| 1. |
- Abercrombie, Daniel, et al.
(author)
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Dark Matter benchmark models for early LHC Run-2 Searches : Report of the ATLAS/CMS Dark Matter Forum
- 2020
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In: Physics of the Dark Universe. - : Elsevier BV. - 2212-6864. ; 27
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Journal article (peer-reviewed)abstract
- This document is the final report of the ATLAS-CMS Dark Matter Forum, a forum organized by the ATLAS and CMS collaborations with the participation of experts on theories of Dark Matter, to select a minimal basis set of dark matter simplified models that should support the design of the early LHC Run-2 searches. A prioritized, compact set of benchmark models is proposed, accompanied by studies of the parameter space of these models and a repository of generator implementations. This report also addresses how to apply the Effective Field Theory formalism for collider searches and present the results of such interpretations.
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| 2. |
- Hillier, Ladeana W, et al.
(author)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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In: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Journal article (peer-reviewed)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 3. |
- Broadbent, Jeffrey, et al.
(author)
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Conflicting Climate Change Frames in a Global Field of Media Discourse
- 2016
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In: Socius: Sociological Research for a Dynamic World. - : SAGE Publications. - 2378-0231. ; 1:1
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Journal article (peer-reviewed)abstract
- Reducing global emissions will require a global cosmopolitan culture built from detailed attention to conflicting national climate change frames (interpretations) in media discourse. The authors analyze the global field of media climate change discourse using 17 diverse cases and 131 frames. They find four main conflicting dimensions of difference: validity of climate science, scale of ecological risk, scale of climate politics, and support for mitigation policy. These dimensions yield four clusters of cases producing a fractured global field. Positive values on the dimensions show modest association with emissions reductions. Data-mining media research is needed to determine trends in this global field.
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| 4. |
- Diaz, Sandra, et al.
(author)
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The IPBES Conceptual Framework - connecting nature and people
- 2015
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In: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 14, s. 1-16
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Journal article (peer-reviewed)abstract
- The first public product of the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) is its Conceptual Framework. This conceptual and analytical tool, presented here in detail, will underpin all IPBES functions and provide structure and comparability to the syntheses that IPBES will produce at different spatial scales, on different themes, and in different regions. Salient innovative aspects of the IPBES Conceptual Framework are its transparent and participatory construction process and its explicit consideration of diverse scientific disciplines, stakeholders, and knowledge systems, including indigenous and local knowledge. Because the focus on co-construction of integrative knowledge is shared by an increasing number of initiatives worldwide, this framework should be useful beyond IPBES, for the wider research and knowledge-policy communities working on the links between nature and people, such as natural, social and engineering scientists, policy-makers at different levels, and decision-makers in different sectors of society.
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| 5. |
- Fomalont, E. B., et al.
(author)
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THE 2014 ALMA LONG BASELINE CAMPAIGN: AN OVERVIEW
- 2015
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In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 808:1
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Journal article (peer-reviewed)abstract
- A major goal of the Atacama Large Millimeter/submillimeter Array (ALMA) is to make accurate images with resolutions of tens of milliarcseconds, which at submillimeter (submm) wavelengths requires baselines up to similar to 15 km. To develop and test this capability, a Long Baseline Campaign (LBC) was carried out from 2014 September to late November, culminating in end-to-end observations, calibrations, and imaging of selected Science Verification (SV) targets. This paper presents an overview of the campaign and its main results, including an investigation of the short-term coherence properties and systematic phase errors over the long baselines at the ALMA site, a summary of the SV targets and observations, and recommendations for science observing strategies at long baselines. Deep ALMA images of the quasar 3C 138 at 97 and 241 GHz are also compared to VLA 43 GHz results, demonstrating an agreement at a level of a few percent. As a result of the extensive program of LBC testing, the highly successful SV imaging at long baselines achieved angular resolutions as fine as 19 mas at similar to 350 GHz. Observing with ALMA on baselines of up to 15 km is now possible, and opens up new parameter space for submm astronomy.
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| 6. |
- Gagnon, Keith T., et al.
(author)
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Allele-Selective Inhibition of Mutant Huntingtin Expression with Antisense Oligonucleotides Targeting the Expanded CAG Repeat
- 2010
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In: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 49:47, s. 10166-10178
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Journal article (peer-reviewed)abstract
- Huntington's disease (HD) is a currently incurable neurodegenerative disease caused by the expansion of a CAG trinucleotide repeat within the huntingtin (HTT) gene. Therapeutic approaches include selectively inhibiting the expression of the mutated HTT allele while conserving function of the normal allele. We have evaluated a series of antisense oligonucleotides (ASOs) targeted to the expanded CAG repeat within HTT mRNA for their ability to selectively inhibit expression of mutant HTT protein. Several ASOs incorporating a variety of modifications, including bridged nucleic acids and phosphorothioate internucleotide linkages, exhibited allele-selective silencing in patient-derived fibroblasts. Allele-selective ASOs did not affect the expression of other CAG repeat-containing genes and selectivity was observed in cell lines containing minimal CAG repeat lengths representative of most HD patients. Allele-selective ASOs left HTT mRNA intact and did not support ribonuclease H activity in vitro. We observed cooperative binding of multiple ASO molecules to CAG repeat-containing HTT mRNA transcripts in vitro. These results are consistent with a mechanism involving inhibition at the level of translation. ASOs targeted to the CAG repeat of HTT provide a starting point for the development of oligonucleotide-based therapeutics that can inhibit gene expression with allelic discrimination in patients with HD.
