles Formed from Titanate Nanotubes
Authors: Church Jeffrey S. , Fincher Keith , Wang Xingdong
Published: February 2010

Sodium titanate nanotubes were prepared hydrothermally and sodium ions were exchanged for hydrogen ions by washing with water and further treatment with HCl. No anatase or rutile was produced during the exchange. Photo-catalysts were prepared by calcination and their activity was compared in UV-A and simulated sunlight by bleaching methyl orange, which does not adsorb onto the catalyst’s surface. Only photo-catalysts with low sodium content were capable of bleaching the dye. More photo-oxidation occurred in simulated sunlight suggesting that the dye is absorbing visible light and transferring this energy to the TiO2. The preparation of highly active photo-catalysts from sodium titanate nanotubes may well depend on optimizing their preparation to minimize sodium content without the formation of rutile.
Preparation of Azobenzenealkanethiols for Self-Assembled Monolayers with Photoswitchable Properties
Authors: Krakert Simone , Terfort Andreas
Published: February 2010

A series of azobenzenealkanethiol compounds with the structure p-RC6H4N=NC6H4(CH2)nSH (n = 3, 4) was synthesized using a divergent strategy with the two anilines H2NC6H4(CH2)nSAc as central compounds. This strategy provides fast access to a broad variety of the respective azobenzenethiols without (note!) an oxygen atom in the alkyl chain, thus permitting the self-assembly of these compounds onto gold in a predictable conformation, also taking advantage of the previously found odd–even effect in aromatic–aliphatic hybrid systems. Initial experiments indicate that all of these molecules indeed form dense monolayers, in which the orientation of the azobenzene unit is determined by the number of methylene groups in the aliphatic part of the molecules.
The Effect of Ionic Charge on the Adsorption of Organic Dyes onto Titanate Nanotubes
Authors: Bavykin Dmitry V. , Redmond Katherine E. , Nias Benjamin P. , Kulak Alexander N. , Walsh Frank C.
Published: February 2010

The adsorption of dye molecules from aqueous solution onto the surface of titanate nanotubes (which have been synthesized via an alkaline hydrothermal treatment) has been studied. The ionic charge on the dye molecules was found to affect their ability to adsorb onto the titanate nanotube surface. In the case of (cationic) methylene blue, the adsorption was preferable on the negatively charged surface of titanate nanotubes rather than on positively charged P25 TiO2 nanoparticles. In the case of (anionic) Eriochrome Black T dye, the opposite trend was found. Herein, the dynamics of dye adsorption and the effect of pH on the adsorption capacity are considered.
A Facile Strategy to Tune the Chiral Recognition Capabilities of Chiral Ionic Liquids by Changing Achiral Alkyl Chain
Authors: Yu Wei , Zhang Haibo , Zhang Long , Zhou Xiaohai
Published: February 2010

A new series of chiral ionic liquids, utilizing cations derived from l-proline, have been synthesized in multi-gram scale, their specific rotations and chiral recognition capability can be adjusted by the alkylation of l-proline.
Room Temperature Suzuki Reactions in Aqueous Media under Air by Palladium(II) Complexes with Pyrazole Derived Ligands
Authors: Xu Kai , Hao Xin-Qi , Gong Jun-Fang , Song Mao-Ping , Wu Yang-Jie
Published: February 2010

Two new palladium complexes with pyrazole derived ligands 2a–2b have been easily prepared and well characterized by elemental analysis, 1H NMR, 13C NMR, and IR spectra. Their detailed structures are determined by a single-crystal X-ray analysis of 2a. The two compounds were successfully applied to the Suzuki coupling reactions of aryl bromides with phenylboronic acid, in aqueous solution at room temperature under air, giving the desired coupled products in good to excellent yields with catalyst loadings as low as 0.01–0.05 mol-%.
Electrochemistry of Redox Active Centres Encapsulated by Non-Covalent Methods
Authors: Gadde Suresh , Batchelor Elizabeth K. , Kaifer Angel E.
Published: February 2010

This manuscript presents a summary of recent research work on the electrochemical behaviour of redox active guests fully or almost fully encapsulated by suitable molecular receptors or molecular capsules. From the standpoint of their voltammetric behaviour the cyclodextrins have been shown to be very dynamic hosts, which hamper the observation of direct electron transfer to/from their inclusion complexes. Therefore, this Review is essentially concerned with research work on cucurbituril and cavitand-type hosts, which was mostly done in the author’s laboratory. In general terms, the observed voltammetric behaviour for encapsulated guests covers a wide range of possibilities. Cucurbituril and cavitand-type hosts afford more kinetically stable complexes, whose direct electrochemical behaviour is observable and tends to be kinetically slower than that of the free guests. However, the degree of kinetic attenuation varies over a wide range and, in some cases, challenges our ability to rationalize the data. Clearly, more variation in the host structures and more research work are required to improve our understanding of encapsulation effects on these electron transfer reactions.
The Application of the Schmidt Reaction and Beckmann Rearrangement to the Synthesis of Bicyclic Lactams: Some Mechanistic Considerations
Authors: Crosby Ian T. , Shin James K. , Capuano Ben
Published: February 2010

