bluuebunny/crossref_metadata_2025_split huggingface dataset:
An in situ vertebrate bioassay helps identify potential matrices for a predator‐based synthetic management tool
Authors: Parsons Michael H. , Blumstein Daniel T. , Dods Kenneth C. 
Published: June 2012

AbstractTo assist management and conservation needs, researchers have called for active kairomones to be elucidated and synthesized directly from animal exudates. However, the existing literature does not provide guidance on how to initiate this complex process. To our knowledge, composite synthetic predator scents that incorporate multiple compounds to accurately mimic the natural signal have not been produced. One approach to improve the accuracy of synthetics is to identify and recombine all major infochemicals within a benign solvent. Therefore, we tested 2 natural, pre‐existing matrices for their potential as vehicles for delivery of a predator scent, dingo (Canis lupus dingo) urine, which causes a startle reaction among western gray kangaroos (Macropus fuliginosus), and avoidance by European foxes (Vulpes vulpes). We compared 2 putative backbone matrices—aged (3‐yr old) dingo urine from a previously active lot, and 10% methanol—to a distilled water control. We used a novel fence‐crossing assay to observe kangaroo interactions with both solvents and a negative control. Our assay allowed us to control for high feeding motivation by testing compounds away from the food source. We determined that neither free‐ranging kangaroos nor European red foxes were adversely affected by either treatment matrix. Foxes were, however, attracted to the aged dingo urine, and were often observed scent‐rolling in the inactive substance. Our results suggest that dilute methanol could be a possible matrix for predator‐scent applications for kangaroos, while aged scents may act as an attractant for nontarget species, particularly canids. © 2012 The Wildlife Society.
Archive eggs: A research and management tool for avian conservation breeding
Authors: Smith Des H.V. , Moehrenschlager Axel , Christensen Nancy , Knapik Dwight , Gibson Keith , Converse Sarah J. 
Published: June 2012

AbstractWorldwide, approximately 168 bird species are captive‐bred for reintroduction into the wild. Programs tend to be initiated for species with a high level of endangerment. Depressed hatching success can be a problem for such programs and has been linked to artificial incubation. The need for artificial incubation is driven by the practice of multiclutching to increase egg production or by uncertainty over the incubation abilities of captive birds. There has been little attempt to determine how artificial incubation differs from bird‐contact incubation. We describe a novel archive (data‐logger) egg and use it to compare temperature, humidity, and egg‐turning in 5 whooping crane (Grus americana) nests, 4 sandhill crane (G. canadensis) nests, and 3 models of artificial incubator; each of which are used to incubate eggs in whooping crane captive‐breeding programs. Mean incubation temperature was 31.7° C for whooping cranes and 32.83° C for sandhill cranes. This is well below that of the artificial incubators (which were set based on a protocol of 37.6° C). Humidity in crane nests varied considerably, but median humidity in all 3 artificial incubators was substantially different from that in the crane nests. Two artificial incubators failed to turn the eggs in a way that mimicked crane egg‐turning. Archive eggs are an effective tool for guiding the management of avian conservation breeding programs, and can be custom‐made for other species. They also have potential to be applied to research on wild populations. © 2012 The Wildlife Society.
Analysis of protein function in clinical C. albicans isolates
Authors: Gerami‐Nejad Maryam , Forche Anja , McClellan Mark , Berman Judith 
Published: June 2012

AbstractClinical isolates are prototrophic and hence are not amenable to genetic manipulation using nutritional markers. Here we describe a new set of plasmids carrying the NAT1 (nourseothricin) drug resistance marker (Shen et al., ), which can be used both in clinical isolates and in laboratory strains. We constructed novel plasmids containing HA–NAT1 or MYC–NAT1 cassettes to facilitate PCR‐mediated construction of strains with C‐terminal epitope‐tagged proteins and a NAT1–pMet3–GFP plasmid to enable conditional expression of proteins with or without the green fluorescent protein fused at the N‐terminus. Furthermore, for proteins that require both the endogenous N‐ and C‐termini for function, we have constructed a GF–NAT1–FP cassette carrying truncated alleles that facilitate insertion of an intact, single copy of GFP internal to the coding sequence. In addition, GFP–NAT1, RFP–NAT1 and M‐Cherry–NAT1 plasmids were constructed, expressing two differently labelled gene products for the study of protein co‐expression and co‐localization in vivo. Together, these vectors provide a useful set of genetic tools for studying diverse aspects of gene function in both clinical and laboratory strains of C. albicans. Copyright © 2012 John Wiley & Sons, Ltd.
Heterochrony: the Evolution of Development
Authors: McNamara Kenneth J. 
Published: June 2012

