| 1. |
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| 2. |
- Abelev, Betty, et al.
(author)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Journal article (peer-reviewed)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 3. |
- Abelev, Betty, et al.
(author)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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In: Journal of High Energy Physics. - 1029-8479. ; :11
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Journal article (peer-reviewed)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 4. |
- Abelev, Betty, et al.
(author)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
-
In: Journal of High Energy Physics. - 1029-8479. ; :7
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Journal article (peer-reviewed)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 5. |
- Bernal, Ximena E., et al.
(author)
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Empowering Latina scientists
- 2019
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 363:6429, s. 825-826
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Journal article (other academic/artistic)
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| 6. |
- Blancas-Benitez, Francisco J., et al.
(author)
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Indigestible fraction of guava fruit : Phenolic profile, colonic fermentation and effect on HT-29 cells
- 2022
-
In: Food Bioscience. - : Elsevier BV. - 2212-4292. ; 46
-
Journal article (peer-reviewed)abstract
- Guava fruit is rich in phenolic compounds (PCs), whose metabolic fate has not been explored. Non-digestible carbohydrates and PCs in whole guava (WG) and seedless guava (SG) were submitted to an in vitro colonic fermentation, followed by evaluation of the anti-proliferative activity of the fermentation extracts in HT-29 cancer cell lines. The main PCs in both samples were (+)-gallocatechin and gallic acid, while procyanidin B was the most abundant one associated with soluble indigestible fraction and quercetin predominated in the insoluble indigestible fraction. The fermentability index at 24 h was 78.84% in WG and 84.74% for SG, near to the value for raffinose used as reference, with butyric acid as the main short chain fatty acids (SCFA) produced. The greatest antiproliferative effects were observed in the SG at 12 h of fermentation and WG at 24 h of fermentation. These results allow to suggest consumption of guava fruit, either with or without seeds, as a feasible way to maintain colonic health.
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| 7. |
- Elsik, Christine G., et al.
(author)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Journal article (peer-reviewed)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 8. |
- Ermgassen, Philine S. E. Zu, et al.
(author)
-
Fishers who rely on mangroves : Modelling and mapping the global intensity of mangrove-associated fisheries
- 2021
-
In: Estuarine, Coastal and Shelf Science. - : Elsevier. - 0272-7714 .- 1096-0015. ; 248
-
Journal article (peer-reviewed)abstract
- Mangroves are critical nursery habitats for fish and invertebrates, providing livelihoods for many coastal communities. Despite their importance, there is currently no estimate of the number of fishers engaged in mangrove associated fisheries, nor of the fishing intensity associated with mangroves at a global scale. We address these gaps by developing a global model of mangrove associated fisher numbers and mangrove fishing intensity. To develop the model, we undertook a three-round Delphi process with mangrove fisheries experts to identify the key drivers of mangrove fishing intensity. We then developed a conceptual model of intensity of mangrove fishing using those factors identified both as being important and for which appropriate global data could be found or developed. These factors were non-urban population, distance to market, distance to mangroves and other fishing grounds, and storm events. By projecting this conceptual model using geospatial datasets, we were able to estimate the number and distribution of mangrove associated fishers and the intensity of fishing in mangroves. We estimate there are 4.1 million mangrove associated fishers globally, with the highest number of mangrove fishers found in Indonesia, India, Bangladesh, Myanmar, and Brazil. Mangrove fishing intensity was greatest throughout Asia, and to a lesser extent West and Central Africa, and Central and South America.
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| 9. |
- Feliciano, Gustavo T., et al.
