bluuebunny/crossref_metadata_2025 huggingface dataset:
Prototyping scalable digital signal processing systems for radio astronomy using dataflow models
Authors: Sane N. , Ford J. , Harris A. I. , Bhattacharyya S. S.
Published: April 2012

There is a growing trend toward using high‐level tools for design and implementation of radio astronomy digital signal processing (DSP) systems. Such tools, for example, those from the Collaboration for Astronomy Signal Processing and Electronics Research (CASPER), are usually platform‐specific, and lack high‐level, platform‐independent, portable, scalable application specifications. This limits the designer's ability to experiment with designs at a high‐level of abstraction and early in the development cycle. We address some of these issues using a model‐based design approach employing dataflow models. We demonstrate this approach by applying it to the design of a tunable digital downconverter (TDD) used for narrow‐bandwidth spectroscopy. Our design is targeted toward an FPGA platform, called theInterconnect Break‐out Board (IBOB), that is available from the CASPER. We use the term TDD to refer to a digital downconverter for which the decimation factor and center frequency can be reconfigured without the need for regenerating the hardware code. Such a design is currently not available in the CASPER DSP library. The work presented in this paper focuses on two aspects. First, we introduce and demonstrate a dataflow‐based design approach using thedataflow interchange format (DIF) tool for high‐level application specification, and we integrate this approach with the CASPER tool flow. Secondly, we explore the trade‐off between the flexibility of TDD designs and the low hardware cost of fixed‐configuration digital downconverter (FDD) designs that use the available CASPER DSP library. We further explore this trade‐off in the context of a two‐stage downconversion scheme employing a combination of TDD or FDD designs.
Two‐dimensional distribution of volatiles in the lunar regolith from space weathering simulations
Authors: Hurley Dana M. , Lawrence David J. , Bussey D. Benjamin J. , Vondrak Richard R. , Elphic Richard C. , Gladstone G. Randall
Published: April 2012

We present simulations of space weathering effects on ice deposits in regions of permanent shadow on the Moon. These Monte Carlo simulations follow the effects of space weathering processes on the distribution of the volatiles over time. The model output constrains the coherence of volatile deposits with depth, lateral separation, and time. The results suggest that ice sheets become broken and buried with time. As impacts begin to puncture an initially coherent surficial ice sheet, small areas with a deficit of ice compared to surrounding areas are formed first. As time progresses, holes become prevalent and the anomalous regions are local enhancements of ice concentration in a volume. The 3‐D distribution is also heterogeneous because the ice is buried to varying depths in different locations. Analysis of the coherence of ice on 10 cm scales predicts that putative ice sheets in anomalous radar craters are <100 Myr old. Surface frost becomes homogenized within 20 Myr. The simulations show the data from the LCROSS impact and surrounding region are consistent with the ice deposit in Cabeus being >1000 Myr old. For future in situ analysis of cold trap volatiles, a horizontal range of 10 m is sufficient to acquire surface‐based measurements of heterogeneously distributed ice. These results also support previous analyses that Mercury's cold traps are young.
Dynamic dissolution of halite rock during flow of diluted saline solutions
Authors: Weisbrod N. , Alon‐Mordish C. , Konen E. , Yechieli Y.
Published: April 2012

The dynamic dissolution pattern of halite salt rocks taken from coreholes near the Dead Sea was studied in laboratory‐scale experiments. When unsaturated solution (with respect to halite) flowed through salt cores, dissolution developed along preferential flow pathways in a channel structure. The channel structure was related to the salt's properties and internal heterogeneities, flow velocity and impact of gravity. Preferential dissolution pathways developed in areas of minimum resistance to flow, such as large‐pore networks and cracks. Nevertheless, in many cases no structural heterogeneity was observed along the dissolution channels prior to the experiments. The initial formation of channels took place above a critical flow velocity; below this threshold, dissolution developed as a slowly propagating front. In these cases, salt re‐precipitation resulted in clogging and cessation of flow through a few of the salt cores. Solution density was found to be important, as evidenced by the fact that more channels developed upward than downward, due to gravitational fractionation. The development of dissolution channels could have very important implications for the overall permeability of the salt layer in general, and the use of salt formations for industrial waste storage and the development of sinkholes along the Dead Sea shore in particular.
Seasonally active slipface avalanches in the north polar sand sea of Mars: Evidence for a wind‐related origin
Authors: Horgan Briony H. N. , Bell James F.
Published: April 2012

Meter‐scale MRO/HiRISE camera images of dune slipfaces in the north polar sand sea of Mars reveal the presence of deep alcoves above depositional fans. These features are apparently active under current climatic conditions, because they form between observations taken in subsequent Mars years. Recently, other workers have hypothesized that the alcoves form due to destabilization and mass‐wasting during sublimation of CO2 frost in the spring. While there is evidence for springtime modification of these features, our analysis of early springtime images reveals that over 80% of the new alcoves are visible underneath the CO2 frost. Thus, we present an alternative hypothesis that formation of new alcoves and fans occurs prior to CO2deposition. We propose that fans and alcoves form primarily by aeolian processes in the mid‐ to late summer, through a sequence of aeolian deposition on the slipface, over‐steepening, failure, and dry granular flow. An aeolian origin is supported by the orientations of the alcoves, which are consistent with recent wind directions. Furthermore, morphologically similar but much smaller alcoves form on terrestrial dune slipfaces, and the size differences between the terrestrial and Martian features may reflect cohesion in the near‐subsurface of the Martian features. The size and preservation of the largest alcoves on the Martian slipfaces also support the presence of an indurated surface layer; thus, new alcoves might be sites of early spring CO2sublimation and secondary mass‐wasting because they act as a window to looser, less indurated materials that warm up more quickly in the spring.
The role of summer surface wind anomalies in the summer Arctic sea ice extent in 2010 and 2011
Authors: Ogi Masayo , Wallace John M.
Published: April 2012

