scholarly journals Laboratory contamination over time during low-biomass sample analysis

2018 ◽  
Author(s):  
Laura S. Weyrich ◽  
Andrew G. Farrer ◽  
Raphael Eisenhofer ◽  
Luis A. Arriola ◽  
Jennifer Young ◽  
...  
Keyword(s):  
High Throughput ◽  
Ancient Dna ◽  
Negative Control ◽  
Modern Molecular Biology ◽  
Taxonomic Profile ◽  
Metagenomic Study ◽  
Ice Water ◽  
Laboratory Contamination ◽  
Over Time

AbstractBacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g.skin swabs, tissue biopsies, ice, water, degraded forensic samples, or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over five years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a homemade silica-based extraction method, commonly used to analyse low-endogenous samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to the modern molecular biology laboratories, and changed over time according to researchers, month, and season. The commercial kit contained higher microbial diversity and several human-associated taxa in comparison to the homemade silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: 1) extraction blank controls should be included and sequenced with every batch of extractions and 2) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.

scholarly journals Detection of SARS-CoV-2 antibodies formed in response to the BNT162b2 and mRNA-1237 mRNA vaccine by commercial antibody tests

2021 ◽  
Author(s):  
Jamil N Kanji ◽  
Ashley Bailey ◽  
Jayne Fenton ◽  
Sean H Ling ◽  
Rafael Rivera ◽  
...  
Keyword(s):  
High Throughput ◽  
Neutralising Antibodies ◽  
Term Care ◽  
Post Vaccination ◽  
Degree Of Protection ◽  
Group 2 ◽  
Antibody Tests ◽  
Abbott Architect ◽  
Over Time

ABSTRACTPURPOSEWith rapid approval of SARS-CoV-2 vaccines, the ability of clinical laboratories to detect vaccine-induced antibodies with available high-throughput commercial assays is unknown. We aimed to determine if commercial serology assays can detect vaccine-induced antibodies (VIAs) and understand the vaccination response.METHODSThis cohort study recruited healthcare workers and residents of long-term care facilities (receiving the BNT162b2 and mRNA-1273 products, respectively) who underwent serum collection pre-vaccination (BNT162b2 group), 2-weeks post vaccination (both groups), and pre-2nd dose (both groups). Sera were tested for the presence of SARS-CoV-2 IgG using four commercial assays (Abbott Architect SARS-CoV-2 IgG, Abbott Architect SARS-CoV-2 IgG II Quant, DiaSorin Liaison Trimeric S IgG, and GenScript cPASS) to detect VIAs. Secondary outcomes included description of post-vaccination antibody response and correlation with neutralising titers.RESULTS225 participants (177 receiving BNT162b2 and 48 receiving mRNA-1273) were included (median age 41 years,; 66-78% female). Nucleocapsid IgG was found in 4.1% and 21.9% of the BNT162b2 (baseline) and mRNA-1273 (2-weeks post first dose). All anti-spike assays detected antibodies post-vaccination, with an average increase of 87.2% (range 73.8-94.3%; BNT162b2), and 25.2% (range 23.8-26.7%; mRNA-1273) between the first and last sampling time points (all p<0.05). Neutralising antibodies were detected at all post-vaccine timepoints for both vaccine arms, with increasing titers over time (all p<0.05).CONCLUSIONAnti-spike vaccine-induced SARS-CoV-2 IgG are detectable by commercially available high-throughput assays and increases over time. Prior to second dose of vaccination, neutralising antibodies are detectable in 73-89% of individuals, suggesting the majority of individuals would have some degree of protection from subsequent infection.

scholarly journals Fluctuating High Throughput Serological Assay Results in Recurrent Convalescent Plasma Donors

2020 ◽  
Author(s):  
Larry L. Luchsinger ◽  
Shiraz Rehmani ◽  
Andrew Opalka ◽  
Donna Strauss ◽  
Christopher D. Hillyer ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Neutralizing Antibodies ◽  
Accurate Estimation ◽  
Patient Protection ◽  
Donation Process ◽  
Antibody Levels ◽  
Antibody Kinetics ◽  
Over Time

