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11.
  • Baxter, Amanda L., et al. (author)
  • Collaborative experience between scientific software projects using Agile Scrum development
  • 2022
  • In: Software, practice & experience. - : John Wiley & Sons. - 0038-0644 .- 1097-024X. ; 52:10, s. 2077-2096
  • Journal article (peer-reviewed)abstract
    • Developing sustainable software for the scientific community requires expertise in software engineering and domain science. This can be challenging due to the unique needs of scientific software, the insufficient resources for software engineering practices in the scientific community, and the complexity of developing for evolving scientific contexts. While open-source software can partially address these concerns, it can introduce complicating dependencies and delay development. These issues can be reduced if scientists and software developers collaborate. We present a case study wherein scientists from the SuperNova Early Warning System collaborated with software developers from the Scalable Cyberinfrastructure for Multi-Messenger Astrophysics project. The collaboration addressed the difficulties of open-source software development, but presented additional risks to each team. For the scientists, there was a concern of relying on external systems and lacking control in the development process. For the developers, there was a risk in supporting a user-group while maintaining core development. These issues were mitigated by creating a second Agile Scrum framework in parallel with the developers' ongoing Agile Scrum process. This Agile collaboration promoted communication, ensured that the scientists had an active role in development, and allowed the developers to evaluate and implement the scientists' software requirements. The collaboration provided benefits for each group: the scientists actuated their development by using an existing platform, and the developers utilized the scientists' use-case to improve their systems. This case study suggests that scientists and software developers can avoid scientific computing issues by collaborating and that Agile Scrum methods can address emergent concerns.
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12.
  • Peloso, Gina M., et al. (author)
  • Association of Exome Sequences with Cardiovascular Traits among Blacks in the Jackson Heart Study
  • 2016
  • In: Circulation: Cardiovascular Genetics. - 1942-325X. ; 9:4, s. 368-374
  • Journal article (peer-reviewed)abstract
    • Background-The correlation of null alleles with human phenotypes can provide insight into gene function in humans. In individuals of African ancestry, we set out to identify null and damaging missense variants, and test these variants for association with a range of cardiovascular phenotypes. Methods and Results-We performed whole-exome sequencing in 3223 black individuals from the Jackson Heart Study and found a total of 729 666 variant sites with minor allele frequency <5%, including 17 263 null variants and 49 929 missense variants predicted to be damaging by in silico algorithms. We tested null and damaging missense variants within each gene for association with 36 cardiovascular traits. We found 3 associations that met our prespecified level of significance (α=1.1×10-7). Null and damaging missense variants in PCSK9 were associated with 36 mg/dL lower low-density lipoprotein cholesterol (P=3×10-21). Three individuals in their 50s with complete PCSK9 deficiency (each compound heterozygote for PCSK9 p.Y142X and p.C679X) were identified, with one having a coronary artery calcification score in the 83rd percentile despite a low-density lipoprotein cholesterol of 32 mg/dL. A damaging missense variant in HBQ1 (p.G52A) was associated with a 2 pg/cell lower mean corpuscular hemoglobin (P=9×10-13) and rare damaging missense variants in VPS13A with higher red blood cell distribution width (P=9.9×10-8). Conclusions-A limited number of null/damaging alleles with a large effect on cardiovascular traits were detectable in ≈3000 black individuals.
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  • Result 11-12 of 12
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journal article (12)
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peer-reviewed (12)
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Groop, Leif (4)
Melander, Olle (4)
Larsson, Anders (3)
Rolandsson, Olov (3)
Sahebkar, Amirhossei ... (3)
Nilsson, Peter (3)
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Tuomi, Tiinamaija (3)
DeFronzo, Ralph A. (3)
McKee, Martin (3)
Madotto, Fabiana (3)
Fadista, Joao (3)
Salomaa, Veikko (3)
Koyanagi, Ai (3)
Aboyans, Victor (3)
Koul, Parvaiz A. (3)
Lind, Lars (3)
Dhimal, Meghnath (3)
Sheikh, Aziz (3)
Adhikari, Tara Balla ... (3)
Hay, Simon I. (3)
Deloukas, Panos (3)
Freedman, Barry I. (3)
Abbafati, Cristiana (3)
Abebe, Zegeye (3)
Afarideh, Mohsen (3)
Agrawal, Sutapa (3)
Alahdab, Fares (3)
Badali, Hamid (3)
Badawi, Alaa (3)
Bensenor, Isabela M. (3)
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Farzadfar, Farshad (3)
Feigin, Valery L. (3)
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Hassen, Hamid Yimam (3)
Jonas, Jost B. (3)
Kasaeian, Amir (3)
Khalil, Ibrahim A. (3)
Khang, Young-Ho (3)
Kimokoti, Ruth W. (3)
Lotufo, Paulo A. (3)
Malekzadeh, Reza (3)
Mendoza, Walter (3)
Miller, Ted R. (3)
Mokdad, Ali H. (3)
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English (12)
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