scholarly journals q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

mSystems ◽  
2018 ◽  
Vol 3 (6) ◽  
Author(s):  
Nicholas A. Bokulich ◽  
Matthew R. Dillon ◽  
Yilong Zhang ◽  
Jai Ram Rideout ◽  
Evan Bolyen ◽  
...  
Keyword(s):  
Temporal Trends ◽  
Population Heterogeneity ◽  
Data Sets ◽  
Cross Sectional ◽  
Paired Sample ◽  
Link Type ◽  
Paired Samples ◽  
Longitudinal Sampling ◽  
Microbiome Data ◽  
Analysis Platform

ABSTRACTStudies of host-associated and environmental microbiomes often incorporate longitudinal sampling or paired samples in their experimental design. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity, offering advantages over cross-sectional and pre-post study designs. To support the needs of microbiome researchers performing longitudinal studies, we developed q2-longitudinal, a software plugin for the QIIME 2 microbiome analysis platform (https://qiime2.org). The q2-longitudinal plugin incorporates multiple methods for analysis of longitudinal and paired-sample data, including interactive plotting, linear mixed-effects models, paired differences and distances, microbial interdependence testing, first differencing, longitudinal feature selection, and volatility analyses. The q2-longitudinal package (https://github.com/qiime2/q2-longitudinal) is open-source software released under a 3-clause Berkeley Software Distribution (BSD) license and is freely available, including for commercial use.IMPORTANCELongitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity. We describe q2-longitudinal, a software plugin for longitudinal analysis of microbiome data sets in QIIME 2. The availability of longitudinal statistics and visualizations in the QIIME 2 framework will make the analysis of longitudinal data more accessible to microbiome researchers.

scholarly journals q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data

2017 ◽  
Author(s):  
Nicholas A. Bokulich ◽  
Yilong Zhang ◽  
Matthew Dillon ◽  
Jai Ram Rideout ◽  
Evan Bolyen ◽  
...  
Keyword(s):  
Temporal Trends ◽  
Population Heterogeneity ◽  
Cross Sectional ◽  
Paired Sample ◽  
Link Type ◽  
Paired Samples ◽  
Study Designs ◽  
Longitudinal Sampling ◽  
Microbiome Data ◽  
Analysis Platform

AbstractStudies of host-associated and environmental microbiomes often incorporate longitudinal sampling or paired samples in their experimental design. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity, offering advantages over cross-sectional and pre/post study designs. To support the needs of microbiome researchers performing longitudinal studies, we developed q2-longitudinal, a software plugin for the QIIME 2 microbiome analysis platform (https://qiime2.org). The q2-longitudinal plugin incorporates multiple methods for analysis of longitudinal and paired-sample data, including paired differences and distances, linear mixed effects models, microbial interdependence test, first differencing, and volatility analyses. The q2-longitudinal package (https://github.com/qiime2/q2-longitudinal) is open source software released under a BSD-3-Clause license and is freely available, including for commercial use.

scholarly journals Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Gongchao Jing ◽  
Lu Liu ◽  
Zengbin Wang ◽  
Yufeng Zhang ◽  
Li Qian ◽  
...  
Keyword(s):  
Big Data ◽  
User Interface ◽  
Search Engine ◽  
Functional Similarity ◽  
Metagenomic Data ◽  
Data Sets ◽  
Data Space ◽  
Link Type ◽  
Database Platform ◽  
Microbiome Data

ABSTRACT Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes in the global metagenome data space based on the taxonomic or functional similarity of a whole microbiome to those in the database. MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a Web-based graphical user interface for user-friendly searching, data browsing, and tutoring. MSE 2 is freely accessible via http://mse.ac.cn. For standalone searches of customized microbiome databases, the kernel of the MSE 2 search engine is provided at GitHub (https://github.com/qibebt-bioinfo/meta-storms). IMPORTANCE A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird’s-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile. Key improvements include database extension, data compatibility, a search engine kernel, and a user interface. The new ability to search the microbiome space via functional similarity greatly expands the scope of search-based mining of the microbiome big data.