AbstractThe clinical and scientific communities rely on serology testing to analyze the degree of antibody-mediated immunity afforded to recovered patients from SARS-CoV-2 infection. Neutralizing antibodies present in COVID-19 convalescent plasma (CCP) remains a practical therapy to treat COVID-19 patients requiring hospitalization. However, it remains unclear how long antibody levels persist in CCP donors after recovery. An accurate estimation of antibody kinetics in CCP donors provide an important observation to further define the extent of long-term immunity in recovered patient and simultaneously inform CCP collection processes in efforts to improve CCP dosing and therapeutic outcome. In this study, we analyzed 63 donors and measured antibody levels using two high throughput screening assays (HTSA) designed to detect antibodies targeting the spike protein (S1) and nucleocapsid protein (NP) of SARS-CoV-2 and monitored antibody levels between 2-8 consecutive donations. We show that anti-S1 antibody levels, as measured using the Ortho Total Ig HTSA, increased over time in repeat CCP donors while anti-NP antibody levels, as measured using the Abbott IgG HTSA, were unchanged or decreased over time. When we normalized these data, we found that both the absolute levels of anti-S1 antibodies and the ratio between S1 and NP antibodies tends to increase over time. These data have important implications for the convalescent donation process, patient protection from future infection and characterization of the SARS-CoV-2 immune response.

Enhancing community welfare through improved water quality: a case for applying staggered pollution charges in the river Musi sub-basin of Andhra Pradesh, India

Water Policy ◽  
2005 ◽  
Vol 7 (5) ◽  
pp. 469-483
Author(s):  
Tishya Chatterjee
Keyword(s):  
Andhra Pradesh ◽  
Relevant Literature ◽  
Pollution Prevention ◽  
Economic Benefits ◽  
Environmental Damage ◽  
Marginal Costs ◽  
Community Acceptance ◽  
Level Data ◽  
Over Time

In conditions of severe water-pollution and dormant community acceptance of accumulating environmental damage, the regulator's role goes beyond pollution prevention and more towards remediation and solutions based on the community's long-term expectations of economic benefits from clean water. This paper suggests a method to enable these benefits to become perceptible progressively, through participatory clean-up operations, supported by staggered pollution charges. It analyses the relevant literature on pollution prevention and applies a cost-based “willingness to pay” model, using primary basin-level data of total marginal costs. It develops a replicable demand-side approach imposing charge-standard targets over time in urban-industrial basins of developing countries.

The Short-Term and Long-Term Impacts of Sarbanes-Oxley Act on Composition and Characteristics of Corporate Board of Directors

2015 ◽  
Vol 5 (4) ◽  
Author(s):  
Halil Kaya ◽  
Gaurango Banerjee
Keyword(s):  
Board Composition ◽  
Corporate Boards ◽  
Corporate Accountability ◽  
Corporate Board ◽  
Short Term ◽  
Dual Roles ◽  
Board Characteristics ◽  
Sarbanes Oxley ◽  
Over Time

The paper examines the Sarbanes-Oxley (2002) Acts immediate impact on board composition and characteristics as well as possible reversals in its impact over time. Effects on directors age and tenure are analyzed over the 2001-06 sample period. Female participation in corporate boards is also studied in the pre-SOX and post-SOX periods. The dual roles of directors in being a member of the board as well as serving as either CEO, CFO, Chairman, Co-Chair, Founder, or Lead Director of their respective companies is also examined. We observe a short-term impact of SOX on board compositions due to changes seen in board characteristics between 2001 (pre-SOX), and 2003-05 short-term period (post-SOX). Also, we observe a reversal of board characteristics in 2006 to pre-SOX levels implying that the effects of SOX on board composition were short-lived, and needs to be monitored over time to ensure adherence to corporate accountability guidelines over the long-term.

A Downward Spiral? A Panel Study of Misinformation and Media Trust in Chile

2021 ◽  
pp. 194016122110252
Author(s):  
Sebastián Valenzuela ◽  
Daniel Halpern ◽  
Felipe Araneda
Keyword(s):  
News Media ◽  
Panel Study ◽  
Future Research ◽  
Panel Survey ◽  
Downward Spiral ◽  
The Media ◽  
Media Trust ◽  
People’S Attitudes ◽  
Over Time

