bluuebunny/crossref_metadata_2025 huggingface dataset:
Iona College Community Centered Family Health History Project: Lessons Learned from Student Focus Groups
Authors: Moore Penelope J. , Gratzer William , Lieber Caroline , Edelson Vaughn , O'Leary James , Terry Sharon F.
Published: August 2011

The Community Centered Family Health History project was initiated to create accessible family health history tools produced by and for the community. The project goal was to promote increased community engagement in health education by encouraging conversations among family members that would translate knowledge of family health history into healthy lifestyle choices. As one of seven community partners, Iona College participated in customizing and beta‐testing the Does It Run in the Family? toolkit. Twenty‐nine college students were engaged to recruit three relatives related by blood to provide feedback on the utility of the toolkit. The toolkit consists of two booklets—“A Guide to Family Health History” and “A Guide to Understanding Genetics and Health”—explaining the importance of knowing and talking about health within the family as well as basics about how conditions are passed down through generations. Twenty‐two of the twenty‐nine students participated in focus groups to discuss their reactions to participation in the project. Students in the focus group reported that the study participants—students and their family members—found the toolkit to be user friendly and the experience a valuable one that prompted many to take positive steps toward good health.
Biases and Standard Errors of Standardized Regression Coefficients
Authors: Yuan Ke-Hai , Chan Wai
Published: August 2011

The paper obtains consistent standard errors (SE) and biases of order O(1/n) for the sample standardized regression coefficients with both random and given predictors. Analytical results indicate that the formulas for SEs given in popular text books are consistent only when the population value of the regression coefficient is zero. The sample standardized regression coefficients are also biased in general, although it should not be a concern in practice when the sample size is not too small. Monte Carlo results imply that, for both standardized and unstandardized sample regression coefficients, SE estimates based on asymptotics tend to under-predict the empirical ones at smaller sample sizes.
Cardanol‐Based Bis(azo) Dyes as a Gasoline 91 Colorant
Authors: Paebumrung Pimpaporn , Petsom Amorn , Thamyongkit Patchanita
Published: August 2011

Novel bis(azo) dyes were successfully prepared from the coupling of either natural cardanol or its hydrogenated derivative with a series of diazotized aromatic amines and diamines. These new dyes were fully characterized by NMR, infrared and UV–visible spectroscopy and mass spectrometry. The dyes are highly soluble in a variety of common organic solvents and gasoline as a consequence of the cardanol unit. The physical properties of gasoline according to American Society for Testing and Materials standard were unaffected by the presence of the bis(azo) dye derived from 1‐(4aminophenylazo)‐2‐naphthol at a concentration of 6 ppm and the dye showed excellent stability over a 3 month period.
Home and neighbourhood correlates of BMI among children living in socioeconomically disadvantaged neighbourhoods
Authors: Crawford David A. , Ball Kylie , Cleland Verity J. , Campbell Karen J. , Timperio Anna F. , Abbott Gavin , Brug Johannes , Baur Louise A. , Salmon Jo A.
Published: August 2011

A detailed understanding of the underlying drivers of obesity-risk behaviours is needed to inform prevention initiatives, particularly for individuals of low socioeconomic position who are at increased risk of unhealthy weight gain. However, few studies have concurrently considered factors in the home and local neighbourhood environments, and little research has examined determinants among children from low socioeconomic backgrounds. The present study examined home, social and neighbourhood correlates of BMI (kg/m2) in children living in disadvantaged neighbourhoods. Cross-sectional data were collected from 491 women with children aged 5–12 years living in forty urban and forty rural socioeconomically disadvantaged areas (suburbs) of Victoria, Australia in 2007 and 2008. Mothers completed questionnaires about the home environment (maternal efficacy, perceived importance/beliefs, rewards, rules and access to equipment), social norms and perceived neighbourhood environment in relation to physical activity, healthy eating and sedentary behaviour. Children's height and weight were measured at school or home. Linear regression analyses controlled for child sex and age. In multivariable analyses, children whose mothers had higher efficacy for them doing physical activity tended to have lower BMIzscores (B = − 0·04, 95 % CI − 0·06, − 0·02), and children who had a television (TV) in their bedroom (B = 0·24, 95 % CI 0·04, 0·44) and whose mothers made greater use of food as a reward for good behaviour (B = 0·05, 95 % CI 0·01, 0·09) tended to have higher BMIzscores. Increasing efficacy among mothers to promote physical activity, limiting use of food as a reward and not placing TV in children's bedrooms may be important targets for future obesity prevention initiatives in disadvantaged communities.
Oral hydroxycitrate supplementation enhances glycogen synthesis in exercised human skeletal muscle
Authors: Cheng I-Shiung , Huang Shih-Wei , Lu Hsang-Chu , Wu Ching-Lin , Chu Ying-Chieh , Lee Shin-Da , Huang Chih-Yang , Kuo Chia-Hua
Published: August 2011

