scholarly journals Lessons learned from bugs in models of human history

2020 ◽  
Author(s):  
Aaron P. Ragsdale ◽  
Dominic Nelson ◽  
Simon Gravel ◽  
Jerome Kelleher
Keyword(s):  
Population Genetic ◽  
Population Genomics ◽  
Lessons Learned ◽  
Genetic Models ◽  
Human History ◽  
Software Developers ◽  
Demographic Models ◽  
Large Numbers ◽  
Genomic Regions ◽  
Made In

AbstractSimulation plays a central role in population genomics studies. Recent years have seen rapid improvements in software efficiency that make it possible to simulate large genomic regions for many individuals sampled from large numbers of populations. As the complexity of the demographic models we study grows, however, there is an ever-increasing opportunity to introduce bugs in their implementation. Here we describe two errors made in defining population genetic models using the msprime coalescent simulator that have found their way into the published record. We discuss how these errors have affected downstream analyses and give recommendations for software developers and users to reduce the risk of such errors.

Iterative Tutorial Design in the Product Development Cycle

1989 ◽  
Vol 33 (5) ◽  
pp. 268-272 ◽  
Author(s):  
Ronald Perkins ◽  
Louis A. Blatt ◽  
Daniel Workman ◽  
Susan F. Ehrlich
Keyword(s):  
Product Development ◽  
Lessons Learned ◽  
Initial Experience ◽  
Joint Effort ◽  
Software Developers ◽  
Development Cycle ◽  
On Line ◽  
Product Development Cycle ◽  
And Training ◽  
Made In

Early development of a tutorial fostered a joint effort between human factors professionals, software developers and training consultants that resulted in early resolution of many problems during the development of Wang Freestyle™, a new multimedia communication system. It was decided that new users of Freestyle should be able to use the basic annotation features without referring to any hardcopy documentation. To ensure this, iterative tests of evolving prototypes of (1) the software and (2) an on-line tutorial that was designed to teach any features of the system that were not immediately intuitive were carried out. Changes were made in the software and the tutorial, resulting in improvements to both. The methods used and some of the lessons learned from this initial experience with iterative tutorial development are discussed.

scholarly journals Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

2012 ◽  
Vol 367 (1587) ◽  
pp. 409-421 ◽  
Author(s):  
Michael W. Nachman ◽  
Bret A. Payseur
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Dna Sequence ◽  
Population Genetic ◽  
Sequence Variation ◽  
Genetic Models ◽  
Rate Variation ◽  
Ancestral Polymorphism ◽  
Dna Sequence Variation ◽  
Genomic Regions

Recently diverged taxa may continue to exchange genes. A number of models of speciation with gene flow propose that the frequency of gene exchange will be lower in genomic regions of low recombination and that these regions will therefore be more differentiated. However, several population-genetic models that focus on selection at linked sites also predict greater differentiation in regions of low recombination simply as a result of faster sorting of ancestral alleles even in the absence of gene flow. Moreover, identifying the actual amount of gene flow from patterns of genetic variation is tricky, because both ancestral polymorphism and migration lead to shared variation between recently diverged taxa. New analytic methods have been developed to help distinguish ancestral polymorphism from migration. Along with a growing number of datasets of multi-locus DNA sequence variation, these methods have spawned a renewed interest in speciation models with gene flow. Here, we review both speciation and population-genetic models that make explicit predictions about how the rate of recombination influences patterns of genetic variation within and between species. We then compare those predictions with empirical data of DNA sequence variation in rabbits and mice. We find strong support for the prediction that genomic regions experiencing low levels of recombination are more differentiated. In most cases, reduced gene flow appears to contribute to the pattern, although disentangling the relative contribution of reduced gene flow and selection at linked sites remains a challenge. We suggest fruitful areas of research that might help distinguish between different models.

Microanalysis of precipitates in a ferritic steel

1978 ◽  
Vol 36 (1) ◽  
pp. 618-619
Author(s):  
J.M. Titchmarsh
Keyword(s):  
Ferritic Steel ◽  
Particle Identification ◽  
Energy Dispersive ◽  
Objective Lens ◽  
Ferritic Steels ◽  
Replica Technique ◽  
X Ray ◽  
Large Numbers ◽  
Scanning Transmission ◽  
Made In

