scholarly journals DNA barcode reference libraries: Achievements of the DNAqua-Net Working Group 1

2021 ◽  
Vol 4 ◽  
Author(s):  
Torbjørn Ekrem ◽  
Fedor Čiampor Jr
Keyword(s):  
Knowledge Transfer ◽  
Working Group ◽  
Collaborative Work ◽  
Dna Barcode ◽  
Aquatic Organisms ◽  
Aquatic Species ◽  
Short Term ◽  
Scientific Publications ◽  
Reference Databases ◽  
Group 1

The three main aims for the DNAqua-Net working group 1 (WG1) have been i) to identify gaps in the barcode reference libraries of European aquatic species, ii) to fill these gaps in collaboration with ongoing initiatives, and iii) to facilitate knowledge transfer and initiate work on barcode reference libraries in regions where such activity was low (Leese et al. 2016). WG1 currently has 129 members from 39 countries spanning four continents, with a majority of members from Europe. In our presentation we show the achievements of WG1 during the lifetime of the DNAqua-Net COST action (CA15219; 2016-2021), and discuss some of the highlights obtained through collaborative work and joint dissemination. Specifically, we emphasize the outcomes presented in two peer-reviewed scientific publications that focus on standards for building DNA barcode reference libraries, and gaps in reference databases for European aquatic organisms currently used in national biomonitoring programs (Rimet et al. 2021, Weigand et al. 2019). However, major achievements were also obtained in four workshops (Braga, Pécs, Limassol & Bratislava) and through the activities of 16 short-term scientific missions (STSMs).

Health and Medical Informatics Competencies: Call to Participate in Updating the IMIA Recommendations

2002 ◽  
Vol 41 (02) ◽  
pp. 86-88 ◽  
Author(s):  
Judith Douglas ◽  
Evelyn Hovenga
Keyword(s):  
Literature Review ◽  
Small Group ◽  
Learning Outcomes ◽  
Medical Informatics ◽  
Working Group ◽  
International Medical ◽  
Three Dimension ◽  
Virtual University ◽  
Group 1

Summary Objectives: On behalf of the International Medical Informatics Association (IMIA), its Working Group 1 (WG1) addresses health and medical informatics education. Methods: As part of its mission, WG1 developed recommendations for competencies, describing a three-dimension framework and defining learning outcomes. Results: Officially approved by IMIA in 1999, the recommendations have been translated into seven languages. In 2001, WG1 charged a small group with updating the recommendations and consider the work undertaken by others to develop competencies. Additional work underway in support of the recommendations includes a literature review to help extract the fundamental competencies from the recommendations. To ensure the highest quality of input in the updated recommendations, WG1 is issuing a call for participation to the international informatics community. Conclusions: Further work with the competencies will result in updated IMIA guidelines. These are expected to support the creation of a virtual university for health and medical informatics.

scholarly journals The influence of preoperative knee flexion contracture severity on short-term outcome of orthopedic surgery in ambulatory children with bilateral cerebral palsy

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Evelina Pantzar-Castilla ◽  
Brian Po-Jung Chen ◽  
Freeman Miller ◽  
Jacques Riad
Keyword(s):  
Cerebral Palsy ◽  
Motor Function ◽  
Surgical Procedures ◽  
Orthopedic Surgery ◽  
Knee Flexion ◽  
Flexion Contracture ◽  
Short Term ◽  
Knee Flexion Contracture ◽  
Group 2 ◽  
Group 1

