bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylmalonyl
Co
A
Mutase
Authors: Gruber Karl , Kratky Christoph 
Published: April 2006

Abstract

The 5′‐adenosylcobalamin dependent methylmalonyl‐CoA mutase (MCM) catalyzes the reversible and stereospecific equilibration of (
2R
)‐methylmalonyl CoA and succinyl CoA through a radical mechanism. Its occurrence ranges from bacteria to mammals, where it is required for the metabolism or biosynthesis of propionate. MCM from

Propionibacterium shermanii

is an αβ‐heterodimer of total molecular weight 150 kDa, containing an inactive β‐subunit along with an active α‐subunit, the latter binding one adenosylcobalamin molecule close to the active site. The protein was found to occur in two fundamentally different conformations: in the presence of substrates it crystallizes in a “closed” conformation, whereas in the absence of substrates an “open” conformation is observed. This dramatic conformational change suggests a mechanism for the first step of the MCM‐catalyzed reaction cycle, i.e. the substrate‐induced homolysis of the Co–C bond.
Dimethylsulfoxide Reductase
Authors: Li Hung‐Kei , Schindelin Hermann 
Published: April 2006

AbstractDimethylsulfoxide reductase is a molybdenum cofactor‐containing enzyme, which catalyzes the two‐electron reduction of dimethylsulfoxide to dimethylsulfide. The enzyme consists of a single polypeptide chain of 780 amino acids and contains no other cofactor besides the molybdenum cofactor. The overall fold of the enzyme is structurally organized into four domains, which are grouped around the cofactor. The molybdenum cofactor consists of two molybdopterin guanine dinucleotides, which are symmetrically ligating the molybdenum with their dithiolene groups. In the oxidized Mo(VI) form of the enzyme, an oxo group and a serine side chain complete the coordination sphere. The oxo group is the catalytically labile oxygen, which is replaced by an aquo or, possibly, a hydroxo ligand in the reduced Mo(IV) state.
Trimethylamine

N

‐Oxide Reductase
Authors: Iobbi‐Nivol Chantal , Haser Richard , Méjean Vincent , Czjzek Mirjam 
Published: April 2006

Abstract

Trimethylamine
N
‐oxide (TMAO) is a compound widely distributed in marine fish and invertebrates; and TMAO reducing enzymes are found not only in marine bacteria and photosynthetic bacteria living in ponds but also in enterobacteria. The various respiratory systems reducing TMAO, described so far, share a high level of homology either in their general structure, or in the regulation or mechanism of electron transfer. According to their content of molybdenum cofactor, the enzymes in charge of TMAO reduction are classified in the structural dimethylsulfoxide (DMSO) reductase family. TMAO reductases, however, in contrast to DMSO reductases are highly specific enzymes and reduce only their physiological substrate. The crystal structure was determined for the TMAO reductase from
Shewanella massilia
, and its structural differences with DMSO reductases in the environment of the active site. A tyrosine residue in the proximity of the molybdenum ion in DMSO reductases is absent in TMAO reductases and could be related to the differences in substrate specificities.
Rusticyanin
Authors: Shoham Menachem 
Published: April 2006

AbstractRusticyanin is a type 1 blue copper protein that functions as the major electron carrier in the iron respiratory electron transport chain ofThiobacillus ferrooxidans. This bacterium is the main cause of acid mine drainage. Rusticyanin is an extremophilic protein with redox activity as low as pH 0.5 and a redox potential of 680 mV, which is at least twice as high as for any other member of the family of cupredoxins. The ligands to the single copper ion are His85, Cys138, His143, and Met148. The three‐dimensional structure consists of a β‐sandwich of two mixed β‐sheets, one of six and one of seven strands, as well as a single amphipathic helix near the N‐terminus.
On the Fundamentals of Hydrological Sciences
Authors: Blöschl Günter 
Published: April 2006

AbstractAlthough there is no universal theory in hydrology that starts from first principles, the various branches of hydrology show numerous common threads. They relate to the nature of the processes including their space–time variability, the general principles of hydrological measurements, and the types of methods for representing hydrological processes in a quantitative way, either statistically or deterministically. The purpose of this article is to provide some common ground for this Encyclopedia to highlight the particularities of the hydrological sciences.
Hydrologic Concepts of Variability and Scale
Authors: Woods Ross 
Published: April 2006

Abstract
All hydrological phenomena have significant variations in time and space. Typically, these variations are driven by variations in physiographic factors such as climate, soils, vegetation, topography, geology, as well as by human and animal activities. These externally driven variations then propagate through hydrological systems, leading to an extremely rich variety of hydrological variability apparent at different temporal and spatial scales, in different physical settings. Virtually any quantitative approach to this problem requires the selection of a limited set of spatial and temporal scales within a particular physiographic setting. Any particular choice of time and space scales has a major influence on which aspects of this hydrological variability are perceived. This article surveys hydrological variability in both time and space, across a range of scales.
Fractals and Similarity Approaches in Hydrology
Authors: Lanza Luca G , Gallant John 
Published: April 2006

