| 1. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 2. |
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| 3. |
- Abazajian, Kevork, et al.
(författare)
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CMB-S4 : Forecasting Constraints on Primordial Gravitational Waves
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 926:1
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Tidskriftsartikel (refereegranskat)abstract
- CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
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| 4. |
- Ademuyiwa, Adesoji O., et al.
(författare)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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Ingår i: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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| 5. |
- Anderson, N. John, et al.
(författare)
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The Arctic in the Twenty-First Century : Changing Biogeochemical Linkages across a Paraglacial Landscape of Greenland
- 2017
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Ingår i: BioScience. - : Oxford University Press. - 0006-3568 .- 1525-3244. ; 67:2, s. 118-133
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Tidskriftsartikel (refereegranskat)abstract
- The Kangerlussuaq area of southwest Greenland encompasses diverse ecological, geomorphic, and climate gradients that function over a range of spatial and temporal scales. Ecosystems range from the microbial communities on the ice sheet and moisture-stressed terrestrial vegetation (and their associated herbivores) to freshwater and oligosaline lakes. These ecosystems are linked by a dynamic glacio-fluvial-aeolian geomorphic system that transports water, geological material, organic carbon and nutrients from the glacier surface to adjacent terrestrial and aquatic systems. This paraglacial system is now subject to substantial change because of rapid regional warming since 2000. Here, we describe changes in the eco-and geomorphic systems at a range of timescales and explore rapid future change in the links that integrate these systems. We highlight the importance of cross-system subsidies at the landscape scale and, importantly, how these might change in the near future as the Arctic is expected to continue to warm.
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| 6. |
- Aziz, Faisal, et al.
(författare)
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The impact of COVID-19 pandemic on vascular registries and clinical trials
- 2021
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Ingår i: Seminars in Vascular Surgery. - : Elsevier. - 0895-7967 .- 1558-4518. ; 34:2, s. 28-36
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Forskningsöversikt (refereegranskat)abstract
- Quality improvement programs and clinical trial research experienced disruption due to the coronavirus disease 2019 (COVID-19) pandemic. Vascular registries showed an immediate impact with significant declines in second-quarter vascular procedure volumes witnessed across Europe and the United States. To better understand the magnitude and impact of the pandemic, organizations and study groups sent grass roots surveys to vascular specialists for needs assessment. Several vascular registries responded quickly by insertion of COVID-19 variables into their data collection forms. More than 80% of clinical trials have been reported delayed or not started due to factors that included loss of enrollment from patient concerns or mandated institutional shutdowns, weighing the risk of trial participation on patient safety. Preliminary data of patients undergoing vascular surgery with active COVID-19 infection show inferior outcomes (morbidity) and increased mortality. Disease specific vascular surgery study collaboratives about COVID-19 were created for the desire to study the disease in a more focused manner than possible through registry outcomes. This review describes the pandemic effect on multiple VASCUNET registries including Germany (GermanVasc), Sweden (SwedVasc), United Kingdom (UK National Vascular Registry), Australia and New Zealand (bi-national Australasian Vascular Audit), as well as the United States (Society for Vascular Surgery Vascular Quality Initiative). We will highlight the continued collaboration of VASCUNET with the Vascular Quality Initiative in the International Consortium of Vascular Registries as part of the Medical Device Epidemiology Network coordinated registry network. Vascular registries must remain flexible and responsive to new and future real-world problems affecting vascular patients.
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| 7. |
- Back, Jon, 1977-
(författare)
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Designing Activity and Creating Experience : On People’s Play in Public places
- 2013
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis deals with the design of play in public places; this can mean both pervasive games and other freer play activities. In these activities (as well as in many other game activities) the same game can spur many different ways to play it, and the same activity can be experienced differently by different players, and even differently on different occasions for the same player. An activity such as playing must be observed as a whole. The surrounding cul- ture, player preconceptions and the emergent mood within the group will affect the experience.By analysing previous frameworks, and using own design examples, a three level design framework is developed, functioning as a lens towards understanding the design of playful activities. The framework focuses on the player perspective, offering game design as an invitation and encouragement to engage in certain activities. The framework distinguishes between design at three levels:Designed construct (e.g. artefacts and rules)ActivityExperiencesBut it remains to be understood why people engage in the activities that lead to playful experiences. What encourages playful engagement? And why do people want to play one game, and not another?This question can be split into two parts:Engagement: starting to be interested in the activityCommitment: actually caring for the experienceThis issue is identified in the thesis, and examples show how convoluted this problem is, in particular in pervasive game settings. Challenges are pre- sented for future work.
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| 8. |
- Back, Jon, 1977-
(författare)
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Designing Public Play : Playful Engagement, Constructed Activity, and Player Experience
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis sets out to explore why people engage in, and how to design for, play in a public setting. It does this by separating design for play from design of games, describing play as a socially and mentally understood activity, and a playful approach to engaging in that activity. It emphasises that while play is voluntary, design can help shape the players’ mode of engagement.The thesis uses a qualitative and inductive approach to research, with an understanding of knowledge as being constructed in the individual. The research is grounded in human computer interaction and interaction design, and closely related to game studies and design science.The research question concerns how design can influence the player activity in order to create a desired player experience in public, by harnessing playful engagement. It’s foundation is a theory of play which describes play as a framed, or hedged-off, activity with a fragile border; where knowledge and feelings can leak both in and out of the activity, and affect the play as well as what is around it. The theory of enjoyment of play is discussed, and the problem of treating this as ‘fun’ is addressed, concluding in a presentation of how playful engagement can be harnessed through design.The theory is applied in five design cases: I’m Your Body, a locative storytelling app; Codename Heroes, a pervasive game of personal empowerment; Passing On, a slow-paced game about communication; Busking Studies, which involves observing street performers and their shows; and DigiFys, an architectural design exploration of playgrounds and play paths.Finally, three concepts, or design tools, are presented, which address: 1) a structure for understanding a design through three layers, constructs designed by the designer, inspiring play activity with the player, leading to experience; 2) an approach to designing invitations to play; and finally 3), a four faceted structure for understanding play engagement when players engage in non intended ways.
