Microarray sub-grid detection: A novel algorithm

This is the post print version of the article. The official published version can be obtained from the link below - Copyright 2007 Taylor & Francis LtdA novel algorithm for detecting microarray subgrids is proposed. The only input to the algorithm is the raw microarray image, which can be of any resolution, and the subgrid detection is performed with no prior assumptions. The algorithm consists of a series of methods of spot shape detection, spot filtering, spot spacing estimation, and subgrid shape detection. It is shown to be able to divide images of varying quality into subgrid regions with no manual interaction. The algorithm is robust against high levels of noise and high percentages of poorly expressed or missing spots. In addition, it is proved to be effective in locating regular groupings of primitives in a set of non-microarray images, suggesting potential application in the general area of image processing

Modeling policy development: examining national governance of stem cell-based embryo models

Researchers can now coax human pluripotent stem cells to imitate the structure and spontaneous self-organization of the developing human embryo. Although these stem cell-based embryo models present an advantageous alternative to embryo research, they also raise ethical and policy challenges. In 2021, the International Society for Stem Cell Research revised its Guidelines for Stem Cell Research and Clinical Translation, providing contemporaneous best practices for ethical conduct in the field. The Guidelines complement national governance frameworks; however, they also contain contentious and aspirational norms that might catalyze change in research practice and in the enactment of national policies. Using a sample of 11 research-intensive countries, the authors compare research policy frameworks against the International Society for Stem Cell Research Guidelines to showcase how developments in global and national policies might affect stem cell-based embryo model research governance and illustrate fertile areas for ethical reflection and policy development

Mending the gaps: ethically sensitive cells and the evolution of European stem cell policy

The past decades witnessed the slow evolution of Europe's heterogeneous stem cell (SC) policy and substantial scientific advances in the field. Parallel to these developments, professional organizations have grown in influence. With the recently revised International Society for Stem Cell Research's Guidelines as a backdrop, we address the evolution of SC policies in 46 European countries and discuss how they fare against evolving ethical standards, societal views, and scientific advances. We identify areas of convergence, divergence, and the suitability of extant governance mechanisms to meet their stewardship roles. Europe represents a rich case study as it encompasses a wide range of policy approaches present worldwide. Comparative studies provide an opportunity to promote insight into national frameworks and to foster international harmonization

Light is more important than nutrient ratios of fertilization for cymodocea nodosa seedling development

Restoration of seagrass beds through seedlings is an alternative to the transplantation of adult plants that reduces the impact over donor areas and increases the genetic variability of restored meadows. To improve the use of Cymodocea nodosa seedlings, obtained from seeds germinated in vitro, in restoration programs, we investigated the ammonium and phosphate uptake rates of seedlings, and the synergistic effects of light levels (20 and 200 mu mol quanta m(-2) s(-1)) and different nitrogen to phosphorus molar ratios (40 mu M N:10 mu M P, 25 mu M N:25 mu M P, and 10 mu N:40 mu M P) on the photosynthetic activity and growth of seedlings. The nutrient content of seedlings was also compared to the seed nutrient reserves to assess the relative importance of external nutrient uptake for seedling development. Eighty two percent of the seeds germinated after 48 days at a mean rate of 1.5 seeds per day. All seedlings under all treatments survived and grew during the 4 weeks of the experiment. Seedlings of C. nodosa acquired ammonium and phosphate from the incubation media while still attached to the seed, at rates of about twice of adult plants. The relevance of external nutrient uptake was further highlighted by the observation that seedlings' tissues were richer in nitrogen and phosphorus than non-germinated seeds. The uptake of ammonium followed saturation kinetics with a half saturation constant of 32 mu M whereas the uptake of phosphate increased linearly with nutrient concentration within the range tested (5 - 100 mu M). Light was more important than the nutrient ratio of fertilization for the successful development of the young seedlings. The seedlings' photosynthetic and growth rates were about 20% higher in the high light treatment, whereas different nitrogen to phosphorus ratios did not significantly affect growth. The photosynthetic responses of the seedlings to changes in the light level and their capacity to use external nutrient sources showed that seedlings of C. nodosa have the ability to rapidly acclimate to the surrounding light and nutrient environment while still attached to the seeds. C. nodosa seedlings experiencing fertilization under low light levels showed slightly enhanced growth if nourished with a balanced formulation, whereas a slight increase in growth was also observed with unbalanced formulations under a higher light level. Our results highlight the importance of high light availability at the seedling restoration sites.Department of the Environment, Heritage and Climate Change of Gibraltar; FCT, the Portuguese Foundation for Science and Technology [SFRH/BPD/91629/2012]; FCT [UID/Multi/04326/2013

Nutrition and the ageing brain: moving towards clinical applications

The global increases in life expectancy and population have resulted in a growing ageing population and with it a growing number of people living with age-related neurodegenerative conditions and dementia, shifting focus towards methods of prevention, with lifestyle approaches such as nutrition representing a promising avenue for further development. This overview summarises the main themes discussed during the 3 Symposium on "Nutrition for the Ageing Brain: Moving Towards Clinical Applications" held in Madrid in August 2018, enlarged with the current state of knowledge on how nutrition influences healthy ageing and gives recommendations regarding how the critical field of nutrition and neurodegeneration research should move forward into the future. Specific nutrients are discussed as well as the impact of multi-nutrient and whole diet approaches, showing particular promise to combatting the growing burden of age-related cognitive decline. The emergence of new avenues for exploring the role of diet in healthy ageing, such as the impact of the gut microbiome and development of new techniques (imaging measures of brain metabolism, metabolomics, biomarkers) are enabling researchers to approach finding answers to these questions. But the translation of these findings into clinical and public health contexts remains an obstacle due to significant shortcomings in nutrition research or pressure on the scientific community to communicate recommendations to the general public in a convincing and accessible way. Some promising programs exist but further investigation to improve our understanding of the mechanisms by which nutrition can improve brain health across the human lifespan is still required

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

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

Measurement of the cross-section of high transverse momentum vector bosons reconstructed as single jets and studies of jet substructure in pp collisions at √s = 7 TeV with the ATLAS detector

This paper presents a measurement of the cross-section for high transverse momentum W and Z bosons produced in pp collisions and decaying to all-hadronic final states. The data used in the analysis were recorded by the ATLAS detector at the CERN Large Hadron Collider at a centre-of-mass energy of √s = 7 TeV;{\rm Te}{\rm V}$and correspond to an integrated luminosity of$4.6\;{\rm f}{{{\rm b}}^{-1}}$. The measurement is performed by reconstructing the boosted W or Z bosons in single jets. The reconstructed jet mass is used to identify the W and Z bosons, and a jet substructure method based on energy cluster information in the jet centre-of-mass frame is used to suppress the large multi-jet background. The cross-section for events with a hadronically decaying W or Z boson, with transverse momentum${{p}_{{\rm T}}}\gt 320\;{\rm Ge}{\rm V}$and pseudorapidity$|\eta |\lt 1.9$, is measured to be${{\sigma }_{W+Z}}=8.5\pm 1.7$ pb and is compared to next-to-leading-order calculations. The selected events are further used to study jet grooming techniques