| 581. |
- Abrahao, Silvia, et al.
(författare)
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Open Source Software: Communities and Quality
- 2023
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Ingår i: IEEE Software. - 1937-4194 .- 0740-7459. ; 40:4, s. 96-99
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Tidskriftsartikel (refereegranskat)abstract
- This edition of the Practitioner's Digest features recent papers on open source software related to toxicity in open source discussions, newcomers in open source projects, quality of ansible scripts, code review practices, orphan vulnerabilities in open source software, and the relationship between community and design smells.
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| 582. |
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| 583. |
- Abram, Nerilie, et al.
(författare)
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Understanding the climate of the past 2000 years: Phase 3of the PAGES 2k Network
- 2017
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Ingår i: Past Global Changes Magazine. - : Past Global Changes (PAGES). - 2411-605X .- 2411-9180. ; 25:2
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The PAGES 2k Network was created with the aim of reconstructing changes in regional and global surface climate over the past 2000 years. During Phases 1 (2008-2013) and 2 (2014-2016), regional and trans-regional groupings focused on building reconstructions for terrestrial regions and the oceans. The conclusion of Phase 2 coincided with the release of an open and transparent global database of temperature-sensitive proxies spanning the Common Era (Fig. 1; PAGES 2k Consortium 2017). This product will be followed up by a special issue of Climate of the Past, entitled “Climate of the past 2000 years: regional and trans-regional syntheses”
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| 584. |
- Abram, Simone, et al.
(författare)
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Six controversies in search of an epistemology
- 2005
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Public engagement in planning and siting policy has been a political priority for some time, and there are various arguments as to why successful participation consistently proves to be an elusive goal. Emphasis is often laid on the incompatibility of local knowledge and technical knowledge, on the failure to invite "public" involvement at an early stage, and so on. In this paper, we examine a set of controversies about the siting of an upgraded railway line and associated stations in six neighbouring municipalities in western Sweden. Using parallel focus group discussions with different parties to the process, we draw two main conclusions. Firstly, local knowledge may equally be technorational, yet the positioning of actors determines when and how alternative arguments may emerge. This suggests that arguments over the necessity of social capital for successful participation may be a red herring. Secondly, policy processes are long and drawn-out, and new participants appear all the way through these processes. The category of "the public" is a fictional remainder category which undermines participative approaches. We suggest that opposition should be understood as an eternal factor in participative democratic policy processes, rather than a preliminary obstacle which can be alleviated early on. Hence we challenge assumptions about the rightful temporal positioning of participative practices and query the notion that early participation leads to "public ownership" of plans.
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| 585. |
- Abramo, Antonio, et al.
(författare)
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Osteotomy of distal radius fracture malunion using a fast remodeling bone substitute consisting of calcium sulphate and calcium phosphate.
- 2010
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Ingår i: Journal of biomedical materials research. Part B, Applied biomaterials. - : Wiley. - 1552-4981 .- 1552-4973. ; 92:1, s. 281-6
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Tidskriftsartikel (refereegranskat)abstract
- Malunion after a distal radius fracture can be treated with an osteotomy of the distal radius. Autologous iliac crest bone graft is often used to fill the gap, but the procedure is associated with donor site morbidity. In this study a novel fast resorbing biphasic bone substitute consisting of a mixture of calcium sulphate and calcium phosphate is used (Cerament BoneSupport AB, Sweden). Fifteen consecutive patients, with a mean age of 52 (27-71) years were included. All had a malunion after a distal radius fracture and underwent an osteotomy. A fragment specific fixation system, TriMed (TriMed, Valencia, CA), consisting of a Buttress Pin and a Radial Pin Plate were used for fixation and a calcium sulphate and calcium phosphate mixture as bone substitute. The patients were followed for 1 year. Grip strength increased from 61 (28-93)% of the contralateral hand to 85 (58-109)%, p < 0.001. DASH scores decreased from 37 (22-61) to 24 (2-49) p = 0.003. Radiographically all osteotomies healed. An increase of ulnar variance was noted during healing from 1.8 mm immediately postoperatively to 2.6 mm at final follow up. Osteotomy can increase grip strength and decease disability after a malunited fracture. In the present series the bone substitute was replaced by bone, but a minor loss of the achieved radiographic correction was noted in some patients during osteotomy healing. A more rigid fixation may improve the radiographic outcome with this kind of bone substitute.
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| 586. |
- Abramova, Anna, 1990, et al.
(författare)
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A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments
- 2023
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Ingår i: Environment International. - 0160-4120 .- 1873-6750. ; 178
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Tidskriftsartikel (refereegranskat)abstract
- The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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| 587. |
- Abramova, Anna, 1990, et al.
