scholarly journals Clinical Annotation Reference Templates: a resource for consistent variant annotation

2018 ◽  
Vol 3 ◽  
pp. 146
Author(s):  
Shawn Yost ◽  
Márton Münz ◽  
Shazia Mahamdallie ◽  
Anthony Renwick ◽  
Elise Ruark ◽  
...  
Keyword(s):  
Reference Genome ◽  
Selection Process ◽  
Genetic Research ◽  
Open Science ◽  
Stable Set ◽  
Annotate Gene ◽  
Variant Annotation ◽  
Gene Variation ◽  
Clinical Annotation ◽  
The Impact

Annotating the impact of a variant on a gene is a vital component of genetic medicine and genetic research. Different gene annotations for the same genomic variant are possible, because different structures and sequences for the same gene are available. The clinical community typically use RefSeq NMs to annotate gene variation, which do not always match the reference genome. The scientific community typically use Ensembl ENSTs to annotate gene variation. These match the reference genome, but often do not match the equivalent NM. Often the transcripts used to annotate gene variation are not provided, impeding interoperability and consistency. Here we introduce the concept of the Clinical Annotation Reference Template (CART). CARTs are analogous to the reference genome; they provide a universal standard template so reference genomic coordinates are consistently annotated at the protein level. Naturally, there are many situations where annotations using a specific transcript, or multiple transcripts are useful. The aim of the CARTs is not to impede this practice. Rather, the CART annotation serves as an anchor to ensure interoperability between different annotation systems and variant frequency accuracy. Annotations using other explicitly-named transcripts should also be provided, wherever useful. We have integrated transcript data to generate CARTs for over 18,000 genes, for both GRCh37 and GRCh38, based on the associated NM and ENST identified through the CART selection process. Each CART has a unique ID and can be used individually or as a stable set of templates; CART37A for GRCh37 and CART38A for GRCh38. We have made the CARTs available on the UCSC browser and in different file formats on the Open Science Framework: https://osf.io/tcvbq/. We have also made the CARTtools software we used to generate the CARTs available on GitHub. We hope the CARTs will be useful in helping to drive transparent, stable, consistent, interoperable variant annotation.

Students’ Management to Increase the Character and Achievement in MAN 2 Banjarnegara

2018 ◽  
Vol 2 ◽  
Author(s):  
Sidik Wibowo Akhmad
Keyword(s):  
Academic Achievement ◽  
Extracurricular Activities ◽  
Selection Process ◽  
Skill Test ◽  
Spare Time ◽  
New Students ◽  
Strong Motivation ◽  
Character Building ◽  
The Impact ◽  
Enrollment Process

The purpose of this study was to describe the students’ management in increasing the character and achievement in MAN 2 Banjarnegara including: (1) the enrollment process of new students, (2) guiding students through discipline, noble character building, academic and non-academic achievement, and (3) the impact of character building and the achievement for students MAN 2 Banjarnegara. This research implemented descriptive qualitative approach. The data collection techniques were in-depth interview, observation, and documentation study. The validity of the data used three criteria; namely credibility, dependability, and conformability. The findings of this study were: The first, the enrollment process of the new students was made a breakthrough during the registration of academic and non-academic achievement of scholarships, the selection process was conducted through the value of official learning reports, certificate of championship/achievement, academic potential test and non-academic, and also the skill test. For the students who passed the selection process were supposed to sign the achievement contract during the learning process at MAN 2 Banjarnegara. The second, the character building was done by the concept of habituation and activities program that were integrated in curricular and extracurricular activities. The third, students who joined the academic and non-academic achievement programs at MAN 2 Banjarnegara had strong motivation, spirit of competition to achieve higher achievement and more focus on self-development and they could anticipate the usage of spare time for positive things/activities.

scholarly journals The Impact of Social Media Use on Consumers’ Restaurant Consumption Experiences: A Qualitative Study