The syntheses of some methoxy-substituted bicyclic lactams, of the types 3 and 4, are reported employing two different conditions for the Schmidt reaction of appropriate ketones and employing two different conditions for the Beckmann rearrangement of the corresponding ketoximes. The alkyl to aryl migration ratios of the reactions were determined by high-performance liquid chromatography analysis of the reactions. The mechanisms of the reactions reported are discussed, some limitations of the reported mechanisms identified, and an alternative mechanism proposed in light of the outcomes of the various reactions. Application of the Schmidt reaction and Beckmann rearrangement was used for the synthesis of some chloro bicyclic lactams, of the types 3 and 4.
New Highly Selective Colorimetric and Fluorescent Chemodosimeters for Mercury Ion
Authors: Wu Chen-Yu , Lin Chiung-Cheng , Fu Tung-Ming , Yang Chi-Rei , Yen Yao-Pin
Published: February 2010

Three new chemodosimeters 1–3 were prepared, and their chromogenic and fluorogenic behaviours toward various metal cations were investigated. Receptors 1–3 show an exclusive response toward Hg2+ and also distinguish Hg2+ from other metal cations by different colour changes in aqueous DMSO solution. Among them, receptor 1 also exhibits a pronounced Hg2+-induced fluorescence enhancement. Therefore, the receptor 1 can be used as a colorimetric and fluorescent chemodosimeter for the determination of Hg2+ ion.
A Fe(bipy)2 Unit Fused to a Keggin Polyoxotungstate Anion
Authors: Xie Jingli , Gilbert-Wilson Ryan , Moubaraki Boujemaa , Murray Keith S. , Wedd Anthony G.
Published: February 2010

Two new hybrid materials [Fe(bipy)3]3[ZnW12O39(OH)Fe(bipy)2(H2O)]2 and [Fe(bipy)3]2[CoW12O40] were obtained by hydrothermal synthesis. They contain [Fe(bipy)3]
n+ (bipy = 2,2′-bipyridyl; n = 2 or 3) cations and Keggin-type polyoxotungstate anions. Both have been characterized by elemental analysis, FT-IR spectroscopy, 1H-NMR spectrometry, and single crystal X-ray crystallography. The anion in the former salt features [FeII(bipy)2(OH2)]2+ units covalently bound via a W=O-Fe bridge to the protonated anion [ZnW12O39(OH)]5–. The latter salt contains discrete [CoW12O40]6– anions.
Molecular Logic: Ways Forward
Authors: Prasanna de Silva A.
Published: February 2010

How can the young field of molecular logic grow up sensibly? Six general answers to this question are offered. These range from seeing everyday chemical phenomena from a Boolean perspective to demonstrating logic applications in small spaces.
Digital Operations with Molecules - Advances, Challenges, and Perspectives
Authors: Pischel Uwe
Published: February 2010

This Review gives a short introduction into molecular logic and focusses then on the latest advances in the field. With regard to complex logic circuits and functions, molecular devices for arithmetic processing (adders and subtractors), multiplexers/demultiplexers, and encoders/decoders are discussed. Further on, the concept of memory for data storage and sequential logic is considered together with the latest results on molecular keypad locks. Molecular logic has been often connected to the future aim of molecular computing. However, albeit the herein described approaches constitute a starting point, major challenges like concatenation of gates, solid state devices and compartmentalization, and alternative concepts (reversible logic, multivalued logic) are waiting ahead. These points are included, as well as a view on alternative applications of molecular logic in bio-inspired approaches, combinatorial chemistry, and materials science.
Redox-Executed Logic Operations through the Reversible Voltammetric Response Characteristics of Electroactive Self-Assembled Monolayers
Authors: Periyasamy Ganga , Levine R. D. , Remacle F.
Published: February 2010

We propose charge quantization in electrochemical oxidation–reduction (redox) systems as a route to performing logical operations efficiently and reversibly. The theory is based on the interfacial potential distribution for electrodes coated with electroactive self-assembled molecular films. We monitor the change in the oxidation number by studying the current as a function of the working and reference electrode potentials and of the temperature. Diamond-shaped regions can be defined that delineate the stability of a given redox species as a function of the applied and reference potentials. Using these electrochemical Coulomb diamonds, we then show the principles for the design of a complete set of binary gates and a finite-state set–reset machine. We demonstrate the analogies between these redox systems and nanoscale solid-state systems where the charging energy is finite. Redox systems allow simple logic operations at room temperature because typically the standard potential is higher than the thermal energy.
Polymers with Sugar Buckets - The Attachment of Cyclodextrins onto Polymer Chains
Authors: Yhaya Firdaus , Gregory Andrew M. , Stenzel Martina H.
Published: February 2010

