| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
- Berntsson Svensson, Richard, 1978, et al.
(författare)
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The unfulfilled potential of data-driven decision making in agile software development
- 2019
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Ingår i: Lecture Notes in Business Information Processing. - Cham : Springer International Publishing. - 1865-1356 .- 1865-1348. - 9783030190330 ; 355, s. 69-85
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Konferensbidrag (refereegranskat)abstract
- With the general trend towards data-driven decision making (DDDM), organizations are looking for ways to use DDDM to improve their decisions. However, few studies have looked into the practitioners view of DDDM, in particular for agile organizations. In this paper we investigated the experiences of using DDDM, and how data can improve decision making. An emailed questionnaire was sent out to 124 industry practitioners in agile software developing companies, of which 84 answered. The results show that few practitioners indicated a wide-spread use of DDDM in their current decision making practices. The practitioners were more positive to its future use for higher-level and more general decision making, fairly positive to its use for requirements elicitation and prioritization decisions, while being less positive to its future use at the team level. The practitioners do see a lot of potential for DDDM in an agile context; however, currently unfulfilled.
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| 3. |
- Spahiu, Linda, et al.
(författare)
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Global Kinetic Mechanism of Microsomal Glutathione Transferase 1 and Insights into Dynamic Enzyme Activation
- 2017
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Ingår i: Biochemistry. - : AMER CHEMICAL SOC. - 0006-2960 .- 1520-4995. ; 56:24, s. 3089-3098
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Tidskriftsartikel (refereegranskat)abstract
- Microsomal glutathione transferase 1 (MGST1) has a unique ability to be activated, <= 30-fold, by modification with sulfhydryl reagents. MGST1 exhibits one-third-of-the-sites reactivity toward glutathione and hence heterogeneous binding to different active sites in the homotrimer. Limited turnover stopped-flow kinetic measurements of the activated enzyme allowed us to more accurately determine the KD for the "third" low-affinity GSH binding site (1.4 +/- 0.3 mM). The rate of thiolate formation, k(2) (0.77 +/- 0.06 s(-1)), relevant to turnover, could also be determined. By deriving the steadystate rate equation for a random sequential mechanism for MGST1, we can predict K-M, k(cat), and k(cat)/K-M values from these and previously determined pre-steady-state rate constants (all determined at 5 C). To assess whether the pre-steady-state behavior can account for the steady-state kinetic behavior, we have determined experimental values for kinetic parameters at 5 degrees C. For reactive substrates and the activated enzyme, data for the microscopic steps account for the global mechanism of MGST1. For the unactivated enzyme and more reactive electrophilic substrates, pre steady -state and steady-state data can be reconciled only if a more active subpopulation of MGST1 is assumed. We suggest that unactivated MGST1 can be partially activated in its unmodified form. The existence of an activated subpopulation (approximately 10%) could be demonstrated in limited turnover experiments. We therefore suggest that MSGT1 displays a preexisting dynamic equilibrium between high- and low-activity forms.
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| 4. |
- Sunduru, Naresh, et al.
(författare)
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N-aryl 2-aryloxyacetamides as a new class of fatty acid amide hydrolase (FAAH) inhibitors
- 2017
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Ingår i: Journal of enzyme inhibition and medicinal chemistry (Print). - : Informa UK Limited. - 1475-6366 .- 1475-6374. ; 32:1, s. 513-521
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Tidskriftsartikel (refereegranskat)abstract
- Fatty acid amide hydrolase (FAAH) is a promising target for the development of drugs to treat neurological diseases. In search of new FAAH inhibitors, we identified 2-(4-cyclohexylphenoxy)-N-(3-(oxazolo[4,5-b] pyri-din-2-yl) phenyl) acetamide, 4g, with an IC50 of 2.6 mu M as a chemical starting point for the development of potent FAAH inhibitors. Preliminary hit-to-lead optimisation resulted in 2-(4-phenylphenoxy)-N-(3-(oxazolo[4,5-b] pyridin-2-yl)phenyl) acetamide, 4i, with an IC50 of 0.35 mu M.
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| 5. |
- Zheng, Hou-Feng, et al.
(författare)
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Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 526:7571, s. 112-
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Tidskriftsartikel (refereegranskat)abstract
- The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF <= 1%) variants contribute to complex traits and disease in the general population is mainly unknown. Bone mineral density (BMD) is highly heritable, a major predictor of osteoporotic fractures, and has been previously associated with common genetic variants(1-8), as well as rare, population specific, coding variants(9). Here we identify novel non-coding genetic variants with large effects on BMD (n(total) = 53,236) and fracture (n(total) = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD8 (rs11692564(T), MAF51.6%, replication effect size510.20 s.d., P-meta = 2 x 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 x 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1cre/flox mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size +10.41 s.d., P-meta = 1 x 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.
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| 6. |
- Alahyari, Hiva, 1979, et al.
(författare)
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A study of value in agile software development organizations
- 2017
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Ingår i: Journal of Systems and Software. - : Elsevier BV. - 0164-1212 .- 1873-1228. ; 125, s. 271-288
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Tidskriftsartikel (refereegranskat)abstract
- The Agile manifesto focuses on the delivery of valuable software. In Lean, the principles emphasise value, where every activity that does not add value is seen as waste. Despite the strong focus on value, and that the primary critical success factor for software intensive product development lies in the value domain, no empirical study has investigated specifically what value is. This paper presents an empirical study that investigates how value is interpreted and prioritised, and how value is assured and measured. Data was collected through semi-structured interviews with 23 participants from 14 agile software development organisations. The contribution of this study is fourfold. First, it examines how value is perceived amongst agile software development organisations. Second, it compares the perceptions and priorities of the perceived values by domains and roles. Third, it includes an examination of what practices are used to achieve value in industry, and what hinders the achievement of value. Fourth, it characterises what measurements are used to assure, and evaluate value-creation activities. (C) 2016 Elsevier Inc. All rights reserved.
