scholarly journals Degradation factors of environmental DNA evaluated by experiments and meta-analysis

2021 ◽  
Vol 4 ◽  
Author(s):  
Tatsuya Saito ◽  
Hideyuki Doi
Keyword(s):  
Water Temperature ◽  
Degradation Rate ◽  
Meta Analysis ◽  
Environmental Dna ◽  
Resident Species ◽  
Multiple Sources ◽  
Related Factors ◽  
Marine Habitats ◽  
Amplicon Length ◽  
Degradation Rates

Environmental DNA (eDNA) methods have been developed to detect organisms' distributions and abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation, but, the dynamics and mechanisms of eDNA degradation are largely unknown, especially when considering different eDNA sources, e.g., cell-derived and fragmental DNA. In this study, we conducted the degradation experiments (Saito and Doi 2020a) and a meta-analysis (Saito and Doi 2020b). Firstly, we experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA (the DNA of internal positive control, IPC), free cells from Oncorhynchus kisutch, and the resident species (Saito and Doi 2020a). We conducted the experiments with pond and seawater to evaluate the differences between freshwater and marine habitats. Our results showed that eDNA derived from the both cells and fragmental DNA decreased exponentially in the both sea and pond samples. The degradation of eDNA from the resident species showed similar behavior to the cell-derived eDNA. As a meta-analysis, we complied the degradation rates of eDNA in laboratory experiment and field studies from 28 studies (Saito and Doi 2020b). We also collected the related factors, including water sources, water temperature, DNA regions, and PCR amplicon lengths of the measured DNA. Our results suggested that water temperature and amplicon length were significantly related to the degradation rate of eDNA. From the simulation based on the 95% quantile model, we predicted the maximum degradation rate of eDNA in various combinations of water temperature and PCR amplicon length.

scholarly journals A Model and Simulation of the Influence of Temperature and Amplicon Length on Environmental DNA Degradation Rates: A Meta-Analysis Approach

2021 ◽  
Vol 9 ◽  
Author(s):  
Tatsuya Saito ◽  
Hideyuki Doi
Keyword(s):  
Endangered Species ◽  
Water Temperature ◽  
Species Distribution ◽  
Degradation Rate ◽  
Meta Analysis ◽  
Environmental Dna ◽  
Rare And Endangered Species ◽  
Amplicon Length ◽  
Degradation Rates ◽  
Rare And Endangered

Environmental DNA (eDNA) analysis can detect aquatic organisms, including rare and endangered species, in a variety of habitats. Degradation can influence eDNA persistence, impacting eDNA-based species distribution and occurrence results. Previous studies have investigated degradation rates and associated contributing factors. It is important to integrate data from across these studies to better understand and synthesize eDNA degradation in various environments. We complied the eDNA degradation rates and related factors, especially water temperature and amplicon lengths of the measured DNA from 28 studies, and subjected the data to a meta-analysis. In agreement with previous studies, our results suggest that water temperature and amplicon length are significantly related to the eDNA degradation rate. From the 95% quantile model simulation, we predicted the maximum eDNA degradation rate in various combinations of water temperature and amplicon length. Predicting eDNA degradation could be important for evaluating species distribution and inducing innovation (e.g., sampling, extraction, and analysis) of eDNA methods, especially for rare and endangered species with small population size.

scholarly journals Environmental DNA degradation simulation from water temperature and DNA fragment length: A meta-analysis approach

2020 ◽  
Author(s):  
Tatsuya Saito ◽  
Hideyuki Doi
Keyword(s):  
Endangered Species ◽  
Water Temperature ◽  
Fragment Length ◽  
Degradation Rate ◽  
Model Simulation ◽  
Environmental Dna ◽  
Related Factors ◽  
Rare And Endangered Species ◽  
Degradation Rates ◽  
Rare And Endangered

AbstractEnvironmental DNA (eDNA) analysis can detect aquatic organisms, including rare and endangered species, in a variety of habitats. The degradation of eDNA concentration is important to investigate their distribution and has also been experimentally evaluated. It is important to integrate these data to synthesize eDNA degradation in various environments. We collected the eDNA degradation rates and related factors, especially water temperature and fragment lengths of the measured DNA from 28 studies. Our results suggest that water temperature and fragment length are significantly related to the eDNA degradation rate. From the 95% quantile model simulation, we predicted the maximum eDNA degradation rate in various combinations of water temperature and fragment length. Predicting eDNA degradation could be important for evaluating species distribution and inducing innovation of eDNA methods, especially for rare and endangered species with lower DNA concentrations.

scholarly journals Degradation modeling of water environmental DNA: Experiments on multiple DNA sources in pond and seawater