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| 9. |
- Barry, Melissa, et al.
(författare)
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Utility of intracerebral theta burst electrical stimulation to attenuate interhemispheric inhibition and to promote motor recovery after cortical injury in an animal model
- 2014
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Ingår i: Experimental Neurology. - : Academic Press. - 0014-4886 .- 1090-2430. ; 261, s. 258-266
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Tidskriftsartikel (refereegranskat)abstract
- Following a cerebral cortex injury such as stroke, excessive inhibition around the core of the injury is thought to reduce the potential for new motor learning. In part, this may be caused by an imbalance of interhemispheric inhibition (IHI); therefore, treatments that relieve the inhibitory drive from the healthy hemisphere to the peri-lesional area may enhance motor recovery. Theta burst stimulation delivered by transcranial magnetic stimulation has been tested as a means of normalizing IHI, but clinical results have been variable. Here we use a new rat model of synaptic IHI to demonstrate that electrical intracranial theta burst stimulation causes long-lasting changes in motor cortex excitability. Further, we show that contralateral intermittent theta burst stimulation (iTBS) blocks IHI via a mechanism involving cannabinoid receptors. Finally, we show that contralesional iTBS applied during recovery from cortical injury in rats improves the recovery of motor function. These findings suggest that theta burst stimulation delivered through implanted electrodes may be a promising avenue to explore for augmenting rehabilitation from brain injury.
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| 10. |
- Downey, Harriet, et al.
(författare)
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Training future generations to deliver evidence-based conservation and ecosystem management
- 2021
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Ingår i: Ecological Solutions and Evidence. - : Wiley. - 2688-8319. ; 2:1
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Forskningsöversikt (refereegranskat)abstract
- 1. To be effective, the next generation of conservation practitioners and managers need to be critical thinkers with a deep understanding of how to make evidence-based decisions and of the value of evidence synthesis.2. If, as educators, we do not make these priorities a core part of what we teach, we are failing to prepare our students to make an effective contribution to conservation practice.3. To help overcome this problem we have created open access online teaching materials in multiple languages that are stored in Applied Ecology Resources. So far, 117 educators from 23 countries have acknowledged the importance of this and are already teaching or about to teach skills in appraising or using evidence in conservation decision-making. This includes 145 undergraduate, postgraduate or professional development courses.4. We call for wider teaching of the tools and skills that facilitate evidence-based conservation and also suggest that providing online teaching materials in multiple languages could be beneficial for improving global understanding of other subject areas.
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| 11. |
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| 12. |
- Jepson, Paul D., et al.
(författare)
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PCB pollution continues to impact populations of orcas and other dolphins in European waters
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Organochlorine (OC) pesticides and the more persistent polychlorinated biphenyls (PCBs) have well-established dose-dependent toxicities to birds, fish and mammals in experimental studies, but the actual impact of OC pollutants on European marine top predators remains unknown. Here we show that several cetacean species have very high mean blubber PCB concentrations likely to cause population declines and suppress population recovery. In a large pan-European meta-analysis of stranded (n = 929) or biopsied (n = 152) cetaceans, three out of four species:-striped dolphins (SDs), bottlenose dolphins (BNDs) and killer whales (KWs) had mean PCB levels that markedly exceeded all known marine mammal PCB toxicity thresholds. Some locations (e.g. western Mediterranean Sea, south-west Iberian Peninsula) are global PCB "hotspots" for marine mammals. Blubber PCB concentrations initially declined following a mid-1980s EU ban, but have since stabilised in UK harbour porpoises and SDs in the western Mediterranean Sea. Some small or declining populations of BNDs and KWs in the NE Atlantic were associated with low recruitment, consistent with PCB-induced reproductive toxicity. Despite regulations and mitigation measures to reduce PCB pollution, their biomagnification in marine food webs continues to cause severe impacts among cetacean top predators in European seas.
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| 13. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 14. |
- Redpath, Steve M., et al.
(författare)
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Don't forget to look down – collaborative approaches to predator conservation
- 2017
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Ingår i: Biological Reviews. - : John Wiley & Sons. - 1464-7931 .- 1469-185X. ; 92:4, s. 2157-2163
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Tidskriftsartikel (refereegranskat)abstract
- Finding effective ways of conserving large carnivores is widely recognised as a priority in conservation. However, there is disagreement about the most effective way to do this, with some favouring top-down ‘command and control’ approaches and others favouring collaboration. Arguments for coercive top-down approaches have been presented elsewhere; here we present arguments for collaboration. In many parts of the developed world, flexibility of approach is built into the legislation, so that conservation objectives are balanced with other legitimate goals. In the developing world, limited resources, poverty and weak governance mean that collaborative approaches are likely to play a particularly important part in carnivore conservation. In general, coercive policies may lead to the deterioration of political legitimacy and potentially to non-compliance issues such as illegal killing, whereas collaborative approaches may lead to psychological ownership, enhanced trust, learning, and better social outcomes. Sustainable hunting/trapping plays a crucial part in the conservation and management of many large carnivores. There are many different models for how to conserve carnivores effectively across the world, research is now required to reduce uncertainty and examine the effectiveness of these approaches in different contexts.
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| 15. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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