2021 ◽  
Vol 13 (12) ◽  
pp. 6581
Author(s):  
Jooyoung Hwang ◽  
Anita Eves ◽  
Jason L. Stienmetz
Keyword(s):  
Decision Making ◽  
Social Media ◽  
Selection Process ◽  
Decision Making Process ◽  
Structured Interviews ◽  
High Standards ◽  
Tourism And Hospitality Industry ◽  
Tourism And Hospitality ◽  
Search For Information ◽  
The Impact

Travellers have high standards and regard restaurants as important travel attributes. In the tourism and hospitality industry, the use of developed tools (e.g., smartphones and location-based tablets) has been popularised as a way for travellers to easily search for information and to book venues. Qualitative research using semi-structured interviews based on the face-to-face approach was adopted for this study to examine how consumers’ restaurant selection processes are performed with the utilisation of social media on smartphones. Then, thematic analysis was adopted. The findings of this research show that the adoption of social media on smartphones is positively related with consumers’ gratification. More specifically, when consumers regard that process, content and social gratification are satisfied, their intention to adopt social media is fulfilled. It is suggested by this study that consumers’ restaurant decision-making process needs to be understood, as each stage of the decision-making process is not independent; all the stages of the restaurant selection process are organically connected and influence one another.

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

scholarly journals The impact of participation in genetic research for families with cleft lip with and without cleft palate: a qualitative study

2014 ◽  
Vol 5 (3) ◽  
pp. 249-256 ◽  
Author(s):  
Lynley J. Donoghue ◽  
Margaret A. Sahhar ◽  
Ravi Savarirayan ◽  
Supriya Raj ◽  
Nicky M. Kilpatrick ◽  
...  
Keyword(s):  
Qualitative Study ◽  
Cleft Palate ◽  
Cleft Lip ◽  
Genetic Research ◽  
The Impact

Open science reforms: Strengths, challenges, and future directions

2021 ◽  
Author(s):  
Kathryn R. Wentzel
Keyword(s):  
Research Design ◽  
Educational Psychology ◽  
Open Science ◽  
Policy And Practice ◽  
Future Directions ◽  
Science Practices ◽  
Research Findings ◽  
Potential Benefits ◽  
The Impact

In this article, I comment on the potential benefits and limitations of open science reforms for improving the transparency and accountability of research, and enhancing the credibility of research findings within communities of policy and practice. Specifically, I discuss the role of replication and reproducibility of research in promoting better quality studies, the identification of generalizable principles, and relevance for practitioners and policymakers. Second, I suggest that greater attention to theory might contribute to the impact of open science practices, and discuss ways in which theory has implications for sampling, measurement and research design. Ambiguities concerning the aims of preregistration and registered reports also are highlighted. In conclusion, I discuss structural roadblocks to open science reform and reflect on the relevance of these reforms for educational psychology.

Information science’s contributions towards emerging open evaluation practices

2019 ◽  
Vol 20 (1) ◽  
pp. 2-16
Author(s):  
Leonor Gaspar Pinto ◽  
Paula Ochôa
Keyword(s):  
Information Science ◽  
Stakeholder Participation ◽  
Open Science ◽  
General Tendency ◽  
Sustainability Transitions ◽  
Transdisciplinary Approach ◽  
Content Type ◽  
Research On Evaluation ◽  
Social Sciences And Humanities ◽  
The Impact

