bluuebunny/crossref_metadata_2025_split huggingface dataset:
Floodplain catastrophes in the UK Holocene: messages for managing climate change
Authors: Lewin J. , Macklin M. G. 
Published: May 2010

AbstractFloodplains may be transformed when environmental changes or human activity causes alluvial systems to cross channel pattern thresholds. Thresholds between pattern states based on occurrence fields are only available for some pattern distinctions, and these may not encompass the alluvial contexts and range of dynamic factors involved. Pattern changes now known from the UK Holocene are reviewed as a basis for appreciating the potential for future transformations in a changing environment. These involved episodic boulder and gravel spreads in upland environments, and braiding $\leftrightarrow$ meandering, anastomosing → meandering and active $\leftrightarrow$ inactive transformations in more lowland contexts. Concern for possible impacts of climatic change need to be grounded in an appreciation of the nature and scale of these past changes. Some potential future changes may be relatively predictable in location (braiding $\leftrightarrow$ meandering); others are more difficult given both present knowledge and the varying, modified and inheritance‐rich ‘contexts of vulnerability’ that floodplains now represent. Implications for management are discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Multivariate analysis as a tool to infer hydrologic response types and controlling variables in a humid temperate catchment
Authors: Ali Geneviève A. , Roy André G. , Turmel Marie‐Claude , Courchesne François 
Published: May 2010

AbstractWe assess the ability of multivariate statistical analyses applied to event hydrographs parameters, to characterize a catchment hydrological behaviour. Motivation for such an approach lies in the fact that streamflow records have yet to be exploited to their full potential towards hydrological interpretation and can be used to infer a catchment state of connectivity from a qualitative standpoint. We have therefore processed 96 event hydrographs from a small headwater temperate humid forested catchment using principal component analysis, variation partitioning and classification tree analysis. These techniques prove to be promising in discriminating contrasted types of hydrologic responses (e.g. low‐ vs high‐magnitude events, slow vs quick timing events), identifying the main hydro‐meteorological variables that control these responses and determining thresholds values of the hydro‐meteorological variables leading to a switch between catchment response types. Copyright © 2010 John Wiley & Sons, Ltd.
Mechanisms and pathways of lateral flow on aspen‐forested, Luvisolic soils, Western Boreal Plains, Alberta, Canada
Authors: Redding Todd , Devito Kevin 
Published: May 2010

AbstractRainfall simulation experiments by Redding and Devito (2008, Hydrological Processes 23: 4287–4300) on two adjacent plots of contrasting antecedent soil moisture storage on an aspen‐forested hillslope on the Boreal Plain showed that lateral flow generation occurred only once large soil storage capacity was saturated combined with a minimum event precipitation of 15–20 mm. This paper extends the results of Redding and Devito (2008, Hydrological Processes 23: 4287–4300) with detailed analysis of pore pressure, soil moisture and tracer data from the rainfall simulation experiments, which is used to identify lateral flow generation mechanisms and flow pathways. Lateral flow was not generated until soils were wet into the fine textured C horizon. Lateral flow occurred dominantly through the clay‐rich Bt horizon by way of root channels. Lateral flow during the largest event was dominated by event water, and precipitation intensity was critical in lateral flow generation. Lateral flow was initiated as preferential flow near the soil surface into root channels, followed by development of a perched water table at depth, which also interacted with preferential flow pathways to move water laterally by the transmissivity feedback mechanism. The results indicate that lateral flow generated by rainfall on these hillslopes is uncommon because of the generally high available soil moisture storage capacity and the low probability of rainfall events of sufficient magnitude and intensity. Copyright © 2010 John Wiley & Sons, Ltd.
Tracing solute infiltration using a combined method of dye tracer test and electrical resistivity tomography in an undisturbed forest soil profile
Authors: Kim Jae Gon , Park Sam‐Gyu , Yi Myeong‐Jong , Kim Jung‐Ho 
Published: May 2010

