bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directed evolution of a temperature-, peroxide- and alkaline pH-tolerant versatile peroxidase
Authors: Garcia-Ruiz Eva , Gonzalez-Perez David , Ruiz-Dueñas Francisco J. , Martínez Angel T. , Alcalde Miguel 
Published: October 2011

The VPs (versatile peroxidases) secreted by white-rot fungi are involved in the natural decay of lignin. In the present study, a fusion gene containing the VP from Pleurotus eryngii was subjected to six rounds of directed evolution, achieving a level of secretion in Saccharomyces cerevisiae (21 mg/l) as yet unseen for any ligninolytic peroxidase. The evolved variant for expression harboured four mutations and increased its total VP activity 129-fold. The signal leader processing by the STE13 protease at the Golgi compartment changed as a consequence of overexpression, retaining the additional N-terminal sequence Glu-Ala-Glu-Ala that enhanced secretion. The engineered N-terminally truncated variant displayed similar biochemical properties to those of the non-truncated counterpart in terms of kinetics, stability and spectroscopic features. Additional cycles of evolution raised the T50 8°C and significantly increased the enzyme's stability at alkaline pHs. In addition, the Km for H2O2 was enhanced up to 15-fold while the catalytic efficiency was maintained, and there was an improvement in peroxide stability (with half-lives for H2O2 of 43 min at a H2O2/enzyme molar ratio of 4000:1). Overall, the directed evolution approach described provides a set of strategies for selecting VPs with improvements in secretion, activity and stability.
Atomistic simulations of the solid-liquid transition of 1-ethyl-3-methyl imidazolium bromide ionic liquid
Authors: Feng Haijun , Zhou Jian , Qian Yu 
Published: October 2011

Achieving melting point around room temperature is important for applications of ionic liquids. In this work, molecular dynamics simulations are carried out to investigate the solid-liquid transition of ionic liquid 1-ethyl-3-methyl imidazolium bromide ([emim]Br) by direct heating, hysteresis, void-nucleation, sandwich, and microcanonical ensemble approaches. Variations of the non-bonded energy, density, diffusion coefficient, and translational order parameter of [emim]Br are analyzed as a function of temperature, and a coexisting solid-liquid system is achieved in the microcanonical ensemble method. The melting points obtained from the first three methods are 547 ± 8 K, 429 ± 8 K, and 370 ± 6 K; while for the sandwich method, the melting points are 403 ± 4 K when merging along the x-axis by anisotropic isothermal-isobaric (NPT) ensemble, 393 ± 4 K when along the y-axis by anisotropic NPT ensemble, and 375 ± 4 K when along the y-axis by isotropic NPT ensemble. For microcanonical ensemble method, when the slabs are merging along different directions (x-axis, y-axis, and z-axis), the melting points are 364 ± 3 K, 365 ± 3 K, and 367 ± 3 K, respectively, the melting points we get by different methods are approximately 55.4%, 21.9%, 5.1%, 14.5%, 11.6%, 6.5%, 3.4%, 3.7%, and 4.3% higher than the experimental value of 352 K. The advantages and disadvantages of each method are discussed. The void-nucleation and microcanonical ensemble methods are most favorable for predicting the solid-liquid transition.
The 2D plasma potential distribution in a HiPIMS discharge
Authors: Mishra A , Kelly P J , Bradley J W 
Published: October 2011

Using an emissive probe the spatial-temporal distribution of the plasma potential V
p in a high power impulse magnetron sputtering discharge has been measured. The magnetron (with a planar circular titanium target) was operated in argon gas at a fixed pressure of 0.54 Pa, a pulse frequency of 100 Hz with a 100 µs on-time and average power of 650 W. In the early part of the voltage pulse (∼6–8 µs), V
p attains deep negative values (∼−150 V) at positions close to the target (10 mm) and above the racetrack, diminishing with distance, but never reaching ground potential, even at excursions of 80 mm. In the confined plasma region, extraordinarily high axial and radial electric field components, up to several kV m−1, are calculated from the plasma potential measurements.
As the plasma develops and the discharge current reaches a maximum (at ∼40 µs), V
p is elevated everywhere in the plasma, however, still with deep negative values (down to −40 V) at positions closest to the target. From the derived electric fields and modelled (vacuum) magnetic field, the 2D distribution of E × B electron drift velocities has been determined. During the early discharge phase, a broad drift channel is predicted above the racetrack, with drift speeds up to ∼3 × 105 ms−1 centred ∼30 mm above the target racetrack. As the discharge develops, these speeds reduce by about a factor 3 and the centre of the velocity distribution moves further away from the target and inwards towards the discharge axis, resembling that observed in dc and pulsed-dc magnetron operation.
KABOOM! A new suffix array based algorithm for clustering expression data
Authors: Hazelhurst Scott , Lipták Zsuzsanna 
Published: October 2011