Strong summertime anticyclonic wind anomalies over the Arctic Ocean, with anomalous flow toward the Fram Strait, during summer months of 2007 contributed to the record‐low the Arctic sea‐ice extent observed in September of that year. Had the summer winds over the Arctic during the summers of 2010 and 2011 been the same as those in 2007, September sea ice extent would have reached new record lows in those years as well. By regulating the flow of ice toward and through the Fram Strait, variations in low‐level winds over the Arctic have contributed to the month‐to‐month, year‐to‐year, and decade‐to‐decade variability of sea ice extent.
Effect of spectral‐dependent surface albedo on Saharan dust direct radiative forcing
Authors: Ma Xiaoyan , Yu Fangqun
Published: April 2012

Direct radiative forcing (DRF) due to mineral dust has quite large uncertainty. Surface albedo is one of the most important factors affecting dust radiative forcing and climate. Here we investigate the effect of spectral‐dependent surface albedo on dust DRF over the Saharan desert region using MODIS surface albedo data and a size‐resolved global aerosol model. In one simulation, surface albedo in 7 wavebands from MODIS‐retrieved data is interpolated to the corresponding 4 solar wavebands of the radiation transfer model (case 1). In another simulation, surface albedo for visible wavebands is applied to all 4 solar spectral‐bands (case 2), which was previously used by many global model simulations. Our results show that the annual averaged DRF for all sky over the Saharan dust is −2.4 W m−2 and −5.6 W m−2 at TOA, and −9.9 W m−2 and −12.9 W m−2at surface for cases 1 and 2, respectively. Such a large difference highlights the importance of using accurate spectral‐dependent surface albedo, and implies that previous studies employing only visible‐band surface albedo might have significantly overestimated the dust cooling effect over the Saharan dust.
A stochastic method for improving seasonal predictions
Authors: Batté L. , Déqué M.
Published: April 2012

Ensemble seasonal forecasts during boreal winter suffer from insufficient spread and systematic errors. In this study we suggest a new stochastic dynamics method to address both issues at a time. Our technique relies on random additive corrections of initial tendency error estimates of the atmospheric component of the CNRM‐CM5.1 global climate model, using ERA‐Interim as a reference over a 1979–2010 hindcast period. The random method improves deterministic scores for 500‐hPa geopotential height forecasts over the Northern Hemisphere extratropics (NH Z500), and increases the ensemble spread. An optimal method consisting in drawing the error corrections within the current month of the hindcast period illustrates the high potential of future improvements, with NH Z500 anomaly correlation reaching 0.65 and North Atlantic Oscillation index correlation 0.71 with ERA‐Interim. These substantial improvements using current year corrections pave the way for future forecasting methods using classification criteria on the correction population.
Ensemble ENSO hindcasts initialized from multiple ocean analyses
Authors: Zhu Jieshun , Huang Bohua , Marx Lawrence , Kinter James L. , Balmaseda Magdalena A. , Zhang Rong‐Hua , Hu Zeng‐Zhen
Published: April 2012

In this study, the impact of ocean initial conditions (OIC) on the prediction skill in the tropical Pacific Ocean is examined. Four sets of OIC are used to initialize the 12‐month hindcasts of the tropical climate from 1979 to 2007, using the Climate Forecast System, version 2 (CFSv2), the current operational climate prediction model at the National Centers for Environmental Predictions (NCEP). These OICs are chosen from four ocean analyses produced by the NCEP and the European Center for Medium Range Weather Forecasts (ECMWF). For each hindcast starting from a given OIC, four ensemble members are generated with different atmosphere and land initial states. The predictive skill in the tropical Pacific Ocean is assessed based on the ensemble mean hindcasts from each individual as well as multiple oceanic analyses. To reduce the climate drift from various oceanic analyses, an anomaly initialization strategy is used for all hindcasts. The results indicate that there exists a substantial spread in the sea surface temperature (SST) prediction skill with different ocean analyses. Specifically, the ENSO prediction skill in terms of the anomaly correlation of Niño‐3.4 index can differ by as much as 0.1–0.2 at lead times longer than 2 months. The ensemble mean of the predictions initialized from all four ocean analyses gives prediction skill equivalent to the best one derived from the individual ocean analysis. It is suggested that more accurate OIC can improve the ENSO prediction skill and an ensemble ocean initialization has the potential of enhancing the skill at the present stage.
The phases and amplitudes of gravity waves propagating and dissipating in the thermosphere: Application to measurements over Alaska
Authors: Nicolls M. J. , Vadas S. L. , Meriwether J. W. , Conde M. G. , Hampton D.
Published: April 2012

