scholarly journals Analysis, identification and visualization of subgroups in genomics

2020 ◽  
Author(s):  
Gunnar Völkel ◽  
Simon Laban ◽  
Axel Fürstberger ◽  
Silke D Kühlwein ◽  
Nensi Ikonomi ◽  
...  
Keyword(s):  
Large Scale ◽  
Somatic Mutations ◽  
Target Selection ◽  
Gene Mutations ◽  
Use Case ◽  
The Past ◽  
Wide Availability ◽  
Approaches To Study ◽  
User Friendly ◽  
Personalized Intervention

Abstract Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact [email protected], phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502

scholarly journals GDS: A Genomic Database for Strawberries (Fragaria spp.)

Horticulturae ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. 41
Author(s):  
Yuhan Zhou ◽  
Yushan Qiao ◽  
Zhiyou Ni ◽  
Jianke Du ◽  
Jinsong Xiong ◽  
...  
Keyword(s):  
Large Scale ◽  
Genomic Data ◽  
Synteny Analysis ◽  
Genome Sequences ◽  
Community Resource ◽  
Genome Database ◽  
The Past ◽  
Gene Search ◽  
User Friendly ◽  
Integration Analysis

Strawberry species (Fragaria spp.) are known as the “queen of fruits” and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released. The reuse of these large amount of genomic data, and the more large-scale comparative analyses are very challenging to both plant biologists and strawberry breeders. To promote the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools, we have developed the Genome Database for Strawberry (GDS). This platform integrates the genome collection, storage, integration, analysis, and dissemination of large amounts of data for researchers engaged in the study of strawberry. We collected and formatted the eight published strawberry genomes. We constructed the GDS based on Linux, Apache, PHP and MySQL. Different bioinformatic software were integrated. The GDS contains data from eight strawberry species, as well as multiple tools such as BLAST, JBrowse, synteny analysis, and gene search. It has a designed interface and user-friendly tools that perform a variety of query tasks with a few simple operations. In the future, we hope that the GDS will serve as a community resource for the study of strawberries.

Password-Less Authentication

2019 ◽  
pp. 190-212
Author(s):  
Rahul Singh Chowhan ◽  
Rohit Tanwar
Keyword(s):  
Great Benefit ◽  
Use Case ◽  
Unauthorized Access ◽  
Research Opportunities ◽  
Traditional System ◽  
The Past ◽  
Working Principle ◽  
User Friendly ◽  
Use Case Diagram ◽  
The Way

Over the years, passwords have been our safeguards by acting to prevent one's data from unauthorized access. With the advancement of technologies, the way we have been using passwords has changed and transformed into much secure yet more user friendly than they were ever been in the past. However, the vulnerabilities identified and observed in this traditional system has motivated industry and researchers to find some alternate where there is no threat like stealing, hacking, and cracking of password. This chapter discusses the major developed password-less authentication techniques in detail and also puts an effort to explain the in-depth details along with the working principle of each of the technique through a use-case diagram. It would be of great benefit and contribution to the callow trying to explore research opportunities in this area.

scholarly journals Applied translation studies and transdisciplinary action research: Understanding, learning and transforming translation in professional contexts

2021 ◽  
Vol 25 (2) ◽  
pp. 443-461
Author(s):  
Gary Massey
Keyword(s):  
Action Research ◽  
Large Scale ◽  
Translation Studies ◽  
Use Case ◽  
The Past ◽  
Home Institution ◽  
Key Factor ◽  
And Performance ◽  
Professional Contexts

Proceeding from accepted shared definitions of applied linguistics that stress its practical, real-world orientation and instrumentality, this article seeks to move the focus from the interdisciplinarity that has been identified as the nexus of translation studies in the past to how its applied branches should systematically engage with an emerging transdisciplinary research paradigm. It argues that the shift can and will be a key factor, challenge and opportunity in the onward development of applied translation studies as it seeks to adequately address the situated realities of professional translation. The article reveals how transdisciplinarity, operationalised as action research, offers a viable framework for investigating, understanding and learning about what translators really do in working contexts and settings, with a view to identifying issues, improving practices, processes and performance, and ultimately transforming the profession for the good of those it employs and serves. In doing so, it considers approaches from cognitive translatology, based largely on a 4EA cognitive paradigm, and translatorial linguistic ethnography, where researchers are gradually but progressively going out into the field to explore and describe the complex socio-cognitive, socio-technical activity of translation in situ. After presenting a use case from a large-scale research project on translation ergonomics at the authors home institution, the article puts forward a model for transdisciplinary action research in professional settings to guide the necessary transition from interdisciplinarity to transdisciplinarity. Such a model would allow professional processes and practices to be investigated, and the findings productively and transformatively applied, in the situated socio-cognitive and socio-technical contexts of translators workplaces - within, for, with and by the organisations that employ them.

