bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional assignment of MAPK phosphatase domains
Authors: Nordle Anna K.L. , Rios Pablo , Gaulton Anna , Pulido Rafael , Attwood Teresa K. , Tabernero Lydia
Published: June 2007

Mitogen‐activated protein kinase (MAPK) pathways are well conserved in most organisms, from yeast to humans. The principal components of these pathways are MAP kinases whose activity is regulated by phosphorylation, implicating various MAPK protein effectors—in particular, protein phosphatases that inactivate MAPKs by dephosphorylation. The molecular basis of binding specificity of such regulatory phosphatases to MAPKs is poorly understood. To try to pinpoint potential functional regions within the sequences and to help identify new family members, we have applied a multimotif pattern‐recognition approach to characterize two MAPK phosphatase subfamilies (tyrosine‐specific and dual specificity) that are crucial in the regulation of MAPKs. We built “fingerprints” for these two subfamilies that are unique to, and highly discriminatory for, each group of proteins. The fingerprints were used in a genome‐wide screen, identifying more than 80 MAPK phosphatase domains, several of which were in partial sequences or unclassified proteins. We confirmed experimentally that one predicted MAPK phosphatase orthologue in Xenopus binds to ERK1/2, suggesting a role in MAPK signaling and thus supporting our functional predictions. Further analysis, mapping the fingerprints on the three‐dimensional structure of MAPK phosphatases, revealed that some of the fingerprint motifs reside in the N‐terminal noncatalytic regions coinciding with reported MAPK binding sites, while others lie within the catalytic phosphatase domain. These results also suggest the presence of putative allosteric sites in the catalytic region for modulation of protein–protein interactions, and provide a framework for future experimental validation. Proteins 2007. © 2007 Wiley‐Liss, Inc.
The helix–coil transition revisited
Authors: Chen Yantao , Zhou Yaoqi , Ding Jiandong
Published: June 2007

In this article, we perform a dynamic Monte Carlo simulation study of the helix–coil transition by using a bond‐fluctuation lattice model. The results of the simulations are compared with those predicted by the Zimm–Bragg statistical thermodynamic theory with propagation and nucleation parameters determined from simulation data. The Zimm–Bragg theory provides a satisfactory description of the helix–coil transition of a homopolypeptide chain of 32 residues (N = 32). For such a medium‐length chain, however, the analytical equation based on a widely‐used large‐N approximation to the Zimm–Bragg theory is not suitable to predict the average length of helical blocks at low temperatures when helicity is high. We propose an analytical large‐eigenvalue (λ) approximation. The new equation yields a significantly improved agreement on the average helix‐block length with the original Zimm–Bragg theory for both medium and long chain lengths in the entire temperature range. Nevertheless, even the original Zimm–Bragg theory does not provide an accurate description of helix–coil transition for longer chains. We assume that the single‐residue nucleation of helix formation as suggested in the original Zimm–Bragg model might be responsible for this deviation. A mechanism of nucleation by a short helical block is proposed by us and provides a significantly improved agreement with our simulation data. Proteins 2007. © 2007 Wiley‐Liss, Inc.
FireDock: Fast interaction refinement in molecular docking
Authors: Andrusier Nelly , Nussinov Ruth , Wolfson Haim J.
Published: June 2007

Here, we present FireDock, an efficient method for the refinement and rescoring of rigid‐body docking solutions. The refinement process consists of two main steps: (1) rearrangement of the interface side‐chains and (2) adjustment of the relative orientation of the molecules. Our method accounts for the observation that most interface residues that are important in recognition and binding do not change their conformation significantly upon complexation. Allowing full side‐chain flexibility, a common procedure in refinement methods, often causes excessive conformational changes. These changes may distort preformed structural signatures, which have been shown to be important for binding recognition. Here, we restrict side‐chain movements, and thus manage to reduce the false‐positive rate noticeably. In the later stages of our procedure (orientation adjustments and scoring), we smooth the atomic radii. This allows for the minor backbone and side‐chain movements and increases the sensitivity of our algorithm. FireDock succeeds in ranking a near‐native structure within the top 15 predictions for 83% of the 30 enzyme‐inhibitor test cases, and for 78% of the 18 semiunbound antibody‐antigen complexes. Our refinement procedure significantly improves the ranking of the rigid‐body PatchDock algorithm for these cases. The FireDock program is fully automated. In particular, to our knowledge, FireDock's prediction results are comparable to current state‐of‐the‐art refinement methods while its running time is significantly lower. The method is available athttp://bioinfo3d.cs.tau.ac.il/FireDock/.Proteins 2007. © 2007 Wiley‐Liss, Inc.
Structural evidence for a functionally relevant second camphor binding site in P450cam: Model for substrate entry into a P450 active site
Authors: Yao Huili , McCullough Christopher R. , Costache Aurora D. , Pullela Phani Kumar , Sem Daniel S.
Published: June 2007

