bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation
Authors: Xu Meiying , Wu Wei-Min , Wu Liyou , He Zhili , Van Nostrand Joy D , Deng Ye , Luo Jian , Carley Jack , Ginder-Vogel Matthew , Gentry Terry J , Gu Baouhua , Watson David , Jardine Philip M , Marsh Terence L , Tiedje James M , Hazen Terry , Criddle Craig S , Zhou Jizhong 
Published: March 2010

Abstract
A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (&lt;30 μg l−1) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.
On abelian birational sections
Authors: Esnault Hélène , Wittenberg Olivier 
Published: March 2010

For a smooth and geometrically irreducible variety

X
X

over a field

k
k

, the quotient of the absolute Galois group

G

k
(
X
)

G_{k(X)}

by the commutator subgroup of

G

k
¯

(
X
)

G_{\bar k(X)}

projects onto

G
k

G_k

. We investigate the sections of this projection. We show that such sections correspond to “infinite divisions” of the elementary obstruction of Colliot-Thélène and Sansuc. If

k
k

is a number field and the Tate–Shafarevich group of the Picard variety of

X
X

is finite, then such sections exist if and only if the elementary obstruction vanishes. For curves this condition also amounts to the existence of divisors of degree

1
1

. Finally we show that the vanishing of the elementary obstruction is not preserved by extensions of scalars.
A Century‐Long Perspective on Agricultural Development
Authors: Barrett Christopher B. , Carter Michael R. , Timmer C. Peter 
Published: March 2010

AbstractThis article strategically surveys the past century's literature on agricultural development. We organize the discussion around three “grand themes” that reveal the richness of agricultural development as an intellectual endeavor. First, we explore the role of agriculture in the broader development process from a macroeconomic and political economy perspective. We then examine the role of technological and institutional change in successful agricultural development. Finally, the focus turns to a microeconomic perspective on agricultural household decision making and the problems of imperfect and missing markets, asymmetric information, and transactions costs that lead to widespread apparent inefficiency and disequilibrium.
Natural Resource Economics and Conservation: Contributions of Agricultural Economics and Agricultural Economists
Authors: Lichtenberg Erik , Shortle James , Wilen James , Zilberman David 
Published: March 2010

AbstractResearch by agricultural economists on natural resources has been distinguished by an interdisciplinary emphasis and a dynamic perspective. It has recognized technological and institutional constraints, has been oriented toward solving concrete resource management and policy problems, and has emphasized empirical and quantitative analysis. Agricultural economists have introduced methods for evaluating natural resource conservation efforts, for predicting adoption of resource conservation technologies, and for designing efficient and sustainable resource management policies. They have identified ways of improving land management and preventing land degradation, proposed reforms of institutions governing water allocation and water quality, and introduced policies for balancing environmental and efficiency considerations in the management of pests, biodiversity, and livestock diseases. Their research has had substantial impacts on the formulation of resource conservation policies.
A Century of Research on Rural Development and Regional Issues
Authors: Irwin Elena G. , Isserman Andrew M. , Kilkenny Maureen , Partridge Mark D. 
Published: March 2010

AbstractRural North America has undergone a major economic transformation over the past century due to labor‐saving technological progress, reductions in transport costs, and rising household incomes. The results are greater rural economic diversity, selected rural population decline, increased rural–urban interdependence, emergent exurban areas, and amenity‐led rural growth. We summarize key research insights and provide a selected review of the economics literature over the past 100 years with a focus on this economic transformation of rural places, its implications for rural communities, and key modeling innovations and applications. The many important contributions by agricultural economists are highlighted.
The AAEA: Ever Growing and Changing Research Challenges
Authors: McCalla Alex , Castle Emery , Eidman Vernon 
Published: March 2010

AbstractThe changing economic conditions over the past century, along with changes in technology and developments in economic theory and quantitative methods, helped shape the profession we currently refer to as agricultural and applied economics. The broadening of the profession from the original focus on the farm and agricultural industry to encompass international affairs, governmental policies, resources, and environmental and rural affairs is discussed within this context. Emergence of the subdisciplines and some of the major individual contributions are noted. The final section argues that members of the profession are well positioned to continue contributing research that will help society achieve its goals, and notes six challenges that provide such opportunities.
A Century of Research on Agricultural Markets
Authors: Myers Robert J. , Sexton Richard J. , Tomek William G. 
Published: March 2010

AbstractThis article provides a perspective on major innovations in research on agricultural markets over the past century. We review research on market structure and performance, vertical coordination arrangements, and institutions for producer collective action. Contributions to empirical modeling of agricultural price determination and marketing margins are also evaluated, as are innovations in research on spatial market relationships and the role of storage. Finally, we discuss contributions to understanding market information systems and the functioning of market‐based mechanisms for agricultural risk management, including futures, options, and insurance. Although progress over the century has been remarkable, we conclude by highlighting possible directions for future research.
Evolution of the Economics of Agricultural Policy
Authors: Sumner Daniel A. , Alston Julian M. , Glauber Joseph W. 
Published: March 2010