Abstract
Motivation: Second-generation sequencing technology has reinvigorated research using expression data, and clustering such data remains a significant challenge, with much larger datasets and with different error profiles. Algorithms that rely on all-versus-all comparison of sequences are not practical for large datasets.
Results: We introduce a new filter for string similarity which has the potential to eliminate the need for all-versus-all comparison in clustering of expression data and other similar tasks. Our filter is based on multiple long exact matches between the two strings, with the additional constraint that these matches must be sufficiently far apart. We give details of its efficient implementation using modified suffix arrays. We demonstrate its efficiency by presenting our new expression clustering tool, wcd-express, which uses this heuristic. We compare it to other current tools and show that it is very competitive both with respect to quality and run time.
Availability: Source code and binaries available under GPL at http://code.google.com/p/wcdest. Runs on Linux and MacOS X.
Contact: scott.hazelhurst@wits.ac.za; zsuzsa@cebitec.uni-bielefeld.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains
Authors: Woźniak Michał , Wong Limsoon , Tiuryn Jerzy 
Published: October 2011

Abstract
Motivation: A number of inconsistencies in genome annotations are documented among bacterial strains. Visualization of the differences may help biologists to make correct decisions in spurious cases.
Results: We have developed a visualization tool, CAMBerVis, to support comparative analysis of multiple bacterial strains. The software manages simultaneous visualization of multiple bacterial genomes, enabling visual analysis focused on genome structure annotations.
Availability: The CAMBerVis software is freely available at the project website: http://bioputer.mimuw.edu.pl/camber. Input datasets for Mycobacterium tuberculosis and Staphylocacus aureus are integrated with the software as examples.
Contact: m.wozniak@mimuw.edu.pl
Supplementary Information: Supplementary data are available at Bioinformatics online.
Risk Factors for Zaireebolavirus–Specific IgG in Rural Gabonese Populations
Authors: Nkoghe Dieudonne , Padilla Cindy , Becquart Pierre , Wauquier Nadia , Moussavou Ghislain , Akué Jean Paul , Ollomo Benjamin , Pourrut Xavier , Souris Marc , Kazanji Mirdad , Gonzalez Jean-Paul , Leroy Eric 
Published: October 2011

Abstract
Background.  In Gabon, several Ebolavirus outbreaks have occurred exclusively in the northeastern region. We conducted a large serosurvey to identify areas and populations at risk and potential demographic, clinical, and behavioral risk factors.
Methods.  Blood samples and clinical and sociodemographic data were collected from 4349 adults and 362 children in a random sample of 220 villages in the 9 provinces of Gabon. An enzyme-linked immunosorbent assay was used to detect Zaire ebolavirus (ZEBOV)–specific IgG, and thin blood smears were used to detect parasites. Logistic regression was implemented using Stata software (Stata), and a probability level of <.05 was considered to be statistically significant.
Results.  The prevalence of ZEBOV-specific IgG was 15.3% overall, increasing to 32.4% (P< .001) in forest areas. No sociodemographic risk factors were found, but the antibody prevalence increased linearly up to 20 years of age. Chronic arthralgia and amicrofilaremia were the only factors associated with ZEBOV seropositivity.
Conclusions.  These findings confirm the endemicity of ZEBOV in Gabon and its link to the ecosystem. Human antibody positivity would appear to be to the result of exposure to contaminated fruits.
Evaluation of efficacy and safety of finasteride 1 mg in 3177 Japanese men with androgenetic alopecia
Authors: SATO Akio , TAKEDA Akira 
Published: October 2011