(författare)
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CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data
- 2021
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059. ; 37:1, s. 121-122
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Tidskriftsartikel (refereegranskat)abstract
- Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE-Coefficient-based Analysis of Fitness by read Enrichment-a software package that can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition and perform appropriate statistical testing on these fitness coefficients.
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| 588. |
- Abramova, Anna, 1990, et al.
(författare)
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Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments
- 2022
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Ingår i: bioRXIV. - : Cold Spring Harbor Laboratory.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, current AMR monitoring initiatives lack comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish the typical baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey across 2516 scientific papers, 150 of which contained relevant qPCR data on antibiotic resistance genes (ARGs) in environments associated with potential routes of AMR dissemination. The collected data include 1487 samples distributed across 30 different countries and 17 environmental types, in a time span from 2005 to 2018. More than 330 different genes were identified from the collected studies. Most surveyed environments contained a diverse set of ARGs, but generally at low abundances. We used linear mixed models and overrepresentation analysis to identify time trends and associations between ARGs and specific environments. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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| 589. |
- Abramova, Anna, 1990
(författare)
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Molecular biology of barnacle Balanus improvisus settlement
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this thesis was to investigate molecular mechanisms of various aspects of barnacle settlement, using the acorn barnacle Balanus improvisus. This barnacle is a common fouling species and a model organism for studies in settlement biology, in particular in relation to antifouling research. In order to facilitate the development of genomic resources in this species, we conducted a pilot study for the sequencing of the B. improvisus genome and performed an initial genomic characterization. The analysis revealed that B. improvisus genome has an extremely high genetic diversity, with about 5% nucleotide diversity in coding regions. In addition, we experimentally estimated the B. improvisus genome size, based on DNA staining and flow cytometry measurements, resulting in a haploid genome size of 738 Mbp. To investigate molecular changes during the settlement process, transcriptomes of four different settlement stages, ie free-swimming, closesearch, attached and juvenile, were compared. We identified several key genes involved in the hormonal regulation of molting and metamorphosis, including the broad complex, ecdysone receptor and retinoid X receptor, adding a new level of insight to the molecular mechanisms involved in settlement. Furthermore, we used two types of surfaces with different wettability to test if differences in surface preferences are reflected in gene expression. The results revealed that exploration of the “favourable” hydrophobic surface induced more genes and with larger changes in expression than on hydrophilic suggesting a stronger transcriptional response. We also investigated two specific aspects related to barnacle chemical communication during settlement - sensory receptors and pheromones. Analysis of the transcriptome of cyprid antennules resulted in the identification of two receptor classes, the chemosensory ionotropic receptors and mechanosensory receptors represented by several TRP subfamilies. We identified and characterized six homologs of the waterborne pheromone WSP in B. improvisus that showed differential expression during settlement. These results suggest the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components. With the aim to further establish B. improvisus into a potent marine model system, a detailed protocol was developed for an all-year-round culturing of B. improvisus and adapted at Tjärnö Marine Laboratory. Finally, I summarise current knowledge on the molecular mechanisms of barnacle settlement and outline new research directions to further improve our understanding of the settlement biology of this species.
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| 590. |
- Abramova, Anna, 1990, et al.
(författare)
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Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus
- 2019
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 14:5
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Tidskriftsartikel (refereegranskat)abstract
- - Barnacle settlement involves sensing of a variety of exogenous cues. A pair of antennules is the main sensory organ that the cyprid larva uses to explore the surface. Antennules are equipped with a number of setae that have both chemo- and mechanosensing function. The current study explores the repertoire of sensory receptors in Balanus improvisus cyprid antennules with the goal to better understand sensory systems involved in the settling behavior of this species. We carried out transcriptome sequencing of dissected B. improvisus cyprid antennules. The generated transcriptome assembly was used to search for sensory receptors using HMM models. Among potential chemosensory genes, we identified the ionotropic receptors IR25a, IR8a and IR93a, and several divergent IR candidates to be expressed in the cyprid antennules. We found one gustatory-like receptor but no odorant receptors, chemosensory or odorant-binding proteins. Apart from chemosensory receptors, we also identified 13 potential mechanosensory genes represented by several transient receptor potential channels (TRP) subfamilies. Furthermore, we analyzed changes in expression profiles of IRs and TRPs during the B. improvisus settling process. Several of the sensory genes were differentially expressed during the course of larval settlement. This study gives expanded knowledge about the sensory systems present in barnacles, a taxonomic group for which only limited information about receptors is currently available. It furthermore serves as a starting point for more in depth studies of how sensory signaling affects settling behavior in barnacles with implications for preventing biofouling. © 2019 Abramova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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