This Review summarizes the structures obtained when marrying synthetic polymers of varying architectures with cyclodextrins. Polymers with cyclodextrin pendant groups were obtained by directly polymerizing cyclodextrin-based monomers or by postmodification of reactive polymers with cyclodextrins. Star polymers with cyclodextrin as the core with up to 21 arms were usually obtained by using modified cyclodextrins as initiator or controlling agent. Limited reports are available on the synthesis of star polymers by arm-first techniques, which all employed azide-functionalized cyclodextrin and ‘click’ chemistry to attach seven polymer arms to the cyclodextrin core. Polymer chains with one or two cyclodextrin terminal units were reported as well as star polymers carrying a cyclodextrin molecule at the end of each arm. Cyclodextrin polymers were obtained using different polymerization techniques ranging from atom transfer radical polymerization, reversible addition–fragmentation chain transfer polymerization, nitroxide-mediated polymerization, free radical polymerization to (ionic) ring-opening polymerization, and polycondensation. Cyclodextrin polymers touch all areas of polymer science from gene delivery, self-assembled structures, drug carriers, molecular sensors, hydrogels, and liquid crystalline polymers. This Review attempts to focus on the range of work conducted with polymers and cyclodextrins and highlights some of the key areas where these macromolecules have been applied.
The Research Front on Molecular Logic
Authors: Credi Alberto
Published: February 2010

The study of the logic implications of the behaviour of molecular systems stimulates the ingenuity of researchers by introducing new concepts in chemistry, and could lead to applications in fields ranging from medicine to materials science. This Research Front provides a taste of this exciting and rapidly growing research area.
Macroporosity of pasture topsoils after three years of set-stocked and rotational grazing by sheep
Authors: Cattle S. R. , Southorn N. J.
Published: February 2010

Grazing of livestock on pasture land can result in changes to the physical condition of soil, particularly as a result of trampling and changed organic matter status of the topsoil. Over time, changes to pasture botanical composition may also occur, which might further affect soil structure. The extent of the effects, and the rate of soil and pasture recovery when livestock are removed, will depend on the grazing management tactics employed. A field study was established at Orange, New South Wales, to compare soil physical properties under ‘set-stocked’ grazing of Merino sheep, ‘high intensity–short duration’ rotational grazing, an ungrazed control, and pasture cages. Topsoil bulk density, hydraulic conductivity, and organic carbon content were measured annually over 3 years, and image analysis of soil macroporosity was carried out annually to quantify changes in pore geometry. Only the topsoil macropore properties changed significantly between treatments over the 3 years. In particular, the structural quality of the topsoil under set-stocked grazing changed, as indicated by a decrease in total macroporosity and a smaller proportion of macropores. In contrast, stable structural conditions were maintained under rotational grazing. Possibly the best soil structure for plant growth, represented by high values of total macroporosity and macropore surface area, and a large range of pore sizes, was exhibited under the pasture cages, where pasture defoliation occurred in the absence of hoof pressure. It is concluded that grazing tactics are an important factor in the dynamics of soil macroporosity and the vertical continuity of macropores, as a result of the combined effects of hoof pressure and root channel development.
Soil spatial variability of drainage properties in relation to phosphate retention and mineralogy on a river terrace of northern Manawatu, New Zealand
Authors: Senarath A. , Palmer A. S. , Tillman R. W.
Published: February 2010

Spatial variability of soil drainage, topsoil phosphate retention (P-retention), and clay mineralogy were investigated in soils on a Manawatu river terrace developed from a mixture of loamy tephra, loess, and quartzo-feldspathic alluvial parent material. The cause of short-distance variation in soil drainage was investigated on an area of 60 ha from the Last Glacial river aggradation terrace (200–240 m a.s.l.). Three small window areas of 7.5 ha were then selected for grid sampling at 50-m centres within each of 3 map units with contrasting drainage class. Each of the window areas was found to contain 3–4 different drainage classes. Topsoil P-retention also varied (from 20 to 84%) within the window areas. We found a close relationship between soil drainage, P-retention, and clay mineralogy. Well-drained soils have high P-retention and the clay fraction contains 12–13% allophane. Poorly drained soils have low P-retention and the clay fraction has no allophane and contains mainly Kandite (Kaolinite and Halloysite). The short-distance variability in drainage is attributed to slight textural variations of the original alluvial parent material. This gives rise to the formation of different soil structures, which in turn influence the soil hydraulic conductivity and thence variable drainage properties, which influence the clay mineralogy and P-retention.
Limited influence of tillage management on organic matter fractions in the surface layer of silt soils under cereal - root crop rotations
Authors: Kader Mohammed Abdul , Sleutel Steven , D'Haene Karoline , De Neve Stefaan
Published: February 2010