Glycogen stored in skeletal muscle is the main fuel for endurance exercise. The present study examined the effects of oral hydroxycitrate (HCA) supplementation on post-meal glycogen synthesis in exercised human skeletal muscle. Eight healthy male volunteers (aged 22·0 (se 0·3) years) completed a 60-min cycling exercise at 70–75 % \dot {>V}O_{2\hairsp max} and received HCA or placebo in a crossover design repeated after a 7 d washout period. They consumed 500 mg HCA or placebo with a high-carbohydrate meal (2 g carbohydrate/kg body weight, 80 % carbohydrate, 8 % fat, 12 % protein) for a 3-h post-exercise recovery. Muscle biopsy samples were obtained from vastus lateralis immediately and 3 h after the exercise. We found that HCA supplementation significantly lowered post-meal insulin response with similar glucose level compared to placebo. The rate of glycogen synthesis with the HCA meal was approximately onefold higher than that with the placebo meal. In contrast, GLUT4 protein level after HCA supplementation was significantly decreased below the placebo level, whereas expression of fatty acid translocase (FAT)/CD36 mRNA was significantly increased above the placebo level. Furthermore, HCA supplementation significantly increased energy reliance on fat oxidation, estimated by the gaseous exchange method. However, no differences were found in circulating NEFA and glycerol levels with the HCA meal compared with the placebo meal. The present study reports the first evidence that HCA supplementation enhanced glycogen synthesis rate in exercised human skeletal muscle and improved post-meal insulin sensitivity.
La revolución eléctrica en América Latina: una reconstrucción cuantitativa del proceso de electrificación hasta 1930
Authors: Tafunell Xavier
Published: August 2011

Latin America participated in the electric revolution which profoundly transformed the most developed Western economies between 1880 and 1930. The qualitative empirical evidence shows that Latin American electrification began with little delay compared to those economies. This article provides new quantitative evidence consisting of annual series about a reliable indicator of the degree of electrification of the Latin American nations. The database built shows that towards 1930 electricity consumption per inhabitant in Latin America was far below that of most advanced economies, and only Latin American leaders in the electrification process had reached power consumption levels similar to the European late comers. Unlike other newly industrializing economies, the region was not able to quickly incorporate new technology to overcome their backwardness.
Emissions scenarios, costs, and implementation considerations of REDD-plus programs
Authors: SATHAYE JAYANT , ANDRASKO KENNETH , CHAN PETER
Published: August 2011

Greenhouse gas emissions from the forestry sector are estimated to be 8.4 GtCO2-eq./year or about 17% of the global emissions. We estimate that the cost for reducing deforestation is low in Africa and several times higher in Latin America and Southeast Asia. These cost estimates are sensitive to the uncertainties of how much unsustainable high-revenue logging occurs, little understood transaction and program implementation costs, and barriers to implementation including governance issues. Due to lack of capacity in the affected countries, achieving reduction or avoidance of carbon emissions will require extensive REDD-plus programs. Preliminary REDD-plus Readiness cost estimates and program descriptions for Indonesia, Democratic Republic of the Congo, Ghana, Guyana and Mexico show that roughly one-third of potential REDD-plus mitigation benefits might come from avoided deforestation and the rest from avoided forest degradation and other REDD-plus activities.
Interdefinability of defeasible logic and logic programming under the well-founded semantics
Authors: MAIER FREDERICK
Published: August 2011

We provide a method of translating theories of Nute's defeasible logic into logic programs, and a corresponding translation in the opposite direction. Under certain natural restrictions, the conclusions of defeasible theories under the ambiguity propagating defeasible logic ADL correspond to those of the well-founded semantics for normal logic programs, and so it turns out that the two formalisms are closely related. Using the same translation of logic programs into defeasible theories, the semantics for the ambiguity blocking defeasible logic NDL can be seen as indirectly providing an ambiguity blocking semantics for logic programs. We also provide antimonotone operators for both ADL and NDL, each based on the Gelfond–Lifschitz (GL) operator for logic programs. For defeasible theories without defeaters or priorities on rules, the operator for ADL corresponds to the GL operator and so can be seen as partially capturing the consequences according to ADL. Similarly, the operator for NDL captures the consequences according to NDL, though in this case no restrictions on theories apply. Both operators can be used to define stable model semantics for defeasible theories.
Representation sharing for Prolog
Authors: NGUYEN PHUONG-LAN , DEMOEN BART
Published: August 2011