AbstractAn accurate prediction of solute infiltration in a soil profile is important in the area of environmental science, groundwater and civil engineering. We examined the infiltration pattern and monitored the infiltration process using a combined method of dye tracer test and electrical resistivity tomography (ERT) in an undisturbed field soil (1 m × 1 m). A homogeneous matrix flow was observed in the surface soil (A horizon), but a preferential flow along macropores and residual rock structure was the dominant infiltration pattern in the subsurface soil. Saturated interflow along the slopping boundaries of A and C1 horizons and of an upper sandy layer and a lower thin clay layer in the C horizon was also observed. The result of ERT showed that matrix flow started first in A horizon and then the infiltration was followed by the preferential flows along the sloping interfaces and macropores. The ERT did not show as much detail as the dye‐stained image for the preferential flow. However, the area with the higher staining density where preferential flow was dominant showed a relatively lower electrical resistivity. The result of this study indicates that ERT can be applied for the monitoring of solute transportation in the vadose zone. Copyright © 2010 John Wiley & Sons, Ltd.
Characterizing the flush of stream chemical runoff from forested watersheds
Authors: Zhang Zhao , Tao Fulu , Shi Peijun , Xu Wei , Sun Yu , Fukushima Takehiko , Onda Yuichi 
Published: May 2010

AbstractA flush can be defined as stream chemical exhibiting higher concentrations during the prophase of a storm event at an event scale, or exhibiting progressively lower concentrations during several successive storms at a seasonal scale. Investigating the flush characteristics of chemical runoff from forested watersheds is important and helpful to understand the chemical dynamics as well as to design a sampling schedule strategy during storm events. Here, three parameters describing the flush characteristic are quantified and the flush characteristics of chemicals from four Japanese forested watersheds (Mie, Kochi, Nagano and Tokyo) were investigated at both event and seasonal levels. We found that the characteristics of the flush were complicated, and depended on the constituents of the hydrochemistry, climate and runoff quality. Generally, the flush occurs more readily for particulate components than for those in solution; the flush on nitrate‐nitrogen is weaker in regions of nitrogen saturation, such as Nagano and Tokyo, than in Mie and Kochi. Rainfall feature was the main factor controlling the flush of particulate components. However, the source available in a watershed plays a main role on the flushes of dissolve chemicals. Copyright © 2010 John Wiley & Sons, Ltd.
A multi‐year study of rainfall and soil water controls on Scots pine transpiration under Mediterranean mountain conditions
Authors: Llorens P. , Poyatos R. , Latron J. , Delgado J. , Oliveras I. , Gallart F. 
Published: May 2010

AbstractThis study is focused on the analysis of the relationship between sap‐flow‐derived transpiration measured in a Scots pine stand in the Vallcebre research catchments (NE Iberian Peninsula) and meteorological and rainfall data. The first part of the study is focused on the analysis of temperature and rainfall anomalies. Then, the Scots pine transpiration response to inter‐annual rainfall variability, soil water stress and water table depth variations during the period 1997–2000 is analysed. This period includes the extremely dry year of 1998, which allows us to infer the response of Scots pine transpiration to severe droughts. Scots pine transpiration during the summer presented a high inter‐annual variability, largely related to rainfall amounts. Daily transpiration during dry summers was 40% of the transpiration of a summer day with average rainfall. Moreover, during dry summers, transpiration rates were not fully recovered even after significant rainfall events. The analysis of the dependence of Scots pine transpiration on available water indicated the strong limitation on transpiration induced by water content in the whole soil profile as well as by water table position. Under these drought conditions, a reduction of runoff and deep water stores was observed at the catchment scale, suggesting that the predicted increase in the frequency of severe summer droughts may threaten the current role of Mediterranean mountain catchments as suppliers of water resources for lowland areas. Copyright © 2010 John Wiley & Sons, Ltd.
Heat tracing of heterogeneous hyporheic exchange adjacent to in‐stream geomorphic features
Authors: Lautz Laura K. , Kranes Nathan T. , Siegel Donald I. 
Published: May 2010