scholarly journals A Novel Sparse Compositional Technique Reveals Microbial Perturbations

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Cameron Martino ◽  
James T. Morton ◽  
Clarisse A. Marotz ◽  
Luke R. Thompson ◽  
Anupriya Tripathi ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Matrix Completion ◽  
Salient Feature ◽  
Discriminatory Power ◽  
Data Sets ◽  
Link Type ◽  
Compositional Technique ◽  
High Discriminatory Power ◽  
Microbiome Data ◽  
Log Ratio

ABSTRACTThe central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance.IMPORTANCEBy accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained athttps://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this analysis athttps://library.qiime2.org/plugins/q2-deicode.

Twitter Usage Using Common Reference to Tinnitus

2020 ◽  
Vol 29 (2) ◽  
pp. 206-217
Author(s):  
Jianyuan Ni ◽  
Monica L. Bellon-Harn ◽  
Jiang Zhang ◽  
Yueqing Li ◽  
Vinaya Manchaiah
Keyword(s):  
Nonprofit Organizations ◽  
Temporal Trends ◽  
Temporal Analysis ◽  
Cross Sectional ◽  
For Profit ◽  
Common Reference ◽  
Personal Experiences ◽  
Twitter Users ◽  
Sectional Analysis ◽  
Share Information

Objective The objective of the study was to examine specific patterns of Twitter usage using common reference to tinnitus. Method The study used cross-sectional analysis of data generated from Twitter data. Twitter content, language, reach, users, accounts, temporal trends, and social networks were examined. Results Around 70,000 tweets were identified and analyzed from May to October 2018. Of the 100 most active Twitter accounts, organizations owned 52%, individuals owned 44%, and 4% of the accounts were unknown. Commercial/for-profit and nonprofit organizations were the most common organization account owners (i.e., 26% and 16%, respectively). Seven unique tweets were identified with a reach of over 400 Twitter users. The greatest reach exceeded 2,000 users. Temporal analysis identified retweet outliers (> 200 retweets per hour) that corresponded to a widely publicized event involving the response of a Twitter user to another user's joke. Content analysis indicated that Twitter is a platform that primarily functions to advocate, share personal experiences, or share information about management of tinnitus rather than to provide social support and build relationships. Conclusions Twitter accounts owned by organizations outnumbered individual accounts, and commercial/for-profit user accounts were the most frequently active organization account type. Analyses of social media use can be helpful in discovering issues of interest to the tinnitus community as well as determining which users and organizations are dominating social network conversations.

scholarly journals 425. The Utility of Paired Upper and Lower COVID-19 Sampling in Patients with Artificial Airways

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S279-S279
Author(s):  
Eimear Kitt ◽  
Julia S Sammons ◽  
Kathleen Chiotos ◽  
Susan E Coffin ◽  
Susan E Coffin ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Diagnostic Testing ◽  
Cross Sectional Study ◽  
Upper Respiratory Tract ◽  
Cross Sectional ◽  
Mechanically Ventilated ◽  
Paired Samples ◽  
Control And Prevention ◽  
Polymerase Chain

