Diurnal variability of inner-shelf circulation in the lee of a cape under upwelling conditions.

The nearshore circulation in the lee of a cape under upwelling conditions was studied using in-situ data from 3 consecutive summers (2006–2008). Focus was given to a period between 20 July and 04 August 2006 to study the diurnal variability of the cross-shelf circulation. This period was chosen because it had a steady upwellingfavourable wind condition modulated by a diurnal cycle much similar to sea breeze. The daily variability of the observed cross-shelf circulation consisted of three distinct periods: a morning period with a 3-layer vertical structure with onshore velocities at mid-depth, a mid-day period where the flow is reversed and has a 2-layer structure with onshore velocities at the surface and offshore flow below, and, lastly, in the evening, a 2-layer period with intensified offshore velocities at the surface and onshore flow at the bottom. The observed cross-shelf circulation showed a peculiar vertical shape and diurnal variability different from several other systems described in literature. We hypothesize that the flow reversal of the cross-shelf circulation results as a response to the rapid change of the wind magnitude and direction at mid-day with the presence of the cape north of the mooring site influencing this response. A numerical modelling experiment exclusively forced by winds simulated successfully most of the circulation at the ADCP site, especially the mid-day reversal and the evening's upwelling-type structure. This supports the hypothesis that the cross-shelf circulation at diurnal timescales is mostly wind-driven. By analysing the 3D circulation in the vicinity of Cape Sines we came to the conclusion that the diurnal variability of the wind and the flow interaction with topography are responsible for the circulation variability at the ADCP site, though only a small region in the south of the cape showed a similar diurnal variability. The fact that the wind diurnally undergoes relaxation and intensification strongly affects the circulation, promoting superficial onshore flows in the leeside of Cape Sines. Despite the small-scale nature of the observed cross-shelf circulation, onshore flows as the ones described in this study can be particularly helpful to understand the transport and settlement of larvae in this region and in other regions with similar topography and wind characteristics.We thank D. Jacinto and T. Silva for help during field work and the Port of Sines Authority (APS) for providing oceanographic and meteorological data. Financial support was provided by FCT (POCI/ MAR/57630/2004; PTDC/BIA-BEC/103734/2008 and PEst-OE/ MAR/UIO199/2011). The simulations were preformed in the computational facilities provided under FCT contract RECI/GEO-MET/0380/ 2012. Luísa Lamas was funded by the FCT under a Ph.D. grant (SFRH/ BD/69533/2010)

Pattern of reading eye movements during monovision contact lens wear in presbyopes

Monovision can be used as a method to correct presbyopia with contact lenses (CL) but its effect on reading behavior is still poorly understood. In this study eye movements (EM) were recorded in fifteen presbyopic participants, naïve to monovision, whilst they read arrays of words, non-words, and text passages to assess whether monovision affected their reading. Three conditions were compared, using daily disposable CLs: baseline (near correction in both eyes), conventional monovision (distance correction in the dominant eye, near correction in the non-dominant eye), and crossed monovision (the reversal of conventional monovision). Behavioral measures (reading speed and accuracy) and EM parameters (single fixation duration, number of fixations, dwell time per item, percentage of regressions, and percentage of skipped items) were analyzed. When reading passages, no differences in behavioral and EM measures were seen in any comparison of the three conditions. The number of fixations and dwell time significantly increased for both monovision and crossed monovision with respect to baseline only with word and non-word arrays. It appears that monovision did not appreciably alter visual processing when reading meaningful texts but some limited stress of the EM pattern was observed only with arrays of unrelated or meaningless items under monovision, which require the reader to have more in-depth controlled visual processing

An efficient algorithm for systematic analysis of nucleotide strings suitable for siRNA design

<p>Abstract</p> <p>Background</p> <p>The "off-target" silencing effect hinders the development of siRNA-based therapeutic and research applications. Existing solutions for finding possible locations of siRNA seats within a large database of genes are either too slow, miss a portion of the targets, or are simply not designed to handle a very large number of queries. We propose a new approach that reduces the computational time as compared to existing techniques.</p> <p>Findings</p> <p>The proposed method employs tree-based storage in a form of a modified truncated suffix tree to sort all possible short string substrings within given set of strings (i.e. transcriptome). Using the new algorithm, we pre-computed a list of the best siRNA locations within each human gene ("siRNA seats"). siRNAs designed to reside within siRNA seats are less likely to hybridize off-target. These siRNA seats could be used as an input for the traditional "set-of-rules" type of siRNA designing software. The list of siRNA seats is available through a publicly available database located at <url>http://web.cos.gmu.edu/~gmanyam/siRNA_db/search.php</url></p> <p>Conclusions</p> <p>In attempt to perform top-down prediction of the human siRNA with minimized off-target hybridization, we developed an efficient algorithm that employs suffix tree based storage of the substrings. Applications of this approach are not limited to optimal siRNA design, but can also be useful for other tasks involving selection of the characteristic strings specific to individual genes. These strings could then be used as siRNA seats, as specific probes for gene expression studies by oligonucleotide-based microarrays, for the design of molecular beacon probes for Real-Time PCR and, generally, any type of PCR primers.</p

