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

2019 ◽  
Vol 19 (4) ◽  
pp. 982-996 ◽  
Author(s):  
Laura S. Weyrich ◽  
Andrew G. Farrer ◽  
Raphael Eisenhofer ◽  
Luis A. Arriola ◽  
Jennifer Young ◽  
...  
Keyword(s):  
Sample Analysis ◽  
Laboratory Contamination ◽  
Biomass Sample ◽  
Over Time

DNA extraction from concrete v2

2021 ◽  
Author(s):  
Anders Kiledal ◽  
Julia A Maresca
Keyword(s):  
Dna Extraction ◽  
Dental Plaque ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Metagenomic Sequencing ◽  
Sample Analysis ◽  
Larger Sample ◽  
Laboratory Contamination ◽  
Biomass Sample ◽  
Over Time

This is a protocol for extracting DNA from concrete, based on the protocol developed by L. S. Weyrich, et al. for extraction of DNA from ancient calcified dental plaque. We have scaled it up for larger sample sizes and made some additional modifications for the chemistry of concrete. DNA extracted using this method is suitable for metagenomic sequencing by Illumina MiSeq and NextSeq, as well as amplicon sequencing. This protocol should yield 10 ng to 5 μg DNA per 10 g of concrete, depending on the age and integrity of the sample. Reference: L. S. Weyrich et al., Laboratory contamination over time during low-biomass sample analysis. Mol. Ecol. Resour. 19, 982–996 (2019).

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 Measuring Return and Volatility Spillovers among Sectoral Stocks in Nigeria

2019 ◽  
Vol 22 (2) ◽  
pp. 71-93 ◽  
Author(s):  
Ismail Olaleke Fasanya ◽  
Oluwatomisin Oyewole ◽  
Taofeek Agbatogun
Keyword(s):  
Stock Prices ◽  
Stock Return ◽  
Volatility Spillover ◽  
Sample Analysis ◽  
Monthly Data ◽  
Volatility Spillovers ◽  
Major Market ◽  
Over Time

Abstract This paper examines the return and volatility spillovers of different sectoral stock prices in Nigeria using monthly data from January 2007 to December 2016. We employ the Diebold and Yilmaz (2012) spillover approach and rolling sample analysis to capture the inherent secular and cyclical movements in the sector stocks market.We show that there is substantial difference between the behaviour of the sectoral stock return and volatility spillover indices over time. We find evidence of interdependence among sector stocks given the spillover indices. While the return spillover index reveals increased integration among the sectoral stocks, the volatility spillover index experiences significant bursts during major market crises. Interestingly, return and volatility spillovers exhibit both trends and bursts respectively.

Social transmission bias and the cultural evolution of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
David Hirshleifer ◽  
Siew Hong Teoh
Keyword(s):  
Cultural Evolution ◽  
Social Transmission ◽  
Cognitive Approach ◽  
Economic Problems ◽  
Economic Attitudes ◽  
The Social ◽  
Economic Beliefs ◽  
Over Time

AbstractEvolved dispositions influence, but do not determine, how people think about economic problems. The evolutionary cognitive approach offers important insights but underweights the social transmission of ideas as a level of explanation. The need for asocialexplanation for the evolution of economic attitudes is evidenced, for example, by immense variations in folk-economic beliefs over time and across individuals.

Articulatory Generalization in Two Word-Medial, Ambisyllabic Contexts

1988 ◽  
Vol 19 (3) ◽  
pp. 251-258 ◽  
Author(s):  
Virginia I. Wolfe ◽  
Suzanne D. Blocker ◽  
Norma J. Prater
Keyword(s):  
Common View ◽  
Perceptual Salience ◽  
The Common ◽  
Unitary Concept ◽  
Over Time

Articulatory generalization of velar cognates /k/, /g/ in two phonologically disordered children was studied over time as a function of sequential word-morpheme position training. Although patterns of contextual acquisition differed, correct responses to the word-medial, inflected context (e.g., "picking," "hugging") occurred earlier and exceeded those to the word-medial, noninflected context (e.g., "bacon," "wagon"). This finding indicates that the common view of the word-medial position as a unitary concept is an oversimplification. Possible explanations for superior generalization to the word-medial, inflected position are discussed in terms of coarticulation, perceptual salience, and the representational integrity of the word.

Treatment Fidelity Procedures for an Aphasia Intervention Within a Randomized Controlled Trial: Design, Feasibility, and Results

2020 ◽  
Vol 29 (1S) ◽  
pp. 412-424
Author(s):  
Elissa L. Conlon ◽  
Emily J. Braun ◽  
Edna M. Babbitt ◽  
Leora R. Cherney
Keyword(s):  
Randomized Controlled Trial ◽  
Controlled Trial ◽  
Treatment Protocol ◽  
Treatment Fidelity ◽  
Protocol Adherence ◽  
Study Condition ◽  
Randomized Controlled ◽  
Aphasia Therapy ◽  
Percent Accuracy ◽  
Over Time

