What Happens When the Way to “Follow the Medium” Changes?

Digital methods allow social researchers and IT professionals to work together to produce instruments to comprehend current social phenomena. To develop these tools, they felt the need to “follow the medium” by reorganizing their data collection and analysis strategies on what they learned from the medium. For many years, digital research has been based on application programming interfaces (APIs) querying, an approach based on the extraction of records of data made available by the platforms through their programming interfaces. But what happens when the way to “follow the medium” changes? This contribution addresses the methodological challenges and the potential alternatives in research activities that affect the researchers' role due to recent restrictions. Two examples of research experience conducted before the APIs' closure are proposed in order to lead towards an initial reflection on its critical effects.

Multi-Wavelength Analytical Ultracentrifugation of Biopolymer Mixtures and Interactions

Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC is suitable for a wide range of applications and biopolymer systems and is poised to become an essential tool to characterize macromolecular interactions. It adds an orthogonal spectral dimension to the traditional hydrodynamic characterization by exploiting unique chromophores in analyte mixtures that may or may not interact. Here we illustrate the utility of MW-AUC for representative classes of challenging biopolymer systems, including interactions between mixtures of different sized proteins with small molecules, mixtures of loaded and empty viral AAV capsids contaminated with free DNA, and mixtures of different proteins, where some have identical hydrodynamic properties, all of which are difficult to resolve with traditional AUC methods. We explain the improvement in resolution and information content obtained by this technique compared to traditional single- or dual-wavelength approaches. We discuss experimental design considerations and limitations of the method, and address the advantages and disadvantages of the two MW optical systems available today, and the differences in data analysis strategies between the two systems.

Key Methods Used in Qualitative Document Analysis

Carrying out research requires that a researcher is aware of the many things that need to be put into consideration and one of them definitely is document analysis. This article attempts to discuss the document analysis strategies, their use, functions/importance, epistemological approaches, types of documents used for analysis in a qualitative research method, and document analysis evaluation considerations. The author finds it essential to also look into the importance and use of document analysis in research to show its relevance in the research study. The inclusion of document types helps in creating an awareness of what is required for analysis. The consideration of document analysis strategy and evaluation helps invalidate the appropriate strategy to use for a particular research method. While the importance and functions of document analysis help to appreciate the contributions of documents to research. The epistemological approaches to document analysis strategies play a very vital role in indicating and directing the appropriate strategy to use in a research study bearing in mind its theoretical demands.

PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples

Recent advances in technology have made multi-omics datasets increasingly available to researchers. To leverage the wealth of information in multi-omics data, a number of integrative analysis strategies have been proposed recently. However, effectively extracting biological insights from these large, complex datasets remains challenging. In particular, matched samples with multiple types of omics data measured on each sample are often required for multi-omics analysis tools, which can significantly reduce the sample size. Another challenge is that analysis techniques such as dimension reductions, which extract association signals in high dimensional datasets by estimating a few variables that explain most of the variations in the samples, are typically applied to whole-genome data, which can be computationally demanding. Here we present pathwayMultiomics, a pathway-based approach for integrative analysis of multi-omics data with categorical, continuous, or survival outcome variables. The input of pathwayMultiomics is pathway p-values for individual omics data types, which are then integrated using a novel statistic, the MiniMax statistic, to prioritize pathways dysregulated in multiple types of omics datasets. Importantly, pathwayMultiomics is computationally efficient and does not require matched samples in multi-omics data. We performed a comprehensive simulation study to show that pathwayMultiomics significantly outperformed currently available multi-omics tools with improved power and well-controlled false-positive rates. In addition, we also analyzed real multi-omics datasets to show that pathwayMultiomics was able to recover known biology by nominating biologically meaningful pathways in complex diseases such as Alzheimer’s disease.

Conceptualizing and Measuring Appetite Self-Regulation Phenotypes and Trajectories in Childhood: A Review of Person-Centered Strategies

This review uses person-centered research and data analysis strategies to discuss the conceptualization and measurement of appetite self-regulation (ASR) phenotypes and trajectories in childhood (from infancy to about ages 6 or 7 years). Research that is person-centered provides strategies that increase the possibilities for investigating ASR phenotypes. We first examine the utility of examining underlying phenotypes using latent profile/class analysis drawing on cross-sectional data. The use of trajectory analysis to investigate developmental change is then discussed, with attention to phenotypes using trajectories of individual behaviors as well as phenotypes based on multi-trajectory modeling. Data analysis strategies and measurement approaches from recent examples of these person-centered approaches to the conceptualization and investigation of appetite self-regulation and its development in childhood are examined. Where relevant, examples from older children as well as developmental, clinical and educational psychology are drawn on to discuss when and how person-centered approaches can be used. We argue that there is scope to incorporate recent advances in biological and psychoneurological knowledge about appetite self-regulation as well as fundamental processes in the development of general self-regulation to enhance the examination of phenotypes and their trajectories across childhood (and beyond). The discussion and conclusion suggest directions for future research and highlight the potential of person-centered approaches to progress knowledge about the development of appetite self-regulation in childhood.