Molecular Epidemiology and Biomarkers in Etiologic Cancer Research: The New in Light of the Old

2020 ◽  
Author(s):  
Lungwani Muungo
Keyword(s):  
Gene Expression ◽  
Cancer Research ◽  
Molecular Epidemiology ◽  
Exposure Assessment ◽  
Large Scale ◽  
First Generation ◽  
Cancer Epidemiology ◽  
Policy Changes ◽  
The Past ◽  
New Generation

The purpose of this review is to evaluate progress inmolecular epidemiology over the past 24 years in canceretiology and prevention to draw lessons for futureresearch incorporating the new generation of biomarkers.Molecular epidemiology was introduced inthe study of cancer in the early 1980s, with theexpectation that it would help overcome some majorlimitations of epidemiology and facilitate cancerprevention. The expectation was that biomarkerswould improve exposure assessment, document earlychanges preceding disease, and identify subgroupsin the population with greater susceptibility to cancer,thereby increasing the ability of epidemiologic studiesto identify causes and elucidate mechanisms incarcinogenesis. The first generation of biomarkers hasindeed contributed to our understanding of riskandsusceptibility related largely to genotoxic carcinogens.Consequently, interventions and policy changes havebeen mounted to reduce riskfrom several importantenvironmental carcinogens. Several new and promisingbiomarkers are now becoming available for epidemiologicstudies, thanks to the development of highthroughputtechnologies and theoretical advances inbiology. These include toxicogenomics, alterations ingene methylation and gene expression, proteomics, andmetabonomics, which allow large-scale studies, includingdiscovery-oriented as well as hypothesis-testinginvestigations. However, most of these newer biomarkershave not been adequately validated, and theirrole in the causal paradigm is not clear. There is a needfor their systematic validation using principles andcriteria established over the past several decades inmolecular cancer epidemiology.

An Assessment of a Low-Cost Wastewater Disposal System after Twenty-Five Years of Operation

1987 ◽  
Vol 19 (5-6) ◽  
pp. 701-710 ◽  
Author(s):  
B. L. Reidy ◽  
G. W. Samson
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Wastewater Disposal ◽  
Industrial Base ◽  
Industrial Wastewaters ◽  
The Past ◽  
Gasification Process ◽  
Appropriate Treatment ◽  
Environmentally Safe ◽  
Coal Resource

A low-cost wastewater disposal system was commissioned in 1959 to treat domestic and industrial wastewaters generated in the Latrobe River valley in the province of Gippsland, within the State of Victoria, Australia (Figure 1). The Latrobe Valley is the centre for large-scale generation of electricity and for the production of pulp and paper. In addition other industries have utilized the brown coal resource of the region e.g. gasification process and char production. Consequently, industrial wastewaters have been dominant in the disposal system for the past twenty-five years. The mixed industrial-domestic wastewaters were to be transported some eighty kilometres to be treated and disposed of by irrigation to land. Several important lessons have been learnt during twenty-five years of operating this system. Firstly the composition of the mixed waste stream has varied significantly with the passage of time and the development of the industrial base in the Valley, so that what was appropriate treatment in 1959 is not necessarily acceptable in 1985. Secondly the magnitude of adverse environmental impacts engendered by this low-cost disposal procedure was not imagined when the proposal was implemented. As a consequence, clean-up procedures which could remedy the adverse effects of twenty-five years of impact are likely to be costly. The question then may be asked - when the total costs including rehabilitation are considered, is there really a low-cost solution for environmentally safe disposal of complex wastewater streams?