(author)
-
Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems : A QM/MM-NEGF Approach
- 2018
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 122:2, s. 485-492
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Journal article (peer-reviewed)abstract
- The effects of the environment in nanoscopic materials can play a crucial role in device design. Particularly in biosensors, where the system is usually embedded in a solution, water and ions have to be taken into consideration in atomistic simulations of electronic transport for a realistic description of the system. In this work, we present a methodology that combines quantum mechanics/molecular mechanics methods (QM/MM) with the nonequilibrium Green’s function framework to simulate the electronic transport properties of nanoscopic devices in the presence of solvents. As a case in point, we present further results for DNA translocation through a graphene nanopore. In particular, we take a closer look into general assumptions in a previous work. For this sake, we consider larger QM regions that include the first two solvation shells and investigate the effects of adding extra k-points to the NEGF calculations. The transverse conductance is then calculated in a prototype sequencing device in order to highlight the effects of the solvent.
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| 10. |
- Feliciano, Gustavo T., et al.
(author)
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Capacitive DNA Detection Driven by Electronic Charge Fluctuations in a Graphene Nanopore
- 2015
-
In: Physical Review Applied. - 2331-7019. ; 3:3
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Journal article (peer-reviewed)abstract
- The advent of parallelized automated methods for rapid whole-genome analysis has led to an exponential drop in costs, thus greatly accelerating biomedical research and discovery. Third-generation sequencing techniques, which would utilize the characteristic electrical conductance of the four different nucleotides, could facilitate longer base read lengths and an even lower price per genome. In this work, we propose and apply a quantum-classical hybrid methodology to quantitatively determine the influence of the solvent on the dynamics of DNA and the resulting electron transport properties of a prototypic sequencing device utilizing a graphene nanopore through which the nucleic-acid chain is threaded. Our results show that charge fluctuations in the nucleotides are responsible for characteristic conductance modulations in this system, which can be regarded as a field-effect transistor tuned by the dynamic aqueous environment.
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| 11. |
- Marques, Maria, et al.
(author)
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How Remote Labs Impact on Courses Outcomes : Various Practices Using VISIR
- 2014
-
In: IEEE Transactions on Education. - : IEEE. - 0018-9359. ; 57:3, s. 151-159
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Journal article (peer-reviewed)abstract
- As technology is increasingly being seen as a facilitator to learning, open remote laboratories are increasingly available and in widespread use around the world. They provide some advantages over traditional hands-on labs or simulations. This paper presents the results of integrating the open remote laboratory VISIR into several courses, in various contexts and using various methodologies. These integrations, all related to higher education engineering, were designed by teachers with different perspectives to achieve a range of learning outcomes. The degree to which these VISIR-related outcomes were accomplished is discussed. The results reflect the levels of student engagement and learning and of teacher involvement. From the analysis, a connection between these two aspects was traced, although only related to the user profiles. VISIR is shown to be always of benefit for more motivated students, but this benefit can be maximized under particular conditions and characteristics.
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| 12. |
- Martins, Ernane de Freitas, et al.
(author)
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A multiscale approach for electronic transport simulation of carbon nanostructures in aqueous solvent
- 2022
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:39, s. 24404-24412
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Journal article (peer-reviewed)abstract
- Theoretical works addressing electronic nano-devices operating in an aqueous environment often neglect solvent effects. In order to assess the role played by the polarization effects on the electronic transport properties of solvated graphene, for example in possible bio-sensing applications, we have used here a combination of polarizable force-field molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) approach, density functional theory, and non-equilibrium Green's function method. We considered different solvation conditions, the presence of defects in graphene, as well as various choices for the partitions between the quantum and classical regions in QM/MM, in which we explicitly account for polarization effects. Our results show that the polarization effects on graphene lead to changes in the structure of interfacial water molecules which are more pronounced in the vicinity of defects. The presence of water leads to increased scattering due to the long-range charge interactions with graphene. At the same time, changes in the conductance due to polarization or salt concentration are found to be small, paving the way for robust electronic nano-devices operating in aqueous environments.
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| 13. |
- Martins, Ernane de Freitas, et al.
(author)
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Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates
- 2019
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In: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 24:5
-
Journal article (peer-reviewed)abstract
- In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green's functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.
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| 14. |
- Martins, Ernane de Freitas, et al.