Abstract
Heterochrony can be defined as change to the timing or rate of development relative to the ancestor. Because organisms generally change in shape as well as increase in size during their development, any variation to the duration of growth or to the rate of growth of different parts of the organism can cause morphological changes in the descendant form. Heterochrony takes the form of both increased and decreased degrees of development, known as “peramorphosis” and “paedomorphosis,” respectively. These are the morphological consequences of the operation of processes that change the duration of the period of an individual’s growth, either starting or stopping it earlier or later than in the ancestor, or by extending or contracting the period of growth. Heterochrony operates both intra- and interspecifically and is the source of much intraspecific variation. It is often also the cause of sexual dimorphism. Selection of a sequence of species with a specific heterochronic trait can produce evolutionary trends in the form of pera- or paedomorphoclines. Many different life history traits arise from the operation of heterochronic processes, and these may sometimes be the targets of selection rather than morphological features themselves. It has been suggested that some significant steps in evolution, such as the evolution of vertebrates, were engendered by heterochrony. Human evolution was fuelled by heterochrony, with some traits, such as a large brain, being peramorphic, whereas others, such as reduced jaw size, are paedomorphic.
Time perspective and psychosocial positive functioning among Italian adolescents who binge eat and drink
Authors: Laghi Fiorenzo , Liga Francesca , Baumgartner Emma , Baiocco Roberto 
Published: June 2012

ABSTRACTEvidence of an association between binge eating and binge drinking and of related health consequences have stimulated investigators to examine and explore risk and protective factors plus the reasons why individuals engage in these risky behaviours (Benjamin & Wulfert, 2003; Ferriter & Ray, 2011). This study examined the relationship between binge drinking and eating, time perspective and psychological functioning. A cross‐sectional survey of 1350 17–19 year‐old adolescents was conducted. Findings suggested that adolescents engaged in both binge eating and binge drinking behaviours reported negative experiences in the past, and they showed a lower future orientation and a greater inclination to fatalism than did the other students Additionally, they were more likely to report lower feelings of satisfaction with life and self‐esteem than the others. The pattern of results allows to conclude that time perspective may be a salient dimension when exploring the psychosocial correlates of binge behaviours, particularly within adolescents.
Six Sigma adoption: Operating performance impacts and contextual drivers of success
Authors: Swink Morgan , Jacobs Brian W. 
Published: June 2012

AbstractWe assess the operational impacts of Six Sigma program adoptions through an event study methodology, comparing financial data for 200 Six Sigma adopting firms against data for matched firms, which serve as control groups for the analyses. We employ various matching procedures using different combinations of pre‐adoption return on assets (ROA), industry, and size as matching criteria. By comparing performance outcomes across a hierarchy of operating metrics, we establish a pattern of Six Sigma adoption effects that provides strong evidence of a positive impact on ROA. Interestingly, these ROA improvements arise mostly from significant reductions in indirect costs; significant improvements in direct costs and asset productivity are not evident. We also find small improvements in sales growth due to Six Sigma adoption. Cross‐sectional analyses of the performance results reveal that distinctions in Six Sigma impacts across manufacturing and service firms are negligible. Interestingly, we find that the performance impact of Six Sigma adoption is negatively correlated to the firm's quality system maturity (indicated by prior ISO 9000 certification). Further analyses of manufacturing and service firms reveals that Six Sigma benefits are significantly correlated with intensity in manufacturing, and with financial performance before adoption in services. We discuss the implications of these findings for practice and for future research.
Holocene alluvial stratigraphy and response to climate change in the Roaring River valley, Front Range, Colorado, USA
Authors: Madole Richard F. 
Published: June 2012