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| 7. |
- Hu, Jiaxin, et al.
(author)
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Allele-selective inhibition of ataxin-3 (ATX3) expression by antisense oligomers and duplex RNAs
- 2011
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In: Biological chemistry (Print). - 1431-6730 .- 1437-4315. ; 392:4, s. 315-325
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Journal article (peer-reviewed)abstract
- Spinocerebellar ataxia-3 (also known as Machado-Joseph disease) is an incurable neurodegenerative disorder caused by expression of a mutant variant of ataxin-3 (ATX3) protein. Inhibiting expression of ATX3 would provide a therapeutic strategy, but indiscriminant inhibition of both wild-type and mutant ATX3 might lead to undesirable side effects. An ideal silencing agent would block expression of mutant ATX3 while leaving expression of wild-type ATX3 intact. We have previously observed that peptide nucleic acid (PNA) conjugates targeting the expanded CAG repeat within ATX3 mRNA block expression of both alleles. We have now identified additional PNAs capable of inhibiting ATX3 expression that vary in length and in the nature of the conjugated cation chain. We can also achieve potent and selective inhibition using duplex RNAs containing one or more mismatches relative to the CAG repeat. Anti-CAG antisense bridged nucleic acid oligonucleotides that lack a cationic domain are potent inhibitors but are not allele-selective. Allele-selective inhibitors of ATX3 expression provide insights into the mechanism of selectivity and promising lead compounds for further development and in vivo investigation.
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| 8. |
- Mohammed Taha, Hiba, et al.
(author)
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The NORMAN Suspect List Exchange (NORMAN-SLE) : facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
- 2022
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In: Environmental Sciences Europe. - : Springer. - 2190-4707 .- 2190-4715. ; 34:1
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Journal article (peer-reviewed)abstract
- Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/).
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| 9. |
- Staples, Richard, et al.
(author)
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Structure and Chemical Analysis of Major Specialized Metabolites Produced by the Lichen Evernia prunastri
- 2020
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In: Chemistry and Biodiversity. - : Wiley. - 1612-1872 .- 1612-1880. ; 17:1
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Journal article (peer-reviewed)abstract
- We performed comparative profiling of four specialized metabolites in the lichen Evernia prunastri, collected at three different geographic locations, California and Maine, USA, and Yoshkar Ola, Mari El, Russia. Among the compounds produced at high concentrations that were identified in all three specimens, evernic acid, usnic acid, lecanoric acid and chloroatranorin, evernic acid was the most abundant. Two depsidones, salazinic acid and physodic acid, were detected in the Yoshkar‐Ola collection only. The crystalline structure of evernic acid (2‐hydroxy‐4‐[(2‐hydroxy‐4‐methoxy‐6‐methylbenzoyl)oxy]‐6‐methylbenzoate) (hmb) revealed two crystallographically and conformationally distinct hmb anions, along with two monovalent sodium atoms. One hmb moiety contained an exotetradentate binding mode to sodium, whereas the other exhibited an exohexadentate binding mode to sodium. Embedded edge‐sharing {Na2O8}n sodium‐oxygen chains connected the hmb anions into the full three‐dimensional crystal structure of the title compound. The crystal used for single‐crystal X‐ray diffraction exhibited non‐merohedral twinning. The data suggest the importance of the acetyl‐polymalonyl pathway products to processes of maintaining integrity of the lichen holobiont community.
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| 10. |
- Steadman, Randolph H., et al.
(author)
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Screen-Based Simulation for Training and Automated Assessment of Teamwork Skills Comparing 2 Modes With Different Interactivity
- 2021
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In: Simulation in Healthcare. - : LIPPINCOTT WILLIAMS & WILKINS. - 1559-2332 .- 1559-713X. ; 16:5, s. 318-326
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Journal article (peer-reviewed)abstract
- Introduction: The need for teamwork training is well documented; however, teaching these skills is challenging given the logistics of assembling individual team members together to train in person. We designed 2 modes of screen-based simulation for training teamwork skills to assess whether interactivity with nonplayer characters was necessary for in-game performance gains or for player satisfaction with the experience. Methods: Mixed, randomized, repeated measures study with licensed healthcare providers block-stratified and randomized to evaluation-participant observes and evaluates the team player in 3 scenarios-and game play-participant is immersed as the leader in the same 3 scenarios. Teamwork construct scores (leadership, communication, situation monitoring, mutual support) from an ontology-based, Bayesian network assessment model were analyzed using mixed randomized repeated measures analyses of variance to compare performance, across scenarios and modes. Learning was measured by pretest and posttest quiz scores. User experience was evaluated using chi(2) analyses. Results: Among 166 recruited and randomized participants, 120 enrolled in the study and 109 had complete data for analysis. Mean composite teamwork Bayesian network scores improved for successive scenarios in both modes, with evaluation scores statistically higher than game play for every teamwork construct and scenario (r = 0.73, P = 0.000). Quiz scores improved from pretest to posttest (P = 0.004), but differences between modes were not significant. Conclusions: For training teamwork skills using screen-based simulation, interactivity of the player with the nonplayer characters is not necessary for in-game performance gains or for player satisfaction with the experience.
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