Asteroseismology and Interferometry

Asteroseismology provides us with a unique opportunity to improve our understanding of stellar structure and evolution. Recent developments, including the first systematic studies of solar-like pulsators, have boosted the impact of this field of research within Astrophysics and have led to a significant increase in the size of the research community. In the present paper we start by reviewing the basic observational and theoretical properties of classical and solar-like pulsators and present results from some of the most recent and outstanding studies of these stars. We centre our review on those classes of pulsators for which interferometric studies are expected to provide a significant input. We discuss current limitations to asteroseismic studies, including difficulties in mode identification and in the accurate determination of global parameters of pulsating stars, and, after a brief review of those aspects of interferometry that are most relevant in this context, anticipate how interferometric observations may contribute to overcome these limitations. Moreover, we present results of recent pilot studies of pulsating stars involving both asteroseismic and interferometric constraints and look into the future, summarizing ongoing efforts concerning the development of future instruments and satellite missions which are expected to have an impact in this field of research.Comment: Version as published in The Astronomy and Astrophysics Review, Volume 14, Issue 3-4, pp. 217-36

Climate, history, society over the last millennium in southeast Africa

Climate variability has been causally linked to the transformation of society in pre-industrial southeast Africa. A growing critique, however, challenges the simplicity of ideas that identify climate as an agent of past societal change; arguing instead that the value of historical climate–society research lies in understanding human vulnerability and resilience, as well as how past societies framed, responded and adapted to climatic phenomena. We work across this divide to present the first critical analysis of climate–society relationships in southeast Africa over the last millennium. To achieve this, we review the now considerable body of scholarship on the role of climate in regional societal transformation, and bring forward new perspectives on climate–society interactions across three areas and periods using the theoretical frameworks of vulnerability and resilience. We find that recent advances in paleoclimatology and archaeology give weight to the suggestion that responses to climate variability played an important part in early state formation in the Limpopo valley (1000–1300), though evidence remains insufficient to clarify similar debates concerning Great Zimbabwe (1300–1450/1520). Written and oral evidence from the Zambezi-Save (1500–1830) and KwaZulu-Natal areas (1760–1828) nevertheless reveals a plurality of past responses to climate variability. These were underpinned by the organization of food systems, the role of climate-related ritual and political power, social networks, and livelihood assets and capabilities, as well as the nature of climate variability itself. To conclude, we identify new lines of research on climate, history and society, and discuss how these can more directly inform contemporary African climate adaptation challenges

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal

Activities of Rifampin, Rifapentine and Clarithromycin Alone and in Combination against Mycobacterium ulcerans Disease in Mice

Buruli ulcer (BU) is found throughout the world but is particularly prevalent in West Africa. Until 2004, treatment for this disfiguring disease was surgical excision followed by skin grafting, procedures often requiring months of hospitalization. More recently, an 8-week regimen of oral rifampin and streptomycin administered by injection has become the standard of care recommended by the World Health Organization. However, daily injections require sterile needles and syringes to prevent spread of blood borne pathogens and streptomycin has potentially serious side effects, most notably hearing loss. We tested an entirely oral regimen, substituting the long acting rifapentine for rifampin and clarithromycin for streptomycin. We also evaluated each drug separately. We found that rifapentine alone is as good as rifampin plus streptomycin, but the simultaneous addition of effective clarithromycin doses, at least in the mouse, reduces the activity of both rifampin and rifapentine, making it difficult to assess the efficacy of the oral regimens in the model. Studies of serum drug concentrations indicated that separating treatment times by one hour or reducing the clarithromycin dose to one active in humans should overcome this issue in experimental and clinical BU treatment, respectively

Gene Expression Profiling in the Type 1 Diabetes Rat Diaphragm

BACKGROUND:Respiratory muscle contractile performance is impaired by diabetes, mechanisms of which included altered carbohydrate and lipid metabolism, oxidative stress and changes in membrane electrophysiology. The present study examined to what extent these cellular perturbations involve changes in gene expression. METHODOLOGY/PRINCIPAL FINDINGS:Diaphragm muscle from streptozotocin-diabetic rats was analyzed with Affymetrix gene expression arrays. Diaphragm from diabetic rats had 105 genes with at least +/-2-fold significantly changed expression (55 increased, 50 decreased), and these were assigned to gene ontology groups based on over-representation analysis using DAVID software. There was increased expression of genes involved in palmitoyl-CoA hydrolase activity (a component of lipid metabolism) (P = 0.037, n = 2 genes, fold change 4.2 to 27.5) and reduced expression of genes related to carbohydrate metabolism (P = 0.000061, n = 8 genes, fold change -2.0 to -8.5). Other gene ontology groups among upregulated genes were protein ubiquitination (P = 0.0053, n = 4, fold change 2.2 to 3.4), oxidoreductase activity (P = 0.024, n = 8, fold change 2.1 to 6.0), and morphogenesis (P = 0.012, n = 10, fold change 2.1 to 4.3). Other downregulated gene groups were extracellular region (including extracellular matrix and collagen) (P = 0.00032, n = 13, fold change -2.2 to -3.7) and organogenesis (P = 0.032, n = 7, fold change -2.1 to -3.7). Real-time PCR confirmed the directionality of changes in gene expression for 30 of 31 genes tested. CONCLUSIONS/SIGNIFICANCE:These data indicate that in diaphragm muscle type 1 diabetes increases expression of genes involved in lipid energetics, oxidative stress and protein ubiquitination, decreases expression of genes involved in carbohydrate metabolism, and has little effect on expression of ion channel genes. Reciprocal changes in expression of genes involved in carbohydrate and lipid metabolism may change the availability of energetic substrates and thereby directly modulate fatigue resistance, an important issue for a muscle like the diaphragm which needs to contract without rest for the entire lifetime of the organism