| 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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Not all requirements prioritization criteria are equal at all times: A quantitative analysis
- 2024
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Ingår i: Journal of Systems and Software. - 0164-1212. ; 209
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Tidskriftsartikel (refereegranskat)abstract
- Requirement prioritization is recognized as an important decision-making activity in requirements engineering. Requirement prioritization is applied to determine which requirements should be implemented and released. In order to prioritize requirements, there are several approaches/techniques/tools that use different requirements prioritization criteria, which are often identified by gut feeling instead of an in-depth analysis of which criteria are most important to use. Therefore, in this study we investigate which requirements prioritization criteria are most important to use in industry when determining which requirements are implemented and released, and if the importance of the criteria change depending on how far a requirement has reached in the development process. We conducted a quantitative study where quantitative data was collected through a case study of one completed project from one software developing company by extracting 32,139 requirements prioritization decisions based on eight requirements prioritization criteria for 11,110 requirements. The results show that not all requirements prioritization criteria are equally important, and this change depending on how far a requirement has reached in the development process. For example, for requirements prioritization decisions before iteration/sprint planning, having high Business value had an impact on the decisions, but after iteration/sprint planning, having high Business value had no impact. Editor's note: Open Science material was validated by the Journal of Systems and Software Open Science Board.
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| 3. |
- Berntsson Svensson, Richard, et al.
(författare)
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Prioritization of quality requirements : State of practice in eleven companies
- 2011
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Ingår i: 2011 IEEE 19th International Requirements Engineering Conference, RE 2011; Trento; 29 August 2011 through 2 September 2011. - Trento : IEEE. - 9781457709234 ; , s. 69-78, s. 69-78
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Konferensbidrag (refereegranskat)abstract
- Requirements prioritization is recognized as an important but challenging activity in software product development. For a product to be successful, it is crucial to find the right balance among competing quality requirements. Although literature offers many methods for requirements prioritization, the research on prioritization of quality requirements is limited. This study identifies how quality requirements are prioritized in practice at 11 successful companies developing software intensive systems. We found that ad-hoc prioritization and priority grouping of requirements are the dominant methods for prioritizing quality requirements. The results also show that it is common to use customer input as criteria for prioritization but absence of any criteria was also common. The results suggests that quality requirements by default have a lower priority than functional requirements, and that they only get attention in the prioritizing process if decision-makers are dedicated to invest specific time and resources on QR prioritization. The results of this study may help future research on quality requirements to focus investigations on industry-relevant issues.
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| 4. |
- Berntsson Svensson, Richard, et al.
(författare)
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Quality Requirements in Industrial Practice – An Extended Interview Study at Eleven Companies
- 2012
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Ingår i: IEEE Transactions on Software Engineering. - : IEEE. - 0098-5589 .- 1939-3520. ; 38:4, s. 923-935
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Tidskriftsartikel (refereegranskat)abstract
- In order to create a successful software product and assure its quality, it is not enough to fulfill the functional requirements, it is also crucial to find the right balance among competing quality requirements (QR). An extended, previosluy piloted, interview study was performed to identify specific challenges associated with the selection, trade-off, and management of QR in industrial practice. Data was collected through semi-structured interviews with eleven product managers and eleven project leaders from eleven software companies. The contribution of this study is fourfold: First, it compares how QR are handled in two cases, companies working in business-to-business markets, and companies that are working in business-to-consumer markets. These two are also compared in terms of impact on the handling of QRs. Second, it compares the perceptions and priorities of QR by product and project management respectively. Third, it includes an examination of the interdependencies among quality requirements perceived as most important by the practitioners. Fourth, it characterizes the selection and management of QR in down-stream development activities.
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| 5. |
- Berntsson Svensson, Richard, 1978, et al.
(författare)
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Quality Requirements in Industrial Practice - An Extended Interview Study at Eleven Companies
- 2011
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Ingår i: IEEE Transactions on Software Engineering. - 0098-5589 .- 1939-3520.