Purpose This study reports on the treatment fidelity procedures implemented during a 5-year randomized controlled trial comparing intensive and distributed comprehensive aphasia therapy. Specifically, the results of 1 treatment, verb network strengthening treatment (VNeST), are examined. Method Eight participants were recruited for each of 7 consecutive cohorts for a total of 56 participants. Participants completed 60 hr of aphasia therapy, including 15 hr of VNeST. Two experienced speech-language pathologists delivered the treatment. To promote treatment fidelity, the study team developed a detailed manual of procedures and fidelity checklists, completed role plays to standardize treatment administration, and video-recorded all treatment sessions for review. To assess protocol adherence during treatment delivery, trained research assistants not involved in the treatment reviewed video recordings of a subset of randomly selected VNeST treatment sessions and completed the fidelity checklists. This process was completed for 32 participants representing 2 early cohorts and 2 later cohorts, which allowed for measurement of protocol adherence over time. Percent accuracy of protocol adherence was calculated across clinicians, cohorts, and study condition (intensive vs. distributed therapy). Results The fidelity procedures were sufficient to promote and verify a high level of adherence to the treatment protocol across clinicians, cohorts, and study condition. Conclusion Treatment fidelity strategies and monitoring are feasible when incorporated into the study design. Treatment fidelity monitoring should be completed at regular intervals during the course of a study to ensure that high levels of protocol adherence are maintained over time and across conditions.

Assessing Functional Language in School-Aged Children Using Language Sample Analysis

2020 ◽  
Vol 5 (3) ◽  
pp. 622-636
Author(s):  
John Heilmann ◽  
Alexander Tucci ◽  
Elena Plante ◽  
Jon F. Miller
Keyword(s):  
Computer Hardware ◽  
School Age Children ◽  
Functional Language ◽  
School Age ◽  
Clinical Use ◽  
Sample Analysis ◽  
Validity And Reliability ◽  
Language Sample Analysis ◽  
Accuracy And Repeatability ◽  
Language Sample

Purpose The goal of this clinical focus article is to illustrate how speech-language pathologists can document the functional language of school-age children using language sample analysis (LSA). Advances in computer hardware and software are detailed making LSA more accessible for clinical use. Method This clinical focus article illustrates how documenting school-age student's communicative functioning is central to comprehensive assessment and how using LSA can meet multiple needs within this assessment. LSA can document students' meaningful participation in their daily life through assessment of their language used during everyday tasks. The many advances in computerized LSA are detailed with a primary focus on the Systematic Analysis of Language Transcripts (Miller & Iglesias, 2019). The LSA process is reviewed detailing the steps necessary for computers to calculate word, morpheme, utterance, and discourse features of functional language. Conclusion These advances in computer technology and software development have made LSA clinically feasible through standardized elicitation and transcription methods that improve accuracy and repeatability. In addition to improved accuracy, validity, and reliability of LSA, databases of typical speakers to document status and automated report writing more than justify the time required. Software now provides many innovations that make LSA simpler and more accessible for clinical use. Supplemental Material https://doi.org/10.23641/asha.12456719

Issues in Language Sample Collection and Analysis With Children Using AAC

2014 ◽  
Vol 23 (2) ◽  
pp. 65-74 ◽  
Author(s):  
Gail Van Tatenhove
Keyword(s):  
Clinical Practice ◽  
Augmentative And Alternative Communication ◽  
Language Production ◽  
Expressive Language ◽  
Sample Analysis ◽  
Alternative Communication ◽  
Sample Collection ◽  
Speech Language Pathologists ◽  
Language Sample Analysis ◽  
Language Sample

Language sample analysis is considered one of the best methods of evaluating expressive language production in speaking children. However, the practice of language sample collection and analysis is complicated for speech-language pathologists working with children who use augmentative and alternative communication (AAC) devices. This article identifies six issues regarding use of language sample collection and analysis in clinical practice with children who use AAC devices. The purpose of this article is to encourage speech-language pathologists practicing in the area of AAC to utilize language sample collection and analysis as part of ongoing AAC assessment.

Percutaneous Tracheostomy: A Multidisciplinary Approach

2008 ◽  
Vol 18 (2) ◽  
pp. 87-98 ◽  
Author(s):  
Vinciya Pandian ◽  
Thai Tran Nguyen ◽  
Marek Mirski ◽  
Nasir Islam Bhatti
Keyword(s):  
Health Care ◽  
Quality Assurance ◽  
Data Collection ◽  
Health Care Professionals ◽  
Multidisciplinary Approach ◽  
Percutaneous Tracheostomy ◽  
Johns Hopkins Hospital ◽  
Prospective Data ◽  
Comprehensive Service ◽  
Over Time

Abstract The techniques of performing a tracheostomy has transformed over time. Percutaneous tracheostomy is gaining popularity over open tracheostomy given its advantages and as a result the number of bedside tracheostomies has increased necessitating the need for a Percutaneous Tracheostomy Program. The Percutaneous Tracheostomy Program at the Johns Hopkins Hospital is a comprehensive service that provides care to patients before, during, and after a tracheostomy with a multidisciplinary approach aimed at decreasing complications. Education is provided to patients, families, and health-care professionals who are involved in the management of a tracheostomy. Ongoing prospective data collection serves as a tool for Quality Assurance.

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