Representation sharing can reduce the memory footprint of a program by sharing one representation between duplicate terms. The most common implementation of representation sharing in functional programming systems is known as hash-consing. In the context of Prolog, representation sharing has been given little attention. Some current techniques that deal with representation sharing are reviewed. The new contributions are (1) an easy implementation ofinput sharingforfindall/3; and (2) a description of asharermodule that introduces representation sharing at runtime. Their realization is shown in the context of the Warren Abstract Machine (WAM) as implemented by hProlog. Both can be adapted to any WAM-like Prolog implementation. The sharer works independently of the garbage collector, but it can be made to cooperate with the garbage collector. Benchmark results show that the sharer has a cost comparable to the heap garbage collector, that its effectiveness is highly application-dependent, and that its policy must be tuned to the collector.
POLYTHERMAL GLACIER HYDROLOGY: A REVIEW
Authors: Irvine‐Fynn Tristram D. L. , Hodson Andrew J. , Moorman Brian J. , Vatne Geir , Hubbard Alun L.
Published: August 2011

The manner by which meltwater drains through a glacier is critical to ice dynamics, runoff characteristics, and water quality. However, much of the contemporary knowledge relating to glacier hydrology has been based upon, and conditioned by, understanding gleaned from temperate valley glaciers. Globally, a significant proportion of glaciers and ice sheets exhibit nontemperate thermal regimes. The recent, growing concern over the future response of polar glaciers and ice sheets to forecasts of a warming climate and lengthening summer melt season necessitates recognition of the hydrological processes in these nontemperate ice masses. It is therefore timely to present an accessible review of the scientific progress in glacial hydrology where nontemperate conditions are dominant. This review provides an appraisal of the glaciological literature from nontemperate glaciers, examining supraglacial, englacial, and subglacial environments in sequence and their role in hydrological processes within glacierized catchments. In particular, the variability and complexity in glacier thermal regimes are discussed, illustrating how a unified model of drainage architecture is likely to remain elusive due to structural controls on the presence of water. Cold ice near glacier surfaces may reduce meltwater flux into the glacier interior, but observations suggest that the transient thermal layer of near surface ice holds a hydrological role as a depth‐limited aquifer. Englacial flowpaths may arise from the deep incision of supraglacial streams or the propagation of hydrofractures, forms which are readily able to handle varied meltwater discharge or act as locations for water storage, and result in spatially discrete delivery of water to the subglacial environment. The influence of such drainage routes on seasonal meltwater release is explored, with reference to summer season upwellings and winter icing formation. Moreover, clear analogies emerge between nontemperate valley glacier and ice sheet hydrology, the discussion of which indicates how persistent reassessment of our conceptualization of glacier drainage systems is required. There is a clear emphasis that continued, integrated endeavors focused on process glaciology at nontemperate glaciers are a scientific imperative to augmenting the existing body of research centered on ice mass hydrology.
Late Cretaceous‐Miocene diachronous onset of back thrusting along the South Caribbean deformed belt and its importance for understanding processes of arc collision and crustal growth
Authors: Kroehler Margaret E. , Mann Paul , Escalona Alejandro , Christeson Gail. L.
Published: August 2011

The Venezuelan basin is obliquely subducted to the east‐southeast beneath the continental South American plate at the east‐west‐trending South Caribbean deformed belt (SCDB), a 50–100‐km‐wide wedge of accreted sedimentary rocks derived both from offscraping of the 0.5 to 1 km‐thick sedimentary cover of the subducting Venezuelan basin and from incorporation of clastic sediments derived from the continental margin of South America. In this paper we describe the structure and sequence stratigraphy of five Late Cretaceous to recent sedimentary sequences overlying a 230,000 km2 area of the southern Venezuelan basin and Beata Ridge. The data set includes 5900 km of 2D seismic reflection data that are tied to lithologic and age data taken from DSDP sites 146/149 and 150 in the central part of the Venezuelan basin. We use observed patterns of wedging in mapped and dated sedimentary sequences adjacent to the SCDB to determine the age of the diachronous west‐to‐east initiation of thrusting and subduction at the SCDB. The onset of subduction in the SCDB corresponds with the cessation of thrusting from west to east along the zone of collision between the intraoceanic Caribbean arc and the South American continent. This correlation in the age of deformation indicates that collision between the Caribbean arc and the South American continent led to subduction polarity reversal, a process that is commonly observed at various stages of tectonic evolution in other areas of active, arc‐continent collision including Japan and Sunda.
A new analytical solution of topography‐driven flow in a drainage basin with depth‐dependent anisotropy of permeability
Authors: Wang Xu‐Sheng , Jiang Xiao‐Wei , Wan Li , Ge Shemin , Li Hailong
Published: August 2011