AbstractStratigraphic analyses and radiocarbon geochronology of alluvial deposits exposed along the Roaring River, Colorado, lead to three principal conclusions: (1) the opinion that stream channels in the higher parts of the Front Range are relics of the Pleistocene and nonalluvial under the present climate, as argued in a water-rights trial USA v. Colorado, is untenable, (2) beds of clast-supported gravel alternate in vertical succession with beds of fine-grained sediment (sand, mud, and peat) in response to centennial-scale changes in snowmelt-driven peak discharges, and (3) alluvial strata provide information about Holocene climate history that complements the history provided by cirque moraines, periglacial deposits, and paleontological data. Most alluvial strata are of late Holocene age and record, among other things, that: (1) the largest peak flows since the end of the Pleistocene occurred during the late Holocene; (2) the occurrence of a mid- to late Holocene interval (~ 2450–1630(?) cal yr BP) of warmer climate, which is not clearly identified in palynological records; and (3) the Little Ice Age climate seems to have had little impact on stream channels, except perhaps for minor (~ 1 m) incision.
Spatiotemporal interpolation of elevation changes derived from satellite altimetry for Jakobshavn Isbræ, Greenland
Authors: Hurkmans R. T. W. L. , Bamber J. L. , Sørensen L. S. , Joughin I. R. , Davis C. H. , Krabill W. B. 
Published: June 2012

Estimation of ice sheet mass balance from satellite altimetry requires interpolation of point‐scale elevation change (dH/dt) data over the area of interest. The largest dH/dtvalues occur over narrow, fast‐flowing outlet glaciers, where data coverage of current satellite altimetry is poorest. In those areas, straightforward interpolation of data is unlikely to reflect the true patterns ofdH/dt. Here, four interpolation methods are compared and evaluated over Jakobshavn Isbræ, an outlet glacier for which widespread airborne validation data are available from NASA's Airborne Topographic Mapper (ATM). The four methods are ordinary kriging (OK), kriging with external drift (KED), where the spatial pattern of surface velocity is used as a proxy for that of dH/dt, and their spatiotemporal equivalents (ST‐OK and ST‐KED). KED assumes a linear relationship between spatial gradients of velocity anddH/dt, which is confirmed for both negative (Pearson's correlation ρ < −0.85) and, to a lesser degree, positive (ρ = 0.73) dH/dtvalues. When compared to ATM data, KED and ST‐KED yield more realistic spatial patterns and higher thinning rates (over 20 m yr−1 as opposed to 7 m yr−1for OK). Spatiotemporal kriging smooths inter‐annual variability and improves interpolation in periods with sparse data coverage and we conclude, therefore, that ST‐KED produces the best results. Using this method increases volume loss estimates from Jakobshavn Isbræ by up to 20% compared to those obtained by OK. The proposed interpolation method will improve ice sheet mass balance reconstructions from existing and past satellite altimeter data sets, with generally poor sampling of outlet glaciers.
Modeling glacier thickness distribution and bed topography over entire mountain ranges with GlabTop: Application of a fast and robust approach
Authors: Linsbauer A. , Paul F. , Haeberli W. 
Published: June 2012

The combination of glacier outlines with digital elevation models (DEMs) opens new dimensions for research on climate change impacts over entire mountain chains. Of particular interest is the modeling of glacier thickness distribution, where several new approaches were proposed recently. The tool applied herein, GlabTop (Glacier bed Topography) is a fast and robust approach to model thickness distribution and bed topography for large glacier samples using a Geographic Information System (GIS). The method is based on an empirical relation between average basal shear stress and elevation range of individual glaciers, calibrated with geometric information from paleoglaciers, and validated with radio echo soundings on contemporary glaciers. It represents an alternative and independent test possibility for approaches based on mass‐conservation and flow. As an example for using GlabTop in entire mountain ranges, we here present the modeled ice thickness distribution and bed topography for all Swiss glaciers along with a geomorphometric analysis of glacier characteristics and the overdeepenings found in the modeled glacier bed. These overdeepenings can be seen as potential sites for future lake formation and are thus highly relevant in connection with hydropower production and natural hazards. The thickest ice of the largest glaciers rests on weakly inclined bedrock at comparably low elevations, resulting in a limited potential for a terminus retreat to higher elevations. The calculated total glacier volume for all Swiss glaciers is 75 ± 22 km3 for 1973 and 65 ± 20 km3 in 1999. Considering an uncertainty range of ±30%, these results are in good agreement with estimates from other approaches.
On the space‐time distribution of major explosive volcanic eruptions on Earth
Authors: Palladino Danilo M. , Sottili Gianluca 
Published: June 2012

