Tatajuba: exploring the distribution of homopolymer tracts.

Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialized bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and help predict their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source licence GNU GPLv3

Tatajuba: exploring the distribution of homopolymer tracts.

Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialized bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and help predict their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source licence GNU GPLv3

ESCADARIAS DE TERRAÇOS MARINHOS EM PORTUGAL CENTROOCIDENTAL – RELEVÂNCIA COMO INDICADORES DE SOERGUIMENTO CRUSTAL STAIRCASES OF WAVE-CUT PLATFORMS IN WESTERN CENTRAL PORTUGAL – RELEVANCE AS INDICATORS OF CRUSTAL UPLIFT

This study addresses the coastal terrace staircases of western central Portugal (Cape Mondego to Cape Espichel). Below the culminant marine unit that records the last episode of aggradation before the ongoing stage of incision, several terrace levels ar identified. The following methodology was used: a) production of geomorphological maps, combining analysis of detailed MDT’s and aerial photos, with field surveys calibrated with GPS; b) stratigraphic and sedimentological study of the sedimentary deposits associated with the marine platforms; c) luminescence dating. On each terrace staircase, the number of platforms and their elevations are different, indicating differential uplift. Quartz OSL provided age estimates up ca. 150 kyr and post-IR IRSL on K-feldspar up to ca. 700 kyr for the marine terraces under study. Using the culminant platform as reference and assuming that it is ca. 3.6 Ma old, uplift rates were estimated as ranging spatially from 0.071 m/ky to 0.019 m/ky. The ongoing luminescence dating will provide uplift rates estimated for the lower and middle marineterraces, clarifying if an acceleration of the crustal uplift is going on

Fast spin exchange between two distant quantum dots

The Heisenberg exchange interaction between neighboring quantum dots allows precise voltage control over spin dynamics, due to the ability to precisely control the overlap of orbital wavefunctions by gate electrodes. This allows the study of fundamental electronic phenomena and finds applications in quantum information processing. Although spin-based quantum circuits based on short-range exchange interactions are possible, the development of scalable, longer-range coupling schemes constitutes a critical challenge within the spin-qubit community. Approaches based on capacitative coupling and cavity-mediated interactions effectively couple spin qubits to the charge degree of freedom, making them susceptible to electrically-induced decoherence. The alternative is to extend the range of the Heisenberg exchange interaction by means of a quantum mediator. Here, we show that a multielectron quantum dot with 50-100 electrons serves as an excellent mediator, preserving speed and coherence of the resulting spin-spin coupling while providing several functionalities that are of practical importance. These include speed (mediated two-qubit rates up to several gigahertz), distance (of order of a micrometer), voltage control, possibility of sweet spot operation (reducing susceptibility to charge noise), and reversal of the interaction sign (useful for dynamical decoupling from noise).Comment: 6 pages including 4 figures, plus 8 supplementary pages including 5 supplementary figure

Association Between Sarcopenia and Functional Status in Liver Transplant Patients

OBJECTIVES: A growing body of evidence shows that frailty and functional performance predict liver transplant outcomes. The Organ Procurement and Transplant Network uses the Karnofsky Performance Status scale to adjust for transplant center case mix in assessing quality measures. This study explores the strength of the relationship between Karnofsky Performance Status scores and objective measures of frailty. MATERIALS AND METHODS: This observational study includes 136 adult, first-time liver transplant recipients at UMass Memorial (2006-2015) who had 2 abdominal computed tomography scans available (at \u3c /= 90 days pretransplant and \u3e /= 7 days before that). We analyzed the relationship between Karnofsky Performance Status and muscle wasting using absolute and change in psoas muscle size and quality pretransplant. RESULTS: The mean age was 55 years, mean Model for End-Stage Liver Disease was 22, and 34% of patients were women. In the study group, 50% of patients had sarcopenia pretransplant and 71.3% demonstrated declined lean psoas area at an average rate of 11% per month. Patients who experienced muscle wasting at a rate of \u3e /= 1% per month had 2.83 times the risk (95% confidence interval, 1.18-6.80) of being severely impaired/disabled pretransplant. The risk increased by 2.32-fold (95% confidence interval, 1.44-3.75) for every standard deviation decrease in pretransplant lean psoas area. CONCLUSIONS: Provider-assessed physical health status moderately correlates with objective measures of frailty

Note on the Existence of Hydrogen Atoms in Higher Dimensional Euclidean Spaces

The question of whether hydrogen atoms can exist or not in spaces with a number of dimensions greater than 3 is revisited, considering higher dimensional Euclidean spaces. Previous results which lead to different answers to this question are briefly reviewed. The scenario where not only the kinematical term of Schr\"odinger equation is generalized to a D-dimensional space but also the electric charge conservation law (expressed here by the Poisson law) should actually remains valid is assumed. In this case, the potential energy in the Schr\"odinger equation goes like 1/r^{D-2}. The lowest quantum mechanical bound states and the corresponding wave functions are determined by applying the Numerov numerical method to solve Schr\"odinger's eigenvalue equation. States for different angular momentum quantum number (l = 0; 1) and dimensionality (5 \leq D \leq 10) are considered. One is lead to the result that hydrogen atoms in higher dimensions could actually exist. For the same range of the dimensionality D, the energy eigenvalues and wave functions are determined for l = 1. The most probable distance between the electron and the nucleus are then computed as a function of D showing the possibility of tiny bound states.Comment: 19 pages, 6 figure

Ozone Profiles in the Baltimore-Washington Region (2006-2011): Satellite Comparisons and DISCOVER-AQ Observations