2020 ◽  
Author(s):  
Tatsuya Saito ◽  
Hideyuki Doi
Keyword(s):  
Environmental Dna ◽  
Degradation Process ◽  
Exponential Model ◽  
Natural Environments ◽  
Multiple Sources ◽  
Marine Habitats ◽  
Fundamental Information ◽  
Degradation Rates ◽  
Free Cells ◽  
Degradation Models

ABSTRACTEnvironmental DNA (eDNA) methods have been developed to detect organism distribution and abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation. However, the dynamics and mechanisms of eDNA degradation are largely unknown, especially when considering different eDNA sources, e.g., cells and fragmental DNA. We experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA, free cells, and inhabiting species. We conducted the experiment with pond and seawater to evaluate the differences between freshwater and marine habitats. We quantified the eDNA copies of free cells, fragmental DNA, and inhabiting species (Cyprinus carpio in the pond and Trachurus japonicus in the sea). Our results show that eDNA derived from both cells and fragmental DNA decreased exponentially in both the sea and pond samples. The degradation of eDNA from inhabiting species showed similar behavior to the cell-derived eDNA. We evaluated three degradation models with different assumptions and degradation steps and found that a simple exponential model is effective in most cases. Our findings on cell- and fragmental DNA-derived eDNA provide fundamental information about the eDNA degradation process and can be applied to elucidate eDNA behavior in natural environments.

Quantifying Shedding and Degradation Rates of Environmental DNA (eDNA) from Pacific Crown-of-thorns Seastar (Acanthaster cf. Solaris)

2021 ◽  
Author(s):  
Sarah Lok Ting Kwong ◽  
Cecilia Villacorta-Rath ◽  
Jason Doyle ◽  
Sven Uthicke
Keyword(s):  
Degradation Rate ◽  
Abiotic Factors ◽  
Feeding Activity ◽  
Environmental Dna ◽  
Aquatic Environments ◽  
Early Life Stages ◽  
Factors Affecting ◽  
Degradation Rates ◽  
Population Outbreaks ◽  
Two Temperatures

Abstract Population outbreaks of the corallivorous crown-of-thorns seastar (CoTS; Acanthaster spp.) are significant threats to the Indo-Pacific reefs. Although recent research demonstrated that environmental DNA (eDNA) techniques could improve CoTS monitoring and management, the interpretation of surveillance results has been limited by uncertainties about eDNA dynamics in aquatic environments. Here, we aimed to identify biotic and abiotic factors affecting the shedding and degradation rates of CoTS eDNA. Using laboratory-raised 8-month-old juvenile CoTS, aquarium experiments were conducted to test the effect of two temperatures (24 and 28°C) and three feeding treatments (no food, food available and food inaccessible) on eDNA shedding rate. Additionally, CoTS eDNA degradation rate was quantified under three temperatures (24, 26 and 28°C). We found that eDNA shedding rate was affected by feeding treatment (p < 0.0001) but not temperature. Specifically, the shedding rate under food accessible treatment was about 7 times higher than that of food inaccessible treatment (p < 0.0001), whereas the presence of coral reduced the shedding rate by half (food inaccessible vs no food, p = 0.0249). Degradation of CoTS eDNA was rapid (half-life = 14h) and not affected by temperature. Our results demonstrated that feeding activity increased eDNA release, but some of the released DNA was lost potentially due to binding to coral surface mucus layer or skeleton. The rapid degradation rate indicated that results of eDNA surveillance likely reflects recent and local occurrence of CoTS. Although further testing is needed, this study provided support for using eDNA as a novel detection tool for early life stages of CoTS on coral reefs.

scholarly journals Prognostic factors for chronic post-surgical pain after lung or pleural surgery: a protocol for a systematic review and meta-analysis

BMJ Open ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. e051554
Author(s):  
Pascal Richard David Clephas ◽  
Sanne Elisabeth Hoeks ◽  
Marialena Trivella ◽  
Christian S Guay ◽  
Preet Mohinder Singh ◽  
...  
Keyword(s):  
Systematic Review ◽  
Prognostic Factors ◽  
Prognostic Factor ◽  
Meta Analysis ◽  
Case Series ◽  
Related Factors ◽  
Surgical Pain ◽  
Literature Reviews ◽  
Chronic Post Surgical Pain