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| 7. |
- Alahyari, Hiva, 1979, et al.
(författare)
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An exploratory study of waste in software development organizations using agile or lean approaches : A multiple case study at 14 organizations
- 2019
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Ingår i: Information and Software Technology. - : Elsevier B.V.. - 0950-5849 .- 1873-6025. ; 107, s. 78-94
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Tidskriftsartikel (refereegranskat)abstract
- Context: The principal focus of lean is the identification and elimination of waste from the process with respect to maximizing customer value. Similarly, the purpose of agile is to maximize customer value and minimize unnecessary work and time delays. In both cases the concept of waste is important. Through an empirical study, we explore how waste is approached in agile software development organizations. Objective: This paper explores the concept of waste in agile/lean software development organizations and how it is defined, used, prioritized, reduced, or eliminated in practice Method: The data were collected using semi-structured open-interviews. 23 practitioners from 14 embedded software development organizations were interviewed representing two core roles in each organization. Results: Various wastes, categorized in 10 different categories, were identified by the respondents. From the mentioned wastes, not all were necessarily waste per se but could be symptoms caused by wastes. From the seven wastes of lean, Task-switching was ranked as the most important, and Extra-features, as the least important wastes according to the respondents’ opinion. However, most companies do not have their own or use an established definition of waste, more importantly, very few actively identify or try to eliminate waste in their organizations beyond local initiatives on project level. Conclusion: In order to identify, recognize and eliminate waste, a common understanding, and a joint and holistic view of the concept is needed. It is also important to optimize the whole organization and the whole product, as waste on one level can be important on another, thus sub-optimization should be avoided. Furthermore, to achieve a sustainable and effective waste handling, both the short-term and the long-term perspectives need to be considered. © 2018 Elsevier B.V.
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| 8. |
- Ameller, D., et al.
(författare)
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Handling Non-functional Requirements in Model-Driven Development: An Ongoing Industrial Survey
- 2015
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Ingår i: 2015 IEEE 23rd International Requirements Engineering Conference (Re). - : IEEE. - 9781467369053
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Konferensbidrag (refereegranskat)abstract
- Model-Driven Development (MDD) is no longer a novel development paradigm. It has become mature from a research perspective and recent studies show its adoption in industry. Still, some issues remain a challenge. Among them, we are interested in the treatment of non-functional requirements (NFRs) in MDD processes. Very few MDD approaches have been reported to deal with NFRs (and they do it in a limited way). However, it is clear that NFRs need to be considered somehow in the final product of the MDD process. To better understand how NFRs are integrated into the existing MDD approaches, we have initiated the NFR4MDD project, a multi-national empirical study, based on interviews with companies working on MDD projects. Our project aims at surveying the state of the practice for this topic. In this paper, we summarize our research protocol and present the current status of our study. The discussion will focus on the peculiarities of our study's context and organization involving about 20 researchers from 8 European countries.
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| 9. |
- Berntsson Svensson, Richard, 1978, et al.
(författare)
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A Case Study Evaluation of the Guideline-Supported QUPER Model for Elicitation of Quality Requirements
- 2015
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Ingår i: Requirements Engineering: Foundation for Software Quality. - Cham : Springer-Verlag Berlin. - 0302-9743 .- 1611-3349. - 9783319161013 - 9783319161006 ; 9013, s. 230-246
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Konferensbidrag (refereegranskat)abstract
- For market-driven software product developing organizations operating on a competitive open market, it is important to plan the product's releases so that they can reach the market as early as possible with a competitive level of quality compared to its competitors' products. Hence, quality requirements can be seen as a key competitive advantage. The QUPER model was developed with the aim to support high-level decision-making in release planning of quality requirements. As a follow up on previous studies on QUPER, this study investigates: What are practitioners' views on the utilities of QUPER extended with guidelines including domain-specific examples? [Principal ideas/results] In the presented case study, a set of detailed guidelines of how to apply QUPER in practice, including how to handle cost dependencies between quality requirements, was evaluated at a case company in the mobile handset domain with 24 professionals using real quality requirements. The results point to the importance of having concrete guidelines combined with instructive examples from real practice, while it is not always obvious for a practitioner to transfer cost-dependency examples into the domains that are different from the example domain. The transferability of guidelines and examples to support methodology adoption is an interesting issue for further research.
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| 10. |
- Berntsson Svensson, Richard, 1978, et al.
(författare)
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Aligning Quality Requirements and Test Results with QUPER's Roadmap View for Improved High-Level Decision-Making
- 2015
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Ingår i: 2015 Ieee/Acm 2nd International Workshop on Requirements Engineering and Testing (Ret). - : IEEE. - 9781479919345
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Konferensbidrag (refereegranskat)abstract
- Weak alignment of requirements engineering (RE) and Software Testing (ST) may lead to problems in delivering the required products in time with the right quality. Despite the importance of aligning RE and ST, the research have mainly been focused on one or the other of RE and ST. Previous work has identified several challenges in aligning RE and ST related to Quality Requirements, for example, the need for tool support for QR, defining and managing QR, and verification of QR. In this position paper, we introduce a new view of the QUPER model, namely aligning QR targets and test results in QUPERs roadmap view. The alignment view was evaluated at a case company with 13 practitioners. The results show that the alignment of QR and test results using QUPER's roadmap view was viewed as an important input to the decision-making process.
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