Recent Progress in Machine Learning-based Prediction of Peptide Activity for Drug Discovery

2019 ◽  
Vol 19 (1) ◽  
pp. 4-16 ◽  
Author(s):  
Qihui Wu ◽  
Hanzhong Ke ◽  
Dongli Li ◽  
Qi Wang ◽  
Jiansong Fang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Large Scale ◽  
Recent Progress ◽  
High Specificity ◽  
Learning Approaches ◽  
Anticancer Peptides ◽  
The Past ◽  
Traditional Approaches ◽  
Large Scale Screening

Over the past decades, peptide as a therapeutic candidate has received increasing attention in drug discovery, especially for antimicrobial peptides (AMPs), anticancer peptides (ACPs) and antiinflammatory peptides (AIPs). It is considered that the peptides can regulate various complex diseases which are previously untouchable. In recent years, the critical problem of antimicrobial resistance drives the pharmaceutical industry to look for new therapeutic agents. Compared to organic small drugs, peptide- based therapy exhibits high specificity and minimal toxicity. Thus, peptides are widely recruited in the design and discovery of new potent drugs. Currently, large-scale screening of peptide activity with traditional approaches is costly, time-consuming and labor-intensive. Hence, in silico methods, mainly machine learning approaches, for their accuracy and effectiveness, have been introduced to predict the peptide activity. In this review, we document the recent progress in machine learning-based prediction of peptides which will be of great benefit to the discovery of potential active AMPs, ACPs and AIPs.

Evaluating Qualitative Research

2017 ◽  
Author(s):  
Jeasik Cho
Keyword(s):  
Qualitative Research ◽  
Large Scale ◽  
Academic Research ◽  
Research Community ◽  
Assessment Tools ◽  
Journal Articles ◽  
Journal Editors ◽  
The Past ◽  
Grant Proposals

This book provides the qualitative research community with some insight on how to evaluate the quality of qualitative research. This topic has gained little attention during the past few decades. We, qualitative researchers, read journal articles, serve on masters’ and doctoral committees, and also make decisions on whether conference proposals, manuscripts, or large-scale grant proposals should be accepted or rejected. It is assumed that various perspectives or criteria, depending on various paradigms, theories, or fields of discipline, have been used in assessing the quality of qualitative research. Nonetheless, until now, no textbook has been specifically devoted to exploring theories, practices, and reflections associated with the evaluation of qualitative research. This book constructs a typology of evaluating qualitative research, examines actual information from websites and qualitative journal editors, and reflects on some challenges that are currently encountered by the qualitative research community. Many different kinds of journals’ review guidelines and available assessment tools are collected and analyzed. Consequently, core criteria that stand out among these evaluation tools are presented. Readers are invited to join the author to confidently proclaim: “Fortunately, there are commonly agreed, bold standards for evaluating the goodness of qualitative research in the academic research community. These standards are a part of what is generally called ‘scientific research.’ ”

scholarly journals Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shumaila Sayyab ◽  
Anders Lundmark ◽  
Malin Larsson ◽  
Markus Ringnér ◽  
Sara Nystedt ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Large Scale ◽  
Somatic Mutations ◽  
Lymphoblastic Leukemia ◽  
Clonal Evolution ◽  
Point Mutations ◽  
Driver Genes ◽  
Protein Coding ◽  
Pediatric Acute Lymphoblastic Leukemia ◽  
Evolutionary Trajectories

AbstractThe mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.

scholarly journals Global climatology and trends in convective environments from ERA5 and rawinsonde data

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mateusz Taszarek ◽  
John T. Allen ◽  
Mattia Marchio ◽  
Harold E. Brooks
Keyword(s):  
Large Scale ◽  
Climate Models ◽  
Global Climate ◽  
Convective Available Potential Energy ◽  
Global Climate Models ◽  
Convective Precipitation ◽  
The Past ◽  
The Tropics ◽  
Rawinsonde Data

AbstractGlobally, thunderstorms are responsible for a significant fraction of rainfall, and in the mid-latitudes often produce extreme weather, including large hail, tornadoes and damaging winds. Despite this importance, how the global frequency of thunderstorms and their accompanying hazards has changed over the past 4 decades remains unclear. Large-scale diagnostics applied to global climate models have suggested that the frequency of thunderstorms and their intensity is likely to increase in the future. Here, we show that according to ERA5 convective available potential energy (CAPE) and convective precipitation (CP) have decreased over the tropics and subtropics with simultaneous increases in 0–6 km wind shear (BS06). Conversely, rawinsonde observations paint a different picture across the mid-latitudes with increasing CAPE and significant decreases to BS06. Differing trends and disagreement between ERA5 and rawinsondes observed over some regions suggest that results should be interpreted with caution, especially for CAPE and CP across tropics where uncertainty is the highest and reliable long-term rawinsonde observations are missing.

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