In a companion paper, we derived the high‐frequency, compressible, dissipative polarization relations for gravity waves (GWs) propagating in the thermosphere. In this paper, we apply the results to nighttime thermospheric observations of a GW over Alaska on 9–10 January 2010. Using a vertically‐pointed Fabry‐Perot interferometer (FPI) at Poker Flat that measured vertical wind perturbations (w′) and two FPIs that measured the line‐of‐sight (LOS) velocities in four common volumes, we inferred a GW ground‐based period ∼32.7 ± 0.3 min, horizontal wavelength λH = 1094 ± 408 km, horizontal ground‐based phase speed cH ∼ 560 ± 210 m/s, and propagation azimuth θ ∼ 33.5 ± 15.8° east‐of‐north. We compared the phase shifts and amplitude ratios of this GW with that predicted by the GW dissipative polarization relations derived in the companion paper, enabled by the ability of the FPIs to measure fundamental GW parameters (wind and temperature perturbations). We find that GWs with λH ∼ 700–1100 km, λz ∼ −500 to −350 km, θ ∼ 15 to 50°, and cH ∼ 350–560 m/s agree with the observations if the primary contribution to the 630‐nm emission was near the upper portion of that layer. The source of GW was likely thermospheric given the large intrinsic phase speed of the wave. Possible sources are discussed, the most likely of which are related to the onset of auroral activity near the time that the wave was initially observed.
Imaging of Perfusion, Angiogenesis, and Tissue Elasticity after Stroke
Authors: Martín Abraham , Macé Emilie , Boisgard Raphael , Montaldo Gabriel , Thézé Benoit , Tanter Mickael , Tavitian Bertrand
Published: April 2012

Blood flow interruption in a cerebral artery causes brain ischemia and induces dramatic changes of perfusion and metabolism in the corresponding territory. We performed in parallel positron emission tomography (PET) with [15O]H2O, single photon emission computed tomography (SPECT) with [99mTc]hexamethylpropylene-amino-oxime ([99mTc]HMPAO) and ultrasonic ultrafast shear wave imaging (SWI) during, immediately after, and 1, 2, 4, and 7 days after middle cerebral artery occlusion (MCAO) in rats. Positron emission tomography and SPECT showed initial hypoperfusion followed by recovery at immediate reperfusion, hypoperfusion at day 1, and hyperperfusion at days 4 to 7. Hyperperfusion interested the whole brain, including nonischemic areas. Immunohistochemical analysis indicated active angiogenesis at days 2 to 7, strongly suggestive that hyperperfusion was supported by an increase in microvessel density in both brain hemispheres after ischemia. The SWI detected elastic changes of cerebral tissue in the ischemic area as early as day 1 after MCAO appearing as a softening of cerebral tissue whose local internal elasticity decreased continuously from day 1 to 7. Taken together, these results suggest that hyperperfusion after cerebral ischemia is due to formation of neovessels, and indicate that brain softening is an early and continuous process. The SWI is a promising novel imaging method for monitoring the evolution of cerebral ischemia over time in animals.
β2-Glycoprotein I inhibits endothelial cell migration through the nuclear factor κB signalling pathway and endothelial nitric oxide synthase activation
Authors: Chiu Wen-Chin , Chiou Tzeon-Jye , Chiang An-Na
Published: April 2012

β2-GPI (β2-glycoprotein I) is a plasma glycoprotein ascribed with an anti-angiogenic function; however, the biological role and molecular basis of its action in cell migration remain unknown. The aim of the present study was to assess the contribution of β2-GPI to HAEC (human aortic endothelial cell) migration and the details of its underlying mechanism. Using wound healing and Boyden chamber assays, we found that β2-GPI inhibited endothelial cell migration, which was restored by its neutralizing antibody. NF-κB (nuclear factor κB) inhibitors and lentiviral siRNA (small interfering RNA) silencing of NF-κB significantly attenuated the inhibitory effect of β2-GPI on cell migration. Moreover, β2-GPI was found to induce IκBα (inhibitor of NF-κB) phosphorylation and translocation of p65 and p50. We further demonstrated that mRNA and protein levels of eNOS [endothelial NO (nitric oxide) synthase] and NO production were all increased by β2-GPI and these effects were remarkably inhibited by NF-κB inhibitors and siRNAs of p65 and p50. Furthermore, β2-GPI-mediated inhibition of cell migration was reversed by eNOS inhibitors and eNOS siRNAs. The findings of the present study provide novel insight into the ability of β2-GPI to inhibit endothelial cell migration predominantly through the NF-κB/eNOS/NO signalling pathway, which indicates a potential direction for clinical therapy in vascular diseases.
Distinctive binding of three antagonistic peptides to the ephrin-binding pocket of the EphA4 receptor
Authors: Lamberto Ilaria , Qin Haina , Noberini Roberta , Premkumar Lakshmanane , Bourgin Caroline , Riedl Stefan J. , Song Jianxing , Pasquale Elena B.
Published: April 2012

The EphA4 receptor tyrosine kinase interacts with ephrin ligands to regulate many processes, ranging from axon guidance and nerve regeneration to cancer malignancy. Thus antagonists that inhibit ephrin binding to EphA4 could be useful for a variety of research and therapeutic applications. In the present study we characterize the binding features of three antagonistic peptides (KYL, APY and VTM) that selectively target EphA4 among the Eph receptors. Isothermal titration calorimetry analysis demonstrated that all three peptides bind to the ephrin-binding domain of EphA4 with low micromolar affinity. Furthermore, the effects of a series of EphA4 mutations suggest that the peptides interact in different ways with the ephrin-binding pocket of EphA4. Chemical-shift changes observed by NMR spectroscopy upon binding of the KYL peptide involve many EphA4 residues, consistent with extensive interactions and possibly receptor conformational changes. Additionally, systematic replacement of each of the 12 amino acids of KYL and VTM identify the residues critical for EphA4, binding. The peptides exhibit a long half-life in cell culture medium which, with their substantial binding affinity and selectivity for EphA4, makes them excellent research tools to modulate EphA4 function.
Ultrastructure and anatomy of Macadamia (Proteaceae) kernels
Authors: Walton David A. , Wallace Helen M. , Webb Richard
Published: April 2012