AbstractBefore now, there has been no study of finasteride use exceeding 1 year in Japanese men with androgenetic alopecia (AGA) except the study subsequently conducted from the development phase. Since the launch of finasteride, no study in a larger population had been reported. Ethnic variation of the onset age, progressive nature and degree of hair loss of androgenetic alopecia are known. The therapeutic effect of oral finasteride (Propecia) was examined on androgenetic alopecia of Japanese men. The efficacy and safety of finasteride (1 mg tablet) was evaluated in Japanese men with AGA in the long term. The study enrolled 3177 men given finasteride 1 mg/day from January 2006 to June 2009 at our clinic. Efficacy was evaluated in 2561 men by the modified global photographic assessment; the photographs were assessed using the standardized 7‐point rating scale. Safety data were assessed by interviews and laboratory tests in all men enrolled in the study. The overall effect of hair growth was seen in 2230 of 2561 men (87.1%), in whom hair greatly (11.1%), moderately (36.5%) and slightly (39.5%) increased. The response rate improved with increasing duration of treatment. Adverse reactions occurred in 0.7% (23/3177) of men; seven men discontinued treatment based on risk–benefit considerations. No specific safety problems associated with long‐term use were observed. This study represents data collected at a single institution. Many patients did not receive follow‐up examination. In Japanese men with AGA, oral finasteride used in the long‐term study maintained progressive hair regrowth without recognized side‐effect.
Design considerations for legalizing cannabis: lessons inspired by analysis of California's Proposition 19
Authors: Caulkins Jonathan P. , Kilmer Beau , MacCoun Robert J. , Pacula Rosalie Liccardo , Reuter Peter 
Published: October 2011

ABSTRACTAims  No modern jurisdiction has ever legalized commercial production, distribution and possession of cannabis for recreational purposes. This paper presents insights about the effect of legalization on production costs and consumption and highlights important design choices.Methods  Insights were uncovered through our analysis of recent legalization proposals in California. The effect on the cost of producing cannabis is largely based on existing estimates of current wholesale prices, current costs of producing cannabis and other legal agricultural goods, and the type(s) of production that will be permitted. The effect on consumption is based on production costs, regulatory regime, tax rate, price elasticity of demand, shape of the demand curve and non‐price effects (e.g. change in stigma).Results  Removing prohibitions on producing and distributing cannabis will dramatically reduce wholesale prices. The effect on consumption and tax revenues will depend on many design choices, including: the tax level, whether there is an incentive for a continued black market, whether to tax and/or regulate cannabinoid levels, whether there are allowances for home cultivation, whether advertising is restricted, and how the regulatory system is designed and adjusted.Conclusions  The legal production costs of cannabis will be dramatically below current wholesale prices, enough so that taxes and regulation will be insufficient to raise retail price to prohibition levels. We expect legalization will increase consumption substantially, but the size of the increase is uncertain since it depends on design choices and the unknown shape of the cannabis demand curve.
In vitro effect of anti-human immunodeficiency virus CCR5 antagonist maraviroc on chemotactic activity of monocytes, macrophages and dendritic cells
Authors: Rossi R , Lichtner M , De Rosa A , Sauzullo I , Mengoni F , Massetti A P , Mastroianni C M , Vullo V 
Published: October 2011

