Southern Ocean isopycnal mixing and ventilation changes driven by winds

Observed and predicted changes in the strength of the westerly winds blowing over the Southern Ocean have motivated a number of studies of the response of the Antarctic Circumpolar Current and Southern Ocean Meridional Overturning Circulation (MOC) to wind perturbations and led to the discovery of the``eddy-compensation" regime, wherein the MOC becomes insensitive to wind changes. In addition to the MOC, tracer transport also depends on mixing processes. Here we show, in a high-resolution process model, that isopycnal mixing by mesoscale eddies is strongly dependent on the wind strength. This dependence can be explained by mixing-length theory and is driven by increases in eddy kinetic energy; the mixing length does not change strongly in our simulation. Simulation of a passive ventilation tracer (analogous to CFCs or anthropogenic CO$_2$) demonstrates that variations in tracer uptake across experiments are dominated by changes in isopycnal mixing, rather than changes in the MOC. We argue that, to properly understand tracer uptake under different wind-forcing scenarios, the sensitivity of isopycnal mixing to winds must be accounted for.

Climate-driven expansion of blanket bogs in Britain during the Holocene

Blanket bog occupies approximately 6% of the area of the UK today. The Holocene expansion of this hyperoceanic biome has previously been explained as a consequence of Neolithic forest clearance. However, the present distribution of blanket bog in Great Britain can be predicted accurately with a simple model (PeatStash) based on summer temperature and moisture index thresholds, and the same model correctly predicts the highly disjunct distribution of blanket bog worldwide. This finding suggests that climate, rather than land-use history, controls blanket-bog distribution in the UK and everywhere else. We set out to test this hypothesis for blanket bogs in the UK using bioclimate envelope modelling compared with a database of peat initiation age estimates. We used both pollen-based reconstructions and climate model simulations of climate changes between the mid-Holocene (6000 yr BP, 6 ka) and modern climate to drive PeatStash and predict areas of blanket bog. We compiled data on the timing of blanketbog initiation, based on 228 age determinations at sites where peat directly overlies mineral soil. The model predicts that large areas of northern Britain would have had blanket bog by 6000 yr BP, and the area suitable for peat growth extended to the south after this time. A similar pattern is shown by the basal peat ages and new blanket bog appeared over a larger area during the late Holocene, the greatest expansion being in Ireland,Wales, and southwest England, as the model predicts. The expansion was driven by a summer cooling of about 2 °C, shown by both pollen-based reconstructions and climate models. The data show early Holocene (pre- Neolithic) blanket-bog initiation at over half of the sites in the core areas of Scotland and northern England. The temporal patterns and concurrence of the bioclimate model predictions and initiation data suggest that climate change provides a parsimonious explanation for the early Holocene distribution and later expansion of blanket bogs in the UK, and it is not necessary to invoke anthropogenic activity as a driver of this major landscape change.

MOLES3: implementing an ISO standards driven data catalogue

ISO19156 Observations and Measurements (O&M) provides a standardised framework for organising information about the collection of information about the environment. Here we describe the implementation of a specialisation of O&M for environmental data, the Metadata Objects for Linking Environmental Sciences (MOLES3). MOLES3 provides support for organising information about data, and for user navigation around data holdings. The implementation described here, “CEDA-MOLES”, also supports data management functions for the Centre for Environmental Data Archival, CEDA. The previous iteration of MOLES (MOLES2) saw active use over five years, being replaced by CEDA-MOLES in late 2014. During that period important lessons were learnt both about the information needed, as well as how to design and maintain the necessary information systems. In this paper we review the problems encountered in MOLES2; how and why CEDA-MOLES was developed and engineered; the migration of information holdings from MOLES2 to CEDA-MOLES; and, finally, provide an early assessment of MOLES3 (as implemented in CEDA-MOLES) and its limitations. Key drivers for the MOLES3 development included the necessity for improved data provenance, for further structured information to support ISO19115 discovery metadata export (for EU INSPIRE compliance), and to provide appropriate fixed landing pages for Digital Object Identifiers (DOIs) in the presence of evolving datasets. Key lessons learned included the importance of minimising information structure in free text fields, and the necessity to support as much agility in the information infrastructure as possible without compromising on maintainability both by those using the systems internally and externally (e.g. citing in to the information infrastructure), and those responsible for the systems themselves. The migration itself needed to ensure continuity of service and traceability of archived assets.

The supernova remnant CTB 37B and its associated magnetar CXOU J171405.7-381031: evidence for a magnetar-driven remnant

We discuss the association between the candidate magnetar CXOU J171405.7-381031 and the supernova remnant CTB 37B. The recent detection of the period derivative of the object allowed an estimation of a young characteristic age of only similar to 1000 yr. This value is too small to be compatible even with the minimum radius of the remnant being >= 10 pc, the value corresponding to the lower limit of the estimated distance of 10.2 +/- 3.5 kpc, unless the true distance happens to be even smaller than the lower limit. We argue that a consistent scenario for the remnant`s origin, in which the latter is powered by the energy injected by a young magnetar, is indeed more accurate to explain the young age, and demonstrates its non-standard (i.e. magnetar-driven) nature.

