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- 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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| 4. |
- Alégroth, Emil, 1984-, et al.
(författare)
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Characteristics that affect Preference of Decision Models for Asset Selection : An Industrial Questionnaire Survey
- 2020
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Ingår i: Software quality journal. - : Springer. - 0963-9314 .- 1573-1367. ; 28:4, s. 1675-1707
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Tidskriftsartikel (refereegranskat)abstract
- Modern software development relies on a combination of development and re-use of technical asset, e.g. software components, libraries and APIs.In the past, re-use was mostly conducted with internal assets but today external; open source, customer off-the-shelf (COTS) and assets developed through outsourcing are also common.This access to more asset alternatives presents new challenges regarding what assets to optimally chose and how to make this decision.To support decision-makers, decision-theory has been used to develop decision models for asset selection.However, very little industrial data has been presented in literature about the usefulness, or even perceived usefulness, of these models.Additionally, only limited information has been presented about what model characteristics that determine practitioner preference towards one model over another.Objective: The objective of this work is to evaluate what characteristics of decision models for asset selection that determine industrial practitioner preference of a model when given the choice of a decision-model of high precision or a model with high speed.Method: An industrial questionnaire survey is performed where a total of 33 practitioners, of varying roles, from 18 companies are tasked to compare two decision models for asset selection.Textual analysis and formal and descriptive statistics are then applied on the survey responses to answer the study's research questions.Results: The study shows that the practitioners had clear preference towards the decision model that emphasised speed over the one that emphasised decision precision.This conclusion was determined to be because one of the models was perceived faster, had lower complexity, had, was more flexible in use for different decisions, was more agile how it could be used in operation, its emphasis on people, its emphasis on ``good enough'' precision and ability to fail fast if a decision was a failure.Hence, seven characteristics that the practitioners considered important for their acceptance of the model.Conclusion: Industrial practitioner preference, which relates to acceptance, of decision models for asset selection is dependent on multiple characteristics that must be considered when developing a model for different types of decisions such as operational day-to-day decisions as well as more critical tactical or strategic decisions.The main contribution of this work are seven identified characteristics that can serve as industrial requirements for future research on decision models for asset selection.
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| 5. |
- Ali, Nauman Bin, et al.
(författare)
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A consolidated process for software process simulation : State of the Art and Industry Experience
- 2012
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Konferensbidrag (refereegranskat)abstract
- Software process simulation is a complex task and in order to conduct a simulation project practitioners require support through a process for software process simulation modelling (SPSM), including what steps to take and what guidelines to follow in each step. This paper provides a literature based consolidated process for SPSM where the steps and guidelines for each step are identified through a review of literature and are complemented by experience from using these recommendations in an action research at a large Telecommunication vendor. We found five simulation processes in SPSM literature, resulting in a seven-step process. The consolidated process was successfully applied at the studied company, with the experiences of doing so being reported.
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| 6. |
- Ali, Nauman bin, et al.
(författare)
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FLOW-assisted value stream mapping in the early phases of large-scale software development
- 2016
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Ingår i: Journal of Systems and Software. - : Elsevier. - 0164-1212 .- 1873-1228. ; 111, s. 213-227
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Tidskriftsartikel (refereegranskat)abstract
- Value stream mapping (VSM) has been successfully applied in the context of software process improvement. However, its current adaptations from Lean manufacturing focus mostly on the flow of artifacts and have taken no account of the essential information flows in software development. A solution specifically targeted toward information flow elicitation and modeling is FLOW. This paper aims to propose and evaluate the combination of VSM and FLOW to identify and alleviate information and communication related challenges in large-scale software development. Using case study research, FLOW-assisted VSM was used for a large product at Ericsson AB, Sweden. Both the process and the outcome of FLOW-assisted VSM have been evaluated from the practitioners’ perspective. It was noted that FLOW helped to systematically identify challenges and improvements related to information flow. Practitioners responded favorably to the use of VSM and FLOW, acknowledged the realistic nature and impact on the improvement on software quality, and found the overview of the entire process using the FLOW notation very useful. The combination of FLOW and VSM presented in this study was successful in systematically uncovering issues and characterizing their solutions, indicating their practical usefulness for waste removal with a focus on information flow related issues.
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| 7. |
- Ali, Nauman Bin, et al.