Summary
Compounds targeting the chemokine receptor CCR5 have recently been approved for treatment of human immunodeficiency virus (HIV) infection. Given the central role of CCR5 in inflammation and recruitment of antigen-presenting cells (APC), it is important to investigate the immunological consequences of pharmacological inhibition of CCR5. We evaluated the in vitro effect of different concentrations of CCR5 antagonist maraviroc (MVC) on cell migration of monocytes, macrophages (MO) and monocyte-derived dendritic cells (MDC) towards peptide formyl-methionyl-leucyl-phenylalanine (fMLP) and chemokines regulated upon activation normal T cell expressed and secreted (RANTES) and CCL4/macrophage inflammatory protein-1 (MIP-1β) and CCL2/monocyte chemotactic protein-1 (MCP-1). Results of flow cytometric analysis showed that monocytes treated in vitro with MVC exhibited a significant dose-dependent reduction of chemotaxis towards MIP-1β and MCP-1. fMLP-induced chemotactic activity decreased only at higher concentration (1 µM and 10 µM of MVC). In addition, all concentrations of MVC (0·1, 1 and 10 µM) induced in vitro a significant inhibition of chemotaxis of MO and MDC in response to all tested chemoattractants. No change in phenotype (CD1a and CD14) and CCR1, CCR4, CCR5 and formyl peptide receptor (FPR) expression was seen after in vitro treatment with MVC. These findings suggest that CCR5 antagonist MVC may have the in vitro ability of inhibiting the migration of innate immune cells by mechanism which could be independent from the pure anti-HIV effect. The drug might have a potential role in the down-regulation of HIV-associated chronic inflammation by blocking the recirculation and trafficking of MO and MDC.
River drying lowers the diversity and alters the composition of an assemblage of desert riparian arthropods
Authors: McCLUNEY KEVIN E. , SABO JOHN L. 
Published: October 2011

Summary 1. Many studies have shown negative effects of river drying on in‐stream animals. However, the influence of river drying on riparian animals remains poorly studied. We examined ground‐dwelling riparian arthropod assemblages along a drying section of the semi‐arid San Pedro River in southeastern Arizona, U.S.A.2. We found strong differences in assemblage composition, taxon diversity and the abundance of key taxa between dry and flowing sites, with higher diversity and abundance of most taxa at flowing sites.3. Changes in assemblage composition, taxon diversity and abundance of representative taxa were associated with a combined measure of water availability that included distance to water and type of water. Other environmental variables showed a weaker association with changes in these arthropod assemblages.4. Thus, we found evidence that desert riparian arthropods are sensitive to river drying and to reduction in water resources. Increases in drying along this river may reduce the diversity and the abundance of many groups of ground‐dwelling arthropods, leading to marked shifts in community composition.
Unravelling complex associations between testosterone and parasite infection in the wild
Authors: Ezenwa Vanessa O. , Stefan Ekernas L. , Creel Scott 
Published: October 2011

Summary1. Testosterone has emerged as an important mechanism linking variation in male reproductive behaviour to parasite infection in vertebrates, and there are numerous pathways by which testosterone can influence infection risk, particularly in free‐living animals.2. The immunocompetence handicap hypothesis posits that the positive effects of testosterone on sexual signalling and behaviour are traded off with negative effects on immune function. While this obligate trade‐off may sometimes explain the association between testosterone and parasite infection, testosterone–parasite relationships may also be mediated by correlated changes in stress, condition and exposure to parasites.3. In this study, we explored associations between testosterone and reproductive behaviour, immune function and parasitism in free‐living Grant’s gazelle (Nanger granti). In particular, we examined how stress (glucocorticoids), behaviour and condition might mediate associations between testosterone, immunity and parasitism.4. We found that variation in endogenous testosterone in male gazelle was correlated with mating behaviour in terms of sexual signal intensity (horn size) and resource‐holding potential (territoriality). We also showed that these same levels of testosterone were associated with immunity and parasite infection, but associations between testosterone, immunity and parasitism were complex. Testosterone was negatively associated with adaptive immunity, but positively associated with innate immunity. Relationships between testosterone and parasitism varied for different parasites.5. Our results suggest that the effects of testosterone on male immunity are not universally suppressive and that immunoenhancement may also occur. In addition, testosterone–parasite relationships vary depending on the parasite, most likely due to the opposing effects of testosterone on different aspects of immunity and indirect effects on parasite exposure mediated by changes in behaviour.
Failure to migrate: lack of tree range expansion in response to climate change
Authors: Zhu Kai , Woodall Christopher W. , Clark James S. 
Published: October 2011