Multi-Wavelength Analytical Ultracentrifugation of Biopolymer Mixtures and Interactions

Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC is suitable for a wide range of applications and biopolymer systems and is poised to become an essential tool to characterize macromolecular interactions. It adds an orthogonal spectral dimension to the traditional hydrodynamic characterization by exploiting unique chromophores in analyte mixtures that may or may not interact. Here we illustrate the utility of MW-AUC for representative classes of challenging biopolymer systems, including interactions between mixtures of different sized proteins with small molecules, mixtures of loaded and empty viral AAV capsids contaminated with free DNA, and mixtures of different proteins, where some have identical hydrodynamic properties, all of which are difficult to resolve with traditional AUC methods. We explain the improvement in resolution and information content obtained by this technique compared to traditional single- or dual-wavelength approaches. We discuss experimental design considerations and limitations of the method, and address the advantages and disadvantages of the two MW optical systems available today, and the differences in data analysis strategies between the two systems.

The Journey of a Word: An Action Research Intervention of Morphemic Analysis and Etymology for a Middle School Gifted and Talented Class

Sixth-grade students who had been identified as gifted and talented participated in a literacy intervention designed and implemented by the first author as part of an action research project. These students were meeting the grade-level standards in literacy, so the project aimed to push their vocabulary knowledge further in order to prepare them for the complex vocabulary they encounter in their independent reading and assigned content units. This daily intervention directly taught students the origins and histories of words and word parts from Latin, Greek, Germanic, and French languages, introduced morphemic analysis strategies, and gave them techniques to analyze the words’ meanings based on that information. Content-specific vocabulary, as well as general vocabulary knowledge of the participating students increased significantly. Throughout the intervention, students’ confidence in vocabulary knowledge improved, and they gained a deeper understanding of the nuances of language as their ability to apply this knowledge in other contexts grew and facilitated better understanding of the words they read.

Search for Multi-Coincidence Cosmic Ray Events over Large Distances with the EEE MRPC Telescopes

The existence of independent, yet time correlated, Extensive Air Showers (EAS) has been discussed over the past years, with emphasis on possible physical mechanisms that could justify their observation. The detector network of the Extreme Energy Events (EEE) Collaboration, with its approximately 60 cosmic ray telescopes deployed over the Italian territory, has the potential to search for such events, employing different analysis strategies. In this paper, we have analyzed a set of EEE data, corresponding to an approximately five month observation period, searching for multi-coincidence events among several far telescopes, within a time window of 1 ms. Events with up to 12 coincident telescopes have been observed. Results were compared to expectations from a random distribution of events and discussed with reference to the relativistic dust grain hypothesis.

Benchmarking different approaches for Norovirus genome assembly in metagenome samples

Background Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for obtaining whole-genome sequences in non-related patients. After polyA RNA isolation and sequencing in eight patients with acute gastroenteritis, we evaluated two de Bruijn graph assemblers (SPAdes and MEGAHIT), combined with four different and common pre-assembly strategies, and compared those yielding whole genome Norovirus contigs. Results Reference-genome guided strategies with both host and target virus did not present any advantages compared to the assembly of non-filtered data in the case of SPAdes, and in the case of MEGAHIT, only host genome filtering presented improvements. MEGAHIT performed better than SPAdes in most samples, reaching complete genome sequences in most of them for all the strategies employed. Read binning with CD-HIT improved assembly when paired with different analysis strategies, and more notably in the case of SPAdes. Conclusions Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to analysis. We may need different approaches even for samples treated equally due to the presence of high intra host variability. We tested and compared different workflows for the accurate assembly of Norovirus genomes and established their assembly capacities for this purpose.

Consensus-based guidance for conducting and reporting multi-analyst studies

Any large dataset can be analyzed in a number of ways, and it is possible that the use of different analysis strategies will lead to different results and conclusions. One way to assess whether the results obtained depend on the analysis strategy chosen is to employ multiple analysts and leave each of them free to follow their own approach. Here, we present consensus-based guidance for conducting and reporting such multi-analyst studies, and we discuss how broader adoption of the multi-analyst approach has the potential to strengthen the robustness of results and conclusions obtained from analyses of datasets in basic and applied research.