The advances in recent years in the microanalytical capabilities of conventional TEM's fitted with probe forming lenses allow much more detailed investigations to be made of the microstructures of complex alloys, such as ferritic steels, than have been possible previously. In particular, the identification of individual precipitate particles with dimensions of a few tens of nanometers in alloys containing high densities of several chemically and crystallographically different precipitate types is feasible. The aim of the investigation described in this paper was to establish a method which allowed individual particle identification to be made in a few seconds so that large numbers of particles could be examined in a few hours.A Philips EM400 microscope, fitted with the scanning transmission (STEM) objective lens pole-pieces and an EDAX energy dispersive X-ray analyser, was used at 120 kV with a thermal W hairpin filament. The precipitates examined were extracted using a standard C replica technique from specimens of a 2¼Cr-lMo ferritic steel in a quenched and tempered condition.

scholarly journals H3ABioNet genomic medicine and microbiome data portals hackathon proceedings

Database ◽  
2021 ◽  
Vol 2021 ◽  
Author(s):  
Faisal M Fadlelmola ◽  
Kais Ghedira ◽  
Yosr Hamdi ◽  
Mariem Hanachi ◽  
Fouzia Radouani ◽  
...  
Keyword(s):  
Ethnic Groups ◽  
Genomic Medicine ◽  
Lessons Learned ◽  
Team Work ◽  
Significant Progress ◽  
Team Members ◽  
Pan African ◽  
Scientific Expertise ◽  
Microbiome Data ◽  
Made In

Abstract African genomic medicine and microbiome datasets are usually not well characterized in terms of their origin, making it difficult to find and extract data for specific African ethnic groups or even countries. The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for developing data portals for African genomic medicine and African microbiomes to address this and ran a hackathon to initiate their development. The two portals were designed and significant progress was made in their development during the hackathon. All the participants worked in a very synergistic and collaborative atmosphere in order to achieve the hackathon's goals. The participants were divided into content and technical teams and worked over a period of 6 days. In response to one of the survey questions of what the participants liked the most during the hackathon, 55% of the hackathon participants highlighted the familial and friendly atmosphere, the team work and the diversity of team members and their expertise. This paper describes the preparations for the portals hackathon and the interaction between the participants and reflects upon the lessons learned about its impact on successfully developing the two data portals as well as building scientific expertise of younger African researchers. Database URL: The code for developing the two portals was made publicly available in GitHub repositories: [https://github.com/codemeleon/Database; https://github.com/codemeleon/AfricanMicrobiomePortal].

scholarly journals Whither Magnetic Hyperthermia? A Tentative Roadmap

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 706
Author(s):  
Irene Rubia-Rodríguez ◽  
Antonio Santana-Otero ◽  
Simo Spassov ◽  
Etelka Tombácz ◽  
Christer Johansson ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Nanoparticle Synthesis ◽  
Careful Analysis ◽  
Magnetic Hyperthermia ◽  
Lessons Learned ◽  
In Vivo Testing ◽  
Evolution Of Science ◽  
Made In ◽  
Critical Aspects

The scientific community has made great efforts in advancing magnetic hyperthermia for the last two decades after going through a sizeable research lapse from its establishment. All the progress made in various topics ranging from nanoparticle synthesis to biocompatibilization and in vivo testing have been seeking to push the forefront towards some new clinical trials. As many, they did not go at the expected pace. Today, fruitful international cooperation and the wisdom gain after a careful analysis of the lessons learned from seminal clinical trials allow us to have a future with better guarantees for a more definitive takeoff of this genuine nanotherapy against cancer. Deliberately giving prominence to a number of critical aspects, this opinion review offers a blend of state-of-the-art hints and glimpses into the future of the therapy, considering the expected evolution of science and technology behind magnetic hyperthermia.

scholarly journals Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 222
Author(s):  
Bartosz Ulaszewski ◽  
Joanna Meger ◽  
Jaroslaw Burczyk
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Genetic Studies ◽  
Genomic Libraries ◽  
Reduced Representation ◽  
Large Numbers ◽  
Broadleaved Tree Species ◽  
Fagus Sylvatica L ◽  
Reference Genomes ◽  
Future Population

Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.

scholarly journals Deploying triple artemisinin-based combination therapy (TACT) for malaria treatment in Africa: ethical and practical considerations

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Paulina Tindana ◽  
Freek de Haan ◽  
Chanaki Amaratunga ◽  
Mehul Dhorda ◽  
Rob W. van der Pluijm ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Combination Therapy ◽  
Southeast Asia ◽  
Malaria Control ◽  
Lessons Learned ◽  
Line Treatment ◽  
African Continent ◽  
First Line ◽  
First Line Treatment ◽  
Made In