Theoretical analysis and field observations suggest that the depth‐dependent trend of permeability anisotropy is a nature of the geological media accompanying the depth‐decaying permeability. However, the effect of depth‐dependent anisotropy has not been investigated in previous studies of regional groundwater flow. A more general analytical solution of topography‐driven flow in drainage basins is derived in this study. Exponential trend of permeability with depth is assumed, and different decay rates of horizontal permeability (kx) and vertical permeability (kz) are included to account for the depth‐dependent anisotropy. It is found that the shape of the nested flow systems in a drainage basin depends on not only the depth‐dependent permeability but also the depth‐dependent anisotropy ratio (kx/kz). For stagnation points between the flow systems, the number of stagnation points is not influenced by the depth‐dependent permeability and anisotropy; however, an increase inkx/kzcan lead to a decrease in the depth of their location. Whenkxis smaller thankzon the top boundary, this phenomenon is especially significant.
Evolution of superficial lake water temperature profile under diurnal radiative forcing
Authors: Vercauteren Nikki , Huwald Hendrik , Bou‐Zeid Elie , Selker John S. , Lemmin Ulrich , Parlange Marc B. , Lunati Ivan
Published: August 2011

In lentic water bodies, such as lakes, the water temperature near the surface typically increases during the day, and decreases during the night as a consequence of the diurnal radiative forcing (solar and infrared radiation). These temperature variations penetrate vertically into the water, transported mainly by heat conduction enhanced by eddy diffusion, which may vary due to atmospheric conditions, surface wave breaking, and internal dynamics of the water body. These two processes can be described in terms of an effective thermal diffusivity, which can be experimentally estimated. However, the transparency of the water (depending on turbidity) also allows solar radiation to penetrate below the surface into the water body, where it is locally absorbed (either by the water or by the deployed sensors). This process makes the estimation of effective thermal diffusivity from experimental water temperature profiles more difficult. In this study, we analyze water temperature profiles in a lake with the aim of showing that assessment of the role played by radiative forcing is necessary to estimate the effective thermal diffusivity. To this end we investigate diurnal water temperature fluctuations with depth. We try to quantify the effect of locally absorbed radiation and assess the impact of atmospheric conditions (wind speed, net radiation) on the estimation of the thermal diffusivity. The whole analysis is based on the results of fiber optic distributed temperature sensing, which allows unprecedented high spatial resolution measurements (∼4 mm) of the temperature profile in the water and near the water surface.
Factors Affecting the Successful Realisation of Benefits from Systems Development Projects: Findings from Three Case Studies
Authors: Doherty Neil F , Ashurst Colin , Peppard Joe
Published: August 2011

The return that organisations derive from investments in information systems and technology continues to disappoint. While there is a very significant body of literature on the factors that should facilitate a successful outcome from systems development, there is growing concern that these prescriptions are not having their desired effect. In this paper, we argue that the success of a systems development project should be measured in terms of its ability to deliver meaningful benefits, rather than the timely delivery of a technical artefact, and therefore organisations should adopt an explicit and proactive benefits realisation approach when investing in IT. Consequently, we sought to explore those actionable factors that might facilitate the effective realisation of benefits from systems development initiatives. Three organisations were identified that claimed to adopt a proactive approach to benefits realisation, and detailed studies of their systems development practices were conducted. Our analysis found that whilst one organisation had been successful in its adoption of a benefits realisation perspective, the other two had not, and this allowed us to identify those factors that helped to explain this difference in outcomes. In short, this paper makes an important contribution by identifying how a subset of traditional systems success factors might be enhanced, to give them a more explicit benefits realisation orientation. Moreover, it presents a coherent set of principles that can be used for deriving other factors and practices.
Emotional Valence Modulates the Preference for Curved Objects
Authors: Leder Helmut , Tinio Pablo P L , Bar Moshe
Published: August 2011

Previous studies have shown that people prefer objects with curved contours over objects with sharp contours. However, those studies used stimuli that were mainly neutral in emotional valence. We tested here the interplay between visual features and general valence as positive or negative. After replicating curvature preferences for neutral objects, we used positive (cake, chocolate) and negative (snake, bomb) stimuli to examine if emotional valence—through response prioritisation—modulates the preference for curved objects. We found that people indeed preferred the curved versions of objects to the sharp versions of the same objects, but only if the objects were neutral or positive in emotional valence. There were no difference in liking for objects with negative emotional valence. This is evidence that the aesthetic response is adaptive, in this case prioritising valence over contour as demanded by the general semantic classification.
When Walls are No Longer Barriers: Perception of Wall Height in Parkour
Authors: Taylor J Eric T , Witt Jessica K , Sugovic Mila
Published: August 2011

Through training, skilled parkour athletes (traceurs) overcome everyday obstacles, such as walls, that are typically insurmountable. Traceurs and untrained novices estimated the height of walls and reported their anticipated ability to climb the wall. The traceurs perceived the walls as shorter than did novices. This result suggests that perception is scaled by the perceiver's anticipated ability to act, and is consistent with the action-specific account of perception.
Amplitude Spectra of Line-Motion Stimuli
Authors: Skottun Bernt Christian
Published: August 2011

