Posts about reproducible paper (old posts, page 19)

AN INTERNATIONAL INTER-LABORATORY DIGITAL PCR STUDY DEMONSTRATES HIGH REPRODUCIBILITY FOR THE MEASUREMENT OF A RARE SEQUENCE VARIANT

This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate labs. Twenty-one laboratories measured four blinded samples containing different quantities of a KRAS fragment encoding G12D, an important genetic marker for guiding therapy of certain cancers. This marker is challenging to quantify reproducibly using qPCR or NGS due to the presence of competing wild type sequences and the need for calibration. Using dPCR, eighteen laboratories were able to quantify the G12D marker within 12% of each other in all samples. Three laboratories appeared to measure consistently outlying results; however, proper application of a follow-up analysis recommendation rectified their data. Our findings show that dPCR has demonstrable reproducibility across a large number of laboratories without calibration and could enable the reproducible application of molecular stratification to guide therapy, and potentially for molecular diagnostics.

Reprowd: Crowdsourced Data Processing Made Reproducible

Crowdsourcing is a multidisciplinary research area in-cluding disciplines like artificial intelligence, human-computer interaction, database, and social science. One of the main objectives of AAAI HCOMP conferences is to bring together researchers from different fields and provide them opportunities to exchange ideas and share new research results. To facilitate cooperation across disciplines,repro-ducibilityis a crucial factor, but unfortunately it has not got-ten enough attention in the HCOMP community.

Vive la Petite Différence! Exploiting Small Differences for Gender Attribution of Short Texts

This article describes a series of experiments on gender attribution of Polish texts. The research was conducted on the publicly available corpus called "He Said She Said", consisting of a large number of short texts from the Polish version of Common Crawl. As opposed to other experiments on gender attribution, this research takes on a task of classifying relatively short texts, authored by many different people. For the sake of this work, the original "He Said She Said" corpus was filtered in order to eliminate noise and apparent errors in the training data. In the next step, various machine learning algorithms were developed in order to achieve better classification accuracy. Interestingly, the results of the experiments presented in this paper are fully reproducible, as all the source codes were deposited in the open platform Gonito.net. Gonito.net allows for defining machine learning tasks to be tackled by multiple researchers and provides the researchers with easy access to each other’s results.

The Reproducibility and Relative Validity of a Mexican Diet Quality Index (ICDMx) for the Assessment of the Habitual Diet of Adults

The study of diet quality in a population provides information for the development of programs to improve nutritional status through better directed actions. The aim of this study was to assess the reproducibility and relative validity of a Mexican Diet Quality Index (ICDMx) for the assessment of the habitual diet of adults.

Assessing the reproducibility of exome copy number variations predictions

Reproducibility is receiving increased attention across many domains of science and genomics is no exception. Efforts to identify copy number variations (CNVs) from exome sequence (ES) data have been increasing. Many algorithms have been published to discover CNVs from exomes and a major challenge is the reproducibility in other datasets. Here we test exome CNV calling reproducibility under three conditions: data generated by different sequencing centers; varying sample sizes; and varying capture methodology.

Standardized Mixed-Meal Tolerance and Arginine Stimulation Tests Provide Reproducible and Complementary Measures ofb-cell Function: Results From the Foundation for the National Institutes of Health Biomarkers Consortium Investigative Series

Standardized, reproducible, and feasible quantification ofb-cell function (BCF) is necessary for the evaluation of interventions to improve insulin secretion and important for comparison across studies. We therefore characterized the re-sponses to, and reproducibility of, standardized methods of in vivo BCF across different glucose tolerance states. Reproducibility for the AST was very good, with ICC values >0.8 across all variables and populations.