Macadamia integrifolia Maiden & Betche and M. tetraphylla L.A.S.Johnson, and their hybrids, are cultivated for their edible kernels (mature embryos). Some kernels separate into halves (cotyledons) during post-harvest handling, and embryo cuticular characteristics may influence breakage. Some kernels have a gap between cotyledons before nut cracking, and this anatomical feature may be related to breakage. Kernels from cultivars producing high or low frequency of breakage were examined by transmission electron microscopy and scanning electron microscopy to identify differences in inner-cuticular wax. Whole seeds of each cultivar were opened without cracking to measure gaps between cotyledons and determine relationships between gaps and embryo breakage. Kernels from cultivars with low frequency of breakage had inner-epicuticular wax layers that were of the sculptured crust type whereas those of cultivars with high frequency of breakage were mainly of a wax-film type. Gap width and length of kernels separate at nut opening were more than twice those for intact kernels. There was a negative relationship between whole-kernel percentage and gap width between cotyledons.
Pollen morphology of the Myrtaceae. Part 1: tribes Eucalypteae, Lophostemoneae, Syncarpieae, Xanthostemoneae and subfamily Psiloxyloideae
Authors: Thornhill Andrew H. , Hope Geoff S. , Craven Lyn A. , Crisp Michael D.
Published: April 2012

A family-wide palynological study of Myrtaceae was conducted using scanning electron microscopy (SEM) and light microscopy (LM). In this part of the study, the pollen morphology of 18 genera and 150 species from the Myrtaceae tribes of subfamily Myrtoideae, Eucalypteae, Lophostemoneae, Syncarpieae, Xanthostemoneae and subfamily Psiloxyloideae are presented. It was found that the most commonly observed pollen in these groups was parasyncolpate with a rugulate exine, whereas some species possessed an apocolpial island. The large, and sometimes syndemicolpate, pollen of Eucalypteae genera Angophora and Corymbia differed from all other genera. Most Eucalyptus pollen had endopores with a thickened exine.
Pollen morphology of the Myrtaceae. Part 3: tribes Chamelaucieae, Leptospermeae and Lindsayomyrteae
Authors: Thornhill Andrew H. , Wilson Peter G. , Drudge Jeff , Barrett Matthew D. , Hope Geoff S. , Craven Lyn A. , Crisp Michael D.
Published: April 2012

The pollen morphology of 36 genera and 147 species from the Myrtaceae tribes Chamelaucieae, Leptospermeae and Lindsayomyrteae was surveyed using scanning electron microscopy (SEM) and light microscopy (LM). Syncolpate pollen were observed in all genera of Leptospermeae and some genera of Chamelaucieae. Genera of tribe Chamelaucieae displayed five distinct colpal morphologies, which makes it the tribe with the most diverse pollen in Myrtaceae. Six genera of Chamelaucieae, including Actinodium, Chamelaucium, Darwinia, Homoranthus, Pileanthus and Verticordia, produce large acolpate pollen not observed in any other Myrtaceae. Two of these genera produce distinct pollen; Actinodium is the only genus to have prolate-spheroidal shaped pollen, and Pileanthus pollen is large and dicolporate. A number of anomalous aperture types occurred in species of Chamelaucieae, including monocolporate (Homoranthus thomasii), pentacolporate (Calytrix oldfieldii) and hexacolporate (Sannantha tozerensis). Pollen of Lindsayomyrteae appeared similar to those of Leptospermeae and Chamelaucieae, and on the basis of pollen features, could be related to these two tribes.
Loss of XLαs (extra-large αs) imprinting results in early postnatal hypoglycemia and lethality in a mouse model of pseudohypoparathyroidism Ib
Authors: Fernández-Rebollo Eduardo , Maeda Akira , Reyes Monica , Turan Serap , Fröhlich Leopold F. , Plagge Antonius , Kelsey Gavin , Jüppner Harald , Bastepe Murat
Published: April 2012

Maternal deletion of the NESP55 differentially methylated region (DMR) (delNESP55/ASdel3-4
m
, delNAS
m
) from the
GNAS
locus in humans causes autosomal dominant pseudohypoparathyroidism type Ib (AD-PHP-Ib
delNASm
), a disorder of proximal tubular parathyroid hormone (PTH) resistance associated with loss of maternal
GNAS
methylation imprints. Mice carrying a similar, maternally inherited deletion of the Nesp55 DMR (
ΔNesp55
m
) replicate these
Gnas
epigenetic abnormalities and show evidence for PTH resistance, yet these mice demonstrate 100% mortality during the early postnatal period. We investigated whether the loss of extralarge αs (XLαs) imprinting and the resultant biallelic expression of XLαs are responsible for the early postnatal lethality in
ΔNesp55
m
mice. First, we found that
ΔNesp55
m
mice are hypoglycemic and have reduced stomach-to-body weight ratio. We then generated mice having the same epigenetic abnormalities as the
ΔNesp55
m
mice but with normalized XLαs expression due to the paternal disruption of the exon giving rise to this
Gnas
product. These mice (
ΔNesp55
m
/
Gnasxl
m+/p−
) showed nearly 100% survival up to postnatal day 10, and a substantial number of them lived to adulthood. The hypoglycemia and reduced stomach-to-body weight ratio observed in 2-d-old
ΔNesp55
m
mice were rescued in the
ΔNesp55
m
/
Gnasxl
m+/p−
mice. Surviving double-mutant animals had significantly reduced Gαs mRNA levels and showed hypocalcemia, hyperphosphatemia, and elevated PTH levels, thus providing a viable model of human AD-PHP-Ib. Our findings show that the hypoglycemia and early postnatal lethality caused by the maternal deletion of the Nesp55 DMR result from biallelic XLαs expression. The double-mutant mice will help elucidate the pathophysiological mechanisms underlying AD-PHP-Ib.
Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf
Authors: Wenden Bénédicte , Toner David L. K. , Hodge Sarah K. , Grima Ramon , Millar Andrew J.
Published: April 2012