(author)
-
The role of water on the electronic transport in graphene nanogap devices designed for DNA sequencing
- 2020
-
In: Carbon. - : Elsevier BV. - 0008-6223 .- 1873-3891. ; 158, s. 314-319
-
Journal article (peer-reviewed)abstract
- Innovative methodologies for reliably and inexpensively sequencing DNA can lead to a new era of personalized medicine. In this work, we performed a theoretical investigation of a nanogap-based all electronic DNA sequencing device. To do so, we used a nitrogen-terminated nanogap on a graphene sheet with the aqueous environment fully taken into account. Our investigation is performed using a hybrid methodology combining quantum and classical mechanics coupled to non-equilibrium Green's functions for solving the electron transport across the device. The obtained results show that the DNA nucleotides can be both detected and distinguished in such a device, which indicates that it can be used as a DNA sequencing device providing very high sensitivity and selectivity. Furthermore, our results show that water plays a major role in electronic transport in nanoscopic tunneling devices, not only from an electrostatics point of view, but also by providing states that significantly increase the conductance in nanogap-based DNA sequencing devices.
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| 15. |
- Moraes, Gustavo Hermínio Salati Marcondes de, et al.
(author)
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An inquiry into the linkages between university ecosystem and students’ entrepreneurial intention and self-efficacy
- 2023
-
In: Innovations in Education and Teaching International. - : Informa UK Limited. - 1470-3297 .- 1470-3300. ; 60:1, s. 134-145
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Journal article (peer-reviewed)abstract
- The purpose of this article is to evaluate the impact of university ecosystems on entrepreneurial intention and self-efficacy of Brazilian undergraduate students. The empirical exercise relies on Structural Equations Modelling based on data of 468 students from 70 universities across the country. Results indicate that traditional approaches to foment entrepreneurship are less effective than nurturing linkages between universities and the broader entrepreneurial ecosystem, and that private universities are more effective in promoting entrepreneurial behaviour. From a practical standpoint, our assessment suggests the need for universities to approach entrepreneurial education in a more flexible way, fostering interactions with businesses.
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| 16. |
- Oliveira, Aldair J., et al.
(author)
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Psychosocial and environmental determinants of physical activity in a Brazilian public university employees - ELDAF : A prospective cohort study protocol
- 2022
-
In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 17:2
-
Journal article (peer-reviewed)abstract
- BackgroundIncreased physical activity levels and their determinations are essential issues worldwide. The Longitudinal Study of Physical Activity Determinants (ELDAF) aims to understand the roles of psychosocial and environmental factors in workers’ physical activity levels.MethodsA prospective cohort study of non-faculty civil servants from a public university (approximately 1,200 individuals) will start in 2022 (baseline). The primary measurements will be accelerometer- and questionnaire-based physical activity, social support, social network, socioeconomic status, bereavement, job stress, body image, common mental disorders, depression, and neighborhood satisfaction. Additional measurements will include necessary sociodemographic, physical morbidity, lifestyle and anthropometric information. Participants’ places of residence will be geocoded using complete addresses. All participants will furnish written, informed consent before the beginning of the study. Pilot studies were performed to identify and correct potential problems in the data collection instruments and procedures. ELDAF will be the first cohort study conducted in Latin America to investigate physical activity and its determinants.
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| 17. |
- Prasongkit, Jariyanee, et al.
(author)
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Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene
- 2015
-
In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 5
-
Journal article (peer-reviewed)abstract
- Fast, cost effective, single-shot DNA sequencing could be the prelude of a new era in genetics. As DNA encodes the information for the production of proteins in all known living beings on Earth, determining the nucleobase sequences is the first and necessary step in that direction. Graphene-based nanopore devices hold great promise for next-generation DNA sequencing. In this work, we develop a novel approach for sequencing DNA using bilayer graphene to read the interlayer conductance through the layers in the presence of target nucleobases. Classical molecular dynamics simulations of DNA translocation through the pore were performed to trace the nucleobase trajectories and evaluate the interaction between the nucleobases and the nanopore. This interaction stabilizes the bases in different orientations, resulting in smaller fluctuations of the nucleobases inside the pore. We assessed the performance of a bilayer graphene nanopore setup for the purpose of DNA sequencing by employing density functional theory and non-equilibrium Green's function method to investigate the interlayer conductance of nucleobases coupling simultaneously to the top and bottom graphene layers. The obtained conductance is significantly affected by the presence of DNA in the bilayer graphene nanopore, allowing us to analyze DNA sequences.