-
Tidskriftsartikel (refereegranskat)abstract
- In order to create a successful software product and assure its quality, it is not enough to fulfill the functional requirements, it is also crucial to find the right balance among competing quality requirements (QR). An extended, previously piloted, interview study was performed to identify specific challenges associated with the selection, trade-off, and management of QR in industrial practice. Data was collected through semi-structured interviews with eleven product managers and eleven project leaders from eleven software companies. The contribution of this study is fourfold: First, it compares how QR are handled in two cases, companies working in business-to-business markets, and companies that are working in business-to-consumer markets. These two are also compared in terms of impact on the handling of QRs. Second, it compares the perceptions and priorities of QR by product and project management respectively. Third, it includes an examination of the interdependencies among quality requirements perceived as most important by the practitioners. Fourth, it characterizes the selection and management of QR in down-stream development activities.
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| 6. |
- 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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| 7. |
- Estrada, Karol, et al.
(författare)
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Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
- 2012
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 44:5, s. 491-501
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Tidskriftsartikel (refereegranskat)abstract
- Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P < 5 × 10(-8)). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P < 5 × 10(-4), Bonferroni corrected), of which six reached P < 5 × 10(-8), including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility.
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| 8. |
- Gad, Helge, et al.
(författare)
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MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool
- 2014
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 508:7495, s. 215-221
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Tidskriftsartikel (refereegranskat)abstract
- Cancers have dysfunctional redox regulation resulting in reactive oxygen species production, damaging both DNA and free dNTPs. The MTH1 protein sanitizes oxidized dNTP pools to prevent incorporation of damaged bases during DNA replication. Although MTH1 is non-essential in normal cells, we show that cancer cells require MTH1 activity to avoid incorporation of oxidized dNTPs, resulting in DNA damage and cell death. We validate MTH1 as an anticancer target in vivo and describe small molecules TH287 and TH588 as first-in-class nudix hydrolase family inhibitors that potently and selectively engage and inhibit the MTH1 protein in cells. Protein co-crystal structures demonstrate that the inhibitors bindin the active site of MTH1. The inhibitors cause incorporation of oxidized dNTPs in cancer cells, leading to DNA damage, cytotoxicity and therapeutic responses in patient-derived mouse xenografts. This study exemplifies the non-oncogene addiction concept for anticancer treatment and validates MTH1 as being cancer phenotypic lethal.
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| 9. |
- Glantz, Maria, et al.
(författare)
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Impact of protease and lipase activities on quality of Swedish raw milk
- 2020
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Ingår i: International Dairy Journal. - : Elsevier BV. - 0958-6946. ; 107
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Tidskriftsartikel (refereegranskat)abstract
- An increasing demand for dairy products with long shelf-life is foreseen. A limiting factor for maintaining high quality of these products is the activity of spoilage enzymes during storage. Lipase and protease activities in Swedish raw milk at farm and dairy level were investigated, analysing milk samples from three geographical regions and two seasons. Lipase activity in milk at farm level was affected by regional and seasonal variations, whereas at dairy level only season had an effect. Lipase activity was positively correlated with ionic calcium. For protease activity, no effect of either region or season was seen. Degradation products, e.g., free fatty acids, peptides and plasmin proteolysis products, varied differently between season and geographical origin at both farm and dairy level. The results indicate that lipase and protease activities are important for raw milk quality, while ionic calcium might be a future indicator for milk fat stability.
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| 10. |
- Kuang, Qie, et al.
(författare)
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A refined atomic model for microsomal glutathione transferase 1 from electron crystallography
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used electron crystallography of two-dimensional (2D) crystals in order to determine an atomic model of rat MGST1 in a lipid environment. The 2D crystals were of the p6 two-sided plane group symmetry. For the refinement, information to 3.5 Å resolution from 225 electron diffraction patterns recorded from specimens at tilt angles up to 66° was used. The model comprises 123 of the 155 amino acid residues, two structured phospholipid molecules, two hydrocarbon chains, and one glutathione (GSH) molecule. Interactions between subunits form trimers centered on the crystallographic three-fold axes of the unit cell. The GSH substrate binds in an extended conformation at the interface between two subunits of the trimer. The location of GSH is supported by mutagenesis data in vitro.
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