The circadian clocks that drive daily rhythms in animals are tightly coupled among the cells of some tissues. The coupling profoundly affects cellular rhythmicity and is central to contemporary understanding of circadian physiology and behavior. In contrast, studies of the clock in plant cells have largely ignored intercellular coupling, which is reported to be very weak or absent. We used luciferase reporter gene imaging to monitor circadian rhythms in leaves of
Arabidopsis thaliana
plants, achieving resolution close to the cellular level. Leaves grown without environmental cycles for up to 3 wk reproducibly showed spatiotemporal waves of gene expression consistent with intercellular coupling, using several reporter genes. Within individual leaves, different regions differed in phase by up to 17 h. A broad range of patterns was observed among leaves, rather than a common spatial distribution of circadian properties. Leaves exposed to light–dark cycles always had fully synchronized rhythms, which could desynchronize rapidly. After 4 d in constant light, some leaves were as desynchronized as leaves grown without any rhythmic input. Applying light–dark cycles to such a leaf resulted in full synchronization within 2–4 d. Thus, the rhythms of all cells were coupled to external light–dark cycles far more strongly than the cellular clocks were coupled to each other. Spontaneous desynchronization under constant conditions was limited, consistent with weak intercellular coupling among heterogeneous clocks. Both the weakness of coupling and the heterogeneity among cells are relevant to interpret molecular studies and to understand the physiological functions of the plant circadian clock.
Long identical multispecies elements in plant and animal genomes
Authors: Reneker Jeff , Lyons Eric , Conant Gavin C. , Pires J. Chris , Freeling Michael , Shyu Chi-Ren , Korkin Dmitry
Published: April 2012

Ultraconserved elements (UCEs) are DNA sequences that are 100% identical (no base substitutions, insertions, or deletions) and located in syntenic positions in at least two genomes. Although hundreds of UCEs have been found in animal genomes, little is known about the incidence of ultraconservation in plant genomes. Using an alignment-free information-retrieval approach, we have comprehensively identified all long identical multispecies elements (LIMEs), which include both syntenic and nonsyntenic regions, of at least 100 identical base pairs shared by at least two genomes. Among six animal genomes, we found the previously known syntenic UCEs as well as previously undescribed nonsyntenic elements. In contrast, among six plant genomes, we only found nonsyntenic LIMEs. LIMEs can also be classified as either simple (repetitive) or complex (nonrepetitive), they may occur in multiple copies in a genome, and they are often spread across multiple chromosomes. Although complex LIMEs were found in both animal and plant genomes, they differed significantly in their composition and copy number. Further analyses of plant LIMEs revealed their functional diversity, encompassing elements found near rRNA and enzyme-coding genes, as well as those found in transposons and noncoding DNA. We conclude that despite the common presence of LIMEs in both animal and plant lineages, the evolutionary processes involved in the creation and maintenance of these elements differ in the two groups and are likely attributable to several mechanisms, including transfer of genetic material from organellar to nuclear genomes, de novo sequence manufacturing, and purifying selection.
Cavities determine the pressure unfolding of proteins
Authors: Roche Julien , Caro Jose A. , Norberto Douglas R. , Barthe Philippe , Roumestand Christian , Schlessman Jamie L. , Garcia Angel E. , García-Moreno E. Bertrand , Royer Catherine A.
Published: April 2012

It has been known for nearly 100 years that pressure unfolds proteins, yet the physical basis of this effect is not understood. Unfolding by pressure implies that the molar volume of the unfolded state of a protein is smaller than that of the folded state. This decrease in volume has been proposed to arise from differences between the density of bulk water and water associated with the protein, from pressure-dependent changes in the structure of bulk water, from the loss of internal cavities in the folded states of proteins, or from some combination of these three factors. Here, using 10 cavity-containing variants of staphylococcal nuclease, we demonstrate that pressure unfolds proteins primarily as a result of cavities that are present in the folded state and absent in the unfolded one. High-pressure NMR spectroscopy and simulations constrained by the NMR data were used to describe structural and energetic details of the folding landscape of staphylococcal nuclease that are usually inaccessible with existing experimental approaches using harsher denaturants. Besides solving a 100-year-old conundrum concerning the detailed structural origins of pressure unfolding of proteins, these studies illustrate the promise of pressure perturbation as a unique tool for examining the roles of packing, conformational fluctuations, and water penetration as determinants of solution properties of proteins, and for detecting folding intermediates and other structural details of protein-folding landscapes that are invisible to standard experimental approaches.
Sex differences in estimating multiple intelligences in self and others: A replication in Russia
Authors: Furnham Adrian , Shagabutdinova Ksenia
Published: April 2012