The line-motion illusion has been regarded as the result of attention. An alternative interpretation is that the illusion is related to apparent motion which would predict the stimuli to contain motion energy associated with the direction of the illusory motion. In order to examine this possibility Fourier transforms of x – t plots of line-motion stimuli were generated under a variety of conditions. The sums of amplitudes associated with movement in the directions away from the cue relative to that towards the cue were compared to previously published psychophysical observations. It was found that the amplitude sums are largely consistent with the psychophysical results. In the few cases where there were discrepancies between results based on amplitude spectra and psychophysical findings, these discrepancies could be accounted for by making relatively simple and plausible assumptions. The present observations suggest that motion energy may be sufficient to account for the line-motion illusion.
Shedding Light on Photosensitive Behaviour in Brown Planaria (Dugesia Tigrina)
Authors: Davidson Colin , Prados Jose , Gibson Claire L , Young Andrew M J , Barnes Darrel , Sherlock Rachel , Hutchinson Claire V
Published: August 2011

The planarian flatworm is one of the simplest animals to develop two eyecups that enable them to detect the presence and direction of light, which they typically avoid. In this study we assessed responses of planaria to different intensities of light. We found that they exhibited a graded, sigmoidal, photonegative response to light intensity. A two-octave increase in luminance (on the upward slope of the sigmoid) corresponded to a 9% increase in the speed planaria travelled to avoid light.
Individual Differences in Visual Search: Relationship to Autistic Traits, Discrimination Thresholds, and Speed of Processing
Authors: Brock Jon , Xu Jing Y , Brooks Kevin R
Published: August 2011

Enhanced visual search is widely reported in autism. Here we note a similar advantage for university students self-reporting higher levels of autism-like traits. Contrary to prevailing theories of autism, performance was not associated with perceptual-discrimination thresholds for the same stimuli, but was associated with inspection-time threshold—a measure of speed of perceptual processing. Enhanced visual search in autism may, therefore, at least partially be explained by faster speed of processing.
Role of egg predation by haddock in the decline of an Atlantic herring population
Authors: Richardson David E. , Hare Jonathan A. , Fogarty Michael J. , Link Jason S.
Published: August 2011

Theoretical studies suggest that the abrupt and substantial changes in the productivity of some fisheries species may be explained by predation-driven alternate stable states in their population levels. With this hypothesis, an increase in fishing or a natural perturbation can drive a population from an upper to a lower stable-equilibrium population level. After fishing is reduced or the perturbation ended, this low population level can persist due to the regulatory effect of the predator. Although established in theoretical studies, there is limited empirical support for predation-driven alternate stable states in exploited marine fish populations. We present evidence that egg predation by haddock (
Melanogrammus aeglefinus
) can cause alternate stable population levels in Georges Bank Atlantic herring (
Clupea harengus
). Egg predation by haddock explains a substantial decoupling of herring spawning stock biomass (an index of egg production) from observed larval herring abundance (an index of egg hatching). Estimated egg survival rates ranged from <2–70% from 1971 to 2005. A population model incorporating egg predation and herring fishing explains the major population trends of Georges Bank herring over four decades and predicts that, when the haddock population is high, seemingly conservative levels of fishing can still precipitate a severe decline in the herring population. These findings illustrate how efforts to rebuild fisheries can be undermined by not incorporating ecological interactions into fisheries models and management plans.
Antagonistic VEGF variants engineered to simultaneously bind to and inhibit VEGFR2 and
α

v

β
3
integrin
Authors: Papo Niv , Silverman Adam P. , Lahti Jennifer L. , Cochran Jennifer R.
Published: August 2011

Significant cross-talk exists between receptors that mediate angiogenesis, such as VEGF receptor-2 (VEGFR2) and
α

v

β
3
integrin. Thus, agents that inhibit both receptors would have important therapeutic potential. Here, we used an antagonistic VEGF ligand as a molecular scaffold to engineer dual-specific proteins that bound to VEGFR2 and
α

v

β
3
integrin with antibody-like affinities and inhibited angiogenic processes in vitro and in vivo. Mutations were introduced into a single-chain VEGF (scVEGF) ligand that retained VEGFR2 binding, but prevented receptor dimerization and activation. Yeast-displayed scVEGF mutant libraries were created and screened by high-throughput flow cytometric sorting to identify several variants that bound with high affinity to both VEGFR2 and
α

v

β
3
integrin. These engineered scVEGF mutants were specific for
α

v

β
3
integrin and did not bind to the related integrins
α

v

β
5
,
α
iib
β
3
, or
α
5
β
1
. In addition, surface plasmon resonance and cell binding assays showed that dual-specific scVEGF proteins can simultaneously engage both receptors. Compared to monospecific scVEGF mutants that bind VEGFR2 or
α

v

β
3
integrin, dual-specific scVEGF proteins more strongly inhibited VEGF-mediated receptor phosphorylation, capillary tube formation, and proliferation of endothelial cells cultured on Matrigel or vitronectin-coated surfaces. Moreover, dual specificity conferred strong inhibition of VEGF-mediated blood vessel formation in Matrigel plugs in vivo, whereas monospecific scVEGF mutants that bind VEGFR2 or
α

v

β
3
integrin were only marginally effective. Instead of relying on antibody associating domains or physical linkage, this work highlights an approach to creating dual-specific proteins where additional functionality is introduced into a protein ligand to complement its existing biological properties.
Cytoskeletal actin networks in motile cells are critically self-organized systems synchronized by mechanical interactions
Authors: Cardamone Luca , Laio Alessandro , Torre Vincent , Shahapure Rajesh , DeSimone Antonio
Published: August 2011