Reduced tillage (RT) management may increase surface soil organic carbon (SOC) and nitrogen (N), particularly due to accumulation of labile organic matter (OM). We investigated the effect of RT compared with conventional tillage (CT) on the distribution of SOC and N over different soil fractions from 7 pairs of fields with cereal–root crop rotations, in the Belgian loess belt. Surface soil samples (0–100 mm) were physically fractionated according to a sequential sieving and density separation method into stable microaggregates, silt and clay, and free and occluded particulate OM fractions. RT management was previously found effective in increasing the organic C and organic N content of the surface soil (0–100 mm) at these 7 sites. Here, physical fractionation showed that the difference in amount of organic C and N in free particulate OM (fPOM), intra-microaggregate particulate OM (iPOM), and silt and clay associated OM between the RT and CT soils contributed 34, 29, and 37% of the increase in SOC and 35, 32, and 33% of the increase in N. The contribution of OC and N in iPOM and fPOM increased significantly on a relative basis under RT management. Only a modest increase in iPOM and slight enhancement of microaggregation was observed in RT compared with CT soils. We suggest that the repeated disturbance of soil by harvest of root crops and repeated use of cultivators and harrows may limit the accumulation of physically protected POM under RT management of these Western European cereal–root crop rotations. Instead, most of the accumulated OC and N in the surface horizons under RT management is present as free unprotected POM, which could be prone to rapid loss after (temporary) abandonment of RT management.
Using digital photogrammetry to monitor soil erosion under conditions of simulated rainfall and wind
Authors: Moritani S. , Yamamoto T. , Andry H. , Inoue M. , Kaneuchi T.
Published: February 2010

We investigated a method to measure sheet erosion by characterising the soil erosion of an upland field in a dryland environment. Digital photogrammetry was used to measure the erosion rates of soil surfaces packed to different densities under simulated rainfall or wind conditions. The photogrammetry system consisted of 2 digital cameras, a rainfall simulator, a wind tunnel, and a computer program for 3-dimensional algorithm analysis. First, we assessed the accuracy of our method by comparing conventionally measured data to photogrammetric data under conditions of either no rainfall or no wind application. Two statistical parameters were used to evaluate the soil surface evolution: the mean absolute error (MAE) and the mean relative error (MRE). Their values were 0.21 mm and 15.8%, respectively. We then assessed the precision of our system under simulated rainfall conditions using 3 different dry bulk densities for the packed saturated soil surface. At densities of 0.91, 0.98, and 1.09 g/cm3, the MAE (MRE) values were 2.21 mm (392.5%), 1.07 mm (126.4%), and 0.59 mm (57.6%), respectively. It was possible to monitor and evaluate both the amount of eroded soil and the erosion mechanism in a specific area. Moreover, this system could be applied to measuring wind erosion with an MAE accuracy as high as 0.21 mm. The digital elevation models (DEMs) allowed for detailed analyses of soil surface evolution, and it was also possible to monitor sheet erosion with high spatial and temporal resolutions.
The need for better links between pedology and soil carbon research in Australia
Authors: Biggs A. J. W. , Grundy M. J.
Published: February 2010

Considerable soil carbon research has occurred in Australia in recent years. A review of published literature suggests there are gaps in both the collection of associated data and the long-term storage of soil carbon data, thus limiting the potential use of these data beyond the original purpose. A more co-operative approach between researchers and pedologists is essential to ensure maximum value is obtained from research investment. Further capacity needs to develop to capture data from all sources and especially non-government scientists. ASRIS can be the national focal point; it is recommended that it be more effectively utilised as a data management tool for Australian soil carbon data.
Modelling shows that the high rates of deep drainage in parts of the Goondoola Basin in semi-arid Queensland can be reduced with changes to the farming systems
Authors: Robinson J. B. , Silburn D. M. , Rattray D. , Freebairn D. M. , Biggs A. , McClymont D. , Christodoulou N.
Published: February 2010