AbstractThe application of fractals and similarity concepts in hydrology has given rise to a better understanding of the space‐time organization of forms and processes that are relevant to the hydrologic cycle. Indeed, a variety of literature results support the conjecture that scaling holds for most hydrological variables in time and space.This chapter concentrates on fields where fractals and similarity approaches have proved helpful in fostering advances in specific hydrological studies. In particular, precipitation and drainage network morphology are addressed. A few specific applications to the study of natural forms and patterns relevant to the hydrological sciences are presented first, while the application of scaling concepts to the study of processes themselves is later discussed.Because of its highly irregular behavior, the rainfall process is one ideal candidate to be approached by means of self‐similarity and/or (multi)fractal description models. Such models involve increasing complexity and computational burden as soon as the interest moves from the one‐dimensional time series to the three‐dimensional case, where the full space‐time pattern of rainfall is considered. Examples of recent interesting results are presented with reference to the one‐, two‐, and three‐dimensional approaches to rainfall modeling based on similarity concepts.
Hydrological and Environmental Modeling of Transport Processes in Rivers and Estuaries
Authors: Lin Binliang , Falconer Roger A 
Published: April 2006

AbstractHydroinformatics tools are increasingly being used for predicting hydrodynamic, hydrological, and water quality processes in river and estuarine waters. The numerical solutions of the governing hydrodynamic and solute and sediment transport equations form the basis of these software tools. Details are given herein of the governing equations for three‐, two‐ and one‐dimensional flow‐field predictions and the transport of water quality indicators and sediment transport processes within the water column. Two case studies are then discussed. In the first of these studies linked 1‐D and 2‐D models are used to predict the velocity and fecal coliform distributions for a relatively large river and estuarine system, including the Ribble Estuary, its tributaries, and the Fylde coast. In the second of these studies, the velocity, suspended sediment, and heavy metal concentration distributions are predicted along the Humber Estuary using 2‐D and 3‐D models, with dynamic partitioning coefficients being used to link the metal concentrations and sediments. Details are also given of the hydrological models used to specify the pollutant discharge loads from land used models.
Evolutionary Computing in Hydrological Sciences
Authors: Savic Dragan , Khu Soon‐Thiam 
Published: April 2006

Abstract

With the advent of data acquisition techniques and data processing capabilities (computers + algorithms),
evolutionary computing
(
EC
) has found its way into a wide range of applications in hydrological science as demonstrated in this article. These applications range from the use of EC to assist in the understanding of hydrological processes, to improve the performance of simulation models for almost all aspects of hydrologic applications, and most recently, to quantify risk and uncertainty with the aim of providing decision support.

In this article, an attempt is made to provide a detailed review of the applications of EC in different hydrological science topics. References are divided into six main categories: hydrologic processes research, rainfall‐runoff modeling, reservoir operations and control, groundwater systems, urban water systems, and water quality studies. These are broad categorizations, and many applications of EC span across multiple groupings.
Evolutionary Computing is a continuously and rapidly growing area of academic research for computer science, mathematics, economics and management, engineering, physical science, and many others. As such, it is futile to try to provide a comprehensive overview of the currently available EC tools and techniques and therefore, no such attempt is made in this article.
Artificial Neural Network Concepts in Hydrology
Authors: Minns Anthony W , Hall Michael J 
Published: April 2006

AbstractThe solution of many applied hydrological problems, such as the forecasting of floods, has for several decades been based upon the concepts of linear systems analysis. However, the introduction of informatics tools, such as Artificial Neural Networks (ANNs), with their origins in cognitive sciences and pattern recognition, has made available new lines of investigation. Nevertheless, despite their apparent structural simplicity, the use of ANNs to encapsulate the transformation of rainfall over a catchment into streamflow at its outlet requires at least as much hydrological insight as a conventional physical/conceptual hydrological model. Of particular importance are: the choice of the input data streams; and the maintenance of the ability of the ANN to generalize and extrapolate beyond its training data set. Attention to these aspects invariably provides a model whose goodness‐of‐fit to an independent testing data set is superior to that of parameter‐based hydrological modeling systems.
Network Distributed Decision Support Systems and the Role of Hydrological Knowledge
Authors: Jonoski Andreja 
Published: April 2006

