bluuebunny/crossref_metadata_2025_split huggingface dataset:
Migrants and Mutineers: The Rebellion of Kong Youde and Seventeenth-Century Northeast Asia
Authors: Agnew Christopher 
Published: June 2009

AbstractThis article analyzes the 1631-33 mutiny led by Kong Youde against the Ming state on the Shandong peninsula and argues that the conflict emerged directly out of the social tensions between local populations and the displaced migrant refugees of the Bohai gulf region. The maritime integration of the Shandong coast city of Dengzhou with the commercial networks of the Liaodong peninsula and the island archipelagoes of the Bohai, together with the militarization of this regional space, created the social conditions in which Kong Youde could mobilize migrant discontent and attempt to construct his own independent military regime. Cette contribution examine la révolte de 1631-1633 dans la presqu'île de Shantung (Shangdong) mené par Kong Youde contre l'Empire Ming. L'auteur estime que ce conflit est en rapport direct avec les tensions sociales entre les populations locales et des migrants déplacés, des réfugés de la région du Golfe de Bohai. D'une part l'intégration maritime de Dengzhou, ville cotière de Shantung avec les réseaux commerciaux de la presqu'île Liaodong, et d'autre part celle avec les archipels de Bohai, ainsi que la militarisation de la région en surcroît, créèrent des conditions sociales qui permîrent à Kong Youde de mobiliser des migrants mécontants qui lui servîrent dans son régime militaire indépendant prévu.
Improving SCIPUFF Dispersion Forecasts with NWP Ensembles
Authors: Lee Jared A. , Peltier L. Joel , Haupt Sue Ellen , Wyngaard John C. , Stauffer David R. , Deng Aijun 
Published: June 2009

Abstract
The relationships between atmospheric transport and dispersion (AT&D) plume uncertainty and uncertainties in the transporting wind fields are investigated using the Second-Order Closure, Integrated Puff (SCIPUFF) AT&D model driven by numerical weather prediction (NWP) meteorological fields. Modeled contaminant concentrations for episode 1 of the 1983 Cross-Appalachian Tracer Experiment (CAPTEX-83) are compared with recorded ground-level concentrations of the inert tracer gas C7F14. This study evaluates a Taylor-diffusion-based parameterization of dispersion uncertainty for SCIPUFF that uses Eulerian meteorological ensemble velocity statistics and a Lagrangian integral time scale as input. These values are diagnosed from NWP ensemble data. Individual simulations of the tracer release fail to reproduce some of the monitored surface concentrations of the tracer. The plumes that are predicted using the uncertainty model in SCIPUFF are broader, improving the overlap between the predicted and observed results. Augmenting the meteorological input to SCIPUFF with meteorological ensemble-uncertainty parameters therefore provides both a better estimate of the expected plume location and the relative uncertainties in the predicted concentrations than single deterministic forecasts. These results suggest that this new parameterization of NWP wind field uncertainty for dispersion may provide more sophisticated information that may benefit emergency response and decision making.
Mechanisms for Spontaneous Gravity Wave Generation within a Dipole Vortex
Authors: Snyder Chris , Plougonven Riwal , Muraki David J. 
Published: June 2009

Abstract
Previous simulations of dipole vortices propagating through rotating, stratified fluid have revealed small-scale inertia–gravity waves that are embedded within the dipole near its leading edge and are approximately stationary relative to the dipole. The mechanism by which these waves are generated is investigated, beginning from the observation that the dipole can be reasonably approximated by a balanced quasigeostrophic (QG) solution. The deviations from the QG solution (including the waves) then satisfy linear equations that come from linearization of the governing equations about the QG dipole and are forced by the residual tendency of the QG dipole (i.e., the difference between the time tendency of the QG solution and that of the full primitive equations initialized with the QG fields). The waves do not appear to be generated by an instability of the balanced dipole, as homogeneous solutions of the linear equations amplify little over the time scale for which the linear equations are valid. Linear solutions forced by the residual tendency capture the scale, location, and pattern of the inertia–gravity waves, although they overpredict the wave amplitude by a factor of 2. There is thus strong evidence that the waves are generated as a forced linear response to the balanced flow. The relation to and differences from other theories for wave generation by balanced flows, including those of Lighthill and Ford et al., are discussed.
A Wave Amplitude Transition in a Quasi-Linear Model with Radiative Forcing and Surface Drag
Authors: Lachmy Orli , Harnik Nili 
Published: June 2009