Abstract Background The Centers for Disease Control and Prevention (CDC) recommends upper respiratory tract (URT) polymerase chain reaction (PCR) testing as the initial diagnostic test for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Lower respiratory tract (LRT) testing for patients requiring mechanical ventilation is also recommended. The goal of this study was to evaluate concordance between paired URT and LRT specimens in children undergoing pre-admission/procedure screening or diagnostic testing. We hypothesized that &lt; 10% of paired tests would have discordant results. Methods Single center cross-sectional study including children with artificial airways who had paired URT and LRT SARS-CoV-2 PCR testing between 4/1/2020 and 6/8/2020. URT specimens included nasopharyngeal (NP) swabs and aspirates. LRT specimens included tracheal aspirates and bronchoalveolar lavages. URT and LRT specimens were classified as paired if the two specimens were collected within 24 hours. Artificial airways included tracheostomies and endotracheal tubes. Tests were classified as diagnostic versus screening based on the indication selected in the order. Results 102 paired specimens were obtained during the study period. Fifty-nine were performed for screening and 43 were performed for diagnosis of suspected SARS-CoV-2. Overall, 94 specimens (92%) were concordant, including 89 negative from both sources and 5 positive from both sources. Eight specimens (8%) were discordant, all of which were positive from the URT and negative from the LRT (Figure 1). Among patients undergoing screening, 3 of 4 positive tests were discordant and among symptomatic patients, 5 of 9 positive tests were discordant. There were no instances of a positive LRT specimen with a negative URT specimen. Figure 1. Performance of upper and lower respiratory tract SARS-CoV-2 PCR testing in children with artificial airways Conclusion Overall, most paired samples from the URT and LRT yielded concordant results with no pairs positive from the LRT and negative from the URT. These data support the CDC recommendation that URT specimens are the preferred initial SARS-CoV-2 test, while LRT specimens should be collected only from mechanically ventilated with suspected SARS-CoV-2. Disclosures All Authors: No reported disclosures

scholarly journals Lifestyle modifications result in alterations in the gut microbiota in obese children

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ky Young Cho
Keyword(s):  
Gut Microbiota ◽  
Normal Weight ◽  
Rrna Gene ◽  
Weight Changes ◽  
Obese Children ◽  
Lifestyle Modifications ◽  
Cross Sectional ◽  
Fat Loss ◽  
Link Type ◽  
Firmicutes Phylum

Abstract Background The association between the gut microbiota and pediatric obesity was analyzed in a cross-sectional study. A prospective study of obese children was conducted to assess the gut microbial alterations after a weight change. We collected fecal samples from obese children before and after a 2-month weight reduction program that consisted of individual counseling for nutritional education and physical activity, and we performed 16S rRNA gene amplicon sequencing using an Illumina MiSeq platform. Results Thirty-six participants, aged 7 to 18 years, were classified into the fat loss (n = 17) and the fat gain (n = 19) groups according to the change in total body fat (%) after the intervention. The baseline analysis of the gut microbiota in the preintervention stages showed dysbiotic features of both groups compared with those of normal-weight children. In the fat loss group, significantly decreased proportions of Bacteroidetes phylum, Bacteroidia class, Bacteroidales order, Bacteroidaceae family, and Bacteroides genus, along with increased proportions of Firmicutes phylum, Clostridia class, and Clostridiales order, were observed after intervention. The microbial richness was significantly reduced, without a change in beta diversity in the fat loss group. The fat gain group showed significantly deceased proportions of Firmicutes phylum, Clostridia class, Clostridiales order, Lachnospiraceae family, and Eubacterium hallii group genus, without a change in diversity after the intervention. According to the functional metabolic analysis by the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, the “Nitrate Reduction VI” and “Aspartate Superpathway” pathways were predicted to increase significantly in the fat loss group. The cooccurring networks of genera were constructed and showed the different microbes that drove the changes between the pre- and postintervention stages in the fat loss and fat gain groups. Conclusions This study demonstrated that lifestyle modifications can impact the composition, richness, and predicted functional profiles of the gut microbiota in obese children after weight changes. Trial registration ClinicalTrials.govNCT03812497, registration date January 23, 2019, retrospectively registered.

scholarly journals Is T2 mapping reliable in evaluation of native and repair cartilage tissue of the knee?