AbstractTree species are expected to track warming climate by shifting their ranges to higher latitudes or elevations, but current evidence of latitudinal range shifts for suites of species is largely indirect. In response to global warming, offspring of trees are predicted to have ranges extend beyond adults at leading edges and the opposite relationship at trailing edges. Large‐scale forest inventory data provide an opportunity to compare present latitudes of seedlings and adult trees at their range limits. Using theUSDAForest Service's Forest Inventory and Analysis data, we directly compared seedling and tree 5th and 95th percentile latitudes for 92 species in 30 longitudinal bands for 43 334 plots across the eastern United States. We further compared these latitudes with 20th century temperature and precipitation change and functional traits, including seed size and seed spread rate. Results suggest that 58.7% of the tree species examined show the pattern expected for a population undergoing range contraction, rather than expansion, at both northern and southern boundaries. Fewer species show a pattern consistent with a northward shift (20.7%) and fewer still with a southward shift (16.3%). Only 4.3% are consistent with expansion at both range limits. When compared with the 20th century climate changes that have occurred at the range boundaries themselves, there is no consistent evidence that population spread is greatest in areas where climate has changed most; nor are patterns related to seed size or dispersal characteristics. The fact that the majority of seedling extreme latitudes are less than those for adult trees may emphasize the lack of evidence for climate‐mediated migration, and should increase concerns for the risks posed by climate change.
Tree species traits cause divergence in soil acidification during four decades of postagricultural forest development
Authors: de Schrijver An , de Frenne Pieter , Staelens Jeroen , Verstraeten Gorik , Muys Bart , Vesterdal Lars , Wuyts Karen , van Nevel Lotte , Schelfhout Stephanie , de Neve Stefaan , Verheyen Kris 
Published: October 2011

AbstractA change in land use from agriculture to forest generally increases soil acidity. However, it remains unclear to what extent plant traits can enhance or mitigate soil acidification caused by atmospheric deposition. Soil acidification is detrimental for the survival of many species. An in‐depth understanding of tree species‐specific effects on soil acidification is therefore crucial, particularly in view of the predicted global increases in acidifying nitrogen (N) deposition. Here, we report soil acidification rates in a chronosequence of broadleaved deciduous forests planted on former arable land in Belgium. This region receives one of the highest loads of potentially acidifying atmospheric deposition in Europe, which allowed us to study a ‘worst case scenario’. We show that less than four decades of forest development caused significant soil acidification. Atmospheric deposition undoubtedly and unequivocally drives postagricultural forests towards more acidic conditions, but the rate of soil acidification is also determined by the tree species‐specific leaf litter quality and litter decomposition rates. We propose that the intrinsic differences in leaf litter quality among tree species create fundamentally different nutrient cycles within the ecosystem, both directly through the chemical composition of the litter and indirectly through its effects on the size and composition of earthworm communities. Poor leaf litter quality contributes to the absence of a burrowing earthworm community, which retards leaf litter decomposition and, consequently, results in forest‐floor build‐up and soil acidification. Also nutrient uptake andN2fixation are causing soil acidification, but were found to be less important. Our results highlight the fact that tree species‐specific traits significantly influence the magnitude of human pollution‐induced soil acidification.
Controls on carbon consumption during Alaskan wildland fires
Authors: Kasischke Eric S. , Hoy Elizabeth E. 
Published: October 2011

AbstractA method was developed to estimate carbon consumed during wildland fires in interior Alaska based on medium‐spatial scale data (60 m cell size) generated on a daily basis. Carbon consumption estimates were developed for 41 fire events in the large fire year of 2004 and 34 fire events from the small fire years of 2006–2008. Total carbon consumed during the large fire year (2.72 × 106 ha burned) was 64.7 Tg C, and the average carbon consumption during the small fire years (0.09 × 106 ha burned) was 1.3 Tg C. Uncertainties for the annual carbon emissions ranged from 13% to 21%. Carbon consumed from burning of black spruce forests represented 76% of the total during large fire years and 57% during small fire years. This was the result of the widespread distribution of black spruce forests across the landscape and the deep burning of the surface organic layers common to these ecosystems. Average carbon consumed was 3.01 kg m−2 during the large fire year and 1.69 kg m−2 during the small fire years. Most of the carbon consumption was from burning of ground layer fuels (85% in the large fire year and 78% in small fire years). Most of the difference in average carbon consumption between large and small fire years was in the consumption of ground layer fuels (2.60 vs. 1.31 kg m−2 during large and small fire years, respectively). There was great variation in average fuel consumption between individual fire events (0.56–5.06 kg m−2) controlled by variations in fuel types and topography, timing of the fires during the fire season, and variations in fuel moisture at the time of burning.