AbstractThere are many field techniques used to quantify rates of hyporheic exchange, which can vary in magnitude and direction spatially over distances of only a few metres, both within and between morphological features. We used in‐stream mini‐piezometers and heat transport modelling of stream and streambed temperatures to quantify the rates and directions of water flux across the streambed interface upstream and downstream of three types of in‐stream geomorphic features: a permanent dam, a beaver dam remnant and a stream meander. We derived hyporheic flux estimates at three different depths at six different sites for a month and then paired those flux rates with measurements of gradient to derive hydraulic conductivity (K) of the streambed sediments. Heat transport modelling provided consistent daily flux estimates that were in agreement directionally with hydraulic gradient measurements and also identified vertical heterogeneities in hydraulic conductivity that led to variable hyporheic exchange. Streambed K varied over an order of magnitude (1·9 × 10−6 to 5·7 × 10−5 m/s). Average rates of hyporheic flux ranged from static (q < ±0·02 m/day) to 0·42 m/day. Heat transport modelling results suggest three kinds of flow around the dams and the meander. Copyright © 2010 John Wiley & Sons, Ltd.
Evaluating the use of a gridded climate surface for modelling groundwater recharge in a semi‐arid region (Okanagan Basin, Canada)
Authors: Smerdon B. D. , Allen D. M. , Neilsen D. 
Published: May 2010

AbstractSpatially distributed groundwater recharge was simulated for a segment of a semi‐arid valley using three different treatments of meteorological input data and potential evapotranspiration (PET). For the same area, timeframe, land cover characteristics and soil properties, groundwater recharge was estimate using (i) single‐station climate data with monthly PET calculated by the Thornthwaite method; (ii) single‐station climate data with daily PET calculated by the Penman–Monteith method; and (iii) daily gridded climate data with spatially distributed PET calculated using the Penman–Monteith method. For each treatment, the magnitude and distribution of actual evapotranspiration (AET) for summer months compared well with those estimated for a 5‐year crop study, suggesting that the near‐surface hydrological processes were replicated and that subsequent groundwater recharge rates are realistic. However, for winter months, calculated AET was near zero when using the Thornthwaite PET method. Mean annual groundwater recharge varied from ∼3·2 to 10·0 mm when PET was calculated by the Thornthwaite method, and from ∼1·8 to 7·5 mm when PET was calculated by the Penman–Monteith method. Comparisons of bivariate plots of seasonal recharge rates estimated from single‐station versus gridded surface climate reveal that there is greater variability between the different methods for spring months, which is the season of greatest recharge. Furthermore, these seasonal differences are shown to provide different results when compared to the depth to water table, which could lead to different results of evaporative extinction depth. These findings illustrate potential consequences of using different approaches for representing spatial meteorological input data, which could provide conflicting predictions when modelling the influence of climate change on groundwater recharge. Copyright © 2010 John Wiley & Sons, Ltd.
A field‐based investigation to examine underwater soundscapes of five common river habitats
Authors: Tonolla Diego , Acuña Vicenç , Lorang Mark S. , Heutschi Kurt , Tockner Klement 
Published: May 2010

AbstractAquatic river habitat types have been characterized and classified for over five decades based on hydrogeomorphic and ecological variables. However, few studies considered the generation of underwater sound as a unique property of aquatic habitats, and therefore as a potential information source for freshwater organisms. In this study, five common habitat types along 12 rivers in Switzerland (six replicates per habitat type) were acoustically compared. Acoustic signals were recorded by submerging two parallel hydrophones and were analysed by calculating the energetic mean as well as the temporal variance of ten octave bands (31·5 Hz–16 kHz). Concurrently, each habitat type was characterized by hydraulic and geomorphic variables, respectively. The average relative roughness, velocity‐to‐depth ratio, and Froude number explained most of the variance of the acoustic signals created in different habitat types. The average relative roughness predominantly affected middle frequencies (63 Hz–1 kHz), while streambed sediment transport increased high‐frequency sound pressure levels (2–16 kHz) as well as the temporal variability of the recorded signal. Each aquatic habitat type exhibited a distinct acoustic signature or soundscape. These soundscapes may be a crucial information source for many freshwater organisms about their riverine environment. Copyright © 2010 John Wiley & Sons, Ltd.
Histone deacetylases in viral infections
Authors: Herbein Georges , Wendling Daniel 
Published: May 2010