IntroductionChronic post-surgical pain (CPSP) after lung or pleural surgery is a common complication and associated with a decrease in quality of life, long-term use of pain medication and substantial economic costs. An abundant number of primary prognostic factor studies are published each year, but findings are often inconsistent, methods heterogeneous and the methodological quality questionable. Systematic reviews and meta-analyses are therefore needed to summarise the evidence.Methods and analysisThe reporting of this protocol adheres to the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) checklist. We will include retrospective and prospective studies with a follow-up of at least 3 months reporting patient-related factors and surgery-related factors for any adult population. Randomised controlled trials will be included if they report on prognostic factors for CPSP after lung or pleural surgery. We will exclude case series, case reports, literature reviews, studies that do not report results for lung or pleural surgery separately and studies that modified the treatment or prognostic factor based on pain during the observation period. MEDLINE, Scopus, Web of Science, Embase, Cochrane, CINAHL, Google Scholar and relevant literature reviews will be searched. Independent pairs of two reviewers will assess studies in two stages based on the PICOTS criteria. We will use the Quality in Prognostic Studies tool for the quality assessment and the CHARMS-PF checklist for the data extraction of the included studies. The analyses will all be conducted separately for each identified prognostic factor. We will analyse adjusted and unadjusted estimated measures separately. When possible, evidence will be summarised with a meta-analysis and otherwise narratively. We will quantify heterogeneity by calculating the Q and I2 statistics. The heterogeneity will be further explored with meta-regression and subgroup analyses based on clinical knowledge. The quality of the evidence obtained will be evaluated according to the Grades of Recommendation Assessment, Development and Evaluation guideline 28.Ethics and disseminationEthical approval will not be necessary, as all data are already in the public domain. Results will be published in a peer-reviewed scientific journal.PROSPERO registration numberCRD42021227888.

scholarly journals Identification and inclusion of gender factors in retrospective cohort studies: the GOING-FWD framework

2021 ◽  
Vol 6 (4) ◽  
pp. e005413
Author(s):  
Valeria Raparelli ◽  
Colleen M. Norris ◽  
Uri Bender ◽  
Maria Trinidad Herrero ◽  
Alexandra Kautzky-Willer ◽  
...  
Keyword(s):  
Outcome Measurement ◽  
Meta Analysis ◽  
Synthetic Data ◽  
Well Being ◽  
Pooled Analysis ◽  
Research Network ◽  
Local Analysis ◽  
Related Factors ◽  
Measurement Framework ◽  
Definition Of

Gender refers to the socially constructed roles, behaviours, expressions and identities of girls, women, boys, men and gender diverse people. Gender-related factors are seldom assessed as determinants of health outcomes, despite their powerful contribution. The Gender Outcomes INternational Group: to Further Well-being Development (GOING-FWD) project developed a standard five-step methodology applicable to retrospectively identify gender-related factors and assess their relationship to outcomes across selected cohorts of non-communicable chronic diseases from Austria, Canada, Spain, Sweden. Step 1 (identification of gender-related variables): Based on the gender framework of the Women Health Research Network (ie, identity, role, relations and institutionalised gender), and available literature for a certain disease, an optimal ‘wish-list’ of gender-related variables was created and discussed by experts. Step 2 (definition of outcomes): Data dictionaries were screened for clinical and patient-relevant outcomes, using the International Consortium for Health Outcome Measurement framework. Step 3 (building of feasible final list): a cross-validation between variables per database and the ‘wish-list’ was performed. Step 4 (retrospective data harmonisation): The harmonisation potential of variables was evaluated. Step 5 (definition of data structure and analysis): The following analytic strategies were identified: (1) local analysis of data not transferable followed by a meta-analysis combining study-level estimates; (2) centrally performed federated analysis of data, with the individual-level participant data remaining on local servers; (3) synthesising the data locally and performing a pooled analysis on the synthetic data and (4) central analysis of pooled transferable data. The application of the GOING-FWD multistep approach can help guide investigators to analyse gender and its impact on outcomes in previously collected data.

scholarly journals Burnout in nurses: A meta analysis of related factorsHemşirelerde tükenmişlik: İlgili faktörlerin meta analizi

2017 ◽  
Vol 14 (2) ◽  
pp. 1242 ◽  
Author(s):  
Filiz Kantek ◽  
Kamile Kabukcuoğlu
Keyword(s):  
Fixed Effects ◽  
Web Of Science ◽  
Meta Analysis ◽  
Personal Accomplishment ◽  
Burnout Syndrome ◽  
Related Factors ◽  
Work Shift ◽  
Ebsco Host ◽  
Fail Safe ◽  
Type Of Institution