Abstract
A quasi-linear two-layer quasigeostrophic β-plane model of the interaction between a baroclinic jet and a single zonal wavenumber perturbation is used to study the mechanics leading to a wave amplitude bifurcation—in particular, the role of the critical surfaces in the upper-tropospheric jet flanks. The jet is forced by Newtonian heating toward a radiative equilibrium state, and Ekman damping is applied at the surface. When the typical horizontal scale is approximately the Rossby radius of deformation, the waves equilibrate at a finite amplitude that is comparable to the mean flow. This state is obtained as a result of a wave-induced temporary destabilization of the mean flow, during which the waves grow to their finite-equilibrium amplitude. When the typical horizontal scale is wider, the model also supports a state in which the waves equilibrate at negligible amplitudes. The transition from small to finite-amplitude waves, which occurs at weak instabilities, is abrupt as the parameters of the system are gradually varied, and in a certain range of parameter values both equilibrated states are supported.
The simple two-layer quasi-linear setting of the model allows a detailed examination of the temporary destabilization process inherent in the large-amplitude equilibration. As the waves grow they reduce the baroclinic growth by reducing the vertical shear of the mean flow, and reduce the barotropic decay by reducing the mean potential vorticity gradient at the inner sides of the upper-layer critical levels. Temporary destabilization occurs when the reduction in barotropic decay is larger than the reduction in baroclinic growth, leading to a larger total growth rate. Ekman friction and radiative damping are found to play a major role in sustaining the vertical shear of the mean flow and enabling the baroclinic growth to continue. By controlling the mean flow potential vorticity gradient near the critical level, the model evolution can be changed from one type of equilibration to the other.
Can a Convective Cloud Feedback Help to Eliminate Winter Sea Ice at High CO2 Concentrations?
Authors: Abbot Dorian S. , Walker Chris C. , Tziperman Eli 
Published: June 2009

Abstract
Winter sea ice dramatically cools the Arctic climate during the coldest months of the year and may have remote effects on global climate as well. Accurate forecasting of winter sea ice has significant social and economic benefits. Such forecasting requires the identification and understanding of all of the feedbacks that can affect sea ice.
A convective cloud feedback has recently been proposed in the context of explaining equable climates, for example, the climate of the Eocene, which might be important for determining future winter sea ice. In this feedback, CO2-initiated warming leads to sea ice reduction, which allows increased heat and moisture fluxes from the ocean surface, which in turn destabilizes the atmosphere and leads to atmospheric convection. This atmospheric convection produces optically thick convective clouds and increases high-altitude moisture levels, both of which trap outgoing longwave radiation and therefore result in further warming and sea ice loss.
Here it is shown that this convective cloud feedback is active at high CO2 during polar night in the coupled ocean–sea ice–land–atmosphere global climate models used for the 1% yr−1 CO2 increase to the quadrupling (1120 ppm) scenario of the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report. At quadrupled CO2, model forecasts of maximum seasonal (March) sea ice volume are found to be correlated with polar winter cloud radiative forcing, which the convective cloud feedback increases. In contrast, sea ice volume is entirely uncorrelated with model global climate sensitivity. It is then shown that the convective cloud feedback plays an essential role in the elimination of March sea ice at quadrupled CO2 in NCAR’s Community Climate System Model (CCSM), one of the IPCC models that loses sea ice year-round at this CO2 concentration. A new method is developed to disable the convective cloud feedback in the Community Atmosphere Model (CAM), the atmospheric component of CCSM, and to show that March sea ice cannot be eliminated in CCSM at CO2 = 1120 ppm without the aide of the convective cloud feedback.
An Analysis of Tropospheric Humidity Trends from Radiosondes
Authors: McCarthy Mark P. , Thorne P. W. , Titchner H. A. 
Published: June 2009

