Do Instructional Videos on Sputum Submission Result in Increased Tuberculosis Case Detection? A Randomized Controlled Trial

Objective

We examined the effect of an instructional video about the production of diagnostic sputum on case detection of tuberculosis (TB), and evaluated the acceptance of the video.

Trial Design

Randomized controlled trial.

Methods

We prepared a culturally adapted instructional video for sputum submission. We analyzed 200 presumptive TB cases coughing for more than two weeks who attended the outpatient department of the governmental Municipal Hospital in Mwananyamala (Dar es Salaam, Tanzania). They were randomly assigned to either receive instructions on sputum submission using the video before submission (intervention group, n = 100) or standard of care (control group, n = 100). Sputum samples were examined for volume, quality and presence of acid-fast bacilli by experienced laboratory technicians blinded to study groups.

Results

Median age was 39.1 years (interquartile range 37.0–50.0); 94 (47%) were females, 106 (53%) were males, and 49 (24.5%) were HIV-infected. We found that the instructional video intervention was associated with detection of a higher proportion of microscopically confirmed cases (56%, 95% confidence interval [95% CI] 45.7–65.9%, sputum smear positive patients in the intervention group versus 23%, 95% CI 15.2–32.5%, in the control group, p <0.0001), an increase in volume of specimen defined as a volume ≥3ml (78%, 95% CI 68.6–85.7%, versus 45%, 95% CI 35.0–55.3%, p <0.0001), and specimens less likely to be salivary (14%, 95% CI 7.9–22.4%, versus 39%, 95% CI 29.4–49.3%, p = 0.0001). Older age, but not the HIV status or sex, modified the effectiveness of the intervention by improving it positively. When asked how well the video instructions were understood, the majority of patients in the intervention group reported to have understood the video instructions well (97%). Most of the patients thought the video would be useful in the cultural setting of Tanzania (92%).

Conclusions

Sputum submission instructional videos increased the yield of tuberculosis cases through better quality of sputum samples. If confirmed in larger studies, instructional videos may have a substantial effect on the case yield using sputum microscopy and also molecular tests. This low-cost strategy should be considered as part of the efforts to control TB in resource-limited settings.

Trial Registration

Pan African Clinical Trials Registry PACTR201504001098231     

GB2sequin - A file converter preparing custom GenBank files for database submission

The typical wet lab user often annotates smaller sequences in the GenBank format, but resulting files are not accepted for database submission by NCBI. This makes submission of such annotations a cumbersome task. Here we present “GB2sequin” an easy-to-use web application that converts custom annotations in the GenBank format into the NCBI direct submission format Sequin. Additionally, the program generates a “five-column, tab-delimited feature table” and a FASTA file. Those are required for submission through BankIt or the update of an existing GenBank entry. We specifically developed “GB2sequin” for the regular wet lab researcher with strong focus on user-friendliness and flexibility. The application is equipped with an intuitive graphical interface and a comprehensive documentation. It can be employed to prepare any GenBank file for database submission and is freely available online at https://chlorobox.mpimp-golm.mpg.de/GenBank2Sequin.html.     

DNA Data Bank of Japan dealing with large-scale data submission.

The DNA Data Bank of Japan (DDBJ) (http//:www.ddbj.nig.ac.jp) has developed a software system for mass submissions to cope with a recent expansion of EST and genome data submissions. The system is composed of four parts, the WWW data submission, large-scale submission, submission management and storing. Using this system one can submit data on a large number of sequences or a very long sequence while checking the consistency between the annotation and sequence without much effort. DDBJ has received large scale data of Homo sapiens, Arabidopsis and Pyrococcus from Japanese researchers who made full use of the new submission system.     

Submission: Its Features and Function in the Wolf and Dog

Submission in the wolf and dog is defined on the basis ot itsmotivation: submission is the effort of the inferior to attainfriendly or harmonic social integration. Submission functions as an appeal or a contribution to socialintegration, but only if it meets a corresponding attitude inthe superior. The form of submissive behavior in wolf and dogis ritualized and symbolized cub-behavior. Two main forms ofsubmissive behavior occur in wolf and dog: active submission,derived from begging for milk or food, and passive submission,derived from the posture which the cub adopts when cleaned byits mother. The definition of submission is generally applicable to vertebratesliving in groups based on intimacy and a social hierarchicalorder. The concept of submission as the role of the defeatedin the terminal phase of fight with the function to inhibitautomatically aggression in the superior should be dismissed.In vertebrates at least three types of conflict with differentterminal phases occur: (1). Severe fight based on intolerance;ends with flight by the inferior or with his death. (2). Ritualizedfight over a privilege; ends with the "giving-up-the-claim ritual"of the inferior, which automatically blocks the aggression ofthe superior. (3). Minor conflict in closed groups; settledby submissive behavior of the inferior. In closed vertebrate groups, intermediate forms between (1)and (3) occur, depending on the proportion between activatedintimacy and intolerance.     