AbstractAgricultural economists helped develop farm programs to respond to the dire economic situation of the 1920s and 1930s. Some early authors appreciated that such policies created problems in markets for commodities and inputs. Over time, our understanding of agricultural issues and policies has deepened. Through the application of improved models and tools of analysis to more extensive data, we have developed better answers to old questions, and have responded to changing policy instruments, market contexts, and policy concerns. This article traces the evolution of our deepening economic understanding of the causes and consequences of agricultural policy.
Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?
Authors: Fernandes Andrew D. , Gloor Gregory B. 
Published: March 2010

Abstract
Motivation: Mutual information (MI) is a quantity that measures the dependence between two arbitrary random variables and has been repeatedly used to solve a wide variety of bioinformatic problems. Recently, when attempting to quantify the effects of sampling variance on computed values of MI in proteins, we encountered striking differences among various novel estimates of MI. These differences revealed that estimating the ‘true’ value of MI is not a straightforward procedure, and minor variations of assumptions yielded remarkably different estimates.
Results: We describe four formally equivalent estimates of MI, three of which explicitly account for sampling variance, that yield non-equal values of MI given exact frequencies. These MI estimates are essentially non-predictive of each other, converging only in the limit of implausibly large datasets. Lastly, we show that all four estimates are biologically reasonable estimates of MI, despite their disparity, since each is actually the Kullback–Leibler divergence between random variables conditioned on equally plausible hypotheses.
Conclusions: For sparse contingency tables of the type universally observed in protein coevolution studies, our results show that estimates of MI, and hence inferences about physical phenomena such as coevolution, are critically dependent on at least three prior assumptions. These assumptions are: (i) how observation counts relate to expected frequencies; (ii) the relationship between joint and marginal frequencies; and (iii) how non-observed categories are interpreted. In any biologically relevant data, these assumptions will affect the MI estimate as much or more-so than observed data, and are independent of uncertainty in frequency parameters.
Contact: andrew@fernandes.org
Supplementary information: Supplementary data are available at Bioinformatics online.
A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
Authors: Ballester Pedro J. , Mitchell John B. O. 
Published: March 2010

Abstract
Motivation: Accurately predicting the binding affinities of large sets of diverse protein–ligand complexes is an extremely challenging task. The scoring functions that attempt such computational prediction are essential for analysing the outputs of molecular docking, which in turn is an important technique for drug discovery, chemical biology and structural biology. Each scoring function assumes a predetermined theory-inspired functional form for the relationship between the variables that characterize the complex, which also include parameters fitted to experimental or simulation data and its predicted binding affinity. The inherent problem of this rigid approach is that it leads to poor predictivity for those complexes that do not conform to the modelling assumptions. Moreover, resampling strategies, such as cross-validation or bootstrapping, are still not systematically used to guard against the overfitting of calibration data in parameter estimation for scoring functions.
Results: We propose a novel scoring function (RF-Score) that circumvents the need for problematic modelling assumptions via non-parametric machine learning. In particular, Random Forest was used to implicitly capture binding effects that are hard to model explicitly. RF-Score is compared with the state of the art on the demanding PDBbind benchmark. Results show that RF-Score is a very competitive scoring function. Importantly, RF-Score's performance was shown to improve dramatically with training set size and hence the future availability of more high-quality structural and interaction data is expected to lead to improved versions of RF-Score.
Contact: pedro.ballester@ebi.ac.uk; jbom@st-andrews.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Regularity and singularity in solutions of the three-dimensional Navier–Stokes equations
Authors: Gibbon J. D. 
Published: March 2010

Higher moments of the vorticity field
Ω

m

(
t
) in the form of
L

2
m

-norms (

) are used to explore the regularity problem for solutions of the three-dimensional incompressible Navier–Stokes equations on the domain

. It is found that the set of quantities

provide a natural scaling in the problem resulting in a bounded set of time averages 〈
D

m

〉

T

on a finite interval of time [0,
T
]. The behaviour of
D

m
+1

/
D

m

is studied on what are called ‘good’ and ‘bad’ intervals of [0,
T
], which are interspersed with junction points (neutral)
τ

i

. For large but finite values of
m
with large initial data (
Ω

m

(0)≤
ϖ
0
O
(
Gr
4
)), it is found that there is an upper bound

which is punctured by infinitesimal gaps or windows in the vertical walls between the good/bad intervals through which solutions may escape. While this result is consistent with that of Leray (Leray 1934
Acta Math.
63
, 193–248 (
doi:10.1007/BF02547354
)) and Scheffer (Scheffer 1976
Pacific J. Math.
66
, 535–552),— this estimate for
Ω

m

corresponds to a length scale well below the validity of the Navier–Stokes equations.
The Role of Ethylene and Cold Temperature in the Regulation of the Apple POLYGALACTURONASE1 Gene and Fruit Softening
Authors: Tacken Emma , Ireland Hilary , Gunaseelan Kularajathevan , Karunairetnam Sakuntala , Wang Daisy , Schultz Keith , Bowen Judith , Atkinson Ross G. , Johnston Jason W. , Putterill Jo , Hellens Roger P. , Schaffer Robert J. 
Published: March 2010