Clearing native vegetation and introducing crops and pastures may increase deep drainage and result in dryland salinity. In south-west Queensland, native vegetation of the Goondoola Basin has been substantially cleared for cropping and pastoral activities, resulting in shallow groundwater and localised salinity. Simulation modelling was used to estimate the water balance of a range of vegetation and soil types. Six soils were studied, with plant-available water capacity (PAWC) of 71 mm (a Kandosol) to 198 mm (a Vertosol) for 1200 mm depth. Vegetation types were annual wheat, opportunity cropping, and perennial pastures in poor and good condition, and high quality perennial pasture with deep roots growing on deep (2400 mm) variants of the 6 soil types. Opportunity cropping did not reduce deep drainage. Substantial differences were found in long-term average deep drainage (mm/year) between wheat crops and pastures for all soil types. The differences in deep drainage between wheat cropping and pasture in good condition were greatest for the 2 Kandosols, which had the lowest PAWC (34 and 21 mm/year less deep drainage, reductions of 53% and 62%, respectively), and a Vertosol with intermediate PAWC (23 mm/year less deep drainage). A Chromosol and a Dermosol with intermediate PAWC had smaller reductions in deep drainage (14 and 11 mm/year, respectively). In the case of a Vertosol with high PAWC (198 mm), deep drainage was negligible with all pastures. Due to increased infiltration and reduced soil evaporation, more deep drainage was simulated with pasture in good condition than pastures in poor condition, especially for 2 Kandosols. Pasture with deep roots (2400 mm) growing on deep variants (2400 mm) of the 6 soils had lower rates of deep drainage than the other pastures. Simulated deep drainage and other components of the water balance were in good agreement with field measurements and expectations. These results indicate that large reductions in deep drainage can be achieved in the Goondoola Basin by replacing cropping with pastoral activities. Kandosol soils used for wheat cropping should be the primary target for land use change.
The No-Miracles Argument for Realism: Inference to an Unacceptable Explanation
Authors: Frost-Arnold Greg
Published: February 2010

I argue that a certain type of naturalist should not accept a prominent version of the no-miracles argument (NMA). First, scientists (usually) do not accept explanations whose explanans-statements neither generate novel predictions nor unify apparently disparate established claims. Second, scientific realism (as it appears in the NMA) is an explanans that makes no new predictions and fails to unify disparate established claims. Third, many proponents of the NMA explicitly adopt a naturalism that forbids philosophy of science from using any methods not employed by science itself. Therefore, such naturalistic philosophers of science should not accept the version of scientific realism that appears in the NMA.
Specious Intrinsicalism
Authors: Barker Matthew J.
Published: February 2010

Over the last 2,300 years or so, many philosophers have believed that species are individuated by essences that are at least in part intrinsic. Psychologists tell us most folks also believe this view. But most philosophers of biology have abandoned the view, in light of evolutionary conceptions of species. In defiance, Michael Devitt has attempted in this journal to resurrect a version of the view, which he calls Intrinsic Biological Essentialism. I show that his arguments for the resurrection fail, and I identify challenges that face anyone wishing to defend Intrinsic Biological Essentialism.
Social Construction Revisited: Epistemology and Scientific Practice
Authors: Fagan Melinda B.
Published: February 2010

Philosophy of scientific practice aims to critically evaluate as well as describe scientific inquiry. Epistemic norms are required for such evaluation. Social constructivism is widely thought to oppose this critical project. I argue, however, that one variety of social constructivism, focused on epistemic justification, can be a basis for critical epistemology of scientific practice, while normative accounts that reject this variety of social constructivism (SCj) cannot. Abstract, idealized epistemic norms cannot ground effective critique of our practices. I propose a new approach, placing SCj within a general framework of social action theory. This framework can be used to explicate epistemic norms implicit in our scientific practices.
Biased hosting of intronic microRNA genes
Authors: Golan David , Levy Carmit , Friedman Brad , Shomron Noam
Published: February 2010

Motivation: MicroRNAs (miRNAs) are involved in an abundant class of post-transcriptional regulation activated through binding to the 3′ -untranslated region (UTR) of mRNAs. The current wealth of mammalian miRNA genes results mostly from genomic duplication events. Many of these events are located within introns of transcriptional units. In order to better understand the genomic expansion of miRNA genes, we investigated the distribution of intronic miRNAs.

Results: We observe that miRNA genes are hosted within introns of short genes much larger than expected by chance.

Implementation: We explore several explanations for this phenomenon and conclude that miRNA integration into short genes might be evolutionary favorable due to interaction with the pre-mRNA splicing mechanism.

Contact:  nshomron@post.tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
End‐systolic volume following surgical ventricular reconstruction impacts survival in patients with ischaemic dilated cardiomyopathy
Authors: Di Donato Marisa , Castelvecchio Serenella , Menicanti Lorenzo
Published: February 2010

Aims

A left ventricular end‐systolic volume (LVESV) ≥60 mL/m2 has been shown to be associated with increased cardiac mortality after a reperfused myocardial infarction (MI). The reduction in LVESV following surgical ventricular reconstruction (SVR) is reported to be between 19% and 50% but its impact on prognosis is not well‐established. The aim of this study was therefore to assess the impact on survival of a residual LVESV index (LVESVI) of ≥ or <60 mL/m2 following SVR.