Despite widespread concern, research on the consequences of misinformation on people's attitudes is surprisingly scant. To fill in this gap, the current study examines the long-term relationship between misinformation and trust in the news media. Based on the reinforcing spirals model, we analyzed data from a three-wave panel survey collected in Chile between 2017 and 2019. We found a weak, over-time relationship between misinformation and media skepticism. Specifically, initial beliefs on factually dubious information were negatively correlated with subsequent levels of trust in the news media. Lower trust in the media, in turn, was related over time to higher levels of misinformation. However, we found no evidence of a reverse, parallel process where media trust shielded users against misinformation, further reinforcing trust in the news media. The lack of evidence of a downward spiral suggests that the corrosive effects of misinformation on attitudes toward the news media are less serious than originally suggested. We close with a discussion of directions for future research.

scholarly journals Personality dynamics at work: The effects of form, time, and context of variability

2021 ◽  
pp. 089020702110173
Author(s):  
Nadin Beckmann ◽  
Damian P Birney ◽  
Amirali Minbashian ◽  
Jens F Beckmann
Keyword(s):  
Individual Differences ◽  
Cognitive Ability ◽  
Temporal Stability ◽  
Limited Evidence ◽  
Short Term ◽  
State Data ◽  
The Status ◽  
Over Time ◽  
Trait Variability

The study aimed to investigate the status of within-person state variability in neuroticism and conscientiousness as individual differences constructs by exploring their (a) temporal stability, (b) cross-context consistency, (c) empirical links to selected antecedents, and (d) empirical links to longer term trait variability. Employing a sample of professionals ( N = 346) from Australian organisations, personality state data together with situation appraisals were collected using experience sampling methodology in field and repeatedly in lab-like settings. Data on personality traits, cognitive ability, and motivational mindsets were collected at baseline and after two years. Contingent (situation contingencies) and non-contingent (relative SD) state variability indices were relatively stable over time and across contexts. Only a small number of predictive effects of state variability were observed, and these differed across contexts. Cognitive ability appeared to be associated with state variability under lab-like conditions. There was limited evidence of links between short-term state and long-term trait variability, except for a small effect for neuroticism. Some evidence of positive manifold was found for non-contingent variability. Systematic efforts are required to further elucidate the complex pattern of results regarding the antecedents, correlates and outcomes of individual differences in state variability.

scholarly journals Agritourism—A Business Reality of the Moment for Romanian Rural Area’s Sustainability

2021 ◽  
Vol 13 (11) ◽  
pp. 6313
Author(s):  
Ramona Ciolac ◽  
Tiberiu Iancu ◽  
Ioan Brad ◽  
Tabita Adamov ◽  
Nicoleta Mateoc-Sîrb
Keyword(s):  
Rural Communities ◽  
Distribution Channels ◽  
Scientific Paper ◽  
Business Owners ◽  
The Future ◽  
Tourism Potential ◽  
The Moment ◽  
Managerial Experience ◽  
Over Time

The agritourism activity can be a characteristic reality of the present, considering rural area’s sustainability, being at the same time a business reality for rural entrepreneurs and a “must have” for rural communities that have tourism potential. It is a form of tourism, through which the tourist can receive a qualitative product at a reasonable price, but also a field that can ensure sustainable development over time, being at the same time environmentally friendly. The purpose of this scientific paper is to identify the aspects that make agritourism “a possible business reality of the moment”, for Romanian rural area’s sustainability. We take into account the following areas: Bran-Moieciu area—considered “the oldest” in terms of agritourism experience, and Apuseni Mountains area, with a great inclination and potential for this activity. The study conducted for these two areas is focused on several aspects: the degree of involvement in agritourism activities, considering the number of years and managerial experience, the analysis of the types of activities/experiences offered by agritourism structures, the identification of the main reasons/motivations for the orientation towards agritourism and the manner in which this field is perceived. Aspects related to the marketing-finance part of the agritourism business are also taken into account: customers, distribution channels, financial sources, shortcomings observed by agritourism business owners and possible action directions so as to improve the activity/agritourism product. Agritourism may be “a possible business reality of the moment” for the studied areas and not only, but in the future, the entrepreneur/farmer must be constantly updated because of the changing situations that appear on the market, be able to make sustainable decisions for his/her own business, which in the future will ensure its viability and obviously its long-term profitability and development, and in the same time rural area’s sustainability.

scholarly journals INTRODUCTION TO THE SPECIAL SECTION: BORDERS, FRONTIERS, AND BOUNDARIES IN THE MAYA WORLD: CONCEPTS AND THEORY