P450cam has long served as a prototype for the cytochrome P450 (CYP) gene family. But, little is known about how substrate enters its active site pocket, and how access is achieved in a way that minimizes exposure of the reactive heme. We hypothesize that P450cam may first bind substrate transiently near the mobile F‐G helix that covers the active site pocket. Such a two‐step binding process is kinetically required if P450cam rarely populates an open conformation—as suggested by previous literature and the inability to obtain a crystal structure of P450cam in an open conformation. Such a mechanism would minimize exposure of the heme by allowing P450cam to stay in a closed conformation as long as possible, since only brief flexing into an open conformation would be required to allow substrate entry. To test this model, we have attempted to dock a second camphor molecule into the crystal structure of camphor‐bound P450cam. The docking identified only one potential entry site pocket, a well‐defined cavity on the F‐helix side of the F‐G flap, 16 Å from the heme iron. Location of this entry site pocket is consistent with our NMR T1 relaxation‐based measurements of distances for a camphor that binds in fast exchange (active site camphor is known to bind in slow exchange). Presence of a second camphor binding site is also confirmed with [1H‐13C] HSQC titrations of 13CH3‐threonine labeled P450cam. To confirm that camphor can bind outside of the active site pocket, 13CH3S‐pyridine was bound to the heme iron to physically block the active site, and to serve as an NMR chemical shift probe. Titration of this P450cam‐pyridine complex confirms that camphor can bind to a site outside the active site pocket, with an estimated Kd of 43 μM. The two‐site binding model that is proposed based on these data is analogous to that recently proposed for CYP3A4, and is consistent with recent crystal structures of P450cam bound to tethered‐substrates, which force a partially opened conformation. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations
Authors: Hansia Priti , Dev Sagarika , Surolia Avadhesha , Vishveshwara Saraswathi
Published: June 2007

Peanut agglutinin is a homotetrameric nonglycosylated protein. The protein has a unique open quaternary structure. Molecular dynamics simulations have been employed to follow the atomistic details of its unfolding at different temperatures. The early events of the deoligomerization of the protein have been elucidated in the present study. Simulation trajectories of the monomer as well as those of the tetramer have been compared and the tetramer is found to be substantially more stable than its monomeric counterpart. The tetramer shows retention of most of its secondary structure but considerable loss of the tertiary structure at high temperature. This observation implies the generation of a molten globule‐like intermediate in the later stages of deoligomerization. The quaternary structure of the protein has weakened to a large extent, but none of the subunits are separated. In addition, the importance of the metal‐binding to the stability of the protein structure has also been investigated. Binding of the metal ions not only enhances the local stability of the metal‐ion binding loop, but also imparts a global stability to the overall structure. The dynamics of different interfaces vary significantly as probed through interface clusters. The differences are substantially enhanced at higher temperatures. The dynamics and the stability of the interfaces have been captured mainly by cluster analysis, which has provided detailed information on the thermal deoligomerization of the protein. Proteins 2007. © 2007 Wiley‐Liss, Inc.
High incidence of ubiquitin‐like domains in human ubiquitin‐specific proteases
Authors: Zhu Xiao , Ménard Robert , Sulea Traian
Published: June 2007

Ubiquitin‐specific proteases (USPs) emerge as key regulators of numerous cellular processes and account for the bulk of human deubiquitinating enzymes (DUBs). Their modular structure, mostly annotated by sequence homology, is believed to determine substrate recognition and subcellular localization. Currently, a large proportion of known human USP sequences are not annotated either structurally or functionally, including regions both within and flanking their catalytic cores. To extend the current understanding of human USPs, we applied consensus fold recognition to the unannotated content of the human USP family. The most interesting discovery was the marked presence of reliably predicted ubiquitin‐like (UBL) domains in this family of enzymes. The UBL domain thus appears to be the most frequently occurring domain in the human USP family, after the characteristic catalytic domain. The presence of multiple UBL domains per USP protein, as well as of UBL domains embedded in the USP catalytic core, add to the structural complexity currently recognized for many DUBs. Possible functional roles of the newly uncovered UBL domains of human USPs, including proteasome binding, and substrate and protein target specificities, are discussed. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Phosphine resistance, respiration rate and fitness consequences in stored‐product insects
Authors: Pimentel Marco Aurélio G , Faroni Lêda Rita D'A , Tótola Marcos R , Guedes Raul Narciso C
Published: June 2007

Resistance to fumigants has been frequently reported in insect pests of stored products and is one of the obstacles in controlling these pests. The authors studied phosphine resistance and its physiological basis in adult insects of 12 populations of Tribolium castaneum (Herbst) (Tenebrionidae), ten populations of Rhyzopertha dominica (F.) (Bostrichidae) and eight populations of Oryzaephilus surinamensis L. (Silvanidae) from Brazil, and the possible existence of fitness costs associated with phosphine resistance in the absence of this fumigant. The bioassays for the detection of phosphine resistance followed the FAO standard method. The production of carbon dioxide and the instantaneous rate of population increase (ri) of each population of each species were correlated with their resistance ratios at the LC50. The resistance ratio at LC50 in T. castaneum ranged from 1.0‐ to 186.2‐fold, in R. dominica from 2.0‐ to 71.0‐fold and in O. surinamensis from 1.9‐ to 32.2‐fold. Ten populations of T. castaneum, nine populations of R. dominica and seven populations of O. surinamensis were resistant to phosphine. In all three species there was significant association (P < 0.05) between respiration rate and phosphine resistance. The populations with lower carbon dioxide production showed a higher resistance ratio, suggesting that the lower respiration rate is the physiological basis of phosphine resistance by reducing the fumigant uptake in the resistant insects. Conversely, populations with higher ri showed lower resistance ratios, which could indicate a lower rate of reproduction of the resistant populations compared with susceptible populations. Thus, management strategies based on the interruption of phosphine fumigation may result in reestablishment of susceptibility, and shows good potential for more effective management of phosphine‐resistant populations. Copyright © 2007 Society of Chemical Industry
Estimating the Jewish undercount in the 2001 Census: a comment on Graham and Waterman (2005) ‘Underenumeration of the Jewish Population in the UK 2001 Census’: Population, Space and Place 11: 89–102
Authors: Voas David
Published: June 2007