Purpose The purpose of this paper is to discuss emerging practices in open evaluation, namely, the concept of co-evaluation and how research on evaluation developed within information science can contribute to enhance stakeholders and citizens’ involvement in open science. Design/methodology/approach A meta-evaluative and transdisciplinary approach – directed toward the intersection between information science, evaluation, competences management, sustainability transitions management and participatory methodologies – provided the basis for the identification and subsequent reflection on the levels of stakeholder participation embedded into ISO 16439’s (2014) methods for assessing the impact of libraries and on the domains and competences to be mobilized for (co)evaluation. The contributions of Engaged 2020 Action Catalogue, as well as several taxonomies of evaluator competences and the Council of Europe’s (2016) conceptual model of competences for a democratic culture were particularly relevant for this (re)construction process. Findings Two results of the line of research carried out since 2012 at the Faculty of Social Sciences and Humanities of the Universidade NOVA de Lisboa (Portugal) can significantly contribute to improve stakeholders’ participation in Open Science: ISO 16439’s systematization of methods and procedures for assessing the impact of libraries and the (co-)evaluation competency framework. Originality/value This paper presents the transdisciplinary concept of co-evaluation and examines the current epistemological challenges to science by analyzing the general tendency to openness through the lens of research on evaluation and participatory methods developed within information science.

scholarly journals The Project TALENT Twin and Sibling Study

2012 ◽  
Vol 16 (1) ◽  
pp. 437-448 ◽  
Author(s):  
Carol A. Prescott ◽  
Deanna Lyter Achorn ◽  
Ashley Kaiser ◽  
Lindsey Mitchell ◽  
John J. McArdle ◽  
...  
Keyword(s):  
Genetic Research ◽  
Original Data ◽  
Family Characteristics ◽  
Shared Environment ◽  
Occupational Outcomes ◽  
School Based ◽  
The Family ◽  
Specific Factors ◽  
The Impact

Project TALENT is a US national longitudinal study of about 377,000 individuals born in 1942–1946, first assessed in 1960. Students in about 1,200 schools participated in a 2-day battery covering aptitudes, abilities, interests, and individual and family characteristics (Flanagan, 1962; www.projectTALENT.org). Follow-up assessments 1, 5, and 11 years later assessed educational and occupational outcomes. The sample includes approximately 92,000 siblings from 40,000 families, including 2,500 twin pairs and 1,200 other siblings of twins. Until recently, almost no behavior genetic research has been conducted with the sample. In the original data collection information was not collected with the intent to link family members. Recently, we developed algorithms using names, addresses, birthdates, and information about family structure to link siblings and identify twins. We are testing several methods to determine zygosity, including use of yearbook photographs. In this paper, we summarize the design and measures in Project TALENT, describe the Twin and Sibling sample, and present our twin-sib-classmate model. In most twin and family designs, the ‘shared environment’ includes factors specific to the family combined with between-family differences associated with macro-level variables such as socioeconomic status. The school-based sampling design used in Project TALENT provides a unique opportunity to partition the shared environment into variation shared by siblings, specific to twins, and associated with school- and community-level factors. The availability of many measured characteristics on the family, schools, and neighborhoods enhances the ability to study the impact of specific factors on behavioral variation.

scholarly journals An open toolkit for tracking open science partnership implementation and impact

2019 ◽  
Vol 3 ◽  
pp. 1442 ◽  
Author(s):  
E. Richard Gold ◽  
Sarah E. Ali-Khan ◽  
Liz Allen ◽  
Lluis Ballell ◽  
Manoel Barral-Netto ◽  
...  
Keyword(s):  
Annual Report ◽  
Open Data ◽  
Structured Interview ◽  
Open Science ◽  
Social Scientists ◽  
Policy Makers ◽  
Ethical Concerns ◽  
Research And Innovation ◽  
Survey Form ◽  
The Impact