2020 ◽  
Vol 31 (3) ◽  
pp. 453-460 ◽  
Author(s):  
Christina Halperin ◽  
Carolyn Freiwald ◽  
Gyles Iannone
Keyword(s):  
Special Section ◽  
Economic Networks ◽  
Maya Area ◽  
Cultural Connections ◽  
Over Time

AbstractThe Maya area has long been characterized as a mosaic of polities large and small, with cultural connections, linguistic dialects, ethnicities, and economic networks that shifted, expanded, and contracted over time. In this paper, we examine different ways of constructing boundaries. From physical demarcations in the landscape to habitual practices of interaction and affiliation, the lines that tied and divided were both unstable and multiple. We draw on definitions and theories from anthropology, history, and geography to review the concepts of borders, frontiers, and boundaries and their implications for the Maya area over the long term.

scholarly journals A Holistic Framework for Evaluating Adaptation Approaches to Coastal Hazards and Sea Level Rise: A Case Study from Imperial Beach, California

Water ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1324
Author(s):  
David Revell ◽  
Phil King ◽  
Jeff Giliam ◽  
Juliano Calil ◽  
Sarah Jenkins ◽  
...  
Keyword(s):  
Sea Level Rise ◽  
Sea Level ◽  
Public Trust ◽  
Adaptation Strategy ◽  
Public Benefits ◽  
Study Results ◽  
Local Risk ◽  
Over Time

Sea level rise increases community risks from erosion, wave flooding, and tides. Current management typically protects existing development and infrastructure with coastal armoring. These practices ignore long-term impacts to public trust coastal recreation and natural ecosystems. This adaptation framework models physical responses to the public beach and private upland for each adaptation strategy over time, linking physical changes in widths to damages, economic costs, and benefits from beach recreation and nature using low-lying Imperial Beach, California, as a case study. Available coastal hazard models identified community vulnerabilities, and local risk communication engagement prioritized five adaptation approaches—armoring, nourishment, living shorelines, groins, and managed retreat. This framework innovates using replacement cost as a proxy for ecosystem services normally not valued and examines a managed retreat policy approach using a public buyout and rent-back option. Specific methods and economic values used in the analysis need more research and innovation, but the framework provides a scalable methodology to guide coastal adaptation planning everywhere. Case study results suggest that coastal armoring provides the least public benefits over time. Living shoreline approaches show greater public benefits, while managed retreat, implemented sooner, provides the best long-term adaptation strategy to protect community identity and public trust resources.

scholarly journals Acute symptoms of mild to moderate COVID-19 are highly heterogeneous across individuals and over time

2021 ◽  
Author(s):  
Thomas L Rodebaugh ◽  
Madelyn R Frumkin ◽  
Angela M Reiersen ◽  
Eric J Lenze ◽  
Michael S Avidan ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Survey Methods ◽  
Clinical Care ◽  
Clinical Deterioration ◽  
Symptom Profiles ◽  
Fluctuating Course ◽  
The Common ◽  
Symptom Changes ◽  
Over Time

Abstract Background The symptoms of COVID-19 appear to be heterogenous, and the typical course of these symptoms is unknown. Our objectives were to characterize the common trajectories of COVID-19 symptoms and assess how symptom course predicts other symptom changes as well as clinical deterioration. Methods 162 participants with acute COVID-19 responded to surveys up to 31 times for up to 17 days. Several statistical methods were used to characterize the temporal dynamics of these symptoms. Because nine participants showed clinical deterioration, we explored whether these participants showed any differences in symptom profiles. Results Trajectories varied greatly between individuals, with many having persistently severe symptoms or developing new symptoms several days after being diagnosed. A typical trajectory was for a symptom to improve at a decremental rate, with most symptoms still persisting to some degree at the end of the reporting period. The pattern of symptoms over time suggested a fluctuating course for many patients. Participants who showed clinical deterioration were more likely to present with higher reports of severity of cough and diarrhea. Conclusion The course of symptoms during the initial weeks of COVID-19 is highly heterogeneous and is neither predictable nor easily characterized using typical survey methods. This has implications for clinical care and early-treatment clinical trials. Additional research is needed to determine whether the decelerating improvement pattern seen in our data is related to the phenomenon of patients reporting long-term symptoms, and whether higher symptoms of diarrhea in early illness presages deterioration.

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