Methods and results

All patients undergoing SVR at our Centre between July 2001 and March 2009 were eligible to be included in this study if they had a preoperative LVESVI of ≥60 mL/m2 and an LVESVI measurement performed at discharge (7–10 days after surgery). Two hundred and sixteen patients (aged 64 ± 9 years, 33 women) satisfied these criteria. Coronary artery bypass graft was performed in 197 patients (91.2%) and mitral repair in 63 patients (29%). Left ventricular ESVI had decreased by 41% at discharge in the overall population. Patients were grouped according to the residual LVESVI at discharge as follows: Group 1, LVESVI ≥ 60 mL/m2 (n = 71), and Group 2, LVESVI < 60 mL/m2 (n = 145). In both groups, LVESVI decreased significantly with respect to baseline, by 29% in Group 1 and by 47% in Group 2. At multivariate analysis, the presence of a non‐Q‐wave MI and a preoperative internal diastolic diameter of 65 mm were the strongest predictors of a residual post‐operative LVESVI of ≥60 mL/m2. Risk of all‐cause death was significantly higher in Group 1. Post‐operative LVESVI of ≥60 mL/m2 was an independent predictor of mortality at follow‐up [Exp(B) = 10.7, CI: 2.67–42.9, P = 0.001].

Conclusion

Our findings confirm the role of LVESVI in predicting survival following SVR; the lack of additional improvement in survival with SVR observed in the STICH trial might be due to the inadequate volume reduction (−19%).
Estimating total mortality and asymptotic length of Crangon crangon between 1955 and 2006
Authors: Hufnagl Marc , Temming Axel , Siegel Volker , Tulp Ingrid , Bolle Loes
Published: February 2010

Hufnagl, M., Temming, A., Siegel, V., Tulp, I., and Bolle, L. 2010. Estimating total mortality and asymptotic length of Crangon crangon between 1955 and 2006. – ICES Journal of Marine Science, 67: 875–884. Total mortality (Z, year−1) of southern North Sea brown shrimp (Crangon crangon) was determined as Z = θK, based on the von Bertalanffy length–growth constant (K, year−1) and θ derived from length-based methods. Mortality estimates were based on length frequency distributions obtained from four long-term dataseries (1955–2006): German Demersal Young Fish Survey, Dutch Demersal Fish Survey, and two German Bycatch series (Büsum and East Frisia). Four methods to estimate θ and L∞ were evaluated. Highest total mortality (Z = 8 year−1) was estimated for the early 1990s, and the lowest (Z = 4 year−1) for the 1960s. Accounting for these differences, a median Z rather than mean values was calculated for the whole series, and the value ranged from 5.74 (Ssentongo and Larkin method), through 5.65 (Beverton and Holt method) and 5.64 (Jones and Zalinge method), to 5.35 (length-converted catch curves). Over the whole period, an increase in θ and a decrease in the proportion of shrimps >60 mm in the catch was observed, whereas asymptotic length L∞ remained constant (at 79.3 mm total length).
An expansion of the MSVPA approach for quantifying predator–prey interactions in exploited fish communities
Authors: Garrison Lance P. , Link Jason S. , Kilduff D. Patrick , Cieri Matthew D. , Muffley Brandon , Vaughan Douglas S. , Sharov Alexei , Mahmoudi Behzad , Latour Robert J.
Published: February 2010

Garrison, L. P., Link, J. S., Kilduff, D. P., Cieri, M. D., Muffley, B., Vaughan, D. S., Sharov, A., Mahmoudi, B., and Latour, R. J. 2010. An expansion of the MSVPA approach for quantifying predator–prey interactions in exploited fish communities. – ICES Journal of Marine Science, 67: 856–870. Ecosystem-based fisheries management requires tools to place fish-stock dynamics in the broader context of fishery, predator, and competitive removals. Multispecies virtual population analysis (MSVPA) is an approach to quantifying predator–prey interactions and estimating the rates of predation mortality for exploited fish populations. Here, an extended MSVPA (MSVPA-X) is presented as an alternative to existing MSVPA approaches. Notably, MSVPA-X uses index-tuned VPA methods, applies a more flexible feeding model, and includes an alternative functional feeding response. The MSVPA-X model is applied to a western Atlantic fish community, focusing on Atlantic menhaden and its major fish predators, and a sensitivity analysis of major model parameters is presented. The sensitivity analysis highlights the need for adequate diet sampling. The MSVPA-X represents an improvement over previous approaches by increasing the flexibility to model seasonal and interannual dynamics in the strength of predator–prey interactions. Model results demonstrate that, for menhaden in particular, and forage fish in general, quantifying predation mortality is an important part of effective assessments of forage fish, their predators, and the fisheries of both.
Analysis of methods commonly used for glycopeptide and oxazolidinone susceptibility testing in Enterococcus faecium isolates
Authors: Raponi Giammarco , Ghezzi Maria Cristina , Gherardi Giovanni , Lorino Giulia , Dicuonzo Giordano
Published: February 2010