Explosive volcanic activity on Earth is typically discontinuous in space and time. The occurrence of spatial/temporal eruption clusters due to mutual cause‐and‐effect relationships or external triggers (e.g., tectonic and/or tidal forcing) is still debated. To detect possible clustering of major explosive eruptions, we test the distribution of eruptions with Volcanic Explosivity Index (VEI) ≥ 4 from 1750 to present. The 143 documented VEI ≥ 4 events display a markedly non‐uniform frequency distribution, with the highest relative probability of eruption recurrence within 500 km distance from the preceding event. The analogous frequency pattern obtained from randomized data series of the same catalogue suggests that the observed eruption pattern is primarily imparted by the geodynamic distribution of volcanoes (mostly located along tectonically active linear belts), with no evidence of mutual or external influence. Our results highlight a counter‐intuitive array of major eruption loci as a consequence of the intrinsic worldwide asymmetry of explosive volcanism, with implications on hazard assessment.
Break detection of annual Swiss temperature series
Authors: Kuglitsch F. G. , Auchmann R. , Bleisch R. , Brönnimann S. , Martius O. , Stewart M. 
Published: June 2012

Instrumental temperature series are often affected by artificial breaks (“break points”) due to (e.g.,) changes in station location, land‐use, or instrumentation. The Swiss climate observation network offers a high number and density of stations, many long and relatively complete daily to sub‐daily temperature series, and well‐documented station histories (i.e., metadata). However, for many climate observation networks outside of Switzerland, detailed station histories are missing, incomplete, or inaccessible. To correct these records, the use of reliable statistical break detection methods is necessary. Here, we apply three statistical break detection methods to high‐quality Swiss temperature series and use the available metadata to assess the methods. Due to the complex terrain in Switzerland, we are able to assess these methods under specific local conditions such as the Foehn or crest situations. We find that the temperature series of all stations are affected by artificial breaks (average = 1 break point / 48 years) with discrepancies in the abilities of the methods to detect breaks. However, by combining the three statistical methods, almost all of the detected break points are confirmed by metadata. In most cases, these break points are ascribed to a combination of factors in the station history.
BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms
Authors: Sosnowski Olivier , Charcosset Alain , Joets Johann 
Published: June 2012

Abstract
Summary: Compilation of genetic maps combined to quantitative trait loci (QTL) meta-analysis has proven to be a powerful approach contributing to the identification of candidate genes underlying quantitative traits. BioMercator was the first software offering a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis. Despite several limitations, the software is still widely used. We developed a new version proposing additional up to date methods and improving graphical representation and exploration of large datasets.
Availability and implementation: BioMercator V3 is implemented in JAVA and freely available (http://moulon.inra.fr/biomercator)
Contact: joets@moulon.inra.fr
POOL server: machine learning application for functional site prediction in proteins
Authors: Somarowthu Srinivas , Ondrechen Mary Jo 
Published: June 2012

Abstract
Summary: We present an automated web server for partial order optimum likelihood (POOL), a machine learning application that combines computed electrostatic and geometric information for high-performance prediction of catalytic residues from 3D structures. Input features consist of THEMATICS electrostatics data and pocket information from ConCavity. THEMATICS measures deviation from typical, sigmoidal titration behavior to identify functionally important residues and ConCavity identifies binding pockets by analyzing the surface geometry of protein structures. Both THEMATICS and ConCavity (structure only) do not require the query protein to have any sequence or structure similarity to other proteins. Hence, POOL is applicable to proteins with novel folds and engineered proteins. As an additional option for cases where sequence homologues are available, users can include evolutionary information from INTREPID for enhanced accuracy in site prediction.
Availability: The web site is free and open to all users with no login requirements at http://www.pool.neu.edu.
Contact: m.ondrechen@neu.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
MobiDB: a comprehensive database of intrinsic protein disorder annotations
Authors: Di Domenico Tomás , Walsh Ian , Martin Alberto J.M. , Tosatto Silvio C.E. 
Published: June 2012