Graham and Waterman (2005) argued that there was a substantial underenumeration of Jews in the UK 2001 Census of Population. Their observations are valuable but some of the specific pieces of evidence and the recommendations that they offer can be criticised. There is an alternative method of estimating the extent to which Jews were undercounted in the census; it produces results that largely support their claims. Copyright © 2007 John Wiley & Sons, Ltd.
Dynamic analysis of less‐than‐truckload shipments and test method to simulate this environment
Authors: Singh S. P. , Joneson E. , Singh J. , Grewal G.
Published: June 2007

This paper provides results from a comprehensive data measurement study that analysed the vibration dynamics produced inside the trailers used for less‐than‐truckload (LTL) shipments. The trailers used for this segment of the package transportation environment are very different in size and suspension than those used for full truckload shipments. This study measured the vertical, lateral and longitudinal vibration inside a trailer as a function of road surface. In addition, the study developed a video showing freight movement inside the trailer to determine physical displacement and shifting of the loads. A set of recommendations was developed to safely load and transport LTL shipments to reduce damage claims. Copyright © 2007 John Wiley & Sons, Ltd.
A new finite sum inequality approach to delay‐dependent H∞ control of discrete‐time systems with time‐varying delay
Authors: Zhang Xian‐Ming , Han Qing‐Long
Published: June 2007

This paper deals with delay‐dependent H∞ control for discrete‐time systems with time‐varying delay. A new finite sum inequality is first established to derive a delay‐dependent condition, under which the resulting closed‐loop system via a state feedback is asymptotically stable with a prescribed H∞ noise attenuation level. Then, an iterative algorithm involving convex optimization is proposed to obtain a suboptimal H∞ controller. Finally, two numerical examples are given to show the effectiveness of the proposed method. Copyright © 2007 John Wiley & Sons, Ltd.
Patterns of primary and heterotrophic productivity in an arid lowland river
Authors: Gawne Ben , Merrick Chester , Williams David G. , Rees Gavin , Oliver Rod , Bowen P. M. , Treadwell Simon , Beattie Gillian , Ellis Iain , Frankenberg Judy , Lorenz Zygmunt
Published: June 2007

Three river conceptual models make differing predictions about the major source of primary production in lowland rivers, acknowledging the importance of primary productivity in the ecology and management of lowland rivers. Patterns of primary production in lowland rivers are still an area of considerable uncertainty. The objective of this study was to examine the major sources and transformations of organic matter in an Australian lowland river and compare them to the predictions of existing models. The broad approach adopted was to quantify the contribution from the major ecosystem components and compare these with estimates of system metabolism determined using open water measures of diel oxygen change. Three 4‐km river reaches were selected to represent the extent of variation found along the free‐flowing lowland sections of the Murray River, one of Australia's largest and most regulated rivers. Annual open water gross primary production (GPP) estimates for the Murray R. during this study ranged from 221 to 376 gC m−2 y−1 and were similar to other large rivers. Examination of the net contribution of organic matter to the channel indicates that primary productivity in the Murray R. is derived from a combination of phytoplankton, riparian vegetation and macrophytes, but that the major source varies both spatially and temporally. The present study confirms that the River Continuum Concept (RCC), the Flood Pulse Concept (FPC) and Riverine Productivity Model (RPM) all have some application to Australian lowland rivers, but that synthesis of the models will be difficult until we can incorporate the extent, causes and consequences of primary production variability. This study also highlights the importance of the microbial loop and macrophytes in the ecology of the Murray R. Copyright © 2007 John Wiley & Sons, Ltd.
Concentration Dependent Different Action of Tamoxifen on Membrane Fluidity
Authors: Kazanci Nadide , Severcan Feride
Published: June 2007

Tamoxifen (TAM) is a non-steroidal antiestrogen drug, which is widely used to prevent and treat breast, liver, pancreas and brain cancers. The present work investigates, in detail, the concentration dependent behavior of TAM (varying from 1 mol% to 45 mol%) on membrane fluidity. The differential scanning calorimetry (DSC) studies showed that tamoxifen eliminates the pre-transition and decreases the main phase transition to lower temperatures. Using visible spectroscopy at 440 nm and Fourier transform infrared (FTIR) spectroscopy it was found that membrane dynamics decreases for 1 and 3 mol% tamoxifen in both the gel and liquid crystalline phases. Above these concentrations up to 18–24 mol%, it increases and reaches its maximum values. As tamoxifen concentration was further increased, the membrane dynamics is found to be gradually decreased, although TAM still has fluidifying effect in comparison to pure phospholipid membrane. These findings are important for the effective use of tamoxifen in the cancer therapy to eliminate its dose dependent side effects reported in the literature.
Temporal trends in the frequency and longer‐term outcome of heart failure complicating myocardial infarction
Authors: Najafi Farid , Dobson Annette J. , Hobbs Michael , Jamrozik Konrad
Published: June 2007

Aims:

To investigate trends in incidence and long‐term outcome of heart failure (HF) developing within 28 days of first‐ever acute myocardial infarction (AMI).

