| 1. |
- Abdekhodaie, Ehsan, et al.
(författare)
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WordCommentsAnalyzer : A windows software tool for qualitative research
- 2018
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- There is a lack of free software that provides a professional and smooth experience in text editing and markup for qualitative data analysis. Word processing software like Microsoft Word provides a good editing experience, allowing the researcher to effortlessly add comments to text portions. However, organizing the keywords and categories in the comments can become a more difficult task when the amount of data increases. We present WordCommentsAnalyzer, a software tool that is written in C# using .NET Framework and OpenXml, which helps a qualitative researcher to organize codes when using Microsoft Word as the primary text markup software. WordCommentsAnalyzer provides an effective user interface to count codes, to organize codes in a code hierarchy, and to see various data extracts belonging to each code. It also offers basic visualization tools. We illustrate how to use this software by conducting a preliminary content analysis on Tweets with the #successfulaging hashtag. We also demonstrate that the software has satisfactory performance on a large dataset of Iranian journals abstracts. We hope this open-source software will facilitate qualitative data analysis by researchers who are interested in using Word for this purpose.
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| 2. |
- Af Petersens, M, et al.
(författare)
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Workplace exposure to carbon dioxide during routine laparoscopy - is it safe?
- 2020
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Ingår i: F1000Research. - : F1000 Research Ltd. - 2046-1402. ; 9, s. 571-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Minimally invasive surgeries have increased dramatically during the last decades. Carbon dioxide (CO2) is the gas used for insufflation during laparoscopies, creating space and visibility. The CO2 leaks into ambient air through ports where instruments are inserted. If the CO2 reaches a certain concentration it affects personnel health. There are national occupational exposure limits (OEL) for CO2, including a level limit value (LLV) of 5000 ppm. We are not aware of any previous studies addressing occupational exposure to CO2 during laparoscopies. The aim of this study was to assess the compliance to national OELs for CO2 during laparoscopies. Methods: A gas detector was placed in the breathing zone of personnel in the operating theatre. The detector measured CO2 concentrations every tenth minute during laparoscopies in three locations. Results: During 27 laparoscopies, the measured CO2 reached a maximum concentration of 1100 ppm, less than one fourth of the LLV. Median CO2 concentration was 700 ppm. Conclusion: Results show that the occupational exposure to CO2 during laparoscopies is well below set OELs. Our findings support personnel safety associated with routine use of CO2 during laparoscopies.
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| 3. |
- Andeer, Robin, et al.
(författare)
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Chanjo : Clincal grade sequence coverage analysis
- 2020
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Coverage analysis is essential when analysing massive parallel sequencing (MPS) data. The analysis indicates existence of false negatives or positives in a region of interest or poorly covered genomic regions. There are several tools that have excellent performance when doing coverage analysis on a few samples with predefined regions. However, there is no current tool for collecting samples over a longer period of time for aggregated coverage analysis of multiple samples or sequencing methods. Furthermore, current coverage analysis tools do not generate customized coverage reports or enable exploratory coverage analysis without extensive bioinformatic skill and access to the original alignment files. We present Chanjo, a user friendly coverage analysis tool for persistent storage of coverage data, that, accompanied with Chanjo Report, produces coverage reports that summarize coverage data for predefined regions in an elegant manner. Chanjo Report can produce both structured coverage reports and dynamic reports tailored to a subset of genomic regions, coverage cut-offs or samples. Chanjo stores data in an SQL database where thousands of samples can be added over time, which allows for aggregate queries to discover problematic regions. Chanjo is well tested, supports whole exome and genome sequencing, and follows common UNIX standards, allowing for easy integration into existing pipelines. Chanjo is easy to install and operate, and provides a solution for persistent coverage analysis and clinical-grade reporting. It makes it easy to set up a local database and automate the addition of multiple samples and report generation. To our knowledge there is no other tool with matching capabilities. Chanjo handles the common file formats in genetics, such as BED and BAM, and makes it easy to produce PDF coverage reports that are highly valuable for individuals with limited bioinformatic expertise. We believe Chanjo to be a vital tool for clinicians and researchers performing MPS analysis.
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| 4. |
- Angers-Loustau, A., et al.