Abstract
A new analysis of historical radiosonde humidity observations is described. An assessment of both known and unknown instrument and observing practice changes has been conducted to assess their impact on bias and uncertainty in long-term trends. The processing of the data includes interpolation of data to address known sampling bias from missing dry day and cold temperature events, a first-guess adjustment for known radiosonde model changes, and a more sophisticated ensemble of estimates based on 100 neighbor-based homogenizations. At each stage the impact and uncertainty of the process has been quantified. The adjustments remove an apparent drying over Europe and parts of Asia and introduce greater consistency between temperature and specific humidity trends from day and night observations. Interannual variability and trends at the surface are shown to be in good agreement with independent in situ datasets, although some steplike discrepancies are apparent between the time series of relative humidity at the surface.
Adjusted trends, accounting for documented and undocumented break points and their uncertainty, across the extratropical Northern Hemisphere lower and midtroposphere show warming of 0.1–0.4 K decade−1 and moistening on the order of 1%–5% decade−1 since 1970. There is little or no change in the observed relative humidity in the same period, consistent with climate model expectation of a positive water vapor feedback in the extratropics with near-constant relative humidity.
New Efficient Sparse Space–Time Algorithms for Superparameterization on Mesoscales
Authors: Xing Yulong , Majda Andrew J. , Grabowski Wojciech W. 
Published: June 2009

Abstract
Superparameterization (SP) is a large-scale modeling system with explicit representation of small-scale and mesoscale processes provided by a cloud-resolving model (CRM) embedded in each column of a large-scale model. New efficient sparse space–time algorithms based on the original idea of SP are presented. The large-scale dynamics are unchanged, but the small-scale model is solved in a reduced spatially periodic domain to save the computation cost following a similar idea applied by one of the authors for aquaplanet simulations. In addition, the time interval of integration of the small-scale model is reduced systematically for the same purpose, which results in a different coupling mechanism between the small- and large-scale models. The new algorithms have been applied to a stringent two-dimensional test suite involving moist convection interacting with shear with regimes ranging from strong free and forced squall lines to dying scattered convection as the shear strength varies. The numerical results are compared with the CRM and original SP. It is shown here that for all of the regimes of propagation and dying scattered convection, the large-scale variables such as horizontal velocity and specific humidity are captured in a statistically accurate way (pattern correlations above 0.75) based on space–time reduction of the small-scale models by a factor of ⅓; thus, the new efficient algorithms for SP result in a gain of roughly a factor of 10 in efficiency while retaining a statistical accuracy on the large-scale variables. Even the models with ⅙ reduction in space–time with a gain of 36 in efficiency are able to distinguish between propagating squall lines and dying scattered convection with a pattern correlation above 0.6 for horizontal velocity and specific humidity. These encouraging results suggest the possibility of using these efficient new algorithms for limited-area mesoscale ensemble forecasting.
Genetic evidence for a predominant role of PI3Kβ catalytic activity in ITAM- and integrin-mediated signaling in platelets
Authors: Canobbio Ilaria , Stefanini Lucia , Cipolla Lina , Ciraolo Elisa , Gruppi Cristian , Balduini Cesare , Hirsch Emilio , Torti Mauro 
Published: June 2009

Abstract
Phosphatidylinositol 3-kinase (PI3K) isoforms PI3Kβ and PI3Kγ are implicated in platelet adhesion, activation, and aggregation, but their relative contribution is still unclear or controversial. Here, we report the first comparative functional analysis of platelets from mice expressing a catalytically inactive form of PI3Kβ or PI3Kγ. We demonstrate that both isoforms were similarly required for maximal activation of the small GTPase Rap1b and for complete platelet aggregation upon stimulation of G protein–coupled receptors for adenosine 5′-diphosphate (ADP) or U46619. Their contribution to these events, however, was largely redundant and dispensable. However, PI3Kβ, but not PI3Kγ, enzymatic activity was absolutely required for Akt phosphorylation, Rap1 activation, and platelet aggregation downstream of the immunoreceptor tyrosine-based activation motif (ITAM)–bearing receptor glycoprotein VI (GPVI). Moreover, PI3Kβ was a major essential regulator of platelet adhesion to fibrinogen and of integrin αIIbβ3-mediated spreading. These results provide genetic evidence for a crucial and selective role of PI3Kβ in signaling through GPVI and integrin αIIbβ3.
Pretargeting CD45 enhances the selective delivery of radiation to hematolymphoid tissues in nonhuman primates
Authors: Green Damian J. , Pagel John M. , Nemecek Eneida R. , Lin Yukang , Kenoyer Aimee , Pantelias Anastasia , Hamlin Donald K. , Wilbur D. Scott , Fisher Darrell R. , Rajendran Joseph G. , Gopal Ajay K. , Park Steven I. , Press Oliver W. 
Published: June 2009