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hasan Banitalebi ◽  
Christian Owesen ◽  
Asbjørn Årøen ◽  
Hang Thi Tran ◽  
Tor Åge Myklebust ◽  
...  
Keyword(s):  
T2 Mapping ◽  
Intraclass Correlation ◽  
Cartilage Tissue ◽  
Intraobserver Agreement ◽  
Level Of Evidence ◽  
Cross Sectional ◽  
Repair Tissue ◽  
Native Cartilage ◽  
Link Type ◽  
Imaging Plane

Abstract Purpose To evaluate the effect of imaging plane and experience of observers on the reliability of T2 mapping of native and repair cartilage tissue of the knee. Methods Fifteen consecutive patients from two randomised controlled trials (RCTs) were included in this cross-sectional study. Patients with an isolated knee cartilage lesion were randomised to receive either debridement or microfracture (RCT 1) or debridement or autologous chondrocyte implantation (RCT 2). T2 mapping was performed in coronal and sagittal planes two years postoperatively. A musculoskeletal radiologist, a resident of radiology and two orthopaedic surgeons measured the T2 values independently. Intraclass Correlation Coefficient (ICC) with 95% Confidence Intervals was used to calculate the inter- and intraobserver agreement. Results Mean age for the patients was 36.8 ± 11 years, 8 (53%) were men. The overall interobserver agreement varied from poor to good with ICCs in the range of 0.27– 0.76 for native cartilage and 0.00 – 0.90 for repair tissue. The lowest agreement was achieved for evaluations of repair cartilage tissue. The estimated ICCs suggested higher inter- and intraobserver agreement for radiologists. On medial femoral condyles, T2 values were higher for native cartilage on coronal images (p < 0.001) and for repair tissue on sagittal images (p < 0.001). Conclusions The reliability of T2 mapping of articular cartilage is influenced by the imaging plane and the experience of the observers. This influence may be more profound for repair cartilage tissue. This is important to consider when using T2 mapping to measure outcomes after cartilage repair surgery. Trial registration ClinicalTrials.gov, NCT02637505 and NCT02636881, registered December 2015. Level of evidence II, based on prospective data from two RCTs.

scholarly journals FRI0056 LUNG COMPROMISE SCREENING IN PATIENTS WITH EARLY RA. A MULTICENTRIC CROSS SECTIONAL STUDY

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 604.1-604
Author(s):  
F. Benavidez ◽  
G. Rodriguez ◽  
A. Riopedre ◽  
D. Mata ◽  
A. Benitez ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Physical Examination ◽  
Lung Disease ◽  
Lung Involvement ◽  
High Resolution Computed Tomography ◽  
Cross Sectional ◽  
Multicentric Study ◽  
Link Type ◽  
Immunological Tests ◽  
Pulmonary Manifestations