(författare)
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The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
- 2018
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Ingår i: F1000Research. - : F1000 Research Ltd. - 2046-1402. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms. In the implementation of any novel technology for regulatory purposes, important considerations such as harmonisation, validation and quality assurance need to be addressed. NGS technologies pose unique challenges in these regards, in part due to their reliance on bioinformatics for the processing and proper interpretation of the data produced. Well-designed benchmark resources are thus needed to evaluate, validate and ensure continued quality control over the bioinformatics component of the process. This concept was explored as part of a workshop on "Next-generation sequencing technologies and antimicrobial resistance" held October 4-5 2017. Challenges involved in the development of such a benchmark resource, with a specific focus on identifying the molecular determinants of AMR, were identified. For each of the challenges, sets of unsolved questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the requirement for monitoring of AMR bacteria in humans, animals, food and the environment, which is aligned with the principles of a "One Health" approach.
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| 5. |
- Anzt, Hartwig, et al.
(författare)
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An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action
- 2020
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
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| 6. |
- Auffray, C., et al.
(författare)
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COVID-19 and beyond : a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight
- 2020
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 9, s. 1130-18
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Tidskriftsartikel (refereegranskat)abstract
- Background: Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) belongs to a subgroup of coronaviruses rampant in bats for centuries. It caused the coronavirus disease 2019 (COVID-19) pandemic. Most patients recover, but a minority of severe cases experience acute respiratory distress or an inflammatory storm devastating many organs that can lead to patient death. The spread of SARS-CoV-2 was facilitated by the increasing intensity of air travel, urban congestion and human contact during the past decades. Until therapies and vaccines are available, tests for virus exposure, confinement and distancing measures have helped curb the pandemic. Vision: The COVID-19 pandemic calls for safeguards and remediation measures through a systemic response. Self-organizing initiatives by scientists and citizens are developing an advanced collective intelligence response to the coronavirus crisis. Their integration forms Olympiads of Solidarity and Health. Their ability to optimize our response to COVID-19 could serve as a model to trigger a global metamorphosis of our societies with far-reaching consequences for attacking fundamental challenges facing humanity in the 21st century. Mission: For COVID-19 and these other challenges, there is no alternative but action. Meeting in Paris in 2003, we set out to "rethink research to understand life and improve health." We have formed an international coalition of academia and industry ecosystems taking a systems medicine approach to understanding COVID-19 by thoroughly characterizing viruses, patients and populations during the pandemic, using openly shared tools. All results will be publicly available with no initial claims for intellectual property rights. This World Alliance for Health and Wellbeing will catalyze the creation of medical and health products such as diagnostic tests, drugs and vaccines that become common goods accessible to all, while seeking further alliances with civil society to bridge with socio-ecological and technological approaches that characterise urban systems, for a collective response to future health emergencies.
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| 7. |
- Bartomeus, Ignasi
(författare)
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Pollinator declines: reconciling scales and implications for ecosystem services
- 2013
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Ingår i: F1000Research. - : F1000 Research Ltd. - 2046-1402. ; 2
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Annan publikation (refereegranskat)abstract
- Despite the widespread concern about the fate of pollinators and the ecosystem services they deliver, we still have surprisingly scarce scientific data on the magnitude of pollinator declines and its actual contribution to crop pollination and food security. We use recently published data from northeastern North America to show that studies at both the local and regional scales are needed to understand pollinator declines, and that species-specific responses to global change are broadly consistent across scales. Second, we show that bee species that are currently delivering most of the ecosystem services (i.e. crop pollination) are not among the species showing declining trends, but rather appear to thrivein human-dominated landscapes. - See more at: http://f1000research.com/articles/2-146/v1#sthash.7jLf7zFE.dpuf
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| 8. |
- Biswas, A., et al.
(författare)
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Adolescent girls’ attitudes toward female genital mutilation : A study in seven African countries [version 1; referees: 2 approved]
- 2018
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Background: The study’s aim is to examine adolescent girls’ attitudes toward the continuation or discontinuation of female genital mutilation (FGM) in association with their demographics in seven different countries in Africa. Methods: Data from the women’s survey of the Demographic and Health Surveys (DHS) conducted by the respective ministries (of Health and Family Welfare) in Egypt, Guinea, Kenya, Mali, Niger, Senegal and Sierra Leone were used. Adolescent girls (15-19 years) were included in the current analysis: Egypt (N=636), Guinea (N=1994), Kenya (N= 1767), Mali (N=2791), Niger (N=1835), Senegal (N=3604), Sierra Leone (N=1237). Results: Prevalence of supporting the continuation of FGM among adolescent girls was in Egypt 58%, Guinea 63%, Kenya 16%, Mali 72%, Niger 3%, Senegal 23%, and Sierra Leone 52%. Being Muslim and having low economic status were significantly associated with supporting the continuation of FGM in five of the participating countries. Girls having no education or only primary education in Guinea, Kenya, Mali and Sierra Leone exhibited a higher likelihood of supporting FGM than girls with secondary or higher education. In Egypt, Niger and Senegal there was no association between education and supporting FGM. The girls who stated that they had no exposure to media showed the higher likelihood of supporting FGM in Guinea, Kenya, and Senegal than those with exposure to media. Conclusions: The current study argues that increasing media coverage and education, and reducing poverty are of importance for shifting adolescent girls’ attitudes in favor of discontinuation of FGM. © 2018 Dalal K et al.