Methods and results:

We identified all residents of Perth, Western Australia aged 25–64 years, with no history of HF, who experienced a non‐fatal, first‐ever AMI between 1984 and 1993, and followed them for ten years. All patients (N=4006) met the criteria for ‘definite AMI’ in WHO MONItoring trends and determinants of CArdiovascular disease (MONICA) Project and 897 (22.4%) had early‐onset HF complicating the index event. After adjustment for age, current smoking, history of diabetes and hypertension, Q‐wave and anterior wall AMI, the odds of developing HF declined by 9% (odds ratio for period 1989–1993 relative to 1984–1988=0.91, 95% confidence interval (957percnt;CI): 0.78 to 1.06). Over 10 years of follow‐up, patients with early‐onset HF had a cumulative average number of re‐admissions of 28 per 100 as compared with 9 per 100 in patients without HF. After adjustment for age, history of diabetes and hypertension, the hazard of death in patients with early‐onset HF declined by 26% (HR for the period 1989–1993 relative to 1984–1988=0.74, 95%CI: 0.57 to 0.96).

Conclusion:

Our data suggest a decline in the incidence of, and show encouraging evidence of improvement in survival after, early‐onset HF complicating AMI.
Osmotic regulation of transcription in Lactococcus lactis: Ionic strength‐dependent binding of the BusR repressor to the busA promoter
Authors: Romeo Yves , Bouvier Jean , Gutierrez Claude
Published: June 2007

The busA locus of Lactococcus lactis encodes a glycine betaine uptake system. At low osmolarity, the transcription of busA is repressed by the BusR protein, which is responsible for the osmotic inducibility of the busA promoter (busAp). In this work, we investigated the mechanism of the osmo‐dependent repression by BusR. We found that BusR binding to the busA promoter is dependent on the ionic strength in vitro. Using a BusR derivative carrying a phosphorylation site and the Escherichia coli RNA polymerase holoenzyme, we showed that these proteins are able to form a stable ternary complex by both binding to the same busAp fragment. The association/dissociation of BusR to the RNA polymerase–busAp complex is strictly correlated to the surrounding ionic strength. Together, these results suggest that during growth at low osmolarity BusR represses transcription from busAp at a step further the recruitment of the RNA polymerase. At high osmolarity, an elevated cytoplasmic ionic strength would dissociate BusR from busAp, resulting in the osmotic induction of the busA operon.
The helminth parasites of the wild rabbitOryctolagus cuniculusand their effect on host condition in Dunas de Mira, Portugal
Authors: Eira C. , Torres J. , Miquel J. , Vingada J.
Published: June 2007

The present study focuses on the helminth parasite community of the wild rabbit in a sand dune area in Portugal over a 5-year period. The influence of host sex and year on the composition of the helminth community is assessed, along with the potential effect of the detected helminths on host body condition. The basic structure of the helminth community comprisesMosgovoyia ctenoides,Graphidium strigosum,Trichostrongylus retortaeformis,Nematodiroides zembraeandPassalurus ambiguus. Mean intensities ofG. strigosumvaried between years. GeneralG. strigosumintensities were also found to vary according to both year and host sex, but not according to the interaction of both factors. When assessing the effect of helminths on rabbit body condition (expressed by the kidney fat index), higher burdens ofM. ctenoides, a cestode that presents a relatively large body mass, were found to induce a reduction in rabbit condition.
Thek-Core and Branching Processes
Authors: RIORDAN OLIVER
Published: June 2007

Thek-coreof a graphGis the maximal subgraph ofGhaving minimum degree at leastk. In 1996, Pittel, Spencer and Wormald found the threshold λcfor the emergence of a non-trivialk-core in the random graphG(n, λ/n), and the asymptotic size of thek-core above the threshold. We give a new proof of this result using a local coupling of the graph to a suitable branching process. This proof extends to a general model of inhomogeneous random graphs with independence between the edges. As an example, we study thek-core in a certain power-law or ‘scale-free’ graph with a parameterccontrolling the overall density of edges. For eachk≥ 3, we find the threshold value ofcat which thek-core emerges, and the fraction of vertices in thek-core whencis ϵ above the threshold. In contrast toG(n, λ/n), this fraction tends to 0 as ϵ→0.
The role of path dependence in the development of US bankruptcy law, 1880–1938
Authors: HANSEN BRADLEY A. , HANSEN MARY ESCHELBACH
Published: June 2007