Protein identification pipeline for the homology-driven proteomics

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.

Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair

Recurrent submicroscopic genomic copy number changes are the result of nonallelic homologous recombination (NAHR). Nonrecurrent aberrations, however, can result from different nonexclusive recombination-repair mechanisms. We previously described small microduplications at Xq28 containing MECP2 in four male patients with a severe neurological phenotype. Here, we report on the fine-mapping and breakpoint analysis of 16 unique microduplications. The size of the overlapping copy number changes varies between 0.3 and 2.3 Mb, and FISH analysis on three patients demonstrated a tandem orientation. Although eight of the 32 breakpoint regions coincide with low-copy repeats, none of the duplications are the result of NAHR. Bioinformatics analysis of the breakpoint regions demonstrated a 2.5-fold higher frequency of Alu interspersed repeats as compared with control regions, as well as a very high GC content (53%). Unexpectedly, we obtained the junction in only one patient by long-range PCR, which revealed nonhomologous end joining as the mechanism. Breakpoint analysis in two other patients by inverse PCR and subsequent array comparative genomic hybridization analysis demonstrated the presence of a second duplicated region more telomeric at Xq28, of which one copy was inserted in between the duplicated MECP2 regions. These data suggest a two-step mechanism in which part of Xq28 is first inserted near the MECP2 locus, followed by breakage-induced replication with strand invasion of the normal sister chromatid. Our results indicate that the mechanism by which copy number changes occur in regions with a complex genomic architecture can yield complex rearrangements.

Retinoic acid inhibits dendritic cell differentiation driven by interleukin-4

All-trans-retinoic acid (atRA) appears to affect Th1-Th2 differentiation and its effects on immune responses might also be mediated by dendritic cell (DC). Nonetheless, studies have been showing contradictory results since was observed either induction or inhibition of DC differentiation. Our aim was to investigate atRA action on human monocyte derived DC differentiation. For this purpose we tested pharmacological and physiological doses of atRA with or without cytokines. Cell phenotypes were analyzed by flow cytometry and function was investigated by phagocytosis and respiratory burst. DC, positive control group, was differentiated with GM-CSF and IL-4 and maturated with TNF-alpha. We demonstrated that atRA effects depend on the dose used as pharmacological doses inhibited expression of all phenotypic markers tested while a physiological dose caused cell differentiation. However, atRA combined or not with cytokines did not promote DC differentiation. In fact, atRA was detrimental on IL-4 property as a DC inductor. (C) 2009 Elsevier Inc. All rights reserved.

Development of an adenoviral vector with robust expression driven by p53

Here we introduce a new adenoviral vector where transgene expression is driven by p53. We first developed a synthetic promoter, referred to as PGTx beta containing a p53-responsive element, a minimal promoter and the first intron of the rabbit P-globin gene. Initial assays using plasmid-based vectors indicated that expression was tightly controlled by p53 and was 5-fold stronger than the constitutive CMV immediate early promoter/enhancer. The adenoviral vector, AdPG, was also shown to offer p53-responsive expression in prostate carcinoma cells LNCaP (wt p53), DU-145 (temperature sensitive mutant of p53) and PC3 (p53-null, but engineered to express temperature-sensitive p53 mutants). AdPG served as a sensor of p53 activity in LNCaP cells treated with chemotherapeutic agents. Since p53 can be induced by radiotherapy and chemotherapy, this new vector could be further developed for use in combination with conventional therapies to bring about cooperation between the genetic and pharmacologic treatment modalities. (c) 2007 Elsevier Inc. All rights reserved.

Preventive and curative glycoside kaempferol treatments attenuate the TH2-driven allergic airway disease

Asthma is a chronic respiratory disease characterized by airway inflammation and airway hyperresponsiveness (AHR). One strategy to treat allergic diseases is the development of new drugs. Flavonoids are compounds derived from plants and are known to have antiallergic, anti-inflammatory, and antioxidant properties. To investigate whether the flavonoid kaempferol glycoside 3-O-[beta-D-glycopiranosil-(1 -> 6)-alpha-L-ramnopiranosil]-7-O-alpha-L-ramnopiranosil-kaempferol (GRRK) would be capable of modulating allergic airway disease (AAD) either as a preventive (GRRK P) or curative (GRRK C) treatment in an experimental model of asthma. At weekly intervals, BALB/c mice were subcutaneously (sc) sensitized twice with ovalbumin (OVA)/alum and challenged twice with OVA administered intranasally. To evaluate any preventive effects GRRK was administered 1 h (hour) before each OVA-sensitization and challenge, while to analyze the curative effects mice were first sensitized with OVA, followed by GRRK given at day 18 through 21. The onset: of AAD was evaluated 24 h after the last OVA challenge. Both treatments resulted in a dose-dependent reduction in total leukocyte and eosinophil counts in the bronchoalveolar lavage fluid (BAL). GRRK also decreased CD4(+), B220(+), MHC class II and CD40 molecule expressions in BAL cells. Histology and lung mechanic showed that GRRK suppressed mucus production and ameliorated the AHR induced by OVA challenge. Furthermore, GRRK impaired Th2 cytokine production (IL-5 and IL-13) and did not induce a Th1 pattern of inflammation. These findings demonstrate that GRRK treatment before or after established allergic lung disease down-regulates key asthmatic features. Therefore. GRRK has a potential clinical use for the treatment of allergic asthma. (C) 2009 Elsevier B.V. All rights reserved.