Abstract
Fruit softening in apple (Malus × domestica) is associated with an increase in the ripening hormone ethylene. Here, we show that in cv Royal Gala apples that have the ethylene biosynthetic gene ACC OXIDASE1 suppressed, a cold treatment preconditions the apples to soften independently of added ethylene. When a cold treatment is followed by an ethylene treatment, a more rapid softening occurs than in apples that have not had a cold treatment. Apple fruit softening has been associated with the increase in the expression of cell wall hydrolase genes. One such gene, POLYGALACTURONASE1 (PG1), increases in expression both with ethylene and following a cold treatment. Transcriptional regulation of PG1 through the ethylene pathway is likely to be through an ETHYLENE-INSENSITIVE3-like transcription factor, which increases in expression during apple fruit development and transactivates the PG1 promoter in transient assays in the presence of ethylene. A cold-related gene that resembles a COLD BINDING FACTOR (CBF) class of gene also transactivates the PG1 promoter. The transactivation by the CBF-like gene is greatly enhanced by the addition of exogenous ethylene. These observations give a possible molecular mechanism for the cold- and ethylene-regulated control of fruit softening and suggest that either these two pathways act independently and synergistically with each other or cold enhances the ethylene response such that background levels of ethylene in the ethylene-suppressed apples is sufficient to induce fruit softening in apples.
Sugar Levels Regulate Tryptophan-Dependent Auxin Biosynthesis in Developing Maize Kernels
Authors: LeClere Sherry , Schmelz Eric A. , Chourey Prem S. 
Published: March 2010

Abstract
The maize (Zea mays) Miniature1 (Mn1) locus encodes the cell wall invertase INCW2, which is localized predominantly in the basal endosperm transfer layer of developing kernels and catalyzes the conversion of sucrose into glucose and fructose. Mutations in Mn1 result in pleiotropic changes, including a reduction in kernel mass and a recently reported decrease in indole-3-acetic acid (IAA) levels throughout kernel development. Here, we show that mn1-1 basal kernel regions (pedicels and basal endosperm transfer layer) accumulate higher levels of sucrose and lower levels of glucose and fructose between 8 and 28 d after pollination when compared with the wild type, whereas upper regions of mn1 accumulate similar or increased concentrations of sugars. To determine the cause of the reduction in IAA accumulation, we investigated transcript levels of several potential IAA biosynthetic enzymes. We demonstrate that reduced IAA levels most closely correspond to reduced transcript levels of ZmYUCCA (ZmYUC), a newly identified homolog of the Arabidopsis (Arabidopsis thaliana) gene YUCCA. We further demonstrate that ZmYUC catalyzes the N-hydroxylation of tryptamine and that sugar levels regulate transcript levels of ZmYUC, both in in vitro-cultured kernels and in a promoter-reporter fusion in Arabidopsis. These results indicate that developing seeds may modulate growth by altering auxin biosynthesis in response to sugar concentrations.
Elevation of CSF albumin in old sheep: relations to CSF turnover and albumin extraction at blood‐CSF barrier
Authors: Chen Ruo‐Li , Chen Carl Pai‐Chu , Preston Jane Elizabeth 
Published: March 2010

J. Neurochem.(2010)113, 1230–1239.AbstractAlbumin is the most abundant protein in both CSF and plasma, and albumin quotient is often used to assess the functions of brain barriers especially that of the blood‐CSF barrier [i.e. the choroid plexus (CP) which also secretes CSF]. In this study, we took albumin as a model molecule to investigate ageing‐related alterations in the CSF‐CP system in sheep. We found significant ageing‐related increases in the weight of lateral CP [122.4 ± 14.0 mg in the young, 198.6 ± 35.4 mg in the middle aged, 286.1 ± 25.1 mg in the old (p < 0.05)], in the CSF albumin as well as the albumin quotient. Albumin protein spots in old CSF displayed wider on 2D western immunoblotting images, and had higher densities on images of 2D large gels stained with Pro‐Q Emerald 488 compared to the young samples, suggesting ageing‐related post‐translational modification in the albumin. CSF secretion was reduced with age: 0.148 ± 0.013 mL/min/g in the young, 0.092 ± 0.02 mL/min/g in the middle aged, 0.070 ± 0.013 mL/min/g in the old (p < 0.05). The125I‐BSA extraction was not different among the sheep groups, nor was altered by temperature reduction, monensin, nocodazole, anti‐transforming growth factor β receptor II antibody, as well as unlabelled albumins. In conclusion, elevation of albumin in old CSF is associated with reduced CSF secretion by the CP, which size increases with age.125I‐BSA extract, reflecting the extracellular space rather than the active albumin uptake in the CP, is not different between ages. These early changes in health ageing may result in the accumulation and modifications of CSF proteins leading to neurotoxicity.
Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin
Authors: Mead Carri‐Lyn R. , Kuzyk Michael A. , Moradian Annie , Wilson Gary M. , Holt Robert A. , Morin Gregg B. 
Published: March 2010