We illustrate mechanisms that can give rise to path dependence in legislation. Specifically, we show how debtor-friendly bankruptcy law arose in the United States as a result of a path dependent process. The 1898 Bankruptcy Act was not regarded as debtor-friendly at the time of its enactment, but the enactment of the law gave rise to changes in interest groups, changes in beliefs about the purpose of bankruptcy law, and changes in the Democratic Party's position on bankruptcy that set the United States on a path to debtor-friendly bankruptcy law. An analysis of the path dependence of bankruptcy law produces an interpretation that is more consistent with the evidence than the conventional interpretation that debtor-friendliness in bankruptcy law began with political compromises to obtain the 1898 Bankruptcy Act.
Unterschiede und Gemein-samkeiten zwischen plötzlichem Säuglingstod (SIDS), Münchhausen-Syndrom by proxy (MSBP) mit tödlichem Ausgang und Infantizid
Authors: Häßler Frank , Zamorski Henryk , Weirich Steffen
Published: June 2007

Zusammenfassung: Einleitung: Plötzlicher Säuglingstod - sudden infant death syndrome (SIDS) - ist die häufigste Todesursache im ersten Lebensjahr. Er ist definiert als der plötzliche und unerwartete Tod eines Säuglings, welcher weder durch die Vorgeschichte noch durch post-mortem Untersuchungen erklärt werden kann. Die Inzidenz in der BRD hat von 1,7 auf 1000 Lebendgeburten im Jahre 1990 auf 0,62 im Jahre 2000 abgenommen. Hinter 5 bis 11% der SIDS Fälle verbergen sich Infantizide. Diese Kindstötungen können durch ein Münchhausen-Syndrom by proxy (MSBP) verursacht sein. MSBP ist eine Form der Kindesmisshandlung, bei der die Eltern bzw. Sorgeberechtigten über einen längeren Zeitraum Symptome oder Krankheiten ihres Kindes erfinden oder gar induzieren (provozieren), was dem Kind zweifelsfrei Schaden zufügt. Kasuistik: In einer Familie mit drei Kindern starb die jüngste Tochter im Alter von 17 Monaten an einer Apnoe-Attacke. Zuvor war sie 11mal stationär in den verschiedensten Kinderkliniken der Region behandelt worden, ohne dass die Eingangssymptome wie Krampfanfälle, Atemnotsyndrom und Durchfälle objektiviert werden konnten. Die rechtsmedizinisch toxikologische Untersuchung wies post mortem Koffein im Blut nach. Eine natürliche Todesursache bzw. ein Unfall schienen klinisch eher unwahrscheinlich. Schlussfolgerungen: Für die Unterscheidung zwischen SIDS, MSBP und Infantiziden sollte auf sich wiederholende Krankheitssymptome, häufige Krankenhausaufenthalte bzw. ambulante Vorstellungen, keine verifizierbare Diagnose, eine gewisse Therapieresistenz, unklare Krankheiten oder Todesfälle bei Geschwistern, wiederholte Vergiftungs- bzw. Erstickungserscheinungen geachtet werden. Die Differenzierung sollte sehr sorgfältig und tiefgründig erfolgen, da die zu ziehenden Konsequenzen von Fall zu Fall variieren und weitreichend sein können.
Fragebogen zur Erfassung sozial ängstlicher Kognitionen bei Kindern und Jugendlichen
Authors: Gra Antje , Gerlach Alexander L. , Melfsen Siebke
Published: June 2007

Zusammenfassung: In der vorliegenden Studie wurde auf der Grundlage des Children’s Cognitive Assessment Questionnaire (CCAQ) ein Fragebogen zur Erfassung sozial ängstlicher Kognitionen bei Kindern und Jugendlichen (SÄKK) entwickelt und hinsichtlich seiner psychometrischen Eigenschaften überprüft. 600 Schülerinnen und Schüler füllten den SÄKK sowie das «Sozialphobie und -angstinventar für Kinder» (SPAIK) aus. Das neue Instrument weist gute psychometrische Eigenschaften auf. Normen für die 3. bis 6. Klassenstufe wurden erstellt.
Similarity solutions for fluvial sediment fining by selective deposition
Authors: Fedele Juan J. , Paola Chris
Published: June 2007

Current models for downstream sediment sorting by selective deposition generally perform well at describing observed sorting data. However, since most were developed initially for application to modern rivers, they are typically formulated in terms of hydraulic and bed‐surface variables that are not readily measurable in the sedimentary record. Moreover, their algebraic complexity obscures some of the underlying simplicity of the segregation process. Here we show how a pair of hydraulically based sorting models developed by Parker et al. can be reformulated, with minimal loss of accuracy, in terms of the size distribution of the supplied sediment and the downstream depositional mass balance. By invoking constant dimensionless shear stress within either the gravel or sand regimes, reach‐scale, short‐term details of hydraulics and sediment transport are summarized via a pair of dimensionless relative mobility functions, one for gravel and one for sand. Our approach yields simplified similarity solutions in which the long‐term longitudinal grain‐size distribution of the substrate and the relative mobility functions can be collapsed into self‐similar forms in which only local mean and standard deviation of sizes in transport are used as scaling parameters. The formulation we propose offers a simple means to explore the impact of controlling variables on fining profiles and can be easily incorporated in long‐term, basin‐scale numerical stratigraphic models, avoiding the necessity of modeling the details of hydraulics and sediment transport. The model involves a minimum number of physically based parameters, the numerical values of which can be determined from the spatial distribution of rate of deposition, dimensionless shear stress, and the coefficient of variation of the supply gravel or sand size distributions.
Nitrification amplifies the decreasing trends of atmospheric oxygen and implies a larger land carbon uptake
Authors: Ciais P. , Manning A. C. , Reichstein M. , Zaehle S. , Bopp L.
Published: June 2007