Abstract
Chromatin remodeling and gene expression are regulated by histone deacetylases (HDACs) that condense the chromatin structure by deacetylating histones. HDACs comprise a group of enzymes that are responsible for the regulation of both cellular and viral genes at the transcriptional level. In mammals, a total of 18 HDACs have been identified and grouped into four classes, i.e., class I (HDACs 1, 2, 3, 8), class II (HDACs 4, 5, 6, 7, 9, 10), class III (Sirt1–Sirt7), and class IV (HDAC11). We review here the role of HDACs on viral replication and how HDAC inhibitors could potentially be used as new therapeutic tools in several viral infections.
A multi-criteria distribution model for global software development projects
Authors: Lamersdorf Ansgar , Münch Jürgen 
Published: May 2010

Abstract
The allocation of development tasks to sites is one of the most important activities in the management of global software development projects. Its various influences on the risks and benefits of distributed projects require careful consideration of multiple allocation criteria in a systematic way. In practice, however, work is often allocated based on only one single criterion such as cost, and defined processes or algorithms for task allocation are typically not used. Existing research approaches mainly focus on selected aspects such as the minimization of cross-site communication and are difficult to adapt to specific environments. This article presents a customizable multi-criteria model for task allocation in global software development projects. Based on an analysis of the state of the practice, a set of requirements was derived and used for evaluating existing task allocation models from different domains. The Bokhari algorithm was identified as a suitable starting point and modified with respect to the fulfillment of the requirements. The modification includes the development of mechanisms for customization, the incorporation of cause-effect relationships, and the use of probabilistic modeling of uncertainty with Bayesian networks. The application of the model is demonstrated in different scenarios that represent typical hypothetical and real distribution decision problems in industrial contexts. Experience from applying the model to such problems has shown, for instance, that depending on the weight of different criteria, very different task distributions will result. This demonstrates, in consequence, the need for systematic multi-criteria task allocation support in global software development.
Global analysis of microarray data reveals intrinsic properties in gene expression and tissue selectivity
Authors: Kim Changsik , Choi Jiwon , Park Hyunjin , Park Yunsun , Park Jungsun , Park Taesung , Cho Kwanghui , Yang Young , Yoon Sukjoon 
Published: May 2010

Abstract
Motivation: It is expected that individual genes have intrinsically different variability in the global expressional trend among them. Thus, the consideration of gene-specific expressional properties will help us to distinguish target-selective gene expression over non-selective over-expression.
Results: The re-standardization and integration of heterogeneous microarray datasets, available from public databases, have enabled us to determine the global expression properties of individual genes across a wide variety of experimental conditions and samples. The global averages and SDs of expression for each gene in the integrated microarray datasets were found to be intrinsic properties, which were consistent among independent collections of datasets using different microarray platforms. Using the gene-specific intrinsic parameters to rescale the microarray data, we were able to distinguish novel selective gene expression [cartilage oligomeric matrix protein (COMP) and Collagen X] in breast cancer tissues from non-selective over-expression, a difference that has not been detectable by conventional methods.
Availability and Implementation: The web-based tool for GS-LAGE is available at http://lage.sookmyung.ac.kr
Contact: yoonsj@sookmyung.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Arabidopsis RING E3 Ligase XBAT32 Regulates Lateral Root Production through Its Role in Ethylene Biosynthesis
Authors: Prasad Madhulika E. , Schofield Andrew , Lyzenga Wendy , Liu Hongxia , Stone Sophia L. 
Published: May 2010