AbstractThis article introduces the hydroinformatics concept of new kinds of environments for supporting decision‐making processes in the fields of water and the environment, under the name of Network Distributed Decision Support Systems(NDDSSs). These environments are designed to enable active participation of large numbers of interested stakeholders including the general public. The platforms for their development and deployment are the electronic networks such as the Internet and the wireless mobile telephony networks. Core components of such systems are instantiated hydrological models, acting as main fact providers for the participants' judgments and evaluations of the proposed courses of actions. For achieving the required performance within NDDSSs, these models need to be distributed (viz. capable of representing spatial variability as encountered in real situations) and capable of simulating integrated physical processes in the hydrological system, and open for wider integration with other kinds of models such as ecological or socioeconomic models. A brief overview of the software agent technology is presented, with its potential for the design and development of these new decision support environments. The manners in which full‐fledged NDDSSs can be implemented into our present societies are also presented.
Atmospheric Boundary‐Layer Climates and Interactions with the Land Surface
Authors: Holtslag Albert AM , Ek Michael B 
Published: April 2006

AbstractThe purpose of this article is to provide an overview of the relevant processes and interactions in the Atmospheric Boundary Layer (ABL) over land. Modeling principles for the ABL are summarized and discussed, including the formulation and role of the surface fluxes. It is shown that both the ABL and the coupled soil‐vegetation‐atmosphere system can be well represented in the well‐defined cases examined. The interactions between the ABL and the land surface are illustrated with the role of soil moisture on boundary‐layer cloud initiation. As such, a new analytical development is discussed and illustrated for the tendency of relative humidity at boundary‐layer top. Typically, increased soil moisture leads to a higher potential for boundary‐layer clouds, but in some cases, the largest potential for boundary‐layer clouds is predicted over dry soils. For readers not familiar with atmospheric turbulence and meteorological definitions, some background is given as well.
Evaporation from Lakes
Authors: Finch Jonathan W , Hall Robin L 
Published: April 2006

AbstractLakes are an important part of the hydrological cycle, but quantifying the evaporation rates from them is not a trivial task. The amount of radiant energy captured by a lake is generally the dominant control on the annual evaporation rate. At shorter time periods, the major factors affecting lake evaporation are: the albedo, the heat‐storage term of the energy budget, and the atmospheric diffusion processes. The albedo is a function of the solar elevation angle and the proportion of downward diffuse radiation, and can be predicted from empirical relationships. The heat‐storage term can decouple the evaporation rates from the net radiation, but can be estimated simply in the case of well‐mixed water. However, in the situation where the lake becomes thermally stratified, more complex, hydrodynamic models are required. The three commonly used methods of estimating lake evaporation are: mass transfer, energy balance, and combination equations. There are strengths and limitations to each of these methods.
Ground‐Based and Airborne Lidar
Authors: Hardesty R Michael , Darby Lisa S 
Published: April 2006

Abstract
Lidar remote sensing techniques can be applied to measure a wide variety of atmospheric parameters important in the hydrological sciences, including aerosol distribution, cloud properties, ozone and water vapor concentration, and wind fields. Lidar measurements make use of scattering and extinction of laser radiation in the atmosphere. Instruments are deployed on surface and aircraft platforms to investigate phenomena such as moisture spatial distribution and temporal evolution, ozone sources and transport, boundary‐layer height, aerosol distribution, cloud microphysics, and wind structure. New satellite‐based instruments enable lidar techniques to be applied on a global scale.
Spatially Resolved Measurements of Evapotranspiration by Lidar
Authors: Eichinger William E 
Published: April 2006

Abstract
Spatially resolved estimates of evapotranspiration may be made over an area of about a square kilometer, with relatively fine (25 m) spatial resolution, derived from three‐dimensional measurements of water vapor concentration made by a scanning Raman lidar. The method is based upon the Monin–Obukhov similarity theory applied to spatially and temporally averaged data. The method has been applied at several locations to produce maps of the spatial distribution of evapotranspiration rates at regular intervals throughout the day. The estimates of evapotranspiration rates made compare favorably with estimates made using eddy correlation methods. The method is limited in that it assumes that the surface roughness, friction velocity, and Obukhov length are assumed constant over the examined areas. Values for the friction velocity and Obukhov length are required from conventional point instruments. The three‐dimensional water vapor concentration and the evaporation maps can be used in a wide variety of ways to study the spatial variations in evapotranspiration caused by changes in soil type and moisture content, canopy type, and topography.
Estimation of River and Water‐Body Stage, Width and Gradients Using Radar Altimetry, Interferometric
SAR
and Laser Altimetry
Authors: Birkett Charon , Alsdorf Doug , Harding David 
Published: April 2006

Abstract
Major advances in the application of satellite radar altimetry have led the way to a proven ability to determine surface water height, or stage, for some of the largest rivers, wetlands, and lakes around the world. These developments have come at a time when global water resources are of major concern, and there is a much‐noted decline in ground‐based monitoring networks. Recent interferometric synthetic aperture radar studies have also demonstrated the ability to retrieve stage changes over a wide expanse of inundated floodplain or wetland. While the performance of these radar instruments is continuously being assessed, focus is also on the potential of satellite‐based laser altimetry, which may offer smaller observable targets and improved stage accuracies. With these technological capabilities, we have the capacity to determine inland water stage, and to some degree, river width and gradient.
Freezing and Thawing Phenomena in Soils
Authors: Stähli Manfred 
Published: April 2006