Atmospheric O2 trend measurements are used to partition global oceanic and land biotic carbon sinks on a multiannual basis. The underlying principle is that a terrestrial uptake or release of CO2 is accompanied by an opposite flux of O2. The molar ratio of the CO2 and O2 terrestrial fluxes should be 1, if no other elements are considered. However, reactive nitrogen produced by human activities (e.g., fertilizers, N deposition) is also being incorporated into plant tissues. The various reaction pathways of the terrestrial nitrogen cycle cause fluxes of atmospheric O2. Thus the cycles of nitrogen, carbon, and oxygen must be linked together. We report here on previously unconsidered anthropogenic nitrogen‐related mechanisms which impact atmospheric O2 trends and thus the derived global carbon sinks. In particular, we speculate that anthropogenic‐driven changes are driving the global nitrogen cycle to a more oxidized state, primarily through nitrification, nitrate fertilizer industrial production, and combustion of fossil fuels and anthropogenic biomass burning. The sum of these nitrogen‐related processes acts to additionally decrease atmospheric O2 and slightly increase atmospheric CO2. We have calculated that the effective land biotic O2:CO2 molar ratio ranges between 0.76 and 1.04 rather than 1.10 (moles of O2 produced per mole of CO2 consumed) over the period 1993–2003, depending on which of four contrasting nitrogen oxidation and reduction pathway scenarios is used. Using the scenario in which we have most confidence, this implies a 0.23 PgC yr−1 correction to the global land biotic and oceanic carbon sinks of most recently reported estimates over 1993–2003, with the land biotic sink becoming larger and the oceanic sink smaller. We have attributed large uncertainties of 100% to all nitrogen‐related O2 and CO2 fluxes and this corresponds up to ±0.09 PgC yr−1 increase in global carbon sink uncertainties. Thus accounting for anthropogenic nitrogen‐related terrestrial fluxes of O2 results in a 45% larger land biotic sink of 0.74 ± 0.78 PgC yr−1 and a slightly smaller oceanic sink of 2.01 ± 0.66 PgC yr−1 for the decade 1993–2003.
Identity and emplacement of domical structures in the western Arcadia Planitia, Mars
Authors: Rampey Michael L. , Milam Keith A. , McSween Harry Y. , Moersch Jeffrey E. , Christensen Philip R.
Published: June 2007

Morphologic, morphometric, and thermophysical aspects of domical structures in a restricted part of the Mars northern plains were characterized using Mars Odyssey and Mars Global Surveyor data. The majority of domical structures consist of relatively high thermal inertia, subcircular to irregularly shaped “core' bodies surrounded by adjacent, relatively low‐albedo, low thermal inertia “annuli,” and dispersed aureoles of apparently disaggregated material. Core profiles vary considerably from low to high aspect ratios. Elongate “arms” of material extend from the central, summit regions in some of the structures. Core features include apparent blocky surface texture, summit fissures and pits, apparent summit and flank ruptures suggestive of “eruption” of material, and concentric and straight summit ridges. Core heights range from ∼30 to 400 m, mean = 160 m, diameters range from ∼620 to 3090 m, mean = 1550 m, aspect ratios range from 0.02 to 0.36, mean = 0.11, and volumes range from ∼0.1 to ∼1.8 km3. An additional morphologic type consists of subcircular, domical mounds that are apparently covered by plains materials. We propose that the majority of the structures are partially extrusive cryptodomes and lava domes, whereas the mounds are entirely intrusive cryptodomes.
Deposition and degradation of a volatile‐rich layer in Utopia Planitia and implications for climate history on Mars
Authors: Morgenstern Anne , Hauber Ernst , Reiss Dennis , van Gasselt Stephan , Grosse Guido , Schirrmeister Lutz
Published: June 2007

We investigate the surface morphology of a study area in western Utopia Planitia, Mars, which is characterized by a variety of landforms that resemble those of terrestrial periglacial landscapes. Polygonally fractured ground and thermokarst‐like depressions are found to be located in a young mantling deposit with a thickness of several tens of meters. We observe a latitudinal dependence of the degradation of this mantling deposit. Larger depressions, whose floors reveal the underlying basement rocks, cover a higher fraction of the total terrain in the southern part of the study area than in the northern part, indicating a more intense degradation of the mantle in the south. All depressions have an asymmetric cross section in north‐south direction, interpreted to be the result of the different solar radiation on differently oriented slopes. On the basis of our morphological observations, we develop a conceptual model for landscape evolution in western Utopia Planitia. It involves subaerial deposition of a layered, ice‐rich mantle and its subsequent degradation by polygon formation and sublimation. A terrestrial analog to the polygonally fractured mantling deposit and its thermokarst‐like depressions is the Siberian Ice Complex or “Yedoma,” which consists of subaerial ice‐rich deposits and is connected to nonglaciated landscapes with highly continental cold‐climatic environmental conditions. Our comparison suggests that no unusual or exotic processes need to be invoked to explain the current morphology of western Utopia. However, the young age of the deposition and degradation implies climatic excursions in the very recent past on Mars.
Effects of 20th century warming and climate variability on flood risk in the western U.S.
Authors: Hamlet Alan F. , Lettenmaier Dennis P.
Published: June 2007