The susceptibility to teicoplanin, vancomycin and linezolid of 30 clinical isolates of Enterococcus faecium was tested by Vitek 2, Phoenix, Etest, broth microdilution and disc diffusion tests. The vanA and vanB resistance genes and the 23S rRNA gene G2576T mutation were detected by PCR and PCR-RFLP, respectively. Resistance rates to teicoplanin ranged from 3 % for Vitek 2 to 57.6 % for the Phoenix test, and those to vancomycin ranged from 56.7 % for Vitek 2 to 86.7 % for the Phoenix test. Only two out of 25 strains carrying the vanA gene were univocally recognized as the VanA phenotype. The only strain with the G2576T mutation did not carry the vanA gene and showed resistance to linezolid by the disc diffusion, Vitek 2 and broth dilution methods (MIC >8 μg ml−1), but was susceptible when tested with the Phoenix test and Etest (MIC ≤4 μg ml−1). Therefore, the resistance to glycopeptides and linezolid was not univocally detected by the susceptibility testing methods used in this study.
Mycoplasma pneumoniae as a cause of non-resolving pneumonia in a neonate
Authors: Kumar Surinder , Maria Arti , Saigal Sanjeev R. , Maheshwari Megha
Published: February 2010

Mycoplasma pneumoniae is known to be the chief causative organism for community-acquired non-lobar pneumonia in children of 5–15 years of age. M. pneumoniae as an aetiological agent for pneumonia among neonates and infants has rarely been reported. We report here a case of persistent pneumonia due to M. pneumoniae in a 3-week-old neonate.
Approaches to measure the fitness of Burkholderia cepacia complex isolates
Authors: Pope C. F. , Gillespie S. H. , Moore J. E. , McHugh T. D.
Published: February 2010

Members of the Burkholderia cepacia complex (Bcc) are highly resistant to many antibacterial agents and infection can be difficult to eradicate. A coordinated approach has been used to measure the fitness of Bcc bacteria isolated from cystic fibrosis (CF) patients with chronic Bcc infection using methods relevant to Bcc growth and survival conditions. Significant differences in growth rate were observed among isolates; slower growth rates were associated with isolates that exhibited higher MICs and were resistant to more antimicrobial classes. The nucleotide sequences of the quinolone resistance-determining region of gyrA in the isolates were determined and the ciprofloxacin MIC correlated with amino acid substitutions at codons 83 and 87. Biologically relevant methods for fitness measurement were developed and could be applied to investigate larger numbers of clinical isolates. These methods were determination of planktonic growth rate, biofilm formation, survival in water and survival during drying. We also describe a method to determine mutation rate in Bcc bacteria. Unlike in Pseudomonas aeruginosa where hypermutability has been detected in strains isolated from CF patients, we were unable to demonstrate hypermutability in this panel of Burkholderia cenocepacia and Burkholderia multivorans isolates.
Transmission of a Klebsiella pneumoniae clone harbouring genes for CTX-M-15-like and SHV-112 enzymes in a neonatal intensive care unit of a Kuwaiti hospital
Authors: Dashti Ali A. , Jadaon Mehrez M. , Gomaa Huda H. , Noronha Bobby , Udo Edet E.
Published: February 2010

The spread of antibiotic-resistant bacteria has become a large problem in most countries including Kuwait. This antibiotic resistance is usually due to the production of extended-spectrum β-lactamase (ESBL) enzymes such as SHV, TEM and CTX-M. This study reports the emergence and spread of an ESBL-producing Klebsiella pneumoniae clone in a neonatal intensive care unit (NICU) in a Kuwaiti hospital. Eight ESBL-producing K. pneumoniae isolates were from blood cultures of seven neonates, and two were from the fingers of two healthcare workers in a NICU in Al Jahra Hospital, Kuwait. All isolates were obtained in February–March 2006, except for one, which was obtained in August 2005. Identification of the bacteria was based on traditional bacteriological and biochemical tests using the Vitek system. Antibiotic susceptibility was tested by the disc diffusion method using 16 different antibiotics. ESBLs were detected using disc approximation and double-disc synergy methods and confirmed as ESBLs using Etest. PCR and DNA sequencing were performed to determine the genotypes and mutations in the β-lactamase genes (bla
TEM, bla
SHV and bla
CTX-M). Genetic relatedness was determined by PFGE. All isolates were confirmed to have ESBLs by the Vitek system, disc approximation test, double-disc diffusion test and Etest, being resistant to cefotaxime, ceftazidime, cefepime, gentamicin, tobramycin and ciprofloxacin but susceptible to tetracycline and trimethoprim–sulfamethoxazole. Molecular studies showed the isolates to have TEM-1 β-lactamase, a CTX-M-15-like ESBL and the newly discovered SHV-112 ESBL. PFGE showed that all isolates had identical banding patterns. The results indicate that a single clone of ESBL-producing K. pneumoniae caused bloodstream infections among babies in a NICU of a Kuwaiti hospital, and may have emerged at least 5 years ago. This clone was also present on the hands of healthcare workers, suggesting that they may have been involved in its transmission. Further studies are recommended to determine whether this clone is also spreading in other Kuwaiti hospitals.
Transcriptional regulation of the Bacillus subtilis asnH operon and role of the 5′-proximal long sequence triplication in RNA stabilization
Authors: Morinaga Tetsuro , Kobayashi Kazuo , Ashida Hitoshi , Fujita Yasutaro , Yoshida Ken-ichi
Published: February 2010