AbstractPretargeted radioimmunotherapy (PRIT) is designed to enhance the directed delivery of radionuclides to malignant cells. Through a series of studies in 19 nonhuman primates (Macaca fascicularis), the potential therapeutic advantage of anti-CD45 PRIT was evaluated. Anti-CD45 PRIT demonstrated a significant improvement in target-to-normal organ ratios of absorbed radiation compared with directly radiolabeled bivalent antibody (conventional radioimmunotherapy [RIT]). Radio-DOTA-biotin administered 48 hours after anti-CD45 streptavidin fusion protein (FP) [BC8 (scFv)4SA] produced markedly lower concentrations of radiation in nontarget tissues compared with conventional RIT. PRIT generated superior target:normal organ ratios in the blood, lung, and liver (10.3:1, 18.9:1, and 9.9:1, respectively) compared with the conventional RIT controls (2.6:1, 6.4:1, and 2.9:1, respectively). The FP demonstrated superior retention in target tissues relative to comparable directly radiolabeled bivalent anti-CD45 RIT. The time point of administration of the second step radiolabeled ligand (radio-DOTA-biotin) significantly impacted the biodistribution of radioactivity in target tissues. Rapid clearance of the FP from the circulation rendered unnecessary the addition of a synthetic clearing agent in this model. These results support proceeding to anti-CD45 PRIT clinical trials for patients with both leukemia and lymphoma.
Complete remission in multiple myeloma examined as time-dependent variable in terms of both onset and duration in Total Therapy protocols
Authors: Hoering Antje , Crowley John , Shaughnessy John D , Hollmig Klaus , Alsayed Yazan , Szymonifka Jackie , Waheed Sarah , Nair Bijay , van Rhee Frits , Anaissie Elias , Barlogie Bart 
Published: June 2009

AbstractLandmark analyses are used to investigate the importance for survival of achieving complete response (CR), an important initial goal of myeloma therapy. With median times to CR in Total Therapy (TT) trials of approximately 1 year, this approach excludes a sizeable fraction of patients dying before such a landmark. To permit inclusion of all trial participants, we investigated the prognostic implications of both onset and duration of CR as time-dependent variables. Superseding the adverse effects of cytogenetic abnormalities and other standard prognostic parameters, both failure to achieve CR (non-CR) and, especially, loss of CR (los-CR) were independently associated with inferior survival in TT1, TT2, and TT3 protocols. In the context of gene array–defined risk, available in TT2 and TT3 subsets, both los-CR and non-CR terms were retained in the survival model as dominant adverse variables, stressing the prognostic importance of sustaining CR status, especially in high-risk disease.
Analysis of DNA relaxation and cleavage activities of recombinant Mycobacterium tuberculosis DNA topoisomerase I from a new expression and purification protocol
Authors: Annamalai Thirunavukkarasu , Dani Neil , Cheng Bokun , Tse-Dinh Yuk-Ching 
Published: June 2009

Abstract

Background

Mycobacterium tuberculosis DNA topoisomerase I is an attractive target for discovery of novel TB drugs that act by enhancing the accumulation of the topoisomerase-DNA cleavage product. It shares a common transesterification domain with other type IA DNA topoisomerases. There is, however, no homology between the C-terminal DNA binding domains of Escherichia coli and M. tuberculosis DNA topoisomerase I proteins.

Results
A new protocol for expression and purification of recombinant M. tuberculosis DNA topoisomerase I (MtTOP) has been developed to produce enzyme of much higher specific activity than previously characterized recombinant enzyme. MtTOP was found to be less efficient than E. coli DNA topoisomerase I (EcTOP) in removal of remaining negative supercoils from partially relaxed DNA. DNA cleavage by MtTOP was characterized for the first time. Comparison of DNA cleavage site selectivity with EcTOP showed differences in cleavage site preferences, but the preferred sites of both enzymes have a C nucleotide in the -4 position.