Using precipitation and temperature data for the 20th century in combination with a macroscale hydrologic model, we evaluate changes in flood risk in the western U.S. associated both with century‐scale warming and interannual climate variations. In addition, we examine the implications of apparent increases in precipitation variability over the region since the mid‐1970s. We use detrended temperature data representing early and late 20th century climate to force the variable infiltration capacity hydrologic model and show that spatially homogeneous temperature changes over the western U.S. in the 20th century on the order of +1°C per century have resulted in substantial changes in flood risks over much of the region. Although changes specific to particular geographic areas are apparent in some cases, the overall changes due to observed warming trends are well categorized by midwinter temperature regimes in each watershed. Cold river basins where snow processes dominate the annual hydrologic cycle (<−6°C average in midwinter) typically show reductions in flood risk due to overall reductions in spring snowpack. Relatively warm rain‐dominant basins (>5°C average in midwinter) show little systematic change. Intermediate or transient basins show a wide range of effects depending on competing factors such as the relative role of antecedent snow and contributing basin area during storms that cause flooding. Warmer transient basins along the coast in Washington, Oregon, and California, in particular, tend to show increased flood risk. While the absolute value of simulated changes in flood risk is affected by basin scale, the nature of the relationship of flood risk to basin temperatures in midwinter is largely scale‐independent. Climate variations associated with Pacific Decadal Oscillation (PDO) and El Niño Southern Oscillation (ENSO) also have strong effects on flood risks. In contrast to the effects associated with 20th century warming, the climate variability signal is characterized by regional scale patterns related to the geographic distribution of cool season precipitation also identified in many previous studies. In general, the largest changes in simulated flood risks are associated with years when PDO and ENSO are “in phase,” particularly in the southwest. Changes in the variability of cool season precipitation after about 1973, the causes of which are uncertain, are shown to result in increased flood risk over much of the western U.S. in the simulations.
Empirical assessment of coral Sr/Ca and Mg/Ca ratios as climate proxies using colonies grown at different temperatures
Authors: Inoue Mayuri , Suzuki Atsushi , Nohara Masato , Hibino Kohei , Kawahata Hodaka
Published: June 2007

Coral strontium/calcium (Sr/Ca) and magnesium/calcium (Mg/Ca) ratios might be useful for reconstructing past sea surface temperature (SST) in tropical oceans where instrumental data are limited. However, the link between coral skeletal trace elements and SST is disputed, and biological factors such as skeletal growth rate may also affect trace elements in a coral. We studied the relationships between growth rate and SST and Sr/Ca and Mg/Ca ratios using corals (Porites spp.) cultured in thermostated tanks. Sr/Ca was controlled primarily by SST, while Mg/Ca mainly reflected the growth rate with negligible contribution from species on both the variations. These relationships are consistent with modeled results of cation partitioning during aragonite crystal formation.
The Scarecrow and the Tin Man: The Vicissitudes of Human Sympathy and Caring
Authors: Loewenstein George , Small Deborah A.
Published: June 2007

Why do some victims elicit outpourings of sympathy from those who are unaffected, while others do not? The authors propose a theoretical framework for making sense of the vicissitudes of sympathy based on the interaction between two qualitatively different mental processes. One, which the authors term “sympathy,” is caring but immature and irrational. The other process, which the authors term “deliberation,” is rational but uncaring. After proposing a framework for how these two factors interact, the authors first discuss a variety of factors that affect the strength of sympathy, including whether one is in the same state as the victim, one's past and vicarious experiences, proximity, similarity, vividness, and newness. Next, the authors discuss factors that affect the relative influence of deliberation. The framework helps to integrate a wide range of disparate experimental findings and provides a possible resolution to parallel debates taking place in psychology and economics over the nature of altruism.
Feeling Duped: Emotional, Motivational, and Cognitive Aspects of Being Exploited by Others
Authors: Vohs Kathleen D. , Baumeister Roy F. , Chin Jason
Published: June 2007

Feeling duped is an aversive emotional response to the perception of having been taken advantage of in a interpersonal transaction (primarily those involving economic exchange), partly as a result of one's own decisions. The actual likelihood of being duped, as well as the heightened vigilance for it, should increase as a function of opportunity (e.g., information asymmetry that gives one side a big advantage in knowledge) and motivation (e.g., an exceptionally huge payoff may make it worth defrauding a long-term business partner). Being duped produces an aversive self-conscious emotion with a threat of self-blame. There appears to be stable individual differences in the motivation (called sugrophobia) to avoid being a sucker. High sugrophobes will be vigilant and skeptical of potential deals. Low sugrophobes may not even realize in some instances that they were duped. The aversive reaction to feeling duped stimulates counterfactual ruminations that may intensify sugrophobia but also aids in extracting useful lessons.
Affect and the Motivational Foundations of Social Capital
Authors: Goette Lorenz , Huffman David
Published: June 2007