Abstract Background Indications and cutoff value of deformities to determine surgical procedures for flexed knee gait are not clear. The aim was to determine the influence of none or mild, and moderate preoperative knee flexion contracture on the improvement of gait after orthopedic surgery in children with bilateral cerebral palsy (CP). Methods Inclusion criteria; bilateral CP, Gross Motor Function Classification System level I-III, and pre- and post operative-gait analysis. The 132 individuals identified were categorized into 2 groups based on the severity of knee flexion contracture (group 1: none or less than 11°; group 2: greater than or equal to 11°), and then matched according to the exact same soft tissue and/or bony orthopedic surgical procedures performed. The indication for surgery was to prevent progressive development of knee flexion contracture and stance phase flexed knee gait. Pre- and postoperative physical examination and gait analysis data were analyzed retrospectively. Results Sixty (30 + 30) children, with mean age 10.6 years in each group, were included. The average follow-up time was 17 months. Gait Deviation Index (GDI) improved in group 1 from mean 66 (SD 19) to 74 (15), p = 0.004, and in group 2 from 60 (13) to 69 (15), p = 0.001. Knee flexion in stance improved in group 1 from 21.4 (16.1) to 12.1 (16.0) degrees, p = 0.002, and in group 2 from 32.2 (14.2) to 17.0 (15.9), p = 0.001. Step length improved in both groups, p = 0.017 and p = 0.008, respectively. Only in group 2 significant improvement was noted in walking speed, p = 0.018 and standing function, Gross Motor Function Measure (GMFM-D), p = 0.001. Knee flexion contracture decreased in group 1 from mean 4.6 (5.3) to 2.1 (8.3) degrees, p = 0.071 and in group 2 from 17.2 (4.9) to 9.6 (9.3), p = 0.001. There was no statistical difference between groups in pre-post improvement of GDI or other variables, except GMFM-D. Conclusions Relative mild to moderate preoperative knee flexion contracture does not influence the short-term improvement of gait after orthopedic surgery in children with bilateral CP.

Working Group 1: Energy Model and Data Support and Operation

1981 ◽  
pp. 63-78
Author(s):  
B. A. Bayraktar ◽  
E. A. Cherniavsky ◽  
M. A. Laughton ◽  
L. E. Ruff
Keyword(s):  
Working Group ◽  
Energy Model ◽  
Data Support ◽  
Group 1

scholarly journals Taming the Wild West of Molecular Tools Application in Aquatic Research and Biomonitoring

2019 ◽  
Vol 3 ◽  
Author(s):  
Alexander Weigand ◽  
Agnès Bouchez ◽  
Pieter Boets ◽  
Kat Bruce ◽  
Fedor Ciampor ◽  
...  
Keyword(s):  
Working Group ◽  
High Throughput Sequencing ◽  
Group Structure ◽  
Time Budget ◽  
Good Practice ◽  
Dna Barcode ◽  
Environmental Parameters ◽  
Full Potential ◽  
Molecular Tools ◽  
Wild West

Modern high-throughput sequencing technologies are becoming a game changer in many fields of aquatic research and biomonitoring. To unfold their full potential, however, the independent development of approaches has to be streamlined. This discussion must be fuelled by stakeholders and practitioners and, scientific results collaboratively filtered to identify the most promising avenues. Furthermore, aspects such as time, budget, skills and the application context have to be considered, finally communicating good practice strategies to target audiences. Since 2016, the EU COST Action DNAqua-Net is taming the wild west of molecular tools application in aquatic research and biomonitoring. After nucleating available knowledge by the formation of a highly international and transdisciplinary network of scientists, stakeholders, practitioners and enterprises, fields of high methodological diversity were identified. Relevant aspects are currently ground truthed, thereby reducing the plethora of pipelines, parameters and protocols to a subset of good practices or standardisations. To effectively bridge the science-application interface, the very same network is exploited for the dissemination of results (Leese et al. 2018). The internal working group structure of DNAqua-Net is used to provide an overview of existing methodological fields of diversity in DNA-based aquatic biomonitoring: WG1 -DNA Barcode References: Different marker systems are targeted for the same organism group. Even in case the same molecular marker is investigated, different primer pairs are frequently applied for DNA metabarcoding. Both aspects challenge the further development of high-quality and complete DNA barcode reference libraries (Weigand et al. 2019). WG2 -Biotic Indices & Metrics: Index systems are developed from molecular data in various ways: from the estimation of species' biomass (as a proxy for abundance) from sequence reads, to the correlation of presence/absence data of molecular operational taxonomic units (MOTUs) with environmental parameters (Pawlowski et al. 2018). WG3 -Field & Lab Protocols: Using environmental DNA (eDNA) metabarcoding as an example, diverse sampling techniques based on varying water volumes, different filter systems and collection devices as well as a multitude of laboratory protocols for PCR, replication and sequencing are considered. WG4 -Data Analysis & Storage: During the process of MOTU identification, varying threshold values and conceptually different pipelines are used, potentially impacting the final list of MOTUs or species retrieved. Furthermore, routine storage concepts for big biodiversity data are only in development and some sample types (e.g. eDNA) have no sophisticated metadata descriptions. WG5 -Implementation Strategy & Legal Issues: The working group picks up collaboratively filtered good practice strategies and generates room for discussions at the science-policy interface (Hering et al. 2018). The CEN working group WG28 "DNA methods" has been initiated and the development of standardisations is fostered.