Serious concerns about the way research is organized collectively are increasingly being raised. They include the escalating costs of research and lower research productivity, low public trust in researchers to report the truth, lack of diversity, poor community engagement, ethical concerns over research practices, and irreproducibility. Open science (OS) collaborations comprise of a set of practices including open access publication, open data sharing and the absence of restrictive intellectual property rights with which institutions, firms, governments and communities are experimenting in order to overcome these concerns. We gathered two groups of international representatives from a large variety of stakeholders to construct a toolkit to guide and facilitate data collection about OS and non-OS collaborations. Ultimately, the toolkit will be used to assess and study the impact of OS collaborations on research and innovation. The toolkit contains the following four elements: 1) an annual report form of quantitative data to be completed by OS partnership administrators; 2) a series of semi-structured interview guides of stakeholders; 3) a survey form of participants in OS collaborations; and 4) a set of other quantitative measures best collected by other organizations, such as research foundations and governmental or intergovernmental agencies. We opened our toolkit to community comment and input. We present the resulting toolkit for use by government and philanthropic grantors, institutions, researchers and community organizations with the aim of measuring the implementation and impact of OS partnership across these organizations. We invite these and other stakeholders to not only measure, but to share the resulting data so that social scientists and policy makers can analyse the data across projects.

scholarly journals Exploring the Impact of Applicants’ Gender and Religion on Principals’ Screening Decisions for Assistant Principal Applicants

2009 ◽  
Vol 4 (1) ◽  
Author(s):  
Susan C. Bon
Keyword(s):  
High School Principals ◽  
Assistant Principals ◽  
Selection Process ◽  
Leadership Positions ◽  
Employment Selection ◽  
Female Principals ◽  
Selection Decisions ◽  
Potential Impact ◽  
And Gender ◽  
The Impact

In this experimental study, a national random sample of high school principals (stratified by gender) were asked to evaluate hypothetical applicants whose resumes varied by religion (Jewish, Catholic, nondenominational) and gender (male, female) for employment as assistant principals. Results reveal that male principals rate all applicants higher than female principals and that the gender and religion of applicants failed to negatively or positively affect principals’ evaluations. These results suggest that discrimination based on an applicant’s gender and religion failed to be manifested during the pre-interview stage of the selection process. The paper concludes with a theoretical discussion of the distinction between explicit and implicit prejudice, and encourages future researchers to investigate the potential impact of prejudice on employment selection decisions and to consider whether schools should promote diversity in leadership positions.

scholarly journals Weather and Climate Science in the Digital Era

2019 ◽  
Author(s):  
Martine G. de Vos ◽  
Wilco Hazeleger ◽  
Driss Bari ◽  
Jorg Behrens ◽  
Sofiane Bendoukha ◽  
...  
Keyword(s):  
Climate Science ◽  
Open Science ◽  
Added Value ◽  
The Road ◽  
Research Software ◽  
Digital Era ◽  
Combining Data ◽  
Weather And Climate ◽  
Computer Scientists ◽  
The Impact

Abstract. The need for open science has been recognized by the communities of meteorology and climate science. However, while these domains are mature in terms of applying digital technologies, these are lagging behind where the implementation of open science methodologies is concerned. In a session on Weather and Climate Science in the Digital Era at the 14th IEEE International eScience conference domain specialists and data and computer scientists discussed the road towards open weather and climate science. The studies presented in the conference session showed the added value of shared data, software and platforms through, for instance, combining data sets from disparate sources, increased accuracy and skill of simulations and forecasts at local scales, and improved consistency of data products. We observed that sharing data and code is important, but not sufficient to achieve open weather and climate science and that here are important issues to address. At the level of technology, the implementation of the FAIR principles to many datasets used in weather and climate science remains a challenge due to their origin, scalability, or legal barriers. Furthermore, the complexity of current software platforms limits collaboration between researchers and optimal use of open science tools and methods. The main challenges we observed, however, were non-technical and impact the system of science as a whole. There is a need for new roles and responsibilities at the interface of science and digital technology, e.g., data stewards and research software engineers. This requires the personnel portfolio of academic institutions to be more diverse, and in addition, a broader consideration of the impact of academic work, beyond publishing and teaching. Besides, new policies regarding open weather and climate science should be developed in an inclusive way to engage all stakeholders, including non-academic parties such as meteorological institutions. We acknowledge that open weather and climate science requires effort to change, but the benefits are large. As can already be observed from the studies presented in the conference it leads to much faster progress in understanding the world.

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