Growing networks of actin fibers are able to organize into compact, stiff two-dimensional structures inside lamellipodia of crawling cells. We put forward the hypothesis that the growing actin network is a critically self-organized system, in which long-range mechanical stresses arising from the interaction with the plasma membrane provide the selective pressure leading to organization. We show that a simple model based only on this principle reproduces the stochastic nature of lamellipodia protrusion (growth periods alternating with fast retractions) and several of the features observed in experiments: a growth velocity initially insensitive to the external force; the capability of the network to organize its orientation; a load-history-dependent growth velocity. Our model predicts that the spectrum of the time series of the height of a growing lamellipodium decays with the inverse of the frequency. This behavior is a well-known signature of self-organized criticality and is confirmed by unique optical tweezer measurements performed in vivo on neuronal growth cones.
Bacterial community assembly based on functional genes rather than species
Authors: Burke Catherine , Steinberg Peter , Rusch Doug , Kjelleberg Staffan , Thomas Torsten
Published: August 2011

The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga
Ulva australis
, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different
U. australis
(only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be “species” (by means of rRNA taxonomy), but rather the more functional level of genes.
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in
Clostridium thermocellum
Authors: Brown Steven D. , Guss Adam M. , Karpinets Tatiana V. , Parks Jerry M. , Smolin Nikolai , Yang Shihui , Land Miriam L. , Klingeman Dawn M. , Bhandiwad Ashwini , Rodriguez Miguel , Raman Babu , Shao Xiongjun , Mielenz Jonathan R. , Smith Jeremy C. , Keller Martin , Lynd Lee R.
Published: August 2011

Clostridium thermocellum
is a thermophilic, obligately anaerobic, Gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass into ethanol through consolidated bioprocessing. Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (
adhE
), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays. Biochemical assays confirm a complete loss of NADH-dependent activity with concomitant acquisition of NADPH-dependent activity, which likely affects electron flow in the mutant. The simplicity of the genetic basis for the ethanol-tolerant phenotype observed here informs rational engineering of mutant microbial strains for cellulosic ethanol production.
Marine microgels as a source of cloud condensation nuclei in the high Arctic
Authors: Orellana Mónica V. , Matrai Patricia A. , Leck Caroline , Rauschenberg Carlton D. , Lee Allison M. , Coz Esther
Published: August 2011

Marine microgels play an important role in regulating ocean basin-scale biogeochemical dynamics. In this paper, we demonstrate that, in the high Arctic, marine gels with unique physicochemical characteristics originate in the organic material produced by ice algae and/or phytoplankton in the surface water. The polymers in this dissolved organic pool assembled faster and with higher microgel yields than at other latitudes. The reversible phase transitions shown by these Arctic marine gels, as a function of pH, dimethylsulfide, and dimethylsulfoniopropionate concentrations, stimulate the gels to attain sizes below 1 μm in diameter. These marine gels were identified with an antibody probe specific toward material from the surface waters, sized, and quantified in airborne aerosol, fog, and cloud water, strongly suggesting that they dominate the available cloud condensation nuclei number population in the high Arctic (north of 80°N) during the summer season. Knowledge about emergent properties of marine gels provides important new insights into the processes controlling cloud formation and radiative forcing, and links the biology at the ocean surface with cloud properties and climate over the central Arctic Ocean and, probably, all oceans.
Unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen
Authors: Rocha Rita , Pereira Pedro José Barbosa , Santos Manuel A. S. , Macedo-Ribeiro Sandra
Published: August 2011

In a restricted group of opportunistic fungal pathogens the universal leucine CUG codon is translated both as serine (97%) and leucine (3%), challenging the concept that translational ambiguity has a negative impact in living organisms. To elucidate the molecular mechanisms underlying the in vivo tolerance to a nonconserved genetic code alteration, we have undertaken an extensive structural analysis of proteins containing CUG-encoded residues and solved the crystal structures of the two natural isoforms of
Candida albicans
seryl-tRNA synthetase. We show that codon reassignment resulted in a nonrandom genome-wide CUG redistribution tailored to minimize protein misfolding events induced by the large-scale leucine-to-serine replacement within the CTG clade. Leucine or serine incorporation at the CUG position in
C. albicans
seryl-tRNA synthetase induces only local structural changes and, although both isoforms display tRNA serylation activity, the leucine-containing isoform is more active. Similarly, codon ambiguity is predicted to shape the function of
C. albicans
proteins containing CUG-encoded residues in functionally relevant positions, some of which have a key role in signaling cascades associated with morphological changes and pathogenesis. This study provides a first detailed analysis on natural reassignment of codon identity, unveiling a highly dynamic evolutionary pattern of thousands of fungal CUG codons to confer an optimized balance between protein structural robustness and functional plasticity.
High-level recombinant protein expression in transgenic plants by using a double-inducible viral vector
Authors: Werner Stefan , Breus Oksana , Symonenko Yuri , Marillonnet Sylvestre , Gleba Yuri
Published: August 2011