An approach for solving the lot-sizing problem of a market-driven foundry

Foundries can be found all over Brazil and they are very important to its economy. In 2008, a mixed integer-programming model for small market-driven foundries was published, attempting to minimize delivery delays. We undertook a study of that model. Here, we present a new approach based on the decomposition of the problem into two sub-problems: production planning of alloys and production planning of items. Both sub-problems are solved using a Lagrangian heuristic based on transferences. An important aspect of the proposed heuristic is its ability to take into account a secondary practice objective solution: the furnace waste. Computational tests show that the approach proposed here is able to generate good quality solutions that outperform prior results. Journal of the Operational Research Society (2010) 61, 108-114. doi:10.1057/jors.2008.151

Fault Coverage-Driven Incremental Test Generation

In this paper, we consider a classical problem of complete test generation for deterministic finite-state machines (FSMs) in a more general setting. The first generalization is that the number of states in implementation FSMs can even be smaller than that of the specification FSM. Previous work deals only with the case when the implementation FSMs are allowed to have the same number of states as the specification FSM. This generalization provides more options to the test designer: when traditional methods trigger a test explosion for large specification machines, tests with a lower, but yet guaranteed, fault coverage can still be generated. The second generalization is that tests can be generated starting with a user-defined test suite, by incrementally extending it until the desired fault coverage is achieved. Solving the generalized test derivation problem, we formulate sufficient conditions for test suite completeness weaker than the existing ones and use them to elaborate an algorithm that can be used both for extending user-defined test suites to achieve the desired fault coverage and for test generation. We present the experimental results that indicate that the proposed algorithm allows obtaining a trade-off between the length and fault coverage of test suites.

Spallation product distributions and neutron multiplicities for accelerator-driven system using the CRISP code

Neutron multiplicities for several targets and spallation products of proton-induced reactions in thin targets of interest to an accelerator-driven system obtained with the CRISP code have been reported. This code is a Monte Carlo calculation that simulates the intranuclear cascade and evaporationl fission competition processes. Results are compared with experimental data, and agreement between each other can be considered quite satisfactory in a very broad energy range of incitant particles and different targets.

The dynamics of cargo driven by molecular motors in the context of asymmetric simple exclusion processes

We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of ail asymmetric simple exclusion process (ASEP). The model is formulated to account for (i) excluded-volume interactions, (ii) the observed asymmetry of the stochastic movement of individual motors and (iii) interactions between motors and cargo. Items (i) and (ii) form the basis of ASEP models and have already been considered to study the behavior of motor density profile [A. Parmeggiani. T. Franosch, E. Frey, Phase Coexistence in driven one-dimensional transport, Phys. Rev. Lett. 90 (2003) 086601-1-086601-4]. Item (iii) is new. It is introduced here as an attempt to describe explicitly the dependence of cargo movement on the dynamics of motors in this context. The steady-state Solutions Of the model indicate that the system undergoes a phase transition of condensation type as the motor density varies. We study the consequences of this transition to the behavior of the average cargo velocity. (C) 2009 Elsevier B.V. All rights reserved.

Orbitally driven east-west antiphasing of South American precipitation

The variations of tropical precipitation are antiphased between the hemispheres on orbital timescales. This antiphasing arises through the alternating strength of incoming solar radiation in the two hemispheres, which affects monsoon intensity and hence the position of the meridional atmospheric circulation of the Hadley cells(1-4). Here we compare an oxygen isotopic record recovered from a speleothem from northeast Brazil for the past 26,000 years with existing reconstructions of precipitation in tropical South America(5-8). During the Holocene, we identify a similar, but zonally oriented, antiphasing of precipitation within the same hemisphere: northeast Brazil experiences humid conditions during low summer insolation and aridity when summer insolation is high, whereas the rest of southern tropical South America shows opposite characteristics. Simulations with a general circulation model that incorporates isotopic variations support this pattern as well as the link to insolation-driven monsoon activity. Our results suggest that convective heating over tropical South America and associated adjustments in large-scale subsidence over northeast Brazil lead to a remote forcing of the South American monsoon, which determines most of the precipitation changes in the region on orbital timescales.