Much progress has been made in creating satellite products for tracking the pollutants ozone and NO2 in the troposphere. Yet, in mid-latitude regions where meteorological interactions with pollutants are complex, accuracy can be difficult to achieve, largely due to persistent layering of some constituents. We characterize the layering of ozone soundings and related species measured from aircraft over two ground sites in suburban Washington, DC (Beltsville, MD, 39.05N; 76.9W) and Baltimore (Edgewood, MD, 39.4N; 76.3W) during the July 2011 DISCOVER-AQ (Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality) experiment. First, we compare column-ozone amounts from the Beltsville and Edgewood sondes with data from overpassing satellites. Second, processes influencing ozone profile structure are analyzed using Laminar Identification and tracers: sonde water vapor, aircraft CO and NOy. Third, Beltsville ozone profiles and meteorological influences in July 2011 are compared to those from the summers of 2006-2010. Sonde-satellite offsets in total ozone during July 2011 at Edgewood and Beltsville, compared to the Ozone Monitoring Instrument (OMI), were 3 percent mean absolute error, not statistically significant. The disagreement between an OMIMicrowave Limb Sounder-based tropospheric ozone column and the sonde averaged 10 percent at both sites, with the sonde usually greater than the satellite. Laminar Identification (LID), that distinguishes ozone segments influenced by convective and advective transport, reveals that on days when both stations launched ozonesondes, vertical mixing was stronger at Edgewood. Approximately half the lower free troposphere sonde profiles have very dry laminae, with coincident aircraft spirals displaying low CO (80-110 ppbv), suggesting stratospheric influence. Ozone budgets at Beltsville in July 2011, determined with LID, as well as standard meteorological indicators, resemble those of 4 of the previous 5 summers. The penetration of stratospheric air throughout the troposphere appears to be typical for summer conditions in the Baltimore-Washington region

Estimating HIV incidence and number of undiagnosed individuals living with HIV in the European Union/European Economic Area, 2015

Helena Cortes Martins, Departamento de Doenças Infeciosas do Instituto Nacional de Saúde Doutor Ricardo Jorge, IPSince 2011, human immunodeficiency virus (HIV) incidence appears unchanged in the European Union/European Economic Area with between 29,000 and 33,000 new cases reported annually up to 2015. Despite evidence that HIV diagnosis is occurring earlier post-infection, the estimated number of people living with HIV (PLHIV) who were unaware of being infected in 2015 was 122,000, or 15% of all PLHIV (n=810,000). This is concerning as such individuals cannot benefit from highly effective treatment and may unknowingly sustain transmission.Members of the ECDC HIV/AIDS Surveillance and Dublin Declaration Monitoring Networks: Portugal: Kamal Mansinho, Helena Cortes Martins, Teresa Melo.info:eu-repo/semantics/publishedVersio

Striatal Dopamine Transporter Function Is Facilitated by Converging Biology of α-Synuclein and Cholesterol

Striatal dopamine transporters (DAT) powerfully regulate dopamine signaling, and can contribute risk to degeneration in Parkinson’s disease (PD). DATs can interact with the neuronal protein α-synuclein, which is associated with the etiology and molecular pathology of idiopathic and familial PD. Here, we tested whether DAT function in governing dopamine (DA) uptake and release is modified in a human-α-synuclein-overexpressing (SNCA-OVX) transgenic mouse model of early PD. Using fast-scan cyclic voltammetry (FCV) in ex vivo acute striatal slices to detect DA release, and biochemical assays, we show that several aspects of DAT function are promoted in SNCA-OVX mice. Compared to background control α-synuclein-null mice (Snca-null), the SNCA-OVX mice have elevated DA uptake rates, and more pronounced effects of DAT inhibitors on evoked extracellular DA concentrations ([DA] ) and on short-term plasticity (STP) in DA release, indicating DATs play a greater role in limiting DA release and in driving STP. We found that DAT membrane levels and radioligand binding sites correlated with α-synuclein level. Furthermore, DAT function in Snca-null and SNCA-OVX mice could also be promoted by applying cholesterol, and using Tof-SIMS we found genotype-differences in striatal lipids, with lower striatal cholesterol in SNCA-OVX mice. An inhibitor of cholesterol efflux transporter ABCA1 or a cholesterol chelator in SNCA-OVX mice reduced the effects of DAT-inhibitors on evoked [DA] . Together these data indicate that human α-synuclein in a mouse model of PD promotes striatal DAT function, in a manner supported by extracellular cholesterol, suggesting converging biology of α-synuclein and cholesterol that regulates DAT function and could impact DA function and PD pathophysiology

Strategies to improve retention in randomised trials

Acknowledgements We thank Jayne Tierney, Sally Stenning, Seeromanie Harding, Sarah Meredith, and Irwin Nazareth for their contributions to earlier versions of this review. We also thank all authors of included published studies who provided additional or unreported data and Principal investigators for data on studies in progress or completed and unpublished. This update was funded by a National Institute for Health Research (NIHR) Incentive Award Scheme 2019 Reference 130660. The Health Services Research Unit, University of Aberdeen receives core funding from the Chief Scientist Office of the Scottish Government Health Directorates. The views expressed in this review are those of the authors and do not necessarily reflect those of the NIHR, the Department of Health and Social Care or these other funders. Sources of support Internal sources: No sources of support supplied External sources: National Institue for Health Research Incentive Award, UK; This update was funded by a National Institue for Health Research Incentive Award [NIHR IA 130660].Peer reviewedPublisher PD