We describe here a unique ethanol-inducible process for expression of recombinant proteins in transgenic plants. The process is based on inducible release of viral RNA replicons from stably integrated DNA proreplicons. A simple treatment with ethanol releases the replicon leading to RNA amplification and high-level protein production. To achieve tight control of replicon activation and spread in the uninduced state, the viral vector has been deconstructed, and its two components, the replicon and the cell-to-cell movement protein, have each been placed separately under the control of an inducible promoter. TransgenicNicotiana benthamianaplants incorporating this double-inducible system demonstrate negligible background expression, high (over 0.5 × 104-fold) induction multiples, and high absolute levels of protein expression upon induction (up to 4.3 mg/g fresh biomass). The process can be easily scaled up, supports expression of practically important recombinant proteins, and thus can be directly used for industrial manufacturing.
Bacteria-induced natural product formation in the fungus
Aspergillus nidulans
requires Saga/Ada-mediated histone acetylation
Authors: Nützmann Hans-Wilhelm , Reyes-Dominguez Yazmid , Scherlach Kirstin , Schroeckh Volker , Horn Fabian , Gacek Agnieszka , Schümann Julia , Hertweck Christian , Strauss Joseph , Brakhage Axel A.
Published: August 2011

Sequence analyses of fungal genomes have revealed that the potential of fungi to produce secondary metabolites is greatly underestimated. In fact, most gene clusters coding for the biosynthesis of antibiotics, toxins, or pigments are silent under standard laboratory conditions. Hence, it is one of the major challenges in microbiology to uncover the mechanisms required for pathway activation. Recently, we discovered that intimate physical interaction of the important model fungus
Aspergillus nidulans
with the soil-dwelling bacterium
Streptomyces rapamycinicus
specifically activated silent fungal secondary metabolism genes, resulting in the production of the archetypal polyketide orsellinic acid and its derivatives. Here, we report that the streptomycete triggers modification of fungal histones. Deletion analysis of 36 of 40 acetyltransferases, including histone acetyltransferases (HATs) of
A. nidulans
, demonstrated that the Saga/Ada complex containing the HAT GcnE and the AdaB protein is required for induction of the orsellinic acid gene cluster by the bacterium. We also showed that Saga/Ada plays a major role for specific induction of other biosynthesis gene clusters, such as sterigmatocystin, terrequinone, and penicillin. Chromatin immunoprecipitation showed that the Saga/Ada-dependent increase of histone 3 acetylation at lysine 9 and 14 occurs during interaction of fungus and bacterium. Furthermore, the production of secondary metabolites in
A. nidulans
is accompanied by a global increase in H3K14 acetylation. Increased H3K9 acetylation, however, was only found within gene clusters. This report provides previously undescribed evidence of Saga/Ada dependent histone acetylation triggered by prokaryotes.
A Unified attentional bottleneck in the human brain
Authors: Tombu Michael N. , Asplund Christopher L. , Dux Paul E. , Godwin Douglass , Martin Justin W. , Marois René
Published: August 2011

Human information processing is characterized by bottlenecks that constrain throughput. These bottlenecks limit both what we can perceive and what we can act on in multitask settings. Although perceptual and response limitations are often attributed to independent information processing bottlenecks, it has recently been suggested that a common attentional limitation may be responsible for both. To date, however, evidence supporting the existence of such a “unified” bottleneck has been mixed. Here, we tested the unified bottleneck hypothesis using time-resolved fMRI. Experiment 1 isolated brain regions involved in the response selection bottleneck that limits speeded dual-task performance. These same brain regions were not only engaged by a perceptual encoding task in Experiment 2, their activity also tracked delays to a speeded decision-making task caused by concurrent perceptual encoding (Experiment 3). We conclude that a unified attentional bottleneck, including the inferior frontal junction, superior medial frontal cortex, and bilateral insula, temporally limits operations as diverse as perceptual encoding and decision-making.
Craniometric ratios of microcephaly and LB1,Homo floresiensis, using MRI and endocasts
Authors: Vannucci Robert C. , Barron Todd F. , Holloway Ralph L.
Published: August 2011