Burnout syndrome is still among the leading problems of nursing profession. Reduction and prevention of burnout will be possible with a better understanding of the relevant factors. The purpose of this study is to evaluate the effects of certain variables on burnout levels of nurses in Turkey with a meta analysis. The study was conducted with a meta analysis. A number of online databases were reviewed including Turkish Medical Index, Google scholar, National Thesis Center, Pubmed, EBSCO Host, and Web of Science by searching for certain keywords such as  “Emotional exhaustion”, “Depersonalization”, “personal accomplishment”, “burnout”, “nurse”, and “Turkey”  both in Turkish and English. The results of the review indicated that there were 11 studies for sex, 17 studies for marital status, 20 studies for educational status, 7 studies for the type of institution, and 8 studies for willingness to choose nursing and the work shift that were found eligible for the inclusion criteria. The study data were analyzed with CMA. The homogeneity of the studies was tested with Q and I2 values. The study bias was assessed with Orwin’s Fail-Safe N and Tau coefficients. The effect size was calculated with random effects and fixed effects models.  The study findings indicated that burnout was affected by sex, the type of institution, and the work shift at lower levels and by willingness to choose nursing at moderate levels. It was similarly found that depersonalization dimension was affected by the type of institution, the work shift, and willingness to choose nursing at lower levels. ÖzetTükenmişlik hemşireler için hala önemli problemlerden biridir. Tükenmişliğin azaltılması ve önlenmesi ilgili faktörlerin daha iyi anlaşılması ile mümkün olacaktır. Bu çalışmanın amacı, Meta analiz yöntemi kullanarak Türkiye’deki hemşirelerin tükenmişlik düzeyleri üzerine bazı değişkenlerin etkisini incelemektir. Çalışmada meta analiz yöntemi kullanıldı. İlgili çalışmalara ulaşmak için Türk Tıp Dizini, Google Akademik, YÖK tez merkezi, Pubmed,  EBSCO Host, Web of Science veri tabanları tarandı. Taramada “Tükenmişlik”, “duygusal tükenmişlik”, “Duyarsızlaşma”, “kişisel başarı” “hemşire” ve “Türkiye” anahtar sözcükleri Türkçe ve İngilizce olarak kullanıldı. Cinsiyet için 11, Medeni durum için 17, eğitim durumu için 20, kurum tipi için 7, mesleği isteyerek seçme durumu ve çalışma şekli için 8 çalışma dahil edilme kriterlerine uygundu. Verilerin analizinde CMA istatistik programı kullanıldı. Meta analize dahil edilen çalışmaların homojenliğini test etmek için Q ve I2 değerleri hesaplandı. Yayın yanlılığını test etmek için Orwin’s Fail-Safe N ve Tau-kare katsayısı hesaplaması yapıldı. Etki büyüklüğünün incelenmesinde rastgele etkiler ve sabit etkiler modeli kullanıldı. Bulgular duygusal tükenme üzerine cinsiyet, kurum tipi ve çalışma şeklinin düşük, mesleği isteyerek seçme durumunun orta düzeyde önemli etkiye sahip olduğunu ortaya koydu. Duyarsızlaşma boyutu üzerine kurum tipi, çalışma şekli ve mesleği isteyerek seçme durumu değişkenlerinin düşük düzeyde önemli etkiye sahip olduğu belirlendi.

scholarly journals Does Loneliness Have a Cost? A Population-Wide Study of the Association Between Loneliness and Healthcare Expenditure

2021 ◽  
Vol 66 ◽  
Author(s):  
Rachelle Meisters ◽  
Daan Westra ◽  
Polina Putrik ◽  
Hans Bosma ◽  
Dirk Ruwaard ◽  
...  
Keyword(s):  
Negative Binomial ◽  
Healthcare Expenditure ◽  
Age Groups ◽  
Mental Healthcare ◽  
Multiple Sources ◽  
Related Factors ◽  
Younger Age ◽  
Unhealthy Behavior ◽  
Nationally Representative ◽  
Binomial Models

Objectives: Loneliness has been associated with unhealthy behavior, poorer health, and increased morbidity. However, the costs of loneliness are poorly understood.Methods: Multiple sources were combined into a dataset containing a nationally representative sample (n = 341,376) of Dutch adults (18+). The association between loneliness and total, general practitioner (GP), specialized, pharmaceutical, and mental healthcare expenditure was tested using Poisson and Zero-inflated negative binomial models, controlling for numerous potential confounders (i.e., demographic, socioeconomic, lifestyle-related factors, self-perceived health, and psychological distress), for four age groups.Results: Controlling for demographic, socioeconomic, and lifestyle-related factors, loneliness was indirectly (via poorer health) associated with higher expenditure in all categories. In fully adjusted models, it showed a direct association with higher expenditure for GP and mental healthcare (0.5 and 11.1%, respectively). The association with mental healthcare expenditure was stronger in younger than in older adults (for ages 19–40, the contribution of loneliness represented 61.8% of the overall association).Conclusion: Loneliness contributes to health expenditure both directly and indirectly, particularly in younger age groups. This implies a strong financial imperative to address this issue.