AbstractMalaria remains a major cause of morbidity and mortality in Africa, particularly in children under five years of age. Availability of effective anti-malarial drug treatment is a cornerstone for malaria control and eventual malaria elimination. Artemisinin-based combination therapy (ACT) is worldwide the first-line treatment for uncomplicated falciparum malaria, but the ACT drugs are starting to fail in Southeast Asia because of drug resistance. Resistance to artemisinins and their partner drugs could spread from Southeast Asia to Africa or emerge locally, jeopardizing the progress made in malaria control with the increasing deployment of ACT in Africa. The development of triple artemisinin-based combination therapy (TACT) could contribute to mitigating the risks of artemisinin and partner drug resistance on the African continent. However, there are pertinent ethical and practical issues that ought to be taken into consideration. In this paper, the most important ethical tensions, some implementation practicalities and preliminary thoughts on addressing them are discussed. The discussion draws upon data from randomized clinical studies using TACT combined with ethical principles, published literature and lessons learned from the introduction of artemisinin-based combinations in African markets.

scholarly journals Sex as a Prognostic Factor in Systematic Reviews: Challenges and Lessons Learned

2021 ◽  
Vol 11 (6) ◽  
pp. 441
Author(s):  
Elena Stallings ◽  
Alba Antequera ◽  
Jesús López-Alcalde ◽  
Miguel García-Martín ◽  
Gerard Urrútia ◽  
...  
Keyword(s):  
Prognostic Factor ◽  
Systematic Reviews ◽  
Lessons Learned ◽  
Disease State ◽  
Sex And Gender ◽  
Funding Agencies ◽  
And Gender ◽  
Baseline Factor ◽  
Clinical Domain ◽  
Made In

Sex is a common baseline factor collected in studies that has the potential to be a prognostic factor (PF) in several clinical areas. In recent years, research on sex as a PF has increased; however, this influx of new studies frequently shows conflicting results across the same treatment or disease state. Thus, systematic reviews (SRs) addressing sex as a PF may help us to better understand diseases and further personalize healthcare. We wrote this article to offer insights into the challenges we encountered when conducting SRs on sex as a PF and suggestions on how to overcome these obstacles, regardless of the clinical domain. When carrying out a PF SR with sex as the index factor, it is important to keep in mind the modifications that must be made in various SR stages, such as modifying the PF section of CHARMS-PF, adjusting certain sections of QUIPS and extracting data on the sex and gender terms used throughout the studies. In this paper, we provide an overview of the lessons learned from carrying out our reviews on sex as a PF in different disciplines and now call on researchers, funding agencies and journals to realize the importance of studying sex as a PF.

Online ethnography: a study of software developers and software development

2015 ◽  
Vol 10 (2) ◽  
pp. 188-202 ◽  
Author(s):  
Jose Rodrigo Cordoba-Pachon ◽  
Cecilia Loureiro-Koechlin
Keyword(s):  
Qualitative Research ◽  
Lessons Learned ◽  
Human Interaction ◽  
Research Subjects ◽  
Software Developers ◽  
Online Data ◽  
Social Phenomena ◽  
Content Type ◽  
Online Ethnography ◽  
Area Of Interest

Purpose – Qualitative research has made important contributions to social science by enabling researchers to engage with people and get an in-depth understanding of their views, beliefs and perceptions about social phenomena. With new and electronically mediated forms of human interaction (e.g. the online world), there are new opportunities for researchers to gather data and participate with or observe people in online groups. The purpose of this paper is to present features, challenges and possibilities for online ethnography as an innovative form of qualitative research. Design/methodology/approach – Ethnography is about telling a story about what happens in a particular setting or settings. In order to do this online, it is important to revisit, adopt and adapt some ideas about traditional (offline) ethnography. The paper distinguishes online ethnography from other types of research. It draws some generic features of online ethnography and identifies challenges for it. With these ideas in mind the paper presents and provides a reflection of an online ethnography of software developers. Findings – Online ethnography can provide valuable insights about social phenomena. The paper identifies generic features of this approach and a number of challenges related to its practice. These challenges have to do with to the choice of settings, use of online data for research, representation of people and generation of valuable and useful knowledge. The paper also highlights issues for future consideration in research and practice. Practical implications – The ethnography helped the researcher to identify and address a number of methodological challenges in practice and position herself in relation to relevant audiences she wanted to speak to. The paper also suggests different orientations to online ethnography. Lessons learned highlight potential contributions as well as further possibilities for qualitative research in the online world. Originality/value – Online ethnography offers possibilities to engage with a global audience of research subjects. For academics and practitioners the paper opens up possibilities to use online tools for research and it shows that the use of these tools can help overcome difficulties in access and interaction with people and to study a diversity of research topics, not only those that exist online. The paper offers guidance for researchers about where to start and how to proceed if they want to conduct online ethnography and generate useful and valuable knowledge in their area of interest.

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