Conclusion
Recombinant M. tuberculosis DNA topoisomerase I can be expressed as a soluble protein and purified in high yield from E. coli host with a new protocol. Analysis of DNA cleavage with M. tuberculosis DNA substrate showed that the preferred DNA cleavage sites have a C nucleotide in the -4 position.
Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes
Authors: Gao Lei , Yi Xuan , Yang Yong-Xia , Su Ying-Juan , Wang Ting 
Published: June 2009

Abstract

Background
Ferns have generally been neglected in studies of chloroplast genomics. Before this study, only one polypod and two basal ferns had their complete chloroplast (cp) genome reported. Tree ferns represent an ancient fern lineage that first occurred in the Late Triassic. In recent phylogenetic analyses, tree ferns were shown to be the sister group of polypods, the most diverse group of living ferns. Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae).

Results
The Alsophila cp genome is 156,661 base pairs (bp) in size, and has a typical quadripartite structure with the large (LSC, 86,308 bp) and small single copy (SSC, 21,623 bp) regions separated by two copies of an inverted repeat (IRs, 24,365 bp each). This genome contains 117 different genes encoding 85 proteins, 4 rRNAs and 28 tRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome. A unique trnR-UCG gene (derived from trnR-CCG) is found between rbcL and accD. The Alsophila cp genome shares some unusual characteristics with the previously sequenced cp genome of the polypod fern Adiantum capillus-veneris, including the absence of 5 tRNA genes that exist in most other cp genomes. The genome shows a high degree of synteny with that of Adiantum, but differs considerably from two basal ferns (Angiopteris evecta and Psilotum nudum). At one endpoint of an ancient inversion we detected a highly repeated 565-bp-region that is absent from the Adiantum cp genome. An additional minor inversion of the trnD-GUC, which is possibly shared by all ferns, was identified by comparison between the fern and other land plant cp genomes.

Conclusion
By comparing four fern cp genome sequences it was confirmed that two major rearrangements distinguish higher leptosporangiate ferns from basal fern lineages. The Alsophila cp genome is very similar to that of the polypod fern Adiantum in terms of gene content, gene order and GC content. However, there exist some striking differences between them: the trnR-UCG gene represents a putative molecular apomorphy of tree ferns; and the repeats observed at one inversion endpoint may be a vestige of some unknown rearrangement(s). This work provided fresh insights into the fern cp genome evolution as well as useful data for future phylogenetic studies.
Toad radiation reveals into-India dispersal as a source of endemism in the Western Ghats-Sri Lanka biodiversity hotspot
Authors: Van Bocxlaer Ines , Biju SD , Loader Simon P , Bossuyt Franky 
Published: June 2009

AbstractBackgroundHigh taxonomic level endemism in the Western Ghats-Sri Lanka biodiversity hotspot has been typically attributed to the subcontinent's geological history of long-term isolation. Subsequent out of – and into India dispersal of species after accretion to the Eurasian mainland is therefore often seen as a biogeographic factor that 'diluted' the composition of previously isolated Indian biota. However, few molecular studies have focussed on into-India dispersal as a possible source of endemism on the subcontinent. Using c. 6000 base pairs of mitochondrial and nuclear DNA, we investigated the evolutionary history and biogeography of true toads (Bufonidae), a group that colonized the Indian Subcontinent after the Indo-Asia collision.ResultsContrary to previous studies, Old World toads were recovered as a nested clade within New World Bufonidae, indicating a single colonization event. Species currently classified asAnsoniaandPedostibeswere both recovered as being non-monophyletic, providing evidence for the independent origin of torrential and arboreal ecomorphs on the Indian subcontinent and in South-East Asia. Our analyses also revealed a previously unrecognized adaptive radiation of toads containing a variety of larval and adult ecomorphs. Molecular dating estimates and biogeographic analyses indicate that the early diversification of this clade happened in the Western Ghats and Sri Lanka during the Late Oligocene to Early Miocene.ConclusionPaleoclimate reconstructions have shown that the Early Neogene of India was marked by major environmental changes, with the transition from a zonal- to the current monsoon-dominated climate. After arrival in the Western Ghats-Sri Lanka hotspot, toads diversifiedin situ, with only one lineage able to successfully disperse out of these mountains. Consequently, higher taxonomic level endemism on the Indian Subcontinent is not only the result of Cretaceous isolation, but also of invasion, isolation and radiation of new elements after accretion to the Eurasian mainland.