Social capital is a resource that includes the willingness of members of society to cooperate with each other, even when it is not in their own individual material self-interests to do so, or enforce beneficial social norms, even when this is materially costly for the enforcer. Evidence from economic choice experiments suggests that affect may play an important role in the individual-level decision process that generates these behavioral tendencies. Negative affective responses to uncooperative behavior can lead to a breakdown in social capital, if there is no option to punish. Given a punishment option, however, individuals discipline uncooperative types, even though it is materially costly to do so. This can completely counteract the tendency for social capital to decline in repeated interactions. Positive affect, triggered by punishing uncooperative types, appears to play a role in generating this socially beneficial willingness to sanction.
Affective Influence on Judgments and Decisions: Moving towards Core Mechanisms
Authors: Winkielman Piotr , Knutson Brian , Paulus Martin , Trujillo Jennifer L.
Published: June 2007

This article reviews psychological accounts of affective influence on judgments and decisions and argues that these accounts can be enriched by insights from biopsychology. The authors show how biopsychological research helps (1) reveal the sources of values and feelings; (2) predict when affect will influence attentional, perceptual, memorial, and decision processes; and (3) identify precise mechanisms underlying the interaction between affective and cognitive systems. The authors also propose a specific biopsychological model of affective priming phenomena and show how this model deals with data that are hard to explain with purely psychological accounts. The authors conclude that a multilevel biopsychological perspective will ultimately provide a more constrained and plausible foundation for understanding psychological processes underlying affect, judgment, and decision.
Deciding versus Reacting: Conceptions of Moral Judgment and the Reason-Affect Debate
Authors: Monin Benoît , Pizarro David A. , Beer Jennifer S.
Published: June 2007

Recent approaches to moral judgment have typically pitted emotion against reason. In an effort to move beyond this debate, we propose that authors presenting diverging models are considering quite different prototypical situations: those focusing on the resolution of complex dilemmas conclude that morality involves sophisticated reasoning, whereas those studying reactions to shocking moral violations find that morality involves quick, affect-laden processes. We articulate these diverging dominant approaches and consider three directions for future research (moral temptation, moral self-image, and lay understandings of morality) that we propose have not received sufficient attention as a result of the focus on these two prototypical situations within moral psychology.
Morphological and molecular characterisation of Abyssoanthus nankaiensis,, a new family, new genus and new species of deep-sea zoanthid (Anthozoa:Hexacorallia:Zoantharia) from a north-west Pacific methane cold seep
Authors: Reimer James D. , Sinniger Frederic , Fujiwara Yoshihiro , Hirano Satoshi , Maruyama Tadashi
Published: June 2007

The order Zoantharia (= Zoanthiniaria, Zoanthidea) remains one of the most taxonomically neglected anthozoan groups, primarily owing to the difficulty of examining the internal morphology of sand-encrusted zoanthids, upon which classification has been largely based until very recently. Additionally, relatively few zoanthid species (all belonging to the genus Epizoanthus) have been properly described from the deep-sea. Numerous individuals of an unidentified sediment-encrusting zoanthid-like species were observed and sampled during a Shinkai 6500 deep-sea submersible dive at a methane cold seep (depth 3259 m) off Muroto at the Nankai Trough, Japan. Unlike previously described deep-sea zoanthids, Abyssoanthus nankaiensis, gen. et sp. nov. (Abyssoanthidae fam. nov.) was found to be non-colonial, free-living (non-commensal), and, uniquely, on mudstone in the vicinity of a methane cold seep. Morphologically, A. nankaiensis, gen. et sp. nov. is characterised by its relatively uniform polyp diameter from oral to aboral end with 19–22 mesenteries. Additionally, DNA (mitochondrial 16S rDNA and mitochondrial cytochrome oxidase c subunit I DNA) sequences obtained from these samples also unambiguously place this specimen in a previously undescribed and new family within the order Zoantharia. This is the first reported zoanthid species from a methane cold seep or other so-called ‘extreme’ environment, and the first molecular characterisation of any such deep-sea zoanthid.
Genetic targeting of the kinase activity of the Met receptor in cancer cells
Authors: Arena Sabrina , Pisacane Alberto , Mazzone Massimiliano , Comoglio Paolo Maria , Bardelli Alberto
Published: June 2007

The development of kinase inhibitors is revolutionizing cancer treatment. Assessing the oncogenic potential of individual kinase activities and ensuring that a drug of interest acts by direct inhibition of its putative target kinase are clear priorities. We developed a genetic strategy to selectively inactivate the catalytic activity of kinases. This approach generates isogenic cells in which a given kinase gene is expressed but is devoid of enzymatic activity. As a model to test this approach, we chose the MET receptor, which is involved in multiple cancers and is the focus of several therapeutic efforts. The exon encoding the ATP-binding site of MET was deleted from the genome of colorectal, bladder, and endometrial cancer cells. The derivative isogenic cells expressed a kinase-inactive Met (MET-KD) and were completely unresponsive to its ligand hepatocyte growth factor (HGF), indicating the exclusivity of this ligand–receptor axis. The
in vivo
tumorigenic potential of MET-KD cells was reduced but could be partially restored by HGF, suggesting that concomitant targeting of the receptor and its ligand should be therapeutically exploited. A reportedly selective Met-kinase inhibitor (SU-11274) markedly affected the growth of MET-KD cancer cells, indicating this compound exerts its effects not only through the intended target. The genetic strategy presented here is not limited to kinase genes but could be broadly applicable to any drug/protein combination in which the target enzymatic domain is known.