Abstract
More than one‐third of the Earth's land surface is subjected to seasonal or permanent soil frost. The freezing and thawing of the soil may generate severe geotechnical, hydrological, and environmental problems, such as frost heaving, restricted infiltration, and enhanced overland flow. Each soil has its own specific freezing characteristic, primarily depending on texture and the prevailing solute concentration. Fine‐textured soils tend to form ice lenses at freezingthat causes the soil to heave. In coarse‐textured soil, on the other hand, the ice is more regularly distributed within the matrix. The behavior of the soil is always strongly linked to the prevailing meteorological conditions. The hydraulic conductivity of frozen soils is reduced, similar to very dry soils. Locally, this leads to reduced infiltration and delayed recharge to groundwater during snowmelt. For larger areas, for example, watersheds, the effect of frozen ground on infiltration and runoff is ambiguous, as a number of recent studies showed.
This article summarizes current theories and recent investigations on soil freezing and thawing phenomena with a major emphasis on implications for hydrology.
Models for Indirect Estimation of Soil Hydraulic Properties
Authors: Schaap Marcel G 
Published: April 2006

Abstract
This article describes methods for the indirect estimation of soil hydraulic properties, such as soil water retention and hydraulic conductivity characteristics. Indirect methods can be classified into semiphysical methods that are based on mechanical assumptions regarding particle and pore arrangements, and statistical methods that are known as pedotransfer functions. Both classes are described and evaluated on their merits, and some characteristic examples are given. A list of applicable software is described at the end of the article and an extensive reference list provides sufficient material for further background information.
Erosion and Sediment Transport by Water on Hillslopes
Authors: Parsons Anthony John 
Published: April 2006

AbstractMuch of the terminology and many of the concepts within the field of erosion and sediment transport by water on hillslopes, derive from the literature of agricultural engineering. Of particular importance has been the distinction between rills and interrill areas. One definition of the former is that they are channels small enough to be removed by ploughing; gullies, by contrast, are not. The distinction of gullies, rills, and interrill areas is artificial. None the less, it provides a convenient framework for an examination of the processes of hillslope erosion and sediment transport.In interrill areas, the dominant mechanism of sediment detachment is that of raindrop impact. Sediment detached by raindrops may be split into that which is transported away from the location of detachment in splash droplets (rainsplash), and that which is simply dislodged by the impact of raindrops but which either remains at, or falls back to, the site of detachment. The former is relatively easy to measure; the latter is not, but may be quantitatively much more important. The rate of detachment is a function of the rainfall energy at the soil surface, so that where vegetation intercepts some of the energy of the rainfall, or a layer of surface water exists, some of the energy of the falling rain will be dissipated. The rate of detachment is also affected by surface gradient. Whereas detachment in interrill areas is due to the energy of falling raindrops, sediment transport is mainly controlled by flow energy. Several authors have attempted to apply transport‐capacity equations developed for alluvial rivers even though the hydraulic conditions in shallow overland flow are very different from those in rivers. However, sediment transport by interrill flow needs to consider not only the capacity of the flow, but also its competence.As threads of interrill flow become deeper and faster, a threshold is reached beyond which significant flow detachment begins to take place. Once this occurs the flow begins to erode definable channels, or rills. As with interrill overland flow, the transport capacity of rill flow has typically been estimated using equations taken from the literature developed for alluvial rivers. However, sediment transport by rill flow is equally determined by the competence of the flow. This is particularly the case for stony soils.Gullies have been relatively neglected in the agricultural literature, so that, whereas there is considerable qualitative literature on gully growth and development, quantitative information is limited. However, gullies may account for between 10% and 94% of total soil loss on hillslopes.Modelling of hillslope erosion and sediment transport has been undertaken by both geomorphologists and agricultural engineers. There is a shared history, inasmuch as, through time, both demonstrate increasingly explicit representation of processes in their modelling as understanding of processes has increased and increased computing power has become available.
Microbial Transport in the Subsurface
Authors: Ginn Timothy R , Camesano Terri , Scheibe Timothy D , Nelson Kirk E , Clement T Prabhakar , Wood Brian D 
Published: April 2006

AbstractWe review the processes involved in the transport of bacteria in the saturated subsurface. Our goal is to communicate priority topics in the basic science of bacterial transport processes, and this leads to a focus on the nanometer to micron scales of observation. The scope of this review is the set of physical, chemical, and biological processes involved in the transport of individual cells, and the constitutive theory underlying conceptual depiction of these processes.