J. Neurochem. (2010) 113, 1491–1503.AbstractUsing immunoprecipitation, mass spectrometry, and western blot analysis we investigated cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin in mammalian cells. We identified novel interactions with members of the exocyst, dynactin and chaperonin containing T‐complex protein complexes, and we confirmed interactions reported previously with all members of the biogenesis of lysosome‐related organelles complex‐1 and the adaptor‐related protein complex 3. We report interactions between dysbindin and the exocyst and dynactin complex that confirm a link between two important schizophrenia susceptibility genes: dysbindin and disrupted‐in‐schizophrenia‐1. To expand upon this network of interacting proteins we also investigated protein interactions for members of the exocyst and dynactin complexes in mammalian cells. Our results are consistent with the notion that impairment of aspects of the synaptic vesicle life cycle may be a pathogenic mechanism in schizophrenia.
Controlling the Formation of Silver Nanoparticles on Silica by Photochemical Deposition and Other Means†
Authors: Vinci John Cody , Bilski Piotr , Kotek Richard , Chignell Colin 
Published: March 2010

AbstractSilver nanoparticles (Ag‐NP) on silica were produced in aqueous solution by deposition of silver on colloidal silica in a small cuvette using radiation from a xenon‐mercury lamp. Ag‐NP were also synthesized on a much larger scale with low‐level, long‐term visible light irradiation for several months. In both cases, the nanoparticle production was monitored by the appearance of the surface plasmon resonance (SPR) band at around 410 nm. The growth of the nanoparticles was directly related to the time exposed to radiation, which could be tracked spectrophotometrically over time. We also investigated the possibilities of rapid nanoparticle production without the assistance of radiation though silver oxide by adding alkali hydroxide, which is a relatively unexplored approach for syntheses of Ag‐NP on silica. The SPR absorption of Ag‐NP was used as a tool in evaluating the size and shape of the resulting nanoparticles along with dynamic light scattering and transmission electron microscopy data. In order to better utilize and understand Ag‐NP, we present various ways to control their production through initial concentration adjustments, irradiation effects, gravitational fractionation, sonication and silver oxide formation.
The diffeotopy group of S1×S2 via contact topology
Authors: Ding Fan , Geiges Hansjörg 
Published: March 2010

AbstractAs shown by Gluck in 1962, the diffeotopy group of S1×S2 is isomorphic to ℤ2⊕ℤ2
⊕ℤ2. Here an alternative proof of this result is given, relying on contact topology. We then discuss two applications to contact topology: (i) it is shown that the fundamental group of the space of contact structures on S1×S2, based at the standard tight contact structure, is isomorphic to ℤ; (ii) inspired by previous work of Fraser, an example is given of an integer family of Legendrian knots in S1×S2#S1×S2 (with its standard tight contact structure) that can be distinguished with the help of contact surgery, but not by the classical invariants (topological knot type, Thurston–Bennequin invariant, and rotation number).
Lifting of characters on p-adic orthogonal and metaplectic groups
Authors: Howard Tatiana K. 
Published: March 2010

AbstractLet F be a p-adic field. Consider a dual pair $({\rm SO}(2n+1)_+, \widetilde {{\rm Sp}}(2n)),$ where SO(2n+1)+ is the split orthogonal group and $\widetilde {{\rm Sp}}(2n)$ is the metaplectic cover of the symplectic group Sp(2n) over F. We study lifting of characters between orthogonal and metaplectic groups. We say that a representation of SO(2n+1)+ lifts to a representation of $\widetilde {{\rm Sp}}(2n)$ if their characters on corresponding conjugacy classes are equal up to a transfer factor. We study properties of this transfer factor, which is essentially the character of the difference of the two halves of the oscillator representation. We show that the lifting commutes with parabolic induction. These results were motivated by the paper ‘Lifting of characters on orthogonal and metaplectic groups’ by Adams who considered the case F=ℝ.