BarleyExpress: a web-based submission tool for enriched microarray database annotations

BarleyExpress is a web-based microarray experiment data submission tool for BarleyBase, a public data resource of Affymetrix GeneChip data for plants. BarleyExpress uses the Plant Ontology vocabularies and enhances the MIAME guidelines to standardize the annotation of microarray gene expression experiments. In addition, BarleyExpress provides explicit support for factorial experiment design and template loading methods to ease the submission process for large experiments. AVAILABILITY: http://barleybase.org SUPPLEMENTARY INFORMATION: BarleyExpress Users Manual.     

MUTbase: maintenance and analysis of distributed mutation databases

MOTIVATION: To develop tools for the submission of mutations to databases and maintenance of locus-specific mutation databases. Advanced, integrated computer systems are needed to store and organize the increasing mutation information. RESULTS: The MUTbase program suite provides an easy, interactive and quality-controlled submission of information to mutation databases. For further study of the databases on the World Wide Web, a number of tools are provided. The program package also writes and updates a large number of Web pages, e.g. about the distribution and statistics of disease-causing mutations, and changes in restriction patterns.     

How the Scientific Community Reacts to Newly Submitted Preprints: Article Downloads,Twitter Mentions,and Citations

We analyze the online response to the preprint publication of a cohort of 4,606 scientific articles submitted to the preprint database arXiv.org between October 2010 and May 2011. We study three forms of responses to these preprints: downloads on the arXiv.org site, mentions on the social media site Twitter, and early citations in the scholarly record. We perform two analyses. First, we analyze the delay and time span of article downloads and Twitter mentions following submission, to understand the temporal configuration of these reactions and whether one precedes or follows the other. Second, we run regression and correlation tests to investigate the relationship between Twitter mentions, arXiv downloads, and article citations. We find that Twitter mentions and arXiv downloads of scholarly articles follow two distinct temporal patterns of activity, with Twitter mentions having shorter delays and narrower time spans than arXiv downloads. We also find that the volume of Twitter mentions is statistically correlated with arXiv downloads and early citations just months after the publication of a preprint, with a possible bias that favors highly mentioned articles.     

Derivation and propagation of human embryonic stem cell lines from frozen embryos in an animal product-free environment

The protocols described here are comprehensive instructions for deriving human embryonic stem (hES) cell lines in xeno-free conditions from cryopreserved embryos. Details are included for propagation, cryopreservation and characterization. Initial derivation is on feeder cells and is followed by adaptation to a feeder-free environment; competent technicians can perform these simplified methods easily. From derivation to cryopreservation of fully characterized initial stocks takes 3-4 months. These protocols served as the basis for standard operating procedures (SOPs), with both operational and technical components, that we set to meet good manufacturing practice (GMP) and UK regulatory body requirements for derivation of clinical-grade cells. As such, these SOPs are currently used in our current GMP compliant facility to derive hES cell lines ab initio, in an animal product-free environment; these lines are suitable for research and potentially for clinical use in cell therapy. So far, we have derived eight clinical-grade lines, which will be freely available to the scientific community after submission/accession to the UK Stem Cell Bank.     

The factor VIII Structure and Mutation Resource Site: HAMSTeRS version 4.

Since 1996 the HAMSTeRS (Haemophilia A Mutation, Search, Test and Resource Site) WWW site has provided an online resource for access to data on the molecular pathology of haemophilia A, replacing previous text editions of the Haemophilia A Database published in Nucleic Acids Research . This report describes the continued development of the site (version 4), and in particular the expansion of factor VIII (FVIII) structure-related features. Access to the mutation database itself, both for searching the listings and for submission of new mutations, is via custom-designed forms: more powerful Boolean searches of the point mutations in the database are also available. During 1997 a total of 22 novel missense mutations were reported, increasing the total number of unique variants now described to 252 (238 in exonic sequences and 14 at intronic splice junctions). Currently, a total of 586 individual reports with associated phenotypic data are available for searching by any category including phenotype. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequencies from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Our intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. The HAMSTeRS URL is http://europium.mrc.rpms.ac.uk     

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database

The submission of multiple sequence alignment data to EMBL has grown 30-fold in the past 10 years, creating a problem of archiving them. The EBI has developed a new public database of multiple sequence alignments called EMBL-Align. It has a dedicated web-based submission tool, Webin-Align. Together they represent a comprehensive data management solution for alignment data. Webin-Align accepts all the common alignment formats and can display data in CLUSTALW format as well as a new standard EMBL-Align flat file format. The alignments are stored in the EMBL-Align database and can be queried from the EBI SRS (Sequence Retrieval System) server. AVAILABILITY: Webin-Align: http://www.ebi.ac.uk/embl/Submission/align_top.html, EMBL-Align: ftp://ftp.ebi.ac.uk/pub/databases/embl/align, http://srs.ebi.ac.uk/