This was a crosscultural study that focused on sex differences in self‐ and other‐estimates of multiple intelligences (including 10 that were specified by Gardner, 1999 and three by Sternberg, 1988) as well as in an overall general intelligence estimate. It was one of a programmatic series of studies done in over 30 countries that has demonstrated the female “humility” and male “hubris” effect in self‐estimated and other‐estimated intelligence. Two hundred and thirty Russian university students estimated their own and their parents’ overall intelligence and “multiple intelligences.” Results revealed no sex difference in estimates of overall intelligence for both self and parents, but men rated themselves higher on spatial intelligence. This contradicted many previous findings in the area which have shown that men rate their own overall intelligence and mathematical intelligence significantly higher than do women. Regressions indicated that estimates of verbal, logical, and spatial intelligences were the best predictors of estimates of overall intelligence, which is a consistent finding over many studies. Regressions also showed that participants’ openness to experience and self‐respect were good predictors of intelligence estimates. A comparison with a British sample showed that Russians gave higher mother estimates, and were less likely to believe that IQ tests measure intelligence. Results were discussed in relation to the influence of gender role stereotypes on lay conception of intelligence across cultures.
Exploring the Accuracy and Utility of the Rey Fifteen Item Test (RMT) with Recognition Trial in a Forensic Psychiatric Population
Authors: Stimmel Matthew , Green Debbie , Belfi Brian , Klaver Jessica
Published: April 2012

The Rey Fifteen Item Test (RMT; Rey, 1941 ) is one of the most commonly used measures to assess the validity of cognitive and memory deficits. A recent recognition trial has been developed to enhance sensitivity of the RMT (Boone, Salazar, Lu, Warner-Chacon, & Razani, 2002). The RMT was administered to 116 forensic patients hospitalized for restoration of competency to stand trial who were classified by treating psychiatrists as “genuine” or “feigning,” and 36 community simulators. Consistent with previous research, the recognition trial increased the sensitivity of the RMT from 44% to 64% among suspected feigners, while decreasing specificity from 82.4% to 74.7% among genuine patients. The optimal cut score for maximizing specificity was 11 in this sample, while the optimal cut score for enhancing the utility of the RMT as a screening measure was found to be 24. Implications of using the RMT with recognition trial as a screening tool in forensic psychiatric assessment are discussed.
Changes in Freshness during Frozen Storage of Farmed Coho Salmon: Effect of Replacement of Synthetic Antioxidants by Natural Ones in Fish Feeds
Authors: Ortiz Jaime , Vivanco Juan P , Quitral Vilma , Larraín M A , Concha Gabriela , Aubourg Santiago P
Published: April 2012

The addition of antioxidants to the diets for salmonids is crucial to prevent or delay deterioration of fish muscle. Most of the antioxidants used in these diets are synthetic, and their safety is more and more being questioned. The aim of this research was to compare the effects of substituting synthetic antioxidants with natural ones on selected biochemical freshness indicators of frozen coho salmon Oncorhynchus kisutch muscle. Three different feeds were tested: a conventional diet with the synthetic antioxidants butylated hydroxytoluene and ethoxyquin (diet 1) was supplied to farmed coho salmon in parallel with two different diets that included natural antioxidants (a tocopherol isomer-rich mixture [diet 2] and a tocopherol isomer–rosemary extract mixture [diet 3]). Five individuals of each group were analyzed every 3 months during frozen storage. The biochemical indicators measured were total volatile basic nitrogen (TVB-N), dimethylamine content, formaldehyde content, and tissue pH. Levels of TVB-N were significantly different between the three diets; TVB-N content was the lower for salmon fed diet 3 than for those fed diet 1, a result that was attributed to the antimicrobial action of the rosemary extracts. Formaldehyde content was similar among the salmon fed diets with different antioxidants, and pH values were always lowered to maximum limits allowed by international legislation. These results support the use of natural antioxidants in the diet of Chilean coho salmon for export.
Hybrid simulation of a dc-enhanced radio-frequency capacitive discharge in hydrogen
Authors: Diomede P , Longo S , Economou D J , Capitelli M
Published: April 2012

A PIC-MCC/fluid hybrid model was employed to study a parallel-plate capacitively coupled radio-frequency discharge in hydrogen, under the application of a dc bias voltage. When a negative dc voltage was applied to one of the electrodes of a continuous wave (cw) plasma, a ‘beam’ of secondary electrons was formed that struck the substrate counter-electrode at nearly normal incidence. The energy distribution of the electrons striking the substrate extended all the way to V
RF + |V
dc|, the sum of the peak RF voltage and the absolute value of the applied dc bias. Such directional, energetic electrons may be useful for ameliorating charging damage in etching of high aspect ratio nano-features. The vibrational distribution function of molecular hydrogen was calculated self-consistently, and was found to have a characteristic plateau for intermediate values of the vibrational quantum number, v. When a positive dc bias voltage was applied synchronously during a specified time window in the afterglow of a pulsed plasma, the ion energy distributions (IEDs) of positive ions acquired an extra peak at an energy equivalent of the applied dc voltage. The electron energy distribution function was slightly and temporarily heated during the application of the dc bias pulse. The calculated IEDs of

and

ions in a cw plasma without dc bias were found to be in good agreement with published experimental data.
Sieve methods in group theory I: Powers in linear groups
Authors: Lubotzky Alexander , Meiri Chen
Published: April 2012

A general sieve method for groups is formulated. It enables one to “measure” subsets of a finitely generated group. As an application we show that if

Γ
\Gamma

is a finitely generated non-virtually solvable linear group of characteristic zero, then the set of proper powers in