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| 18. |
- Quaglia, Federica, et al.
(author)
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DisProt in 2022 : improved quality and accessibility of protein intrinsic disorder annotation
- 2022
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:D1, s. D480-D487
-
Journal article (peer-reviewed)abstract
- The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.
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| 19. |
- Sartelli, Massimo, et al.
(author)
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Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action
- 2023
-
In: WORLD JOURNAL OF EMERGENCY SURGERY. - 1749-7922. ; 18:1
-
Research review (peer-reviewed)abstract
- Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.
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| 20. |
- Sen, Partha, et al.
(author)
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Novel FOXF1 Mutations in Sporadic and Familial Cases of Alveolar Capillary Dysplasia with Misaligned Pulmonary Veins Imply a Role for its DNA Binding Domain
- 2013
-
In: Human Mutation. - : Hindawi Limited. - 1059-7794. ; 34:6, s. 801-811
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Journal article (peer-reviewed)abstract
- Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare and lethal developmental disorder of the lung defined by a constellation of characteristic histopathological features. Nonpulmonary anomalies involving organs of gastrointestinal, cardiovascular, and genitourinary systems have been identified in approximately 80% of patients with ACD/MPV. We have collected DNA and pathological samples from more than 90 infants with ACD/MPV and their family members. Since the publication of our initial report of four point mutations and 10 deletions, we have identified an additional 38 novel nonsynonymous mutations of FOXF1 (nine nonsense, seven frameshift, one inframe deletion, 20 missense, and one no stop). This report represents an up to date list of all known FOXF1 mutations to the best of our knowledge. Majority of the cases are sporadic. We report four familial cases of which three show maternal inheritance, consistent with paternal imprinting of the gene. Twenty five mutations (60%) are located within the putative DNA-binding domain, indicating its plausible role in FOXF1 function. Five mutations map to the second exon. We identified two additional genic and eight genomic deletions upstream to FOXF1. These results corroborate and extend our previous observations and further establish involvement of FOXF1 in ACD/MPV and lung organogenesis.
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| 21. |
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| 22. |
- zu Ermgassen, Philine S. E., et al.
(author)
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Fishers who rely on mangroves : Modelling and mapping the global intensity of mangrove-associated fisheries
- 2020
-
In: Estuarine, Coastal and Shelf Science. - : ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD. - 0272-7714 .- 1096-0015. ; 247
-
Journal article (peer-reviewed)abstract
- Mangroves are critical nursery habitats for fish and invertebrates, providing livelihoods for many coastal communities. Despite their importance, there is currently no estimate of the number of fishers engaged in mangrove associated fisheries, nor of the fishing intensity associated with mangroves at a global scale. We address these gaps by developing a global model of mangrove associated fisher numbers and mangrove fishing intensity. To develop the model, we undertook a three-round Delphi process with mangrove fisheries experts to identify the key drivers of mangrove fishing intensity. We then developed a conceptual model of intensity of mangrove fishing using those factors identified both as being important and for which appropriate global data could be found or developed. These factors were non-urban population, distance to market, distance to mangroves and other fishing grounds, and storm events. By projecting this conceptual model using geospatial data sets, we were able to estimate the number and distribution of mangrove associated fishers and the intensity of fishing in mangroves. We estimate there are 4.1 million mangrove associated fishers globally, with the highest number of mangrove fishers found in Indonesia, India, Bangladesh, Myanmar, and Brazil. Mangrove fishing intensity was greatest throughout Asia, and to a lesser extent West and Central Africa, and Central and South America.
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