Background:Rheumatoid arthritis (RA) affects 0.4-1.3% of general population (1). It can affect lungs in different ways, with interstitial lung disease (ILD) as the most severe. Clinically evident ILD has been reported in 10-42% of patients, with a great impact in prognosis (2).Objectives:Toidentify the prevalence of lung involvement in early rheumatoid arthritis patients (ERA) without previous known lung disease and describe the association between high resolution computed tomography (HRCT), lung functional tests (LFT) and clinical findings.Methods:Cross sectional multicentric study. We included ERA patients (1 year or less since diagnose) consecutively. Patients with previous RA related lung disease or biologic/targeted synthetic Dmard treatment were excluded. HRCT, immunological tests (rheumatoid factor, anti-CCP, ANA), LFT and clinical evaluation were performed.Results:We included 74 patients, 63 (85,1%) woman, mean (SD) of 47 (17,7) years. Thirty-seven patients (50%) were current or former smokers. Abnormal findings in HRCT were found in 62 patients (88,6%): ILD in 6 (8,6%), airway involvement in 40 (70%) and emphysema in 7 (10%). Ten patients (13,5%) had abnormal auscultation (2 sibilances, 2 roncus, and 6 crackles). Six patients (8,1%) had digital clubbing. Regarding immunological tests, 54/61 (88,5%) patients were positive for Anti CCP, and 53/61 (86,9%) were positive for FR. We compared features of patients with findings related to RA in HRCT (interstitial and/or airway) with those without them. We found no differences in the mean (SD) of DAS-28 [4,74 (1,38) vs 4,32 (1,39); p= 0,27]. The prevalence of anti- CCP was not higher in patients with abnormal HRCT [38/44 (86,3%) vs 16/17 (94,1%); p=0,39]. Patients with abnormal HRCT were older [median (IQR) 50,5 years (44,5-59,5) vs 43 years (32-51); p=0,008) and showed higher VSG values [mean (SD) 39,09 (24,03) vs 27,38 (17,6); p= 0,043]. Abnormal physical examination or dyspnea (class 2 mMRC or higher) was significantly associated with HRCT abnormalities [26 (50%) vs 3 (13,6%); p=0.003) and the presence of ILD on HRCT was significantly associated with crackles on the auscultation [4/68(6,25%) vs 2/6 (33,33%); p 0,023].Conclusion:This study shows a high prevalence of lung involvement in ERA patients of less 1 year from diagnosis. Also, we showed a significant association between HRCT and physical examination findings. This data highlights the importance of the clinical examination in Rheumatoid Arthritis patients. More studies with bigger samples and longitudinal follow up are needed to confirm and complete our results.References:[1]Rooney BK, Silman AJ. Epidemiology of the rheumatic diseases. Curr Opin Rheumatol [Internet]. 1999 Mar [cited 2016 Jul 19];11(2):91–7. Available from:http://www.ncbi.nlm.nih.gov/pubmed/10319210.[2]Antin-Ozerkis D, Evans J, Rubinowitz A, Homer RJ, Matthay RA. Pulmonary Manifestations of Rheumatoid Arthritis. Clin Chest Med [Internet]. 2010;31(3):451–78. Available from:http://dx.doi.org/10.1016/j.ccm.2010.04.003.Disclosure of Interests:None declared

scholarly journals Trends in the prevalence of anaemia in Japanese adult women, 1989–2003

2008 ◽  
Vol 11 (3) ◽  
pp. 252-257 ◽  
Author(s):  
Fumi Hayashi ◽  
Nobuo Yoshiike ◽  
Katsushi Yoshita ◽  
Kazuo Kawahara
Keyword(s):  
Age Groups ◽  
Data Sets ◽  
Adult Women ◽  
Residential Areas ◽  
Nutrition Survey ◽  
Japanese Adult ◽  
Cross Sectional ◽  
Health And Nutrition ◽  
Trend Data ◽  
National Trends

AbstractObjectiveThere is an increasing concern of anaemia in Japanese women, but no national trend data has existed to date. We analysed long-term national trends of anaemia in adult women.DesignSecondary analyses of 15 consecutive cross-sectional nationwide surveys conducted during the period 1989–2003. Analyses were based on 5-year intervals (1989–1993, 1994–1998, 1999–2003).SettingJapan.SubjectsThe subjects included the National Health and Nutrition Survey of Japan (NHNS-J) population. Analyses were based on 50 967 non-pregnant/non-lactating women aged 20 years and over, with complete data sets. We stratified subjects into six age groups (20–29 years, 30–39 years, 40–49 years, 50–59 years, 60–69 years and 70+ years), and three age groups (20–49 years, 50–69 years, 70+ years) for analyses on residential areas (metropolitan, cities and towns).ResultsDecreases in trends of mean haemoglobin values (intravenous) were significant in all age groups. Changes in the prevalence of anaemia were significant only in women aged 30–39 and 40–49 years. Anaemia (haemoglobin < 12.0 g dl−1) increased from 16.8% to 20.6% in women aged 30–39 years, and from 20.2% to 26.9% in women aged 40–49 years, respectively. Prevalence was highest in women aged 70 years and older in all times, but no significant change was observed.ConclusionsHaemoglobin values have declined significantly in all ages in the last 15 years. Anaemia was especially significant in women aged 30–39 years and 40–49 years. Our findings suggest that a large number of young women in Japan are at risk of anaemia, so continuous monitoring and controlling efforts of this trend are needed.

Sign in / Sign up

Export Citation Format

Share Document