(författare)
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Testing highly complex system of systems : An industrial case study
- 2012
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Ingår i: [Host publication title missing]. - Lund : ACM/IEEE. - 9781450310567 ; , s. 211-220
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Konferensbidrag (refereegranskat)abstract
- Systems of systems (SoS) are highly complex and are integrated on multiple levels (unit, component, system, system of systems). Many of the characteristics of SoS (such as operational and managerial independence, integration of system into system of systems, SoS comprised of complex systems) make their development and testing challenging. Contribution: This paper provides an understanding of SoS testing in large-scale industry settings with respect to challenges and how to address them. Method: The research method used is case study research. As data collection methods we used interviews, documentation, and fault slippage data. Results: We identified challenges related to SoS with respect to fault slippage, test turn-around time, and test maintainability. We also classified the testing challenges to general testing challenges, challenges amplified by SoS, and challenges that are SoS specific. Interestingly, the interviewees agreed on the challenges, even though we sampled them with diversity in mind, which meant that the number of interviews conducted was sufficient to answer our research questions. We also identified solution proposals to the challenges that were categorized under four classes of developer quality assurance, function test, testing in all levels, and requirements engineering and communication. Conclusion: We conclude that although over half of the challenges we identified can be categorized as general testing challenges still SoS systems have their unique and amplified challenges stemming from SoS characteristics. Furthermore, it was found that interviews and fault slippage data indicated that different areas in the software process should be improved, which indicates that using only one of these methods would have led to an incomplete picture of the challenges in the case company.
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| 8. |
- Ali, Nauman, et al.
(författare)
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Evaluating strategies for study selection in systematic literature studies
- 2014
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Ingår i: ESEM '14 Proceedings of the 8th ACM/IEEE International Symposium on Empirical Software Engineering and Measurement. - New York, NY, USA : ACM. - 9781450327749
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Konferensbidrag (refereegranskat)abstract
- Context: The study selection process is critical to improve the reliability of secondary studies. Goal: To evaluate the selection strategies commonly employed in secondary studies in software engineering. Method: Building on these strate- gies, a study selection process was formulated and evalu- ated in a systematic review. Results: The selection process used a more inclusive strategy than the one typically used in secondary studies, which led to additional relevant articles. Conclusions: The results indicates that a good-enough sam- ple could be obtained by following a less inclusive but more efficient strategy, if the articles identified as relevant for the study are a representative sample of the population, and there is a homogeneity of results and quality of the articles.
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| 9. |
- Amundadottir, Laufey, et al.
(författare)
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Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer.
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 41, s. 986-990
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Tidskriftsartikel (refereegranskat)abstract
- We conducted a two-stage genome-wide association study of pancreatic cancer, a cancer with one of the lowest survival rates worldwide. We genotyped 558,542 SNPs in 1,896 individuals with pancreatic cancer and 1,939 controls drawn from 12 prospective cohorts plus one hospital-based case-control study. We conducted a combined analysis of these groups plus an additional 2,457 affected individuals and 2,654 controls from eight case-control studies, adjusting for study, sex, ancestry and five principal components. We identified an association between a locus on 9q34 and pancreatic cancer marked by the SNP rs505922 (combined P = 5.37 x 10(-8); multiplicative per-allele odds ratio 1.20; 95% confidence interval 1.12-1.28). This SNP maps to the first intron of the ABO blood group gene. Our results are consistent with earlier epidemiologic evidence suggesting that people with blood group O may have a lower risk of pancreatic cancer than those with groups A or B.
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| 10. |
- Arslan, Alan A., et al.
(författare)
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Anthropometric Measures, Body Mass Index, and Pancreatic Cancer A Pooled Analysis From the Pancreatic Cancer Cohort Consortium (PanScan)
- 2010
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Ingår i: Archives of Internal Medicine. - 0003-9926. ; 170:9, s. 791-802
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Tidskriftsartikel (refereegranskat)abstract
- Background: Obesity has been proposed as a risk factor for pancreatic cancer. Methods: Pooled data were analyzed from the National Cancer Institute Pancreatic Cancer Cohort Consortium (PanScan) to study the association, between prediagnostic anthropometric measures and risk of pancreatic cancer. PanScan applied a nested case-control study design and included 2170 cases and 2209 control subjects. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using unconditional logistic regression for cohort-specific quartiles of body mass index (BMI [calculated as weight in kilograms divided by height in meters squared]), weight, height, waist circumference, and waist to hip ratio as well as conventional BMI categories (underweight, <18.5; normal weight, 18.5-24.9; overweight, 25.0-29.9; obese, 30.0-34.9; and severely obese, >= 35.0). Models were adjusted for potential confounders. Results: In all of the participants, a positive association between increasing BMI and risk of pancreatic cancer was observed (adjusted OR for the highest vs lowest BMI guartile, 1.33; 95% Cl, 1.12-1.58; P-trend<.001). In men, the adjusted OR for pancreatic cancer for the highest vs lowest quartile of BMI was 1.33 (95% Cl, 1.04-1.69; P-trend<.03), and in women it was 1.34 (95% Cl, 1.05-1.70; P-trend=.01). Increased waist to hip ratio was associated with increased risk of pancreatic cancer in women (adjusted OR for the highest vs lowest quartile, 1.87; 95% Cl, 1.31-2.69; P-trend=.003) but less so in men. Conclusions: These findings provide strong support for a positive association between BMI and pancreatic cancer risk. In addition, centralized fat distribution may increase pancreatic cancer risk, especially in women. Arch Intern Med. 2010;170(9):791 -802
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