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 Impact of Switching from Short-Term Teriparatide Treatment to Denosumab Therapy Compared with Denosumab Alone for Patients with Osteoporotic Hip Fracture: A 1-Year Follow-up Study

2020 ◽  
Author(s):  
Chan Ho Park ◽  
Jun-Il Yoo ◽  
Chang Hyun Choi ◽  
You-Sung Suh
Keyword(s):  
Hip Fracture ◽  
Mineral Density ◽  
Short Term ◽  
Short Term Treatment ◽  
T Score ◽  
The Difference ◽  
Group 2 ◽  
The Impact ◽  
Group 1

Abstract Background: Switching the prescription from bone-forming medication to resorptive agents is reportedly effective for patients with severe osteoporosis. The objective of this study is to determine the impact of implementing short-term teriparatide (TPTD) intervention before denosumab (DMab) therapy compared with DMab therapy alone for 1 year after hip fracture.Methods: TPTD was administered to 24 patients for an average of 12.1 weeks after which the intervention was switched to DMab therapy for 12 months (group 1). DMab alone was administered to 16 patients for 12 months (group 2). Bone mineral density (BMD) was evaluated before and after treatment at the 1-year follow-up. The improvement of BMD and T-score in hip and spine was compared with the levels of bone turnover marker.Results: The difference of hip BMD after osteoporosis treatment was -0.0081±0.03 in group 1 and 0.0074±0.04 in group 2 (p=0.180). The difference of spine BMD was 0.0819±0.04 in group 1 and 0.0145±0.03 in group 2 (p<0.001). BMD and T-score of the spine improved significantly in groups 1 and 2 (p < 0.001). There was no statistical difference in C-terminal telopeptide and osteocalcin level. Conclusion: Short-term TPTD administration followed by DMab alone was effective only in improving spine BMD. Short-term treatment with TPTD caused mild improvement in femur neck BMD compared with DMab alone. However, further research with a longer duration of TPTD treatment is warranted, as our findings lack statistical significance.

scholarly journals Responses of metabolic enzymes (GOT, GPT and LDH) in an Indian major carp Cirrhinus mrigala exposed to titanium dioxide (TiO2 ) nanorods under short-term exposure

2020 ◽  
Vol 15 ◽  
pp. 69-78
Author(s):  
B. Rangasamy ◽  
A.P. Ashokan ◽  
M. Ramesh ◽  
A. Narayanasamy
Keyword(s):  
Titanium Dioxide ◽  
Tio2 Nanoparticles ◽  
Aquatic Organisms ◽  
Tio2 Nanorods ◽  
Freshwater Ecosystem ◽  
X Ray Diffraction ◽  
Short Term ◽  
Indian Major Carp ◽  
Cirrhinus Mrigala ◽  
Short Term Exposure

Titanium dioxide (TiO2) nanoparticles are extensively manufactured due to their potential properties and applications invarious fields such as biomedical, electrical and environmental. These particles are likely to reach the aquatic environmentand may cause adverse effects on aquatic organisms. In this study, we investigated the effects of different concentrations (1, 50 and 100 mg L-l) of TiO2 nanorods (NRs). The enzymatic activity of glutamate oxaloacetate transaminase (GOT), glutamate pyruvate transaminase (GPT), and lactate dehydrogenase (LDH) was measured in the liver and muscle of an Indian major carp, Cirrhinus mrigala, under short-term exposure (96 h). The synthesised particles were characterized using X-ray diffraction (XRD), scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FTIR), UV-Visspectroscopy (UV-Vis) and photoluminescence (PL) techniques before conducting the toxicity assay. The GOT and GPT activities were significantly elevated in both liver and muscle of fish treated with TiO2 nanorods (except 50 mg L-l in muscle for GPT). Similarly, the activity of LDH was also found to be elevated. The findings of the present investigation suggest that TiO2:NRs might have be absorbed, circulated, accumulated in liver and muscles of C. mrigala resulting in alterations in the enzyme activities. The results revealed that TiO2 nanorods induced alterations in GOT, GPT and LDH activities of fish at tested concentrations. The alterations of these enzymatic parameters can be useful for monitoring the environmental contamination of titanium dioxide (TiO2) nanoparticles in freshwater ecosystem.

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