Γ
\Gamma

is exponentially small. This is a far-reaching generalization of a result of Hrushovski, Kropholler, Lubotzky, and Shalev.
First Report of Stem and Leaf Blight Caused by Sclerotinia sclerotiorum on Eustoma in Taiwan
Authors: Shen Y. M. , Chao C. H. , Wang F. C. , Liu H. L. , Huang T. C.
Published: April 2012

Eustoma (Eustoma russellianum) is an economically important cut flower in Taiwan. Each year more than 1.7 million dozen flowers, mainly exported to Japan in the winter, are produced in greenhouses. In January 2011, eustoma plants with stem and leaf blight symptoms were observed in some greenhouses in Changhua County, Taiwan, at an incidence of 2%. Brown and rotten lesions were presented on the stem and nearby leaves, with white mycelia growing on the surface and black sclerotia (up to 7 mm long) produced inside the stem. Infected plants were completely blighted and eventually died. Diseased stem tissues collected from the field were surface sterilized for 3 min in 0.6% NaOCl, rinsed with sterilized distilled water, and plated on potato dextrose agar. White fungal colonies were consistently isolated. The cultures produced large sclerotia at the peripheries of the plates. Internal transcribed spacer (ITS) sequences of two voucher isolates were determined and deposited in GenBank (Accession Nos. JQ653934 and JQ653935). The sequences were 100% identical to that of Sclerotinia sclerotiorum strain ATCC MYA-4521 (Accession No. FJ810516). In addition, PCR amplified DNA fragments (approximately 630 bp) were obtained by the S. sclerotiorum specific primer pair MP_SsF and MP_UniR (1). On the basis of morphology, ITS sequence homology, and the specific PCR detection, the fungus was identified as S. sclerotiorum. The two fungal isolates (BCRC34830 and BCRC34831) were deposited in Bioresource Collection and Research Center, Hsinchu, Taiwan. Pathogenicity tests were conducted on 1-month-old, second flush eustoma cultivars Ex Rosa Pink Flash and Rosina Blue Ver. 2 after primary flowers had been harvested in the greenhouse. Fungal inoculum consisting of Tref horticultural substrate and wet sterilized rice colonized by S. sclerotiorum BCRC34830 (substrate-rice-water ratio of 2:1:1) was placed near the base of the plants. Ten plants of each cultivar were inoculated with about 800 g of the mixture. Sterile mixture applied to an equal number of plants served as negative controls. Eight plants of each cultivar showed blight symptoms after 1 month of incubation at an average temperature of 26°C. All control plants remained healthy. The pathogen reisolated from the inoculated stems produced sclerotia identical to those isolated in the field, fulfilling Koch's postulates. The pathogenicity test was repeated with similar results. S. sclerotiorum has been reported on eustoma in Argentina (2). To our knowledge, this is the first report of Sclerotinia blight on eustoma in Taiwan. Although the disease was not prevalent on eustoma, the inoculum could be dormant in the greenhouse soil. Awareness of the potential perennial problem could increase the quality of the flowers exported and benefit the flower industry.

References: (1) S. Hirschhäuser and J. Fröhlich. Int. J. Food Microbiol. 118:151, 2007. (2) S. Wolcan et al. Plant Dis. 80:223, 1996.
First Report of Blight Disease on Buxus Caused by Cylindrocladium buxicola in France
Authors: Saurat C. , Fourrier C. , Ioos R.
Published: April 2012

Cylindrocladium buxicola Henricot causes twig blight on Buxus spp., severe defoliation, and eventually death of plants, especially in young seedlings (1). The disease was first observed in the United Kingdom and New Zealand in the 1990s and recently, the fungus was detected in other European countries (1). In November 2006, box blight symptoms were observed in a Buxus sempervirens nursery located in the South West of France (La Reole). Since then, more diseased samples from other French sites, including forestry areas and ornamental garden nurseries, have been received, indicating that this disease is spreading. Symptomatic twig samples were sent for lab analysis and dark brown spots were observed on the leaves, sometimes coalescing to cover the entire leaf surface, with black streaks on the stems. Fungal fruiting structures were observed directly on the leaf surface and were examined with a stereomicroscope. Microscopic slides were then prepared by gently pressing a clear adhesive tape onto the surface covered by mycelium and spores, which was further stained with lactic acid and methyl blue. Cylindrical, straight, biseptate, hyaline conidia, 53.8 to 75.3 (64.4) × 4.4 to 5.2 (4.6) μm, were observed, sterile hyphae with terminal vesicles ended with a pointed apex, and conidiophores were penicilliate; all of those characters were consistent with C. buxicola (2). To support the diagnosis, fruiting structures were plated on malt agar media supplemented with 100 ppm of chloramphenicol. The pure culture obtained showed a whitish mycelium with a tan brown center that was in line with the original description of C. buxicola (2). DNA was extracted from the pure culture and the internal transcribed spacer (ITS) region was amplified by PCR using the ITS1-ITS4 primer pair (4). Nucleotide sequence was determined and deposited on GenBank (Accession No. JQ743502). BLAST analysis of the sequence showed 100% identity with all currently available C. buxicola ITS sequences, which confirmed our morphological diagnosis. To our knowledge, this is the first report of C. buxicola (teleomorph Calonectria pseudonaviculata) in France. The occurrence of this disease in France worries the nursery industry since losses can sometimes be dramatic as seen in United Kingdom, where the disease is widespread (3).

