scholarly journals Improving the usability and comprehensiveness of microbial databases

2018 ◽  
Author(s):  
Caitlin Loeffler ◽  
Aaron Karlsberg ◽  
Lana S. Martin ◽  
Eleazar Eskin ◽  
David Koslicki ◽  
...  
Keyword(s):  
Translational Research ◽  
Basic Science ◽  
Reference Genome ◽  
Reference Database ◽  
Data Preparation ◽  
Genome Database ◽  
Reference Databases ◽  
Reference Genome Database

AbstractMetagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibility, hindering their quality and comprehensiveness, and calling for the establishment of recommendations for reference genome database assembly. Here, we analyze existing fungal and bacterial databases and discuss guidelines for the development of a master reference database that promises to improve the quality and quantity of omics research.

scholarly journals Scalable metagenomic taxonomy classification using a reference genome database

2013 ◽  
Vol 29 (18) ◽  
pp. 2253-2260 ◽  
Author(s):  
Sasha K. Ames ◽  
David A. Hysom ◽  
Shea N. Gardner ◽  
G. Scott Lloyd ◽  
Maya B. Gokhale ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genome Database ◽  
Reference Genome Database

scholarly journals Adaptability of Ultrasonic Lamb Wave Touchscreen to the Variations in Touch Force and Touch Area

Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1736
Author(s):  
Zengchong Yang ◽  
Xiucheng Liu ◽  
Bin Wu ◽  
Ren Liu
Keyword(s):  
Lamb Wave ◽  
Weight Coefficient ◽  
The Self ◽  
Reference Database ◽  
Learning Method ◽  
Improved Method ◽  
Large Area ◽  
Localization Model ◽  
Reference Databases ◽  
First Time

Previous studies on Lamb wave touchscreen (LWT) were carried out based on the assumption that the unknown touch had the consistent parameters with acoustic fingerprints in the reference database. The adaptability of LWT to the variations in touch force and touch area was investigated in this study for the first time. The automatic collection of the databases of acoustic fingerprints was realized with an experimental prototype of LWT employing three pairs of transmitter–receivers. The self-adaptive updated weight coefficient of the used transmitter–receiver pairs was employed to successfully improve the accuracy of the localization model established based on a learning method. The performance of the improved method in locating single- and two-touch actions with the reference database of different parameters was carefully evaluated. The robustness of the LWT to the variation of the touch force varied with the touch area. Moreover, it was feasible to locate touch actions of large area with reference databases of small touch areas as long as the unknown touch and the reference databases met the condition of equivalent averaged stress.

scholarly journals Two Approaches for a Genetic Analysis of Pompe Disease: A Literature Review of Patients with Pompe Disease and Analysis Based on Genomic Data from the General Population

Children ◽  
2021 ◽  
Vol 8 (7) ◽  
pp. 601
Author(s):  
Kyung-Sun Park
Keyword(s):  
General Population ◽  
Pompe Disease ◽  
Genomic Data ◽  
Japanese Patients ◽  
Population Database ◽  
Genome Database ◽  
Genetic Database ◽  
Pathogenic Variants ◽  
Reference Genome Database ◽  
Real Patients

In this study, two different approaches were applied in the analysis of the GAA gene. One was analyzed based on patients with Pompe disease, and the other was analyzed based on GAA genomic data from unaffected carriers in a general population genetic database. For this, GAA variants in Korean and Japanese patients reported in previous studies and in patients reported in the Pompe disease GAA variant database were analyzed as a model. In addition, GAA variants in the Korean Reference Genome Database (KRGDB), the Japanese Multi Omics Reference Panel (jMorp), and the Genome Aggregation Database (gnomAD) were analyzed. Overall, approximately 50% of the pathogenic or likely pathogenic variants (PLPVs) found in unaffected carriers were also found in real patients with Pompe disease (Koreans, 57.1%; Japanese, 46.2%). In addition, there was a moderate positive correlation (Spearman’s correlation coefficient of 0.45–0.69) between the proportion of certain PLPVs in patients and the minor allele frequency of their variants in a general population database. Based on the analysis of general population databases, the total carrier frequency for Pompe disease in Koreans and Japanese was estimated to be 1.7% and 0.7%, respectively, and the predicted genetic prevalence was 1:13,657 and 1:78,013, respectively.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals The Future of Restorative Neurosciences in Stroke: Driving the Translational Research Pipeline From Basic Science to Rehabilitation of People After Stroke

2008 ◽  
Vol 23 (2) ◽  
pp. 97-107 ◽  
Author(s):  
◽  
Binith Cheeran ◽  
Leonardo Cohen ◽  
Bruce Dobkin ◽  
Gary Ford ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Translational Research ◽  
Basic Science ◽  
Clinical Importance ◽  
Small Scale ◽  
Front Line ◽  
Pressure Groups ◽  
The United Kingdom ◽  
Public Sector Research

Background. Major advances during the past 50 years highlight the immense potential for restoration of function after neural injury, even in the damaged adult human brain. Yet, the translation of these advances into clinically useful treatments is painstakingly slow. Objective. Here, we consider why the traditional model of a “translational research pipeline” that transforms basic science into novel clinical practice has failed to improve rehabilitation practice for people after stroke. Results. We find that (1) most treatments trialed in vitro and in animal models have not yet resulted in obviously useful functional gains in patients; (2) most clinical trials of restorative treatments after stroke have been limited to small-scale studies; (3) patient recruitment for larger clinical trials is difficult; (4) the determinants of patient outcomes and what patients want remain complex and ill-defined, so that basic scientists have no clear view of the clinical importance of the problems that they are addressing; (5) research in academic neuroscience centers is poorly integrated with practice in front-line hospitals and the community, where the majority of patients are treated; and (6) partnership with both industry stakeholders and patient pressure groups is poorly developed, at least in the United Kingdom where research in the translational restorative neurosciences in stroke depends on public sector research funds and private charities. Conclusions. We argue that interaction between patients, front-line clinicians, and clinical and basic scientists is essential so that they can explore their different priorities, skills, and concerns. These interactions can be facilitated by funding research consortia that include basic and clinical scientists, clinicians and patient/carer representatives with funds targeted at those impairments that are major determinants of patient and carer outcomes. Consortia would be instrumental in developing a lexicon of common methods, standardized outcome measures, data sharing and long-term goals. Interactions of this sort would create a research-friendly, rather than only target-led, culture in front-line stroke rehabilitation services.

Basic Principles of Translational Research

2012 ◽  
Author(s):  
Boris Rubinsky
Keyword(s):  
Translational Research ◽  
Basic Concept ◽  
Basic Science ◽  
Clinical Medicine ◽  
Irreversible Electroporation ◽  
The Public ◽  
Food Engineering ◽  
New Science ◽  
Fda Approval ◽  
Health Laws

Translational research turns fundamental new science and innovations into a product that has value to the public. The process is difficult because it combines a variety of diverse disciplines and skills from basic science, clinical medicine, engineering, business, public health, laws and regulations. These areas are so wide apart that it is very difficult to combine. The author has engaged in translational research since the early 1980’s and will describe the processes, pitfalls and rewards through typical examples from his projects that include: development of imaging monitored cryosurgery from concept to treatment of hundreds of thousands of patients, transgenes in food engineering from basic science to a twenty year wait for FDA approval, microelectroporation from basic concept to incorporation of the technology by numerous companies and non-thermal irreversible electroporation from basic concept to current clinical use in over 50 hospitals and over thousand treated patients.

Sign in / Sign up

Export Citation Format

Share Document