Abstract
Motivation: Disordered protein regions are key to the function of numerous processes within an organism and to the determination of a protein's biological role. The most common source for protein disorder annotations, DisProt, covers only a fraction of the available sequences. Alternatively, the Protein Data Bank (PDB) has been mined for missing residues in X-ray crystallographic structures. Herein, we provide a centralized source for data on different flavours of disorder in protein structures, MobiDB, building on and expanding the content provided by already existing sources. In addition to the DisProt and PDB X-ray structures, we have added experimental information from NMR structures and five different flavours of two disorder predictors (ESpritz and IUpred). These are combined into a weighted consensus disorder used to classify disordered regions into flexible and constrained disorder. Users are encouraged to submit manual annotations through a submission form. MobiDB features experimental annotations for 17 285 proteins, covering the entire PDB and predictions for the SwissProt database, with 565 200 annotated sequences. Depending on the disorder flavour, 6–20% of the residues are predicted as disordered.
Availability: The database is freely available at http://mobidb.bio.unipd.it/.
Contact: silvio.tosatto@unipd.it
Functions of DNA methyltransferase 3‐like in germ cells and beyond
Authors: Liao Hung‐Fu , Tai Kang‐Yu , Chen Wendy S.‐C. , Cheng Luca C.W. , Ho Hong‐Nerng , Lin Shau‐Ping 
Published: June 2012

AbstractDNA methyltransferase 3‐like (DNMT3L) is one of the key players in de novo DNA methylation of imprinting control elements and retrotransposons, which occurs after genome‐wide epigenetic erasure during germ cell development. In this review, we summarise the biochemical properties of DNMT3L and discuss the possible mechanisms behind DNMT3L‐mediated imprinting establishment and retrotransposon silencing in germ cells. We also discuss possible connections between DNMT3L and non‐coding RNA‐mediated epigenetic remodelling, the roles of DNMT3L in germ cell development and the implications in stem cell and cancer research.
Nitrogen dynamics in grain crop and legume pasture systems under elevated atmospheric carbon dioxide concentration: A meta‐analysis
Authors: Lam Shu K. , Chen Deli , Norton Rob , Armstrong Roger , Mosier Arvin R. 
Published: June 2012

AbstractUnderstanding nitrogen (N) removal and replenishment is crucial to crop sustainability under rising atmospheric carbon dioxide concentration ([CO2]). While a significant portion of N is removed in grains, the soil N taken from agroecosystems can be replenished by fertilizer application and N2 fixation by legumes. The effects of elevated [CO2] on N dynamics in grain crop and legume pasture systems were evaluated using meta‐analytic techniques (366 observations from 127 studies). The information analysed for non‐legume crops included grain N removal, residue C : N ratio, fertilizer N recovery and nitrous oxide (N2O) emission. In addition to these parameters, nodule number and mass, nitrogenase activity, the percentage and amount of N fixed from the atmosphere were also assessed in legumes. Elevated [CO2] increased grain N removal of C3 non‐legumes (11%), legumes (36%) and C4 crops (14%). The C : N ratio of residues from C3 non‐legumes and legumes increased under elevated [CO2] by 16% and 8%, respectively, but the increase for C4 crops (9%) was not statistically significant. Under elevated [CO2], there was a 38% increase in the amount of N fixed from the atmosphere by legumes, which was accompanied by greater whole plant nodule number (33%), nodule mass (39%), nitrogenase activity (37%) and %N derived from the atmosphere (10%; non‐significant). Elevated [CO2] increased the plant uptake of fertilizer N by 17%, and N2O emission by 27%. These results suggest that N demand and removal in grain cropping systems will increase under future CO2‐enriched environments, and that current N management practices (fertilizer application and legume incorporation) will need to be revised.