TheBacillus subtilis asnHoperon, comprisingyxbB,yxbA,yxnB,asnHandyxaM, is induced dramatically in the transition between exponential growth and stationary phase in rich sporulation medium. TheasnHoperon is transcribed to produce an unstable long transcript covering the entire operon as well as a short one corresponding to the first three genes. Northern blot analysis revealed that the discrete band corresponding to the short transcript was detectable even 1 h after the addition of excess rifampicin, suggesting its unusual stability. The transcription start site of the operon was determined; its corresponding promoter was most likely sigma-A dependent and under tight control of AbrB and CodY. Within the 5′-proximal region of the transcript precedingyxbB, there is a mysterious long sequence triplication (LST) segment, consisting of a tandem repeat of two highly conserved 118 bp units and a less conserved 129 bp unit. This LST segment was not involved in regulation by AbrB and CodY. Transcriptional fusion of the 5′-region containing the LST segment tolacZresulted in a significant increase inβ-galactosidase synthesis in cells; the LST segment was thought to prevent degradation of the 5′-region–lacZfusion transcript. These results suggest that the 5′-region containing the LST segment could function as an mRNA stabilizer that prolongs the lifetime of the transcript to which it is fused.
Mullite-type Ga4B2O9: structure and order–disorder phenomenon
Authors: Cong Rihong , Yang Tao , Li Kuo , Li Hongmei , You Liping , Liao Fuhui , Wang Yingxia , Lin Jianhua
Published: February 2010

Ga4B2O9, an aluminium-free mullite-type compound, was prepared by a boric-acid flux method and its structure was determined using powder X-ray diffraction techniques, in combination with transmission electron microscopy, solid-state 11B MAS-NMR and IR spectroscopies. GaO6 octahedra share edges in a trans-manner forming one-dimensional chains along the b direction, and the chains are further cross-linked by GaO5, BO3 and BO4 groups into a three-dimensional mullite-type structure. The disorder of the inter-chain groups results in a small unit cell for Ga4B2O9 compared with that for Al4B2O9, an ordered compound with a superstructure. By deconstructing the structure of Ga4B2O9, we were able to identify the fundamental building units and their linking rules which can be used to reconstruct the ordered and disordered structures. For Ga4B2O9, we found that the structure is intrinsically disordered within the ac plane, but ordered along the b axis. The three-dimensional structure can then be constructed by stacking the disordered ac sheets along the b axis (½b) with a ½a shift. The fundamental building units and exclusivity rules identified in this gallium borate mullite may also be useful for understanding other related mullite phases. The structure analysis applying the proposed method is used to recognize the structural features of Al4B2O9 and Al18B4O33.
Precursor effects of the orthorhombic to monoclinic phase transition in benzocaine form (II) revealed by X-ray diffuse scattering
Authors: Chan E. J. , Welberry T. R.
Published: February 2010

We described the development of a Monte Carlo computer model for the room-temperature form (II) polymorph of benzocaine that incorporates, on a local scale, structural features derived from the low-temperature form (III) polymorph. The introduction of this extra information convincingly reproduces those observed diffraction features that an earlier harmonic model was unable to achieve. In both form (I) and form (II) the hydrogen-bonded chains of molecules that extend along the respective a axes tend to slide backward and forward along their lengths. While in form (I) the motion is well modelled by a harmonic potential in form (II) there is a degree of anharmonicity that means that some intermolecular contact vectors, which are identical in the average structure, are distributed bimodally with either longer or shorter vectors being preferred to the average. Moreover there is a tendency for these deviations from average to be correlated to give short-range ordered domains that are the precursors of the two twinned variants of the long-range ordered low-temperature form (III) structure.