AbstractXBAT32, a member of the RING domain-containing ankyrin repeat subfamily of E3 ligases, was previously identified as a positive regulator of lateral root development. Arabidopsis (Arabidopsis thaliana) plants harboring a mutation in XBAT32 produce fewer lateral roots that wild-type plants. We found that xbat32 mutants produce significantly more ethylene than wild-type plants and that inhibition of ethylene biosynthesis or perception significantly increased xbat32 lateral root production. XBAT32 interacts with the ethylene biosynthesis enzymes AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE4 (ACS4) and ACS7 in yeast-two-hybrid assays. XBAT32 is capable of catalyzing the attachment of ubiquitin to both ACS4 and ACS7 in in vitro ubiquitination assays. These results suggest that XBAT32 negatively regulates ethylene biosynthesis by modulating the abundance of ACS proteins. Loss of XBAT32 may promote the stabilization of ACSs and lead to increased ethylene synthesis and suppression of lateral root formation. XBAT32 may also contribute to the broader hormonal cross talk that influences lateral root development. While auxin treatments only partially rescue the lateral root defect of xbat32, they completely restore wild-type levels of xbat32 lateral root production when coupled with ethylene inhibition. Abscisic acid, an antagonist of ethylene synthesis/signaling, was also found to stimulate rather than inhibit xbat32 lateral root formation, and abscisic acid acts synergistically with auxin to promote xbat32 lateral root production.
Conserved Alternative Splicing of Arabidopsis Transthyretin-Like Determines Protein Localization and S-Allantoin Synthesis in Peroxisomes
Authors: Lamberto Ilaria , Percudani Riccardo , Gatti Rita , Folli Claudia , Petrucco Stefania 
Published: May 2010

Abstract
S-allantoin, a major ureide compound, is produced in plant peroxisomes from oxidized purines. Sequence evidence suggested that the Transthyretin-like (TTL) protein, which interacts with brassinosteroid receptors, may act as a bifunctional enzyme in the synthesis of S-allantoin. Here, we show that recombinant TTL from Arabidopsis thaliana catalyzes two enzymatic reactions leading to the stereoselective formation of S-allantoin, hydrolysis of hydroxyisourate through a C-terminal Urah domain, and decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline through an N-terminal Urad domain. We found that two different mRNAs are produced from the TTL gene through alternative use of two splice acceptor sites. The corresponding proteins differ in the presence (TTL1−) and the absence (TTL2−) of a rare internal peroxisomal targeting signal (PTS2). The two proteins have similar catalytic activity in vitro but different in vivo localization: TTL1− localizes in peroxisomes, whereas TTL2− localizes in the cytosol. Similar splice variants are present in monocots and dicots. TTL originated in green algae through a Urad-Urah fusion, which entrapped an N-terminal PTS2 between the two domains. The presence of this gene in all Viridiplantae indicates that S-allantoin biosynthesis has general significance in plant nitrogen metabolism, while conservation of alternative splicing suggests that this mechanism has general implications in the regulation of the ureide pathway in flowering plants.
Plastidial Thioredoxin z Interacts with Two Fructokinase-Like Proteins in a Thiol-Dependent Manner: Evidence for an Essential Role in Chloroplast Development in Arabidopsis and Nicotiana benthamiana
Authors: Arsova Borjana , Hoja Ursula , Wimmelbacher Matthias , Greiner Eva , Üstün Şuayib , Melzer Michael , Petersen Kerstin , Lein Wolfgang , Börnke Frederik 
Published: May 2010

Abstract
Here, we characterize a plastidial thioredoxin (TRX) isoform from Arabidopsis thaliana that defines a previously unknown branch of plastidial TRXs lying between x- and y-type TRXs and thus was named TRX z. An Arabidopsis knockout mutant of TRX z had a severe albino phenotype and was inhibited in chloroplast development. Quantitative real-time RT-PCR analysis of the mutant suggested that the expressions of genes that depend on a plastid-encoded RNA polymerase (PEP) were specifically decreased. Similar results were obtained upon virus-induced gene silencing (VIGS) of the TRX z ortholog in Nicotiana benthamiana. We found that two fructokinase-like proteins (FLN1 and FLN2), members of the pfkB-carbohydrate kinase family, were potential TRX z target proteins and identified conserved Cys residues mediating the FLN–TRX z interaction. VIGS in N. benthamiana and inducible RNA interference in Arabidopsis of FLNs also led to a repression of PEP-dependent gene transcription. Remarkably, recombinant FLNs displayed no detectable sugar-phosphorylating activity, and amino acid substitutions within the predicted active site imply that the FLNs have acquired a new function, which might be regulatory rather than metabolic. We were able to show that the FLN2 redox state changes in vivo during light/dark transitions and that this change is mediated by TRX z. Taken together, our data strongly suggest an important role for TRX z and both FLNs in the regulation of PEP-dependent transcription in chloroplasts.