References: (1) B. Henricot. The Plantsman 9:153, 2006. (2) B. Henricot and A. Culham. Mycologia 94:980, 2002. (3) B. Henricot et al. Plant Pathol. 49:805, 2000. (4) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications, 1990.
Comparative Pathogenicity and Virulence of Fusarium Species on Sugar Beet
Authors: Burlakoti Pragyan , Rivera V. , Secor G. A. , Qi A. , Rio-Mendoza L. E. Del , Khan Mohamed F. R.
Published: April 2012

In all, 98 isolates of three Fusarium spp. (18 Fusarium oxysporum, 30 F. graminearum, and 50 Fusarium sp. nov.) obtained from sugar beet in Minnesota were characterized for pathogenicity and virulence on sugar beet in the greenhouse by a bare-root inoculation method. Among the 98 isolates tested, 80% of isolates were pathogenic: 83% of the F. oxysporum isolates, 57% of the F. graminearum isolates, and 92% of the Fusarium sp. nov. isolates. Symptoms varied from slight to moderate wilting of the foliage, interveinal chlorosis and necrosis, and vascular discoloration of the taproot without any external root symptoms. Among the pathogenic isolates, 14% were highly virulent and 12% were moderately virulent. Most of the highly virulent isolates (91%) and moderately virulent isolates (89%) were Fusarium sp. nov. All pathogenic isolates of F. graminearum and most pathogenic isolates (87%) of F. oxysporum were less virulent. In general, more-virulent isolates induced first foliar symptoms earlier compared with less-virulent isolates. This study indicates that both F. oxysporum and Fusarium sp. nov. should be used in greenhouse and be present in field studies used for screening and developing sugar beet cultivars resistant to Fusarium yellows complex for Minnesota and North Dakota.
Distinguishing Galactomyces citri-aurantii from G. geotrichum and Characterizing Population Structure of the Two Postharvest Sour Rot Pathogens of Fruit Crops in California
Authors: McKay A. H. , Förster H. , Adaskaveg J. E.
Published: April 2012

A growth assay in lemon juice and polymerase chain reaction amplifications using newly designed species-specific primers from endopolygalacturonase and β-tubulin genes rapidly differentiated isolates of the morphologically similar fruit sour rot pathogens Galactomyces citriaurantii and G. geotrichum. Isolates of both species were collected from agricultural soils and decaying fruit at locations within and outside California, including worldwide locations, and were used in population genetic studies based on amplified fragment length polymorphic (AFLP) DNA markers. For all four geographically defined subpopulations (three counties of California and locations outside California) among 97 isolates of G. citri-aurantii and for the two subpopulations (origin within or outside California) among 35 isolates of G. geotrichum, the proportion of polymorphic loci and haplotypic diversity was high. In total, 82 unique haplotypes were identified for G. citri-aurantii for the four subpopulations and, of these, 80 haplotypes were unique among subpopulations. For G. geotrichum, 25 unique haplotypes were identified among the two subpopulations and no haplotype was shared. Indices of genetic differences (FST) between subpopulations within each species were all low (e.g., 0.038 for G. geotrichum and 0.085 to 0.226 for G. citriaurantii), indicating a low level of genetic differentiation. Following clone correction, mating type segregation ratios for G. citri-aurantii did not significantly (P > 0.1) deviate from a 1:1 ratio for all four subpopulations or the entire population. Tests of the index of association (IA) and parsimony tree-length permutation tests (PTLPT) supported a random mating structure for clone-corrected data for the Kern, Tulare, and Ventura County subpopulations and the null hypothesis of random mating could not be rejected. Additionally, PTLPT also supported random mating for the “outside of California” population. For G. geotrichum, random mating was only tested using IA and PTLPT and the null hypothesis of random mating was not rejected (P > 0.05) using clone-corrected data. Further evidence that sexual recombination likely occurs in both species of Galactomyces was the lack of grouping consistency in the unweighted pair-group method with arithmetic mean clustering of AFLP data. A high confidence based on bootstrap values was obtained for only a few of the nodes in each of the two trees. A mixed reproduction system with an out-crossing sexual mating system and a prolific asexual phase is proposed for both species.
Manipulating Inoculum Densities of Verticillium dahliae and Pratylenchus penetrans with Green Manure Amendments and Solarization Influence Potato Yield
Authors: MacGuidwin A. E. , Knuteson D. L. , Connell T. , Bland W. L. , Bartelt K. D.
Published: April 2012

We used cover crops with demonstrated efficacy against Verticillium dahliae and Pratylenchus penetrans in combination with the biocidal practice of solarization to determine the importance of targeting both organisms for managing potato early dying, an issue relevant to the search for alternatives to soil fumigation. Two experiments were conducted in commercial fields using a split-plot design with cover crop treatments of rapeseed, marigold, forage pearl millet, sorghum-sudangrass, and corn as the main plot factor and solarization as the subplot factor. Cover crops were grown and solarization applied in year one, followed by potato in year two. The main effect of solarization was significant for reduced inoculum levels of both organisms in year two and increased tuber yields. The main effect of cover crop was also significant with lower population densities of P. penetrans following the marigold and millet treatments and of V. dahliae following rape and sorghum-sudangrass. The cover crop treatments influenced yield in only one of the experiments in the absence of solarization. The combinatorial effect of cover crops and solarization resulted in a wide range of pathogen population densities. Mean soil inoculum levels were negatively related to yield for V. dahliae in experiment 1, and for P. penetrans and the P. penetrans × V. dahliae interaction in both experiments.