scholarly journals Estimation accuracy of species abundance based on environmental DNA with relation to its production source, state, and assay methodology suggested by meta-analyses

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Hiroki Yamanaka
Keyword(s):  
Meta Analysis ◽  
Empirical Studies ◽  
Species Abundance ◽  
Environmental Dna ◽  
Efficient Estimation ◽  
Estimation Accuracy ◽  
Accurate Estimation ◽  
Abundance Estimation ◽  
Natural Environments ◽  
Promising Tool

Environmental DNA (eDNA) analysis is a promising tool for non-disruptive and cost-efficient estimation of species abundance. However, its practical applicability in natural environments is limited because it is unclear whether eDNA concentrations actually represent species abundance in the field. Although the importance of accounting for eDNA dynamics, such as transport and degradation, has been discussed, the influences of eDNA characteristics, including production source and state, and methodology, including collection and quantification strategy and abundance metrics, on the accuracy of eDNA-based abundance estimation were entirely overlooked. We conducted a meta-analysis using 56 previous eDNA literature and investigated the relationships between the accuracy (R2) of eDNA-based abundance estimation and eDNA characteristics and methodology. Our meta-regression analysis found that R2 values were significantly lower for crustaceans than fish, suggesting that less frequent eDNA production owing to their external morphology and physiology may impede accurate estimation of their abundance via eDNA. Moreover, R2 values were positively associated with filter pore size, indicating that selective collection of larger-sized eDNA, which is typically fresher, could improve the estimation accuracy of species abundance. Furthermore, R2 values were significantly lower for natural than laboratory conditions, while there was no difference in the estimation accuracy among natural environments. Our findings shed a new light on the importance of what characteristics of eDNA should be targeted for more accurate estimation of species abundance. Further empirical studies are required to validate our findings and fully elucidate the relationship between eDNA characteristics and eDNA-based abundance estimation.

scholarly journals The Gender Outcomes International Group: to Further Well-being Development (Going-fwd) Methodology on Identification and Inclusion of Gender Factors in Retrospective Cohort Studies

2020 ◽  
Author(s):  
Valeria Raparelli Raparelli ◽  
Colleen M. Norris ◽  
Uri Bender ◽  
Maria Trinidad Herrero ◽  
Alexandra Kautzky-Willer ◽  
...  
Keyword(s):  
Data Structure ◽  
Meta Analysis ◽  
Synthetic Data ◽  
Well Being ◽  
Pooled Analysis ◽  
Research Network ◽  
Local Analysis ◽  
Related Factors ◽  
Individual Level ◽  
Definition Of

Abstract Background: Gender refers to the socially constructed roles, behaviors, expressions, and identities of girls, women, boys, men, and gender diverse people. It influences self-perception, individual’s actions and interactions, as well as the distribution of power and resources in society. Gender-related factors are seldom assessed as determinants of health outcomes, despite their powerful contribution.Methods: Investigators of the GOING-FWD project developed a standard methodology applicable for observational studies to retrospectively identify gender-related factors to assess their relationship to outcomes and applied this method to selected cohorts of non-communicable chronic diseases from Austria, Canada, Spain, Sweden.Results: The following multistep process was applied. Step 1 (Identification of Gender-related Variables): Based on the gender framework of the Women Health Research Network (i.e. gender identity, role, relations, and institutionalized gender), and available literature for a certain disease, an optimal “wish-list” of gender-related variables/factors was created and discussed by experts. Step 2 (Definition of Outcomes): each of the cohort data dictionaries were screened for clinical and patient relevant outcomes, using the ICHOM framework. Step 3 (Building of Feasible Final List): A cross-validation between gender-related and outcome variables available per database and the “wish-list” was performed. Step 4 (Retrospective Data Harmonization): The harmonization potential of variables was evaluated. Step 5 (Definition of Data Structure and Analysis): Depending on the database data structure, the following analytic strategies were identified: (1) local analysis of data not transferable followed by a meta-analysis combining study-level estimates; (2) centrally performed federated analysis of anonymized data, with the individual-level participant data remaining on local servers; (3) synthesizing the data locally and performing a pooled analysis on the synthetic data; and (4) central analysis of pooled transferable data.Conclusion: The application of the GOING-FWD systematic multistep approach can help guide investigators to analyze gender and its impact on outcomes in previously collected data.

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