The designation ofHomo floresiensisas a new species derived from an ancient population is controversial, because the type specimen, LB1, might represent a pathological microcephalic modernHomo sapiens. Accordingly, two specific craniometric ratios (relative frontal breadth and cerebellar protrusion) were ascertained in 21 microcephalic infants and children by using MRI. Data on 118 age-equivalent control (normocephalic) subjects were collected for comparative purposes. In addition, the same craniometric ratios were determined on the endocasts of 10 microcephalic individuals, 79 normal controls (anatomically modern humans), and 17Homo erectusspecimens. These ratios were then compared with those of two LB1 endocasts. The findings showed that the calculated cerebral/cerebellar ratios of the LB1 endocast [Falk D, et al. (2007)Proc Natl Acad Sci USA104:2513–2518] fall outside the range of living normocephalic individuals. The ratios derived from two LB1 endocasts also fall largely outside the range of modern normal human andH. erectusendocasts and within the range of microcephalic endocasts. The findings support but do not prove the contention that LB1 represents a pathological microcephalicHomo sapiensrather than a new species, (i.e.,H. floresiensis).
Hypoxia-induced methylation of a pontin chromatin remodeling factor
Authors: Lee Jason S. , Kim Yunho , Bhin Jinhyuk , Shin Hi-Jai R. , Nam Hye Jin , Lee Seung Hoon , Yoon Jong-Bok , Binda Olivier , Gozani Or , Hwang Daehee , Baek Sung Hee
Published: August 2011

Pontin is a chromatin remodeling factor that possesses both ATPase and DNA helicase activities. Although Pontin is frequently overexpressed in human cancers of various types and implicated in oncogenic functions, the upstream signaling network leading to the regulation of Pontin that in turn affects transcription of downstream target genes has not been extensively studied. Here, we identify Pontin is methylated by G9a/GLP methyltransferases in hypoxic condition and potentiates HIF-1α-mediated activation by increasing the recruitment of p300 coactivator to a subset of HIF-1α target promoters. Intriguingly, Pontin methylation results in the increased invasive and migratory properties by activating downstream target gene,
Ets1
. In contrast, inhibition of Pontin methylation results in the suppression of tumorigenic and metastatic properties. Together, our data provide new approaches by targeting Pontin methylation and its downstream targets for the development of therapeutic agents for human cancers.
Hierarchical self-assembly of amelogenin and the regulation of biomineralization at the nanoscale
Authors: Fang Ping-An , Conway James F. , Margolis Henry C. , Simmer James P. , Beniash Elia
Published: August 2011

Enamel is a highly organized hierarchical nanocomposite, which consists of parallel arrays of elongated apatitic crystallites forming an intricate three-dimensional microstructure. Amelogenin, the major extracellular matrix protein of dental enamel, regulates the formation of these crystalline arrays via cooperative interactions with forming mineral phase. Using cryoelectron microscopy, we demonstrate that amelogenin undergoes stepwise hierarchical self-assembly. Furthermore, our results indicate that interactions between amelogenin hydrophilic C-terminal telopeptides are essential for oligomer formation and for subsequent steps of hierarchical self-assembly. We further show that amelogenin assemblies stabilize mineral prenucleation clusters and guide their arrangement into linear chains that organize as parallel arrays. The prenucleation clusters subsequently fuse together to form needle-shaped mineral particles, leading to the formation of bundles of crystallites, the hallmark structural organization of the forming enamel at the nanoscale. These findings provide unique insight into the regulation of biological mineralization by specialized macromolecules and an inspiration for bottom-up strategies for the materials design.
Direct inference of protein–DNA interactions using compressed sensing methods
Authors: AlQuraishi Mohammed , McAdams Harley H.
Published: August 2011

Compressed sensing has revolutionized signal acquisition, by enabling complex signals to be measured with remarkable fidelity using a small number of so-called incoherent sensors. We show that molecular interactions, e.g., protein–DNA interactions, can be analyzed in a directly analogous manner and with similarly remarkable results. Specifically, mesoscopic molecular interactions act as incoherent sensors that measure the energies of microscopic interactions between atoms. We combine concepts from compressed sensing and statistical mechanics to determine the interatomic interaction energies of a molecular system exclusively from experimental measurements, resulting in a “de novo” energy potential. In contrast, conventional methods for estimating energy potentials are based on theoretical models premised on a priori assumptions and extensive domain knowledge. We determine the de novo energy potential for pairwise interactions between protein and DNA atoms from (
i
) experimental measurements of the binding affinity of protein–DNA complexes and (
ii
) crystal structures of the complexes. We show that the de novo energy potential can be used to predict the binding specificity of proteins to DNA with approximately 90% accuracy, compared to approximately 60% for the best performing alternative computational methods applied to this fundamental problem. This de novo potential method is directly extendable to other biomolecule interaction domains (enzymes and signaling molecule interactions) and to other classes of molecular interactions.