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| 9. |
- Biswas, Animesh, et al.
(författare)
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Lightning Injury is a disaster in Bangladesh? : Exploring its magnitude and public health needs
- 2016
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Ingår i: F1000 Research. - London, United Kingdom : Faculty of 1000 Ltd.. - 2046-1402. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Lightning injury is a global public health issue. Low and middle-income countries in the tropical and subtropical regions of the world are most affected by lightning. Bangladesh is one of the countries at particular risk, with a high number of devastating lightning injuries in the past years, causing high mortality and morbidity. The exact magnitude of the problem is still unknown and therefore this study investigates the epidemiology of lightning injuries in Bangladesh, using a national representative sample.Methods: A mixed method was used. The study is based on results from a nationwide cross-sectional survey performed in 2003 in twelve randomly selected districts. In the survey, a total of 819,429 respondents from 171,336 households were interviewed using face-to-face interviews. In addition, qualitative information was obtained by reviewing national and international newspaper reports of lightning injuries sustained in Bangladesh between 13 and 15 May 2016.Results: The annual mortality rate was 3.661 (95% CI 0.9313–9.964) per 1,000,000 people. The overall incidence of lightning injury was 19.89/100,000 people. Among the victims, 60.12% (n=98) were males and 39.87% (n=65) were females. Males were particularly vulnerable, with a 1.46 times increased risk compared with females (RR 1.46, 95% CI 1.06–1.99). Rural populations were more vulnerable, with a 8.73 times higher risk, than urban populations (RR 8.73, 95% CI 5.13–14.86). About 43% of injuries occurred between 12 noon and 6 pm. The newspapers reported 81 deaths during 2 days of electric storms in 2016. Lightning has been declared a natural disaster in Bangladesh.Conclusions: The current study indicates that lightning injuries are a public health problem in Bangladesh. The study recommends further investigations to develop interventions to reduce lightning injuries, mortality and related burden in Bangladesh.
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| 10. |
- Biswas, Animesh, 1978-, et al.
(författare)
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Maternal complications in a geographically challenging and hard to reach district of Bangladesh : a qualitative study
- 2016
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Ingår i: F1000 Research. - London, United Kingdom : Faculty of 1000 Ltd.. - 2046-1402. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Maternal complications contribute to maternal deaths in developing countries. Bangladesh still has a high prevalence of maternal mortality, which is often preventable. There are some geographically challenging and hard to reach rural districts in Bangladesh and it is difficult to get information about maternal complications in these areas. In this study, we examined the community lay knowledge of possible pregnancy complications. We also examined the common practices associated with complications and we discuss the challenges for the community.Methods: The study was conducted in Moulvibazar of north east Bangladesh, a geographically challenged, difficult to reach district. Qualitative methods were used to collect the information. Pregnant women, mothers who had recently delivered, their guardians and traditional birth attendants participated in focus group discussions. Additionally, in-depth interviews were conducted with the family members. Thematic analyses were performed.Results: The study revealed that there is a lack of knowledge of maternal complications. In the majority of cases, the mothers did not receive proper treatment for maternal complications. There are significant challenges that these rural societies need to address: problems of ignorance, traditional myths and family restrictions on seeking better treatment. Moreover, traditional birth attendants and village doctors also have an important role in assuring appropriate, effective and timely treatment.Conclusions: The rural community lacks adequate knowledge on maternal complications. Reduction of the societal barriers including barriers within the family can improve overall practices. Moreover, dissemination of adequate information to the traditional birth attendant and village doctors may improve the overall situation, which would eventually help to reduce maternal deaths.
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